title: Patient 17 Post-Treatment Transcriptomics, Male, Stable Disease

description: Library name: Patient-17-POST-TX


title: Patient 18 Baseline Transcriptomics, Male, Progressive Disease

status: Public on Dec 03 2025

type: SRA

city: Buffalo

first: Spencer

last: Rosario

address: Elm & Carlton Sts

country: USA

institute: Roswell Park Comprehensive Cancer Center

description: Library name: Patient-18-BLBX

library_source: transcriptomic

data_processing:
Raw reads that passed thequality filter were demultiplexed and pre-processed using FastQC for sequencing base quality control.
Genome alignment of raw reads to the human reference genome (GRCh38.p13) using STAR
Mapped reads were quantified at the gene level as a raw counts matrix using featureCounts from Subread
Assembly: GRCh38
Supplementary files format and content: Transcripomics_Processed .csv file includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: colorectal tumor

extract_protocol:
The FFPE samples were emulsified in Tissue Lysis Buffer in the presence of Proteinase K on the Covaris E220 sonicator. This was followed by an incubation at 56 °C for a short duration. The RNA-containing supernatant was separated from the DNA-containing tissue by a centrifugation step. RNA was then de-crosslinked, DNAse digested, and purified over an RNA-specific spin column. Sequentially, DNA was released from the DNA-containing tissue by the Covaris E220 sonicator. The resuspension was then put through an additional Proteinase K digestion, following a de-crosslinking step at 80 °C. DNA was then purified over a DNA-specific spin column.
Unique dual-indexed, molecular-barcoded libraries were purified with AMPureXP beads (Beckman Coulter) and validated for appropriate size (225-275bp) on a Tapestation 4200 DNA1000 screentape (Agilent Inc.). 200ng of purified library was then hybridized to the SureSelectXT Human All Exon V6+UTR Capture library (Agilent Inc.). The hybridized regions were then bound to streptavidin magnetic beads and washed to remove any non-specific bound products. Eluted library underwent a second 13 cycle PCR amplification to generate enough material for sequencing. Final libraries were purified, measured by Tapestation 4200 DNA1000 screentape (250-350bp), and quantitated using KAPA qPCR (KAPA Biosystems). Individual libraries were pooled in equimolar 2nM final concentration.

treatment_protocol: Whole transcriptome analysis of FFPE samples was performed using SureSelect XT HS2 RNA Target Enrichment System (Agilent Inc). 200ng of RNA was fragmented and converted to cDNA followed by end repair, duplex UMI adaptor ligation, and 12 cycles of PCR to complete the dual-index adapters.

tag: tissue

value: colorectal tumor

tag: Sex

value: Male

tag: disease status

value: Progressive Disease

tag: genotype

value: RAS wt

tag: time point

value: Baseline


title: Patient 18 Post-Treatment Transcriptomics, Male, Progressive Disease

description: Library name: Patient-18-POST-TX

value: Post-Treatment


title: AK Keratinocytes 49 100 mJ SSR

city: Hamburg

first: Leonardo

last: Elsbroek

address: Beiersdorfstraße 1-9

country: Germany

institute: Beiersdorf AG

description: Library name: 11_AK49_100

data_processing:
For quality control Raw FASTQ reads were processed with fastp (adapter trimming, low-quality filtering, removal of poly-N reads).
Gene-level read counts were quantified using featureCounts v1.5.0-p3.
Assembly: GRCh38 / GENCODE v43.
Supplementary files format and content: Count matrices gene-level read counts csv files include raw RNA counts for each sample.

molecule: polyA RNA

source_name: Epidermis

growth_protocol: Primary human keratinocytes from AK lesions and photo-exposed healthy facial epidermis (HEK) were cultured in vitro in Stem Cell Basal Keratinocyte expansion media with antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, cat. 74104) according to the manufacturer’s instructions. On-column DNase I digestion (Qiagen, cat. 79254) was performed to remove genomic DNA.  RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP. Library quantification was performed via Qubit and real-time PCR; size distribution assessed with a Bioanalyzer

treatment_protocol: Cells received either a single exposure or repeated daily exposures for 3 consecutive days. The UVB-equivalent dose per exposure was 100 mJ/cm² (within the SSR spectrum). Cells were harvested 6 h after the final exposure for RNA extraction. Controls were processed in parallel. Each condition was profiled by RNA-seq in 7 biological replicates per group.

value: Epidermis

tag: cell line

tag: cell type

value: AK Keratinocyte

value: wt

tag: treatment

value: 100 mJ SSR


title: Patient 17 Baseline Transcriptomics, Male, Stable Disease

description: Library name: Patient-17-BLBX

value: Stable Disease


title: AK Keratinocytes Control 49

description: Library name: 10_AK49_C

value: Control


title: AK Keratinocytes 47 3x100 mJ SSR

description: Library name: 9_AK47_3x100

value: 3x100 mJ SSR


title: Patient 12 Post-Treatment Transcriptomics, Male, Stable Disease

description: Library name: Patient-12-POST-TX


title: AK Keratinocytes 47 100 mJ SSR

description: Library name: 8_AK47_100


title: AK Keratinocytes Control 47

description: Library name: 7_AK47_C


title: Patient 12 Baseline Transcriptomics, Male, Stable Disease

description: Library name: Patient-12-BLBX


title: Patient 1 Post-Treatment Transcriptomics, Male, Stable Disease

description: Library name: Patient-01-POST-TX


title: Patient 35 Baseline Transcriptomics, Male, Stable Disease

description: Library name: Patient-35-BLBX


title: AK Keratinocytes Control 54

description: Library name: 13_AK54_C


title: Patient 22 Post-Treatment Transcriptomics, Male, Progressive Disease

description: Library name: Patient-22-POST-TX


title: Patient 1 Baseline Transcriptomics, Male, Stable Disease

description: Library name: Patient-01-BLBX


title: AK Keratinocytes 41 100 mJ SSR

description: Library name: 5_AK41_100


title: AK Keratinocytes 55 100 mJ SSR

description: Library name: 17_AK55_100


title: Patient 14 Post-Treatment Transcriptomics, Male, Stable Disease

description: Library name: Patient-14-POST-TX


title: AK Keratinocytes Control 41

description: Library name: 4_AK41_C


title: shTCF4, TCF4, HUVEC, IP-3

city: Boston

first: Kaifu

last: Chen

state: MA

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

description: Library name: si-TCF4 IP-3

library_source: genomic

data_processing:
The raw reads of CUT&RUN data were preprocessed by the CHIPs pipeline[https://doi.org/10.12688/f1000research.52878.1], which includes read trimming, read mapping to the mouse genome (hg38), read level quality control, and peak level quality control. DANPOS2 dpeak function was used to call peaks using BAM files of uniquely mapped reads
The BigWig files were generated by wigToBigWig based on wig files from DANPOS2 software
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Run

molecule: genomic DNA

source_name: Human Umbilical Vein Endothelial Cells

growth_protocol: HUVECs were cultured in Endothelial Cell Medium (ECM; ScienCell) supplemented with 5% fetal bovine serum, 1% endothelial cell growth supplement (ECGS), and 1% penicillin/streptomycin. Cells were maintained at 37°C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Cells were harvested and subjected to CUT&RUN according to the Cell Signaling Technology (CST) protocol. Briefly, cells were immobilized on concanavalin A–coated magnetic beads, permeabilized, and incubated with specific antibody overnight at 4°C. Samples were then incubated with pA-MNase and activated by calcium addition. Digested chromatin was released and DNA purified using spin columns.
DNA was used to prepare sequencing libraries following a standard protocol for low-input samples. DNA fragments were end-repaired, A-tailed, and ligated to sequencing adapters. Libraries were amplified by PCR, size-selected (typically 150–400 bp), and quality checked using the Agilent High Sensitivity DNA Kit.

value: Human Umbilical Vein Endothelial Cells

tag: chip antibody


title: AK Keratinocytes 35 3x100 mJ SSR

description: Library name: 3_AK35_3x100


title: shTCF4, TCF4, HUVEC, IP-2

description: Library name: si-TCF4 IP-2


title: AK Keratinocytes 35 100 mJ SSR

description: Library name: 2_AK35_100


title: shTCF4, TCF4, HUVEC, IP-1

description: Library name: si-TCF4 IP-1


title: shTCF4, HUVEC, Input-2

description: Library name: si-TCF4 Input-2


title: Patient 14 Baseline Transcriptomics, Male, Stable Disease

description: Library name: Patient-14-BLBX


title: SNAI1, HUVEC, IP-3

description: Library name: SNAIL1 IP-3


title: VisiumHD_1, before treatment

city: Fukuoka

first: Satoshi

last: Nakamura

state: Fukuoka

address: 3-1-1, Maidashi, higashi-ku

department: Respiratory Medicine

country: Japan

institute: Kyushu University

description: Library name: A

data_processing:
Sequencing data (FASTQ files) were processed and analyzed using Space Ranger (version 3.0.0) software to assess data quality and generate spatial gene expression profiles.
Assembly: GRCh38
Supplementary files format and content: A.tar: Tar archive containing the 2μm resolution binning outputs of pre-treatment sample obtained from space ranger and coordinate data after stardist processing
Supplementary files format and content: C.tar: Tar archive containing the 2μm resolution binning outputs of post-treatment sample obtained from space ranger and coordinate data after stardist processing
Library strategy: Spatial Transcriptomics

source_name: Lung

extract_protocol:
In this study, a total of two samples consisting of paired pre- and post-treatment samples from a patient were analyzed. The FFPE tissue sections were then subjected to deparaffinization and H&E staining following the Visium HD FFPE Tissue Preparation protocol provided by 10x Genomics (Visium HD FFPE Tissue Preparation Handbook, CG000684 Rev A).
Gene expression libraries were prepared from the H&E-stained sections following the 10X Genomics protocol (Visium HD Spatial Gene Expression Reagent Kits User Guide CG000685 Rev A). The quality of the prepared libraries was evaluated using the 4200 Tape Station, and all libraries were confirmed to have sufficient concentrations. The Visium libraries were sequenced using the NovaSeq X Plus platform with a paired-end configuration (read1: 150 bp, read2: 150 bp).

value: Lung


title: VisiumHD_2, after treatment

description: Library name: C


title: shTCF4, HUVEC, Input-1

description: Library name: si-TCF4 Input-1


title: hct116-lt4-1

city: Taipei

first: I-CHUAN

last: YEN

address: No.161, Sec. 6, Minquan E. Rd., Neihu Dist.

department: school of pharmacy

country: Taiwan

institute: National Defense Medical Center

description: Library name: hct116-lt4-1

data_processing:
Sequencing reads were processed by fastp (v0.20.0) to remove adapters and low-quality nucleic acid bases.
Trimmed sequences were aligned with the reference genome using HISAT2  (v2.1.0). The resulting SAM (Sequence Alignment Map) is further converted to BAM format by SAMtools (v1.9).
Reads count were calculate using featureCounts (subread v2.0.1) and normalize to TPM.
Assembly: GRCh38
Supplementary files format and content: .xlsx

extract_protocol:
RNA Extraction Procedure Using TRIzol Reagent Cell Lysis  After removing the culture medium, cells were washed once with ice-cold phosphate-buffered saline (PBS), and residual PBS was thoroughly aspirated.  A total of 200 μL TRIzol reagent was added to each well of a 6-well plate and incubated on ice for 5 minutes to ensure complete cell lysis.  Cells were scraped using a cell scraper and the lysate was transferred into a 1.5 mL RNase-free Eppendorf tube and kept on ice for an additional 5–10 minutes.  Phase Separation  Chloroform (80 μL) was added to each tube. The mixture was vortexed vigorously for 15 seconds and then incubated at room temperature for 2–3 minutes.  Samples were centrifuged at 12,000 ×g for 15 minutes at 4 °C to allow phase separation.  RNA Precipitation  The aqueous (upper) phase was carefully transferred to a new RNase-free tube (approximately double the volume of the chloroform used), followed by the addition of 500 μL isopropanol.  The solution was mixed thoroughly and incubated at room temperature for 10 minutes.  RNA was pelleted by centrifugation at 12,000 ×g for 10 minutes at 4 °C.  RNA Washing and Drying  The supernatant was carefully removed, retaining the white RNA pellet at the bottom.  The pellet was washed with 1 mL of 75% ethanol and vortexed gently.  The sample was centrifuged at 12,000 ×g for 5 minutes at 4 °C.  The ethanol was discarded, and the pellet was air-dried under sterile conditions on a biosafety cabinet for 10–20 minutes (avoiding over-drying, which may hinder RNA re-dissolution).  RNA Re-dissolution and Quantification  The dried RNA pellet was dissolved in 15–50 μL of DEPC-treated water.  RNA concentration and purity were assessed using a spectrophotometer. An A260/230 ratio greater than 2.0 was considered indicative of acceptable RNA purity.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following manufacturer's protocols.


title: hct116-lt4-3

description: Library name: hct116-lt4-3


title: hct116-control-3

description: Library name: hct116-control-3


title: hct116-control-2

description: Library name: hct116-control-2


title: SNAI1, HUVEC, IP-1

description: Library name: SNAIL1 IP-1


title: TCF4, HUVEC, IP-2

description: Library name: TCF4 IP-2


title: TCF4, HUVEC, IP-1

description: Library name: TCF4 IP-1


title: hct116-control-1

description: Library name: hct116-control-1


title: Z058_6

city: Gainesville

first: Jason

middle: Orr

last: Brant

state: FL

address: 2197 Mowry Rd

department: Biostatistics

institute: University of Florida

description: Library name: Z058_6

data_processing:
nf-core RNA-Seq pipeline v3.12
Raw sequencing reads in FASTQ format were first evaluated for quality using FastQC v0.11.9.
Adapter sequences were auto detected, and low-quality bases were trimmed using Trim Galore v0.6.7. Reads shorter than 20 bp post-trimming were discarded.
Read alignment was performed with STAR v2.7.10a to the reference genome GRCh37 and gene expression quantification was done using RSEM v1.3.1. Checks for mapping quality, duplicate rates, and GC content were conducted.
Raw counts were corrected using ComBat-Seq   from the sva package v3.52.0 (Lee, 2024) in R programming language to remove batch-induced technical variation.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: csv file includes corrected CPM for each sample

source_name: Pancreatic tissue

extract_protocol:
RNA was purified using miRNeasy mini kit (Qiagen). 600 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit following manufacture's protocols.

