Data_Denise_LT_DNA_Bindung + Data_Denise_LT_K331A_RNASeq

基于您提供的文件列表和已发表的论文背景，以下是 LT (Large Tumor Antigen) 相关未发表数据的完整表格整理。这些数据分为 ChIP-seq（LT蛋白结合位点）和 RNA-seq（LT及突变体转录组影响）。

1. LT 蛋白特异性 ChIP-Seq 数据集

状态: 未发表 (Unpublished) 目的: 绘制 LT 蛋白在全基因组上的直接结合位点。抗体: Cm2b4 (针对 LT/LTtr 蛋白) 或 IgG/Input 对照。注意: 部分样本为 LT+sT 共表达，部分为 LT 单独表达。

样本名称 (Sample ID)	细胞类型	供体/ID	处理条件 (Condition)	对照类型 (Control)	文件名示例 (File Name)	备注
HEK293_r1	HEK293	N/A	LT + sT	Input	`HEK293_LT+sT_r1.fastq.gz` `HEK293_LT+sT_r1_Input.fastq.gz`	重复1
HEK293_r2	HEK293	N/A	LT + sT	Input	`HEK293_LT+sT_r2.fastq.gz`	重复2 (Input可能在其他目录或共用)
HEK293_r3	HEK293	N/A	LT + sT	Input	`HEK293_LT+sT_r3.fastq.gz` `HEK293_LT+sT_r3_Input.fastq.gz`	重复3
HEK293_Mock_r1-3	HEK293	N/A	Mock (Vector)	Input	`HEK293_mock_r1...r3.fastq.gz` `..._Input.fastq.gz`	阴性对照 (之前分析中 r2/r3 质量较差可能被排除)
hTERT_LT_r1	hTERT (BJ5ta)	N/A	LT only	Input?	`hTERT_LT_r1.fastq.gz`	仅 LT 表达 (注意：之前分析中此样本可能因质量被排除，需检查对应 Input)
hTERT_LT_r2	hTERT (BJ5ta)	N/A	LT only	Input	`hTERT_LT_r2.fastq.gz` `hTERT_LT_r2_Input.fastq.gz`	仅 LT 表达，高质量重复
hTERT_LT+sT_r1	hTERT (BJ5ta)	N/A	LT + sT	Input	`hTERT_LT+sT_r1.fastq.gz` `hTERT_LT+sT_r1_Input.fastq.gz`	LT+sT 共表达
hTERT_LT+sT_r2	hTERT (BJ5ta)	N/A	LT + sT	Input	`hTERT_LT+sT_r2.fastq.gz` `hTERT_LT+sT_r2_Input.fastq.gz`	LT+sT 共表达
hTERT_Mock_r1-2	hTERT (BJ5ta)	N/A	Mock (Vector)	Input	`hTERT_mock_r1...r2.fastq.gz` `..._Input.fastq.gz`	阴性对照
NHDF_Donor1	NHDF (Primary)	Donor 1	LT (Cm2b4)	Input	`NHDF_LT_Donor1.fastq.gz` `NHDF_LT_Donor1_Input.fastq.gz`	原代细胞，生理相关性高
NHDF_Donor2	NHDF (Primary)	Donor 2	LT (Cm2b4)	Input	`NHDF_LT_Donor2.fastq.gz` `NHDF_LT_Donor2_Input.fastq.gz`	原代细胞，生理相关性高
p783_DonorI	NHDF (Primary)	Donor I (p783)	LT?/Cm2b4	Input	`p783_ChIP_DonorI.fastq.gz` `p783_input_DonorI.fastq.gz`	2023年新批次数据
p783_DonorII	NHDF (Primary)	Donor II (p783)	LT?/Cm2b4	Input	`p783_ChIP_DonorII.fastq.gz` `p783_input_DonorII.fastq.gz`	2023年新批次数据
PFSK-1A_r1	PFSK-1A	N/A	LT + sT	IgG	`PFSK-1A_LT+sT_r1.fastq.gz` `PFSK-1A_LT+sT_r1_IgG.fastq.gz`	注意: 使用 IgG 作为对照，而非 Input
PFSK-1A_r2	PFSK-1A	N/A	LT + sT	IgG	`PFSK-1A_LT+sT_r2.fastq.gz` `PFSK-1A_LT+sT_r2_IgG.fastq.gz`	注意: 使用 IgG 作为对照
PFSK-1B_r1	PFSK-1B	N/A	LT + sT	Input	`PFSK-1B_LT+sT_r1.fastq.gz` `PFSK-1B_LT+sT_r1_Input.fastq.gz`	使用 Input 作为对照
PFSK-1B_r2	PFSK-1B	N/A	LT + sT	Input	`PFSK-1B_LT+sT_r2.fastq.gz` `PFSK-1B_LT+sT_r2_Input.fastq.gz`	使用 Input 作为对照
PFSK-1A_H3K4	PFSK-1A	N/A	H3K4me3 ChIP	IgG	`PFSK-1A_H3K4_...fastq.gz`	非LT蛋白ChIP，为组蛋白修饰数据，可用于辅助注释

