title: genomic DNA from buccal swab 137

status: Public on Mar 03 2025

city: GAINESVILLE

first: Edward

last: Quinn

state: FL

address: 2033 Mowry Road

department: Anthropology

institute: University of Florida

description:
4-2-F2-F
normal buccal swab

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infinium MethylationEPIC v1.0 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan using standard recommended Illumina scanner settings

data_processing:
SeSame R package
Average Beta after masking non CpG probes, Infinium I Channel inference, non-linear dye-bias correction, p-value detection masking, and noob normalization. The components of the pipeline are described here: https://zhou-lab.github.io/sesame/v1.16/sesame.html#Preprocessing_Function_Code.

label: Cy5 and Cy3

source_name: buccal swab 137

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from buccal cell swabs using either the QIAmp DNA Investigator Kit (catalog number 56504, Qiagen, Germantown, Maryland, United States) or the Isohelix Xtreme DNA Kit (catalog number XME-5/50, Harrietsham, Kent, United Kingdom).

tag: gender

value: Female

tag: epithelial cell proportion

tag: individual

tag: generation

tag: nuclear family

tag: extended family

tag: passed methylation quality control

value: TRUE

tag: included in final analytical sample

value: FALSE

tag: replicate

tag: replicate id

tag: serial number

tag: plate

value: A

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: generation of conflict exposure

tag: material deprivation

tag: socioeconomic status

tag: arabic family food security scale

tag: birth order


title: genomic DNA from buccal swab 139

type: genomic

country: USA

description:
4-2-F3-2-F
normal buccal swab

molecule: genomic DNA

organism: Homo sapiens

source_name: buccal swab 139

tag: gender

tag: epithelial cell proportion

tag: individual

tag: age

tag: generation


title: KrTB-65

status: Public on Mar 19 2025

type: SRA

city: New York City

first: Jorge

last: Baquero

state: NY

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell Medical College

description: Library name: Sample 9

library_source: transcriptomic

data_processing:
Illumina bcl2fastq2 v2.20 was employed for basecalling.
The sequenced reads underwent trimming to eliminate low-quality bases and adapter sequences using cutadapt. Subsequently, these reads were mapped to the mouse GRCm38 reference genome using STAR v2.5.2b.
The extraction of raw read counts was accomplished through HTSeq-count v0.11.2.
Differential expression analysis was conducted using the DESeq2 v1.6.3 package.
We employed the limma package v3.22.7 to remove batch effects from processing samples from different batches.
Assembly: Mouse GRCm38
Supplementary files format and content: Excel file including gene name and log2fold changes (KrTB-D vs. KrTB and KrTB-DN vs. KrTB-N) for each gene

molecule: total RNA

organism: Mus musculus

source_name: Tongue epithelia tissue

extract_protocol:
Qiagen's RNEasy Micro kit (Cat # 74004)
The preparation of RNA libraries utilized the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA), following the protocols provided by the manufacturer. The libraries were sequenced with pair-end 51bp reads on the NovaSeq6000 sequencer.

treatment_protocol: Water, water+doxycycline (2 mg/ml), water+4NQO (50 μg/ml), and water+doxycycline+4NQO (2 mg/ml and 50 μg/ml)

tag: tissue

value: Tongue epithelia tissue

tag: strain

tag: treatment

value: KrTB-N


title: genomic DNA from buccal swab 93

description:
3-23-F3-2-M
normal buccal swab

source_name: buccal swab 93

value: Male

tag: nuclear family

tag: extended family

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: serial number

tag: plate


title: Mouse colon no tumor WT and PHIL CD45 pos, scRNAseq

status: Public on Apr 24 2025

city: Zürich

first: Kristina

last: Handler

address: Winterthurerstrasse

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zürich

description:
Library name: Colon_Mm_no_tumor_WTA
Colon_Mm_no_tumor_Expression_Data.st.txt
feature_README.txt

library_source: transcriptomic single cell

data_processing:
Demultiplexing of BCL files with Bcl2fastq (v2.20.0433, Illumina)
Count matrix generation using the BD Rhapsody™ WTA analysis pipeline (v1.12.1) on the SevenBridges Genomics platform
Assembly: STAR index generation using STAR (v2.5.2b) with gene code GRCm38 v25
Supplementary files format and content: st.txt files: text file showing the input data for the WTA Analysis pipeline at the beginning of the file. Followed by a matrix (first column: “Cell_index”, cell IDs; second column: “Bioproduct”, Gene Symbols; third column: “RSEC_Reads”, Number of UMI reads per cell ID and bioproduct; forth column: “Raw_Molecules”, Reads with the same cell ID, same UMI sequence and same bioproduct collapsed into single molecules; fifth column: “RSEC_Adjusted_Molecules”, Number of molecules detected after RSEC molecular identifier adjustment algorithm, this is the counts used for downstream analysis;
Supplementary files format and content: feature_README.txt: text file that contains the sample tag information

molecule: polyA RNA

source_name: Colon

extract_protocol:
BD Rhapsody Express Single-Cell Analysis System (BD Bioscience)
mRNA Whole Transcriptome Analysis (WTA) and Sample Tag (ST) Library Preparation Protocol (BD Biosciences)

