HemTools public data¶
bulk RNA-seq data¶
/home/yli11/dirs/blood_regulome/chenggrp/HemPortal/HemTools_uniform_processed_files/blood_rna_seq
Blood_gene_expression.2.21.2023.csv bulk RNA-seq data is based on gencode v39.
gene_info.v39.tsv contains ENST, ENSG and gene name.
TSS data¶
hg19 non-redundant TSS from ensembl
/home/yli11/Data/Human/hg19/Ensembl_v99_2020_Jan/hg19.ensembl.TSS.gene_name.bed
hg19 redundant TSS (ensembl + gencode)
In this dataset, each gene can have multiple TSSs, but gene-TSS combination is unique
/home/yli11/Data/Human/hg19/gencode33/hg19.redundant.tss.bed
hg19 data¶
Hi-CHIP¶
Hudep2 GATA1 HiCHIP 20kb: /research_jude/rgs01_jude/groups/chenggrp/projects/blood_regulome/chenggrp/Projects/jchen6/GATA1_TFBS_ABE8e_screening/pre-test_vali/HiChIP/merged/GATA1_ATAC_P_to_all_results/GATA1_H2_HiCHIP/fihichip_results/FitHiChIP_Peak2ALL_b20000_L10000_U2000000/P2PBckgr_0/Coverage_Bias/FitHiC_BiasCorr/Merge_Nearby_Interactions/GATA1_H2_HiCHIP.interactions_FitHiC_Q0.05_MergeNearContacts.bed
H3K27AC Hudep2 2.5kb: /research_jude/rgs01_jude/groups/chenggrp/projects/blood_regulome/chenggrp/HemPortal/HemTools_uniform_processed_files/HICHIP
7880 1374932_1400249_Hudep2_H3K27AC_HiChIP.count.bedpe
13109 1374933_1400250_Hudep2_H3K27AC_HiChIP_FS.count.bedpe
6781 1482819_1512832_Hudep2_D3_H3K27AC_HiChIP.count.bedpe
18979 1482820_1512831_CD34_D13_rep1_H3K27AC.count.bedpe
Jurkat CTCF hichip: /research_jude/rgs01_jude/groups/chenggrp/projects/blood_regulome/common/insulator_screen/insulator_oligo_screen/hichip_dove_raw_data/hichip_dshresth_2022-09-09/ctcf_hichip/merged_CTCF_peak.fithichip_005.results/FitHiChIP_Peak2ALL_b5000_L10000_U2000000/P2PBckgr_0/Coverage_Bias/FitHiC_BiasCorr/ctcf_hichip.interactions_FitHiC_Q0.05.bed
TF histone peaks¶
H1 GATA1 Day0 IDR peak: /research_jude/rgs01_jude/groups/chenggrp/projects/blood_regulome/chenggrp/Projects/fetal_vs_adult/data/GATA1_new/pair_end/PE-chip-seq_qqi_2019-03-21/IDR_peak/idr_peaks_qqi_2020-05-16_13c13bb9aad9/idr_peaks.rmblck.merged_peaks.bed
H2 GATA1 Day0 IDR peak: /home/yli11/dirs/blood_regulome/chenggrp/Projects/fetal_vs_adult/data/GATA1_new/pair_end/PE-chip-seq_qqi_2019-03-21/IDR_peak/idr_peaks_qqi_2020-06-04/idr_peaks.rmblck.merged_peaks.bed
blood_regulome/chenggrp/HemPortal/HemTools_uniform_processed_files/Hudep2/unknown/ATAC_seq/atac_seq_yli11_2020-06-12/peak_files/H2_ATAC_peak.union.bed
blood_regulome/chenggrp/HemPortal/HemTools_uniform_processed_files/
CD34/ChIP_seq/chip_seq_single_yli11_2021-01-28/peak_files/H3K27ac_CD34.merged.bed
Hudep1/ChIP_seq/chip_seq_single_yli11_2021-01-28/peak_files/H3K27ac_H1.merged.bed
./Hudep2/unknown/Histone_chip_seq_single/chip_seq_single_yli11_2021-01-28/peak_files/H3K27ac_H2_D0.merged.bed
Sequencing_runs/Li_data/raw_data_ABE_CRM/ChIP_seq/histone/chip_seq_single_yli11_2020-08-21/peak_files/H3K27ac_H2_D3.merged.bed
Jurkat CTCF merged peak: blood_regulome/chenggrp/HemPortal/HemTools_uniform_processed_files/Jurkat/ChIP_seq/CTCF/Jurkat_CTCF.merged.bed
chromHMM data¶
There is chromatin states (N=10) annotation chromHMM_heatmap.pdf in the same folder.