treatment_protocol: After adding Matrigel, it was immediately removed from the uncultured Day 0 samples by centrifugation at 4°C before solidification. In contrast, Day 6 samples underwent 6 days of ADM incubation at 37°C before Matrigel removal and subsequent collection.

value: Pancreatic tissue

value: Acinar cells

value: ADM 6 Days

tag: batch


title: TCF4, HUVEC, IP-3

description: Library name: TCF4 IP-3


title: CON, HUVEC, Input-2

description: Library name: CON Input-2


title: CON, HUVEC, Input-1

description: Library name: CON Input-1


title: 20164_6

description: Library name: 20164_6


title: AK Keratinocytes Control 35

description: Library name: 1_AK35_C


title: 1930_6

description: Library name: 1930_6


title: siSOX10_2_2

city: Toyama

first: Satoru

last: Yokoyama

state: Toyama

address: 2630 Sugitani

institute: Univeristy of Toyama

description: Library name: 11A0217

data_processing:
Created the fastq file by bcl2fastq.
Mapped and caliculated the TPM by DRAGEN Bio-IT Platform.
Assembly: human genome GRCh 38
Supplementary files format and content: TPM data in xlsx format

source_name: cutaneous melanoma

growth_protocol: A2058 human melanoma cells were cultured in RPMI1640 Medium with 10% fetal bovine serum, 2 mM L-glutamine, 100 units/ml penicillin, and 100 µg/ml streptomycin in 5% CO2 at 37˚C.

extract_protocol:
A2058 cells were transfected with siRNAs for human SOX10 or a negative control for 96 hours. Total RNAs were extracted using RNeasy kit.
SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing and Nextera XT DNA Library Prep Kit were used for the preparation of libraries.

treatment_protocol: In siRNA knockdown experiments, siRNA for human SOX10 (1 or 2)  or negative control was used for transfection at a final concentration of 12.5 nM in melanoma cells by Lipofectamine RNAiMAX reagent.

value: cutaneous melanoma

value: melanoma


title: siSOX10_2_3

description: Library name: 12A0218


title: 1903_6

description: Library name: 1903_6


title: HP5325_6

description: Library name: HP5325_6


title: HP2335_6

description: Library name: HP2335_6


title: siSOX10_1_3

description: Library name: 09A0215


title: siSOX10_2_1

description: Library name: 10A0216


title: SNAI1, HUVEC, IP-2

description: Library name: SNAIL1 IP-2


title: siSOX10_1_1

description: Library name: 07A0213


title: siSOX10_1_2

description: Library name: 08A0214


title: HP21342_6

description: Library name: HP21342_6


title: HP21337_6

description: Library name: HP21337_6


title: siCNTL_3

description: Library name: 06A0212

value: siCNTL-transfected


title: HP21302_6

description: Library name: HP21302_6


title: 2019_6

description: Library name: 2019_6


title: HP21272_6

description: Library name: HP21272_6


title: siCNTL_2

description: Library name: 05A0211


title: siCNTL_1

description: Library name: 04A0210


title: A2058_2

description: Library name: 02A0208

value: non-treatment


title: HP21263_6

description: Library name: HP21263_6


title: HP21243_6

description: Library name: HP21243_6


title: A2058_3

description: Library name: 03A0209


title: A2058_1

description: Library name: 01A0207


title: HP2103_6

description: Library name: HP2103_6


title: HP21247_6

description: Library name: HP21247_6


title: G-CSF mobilized graft and PBMC post-alloHSCT sublib 15

first: Immo

last: Prinz

address: Martinistraße 52, Building N25

department: Institute of Systems Immunology

institute: University Medical Center Hamburg-Eppendorf

description:
Library name: S15
all_genes_S15.csv

library_source: transcriptomic single cell

data_processing:
Raw fastq data were aligned to human genome assembly GRCh38 (hg38) and quantified using split-pipe software suite (Parse Biosciences, v1.1.1).
Assembly: hg38
Supplementary files format and content: Comma-separated values files and matrix files

source_name: Blood

extract_protocol:
Peripheral blood stem cell graft samples were collected at the time of transplantation and were cryopreserved on the next day. The PBMC samples of recipients were collected at day +30 and day +100 and were cryopreserved on the same or the following day. Mononuclear cells were isolated using a Ficoll gradient and cryopreserved in DMSO until they were used for single cell analysis.
Ten adult (>18y) patients with AML in complete remission who underwent alloHSCT with peripheral blood stem cell grafts. Peripheral blood stem cell graft samples were collected at the time of transplantation and were cryopreserved on the next day. The PBMC samples of recipients were collected at day +30 and day +100 and were cryopreserved on the same or the following day. Mononuclear cells were isolated using a Ficoll gradient and cryopreserved in DMSO until they were used for single cell analysis. All live cells (DAPI⁻) were sorted from frozen PBMC samples. The sorted cells were fixed and permeabilized using Evercode™ Cell Fixation v2 (Parse Biosciences, Cat. ECF2001) following the manufacturer’s protocol. Fixed cells were stored at −80°C. All samples were then processed together to prepare single-cell libraries using one Evercode™ WT Mega v2 Kit (Parse Biosciences, Cat. ECW02050), according to the manufacturer’s instructions. Fifteen sub-libraries were sequenced on the Illumina NovaSeq 6000 S4 flow cell platform using PE150 chemistry with a sequencing depth of 25,000 reads per cell.

value: Blood

value: PBMC


title: G-CSF mobilized graft and PBMC post-alloHSCT sublib 13

description:
Library name: S13
all_genes_S13.csv


title: HP1132_6

description: Library name: HP1132_6


title: HP2102_6

description: Library name: HP2102_6


title: AK Keratinocytes 41 3x100 mJ SSR

description: Library name: 6_AK41_3x100

value: Epidermis

value: AK Keratinocyte


title: G-CSF mobilized graft and PBMC post-alloHSCT sublib 12

description:
Library name: S12
all_genes_S12.csv


title: G-CSF mobilized graft and PBMC post-alloHSCT sublib 14

description:
Library name: S14
all_genes_S14.csv


title: HAR.001_6

description: Library name: HAR.001_6


title: G-CSF mobilized graft and PBMC post-alloHSCT sublib 10

description:
Library name: S10
all_genes_S10.csv


title: 9345_6

description: Library name: 9345_6


title: 9318_6

description: Library name: 9318_6


title: G-CSF mobilized graft and PBMC post-alloHSCT sublib 9

description:
Library name: S9
all_genes_S9.csv


title: 7916_6

description: Library name: 7916_6


title: G-CSF mobilized graft and PBMC post-alloHSCT sublib 8

description:
Library name: S8
all_genes_S8.csv


title: G-CSF mobilized graft and PBMC post-alloHSCT sublib 7

description:
Library name: S7
all_genes_S7.csv


title: 80620_6

description: Library name: 80620_6


title: G-CSF mobilized graft and PBMC post-alloHSCT sublib 11

description:
Library name: S11
all_genes_S11.csv


title: 5152_6

description: Library name: 5152_6


title: G-CSF mobilized graft and PBMC post-alloHSCT sublib 5

description:
Library name: S5
all_genes_S5.csv


title: G-CSF mobilized graft and PBMC post-alloHSCT sublib 4

description:
Library name: S4
all_genes_S4.csv


title: 3422_6

description: Library name: 3422_6


title: G-CSF mobilized graft and PBMC post-alloHSCT sublib 3

description:
Library name: S3
all_genes_S3.csv


title: 2017_6

description: Library name: 2017_6


title: G-CSF mobilized graft and PBMC post-alloHSCT sublib 2

description:
Library name: S2
all_genes_S2.csv


title: 20276_6

description: Library name: 20276_6


title: G-CSF mobilized graft and PBMC post-alloHSCT sublib 6

description:
Library name: S6
all_genes_S6.csv


title: 20252_6

description: Library name: 20252_6


title: 100620_6

description: Library name: 100620_6


title: G-CSF mobilized graft and PBMC post-alloHSCT sublib 1

description:
Library name: S1
all_genes_S1.csv


title: S_HP23151_Day_0

description: Library name: HP23151

value: Uncultured


title: HPA064_6

description: Library name: HPA064_6


title: S_HP23135_Day_0

description: Library name: HP23135


title: HP9289_6

description: Library name: HP9289_6


title: S_HP23093_Day_0

description: Library name: HP23093


title: HP2301_6

description: Library name: HP2301_6


title: HP2129_6

description: Library name: HP2129_6


title: 7417_6

description: Library name: 7417_6


title: 6797_6

description: Library name: 6797_6


title: S_HP22316_Day_0

description: Library name: HP22316


title: S_HP23046_Day_0

description: Library name: HP23046


title: HP2121_6

description: Library name: HP2121_6


title: HP2123_6

description: Library name: HP2123_6


title: S_HP22294_Day_0

description: Library name: HP22294


title: HP2110_6

description: Library name: HP2110_6


title: S_HP22310_Day_6

description: Library name: HP22310


title: HP1062_6

description: Library name: HP1062_6


title: NS_3862_9_HP22187

description: Library name: NS-3862_9_HP22187


title: S_HP22076_Day_0

description: Library name: HP22076


title: HAR.002_6

description: Library name: HAR.002


title: S_HP22193_Day_0

description: Library name: HP22193


title: NS_3862_6_20259

description: Library name: NS-3862_6_20259


title: NS_3862_7_HPA071

description: Library name: NS-3862_7_HPA071


title: S_HP22052_Day_0

description: Library name: HP22052


title: S_HP23052_Day_0

description: Library name: HP23052


title: S_HP12623_Day_0

description: Library name: HP12623


title: S_HP22021_Day_0

description: Library name: HP22021


title: NS_3862_5_20228

description: Library name: NS-3862_5_20228


title: S_HP5325_0

description: Library name: HP5325


title: S_HP2335_0

description: Library name: HP2335


title: NS_3862_2_20057

description: Library name: NS-3862_2_20057


title: NS_3862_4_081320

description: Library name: NS-3862_4_081320


title: NS_3862_16_HP24170

description: Library name: NS-3862_16_HP24170


title: S_22265_Day_0

description: Library name: 22265


title: S_HP2301_0

description: Library name: HP2301


title: S_HP21342_0

description: Library name: HP21342


title: NS_3862_15_HP24149

description: Library name: NS-3862_15_HP24149


title: NS_3862_14_HP23256

description: Library name: NS-3862_14_HP23256


title: S_HP21337_0

description: Library name: HP21337


title: S_HP21302_0

description: Library name: HP21302


title: S_HP22068_Day_0

description: Library name: HP22068


title: NS_3862_13_HP23227

description: Library name: NS-3862_13_HP23227


title: NS_3862_12_HP23219

description: Library name: NS-3862_12_HP23219


title: S_HP2129_0

description: Library name: HP2129


title: S_HP21272_0

description: Library name: HP21272


title: S_HP21263_0

description: Library name: HP21263


title: NS_3862_10_VCU1Healthy

description: Library name: NS-3862_10_VCU1Healthy


title: NS_3862_3_K442

description: Library name: NS-3862_3_K442


title: S_HP21247_0

description: Library name: HP21247


title: S_HP21243_0

description: Library name: HP21243


title: FFPE tumor section_31

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

description:
Library name: T201186_ 8T
Column name in CountMatrix.txt: T201186_ 8T

data_processing:
Raw sequencing reads were quality-checked using FastQC (v0.12.1).
Adapter trimming and quality filtering were performed using fastp (v0.23.4) with the following parameters: --trim_poly_x, --trim_poly_g, -q 20, -l 20.
The processed reads were aligned to the reference genome (hg38) using HISAT2 (v2.2.1). Aligned reads were sorted and indexed using Samtools (v1.20).
Gene expression quantification was performed using featureCounts (Subread v2.0.6).
Assembly: hg38
Supplementary files format and content: tab-deliminated txt file includes raw counts for each Sample

source_name: EGFR-mutant lung cancer

extract_protocol:
Tumor tissue was obtained by macrodissection, and RNA was extracted from two FFPE sections (thickness of 10 μm), each with an area of >1 cm², with the use of a MagMAX FFPE DNA/RNA Ultra Kit (#A31881, Thermo Fisher Scientific).
RNA libraries for RNA-seq were prepared using Twist RNA Library Prep Kit along with the Twist Human Core Exome Panel.