treatment_protocol: Cell hasing unsing BD Rhapsody Mouse Single-Cell Multiplexing kit

value: Colon

tag: cellular enrichment

tag: bd rhapsody_capture_bead_version

value: enhanced beads

tag: sample tag_(cell_hashing)_version

value: Single-Cell Multiplex Kit - Mouse

tag: library type

value: Whole transcriptome (WTA)


title: BPD + PH 1

status: Public on Apr 14 2025

city: Nashville

first: Jennifer

last: Sucre

state: TN

address: 2215 B Garland Ave, 1125 Light Hall

department: Division of Neonatology, Department of Pediatrics

institute: Vanderbilt University Medical Center

data_processing:
Reads with read quality less than 30 were filtered out and CellRanger Count v7.1.0 (10x Genomics) was used to align reads onto the GRCh38 reference genome. The ambient RNA was removed from the CellRanger count matrix h5 file outputs using CellBender v0.2.1. The scRNAseq data was analyzed using Seurat (v4.4.0) in R (v4.3.2). The quality control of the ambient RNA corrected cells filtered out cells with >10 % mitochondrial mRNA mapped UMIs, <500 identified genes, and >7000 identified genes. The data was normalized using SCTransform (v0.4.1) with the glmGamPoi (v1.14.0).
Assembly: GRCh38
Supplementary files format and content: .h5 file of counts after ambient RNA removal by cellbender, and two csv.gz files containing compiled cell counts and annotations.

source_name: Lung tissue

extract_protocol:
Human lung tissue from infants who died with BPD, BPD+PH, and term infant controls were digested in an enzymatic cocktail [collagenase I/dispase II (1 μg/ml) tissue or Miltenyi Multi-Tissue Dissociation Kit] using a gentleMACS Octo Dissociator. Tissue lysates were serially filtered through sterile gauze, 100- and 40-μm sterile filters (Fischer). Single-cell suspensions then underwent cell sorting using serial columns (Miltenyi Microbeads, CD235a and CD45).
CD45− and C45+ populations were mixed 2:1 and were used as input for generation of scRNA-seq libraries using the 10x Chromium platform 3' or 5′ library preparation kits (10x Genomics) following the manufacturer's recommendations and targeting 10,000-20,000 cells per sample.

value: Lung tissue


title: Mouse B16 Nanostring CosMx SMI

status: Public on Apr 09 2025

type: RNA

city: Newcastle Upon Tyne

first: Jing Xuan

last: Lim

address: Framlington Place

department: Bioscience Institute

country: United Kingdom

institute: Newcastle University

description: Nanostring CosMx SMI

hyb_protocol: As per manufacturer's instruction

scan_protocol: As per manufacturer's instruction

data_processing:
For Nanostring Cosmx SMI, images were segmented to obtain cell boundaries based on protocol described in He et al, Nature Biotechnology 2022;40(12):1794-806. The transcripts were assigned at the cell-level to obtain a transcript by cell count matrix. Data were processed and exported from the AtoMxTM Spatial Informatics Platform (SIP). The polygon.csv, exprMat.csv, tx.csv, metadata.csv, tx.csv and fov_positions.csv were imported to R using LoadNanostring() function.
CXsea_Newcastle_MsTMA-polygons.csv: global cell boundaries
CXsea_Newcastle_MsTMA_exprMat_file.csv: count matrix file
CXsea_Newcastle_MsTMA_metadata_file.csv: local/global cell coordinates, morphology marker intensities)
CXsea_Newcastle_MsTMA_tx_file.csv: global transcripts file
CXsea_Newcastle_MsTMA_fov_positions_file.csv: global FOV position

source_name: Tumor

label_protocol: As per manufacturer's instruction

extract_protocol: As per manufacturer's instruction

treatment_protocol: Rag1-/- mice were reconstituted with B16 melanoma and then treated with WT Teff and either WT Tregs or PD1KO Tregs at day 7 post-inoculation.

value: Melanoma tumours

tag: cell line

value: B16F10 cells

tag: cell type

value: Tumor microenvironment cells

tag: genotype

value: WTTeff:WT Treg or WTTeff:PD1KO Treg


title: Sample tag library associated with Mouse blood and bone marrow from healthy and AKPS tumor mice eosinophils,ST, scRNAseq

description:
Library name: Blood_bone_marrow_Mm_tumor_no_tumor_ST
Blood_Mm_no_tumor_Expression_Data.st.txt
feature_README.txt
Blood_Mm_tumor_Expression_Data.st.txt
Bone_marrow_Mm_no_tumor_Expression_Data.st.txt
Bone_marrow_Mm_tumor_Expression_Data.st.txt

source_name: Blood and bone marrow

tag: tissue

value: Blood and bone marrow

tag: strain

tag: cell line_injected

value: AKPS organoids (Apc-LOF, p53-LOF, Kras-GOF, Smad4-LOF)

value: Sample tag (ST)


title: Acute preterm injury 1


title: genomic DNA from buccal swab 91

description:
3-23-F2-F
normal buccal swab

source_name: buccal swab 91

tag: gender

value: Female

tag: epithelial cell proportion

tag: individual

tag: age

tag: generation

tag: nuclear family

tag: extended family

value: TRUE

value: FALSE

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: generation of conflict exposure