2. LT-K331A 突变体 RNA-Seq 数据集

状态: 未发表 (Unpublished) 目的: 比较野生型 LT、截短体 LTtr 和解旋酶突变体 K331A 对宿主转录组的影响。 细胞模型: NHDF (原代人真皮成纤维细胞)，两个独立供体 (Donor I & II)。 时间点: 转导后第 8 天 (Day 8)。

样本名称 (Sample ID)	细胞类型	供体 (Donor)	处理条件 (Condition)	文件名 (File Name)	备注
Control_DI	NHDF	Donor I	Vector Control	`control_d8_DonorI.fastq.gz`	空白对照
Control_DII	NHDF	Donor II	Vector Control	`control_d8_DonorII.fastq.gz`	空白对照
Control_DII_Re	NHDF	Donor II	Vector Control	`control-d8-DII_re.fastq.gz`	Donor II 的重复或重测数据
LT_WT_DI	NHDF	Donor I	LT (Wild Type)	`LT_d8_DonorI.fastq.gz`	野生型 LT
LT_WT_DII	NHDF	Donor II	LT (Wild Type)	`LT_d8_DonorII.fastq.gz`	野生型 LT
LTtr_DI	NHDF	Donor I	LTtr (Truncated)	`LTtr_d8_DonorI.fastq.gz`	肿瘤相关截短体
LTtr_DII	NHDF	Donor II	LTtr (Truncated)	`LTtr_d8_DonorII.fastq.gz`	肿瘤相关截短体
LT_K331A_DI	NHDF	Donor I	LT-K331A (Mutant)	`LT_K331A_d8_DonorI.fastq.gz`	解旋酶结构域突变体
LT_K331A_DII	NHDF	Donor II	LT-K331A (Mutant)	`LT_K331A_d8_DonorII.fastq.gz`	解旋酶结构域突变体
LT_K331A_DII_Re	NHDF	Donor II	LT-K331A (Mutant)	`LT-K331A-d8-DII_re.fastq.gz`	Donor II 的重复或重测数据

数据分析建议

ChIP-Seq 分析策略:
- 分组: 将样本分为 LT_only (hTERT_LT_r2, NHDF_Donors), LT+sT (HEK293, hTERT_LT+sT, PFSK), 和 Mock。
- 对照处理: 注意 PFSK-1A 使用 IgG 对照，而其他样本主要使用 Input。在调用峰值 (Peak Calling, 如 MACS2) 时，需针对不同对照类型调整参数或分别处理。
- 整合: 将 LT 结合位点与 RNA-Seq 中的差异基因 (DEGs) 进行重叠分析，特别是关注 LT-K331A 突变是否导致某些关键基因启动子区域的 LT 结合丢失或减弱。
RNA-Seq 分析策略:
- 差异表达: 使用 DESeq2 进行以下对比：
  - LT_WT vs Control
  - LTtr vs Control
  - LT_K331A vs Control
  - LT_K331A vs LT_WT (关键对比：确定 K331A 突变特异性影响的基因)
- 功能富集: 重点关注干扰素信号通路 (ISGs)、细胞周期调控和 DNA 损伤反应基因。根据已发表论文，LT 会诱导 ISGs，而 K331A 突变可能会改变这种诱导能力或影响其他下游通路。
多组学整合:
- 利用 NHDF Donor 1 & 2 的数据进行跨组学整合，因为这部分既有 ChIP-seq (LT 结合) 又有 RNA-seq (LT/K331A 表达影响)，且来自相同的原代细胞系统，生物学一致性最高。

Based on the file list you provided and the background of published papers, here is the complete table of unpublished data related to LT (Large Tumor Antigen). These data are divided into ChIP-seq (LT protein binding sites) and RNA-seq (transcriptomic impact of LT and its mutants).