value: EGFR-mutant lung cancer


title: FFPE tumor section_32

description:
Library name: T21385_4T
Column name in CountMatrix.txt: T21385_4T


title: S_HP2123_0

description: Library name: HP2123


title: S_HP2121_0

description: Library name: HP2121


title: S_HP2110_0

description: Library name: HP2110


title: S_HP2103_0

description: Library name: HP2103


title: FFPE tumor section_26

description:
Library name: S192447_86T
Column name in CountMatrix.txt: S192447_86T


title: NS_3862_1_5391

description: Library name: NS-3862_1_5391


title: S_HP2102_0

description: Library name: HP2102


title: S_HP1132_0

description: Library name: HP1132


title: FFPE tumor section_27

description:
Library name: S200052_84T
Column name in CountMatrix.txt: S200052_84T


title: S_HP1062_0

description: Library name: HP1062


title: FFPE tumor section_25

description:
Library name: S112289_25T
Column name in CountMatrix.txt: S112289_25T


title: FFPE tumor section_22

description:
Library name: Q2017111_25T
Column name in CountMatrix.txt: Q2017111_25T


title: FFPE tumor section_21

description:
Library name: Q2000742_19T
Column name in CountMatrix.txt: Q2000742_19T


title: S_80620_0

description: Library name: 80620


title: S_7916_0

description: Library name: 7916


title: FFPE tumor section_24

description:
Library name: Q2214135_ 20T
Column name in CountMatrix.txt: Q2214135_ 20T


title: S_7417_0

description: Library name: 7417


title: NS_3862_11_HP23159

description: Library name: NS-3862_11_HP23159


title: FFPE tumor section_20

description:
Library name: Q1915032_12T
Column name in CountMatrix.txt: Q1915032_12T


title: S_1903_0

description: Library name: 1903


title: FFPE tumor section_30

description:
Library name: T181029_ 9T
Column name in CountMatrix.txt: T181029_ 9T


title: S_100620_0

description: Library name: 100620


title: FFPE tumor section_18

description:
Library name: Q1903221_15T
Column name in CountMatrix.txt: Q1903221_15T


title: FFPE tumor section_28

description:
Library name: T123396_8T
Column name in CountMatrix.txt: T123396_8T


title: FFPE tumor section_19

description:
Library name: Q1910072_23T
Column name in CountMatrix.txt: Q1910072_23T


title: S_Z058_0

description: Library name: Z058


title: FFPE tumor section_17

description:
Library name: Q1814314_10T
Column name in CountMatrix.txt: Q1814314_10T


title: FFPE tumor section_15

description:
Library name: Q1804524_18T
Column name in CountMatrix.txt: Q1804524_18T


title: S_HP9289_0

description: Library name: HP9289


title: FFPE tumor section_16

description:
Library name: Q1804945_14T
Column name in CountMatrix.txt: Q1804945_14T


title: S_HPA064_0

description: Library name: HPA064


title: S_HAR_002_0

description: Library name: HAR-002


title: FFPE tumor section_14

description:
Library name: Q1714261_17T
Column name in CountMatrix.txt: Q1714261_17T


title: S_HAR_001_0

description: Library name: HAR-001


title: FFPE tumor section_23

description:
Library name: Q2106763_84T
Column name in CountMatrix.txt: Q2106763_84T


title: FFPE tumor section_13

description:
Library name: Q1602098_16T
Column name in CountMatrix.txt: Q1602098_16T


title: FFPE tumor section_11

description:
Library name: P2107839_ 24T
Column name in CountMatrix.txt: P2107839_ 24T


title: FFPE tumor section_12

description:
Library name: Q1515090_T
Column name in CountMatrix.txt: Q1515090_T


title: S_9345_0

description: Library name: 9345


title: S_9318_0

description: Library name: 9318


title: FFPE tumor section_10

description:
Library name: P1900533_T
Column name in CountMatrix.txt: P1900533_T


title: FFPE tumor section_29

description:
Library name: T173622_6T
Column name in CountMatrix.txt: T173622_6T


title: S_20276_0

description: Library name: 20276


title: FFPE tumor section_8

description:
Library name: J2000379_T
Column name in CountMatrix.txt: J2000379_T


title: S_3422_0

description: Library name: 3422


title: FFPE tumor section_7

description:
Library name: J1803706_69T
Column name in CountMatrix.txt: J1803706_69T


title: S_6797_0

description: Library name: 6797


title: FFPE tumor section_6

description:
Library name: J1801384_76T
Column name in CountMatrix.txt: J1801384_76T


title: S_2017_0

description: Library name: 2017


title: FFPE tumor section_5

description:
Library name: J1700274_72T
Column name in CountMatrix.txt: J1700274_72T


title: S_20252_0

description: Library name: 20252


title: FFPE tumor section_9

description:
Library name: J2101898_28T
Column name in CountMatrix.txt: J2101898_28T


title: S_20164_0

description: Library name: 20164


title: FFPE tumor section_4

description:
Library name: E69781_121T
Column name in CountMatrix.txt: E69781_121T


title: FFPE tumor section_3

description:
Library name: E69064_89T
Column name in CountMatrix.txt: E69064_89T


title: FFPE tumor section_2

description:
Library name: E59757_113T
Column name in CountMatrix.txt: E59757_113T


title: N2, week4, ctrl

first: Yu-Hui

last: Wong

state: Taiwan

address: (NYCU) No. 155, Sec. 2, Linong St., Beitou Dist.

institute: National Yang Ming Chiao Tung University

description:
Library name: N2RGCb2Ct
N2RGCb2Ct

data_processing:
The fastq format reads underwent quality filter (score >= Q15, qualified percentage > 60%) and adapter trimming using fastp (0.20.1).
The remain reads were mapped to Human Genome Reference GRCh38 using STAR (2.7.5a) to generate output in the BAM file format.
Expected counts were then estimated using RSEM (1.3.1).
Assembly: Human Genome Reference GRCh38
Supplementary files format and content: tab-delimited text file includes expected counts for each sample

growth_protocol:
Human iPSCs are maintained in StemFlex™ medium (Gibco).
Human iPSCs for RGC differentiation are infected with lentiviruses encoding ubiquitously driven reverse tetracycline transactivator (rtTA) and Tet-On promoter driven ATOH7, BRN3B and SOX4 sequentially.
The differentiation process was started by addition of 2 μg/mL doxycycline, defined as day 0. Cells were then cultured in Medium-1: DMEM/F12 (Gibco) supplemented with N-2 (Gibco), 0.1 mM NEAA and 200 ng/mL mouse laminin (Gibco) with various other supplementary substances, namely brain-derived neurotrophic factor (BDNF, 10 μg/mL, PeproTech), ciliary neurotrophic factor (CNTF, 10 μg/mL, PeproTech), basic fibroblast growth factor (bFGF, 5 μg/mL, PeproTech), and forskolin (10 μM, Sigma-Aldrich). On day 1, Medium-1 was refreshed and 1 μg/mL puromycin and 2 μg/mL zeocin were added to allow selection of successfully induced cells.
On day 2, the cells were then dissociated using 0.5 mM EDTA in DPBS and replated onto poly-L-lysine- and laminin-coated culture plates for culture in Medium-2: DMEM/F12 + Neurobasal (1:1) supplemented with N-2, B-27, GlutaMAX (Gibco) and 200 ng/mL mouse laminin (Gibco) with supplementary substances. Zeocin selection was continued until day 6. On day 4 after doxycycline induction, Medium-2 was refreshed with 25 μM AraC to inhibit proliferation of undifferentiated cells.
On day 6, after 48 hrs of AraC treatment, Medium-2 was replaced by Medium-3: Neurobasal supplemented with N-2, B27 and GlutaMAX with supplementary substances. Hereafter, the cells were cultured in Medium-3 and medium was half refreshed every 3-4 days until treatment.The supplementary substances included doxycycline (2 μg/mL), brain-derived neurotrophic factor (BDNF, 10 μg/mL, PeproTech), ciliary neurotrophic factor (CNTF, 10 μg/mL, PeproTech), neurotrophin-3 (NT-3, 10 μg/mL, PeproTech), basic fibroblast growth factor (bFGF, 5 μg/mL, PeproTech), insulin (5 μg/mL, PeproTech) and forskolin (10 μM, Sigma-Aldrich)

extract_protocol:
Total RNA of iRGCs from day 28 were extracted using RNA Mini Kit (Geneaid).
1 μg of total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

treatment_protocol: On week 4, medium was refreshed into complete medium with 1000 ug/mL (3.6 mM) EMB and treated for 24 h. Equivalent volume of water was added as control.

value: hiPSC-derived retinal ganglion cells

value: Control


title: S_2019_0

description: Library name: 2019


title: FFPE tumor section_1

description:
Library name: E53928_T
Column name in CountMatrix.txt: E53928_T


title: N1, week4, EMB

description:
Library name: N1RGCb2EB
N1RGCb2EB

value: EMB


title: PC9 cells with shIFITM3_3

description:
Library name: PC9ShIFITM3_3
Column name in CountMatrix.txt: PC9ShIFITM3_3

growth_protocol: Cells were cultured at 37°C, 5% CO2, in RPMI supplemented with 10% Fetal Bovine Serum, 1% penicillin streptomycin.

extract_protocol:
Total RNA was isolated with the use of RNeasy Mini Kit (#74016, Qiagen) from PC-9 cells stably expressing IFITM3 or control shRNAs. Three biological replicates were processed for each condition.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep kit following manufacuter's protrcol


title: N1, week4, ctrl

description:
Library name: N1RGCb2Ct
N1RGCb2Ct


title: S_5152_0

description: Library name: 5152


title: PC9 cells with shIFITM3_1

description:
Library name: PC9ShIFITM3_1
Column name in CountMatrix.txt: PC9ShIFITM3_1


title: Allele-iRGC, week 4, ctrl

description:
Library name: ARGCb2Ct
ARGCb2Ct

source_name: Allele

value: Allele


title: Allele-iRGC, week 4, EMB

description:
Library name: ARGCb2EB
ARGCb2EB


title: PC9 cells with shControl_3

description:
Library name: PC9ShEV_3
Column name in CountMatrix.txt: PC9ShEV_3


title: PC9 cells with shControl_2

description:
Library name: PC9ShEV_2
Column name in CountMatrix.txt: PC9ShEV_2


title: Allele-iRGC-1, week 4, ctrl

description:
Library name: ARGCb1Ct
ARGCb1Ct


title: PC9 cells with shControl_1

description:
Library name: PC9ShEV_1
Column name in CountMatrix.txt: PC9ShEV_1


title: Doxy5: ICITED4-CM+Doxy

city: Shanghai

first: Chang

last: Liu

address: Nanchen Road 333

country: China

institute: Shanghai University

description: Library name: Sample10

data_processing:
Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs).
Assembly: GRCh38.p13
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

extract_protocol:
Total RNA was isolated from cells by extraction with Trizol
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: H9-derived cardiomyocytes

value: CITED4 overexpressing

value: doxy


title: Doxy1: ICITED4-CM+Doxy

description: Library name: Sample6


title: Doxy2: ICITED4-CM+Doxy

description: Library name: Sample7


title: Doxy4: ICITED4-CM+Doxy

description: Library name: Sample9


title: ChIP_SIX1-2

city: Manchester

first: Georges

last: Lacaud

state: England

address: Wilmslow Raod

department: Stem Cell Biology

country: United Kingdom

institute: Cancer Research UK Manchester Institute

description: Library name: 87 - SIX1 cell (2)

data_processing:
Raw fastqc sequencing files were run through nextflow on the CRUK-MI (Manchester institute) server to generate merged salmon gene counts and BigWig files
DESeq2 R package was run to infer differentially expressed genes accross samples ChIPpeakAnno bioconductor package was used in R for gene ontology
Assembly: hg38
Supplementary files format and content: Salon merged gene counts were generared by nextflow. All counts concatenated on same tsv file BigWig files generated by nextflow  - ChIP

source_name: 87 - SIX1 cell (2)

growth_protocol: THP1 cells were grown in RPMI media in order to harvest 4x10^8 cells in T225 TC flasks for ChIP. KO and NT cells were cultured in RPMI media for 48hrs before sorting and RNA isolation.

extract_protocol:
Direct RNA isolation with RNeasy Mini Kit [Qiagen Ref. 74004] -RNA Following pulldown - DNA was extracted using Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v), before being further purified with QIAquick PCR Purification Kit
RNA was sent to BMKGENE for library preperation and sequencing

value: Blood (Bone marrow)

value: monocytic


title: Doxy3: ICITED4-CM+Doxy

description: Library name: Sample8


title: Rat #16N 24 hour abstinence following 16 days of methamphetamine self-administration

city: Daegu

first: Taekwon

last: Son

address: 61, Cheomdan-ro, Dong-gu

department: Korea Brain Bank

country: South Korea

institute: Korea Brain Research Institute

description: Library name: MA24-16N

data_processing:
Sequence reads of the 12 independent samples were trimmed for both PCR and sequencing adapters with Cutadapt (version 1.18).
Trimmed reads were aligned to the rn6 rat reference genome using STAR (version 2.7.0e).
Read counts were generated using featureCounts function from the HTSeq (version 0.12.4).
Assembly: rn6
Supplementary files format and content: Tab-delimited text file include raw counts per mRNA per sample.