tag: material deprivation

tag: socioeconomic status

tag: arabic family food security scale

tag: birth order


title: Mouse blood and bone marrow from healthy and AKPS tumor mice eosinophils, scRNAseq

description:
Library name: Blood_bone_marrow_Mm_tumor_no_tumor_WTA
Blood_Mm_no_tumor_Expression_Data.st.txt
feature_README.txt
Blood_Mm_tumor_Expression_Data.st.txt
Bone_marrow_Mm_no_tumor_Expression_Data.st.txt
Bone_marrow_Mm_tumor_Expression_Data.st.txt

tag: tissue

tag: strain

tag: cellular enrichment

tag: bd rhapsody_capture_bead_version

tag: sample tag_(cell_hashing)_version

tag: library type


title: BPD 1


title: genomic DNA from buccal swab 142

description:
2-12-F3-2-F
normal buccal swab

source_name: buccal swab 142

tag: gender

tag: epithelial cell proportion

tag: individual

tag: age

tag: generation

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: serial number

tag: plate

value: A

value: Germline Exposure

value: Laterborn


title: genomic DNA from buccal swab 119

description:
2-12-F2-F
normal buccal swab

source_name: buccal swab 119

tag: nuclear family

tag: extended family

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: generation of conflict exposure

value: Prenatal Exposure

tag: material deprivation

tag: socioeconomic status

tag: arabic family food security scale

tag: birth order


title: genomic DNA from buccal swab 57

description:
2-11-F3-2-F
normal buccal swab

source_name: buccal swab 57

tag: gender

tag: epithelial cell proportion

tag: individual

tag: age

tag: generation

value: B

value: Firstborn


title: genomic DNA from buccal swab 95

description:
3-23-F3-1-F
normal buccal swab

source_name: buccal swab 95

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: serial number


title: KrTB-66

description: Library name: Sample 10

tag: tissue

value: Tongue epithelia tissue

tag: strain

tag: treatment

value: KrTB-N


title: genomic DNA from buccal swab 44

description:
2-11-F1A-F
normal buccal swab

source_name: buccal swab 44

tag: nuclear family

tag: extended family

tag: plate

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: generation of conflict exposure

value: Direct Exposure

tag: material deprivation


title: genomic DNA from buccal swab 120

description:
2-10-F2-F_1
normal buccal swab

source_name: buccal swab 120

tag: gender

tag: epithelial cell proportion

tag: individual

tag: age

tag: generation

tag: socioeconomic status

tag: arabic family food security scale

tag: birth order


title: genomic DNA from buccal swab 144

description:
4-2-F3-1-M
normal buccal swab

source_name: buccal swab 144

value: Male

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: serial number


title: genomic DNA from buccal swab 114

description:
2-10-F3-2-F_2
normal buccal swab

source_name: buccal swab 114

tag: nuclear family

tag: extended family

tag: plate

tag: slide

tag: violence trauma


title: genomic DNA from buccal swab 94

description:
1-6-F3-2-F
normal buccal swab

source_name: buccal swab 94

tag: gender

tag: epithelial cell proportion

tag: conflict exposed to

tag: generation of conflict exposure

tag: material deprivation


title: genomic DNA from buccal swab 54

description:
1-17-F2-F
normal buccal swab

source_name: buccal swab 54

tag: individual

tag: age

tag: generation

value: Control

tag: socioeconomic status

tag: arabic family food security scale


title: genomic DNA from buccal swab 50

description:
1-17-F1A-F
normal buccal swab

source_name: buccal swab 50

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: birth order


title: KrTB-73

description: Library name: Sample 12

source_name: Tongue epithelia tissue

tag: tissue

tag: strain

tag: treatment


title: genomic DNA from buccal swab 40

description:
1-17-F3-2-M
normal buccal swab

source_name: buccal swab 40

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: serial number

tag: plate

tag: slide

tag: violence trauma


title: genomic DNA from buccal swab 92

description:
1-6-F3-1-F
normal buccal swab

source_name: buccal swab 92

tag: individual

tag: age

tag: generation

tag: conflict exposed to

tag: generation of conflict exposure

tag: material deprivation

tag: socioeconomic status

tag: arabic family food security scale


title: genomic DNA from buccal swab 46

description:
2-11-F2-F
normal buccal swab

source_name: buccal swab 46

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: birth order


title: genomic DNA from buccal swab 39

description:
1-17-F3-1-M
normal buccal swab

source_name: buccal swab 39

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: serial number


title: genomic DNA from buccal swab 90

description:
1-6-F2-F
normal buccal swab

source_name: buccal swab 90

tag: individual

tag: age

tag: plate

tag: slide

tag: violence trauma


title: genomic DNA from buccal swab 102

description:
2-10-F3-2-F_1
normal buccal swab

source_name: buccal swab 102

tag: generation

tag: conflict exposed to

tag: generation of conflict exposure

tag: material deprivation

tag: socioeconomic status


title: genomic DNA from buccal swab 141

description:
2-10-F2-F_2
normal buccal swab

source_name: buccal swab 141

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: arabic family food security scale