1. LT Protein-Specific ChIP-Seq Datasets

Status: Unpublished Objective: To map the direct genome-wide binding sites of the LT protein. Antibody: Cm2b4 (targeting LT/LTtr proteins) or IgG/Input controls. Note: Some samples involve co-expression of LT+sT, while others involve LT expression alone.

Sample ID	Cell Type	Donor/ID	Condition	Control Type	Example File Name	Remarks
HEK293_r1	HEK293	N/A	LT + sT	Input	`HEK293_LT+sT_r1.fastq.gz` `HEK293_LT+sT_r1_Input.fastq.gz`	Replicate 1
HEK293_r2	HEK293	N/A	LT + sT	Input	`HEK293_LT+sT_r2.fastq.gz`	Replicate 2 (Input may be in another directory or shared)
HEK293_r3	HEK293	N/A	LT + sT	Input	`HEK293_LT+sT_r3.fastq.gz` `HEK293_LT+sT_r3_Input.fastq.gz`	Replicate 3
HEK293_Mock_r1-3	HEK293	N/A	Mock (Vector)	Input	`HEK293_mock_r1...r3.fastq.gz` `..._Input.fastq.gz`	Negative control (r2/r3 might have been excluded due to poor quality in previous analyses)
hTERT_LT_r1	hTERT (BJ5ta)	N/A	LT only	Input?	`hTERT_LT_r1.fastq.gz`	LT expression only (Note: This sample might have been excluded due to quality in previous analyses; check for corresponding Input)
hTERT_LT_r2	hTERT (BJ5ta)	N/A	LT only	Input	`hTERT_LT_r2.fastq.gz` `hTERT_LT_r2_Input.fastq.gz`	LT expression only, high-quality replicate
hTERT_LT+sT_r1	hTERT (BJ5ta)	N/A	LT + sT	Input	`hTERT_LT+sT_r1.fastq.gz` `hTERT_LT+sT_r1_Input.fastq.gz`	Co-expression of LT+sT
hTERT_LT+sT_r2	hTERT (BJ5ta)	N/A	LT + sT	Input	`hTERT_LT+sT_r2.fastq.gz` `hTERT_LT+sT_r2_Input.fastq.gz`	Co-expression of LT+sT
hTERT_Mock_r1-2	hTERT (BJ5ta)	N/A	Mock (Vector)	Input	`hTERT_mock_r1...r2.fastq.gz` `..._Input.fastq.gz`	Negative control
NHDF_Donor1	NHDF (Primary)	Donor 1	LT (Cm2b4)	Input	`NHDF_LT_Donor1.fastq.gz` `NHDF_LT_Donor1_Input.fastq.gz`	Primary cells, high physiological relevance
NHDF_Donor2	NHDF (Primary)	Donor 2	LT (Cm2b4)	Input	`NHDF_LT_Donor2.fastq.gz` `NHDF_LT_Donor2_Input.fastq.gz`	Primary cells, high physiological relevance
p783_DonorI	NHDF (Primary)	Donor I (p783)	LT?/Cm2b4	Input	`p783_ChIP_DonorI.fastq.gz` `p783_input_DonorI.fastq.gz`	New batch data from 2023
p783_DonorII	NHDF (Primary)	Donor II (p783)	LT?/Cm2b4	Input	`p783_ChIP_DonorII.fastq.gz` `p783_input_DonorII.fastq.gz`	New batch data from 2023
PFSK-1A_r1	PFSK-1A	N/A	LT + sT	IgG	`PFSK-1A_LT+sT_r1.fastq.gz` `PFSK-1A_LT+sT_r1_IgG.fastq.gz`	Note: Uses IgG as control, not Input
PFSK-1A_r2	PFSK-1A	N/A	LT + sT	IgG	`PFSK-1A_LT+sT_r2.fastq.gz` `PFSK-1A_LT+sT_r2_IgG.fastq.gz`	Note: Uses IgG as control
PFSK-1B_r1	PFSK-1B	N/A	LT + sT	Input	`PFSK-1B_LT+sT_r1.fastq.gz` `PFSK-1B_LT+sT_r1_Input.fastq.gz`	Uses Input as control
PFSK-1B_r2	PFSK-1B	N/A	LT + sT	Input	`PFSK-1B_LT+sT_r2.fastq.gz` `PFSK-1B_LT+sT_r2_Input.fastq.gz`	Uses Input as control
PFSK-1A_H3K4	PFSK-1A	N/A	H3K4me3 ChIP	IgG	`PFSK-1A_H3K4_...fastq.gz`	Not LT protein ChIP; histone modification data, useful for auxiliary annotation