organism: Rattus norvegicus

source_name: striatum

extract_protocol:
Total RNA was extracted using TRIzol® reagent (Invitrogen).
The isolated total RNA was processed for preparation of an mRNA sequencing library using a TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: striatum

value: WT

value: methamphetamine


title: control5: ICITED4-CM

description: Library name: Sample5

value: con


title: N2, week4, EMB

description:
Library name: N2RGCb2EB
N2RGCb2EB


title: control3: ICITED4-CM

description: Library name: Sample3


title: control4: ICITED4-CM

description: Library name: Sample4


title: Rat #15N 24 hour abstinence following 16 days of methamphetamine self-administration

description: Library name: MA24-15N


title: S_1930_0

description: Library name: 1930

value: Pancreatic tissue

value: Acinar cells


title: Rat #14N 24 hour abstinence following 16 days of methamphetamine self-administration

description: Library name: MA24-14N


title: control2: ICITED4-CM

description: Library name: Sample2


title: PC9 cells with shIFITM3_2

description:
Library name: PC9ShIFITM3_2
Column name in CountMatrix.txt: PC9ShIFITM3_2


title: ChIP isotype

description: Library name: 87 - IgG

source_name: 87 - IgG


title: ChIP_SIX1-1

description: Library name: 87 - SIX1 cell (1)

source_name: 87 - SIX1 cell (1)


title: Allele-iRGC-1, week 4, EMB

description:
Library name: ARGCb1EB
ARGCb1EB


title: Knock_out_48hrs3

description: Library name: T3

source_name: THP1 KO 3 - 48hr


title: control1: ICITED4-CM

description: Library name: Sample1


title: Rat #9N 24 hour abstinence following 16 days of methamphetamine self-administration

description: Library name: MA24-9N


title: Knock_out_48hrs2

description: Library name: T2

source_name: THP1 KO 2 - 48hr


title: Rat #7N 12 hour abstinence following 16 days of methamphetamine self-administration

description: Library name: MA12-7N


title: HeLa cells, ADAR1-ADAR2-double-knockout, replicate 4

city: Rochester

first: Christian

middle: Karl

last: Pfaller

state: MN

address: 200 First Street SW

department: Molecular Medicine

institute: Mayo Clinic

description: Library name: HeLa_DKO_4

data_processing:
Raw FASTQ files were quality trimmed with fastp (v. 0.23.1): -M 30 -3 -5 -n 0 -l 35 -q 30 -u 15 -w 16 -f 1 -F 1
Trimmmed FASTQ files were aligned to reference genomes with STAR (v. 2.7.9a): --runThreadN 30 --outSAMmapqUnique 60 --outSAMtype BAM SortedByCoordinate --twopassMode Basic --outFilterType Normal --outFilterMultimapNmax 10 --alignSJoverhangMin 5 --alignSJDBoverhangMin 3 --outFilterMismatchNmax 10 --outFilterMismatchNoverReadLmax 1 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --alignIntronMin 21 --alignIntronMax 0 --alignMatesGapMax 0
Optical duplicates were marked and removed with PICARD MarkDuplicates (v. 2.27.5): CREATE_INDEX=true REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT
Reads spanning exon/exon junctions were split using GATK SplitNCigarReads (v. 4.3.0.0) using default settings
Reads were re-aligned with GATK LeftAlignIndels (v. 4.3.0.0): --disable-read-filter WellformedReadFilter
For deNovo analysis: BAM alignments were analyzed with TSniffer deNovo: -wSize 100 -minCov 4 -chunkSize 5000000 -primary (The primary parameter was omitted for analysis of ferret data); https://github.com/maiher/tsniffer_1.0
For Regio analysis: BAM alignments were analyzed with TSniffer Regio using a filtered and cleaned-up set of regions derived from deNovo analysis using default parameters; https://github.com/maiher/tsniffer_1.0
Assembly: hg38 (GCA_000001405.15_GRCh38)
Assembly: MusPutFur1.0 (GCF_000215625.1)
Supplementary files format and content: deNovo analysis: gff file with detected transition regions; annotation column includes transition type, relative transition frequencies, p-value from Fisher's exact test, transition sites count, and nucleotide positions
Supplementary files format and content: Regio analysis: gff file with detected transition regions; annotation column includes transition type, relative transition frequencies, p-value from Fisher's exact test, transition sites count, and nucleotide positions

source_name: HeLa

growth_protocol: HeLa cells were grown in standard growth medium in 6 well plates and harvested at confluency; ferret PBMCs were isolated from fresh whole blood and cultivated in standard growth medium for 3 days before RNA extraction.

extract_protocol:
HeLa/Ferret samples: Total RNA was extracted using Trizol; for HeLa cells, genomic DNA was removed by two Dnase I treatment steps and RNA was cleaned up using phenol/chloroform/isoamyl alcohol
HeLa/Ferret samples: RNA integrity numbers (RIN) were assessed by fragment analyzer and only RNAs with RIN=10 were further  processed; ribosomal RNA was removed before RNA-seq library preparation; strand-specific libraries were generated using a custom protocol at the Paul-Ehrlich-Institute (PMID 35952673) or a standard protocol by Azenta (Leipzig, Germany)
HeLa, Ferret samples: Libraries were sequenced at 2x 150 bp paired-end reads

value: HeLa


title: Visium HD, LR1, LR2

description: Library name: Slide2

data_processing:
Sequencing data (FASTQ files) were processed and analyzed using Space Ranger (version 3.0.0) software to assess data quality and generate spatial gene expression profiles.
Assembly: GRCh38
Supplementary files format and content: slide1.tar: Tar archive containing the 2μm resolution binning outputs of slide1 obtained from space ranger and coordinate data after stardist processing
Supplementary files format and content: slide2.tar: Tar archive containing the 2μm resolution binning outputs of slide2 obtained from space ranger and coordinate data after stardist processing
Library strategy: Spatial Transcriptomics

extract_protocol:
In this study, two capture areas on a Visium HD slide were utilized, with four samples assigned to each capture area. A total of eight samples consisting of paired pre- and post-treatment samples from four patients (ER, SR, LR1 and LR2) were analyzed, and each sample was differentiated from (ER_pre, ER_post, SR_pre, SR_post, LR1_pre, LR1_post, LR2_pre, LR2_post). Specifically, ER and SR samples were assigned to one capture area, while LR1 and LR2 samples were assigned to the other capture area. Initially, RNA was extracted from FFPE tissue sections prepared for RNA quality assessment, and the DV200 value was measured using the 4200 Tape Station. The DV200 value for all samples was greater than or equal to 30%. The FFPE tissue sections were then subjected to deparaffinization and H&E staining following the Visium HD FFPE Tissue Preparation protocol provided by 10x Genomics (Visium HD FFPE Tissue Preparation Handbook, CG000684 Rev A). After staining, tissue sections were imaged using the EVIDENT VS200 microscope in accordance with the 10X Genomics protocol (Visium HD Spatial Applications Image Guidelines CG000688 Rev A).
Gene expression libraries were prepared from the H&E-stained sections following the 10X Genomics protocol (Visium HD Spatial Gene Expression Reagent Kits User Guide CG000685 Rev A). The quality of the prepared libraries was evaluated using the 4200 Tape Station, and all libraries were confirmed to have sufficient concentrations. The Visium libraries were sequenced using the NovaSeq X Plus platform with a paired-end configuration (read1: 150 bp, read2: 150 bp).

value: Lung

value: LR1 LR2


title: Knock_out_48hrs1

description: Library name: T1

source_name: THP1 KO 1 - 48hr


title: Visium HD, ER, SR

description: Library name: Slide1

value: ER SR


title: HeLa cells, ADAR1-ADAR2-double-knockout, replicate 2

description: Library name: HeLa_DKO_2


title: non_targeting_48hrs3

description: Library name: NT3

source_name: THP1 NT3 -48hr


title: Rat #31 12 hour abstinence following 16 days of methamphetamine self-administration

description: Library name: MA12-31


title: HeLa cells, ADAR1-knockout, replicate 5

description: Library name: HeLa_1KO_5


title: HeLa cells, ADAR1-knockout, replicate 4

description: Library name: HeLa_1KO_4


title: HeLa cells, ADAR1-knockout, replicate 3

description: Library name: HeLa_1KO_3


title: Rat #4N 12 hour abstinence following 16 days of methamphetamine self-administration

description: Library name: MA12-4N


title: HeLa cells, ADAR1-knockout, replicate 2

description: Library name: HeLa_1KO_2


title: non_targeting_48hrs1

description: Library name: NT1

source_name: THP1 NT1 -48hr


title: Non-addicted rat #13 after 16 days of methamphetamine self-administration

description: Library name: NA-13


title: Rat #21 12 hour abstinence following 16 days of methamphetamine self-administration

description: Library name: MA12-21


title: HeLa cells, parental, untreated, replicate 5

description: Library name: HeLa_WT_5

value: wild type


title: HeLa cells, parental, untreated, replicate 4

description: Library name: HeLa_WT_4


title: HeLa cells, parental, untreated, replicate 3

description: Library name: HeLa_WT_3


title: Non-addicted rat #12 after 16 days of methamphetamine self-administration

description: Library name: NA-12


title: Knock_out_96hrs2

description: Library name: GL88_01_LC34_S19

source_name: THP1 KO 2 - 96hr


title: Knock_out_96hrs1

description: Library name: GL88_12_LC33_S30

source_name: THP1 KO 1 - 96hr


title: HeLa cells, ADAR1-ADAR2-double-knockout, replicate 3

description: Library name: HeLa_DKO_3


title: RNA-seq of Oocyte4 from the index

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

description:
Library name: Index_Oocyte4
Column name in NXTRA_combined.counts.txt: GHI-F0063-G7_0601486261

data_processing:
Reads were quality-trimmed with bbduk.sh (BBMap v38.69)
Alignment to GRCh37 (hs37d53) using STAR (v2.6.1d).
Gene counts generated with HTSeq-count (v0.9.1).
Normalization with TMMwsp (edgeR).
PCA on CLR-transformed CPM values, batch-corrected, using top 3,000 variable genes.
Assembly: GRCh37
Supplementary files format and content: tsv files. Column1: EnsembleID, Column2: Raw Count

source_name: MII Oocyte

growth_protocol: MII oocytes were retrieved after hCG-triggered ovulation, with 8/14 reaching maturity.

extract_protocol:
cDNA was generated using SMART-Seq v4 (Takara Bio, USA), amplified, purified, and quantified.
Nextera XT (Illumina, USA) was used for tagmentation, barcoding, and sequencing on NovaSeq 6000 (50M reads/sample).

treatment_protocol: MII oocytes underwent ICSI, but none formed pronuclei or cleaved.

value: MII Oocyte

value: Fertilized


title: HeLa cells, parental, untreated, replicate 2

description: Library name: HeLa_WT_2


title: RNA-seq of Oocyte3 from the index

description:
Library name: Index_Oocyte3
Column name in NXTRA_combined.counts.txt: GHI-F0063-G5_0601486251


title: Non-addicted rat #11 after 16 days of methamphetamine self-administration

description: Library name: NA-11


title: Non-addicted rat #9 after 16 days of methamphetamine self-administration

description: Library name: NA-9


title: RNA-seq of Oocyte2 from the index

description:
Library name: Index_Oocyte2
Column name in NXTRA_combined.counts.txt: GHI-F0063-G3_0601486241


title: HeLa cells, ADAR1-ADAR2-double-knockout, replicate 1

description: Library name: HeLa_DKO_1


title: RNA-seq of Oocyte1 from the index

description:
Library name: Index_Oocyte1
Column name in NXTRA_combined.counts.txt: GHI-F0063-G2_0601486231


title: non_targeting_96hrs2

description: Library name: GL88_03_LC32_S21

source_name: THP1 NT 2 - 96hr


title: HUDEP-2, lentiviral empty vector, GATA2 antibody, replicate 1

city: Madison

first: Bresnick

last: Emery

state: WI

address: 600 Highland Avenue

institute: University of Wisconsin Madison

description: Library name: NS.X0106.003.N712---N508.EB-KJ-WISC_1_5A-7A_WT_EV_G2_1

data_processing:
QC with FastQC
Adadptors removed with cutadapt v. 3.3
Reads aligned to hg38 with Bowtie1 v. 2.2.5
bigwig files generated with bamCoverage v. 3.5.3
Peaks called with MACS2 v. 2.2.7.1 and q-value cutoff 1e-6
Assembly: hg38
Supplementary files format and content: bigwig (.bw)
Supplementary files format and content: narrowPeak (.narrowPeak)
Library strategy: CUT&Run

growth_protocol: SFEM II (Stem Cell Technologies, # 09655) supplemented with 2X Pen/Strep (ThermoFisher; #15140-122), 3U/ml Epo (Stem Cell Technology), 50 ng/ml human SCF (Peprotech, #300-07), 1µg/ml Doxycycline (Sigma Aldrich, #D9891)*, and 1uM Dexamethasone (Sigma Aldrich, #D4902).

extract_protocol:
Following tagmentation, samples were treated with Proteinase K and incubated at 37C overnight.  DNA was purified by spin clolumn (Cell Signaling Technology, #14209)
Libraries were prepared with the NEB Next HiFi 2x PCR Master Mix (M0514S) following the manufacturer’s protocol using 16 cycles of amplification. Sample concentration was determined using Qubit 1X dsDNA HS Assay (ThermoFisher Q33231). The quality of the library was assessed using Bioanalyzer High Sensitivity DNA Analysis (Agilent).

treatment_protocol: Lentivally infected cells were sorted for GFP expression prior to Cut & Tag processing

value: immortalized erythroid progenitor

value: Wild-type

tag: expression plasmid

value: Empty vector

value: Rabbit anti-GATA2 (in-house)


title: HUDEP-2, lentiviral empty vector, GATA2 antibody, replicate 2

description: Library name: NS.X0106.003.N712---N503.EB-KJ-WISC_2_5F-7A_WT_EV_G2_2


title: non_targeting_48hrs2

description: Library name: NT2

source_name: THP1 NT2 -48hr

value: Blood (Bone marrow)

value: monocytic


title: non_targeting_96hrs1

description: Library name: GL88_06_LC31_S24

source_name: THP1 NT 1 - 96hr


title: HUDEP-2, lentiviral empty vector, GATA2 antibody, replicate 3

description: Library name: NS.X0106.003.N712---N502.EB-KJ-WISC_3_5G-7A_WT_EV_G2_3


title: Knock_out_72hrs2

description: Library name: GL88_14_LC30_S32

source_name: THP1 KO 2 - 72hr


title: tifx_3

city: Xianyang

first: Young

last: Tang

state: Shaanxi

address: #22 Xinong Road, Yangling District

department: College of Veterinary Medicine

institute: Northwest A&F University

description: Library name: Sample16

data_processing:
1.Clean reads were obtained by removing adapter-containing, poly-N, and low-quality reads from raw data. The reference genome index was built using Hisat2 v2.0.5, and paired-end clean reads were aligned to the reference genome.
2.The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
3.FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
4.Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
5.Used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: ncbi_bos_taurus_gcf_002263795_3_ars_ucd2_0(bECs) ensembl_100_bos_taurus_ars_ucd1_2_toplevel(bESCs)
Supplementary files format and content: Only raw FASTQ files are available.