title: genomic DNA from buccal swab 38

description:
1-16-F3-2-F
normal buccal swab

source_name: buccal swab 38

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: birth order


title: genomic DNA from buccal swab 117

description:
2-12-F3-1-F
normal buccal swab

source_name: buccal swab 117

tag: individual

tag: age

tag: serial number

tag: plate

tag: slide


title: genomic DNA from buccal swab 34

description:
1-16-F2-F
normal buccal swab

source_name: buccal swab 34

tag: generation

tag: violence trauma

tag: conflict exposed to

tag: generation of conflict exposure

tag: material deprivation


title: genomic DNA from buccal swab 76

description:
2-8-F3-1-F
normal buccal swab

source_name: buccal swab 76

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: socioeconomic status


title: genomic DNA from buccal swab 33

description:
1-16-F3-1-M
normal buccal swab

source_name: buccal swab 33

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: arabic family food security scale


title: genomic DNA from buccal swab 17

description:
2-8-F2-F
normal buccal swab

source_name: buccal swab 17

tag: individual

tag: age

tag: serial number

tag: plate

tag: birth order


title: genomic DNA from buccal swab 154

description:
1-15-F2-F
normal buccal swab

source_name: buccal swab 154

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: generation of conflict exposure


title: genomic DNA from buccal swab 160

description:
1-14-F2-F
normal buccal swab

source_name: buccal swab 160

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: material deprivation


title: genomic DNA from buccal swab 19

description:
2-8-F3-2-F
normal buccal swab

source_name: buccal swab 19

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: socioeconomic status


title: genomic DNA from buccal swab 116

description:
2-10-F3-1-F
normal buccal swab

source_name: buccal swab 116

tag: individual

tag: age

tag: serial number

tag: plate

tag: arabic family food security scale


title: genomic DNA from buccal swab 55

description:
1-13-F3-2-M_2
normal buccal swab

source_name: buccal swab 55

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: birth order


title: genomic DNA from buccal swab 56

description:
1-13-F2-F
normal buccal swab

source_name: buccal swab 56

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: generation of conflict exposure


title: genomic DNA from buccal swab 156

description:
1-15-F3-2-F
normal buccal swab

source_name: buccal swab 156

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: material deprivation


title: genomic DNA from buccal swab 97

description:
1-12-F3-1-F
normal buccal swab

source_name: buccal swab 97

tag: individual

tag: age

tag: serial number

tag: plate

tag: socioeconomic status


title: genomic DNA from buccal swab 158

description:
1-14-F3-1-M
normal buccal swab

source_name: buccal swab 158

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: arabic family food security scale


title: genomic DNA from buccal swab 109

description:
1-12-F3-2-F
normal buccal swab

source_name: buccal swab 109

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: birth order


title: genomic DNA from buccal swab 27

description:
3-25-F2-F
normal buccal swab

source_name: buccal swab 27

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: generation of conflict exposure


title: genomic DNA from buccal swab 51

description:
1-13-F3-1-M
normal buccal swab

source_name: buccal swab 51

tag: individual

tag: age

tag: serial number

tag: plate

tag: material deprivation


title: genomic DNA from buccal swab 107

description:
3-24-F3-1-F_2
normal buccal swab

source_name: buccal swab 107

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: socioeconomic status


title: genomic DNA from buccal swab 31

description:
3-25-F3-1-M
normal buccal swab

source_name: buccal swab 31

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: arabic family food security scale


title: genomic DNA from buccal swab 112

description:
3-24-F3-2-M
normal buccal swab

source_name: buccal swab 112

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: birth order


title: genomic DNA from buccal swab 110

description:
3-24-F2-F
normal buccal swab

source_name: buccal swab 110

tag: individual

tag: age

tag: serial number

tag: plate

tag: generation of conflict exposure


title: genomic DNA from buccal swab 155

description:
1-14-F3-2-M
normal buccal swab

source_name: buccal swab 155

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: material deprivation


title: genomic DNA from buccal swab 105

description:
3-24-F3-1-F_1
normal buccal swab

source_name: buccal swab 105

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: socioeconomic status


title: genomic DNA from buccal swab 127

description:
3-22-F2-F
normal buccal swab

source_name: buccal swab 127

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: arabic family food security scale


title: genomic DNA from buccal swab 122

description:
3-22-F3-1-F
normal buccal swab

source_name: buccal swab 122

tag: individual

tag: age

tag: serial number

tag: plate

tag: birth order


title: genomic DNA from buccal swab 124

description:
3-22-F3-2-M
normal buccal swab

source_name: buccal swab 124

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: generation of conflict exposure


title: genomic DNA from buccal swab 3

description:
1-13-F3-2-M_1
normal buccal swab

source_name: buccal swab 3

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: material deprivation


title: genomic DNA from buccal swab 86

description:
3-21-F3-1-F
normal buccal swab

source_name: buccal swab 86

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: socioeconomic status


title: genomic DNA from buccal swab 100

description:
1-12-F2-F
normal buccal swab

source_name: buccal swab 100

tag: individual

tag: age

tag: serial number

tag: plate

tag: arabic family food security scale


title: genomic DNA from buccal swab 53

description:
3-20-F3-2-M
normal buccal swab

source_name: buccal swab 53

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: birth order


title: genomic DNA from buccal swab 71

description:
3-21-F2-F_1
normal buccal swab

source_name: buccal swab 71

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: generation of conflict exposure