Hudep2 Day0: blood_regulome/chenggrp/HemPortal/HemTools_uniform_processed_files/Hudep2/Day0/chromHMM/chromHMM_yli11_2022-09-01/learned_model_10/myCellLine_10_segments.bed
CD34: blood_regulome/chenggrp/HemPortal/HemTools_uniform_processed_files/CD34/chromHMM/chromHMM_yli11_2022-09-01/learned_model_10/myCellLine_10_segments.bed
Data Table¶
Name |
Path |
|---|---|
hg19_BWA_index |
/home/yli11/Data/Human/hg19/index/bwa_16a_index/hg19.fa |
hg19_kallisto_index |
/home/yli11/Data/Human/hg19/index/kallisto/hg19.idx |
hg19_black_list |
/home/yli11/Data/Human/hg19/annotations/hg19.blacklist.bed |
hg19_chrom_size |
/home/yli11/Data/Human/hg19/annotations/hg19.chrom.sizes |
hg19_fasta |
/home/yli11/Data/Human/hg19/fasta/hg19.fa |
hg19_motif |
/home/yli11/Data/Motif_database/Human/human.meme |
hg19_rRNA |
/home/yli11/Data/RSEQC_bed/hg19_rRNA.bed3 |
hg19_HBG |
/home/yli11/Data/Human/hg19/features/HBG.bed |
hg19_hemoglobin |
/home/yli11/Data/Human/hg19/features/hg19.ENCODE_GENE.hem.bed3 |
hg19_t2g |
/home/yli11/Data/Human/hg19/index/kallisto/hg19.ensembl_v75.t2g |
hg19_FANTOM5_enhancer |
/home/yli11/Data/Human/hg19/FANTOM/human_permissive_enhancers_phase_1_and_2.bed |
hg19_FANTOM5_TSS |
/home/yli11/Data/Human/hg19/FANTOM/TSS_human.bed |
hg19_3UTR |
/home/yli11/Data/Human/hg19/UCSC_table_browser/gene_3UTR.bed |
hg19_gene_body |
/home/yli11/Data/Human/hg19/UCSC_table_browser/gene_body.bed |
hg19_gene_end_2000 |
/home/yli11/Data/Human/hg19/UCSC_table_browser/gene_down2000.bed |
hg19_intron |
/home/yli11/Data/Human/hg19/UCSC_table_browser/gene_intron.bed |
hg19_promoter_up2000 |
/home/yli11/Data/Human/hg19/UCSC_table_browser/gene_promoter_up2000.bed |
hg19_intergenic_regions |
/home/yli11/Data/Human/hg19/UCSC_table_browser/intergenic.bed |
hg19_5UTR |
/home/yli11/Data/Human/hg19/UCSC_table_browser/gene_5UTR.bed |
hg19_gene_end_1000 |
/home/yli11/Data/Human/hg19/UCSC_table_browser/gene_down1000.bed |
hg19_exon |
/home/yli11/Data/Human/hg19/UCSC_table_browser/gene_exon.bed |
hg19_promoter_up1000 |
/home/yli11/Data/Human/hg19/UCSC_table_browser/gene_promoter_up1000.bed |
hg38 data¶
Name |
Path |
|---|---|
hg38_motif |
/home/yli11/Data/Motif_database/Human/human.meme |
hg38_t2g |
/home/yli11/Data/Human/hg38/index/kallisto/hg38.ensembl_v67.t2g |
hg38_kallisto_index |
/home/yli11/Data/Human/hg38/index/kallisto/hg38.idx |
mm10 data¶
Name |
Path |
|---|---|
mm10_t2g |
/home/yli11/Data/Mouse/mm10/index/kallisto/mm10.ensembl_v67.t2g |
mm10_kallisto_index |
/home/yli11/Data/Mouse/mm10/index/kallisto/mm10.idx |
mm9 data¶
Name |
Path |
|---|---|
mm9_t2g |
/home/yli11/Data/Mouse/mm9/index/kallisto/mm9.ensembl_v67.t2g |
mm9_kallisto_index |
/home/yli11/Data/Mouse/mm9/index/kallisto/mm9.idx |
chromHMM¶
Name |
Path |
|---|---|
known_association |
/home/yli11/HemTools/share/misc/chromHMM_known_associations.tsv |
chromatin_state_info |
/home/yli11/HemTools/share/misc/chromatin_state_info.tsv |
RNA-seq data¶
Blood lineage data:
Paired-end: /home/yli11/HemPortal/RNA_seq/blood/PRJNA299579
Single-end: /home/yli11/HemPortal/RNA_seq/blood/GSE61566_GSE53983
BE-editor: /research/rgs01/project_space/chenggrp/blood_regulome/chenggrp/Projects/BE_editor/GSE121668