organism: Bos taurus

source_name: Blastocyst

extract_protocol:
RNA was extracted from bECs using the SMART-Seq® mRNA HT LP (Takara, #032124) and from bESCs using the RNeasy Mini Kit (Qiagen, #74104), both following the respective manufacturer’s protocols.
Total RNA was purified to obtain mRNA using poly-T beads. mRNA was fragmented and reverse transcribed into first-strand cDNA with random hexamers and M-MuLV Reverse Transcriptase. Second-strand synthesis was done with DNA Polymerase I and RNase H. DNA ends were blunted and adenylated, followed by ligation of hairpin loop adaptors. cDNA fragments (370–420 bp) were selected using AMPure XP system. PCR amplification was performed with Phusion polymerase, universal primers, and index primers. Final PCR products were purified and library quality assessed on Agilent Bioanalyzer 2100.

value: Blastocyst

value: tifx, bovine embryonic stem cell culture medium

value: embryonic stem cells

value: WT


title: HUDEP-2, lentiviral empty vector, GATA2 antibody, replicate 4

description: Library name: NS.X0106.003.N712---N501.EB-KJ-WISC_4_5H-7A_WT_EV_G2_4


title: tifx_2

description: Library name: Sample15


title: GATA2 low HUDEP-2, lentiviral empty vector, GATA2 antibody, replicate 1

description: Library name: NS.X0106.003.N711---N508.EB-KJ-WISC_5_5A-7B_HET_EV_G2_1


title: non_targeting_72hrs2

description: Library name: GL88_05_LC28_S23

source_name: THP1 NT 2 - 72hr


title: LY_2

description: Library name: Sample13


title: GATA2 low HUDEP-2, lentiviral empty vector, GATA2 antibody, replicate 4

description: Library name: NS.X0106.003.N711---N501.EB-KJ-WISC_8_5H-7B_HET_EV_G2_4


title: Knock_out_72hrs1

description: Library name: GL88_07_LC29_S25

source_name: THP1 KO 1 - 72hr


title: GATA2 low HUDEP-2, lentiviral empty vector, IgG isotype control (GATA2), replicate 1

description: Library name: NS.X0106.003.N710---N508.EB-KJ-WISC_9_5A-7C_HET_EV_IgG_1

value: Rabbit IgG (Invitrogen, #10500C)


title: LY_3

description: Library name: Sample14


title: GATA2 low HUDEP-2, lentiviral empty vector, GATA2 antibody, replicate 2

description: Library name: NS.X0106.003.N711---N503.EB-KJ-WISC_6_5F-7B_HET_EV_G2_2


title: CUTandTag_7860_PAX8ko6_HIF1b

city: Aachen

first: René

last: Krüger

address: Pauwelsstraße 20

department: Institute for Stem Cell Biology

institute: RWTH Aachen University Medical School

description: Library name: CUTandTag_7860_PAX8ko6_HIF1b

data_processing:
RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and aligned to the GRCh38 genome using Bowtie2 version 2.3.4.1.
Reads were sorted using samtools v.1.8.
Reads aligned to mtDNA, low quality reads (MAPQ <30), ENCODE blacklisted regions and duplicates were removed using samtools version 1.8 and Picard version 2.25.2.
Bigwig files were generated using deeptools bamCoverage version 3.5.0, command –normalizeUsing RPGC --binsize 1.
Assembly: GRCh38
Supplementary files format and content: bigWig
Library strategy: CUT&Run

extract_protocol:
CUT&Tag was performed according to the protocol published by Kaya-Okur et al. (DOI: 10.1038/s41467-019-09982-5) with modifications based on the protocol by Bartosovic et al. (DOI: 10.1038/s41587-021-00869-9). In short 250,000-350,000 cells were lysed and resuspended in antibody buffer with 1:50 diluted primary antibody (monoclonal rabbit anti-HIF-1β antibody [5537S, Cell Signaling Technology] or polyclonal rabbit anti-HIF-1β antibody [NB100-110, Novus Biologicals] or monoclonal rabbit anti-H3K27ac antibody [ab177178, Abcam] or polyclonal rabbit anti-HIF-1α antibody [Cay10006421, Cayman Chemicals] or polyclonal rabbit anti-HNF-1β antibody [HPA002083, Atlas Antibodies, Sigma Aldrich]). Cells were washed and incubated with Dig-wash buffer containing 1:50 diluted secondary antibody (ABIN101961, Guinea Pig anti-Rabbit IgG antibody, Antibodies-Online). Cells were washed again and resuspended in Dig-300 buffer with 1:100 diluted protein A–TN5 transposase (C01070002, Diagenode, loaded with mosaic adapters according to manufacturer’s instructions). Following Tn5 loading cells were washed and resuspended in tagmentation buffer. Tagmentation was stopped by addition of 500 mM EDTA, SDS 10% and Proteinase K. DNA was purified using the DNA Clean and Concentrator-5 Kit (Zymo Research, Freiburg, Germany) according to the manufacturer’s protocol. Following purification, library fragments were amplified by using the NEB Next® High-Fidelity 2X PCR Master Mix (New England Biolabs, Ipswich, UK) and custom-made indexed Nextera PCR primers (Sigma Aldrich, St. Louis, MO, USA). Libraries were amplified for a total of 15 cycles. SPRI select beads (Beckman Coulter GmbH, Krefeld, Germany) were used for library clean-up according to the manufacturer’s protocol.
CUT&Tag library preparation was carried out applying the protocol published by Kaya-Okur et al. (DOI: 10.1038/s41467-019-09982-5) Libraries were sequenced on Illumina NovaSeq XPlus platforms following the manufacturer's protocols.

value: Single clone of cells

tag: cut&tag antibody


title: LY10_3

description: Library name: Sample12

value: embryonic cells


title: GATA2 low HUDEP-2, lentiviral empty vector, GATA2 antibody, replicate 3

description: Library name: NS.X0106.003.N711---N502.EB-KJ-WISC_7_5G-7B_HET_EV_G2_3


title: GATA2 low HUDEP-2, lentiviral HA-GATA2, GATA2 antibody, replicate 1

description: Library name: NS.X0106.003.N709---N508.EB-KJ-WISC_11_5A-7D_HET_HAG2_G2_1


title: LY10_2

description: Library name: Sample11


title: GATA2 low HUDEP-2, lentiviral HA-GATA2, GATA2 antibody, replicate 3

description: Library name: NS.X0106.003.N709---N502.EB-KJ-WISC_13_5G-7D_HET_HAG2_G2_3


title: non_targeting_72hrs1

description: Library name: GL88_04_LC27_S22

source_name: THP1 NT 1 - 72hr


title: GATA2 low HUDEP-2, lentiviral empty vector, IgG isotype control (GATA2), replicate 2

description: Library name: NS.X0106.003.N710---N503.EB-KJ-WISC_10_5F-7C_HET_EV_IgG_2


title: GATA2 low HUDEP-2, lentiviral HA-GATA2, GATA2 antibody, replicate2

description: Library name: NS.X0106.003.N709---N503.EB-KJ-WISC_12_5F-7D_HET_HAG2_G2_2


title: GATA2 low HUDEP-2, lentiviral HA-GATA2, GATA2 antibody, replicate 4

description: Library name: NS.X0106.003.N709---N501.EB-KJ-WISC_14_5H-7D_HET_HAG2_G2_4


title: LY10_1

description: Library name: Sample10


title: GATA2 low HUDEP-2, lentiviral HA-GATA2, IgG isotype control, replicate 4

description: Library name: NS.X0106.003.N708---N501.EB-KJ-WISC_16_5H-7E_HET_HAG2_IgG_4


title: GATA2 low HUDEP-2, lentiviral HA-GATA2, IgG isotype control, replicate 3

description: Library name: NS.X0106.003.N708---N502.EB-KJ-WISC_15_5G-7E_HET_HAG2_IgG_3


title: CUTandTag_7860_HNF1bko8_HIF1b

description: Library name: CUTandTag_7860_HNF1bko8_HIF1b


title: DMSO_2

description: Library name: Sample8

value: DMSO


title: CUTandTag_7860_nt4_forHNFandPAXko_HIF1b

description: Library name: CUTandTag_7860_nt4_forHNFandPAXko_HIF1b

value: non-targeting control sgRNAs


title: GATA2 low HUDEP-2, lentiviral HA-GATA2(T354M), GATA2 antibody, replicate 2

description: Library name: NS.X0106.003.N707---N503.EB-KJ-WISC_18_5F-7F_HET_T354M_G2_2


title: GATA2 low HUDEP-2, lentiviral HA-GATA2(T354M), GATA2 antibody, replicate 1

description: Library name: NS.X0106.003.N707---N508.EB-KJ-WISC_17_5A-7F_HET_T354M_G2_1


title: CUTandTag_7860_PAX8ko2_HIF1b

description: Library name: CUTandTag_7860_PAX8ko2_HIF1b


title: CUTandTag_7860_nt3_forHNFandPAXko_HIF1b

description: Library name: CUTandTag_7860_nt3_forHNFandPAXko_HIF1b


title: DMSO_3

description: Library name: Sample9


title: GATA2 low HUDEP-2, lentiviral HA-GATA2(T354M), GATA2 antibody, replicate 3

description: Library name: NS.X0106.003.N707---N502.EB-KJ-WISC_19_5G-7F_HET_T354M_G2_3


title: LY_DMSO_2

description: Library name: Sample6


title: GATA2 low HUDEP-2, lentiviral HA-GATA2(T354M), GATA2 antibody, replicate 4

description: Library name: NS.X0106.003.N707---N501.EB-KJ-WISC_20_5H-7F_HET_T354M_G2_4


title: CUTandTag_7860_E2PAX8ko_HIF1b

description: Library name: CUTandTag_7860_E2PAX8ko_HIF1b


title: GATA2 low HUDEP-2, lentiviral empty vector, HA antibody, replicate 2

description: Library name: NS.X0106.003.N706---N503.EB-KJ-WISC_22_5F-7G_HET_EV_HA_2

value: Rabbit anti-HA (Cell Signaling Technology, #3724)


title: GATA2 low HUDEP-2, lentiviral empty vector, HA antibody, replicate 4

description: Library name: NS.X0106.003.N706---N501.EB-KJ-WISC_24_5H-7G_HET_EV_HA_4


title: GATA2 low HUDEP-2, lentiviral empty vector, HA antibody, replicate 3

description: Library name: NS.X0106.003.N706---N502.EB-KJ-WISC_23_5G-7G_HET_EV_HA_3


title: cell16_LY_2

description: Library name: Sample5


title: GATA2 low HUDEP-2, lentiviral HA-GATA2, HA antibody, replicate 1

description: Library name: NS.X0106.003.N704---N508.EB-KJ-WISC_29_5A-7I_HET_HAG2_HA_1


title: CUTandTag_7860_E2HNF1bko_HIF1b

description: Library name: CUTandTag_7860_E2HNF1bko_HIF1b


title: cell16_LY_1

description: Library name: Sample4


title: GATA2 low HUDEP-2, lentiviral empty vector, IgG isotype control (HA), replicate 4

description: Library name: NS.X0106.003.N705---N501.EB-KJ-WISC_28_5H-7H_HET_EV_IgG_4


description: Library name: CUTandTag_7860_ntforE2HNF1bkoandE2PAX8ko_HIF1b


title: CUTandTag_7860_HNF1bko7_HIF1b

description: Library name: CUTandTag_7860_HNF1bko7_HIF1b


title: GATA2 low HUDEP-2, lentiviral empty vector, IgG isotype control (HA), replicate 2

description: Library name: NS.X0106.003.N705---N503.EB-KJ-WISC_26_5F-7H_HET_EV_IgG_2


title: LY_DMSO_1

description: Library name: Sample3


title: GATA2 low HUDEP-2, lentiviral HA-GATA2, HA antibody, replicate 3

description: Library name: NS.X0106.003.N704---N502.EB-KJ-WISC_31_5G-7I_HET_HAG2_HA_3


title: GATA2 low HUDEP-2, lentiviral HA-GATA2, HA antibody, replicate 2

description: Library name: NS.X0106.003.N704---N503.EB-KJ-WISC_30_5F-7I_HET_HAG2_HA_2


title: CUTandTag_7860_HIF1Bko8_H3K27ac

description: Library name: CUTandTag_7860_HIF1Bko8_H3K27ac


title: DMSO_1

description: Library name: Sample7


title: cell2_LY_2

description: Library name: Sample2


title: GATA2 low HUDEP-2, lentiviral HA-GATA2, HA antibody, replicate 4

description: Library name: NS.X0106.003.N704---N501.EB-KJ-WISC_32_5H-7I_HET_HAG2_HA_4


title: GATA2 low HUDEP-2, lentiviral empty vector, HA antibody, replicate 1

description: Library name: NS.X0106.003.N706---N508.EB-KJ-WISC_21_5A-7G_HET_EV_HA_1


title: GATA2 low HUDEP-2, lentiviral HA-GATA2, IgG isotype control, replicate 1

description: Library name: NS.X0106.003.N703---N508.EB-KJ-WISC_33_5A-7J_HET_HAG2_IgG_1


title: GATA2 low HUDEP-2, lentiviral HA-GATA2, IgG isotype control, replicate 2

description: Library name: NS.X0106.003.N703---N503.EB-KJ-WISC_34_5F-7J_HET_HAG2_IgG_2


title: cell2_LY_1

description: Library name: Sample1


title: CUTandTag_RCC4_HIF1Bko7_H3K27ac

description: Library name: CUTandTag_RCC4_HIF1Bko7_H3K27ac


title: GATA2 low HUDEP-2, lentiviral HA-GATA2(T354M), HA antibody, replicate 1

description: Library name: NS.X0106.003.N702---N508.EB-KJ-WISC_37_5A-7K_HET_T354M_HA_1