title: genomic DNA from buccal swab 49

description:
3-20-F2-F
normal buccal swab

source_name: buccal swab 49

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: material deprivation


title: genomic DNA from buccal swab 32

description:
1-11-F3-2-F_1
normal buccal swab

source_name: buccal swab 32

tag: individual

tag: age

tag: serial number

tag: plate

tag: socioeconomic status


title: genomic DNA from buccal swab 30

description:
3-25-F3-2-M
normal buccal swab

source_name: buccal swab 30

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: arabic family food security scale


title: genomic DNA from buccal swab 126

description:
1-11-F3-2-F_2
normal buccal swab

source_name: buccal swab 126

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: birth order


title: genomic DNA from buccal swab 148

description:
1-10-F2-F
normal buccal swab

source_name: buccal swab 148

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: generation of conflict exposure


title: genomic DNA from buccal swab 89

description:
1-11-F2-F
normal buccal swab

source_name: buccal swab 89

tag: individual

tag: age

tag: serial number

tag: plate

tag: material deprivation


title: genomic DNA from buccal swab 147

description:
1-10-F3-2-F
normal buccal swab

source_name: buccal swab 147

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: socioeconomic status


title: genomic DNA from buccal swab 101

description:
1-9-F3-2-F
normal buccal swab

source_name: buccal swab 101

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: arabic family food security scale


title: genomic DNA from buccal swab 98

description:
1-9-F2-F
normal buccal swab

source_name: buccal swab 98

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: birth order


title: genomic DNA from buccal swab 87

description:
3-19-F2-F
normal buccal swab

source_name: buccal swab 87

tag: individual

tag: age

tag: serial number

tag: plate

tag: generation of conflict exposure


title: genomic DNA from buccal swab 85

description:
3-19-F3-2-M
normal buccal swab

source_name: buccal swab 85

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: material deprivation


title: genomic DNA from buccal swab 78

description:
1-8-F3-2-M
normal buccal swab

source_name: buccal swab 78

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: socioeconomic status


title: genomic DNA from buccal swab 81

description:
3-19-F3-1-M
normal buccal swab

source_name: buccal swab 81

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: arabic family food security scale


title: genomic DNA from buccal swab 83

description:
1-7-F3-2-F
normal buccal swab

source_name: buccal swab 83

tag: individual

tag: age

tag: serial number

tag: plate

tag: birth order


title: genomic DNA from buccal swab 82

description:
1-7-F2-F
normal buccal swab

source_name: buccal swab 82

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: generation of conflict exposure


title: genomic DNA from buccal swab 123

description:
1-4-F3-2-M
normal buccal swab

source_name: buccal swab 123

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: material deprivation


title: genomic DNA from buccal swab 74

description:
1-8-F2-F
normal buccal swab

source_name: buccal swab 74

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: socioeconomic status


title: genomic DNA from buccal swab 69

description:
1-5-F2-F
normal buccal swab

source_name: buccal swab 69

tag: individual

tag: age

tag: serial number

tag: plate

tag: arabic family food security scale


title: genomic DNA from buccal swab 68

description:
1-5-F3-2-M
normal buccal swab

source_name: buccal swab 68

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: birth order


title: genomic DNA from buccal swab 88

description:
3-21-F3-2-M
normal buccal swab

source_name: buccal swab 88

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: generation of conflict exposure


title: genomic DNA from buccal swab 84

description:
3-21-F2-F_2
normal buccal swab

source_name: buccal swab 84

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: material deprivation


title: genomic DNA from buccal swab 65

description:
1-5-F3-1-F
normal buccal swab

source_name: buccal swab 65

tag: individual

tag: age

tag: serial number

tag: plate

tag: socioeconomic status


title: genomic DNA from buccal swab 128

description:
1-4-F2-F
normal buccal swab

source_name: buccal swab 128

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: arabic family food security scale


title: genomic DNA from buccal swab 77

description:
1-3-F2-F
normal buccal swab

source_name: buccal swab 77

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: birth order


title: genomic DNA from buccal swab 52

description:
3-20-F3-1-F
normal buccal swab

source_name: buccal swab 52

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: generation of conflict exposure


title: genomic DNA from buccal swab 75

description:
1-3-F3-1-M
normal buccal swab

source_name: buccal swab 75

tag: individual

tag: age

tag: serial number

tag: plate

tag: material deprivation


title: genomic DNA from buccal swab 73

description:
1-3-F3-2-M
normal buccal swab

source_name: buccal swab 73

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: socioeconomic status


title: genomic DNA from buccal swab 132

description:
1-2-F3-1-M
normal buccal swab

source_name: buccal swab 132

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: arabic family food security scale


title: genomic DNA from buccal swab 129

description:
1-2-F2-F
normal buccal swab

source_name: buccal swab 129

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: birth order


title: genomic DNA from buccal swab 20

description:
1-1-F3-1-F
normal buccal swab

source_name: buccal swab 20

tag: individual

tag: age

tag: serial number

tag: plate

tag: generation of conflict exposure


title: genomic DNA from buccal swab 24

description:
1-1-F2-F
normal buccal swab

source_name: buccal swab 24

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: material deprivation


title: genomic DNA from buccal swab 135

description:
1-2-F3-2-F
normal buccal swab

source_name: buccal swab 135

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: socioeconomic status


title: genomic DNA from buccal swab 23

description:
1-1-F3-2-M
normal buccal swab

source_name: buccal swab 23

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: arabic family food security scale