2. LT-K331A Mutant RNA-Seq Datasets

Status: Unpublished Objective: To compare the impact of Wild-Type LT, Truncated LT (LTtr), and Helicase Mutant K331A on the host transcriptome. Cell Model: NHDF (Primary Human Dermal Fibroblasts), two independent donors (Donor I & II). Time Point: Day 8 post-transduction.

Sample ID	Cell Type	Donor	Condition	File Name	Remarks
Control_DI	NHDF	Donor I	Vector Control	`control_d8_DonorI.fastq.gz`	Blank control
Control_DII	NHDF	Donor II	Vector Control	`control_d8_DonorII.fastq.gz`	Blank control
Control_DII_Re	NHDF	Donor II	Vector Control	`control-d8-DII_re.fastq.gz`	Replicate or re-test data for Donor II
LT_WT_DI	NHDF	Donor I	LT (Wild Type)	`LT_d8_DonorI.fastq.gz`	Wild-Type LT
LT_WT_DII	NHDF	Donor II	LT (Wild Type)	`LT_d8_DonorII.fastq.gz`	Wild-Type LT
LTtr_DI	NHDF	Donor I	LTtr (Truncated)	`LTtr_d8_DonorI.fastq.gz`	Tumor-associated truncated form
LTtr_DII	NHDF	Donor II	LTtr (Truncated)	`LTtr_d8_DonorII.fastq.gz`	Tumor-associated truncated form
LT_K331A_DI	NHDF	Donor I	LT-K331A (Mutant)	`LT_K331A_d8_DonorI.fastq.gz`	Helicase domain mutant
LT_K331A_DII	NHDF	Donor II	LT-K331A (Mutant)	`LT_K331A_d8_DonorII.fastq.gz`	Helicase domain mutant
LT_K331A_DII_Re	NHDF	Donor II	LT-K331A (Mutant)	`LT-K331A-d8-DII_re.fastq.gz`	Replicate or re-test data for Donor II

Data Analysis Recommendations

ChIP-Seq Analysis Strategy:
- Grouping: Divide samples into LT_only (hTERT_LT_r2, NHDF_Donors), LT+sT (HEK293, hTERT_LT+sT, PFSK), and Mock.
- Control Handling: Note that PFSK-1A uses IgG controls, while other samples primarily use Input. When calling peaks (e.g., using MACS2), adjust parameters or process them separately based on the control type.
- Integration: Overlap LT binding sites with Differentially Expressed Genes (DEGs) from RNA-Seq. Pay particular attention to whether the LT-K331A mutation leads to the loss or weakening of LT binding at the promoter regions of key genes.
RNA-Seq Analysis Strategy:
- Differential Expression: Use DESeq2 for the following comparisons:
  - LT_WT vs Control
  - LTtr vs Control
  - LT_K331A vs Control
  - LT_K331A vs LT_WT (Key comparison: Identify genes specifically affected by the K331A mutation)
- Functional Enrichment: Focus on Interferon signaling pathways (ISGs), cell cycle regulation, and DNA damage response genes. According to published literature, LT induces ISGs, and the K331A mutation may alter this induction capacity or affect other downstream pathways.
Multi-Omics Integration:
- Utilize data from NHDF Donor 1 & 2 for cross-omics integration, as these samples have both ChIP-seq (LT binding) and RNA-seq (impact of LT/K331A expression) data from the same primary cell system, offering the highest biological consistency.

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