title: GATA2 low HUDEP-2, lentiviral HA-GATA2(T354M), HA antibody, replicate 2

description: Library name: NS.X0106.003.N702---N503.EB-KJ-WISC_38_5F-7K_HET_T354M_HA_2


title: CUTandTag_7860_nt5_forHIF1Bko_H3K27ac

description: Library name: CUTandTag_7860_nt5_forHIF1Bko_H3K27ac


title: I59,IGRA+,PBMC,DMSO

city: La Jolla

first: Leila

middle: Y

last: Chihab

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

description:
Library name: Sample 542
XT0134_DMSO_S190_L001

data_processing:
Reads that passed illumina filters were filtered to eliminate reads aligning to tRNA, rRNA, and adapter sequences. The reads were then aligned to GRCh38 reference genome using TopHat. DUST scores were calculated with PRINSEQ Lite and low complexity reads (DUST >4) were removed from the BAM files. The alignment results were parsed via SAMtools to generate SAM files. Read counts for each genomic feature were obtained with the htseq-count program.
Assembly: GRCh38
Supplementary files format and content: abundance measurementas as a matrix table

source_name: PBMC

extract_protocol:
RNA was purified using an miRNeasy Micro Kit (QIAGEN).
Purified total RNA (1–5 ng) was amplified following the Smart-Seq2 protocol (16 cycles of cDNA amplification). 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina)

treatment_protocol: No specific treatment involved

value: PBMC

value: IGRA+


title: C59,IGRA-,PBMC,DMSO

description:
Library name: Sample 538
TU0146_Z

value: IGRA-


title: C59,IGRA-,PBMC,MTB300

description:
Library name: Sample 539
TU0146_Y


title: CUTandTag_RCC4_nt2_forHIF1Bko_H3K27ac

description: Library name: CUTandTag_RCC4_nt2_forHIF1Bko_H3K27ac


title: T57,ATB,PBMC,DMSO

description:
Library name: Sample 536
TU0145_Z

value: ATB


title: CUTandTag_7860_HIF1Bko4_H3K27ac

description: Library name: CUTandTag_7860_HIF1Bko4_H3K27ac


title: I54,IGRA+,PBMC,MTB300

description:
Library name: Sample 499
TU0070_MTB300_S173_L001


title: GATA2 low HUDEP-2, lentiviral HA-GATA2(T354M), HA antibody, replicate 3

description: Library name: NS.X0106.003.N702---N502.EB-KJ-WISC_39_5G-7K_HET_T354M_HA_3

value: immortalized erythroid progenitor


title: CUTandTag_7860_nt3_forHIF1Bko_H3K27ac

description: Library name: CUTandTag_7860_nt3_forHIF1Bko_H3K27ac


title: GATA2 low HUDEP-2, lentiviral HA-GATA2(T354M), HA antibody, replicate 4

description: Library name: NS.X0106.003.N702---N501.EB-KJ-WISC_40_5H-7K_HET_T354M_HA_4