title: genomic DNA from buccal swab 72

description:
2-7-F3-2-F
normal buccal swab

source_name: buccal swab 72

tag: individual

tag: age

tag: serial number

tag: plate

tag: birth order


title: genomic DNA from buccal swab 118

description:
2-6-F3-1-F_2
normal buccal swab

source_name: buccal swab 118

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: generation of conflict exposure


title: genomic DNA from buccal swab 115

description:
2-6-F3-1-F_1
normal buccal swab

source_name: buccal swab 115

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: material deprivation


title: genomic DNA from buccal swab 136

description:
2-6-F3-2-M
normal buccal swab

source_name: buccal swab 136

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: socioeconomic status


title: genomic DNA from buccal swab 11

description:
2-4-F2-M
normal buccal swab

source_name: buccal swab 11

tag: individual

tag: age

tag: serial number

tag: plate

tag: arabic family food security scale


title: genomic DNA from buccal swab 113

description:
2-6-F2-F
normal buccal swab

source_name: buccal swab 113

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: birth order


title: genomic DNA from buccal swab 16

description:
2-4-F2-F
normal buccal swab

source_name: buccal swab 16

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: generation of conflict exposure


title: genomic DNA from buccal swab 63

description:
2-3-F3-1-M
normal buccal swab

source_name: buccal swab 63

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: material deprivation


title: genomic DNA from buccal swab 13

description:
2-4-F3-2-M
normal buccal swab

source_name: buccal swab 13

tag: individual

tag: age

tag: serial number

tag: plate

tag: socioeconomic status


title: genomic DNA from buccal swab 151

description:
2-2-F3-2-F
normal buccal swab

source_name: buccal swab 151

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: arabic family food security scale


title: genomic DNA from buccal swab 150

description:
2-2-F3-1-F
normal buccal swab

source_name: buccal swab 150

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: birth order


title: genomic DNA from buccal swab 61

description:
2-3-F3-2-M
normal buccal swab

source_name: buccal swab 61

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: generation of conflict exposure


title: genomic DNA from buccal swab 152

description:
2-1-F3-1-M
normal buccal swab

source_name: buccal swab 152

tag: individual

tag: age

tag: serial number

tag: plate

tag: material deprivation


title: genomic DNA from buccal swab 70

description:
2-7-F2-F
normal buccal swab

source_name: buccal swab 70

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: socioeconomic status


title: genomic DNA from buccal swab 149

description:
2-1-F3-2-F
normal buccal swab

source_name: buccal swab 149

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: arabic family food security scale


title: genomic DNA from buccal swab 146

description:
2-1-F2-F
normal buccal swab

source_name: buccal swab 146

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: birth order


title: genomic DNA from buccal swab 143

description:
3-18-F2-F
normal buccal swab

source_name: buccal swab 143

tag: individual

tag: age

tag: serial number

tag: plate

tag: generation of conflict exposure


title: genomic DNA from buccal swab 121

description:
3-18-F3-2-M
normal buccal swab

source_name: buccal swab 121

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: material deprivation


title: genomic DNA from buccal swab 130

description:
3-17-F3-2-M
normal buccal swab

source_name: buccal swab 130

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: socioeconomic status


title: genomic DNA from buccal swab 125

description:
3-18-F3-1-F
normal buccal swab

source_name: buccal swab 125

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: arabic family food security scale


title: genomic DNA from buccal swab 145

description:
2-2-F2-F
normal buccal swab

source_name: buccal swab 145

tag: individual

tag: age

tag: serial number

tag: plate

tag: birth order


title: genomic DNA from buccal swab 133

description:
3-17-F2-F
normal buccal swab

source_name: buccal swab 133

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: generation of conflict exposure


title: genomic DNA from buccal swab 157

description:
3-16-F3-2-F
normal buccal swab

source_name: buccal swab 157

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: material deprivation


title: genomic DNA from buccal swab 134

description:
3-15-F3-1-F_2
normal buccal swab

source_name: buccal swab 134

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: socioeconomic status


title: genomic DNA from buccal swab 58

description:
3-15-F3-1-F_1
normal buccal swab

source_name: buccal swab 58

tag: individual

tag: age

tag: serial number

tag: plate

tag: arabic family food security scale


title: genomic DNA from buccal swab 153

description:
3-16-F2-F
normal buccal swab

source_name: buccal swab 153

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: birth order


title: genomic DNA from buccal swab 131

description:
3-17-F3-1-M
normal buccal swab

source_name: buccal swab 131

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: generation of conflict exposure


title: genomic DNA from buccal swab 80

description:
3-15-F3-2-M
normal buccal swab

source_name: buccal swab 80

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: material deprivation


title: genomic DNA from buccal swab 79

description:
3-15-F2-F
normal buccal swab

source_name: buccal swab 79

tag: individual

tag: age

tag: serial number

tag: plate

tag: socioeconomic status


title: genomic DNA from buccal swab 12

description:
3-14-F3-2-M
normal buccal swab

source_name: buccal swab 12

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: arabic family food security scale