title: T57,ATB,PBMC,MTB300

description:
Library name: Sample 537
TU0145_Y


title: C60,IGRA-,PBMC,DMSO

description:
Library name: Sample 541
XT0130_DMSO_S188_L001


title: C60,IGRA-,PBMC,MTB300

description:
Library name: Sample 540
XT0130_MTB300_S189_L001


title: CUTandTag_RCC4_HIF1Bko2_H3K27ac

description: Library name: CUTandTag_RCC4_HIF1Bko2_H3K27ac


title: I55,IGRA+,PBMC,DMSO

description:
Library name: Sample 503
TU0075_DMSO_S174_L001


title: I55,IGRA+,PBMC,MTB300

description:
Library name: Sample 502
TU0075_MTB300_S175_L001


title: T56,ATB,PBMC,MTB300

description:
Library name: Sample 535
TU0141_Y


title: C51,IGRA-,PBMC,MTB300

description:
Library name: Sample 491
TU0054_MTB300_S169_L001


title: CUTandTag_RCC4iVHL_Dox_H3K27ac_rep_2

description: Library name: CUTandTag_RCC4iVHL_Dox_H3K27ac_rep_2

value: Doxycycline


title: I54,IGRA+,PBMC,DMSO

description:
Library name: Sample 498
4225_DMSO_S3_L001


title: T55,ATB,PBMC,MTB300

description:
Library name: Sample 533
TU0139_Y


title: CUTandTag_RCC4iVHL_DMSO_H3K27ac_rep_2

description: Library name: CUTandTag_RCC4iVHL_DMSO_H3K27ac_rep_2


title: C53,IGRA-,PBMC,DMSO

description:
Library name: Sample 495
TU0059_DMSO_S170_L001


title: C53,IGRA-,PBMC,MTB300

description:
Library name: Sample 494
TU0059_MTB300_S171_L001


title: T56,ATB,PBMC,DMSO

description:
Library name: Sample 534
TU0141_Z


title: T55,ATB,PBMC,DMSO

description:
Library name: Sample 532
TU0139_Z


title: I46,IGRA+,PBMC,MTB300

description:
Library name: Sample 473
TU0005_MTB300_S165_L001


title: CUTandTag_RCC4_nt5_forHIF1Bko_H3K27ac

description: Library name: CUTandTag_RCC4_nt5_forHIF1Bko_H3K27ac


title: CUTandTag_RCC4iVHL_Dox_H3K27ac_rep_1

description: Library name: CUTandTag_RCC4iVHL_Dox_H3K27ac_rep_1


title: I58,IGRA+,PBMC,MTB300

description:
Library name: Sample 531
TU0137_Y


title: CUTandTag_RCC4iVHL_DMSO_H3K27ac_rep_1

description: Library name: CUTandTag_RCC4iVHL_DMSO_H3K27ac_rep_1


title: T45,ATB,PBMC,DMSO

description:
Library name: Sample 468
TT0121_1_DMSO_S465_L003


title: T43,ATB,PBMC,DMSO

description:
Library name: Sample 464
TT0119_1_DMSO_S457_L003


title: I58,IGRA+,PBMC,DMSO

description:
Library name: Sample 530
TU0137_Z


title: C51,IGRA-,PBMC,DMSO

description:
Library name: Sample 490
TU0054_DMSO_S168_L001


title: I46,IGRA+,PBMC,DMSO

description:
Library name: Sample 472
TU0005_DMSO_S164_L001


title: T45,ATB,PBMC,MTB300

description:
Library name: Sample 467
TT0121_1_MTB300_S467_L003


title: T54,ATB,PBMC,MTB300

description:
Library name: Sample 529
TU0131_Y


title: T44,ATB,PBMC,DMSO

description:
Library name: Sample 466
TT0120_1_DMSO_S461_L003


title: CUTandTag_7860_E2HIFko7_HIF1b

description: Library name: CUTandTag_7860_E2HIFko7_HIF1b


title: CUTandTag_7860_E2HIFko6_HIF1b

description: Library name: CUTandTag_7860_E2HIFko6_HIF1b


title: T53,ATB,PBMC,DMSO

description:
Library name: Sample 527
TU0130_Z


title: T54,ATB,PBMC,DMSO

description:
Library name: Sample 528
TU0131_Z


title: T42,ATB,PBMC,DMSO

description:
Library name: Sample 462
TT0116_1_EX_VIVO_S454_L003


title: T43,ATB,PBMC,MTB300

description:
Library name: Sample 463
TT0119_1_MTB300_S459_L003


title: CUTandTag_7860_nt5_forE2HIFko_HIF1b

description: Library name: CUTandTag_7860_nt5_forE2HIFko_HIF1b


title: T42,ATB,PBMC,MTB300

description:
Library name: Sample 461
TT0116_1_MTB300_S455_L003


title: T41,ATB,PBMC,MTB300

description:
Library name: Sample 460
TT0114_1_MTB300_S451_L003


title: C50,IGRA-,PBMC,MTB300

description:
Library name: Sample 489
TU0053_MTB300_S167_L001


title: CUTandTag_7860_nt3_forE2HIFko_HIF1b

description: Library name: CUTandTag_7860_nt3_forE2HIFko_HIF1b


title: T41,ATB,PBMC,DMSO

description:
Library name: Sample 459
TT0114_1_DMSO_S449_L003


title: T39,ATB,PBMC,DMSO

description:
Library name: Sample 456
TT0112_1_DMSO_S445_L003


title: T53,ATB,PBMC,MTB300

description:
Library name: Sample 526
TU0130_Y


title: CUTandTag_7860_E2HIFko7_H3K27ac

description: Library name: CUTandTag_7860_E2HIFko7_H3K27ac


title: T52,ATB,PBMC,DMSO

description:
Library name: Sample 525
TU0129_Z


title: T39,ATB,PBMC,MTB300

description:
Library name: Sample 455
TT0112_1_MTB300_S447_L003


title: T38,ATB,PBMC,DMSO

description:
Library name: Sample 454
TT0111_1_DMSO_S160_L001


title: CUTandTag_7860_E2HIFko6_H3K27ac

description: Library name: CUTandTag_7860_E2HIFko6_H3K27ac


title: T38,ATB,PBMC,MTB300

description:
Library name: Sample 453
TT0111_1_MTB300_S162_L001


title: T37,ATB,PBMC,MTB300

description:
Library name: Sample 452
TT0109_1_MTB300_S443_L003


title: T52,ATB,PBMC,MTB300

description:
Library name: Sample 524
TU0129_Y


title: T44,ATB,PBMC,MTB300

description:
Library name: Sample 465
TT0120_1_MTB300_S463_L003


title: CUTandTag_7860_PAX8ko6_H3K27ac

description: Library name: CUTandTag_7860_PAX8ko6_H3K27ac


title: T36,ATB,PBMC,DMSO

description:
Library name: Sample 450
TT0108_1_DMSO_S437_L003


title: T37,ATB,PBMC,DMSO

description:
Library name: Sample 451
TT0109_1_DMSO_S441_L003


title: T51,ATB,PBMC,DMSO

description:
Library name: Sample 522
TU0126_Z


title: T51,ATB,PBMC,MTB300

description:
Library name: Sample 523
TU0126_Y


title: CUTandTag_7860_HNF1bko8_H3K27ac

description: Library name: CUTandTag_7860_HNF1bko8_H3K27ac


title: T36,ATB,PBMC,MTB300

description:
Library name: Sample 449
TT0108_1_MTB300_S439_L003


title: T35,ATB,PBMC,DMSO

description:
Library name: Sample 447
TT0107_1_DMSO_S156_L001


title: T35,ATB,PBMC,MTB300

description:
Library name: Sample 448
TT0107_1_MTB300_S158_L001


title: CUTandTag_7860_PAX8ko2_H3K27ac

description: Library name: CUTandTag_7860_PAX8ko2_H3K27ac


title: T34,ATB,PBMC,DMSO

description:
Library name: Sample 446
TT0105_1_EX_VIVO_S149_L001


title: CUTandTag_7860_HNF1bko7_H3K27ac

description: Library name: CUTandTag_7860_HNF1bko7_H3K27ac


title: T50,ATB,PBMC,MTB300

description:
Library name: Sample 520
TU0124_Y


title: T33,ATB,PBMC,DMSO

description:
Library name: Sample 444
TT0106_1_DMSO_S152_L001


description: Library name: CUTandTag_7860_nt4_forHNF1bandPAX8ko_H3K27ac


title: T49,ATB,PBMC,DMSO

description:
Library name: Sample 519
TU0122_Z


title: C44,IGRA-,PBMC,DMSO

description:
Library name: Sample 438
TT0075_DMSO_S144_L001


title: T33,ATB,PBMC,MTB300

description:
Library name: Sample 443
TT0106_1_MTB300_S154_L001


title: C44,IGRA-,PBMC,MTB300

description:
Library name: Sample 437
TT0075_MTB300_S146_L001


description: Library name: CUTandTag_7860_nt3_forHNF1bandPAX8ko_H3K27ac


title: CUTandTag_7860_HNF1b

description: Library name: CUTandTag_7860_HNF1b

value: untreated


title: T32,ATB,PBMC,DMSO

description:
Library name: Sample 435
TT0069_1_DMSO_S140_L001


title: T48,ATB,PBMC,MTB300

description:
Library name: Sample 517
TU0113_Y


title: T31,ATB,PBMC,DMSO

description:
Library name: Sample 433
TT0059_1_DMSO_S136_L001


title: CUTandTag_Caki1_DMOG_HIF1a

description: Library name: CUTandTag_Caki1_DMOG_HIF1a

value: DMOG


title: T49,ATB,PBMC,MTB300

description:
Library name: Sample 518
TU0122_Y


title: T32,ATB,PBMC,MTB300

description:
Library name: Sample 436
TT0069_1_MTB300_S142_L001


title: CUTandTag_ccRCC_5_HIF1b

description: Library name: CUTandTag_ccRCC_5_HIF1b

source_name: primary ccRCC cells

value: primary ccRCC cells


title: T31,ATB,PBMC,MTB300

description:
Library name: Sample 434
TT0059_1_MTB300_S138_L001


title: C43,IGRA-,PBMC,MTB300

description:
Library name: Sample 432
TT0058_MTB300_S435_L003


title: T48,ATB,PBMC,DMSO

description:
Library name: Sample 516
TU0113_Z


title: C58,IGRA-,PBMC,MTB300

description:
Library name: Sample 515
TU0110_Y


title: T34,ATB,PBMC,MTB300

description:
Library name: Sample 445
TT0105_1_MTB300_S150_L001


title: T50,ATB,PBMC,DMSO

description:
Library name: Sample 521
TU0124_Z


title: C42,IGRA-,PBMC,MTB300

description:
Library name: Sample 430
TT0057_MTB300_S431_L003


title: CUTandTag_ccRCC_4_HIF1b

description: Library name: CUTandTag_ccRCC_4_HIF1b


title: C58,IGRA-,PBMC,DMSO

description:
Library name: Sample 514
TU0110_Z


title: C41,IGRA-,PBMC,MTB300

description:
Library name: Sample 428
TT0051_MTB300_S134_L001


title: C41,IGRA-,PBMC,DMSO

description:
Library name: Sample 429
TT0051_DMSO_S132_L001


title: C40,IGRA-,PBMC,DMSO

description:
Library name: Sample 426
TT0050_DMSO_S128_L001


title: CUTandTag_7860_wt_HIF1b

description: Library name: CUTandTag_7860_wt_HIF1b


title: C40,IGRA-,PBMC,MTB300

description:
Library name: Sample 427
TT0050_MTB300_S130_L001


title: CUTandTag_RCC4VHLplus_DMOG_H3K27ac

description: Library name: CUTandTag_RCC4VHLplus_DMOG_H3K27ac


title: C57,IGRA-,PBMC,MTB300

description:
Library name: Sample 512
TU0094_Y


title: I44,IGRA+,PBMC,MTB300

description:
Library name: Sample 423
TT0048_MTB300_S423_L003


title: I45,IGRA+,PBMC,DMSO

description:
Library name: Sample 424
TT0049_DMSO_S425_L003


title: CUTandTag_RCC4VHLplus_ctrl_H3K27ac

description: Library name: CUTandTag_RCC4VHLplus_ctrl_H3K27ac

value: control


title: C56,IGRA-,PBMC,DMSO

description:
Library name: Sample 511
TU0084_Z


title: I44,IGRA+,PBMC,DMSO

description:
Library name: Sample 422
TT0048_DMSO_S421_L003


title: C39,IGRA-,PBMC,MTB300

description:
Library name: Sample 421
TT0047_MTB300_S126_L001


title: C43,IGRA-,PBMC,DMSO

description:
Library name: Sample 431
TT0058_DMSO_S433_L003


title: ATAC_7860_E2HIFko7_rep_2

description: Library name: ATAC_7860_E2HIFko7_rep_2

data_processing:
RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and aligned to the GRCh38 genome using Bowtie2 version 2.3.4.1.
Reads aligned to mtDNA, low quality reads (MAPQ <30), ENCODE blacklisted regions and duplicates were removed using samtools version 1.8 and Picard version 2.25.2.
Bigwig files were generated using deeptools bamCoverage version 3.5.0, command –normalizeUsing RPGC --binsize 1.
Assembly: GRCh38
Supplementary files format and content: bigWig

extract_protocol:
The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) was performed according to the Omni-ATAC protocol published by Corces et al. (Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396). In short, libraries were prepared using the Illumina Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina, San Diego, CA, USA) and purified using the DNA Clean and Concentrator-5 Kit (Zymo Research, Freiburg, Germany) according to the manufacturer’s protocol. Following purification, library fragments were amplified by using the NEB Next® High-Fidelity 2X PCR Master Mix (New England Biolabs, Ipswich, UK) and custom-made indexed Nextera PCR primers (Sigma Aldrich, St. Louis, MO, USA). Libraries were amplified for a total of 8 – 12 cycles. Library clean-up and double-sided size selection was performed using AMPure XP beads (Beckman Coulter GmbH, Krefeld, Germany) according to the manufacturer’s recommendations.
ATAC-seq library preparation was carried out using the Omni-ATAC protocol. Libraries were sequenced on Illumina Novaseq 6000 platforms following the manufacturer's protocols.


title: C39,IGRA-,PBMC,DMSO

description:
Library name: Sample 420
TT0047_DMSO_S124_L001


title: C56,IGRA-,PBMC,MTB300

description:
Library name: Sample 510
TU0084_X


title: I43,IGRA+,PBMC,DMSO

description:
Library name: Sample 419
TT0046_DMSO_S417_L003


title: ATAC_7860_E2HIFko7_rep_1

description: Library name: ATAC_7860_E2HIFko7_rep_1


title: ATAC_7860_E2HIFko6_rep_2

description: Library name: ATAC_7860_E2HIFko6_rep_2


title: I57,IGRA+,PBMC,DMSO

description:
Library name: Sample 509
TU0081_Z


title: I57,IGRA+,PBMC,MTB300

description:
Library name: Sample 508
TU0081_Y


title: C38,IGRA-,PBMC,MTB300

description:
Library name: Sample 417
TT0044_MTB300_S415_L003


title: C57,IGRA-,PBMC,DMSO

description:
Library name: Sample 513
TU0094_Z


title: ATAC_7860_E2HIFko6_rep_1

description: Library name: ATAC_7860_E2HIFko6_rep_1


title: C38,IGRA-,PBMC,DMSO

description:
Library name: Sample 416
TT0044_DMSO_S413_L003


title: I43,IGRA+,PBMC,MTB300

description:
Library name: Sample 418
TT0046_MTB300_S419_L003


title: C37,IGRA-,PBMC,DMSO

description:
Library name: Sample 415
TT0041_DMSO_S120_L001


title: I45,IGRA+,PBMC,MTB300

description:
Library name: Sample 425
TT0049_MTB300_S427_L003


title: C37,IGRA-,PBMC,MTB300

description:
Library name: Sample 414
TT0041_MTB300_S122_L001


title: C36,IGRA-,PBMC,DMSO

description:
Library name: Sample 412
TT0040_DMSO_S116_L001


title: I42,IGRA+,PBMC,DMSO

description:
Library name: Sample 411
TT0039_DMSO_S112_L001


title: C36,IGRA-,PBMC,MTB300

description:
Library name: Sample 413
TT0040_MTB300_S118_L001


title: ATAC_7860_PAX8ko6_rep_2

description: Library name: ATAC_7860_PAX8ko6_rep_2


title: I56,IGRA+,PBMC,DMSO

description:
Library name: Sample 505
TU0078_Z


title: C55,IGRA-,PBMC,DMSO

description:
Library name: Sample 506
TU0079_Z


title: ATAC_7860_PAX8ko6_rep_1

description: Library name: ATAC_7860_PAX8ko6_rep_1


title: I42,IGRA+,PBMC,MTB300

description:
Library name: Sample 410
TT0039_MTB300_S114_L001


title: T30,ATB,PBMC,DMSO

description:
Library name: Sample 409
TT0036_1_DMSO_S409_L003


title: T30,ATB,PBMC,MTB300

description:
Library name: Sample 408
TT0036_1_MTB300_S411_L003


title: C54,IGRA-,PBMC,DMSO

description:
Library name: Sample 501
TU0071_Z


title: ATAC_7860_PAX8ko2_rep_1

description: Library name: ATAC_7860_PAX8ko2_rep_1


title: I41,IGRA+,PBMC,DMSO

description:
Library name: Sample 405
TT0032_DMSO_S405_L003


title: ATAC_7860_HNF1bko8_rep_2

description: Library name: ATAC_7860_HNF1bko8_rep_2


title: C54,IGRA-,PBMC,MTB300

description:
Library name: Sample 500
TU0071_Y


title: C55,IGRA-,PBMC,MTB300

description:
Library name: Sample 507
TU0079_Y


title: ATAC_7860_HNF1bko8_rep_1

description: Library name: ATAC_7860_HNF1bko8_rep_1


title: I40,IGRA+,PBMC,DMSO

description:
Library name: Sample 402
TT0030_DMSO_S104_L001


title: I53,IGRA+,PBMC,DMSO

description:
Library name: Sample 497
TU0064_Z


title: ATAC_7860_HNF1bko7_rep_2

description: Library name: ATAC_7860_HNF1bko7_rep_2


title: I40,IGRA+,PBMC,MTB300

description:
Library name: Sample 403
TT0030_MTB300_S106_L001


title: I39,IGRA+,PBMC,DMSO

description:
Library name: Sample 401
TT0029_DMSO_S401_L003


title: I53,IGRA+,PBMC,MTB300

description:
Library name: Sample 496
TU0064_Y


title: I39,IGRA+,PBMC,MTB300

description:
Library name: Sample 400
TT0029_MTB300_S403_L003


title: ATAC_7860_HNF1bko7_rep_1

description: Library name: ATAC_7860_HNF1bko7_rep_1


title: I38,IGRA+,PBMC,MTB300

description:
Library name: Sample 399
TT0028_MTB300_S102_L001


title: ATAC_7860_nt3_forHNF1bPAX8ko_rep_2

description: Library name: ATAC_7860_nt3_forHNF1bPAX8ko_rep_2


title: I38,IGRA+,PBMC,DMSO

description:
Library name: Sample 398
TT0028_DMSO_S100_L001


title: ATAC_7860_PAX8ko2_rep_2

description: Library name: ATAC_7860_PAX8ko2_rep_2


title: T28,ATB,PBMC,DMSO

description:
Library name: Sample 397
TT0027_1_DMSO_S98_L001


title: C52,IGRA-,PBMC,MTB300

description:
Library name: Sample 492
TU0056_Y


title: T28,ATB,PBMC,MTB300

description:
Library name: Sample 396
TT0027_1_MTB300_S399_L003


title: I56,IGRA+,PBMC,MTB300

description:
Library name: Sample 504
TU0078_Y


title: I37,IGRA+,PBMC,DMSO

description:
Library name: Sample 395
TT0026_DMSO_S94_L001


title: T29,ATB,PBMC,DMSO

description:
Library name: Sample 407
TT0033_1_DMSO_S108_L001


title: T29,ATB,PBMC,MTB300

description:
Library name: Sample 406
TT0033_1_MTB300_S110_L001


title: C50,IGRA-,PBMC,DMSO

description:
Library name: Sample 488
TU0053_Z


title: I37,IGRA+,PBMC,MTB300

description:
Library name: Sample 394
TT0026_MTB300_S96_L001


title: ATAC_7860_nt2_forHNF1bPAX8ko_rep_2

description: Library name: ATAC_7860_nt2_forHNF1bPAX8ko_rep_2


title: I41,IGRA+,PBMC,MTB300

description:
Library name: Sample 404
TT0032_MTB300_S407_L003


title: T27,ATB,PBMC,MTB300

description:
Library name: Sample 393
TT0022_1_MTB300_S397_L003


title: C49,IGRA-,PBMC,MTB300

description:
Library name: Sample 487
TU0052_Y


title: ATAC_7860_nt2_forHNF1bPAX8ko_rep_1

description: Library name: ATAC_7860_nt2_forHNF1bPAX8ko_rep_1


title: C49,IGRA-,PBMC,DMSO

description:
Library name: Sample 486
TU0052_Z


title: T27,ATB,PBMC,DMSO

description:
Library name: Sample 392
TT0022_1_DMSO_S395_L003


title: I36,IGRA+,PBMC,MTB300

description:
Library name: Sample 390
TT0020_MTB300_S393_L003


title: I35,IGRA+,PBMC,MTB300

description:
Library name: Sample 389
TT0019_MTB300_S92_L001


title: ATAC_RCC4_VHLplus_DMOG_rep_2

description: Library name: ATAC_RCC4_VHLplus_DMOG_rep_2


title: I36,IGRA+,PBMC,DMSO

description:
Library name: Sample 391
TT0020_DMSO_S391_L003


title: C48,IGRA-,PBMC,DMSO

description:
Library name: Sample 485
TU0049_Z


title: C52,IGRA-,PBMC,DMSO

description:
Library name: Sample 493
TU0056_Z


title: I35,IGRA+,PBMC,DMSO

description:
Library name: Sample 388
TT0019_DMSO_S90_L001


title: ATAC_RCC4_VHLplus_DMOG_rep_1

description: Library name: ATAC_RCC4_VHLplus_DMOG_rep_1


title: I34,IGRA+,PBMC,DMSO

description:
Library name: Sample 387
TT0017_DMSO_S86_L001


title: I34,IGRA+,PBMC,MTB300

description:
Library name: Sample 386
TT0017_MTB300_S88_L001


title: ATAC_7860_nt3_forHNF1bPAX8ko_rep_1

description: Library name: ATAC_7860_nt3_forHNF1bPAX8ko_rep_1


title: C48,IGRA-,PBMC,MTB300

description:
Library name: Sample 484
TU0049_Y


title: I33,IGRA+,PBMC,MTB300

description:
Library name: Sample 384
TT0016_MTB300_S84_L001


title: I52,IGRA+,PBMC,DMSO

description:
Library name: Sample 483
TU0046_Z


title: ATAC_RCC4_VHLplus_control_rep_1

description: Library name: ATAC_RCC4_VHLplus_control_rep_1


title: I32,IGRA+,PBMC,DMSO

description:
Library name: Sample 382
TT0013_DMSO_S387_L003


title: I32,IGRA+,PBMC,MTB300

description:
Library name: Sample 383
TT0013_MTB300_S389_L003


title: I33,IGRA+,PBMC,DMSO

description:
Library name: Sample 385
TT0016_DMSO_S82_L001


title: I52,IGRA+,PBMC,MTB300

description:
Library name: Sample 482
TU0046_Y


title: I31,IGRA+,PBMC,DMSO

description:
Library name: Sample 381
TT0012_DMSO_S383_L003


title: ATAC_7860_HIF1Bko8_rep_2

description: Library name: ATAC_7860_HIF1Bko8_rep_2


title: I51,IGRA+,PBMC,MTB300

description:
Library name: Sample 480
TU0024_Y


title: ATAC_7860_HIF1Bko8_rep_1

description: Library name: ATAC_7860_HIF1Bko8_rep_1


title: I30,IGRA+,PBMC,MTB300

description:
Library name: Sample 379
TT0011_MTB300_S80_L001


title: I31,IGRA+,PBMC,MTB300

description:
Library name: Sample 380
TT0012_MTB300_S385_L003


title: I29,IGRA+,PBMC,DMSO

description:
Library name: Sample 377
TT0010_DMSO_S74_L001


title: I30,IGRA+,PBMC,DMSO

description:
Library name: Sample 378
TT0011_DMSO_S78_L001


title: I29,IGRA+,PBMC,MTB300

description:
Library name: Sample 376
TT0010_PC_S77_L001


title: I50,IGRA+,PBMC,MTB300

description:
Library name: Sample 479
TU0023_Y


title: C35,IGRA-,PBMC,DMSO

description:
Library name: Sample 374
TT0008_DMSO_S70_L001


title: ATAC_7860_HIF1Bko4_rep_1

description: Library name: ATAC_7860_HIF1Bko4_rep_1


title: ATAC_RCC4_VHLplus_control_rep_2

description: Library name: ATAC_RCC4_VHLplus_control_rep_2


title: I28,IGRA+,PBMC,MTB300

description:
Library name: Sample 373
TT0007_MTB300_S68_L001


title: I27,IGRA+,PBMC,MTB300

description:
Library name: Sample 372
TT0006_MTB300_S381_L003


title: I49,IGRA+,PBMC,MTB300

description:
Library name: Sample 477
TU0022_Y


title: I49,IGRA+,PBMC,DMSO

description:
Library name: Sample 476
TU0022_Z


title: ATAC_7860_nt3_forHIF1Bko_rep_2

description: Library name: ATAC_7860_nt3_forHIF1Bko_rep_2


title: C35,IGRA-,PBMC,MTB300

description:
Library name: Sample 375
TT0008_PC_S73_L001


title: I51,IGRA+,PBMC,DMSO

description:
Library name: Sample 481
TU0024_Z


title: I26,IGRA+,PBMC,DMSO

description:
Library name: Sample 369
TT0005_DMSO_S375_L003


title: I48,IGRA+,PBMC,MTB300

description:
Library name: Sample 475
TU0013_Y


title: T25,ATB,PBMC,MTB300

description:
Library name: Sample 366
TT0003_1_MTB300_S373_L003


title: T25,ATB,PBMC,DMSO

description:
Library name: Sample 365
TT0003_1_DMSO_S371_L003


title: I48,IGRA+,PBMC,DMSO

description:
Library name: Sample 474
TU0013_Z


title: ATAC_7860_HIF1Bko4_rep_2

description: Library name: ATAC_7860_HIF1Bko4_rep_2


title: ATAC_7860_nt3_forHIF1Bko_rep_1

description: Library name: ATAC_7860_nt3_forHIF1Bko_rep_1


title: T24,ATB,PBMC,DMSO

description:
Library name: Sample 363
TT0001_1_DMSO_S367_L003


title: T47,ATB,PBMC,DMSO

description:
Library name: Sample 471
TT0126_DMSO_S38_L004


title: ATAC_RCC4_HIF1Bko7_rep_1

description: Library name: ATAC_RCC4_HIF1Bko7_rep_1


title: ATAC_7860_nt5_forHIF1Bko_rep_2

description: Library name: ATAC_7860_nt5_forHIF1Bko_rep_2


title: I50,IGRA+,PBMC,DMSO

description:
Library name: Sample 478
TU0023_Z


title: I27,IGRA+,PBMC,DMSO

description:
Library name: Sample 371
TT0006_DMSO_S379_L003


title: ATAC_RCC4_HIF1Bko2_rep_2

description: Library name: ATAC_RCC4_HIF1Bko2_rep_2


title: T21,ATB,PBMC,DMSO

description:
Library name: Sample 359
TS0077_DMSO_S60_L001


title: T22,ATB,PBMC,DMSO

description:
Library name: Sample 360
TS0079_DMSO_S62_L001


title: T21,ATB,PBMC,MTB300

description:
Library name: Sample 358
TS0077_MTB300_S61_L001


title: T46,ATB,PBMC,MTB300

description:
Library name: Sample 470
TT0123_MTB300_S105_L004


title: T46,ATB,PBMC,DMSO

description:
Library name: Sample 469
TT0123_DMSO_S43_L004


title: ATAC_7860_nt5_forHIF1Bko_rep_1

description: Library name: ATAC_7860_nt5_forHIF1Bko_rep_1


title: ATAC_RCC4_HIF1Bko2_rep_1

description: Library name: ATAC_RCC4_HIF1Bko2_rep_1


title: T20,ATB,PBMC,MTB300

description:
Library name: Sample 357
TS0074_MTB300_S59_L001


title: T40,ATB,PBMC,MTB300

description:
Library name: Sample 458
T0013_MTB300_S76_L004


title: I26,IGRA+,PBMC,MTB300

description:
Library name: Sample 370
TT0005_MTB300_S377_L003


title: C47,IGRA-,PBMC,MTB300

description:
Library name: Sample 442
TT0113_MTB300_S129_L004


title: T17,ATB,PBMC,DMSO

description:
Library name: Sample 351
TS0051_DMSO_S52_L001


title: T17,ATB,PBMC,MTB300

description:
Library name: Sample 350
TS0051_MTB300_S53_L001


title: T20,ATB,PBMC,DMSO

description:
Library name: Sample 356
TS0074_DMSO_S58_L001


title: ATAC_RCC4_HIF1Bko7_rep_2

description: Library name: ATAC_RCC4_HIF1Bko7_rep_2


title: RNA_7860_clone_E2_HIFko_7_rep_2

description: Library name: RNA_7860_clone_E2_HIFko_7_rep_2

data_processing:
RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the GRCh38 genome using STAR version v2.7.10a.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
RNA was isolated using the peqGold total RNA kit (VWR Peqlab, Erlangen, Germany) according to the manufacturer´s protocol.
Novogene NGS DNA Library Prep Set (Cat No.PT004). Libraries were sequenced on Illumina Novaseq 6000 or NovoSeq XPlus as indicated  (Illumina).


title: C45,IGRA-,PBMC,MTB300

description:
Library name: Sample 440
TT0079_MTB300_S131_L004


title: T19,ATB,PBMC,MTB300

description:
Library name: Sample 355
TS0067_MTB300_S57_L001


title: ATAC_RCC4_nt5_forHIF1Bko_rep_2

description: Library name: ATAC_RCC4_nt5_forHIF1Bko_rep_2


title: T40,ATB,PBMC,DMSO

description:
Library name: Sample 457
T0013_DMSO_S14_L004


title: T24,ATB,PBMC,MTB300

description:
Library name: Sample 364
TT0001_1_MTB300_S369_L003


title: T19,ATB,PBMC,DMSO

description:
Library name: Sample 354
TS0067_DMSO_S56_L001


title: I23,IGRA+,PBMC,MTB300

description:
Library name: Sample 311
GS1758_MTB300_S51_L001


title: C31,IGRA-,PBMC,MTB300

description:
Library name: Sample 307
GS1692_MTB300_S49_L001


title: RNA_7860_clone_E2_HIFko_7_rep_1

description: Library name: RNA_7860_clone_E2_HIFko_7_rep_1


title: I22,IGRA+,PBMC,MTB300

description:
Library name: Sample 305
GS1682_MTB300_S47_L001


title: ATAC_RCC4_nt5_forHIF1Bko_rep_1

description: Library name: ATAC_RCC4_nt5_forHIF1Bko_rep_1


title: T18,ATB,PBMC,DMSO

description:
Library name: Sample 353
TS0066_DMSO_S54_L001


title: T23,ATB,PBMC,MTB300

description:
Library name: Sample 362
TS0080_MTB300_S65_L001


title: T18,ATB,PBMC,MTB300

description:
Library name: Sample 352
TS0066_MTB300_S55_L001


title: ATAC_RCC4_nt2_forHIF1Bko_rep_2

description: Library name: ATAC_RCC4_nt2_forHIF1Bko_rep_2


title: T23,ATB,PBMC,DMSO

description:
Library name: Sample 361
TS0080_DMSO_S64_L001


title: C23,IGRA-,PBMC,DMSO

description:
Library name: Sample 289
GS1536_DMSO_S42_L001


title: T26,ATB,PBMC,MTB300

description:
Library name: Sample 367
TT0046_MTB300_S123_L004


title: C31,IGRA-,PBMC,DMSO

description:
Library name: Sample 308
GS1692_DMSO_S48_L001


title: I22,IGRA+,PBMC,DMSO

description:
Library name: Sample 306
GS1682_DMSO_S46_L001


title: RNA_7860_clone_E2_HIFko_6_rep_1

description: Library name: RNA_7860_clone_E2_HIFko_6_rep_1


title: C47,IGRA-,PBMC,DMSO

description:
Library name: Sample 441
TT0113_DMSO_S67_L004


title: C23,IGRA-,PBMC,MTB300

description:
Library name: Sample 290
GS1536_MTB300_S43_L001


title: T26,ATB,PBMC,DMSO

description:
Library name: Sample 368
TT0046_DMSO_S61_L004


title: RNA_7860_clone_E2_HIFko_6_rep_2

description: Library name: RNA_7860_clone_E2_HIFko_6_rep_2


title: RNA_7860_clone_nt_5_rep_2

description: Library name: RNA_7860_clone_nt_5_rep_2


title: ATAC_RCC4_nt2_forHIF1Bko_rep_1

description: Library name: ATAC_RCC4_nt2_forHIF1Bko_rep_1


title: I10,IGRA+,PBMC,MTB300

description:
Library name: Sample 246
5089_MTB300_S365_L003


title: I10,IGRA+,PBMC,DMSO

description:
Library name: Sample 245
5089_DMSO_S363_L003


title: C45,IGRA-,PBMC,DMSO

description:
Library name: Sample 439
TT0079_DMSO_S69_L004


title: RNA_7860_clone_nt_3_rep_2

description: Library name: RNA_7860_clone_nt_3_rep_2


title: I7,IGRA+,PBMC,MTB300

description:
Library name: Sample 240
5086_MTB300_S353_L003


title: C10,IGRA-,PBMC,DMSO

description:
Library name: Sample 247
5090_DMSO_S39_L001


title: RNA_7860_clone_nt_3_rep_1

description: Library name: RNA_7860_clone_nt_3_rep_1


title: T15,ATB,PBMC,MTB300

description:
Library name: Sample 346
TS0038_Y


title: T16,ATB,PBMC,MTB300

description:
Library name: Sample 349
TS0039_Y


title: I9,IGRA+,PBMC,DMSO

description:
Library name: Sample 244
5088_DMSO_S359_L003


title: I6,IGRA+,PBMC,MTB300

description:
Library name: Sample 237
5085_MTB300_S349_L003


title: T14,ATB,PBMC,MTB300

description:
Library name: Sample 345
TS0037_Y


title: T16,ATB,PBMC,DMSO

description:
Library name: Sample 348
TS0039_Z


title: biopsy_miRNA_GS3

city: Taipei City

first: MIN-HSIU

last: CHEN

address: No. 161, Sec. 6, Minquan E. Rd., Neihu Dist.

institute: National Defense Medical University

description: miRNA

data_processing:
Analysis of data was performed with GENEGLOBE online software (https://geneglobe.qiagen.com/pl/analyze).
DESeq2 was also used to normalize the expression (UMI reads) of each miRNA in a sample by calculating a scaling factor (for detailed information on DESeq2, please refer to the DESeq2 manual: https://www.bioconductor.org/packages/3.3/bioc/vignettes/DESeq2/inst/doc/DESeq2.pdf).
Assembly: miRBase_v22, Homo sapiens
Supplementary files format and content: tab-delimited text files include counts for each sample

source_name: Kidney

extract_protocol:
1. Isolate uEV by SBI ExoQuick-TC kit. 2. Extract miRNA from uEV and biopsied kidney tissues by QIAGEN miRNeasy micro kit.
1 ng of each miRNA sample was used for small RNA library preparation following the standard protocol of the QIAseq miRNA Library Kit.

value: Kidney


title: I9,IGRA+,PBMC,MTB300

description:
Library name: Sample 243
5088_MTB300_S361_L003


title: C9,IGRA-,PBMC,DMSO

description:
Library name: Sample 236
5084_DMSO_S343_L003


title: I8,IGRA+,PBMC,MTB300

description:
Library name: Sample 242
5087_MTB300_S357_L003


title: I8,IGRA+,PBMC,DMSO

description:
Library name: Sample 241
5087_DMSO_S355_L003


title: C9,IGRA-,PBMC,MTB300

description:
Library name: Sample 235
5084_MTB300_S345_L003


title: RNA_7860_clone_nt_5_rep_1

description: Library name: RNA_7860_clone_nt_5_rep_1


title: biopsy_miRNA_GS2

description: miRNA


title: I5,IGRA+,PBMC,MTB300

description:
Library name: Sample 234
5083_MTB300_S341_L003


title: biopsy_miRNA_GS1

description: miRNA


title: T15,ATB,PBMC,DMSO

description:
Library name: Sample 347
TS0038_Z


title: I4,IGRA+,PBMC,MTB300

description:
Library name: Sample 232
5082_MTB300_S337_L003


title: biopsy_miRNA_C3

description: miRNA


title: I7,IGRA+,PBMC,DMSO

description:
Library name: Sample 239
5086_DMSO_S351_L003


title: I6,IGRA+,PBMC,DMSO

description:
Library name: Sample 238
5085_DMSO_S347_L003


title: I5,IGRA+,PBMC,DMSO

description:
Library name: Sample 233
5083_DMSO_S339_L003


title: T14,ATB,PBMC,DMSO

description:
Library name: Sample 344
TS0037_Z


title: T13,ATB,PBMC,DMSO

description:
Library name: Sample 342
TS0030_Z


title: I3,IGRA+,PBMC,MTB300

description:
Library name: Sample 228
5080_MTB300_S329_L003


title: I4,IGRA+,PBMC,DMSO

description:
Library name: Sample 231
5082_DMSO_S335_L003


title: T12,ATB,PBMC,MTB300

description:
Library name: Sample 340
TS0028_Y