title: genomic DNA from buccal swab 22

description:
3-13-F3-2-F
normal buccal swab

source_name: buccal swab 22

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: birth order


title: genomic DNA from buccal swab 64

description:
2-3-F2-F
normal buccal swab

source_name: buccal swab 64

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: generation of conflict exposure


title: genomic DNA from buccal swab 18

description:
3-13-F3-1-M
normal buccal swab

source_name: buccal swab 18

tag: individual

tag: age

tag: serial number

tag: plate

tag: material deprivation


title: genomic DNA from buccal swab 21

description:
3-13-F2-F
normal buccal swab

source_name: buccal swab 21

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: socioeconomic status


title: genomic DNA from buccal swab 9

description:
3-14-F3-1-F
normal buccal swab

source_name: buccal swab 9

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: arabic family food security scale


title: genomic DNA from buccal swab 4

description:
3-12-F3-1-F
normal buccal swab

source_name: buccal swab 4

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: birth order


title: genomic DNA from buccal swab 1

description:
3-12-F2-F
normal buccal swab

source_name: buccal swab 1

tag: individual

tag: age

tag: serial number

tag: plate

tag: generation of conflict exposure


title: genomic DNA from buccal swab 7

description:
3-12-F3-2-M
normal buccal swab

source_name: buccal swab 7

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: material deprivation


title: genomic DNA from buccal swab 138

description:
3-11-F2-F
normal buccal swab

source_name: buccal swab 138

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: socioeconomic status


title: genomic DNA from buccal swab 140

description:
3-11-F3-2-F
normal buccal swab

source_name: buccal swab 140

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: arabic family food security scale


title: genomic DNA from buccal swab 6

description:
3-10-F2-F
normal buccal swab

source_name: buccal swab 6

tag: individual

tag: age

tag: serial number

tag: plate

tag: birth order


title: genomic DNA from buccal swab 104

description:
3-9-F3-2-M
normal buccal swab

source_name: buccal swab 104

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: generation of conflict exposure


title: genomic DNA from buccal swab 2

description:
3-10-F3-2-M
normal buccal swab

source_name: buccal swab 2

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: material deprivation


title: genomic DNA from buccal swab 103

description:
3-9-F3-1-M
normal buccal swab

source_name: buccal swab 103

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: socioeconomic status


title: genomic DNA from buccal swab 99

description:
3-9-F2-F
normal buccal swab

source_name: buccal swab 99

tag: individual

tag: age

tag: serial number

tag: plate

tag: arabic family food security scale


title: genomic DNA from buccal swab 159

description:
3-8-F2-F
normal buccal swab

source_name: buccal swab 159

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: birth order


title: genomic DNA from buccal swab 41

description:
3-8-F3-2-M
normal buccal swab

source_name: buccal swab 41

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: generation of conflict exposure


title: genomic DNA from buccal swab 43

description:
3-8-F3-1-F
normal buccal swab

source_name: buccal swab 43

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: material deprivation


title: genomic DNA from buccal swab 42

description:
3-6-F3-1-M_1
normal buccal swab

source_name: buccal swab 42

tag: individual

tag: age

tag: serial number

tag: plate

tag: socioeconomic status


title: genomic DNA from buccal swab 8

description:
3-5-F3-2-F_1
normal buccal swab

source_name: buccal swab 8

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: arabic family food security scale


title: genomic DNA from buccal swab 48

description:
3-6-F3-2-M
normal buccal swab

source_name: buccal swab 48

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: birth order


title: genomic DNA from buccal swab 14

description:
3-14-F2-F
normal buccal swab

source_name: buccal swab 14

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: generation of conflict exposure


title: genomic DNA from buccal swab 96

description:
3-5-F3-2-F_2
normal buccal swab

source_name: buccal swab 96

tag: individual

tag: age

tag: serial number

tag: plate

tag: material deprivation


title: genomic DNA from buccal swab 47

description:
3-6-F2-F
normal buccal swab

source_name: buccal swab 47

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: socioeconomic status


title: genomic DNA from buccal swab 15

description:
3-5-F3-1-F
normal buccal swab

source_name: buccal swab 15

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: arabic family food security scale


title: genomic DNA from buccal swab 45

description:
3-6-F3-1-M_2
normal buccal swab

source_name: buccal swab 45

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: birth order


title: genomic DNA from buccal swab 29

description:
3-4-F3-2-F
normal buccal swab

source_name: buccal swab 29

tag: individual

tag: age

tag: serial number

tag: plate

tag: generation of conflict exposure


title: genomic DNA from buccal swab 10

description:
3-5-F2-F
normal buccal swab

source_name: buccal swab 10

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: material deprivation


title: genomic DNA from buccal swab 28

description:
3-4-F2-F
normal buccal swab

source_name: buccal swab 28

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: socioeconomic status


title: genomic DNA from buccal swab 67

description:
3-3-F2-F
normal buccal swab

source_name: buccal swab 67

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: arabic family food security scale


title: genomic DNA from buccal swab 111

description:
3-2-F3-1-M
normal buccal swab

source_name: buccal swab 111

tag: individual

tag: age

tag: serial number

tag: plate

tag: birth order


title: genomic DNA from buccal swab 25

description:
3-3-F3-2-F
normal buccal swab

source_name: buccal swab 25

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: generation of conflict exposure


title: genomic DNA from buccal swab 66

description:
3-3-F3-1-F
normal buccal swab

source_name: buccal swab 66

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: material deprivation


title: genomic DNA from buccal swab 108

description:
3-2-F3-2-M
normal buccal swab

source_name: buccal swab 108

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: socioeconomic status


title: genomic DNA from buccal swab 62

description:
3-1-F3-2-M
normal buccal swab

source_name: buccal swab 62

tag: individual

tag: age

tag: serial number

tag: plate

tag: arabic family food security scale


title: genomic DNA from buccal swab 106

description:
3-2-F2-F
normal buccal swab

source_name: buccal swab 106

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: birth order


title: genomic DNA from buccal swab 5

description:
3-10-F3-1-F
normal buccal swab

source_name: buccal swab 5

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: generation of conflict exposure


title: genomic DNA from buccal swab 60

description:
3-1-F3-1-F
normal buccal swab

source_name: buccal swab 60

tag: gender

tag: epithelial cell proportion

tag: nuclear family

tag: extended family

tag: material deprivation


title: genomic DNA from buccal swab 37

description:
2-9-F3-1-M
normal buccal swab

source_name: buccal swab 37

tag: individual

tag: age

tag: serial number

tag: plate

tag: socioeconomic status


title: genomic DNA from buccal swab 36

description:
2-9-F3-2-F
normal buccal swab

source_name: buccal swab 36

tag: generation

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: arabic family food security scale


title: A-498, sgHIF2α, Rep3

status: Public on Feb 20 2025

city: Boston

first: Qinqin

last: Jiang

state: Ma

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Raw sequencing reads were first aligned to the reference human transcriptome (hg19) using bowtie2 (v 2.3.4.3). Reads that failed to map to the human transcriptome were subsequently aligned to the reference ERV genome. Paired-end reads where both ends perfectly matching to at least one ERV reference sequence (PM), or those with no more than one mismatch across both reads (1MM), were preserved. Single ends from read pairs that met the following criteria were also kept for downstream analysis: (i) perfect match to an ERV reference sequence; (ii) not part of any paired-end PM or 1MM matches to any ERV reference sequence; (iii) no matches to the human transcriptome. Duplicated reads were identified and removed using PicardMarkDuplicates. Quantification was performed using HTSeq (v 0.11.0),and the final expression was defined as 2× number of paired-end matches (PM & 1MM) + number of single-end matches to the ERV reference database.The expression of each ERV was normalized by the library size of the corresponding sample as well as the length of the ERV. These normalized ERV counts were used in downstream analyses.
Assembly: hg19
Supplementary files format and content: An excel file, which contains normalized ERV counts for 3173 ERVs (defined by Vargiu et al, Retrovilogy, 2016) under all conditions

growth_protocol: A-498 cells were obtained from American Type Culture Collection and were cultured in DMEM (Gibco 11995073) supplemented with FBS (GeminiBio 100-106), 1% penicillin-streptomycin (Gibco 15140122)

extract_protocol:
A-498 cells were homogenized with QIAshredder columns (Qiagen 79654), and total RNA was extracted from homogenized cell lysates using the RNeasy Mini Kit (Qiagen 74106) according to manufacturer’s protocol. The RNA was quantified on a NanoDrop spectrophotometer (Thermo Scientific ND-8000-GL).
Ribosomal RNA (rRNA)-depleted libraries were prepared using KAPA RNA HyperPrep Kit with RiboErase (Roche) from 100 ng of total RNA according to manufacturer’s protocol. Briefly, mRNA or non-coding RNA were enriched and then purified using KAPA pure beads and fragmented at 94°C for 8 min. 1st strand and 2nd strand were subsequently synthesized. cDNA fragments were end-repaired and adenylated at the 3′ ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment with 14 cycles of PCR post-adapter ligation on a Beckman Coulter Biomek i7. Finished dsDNA libraries were quantified by Qubit fluorometer and Agilent TapeStation 4200. Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance. The final pool was sequenced with paired-end 150 bp reads on an Illumina NovaSeq 6000 at the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

treatment_protocol: A-498 cells were infected with bicistronic vectors (pLX304-EV-IRES-GFP or pLX304-VHL-IRES-Tdtomato), GFP or Tdtomato positive cells were isolated by FACS. For the sorted cells that express pVHL and EV, cells express EV were treated with either 2 uM PT2399 (PT) or vehicle (Veh) for 72 hours, at the same time, cells that express pVHL were also treated with vehicle (Veh) for 72 h. Cells from the three conditions listed above were harvested at the end of 72 hours. A-498 cells that were edited with a HIF2a sgRNA or a contrl sgRNA (sgCtrl) were also collected.

tag: cell line

tag: cell type

value: ccRCC

tag: treatment

value: Infected with a HIF2a giude RNA (sgHIF2a)


title: genomic DNA from buccal swab 59

description:
3-1-F2-F
normal buccal swab

source_name: buccal swab 59

tag: gender

tag: epithelial cell proportion

tag: passed methylation quality control

tag: included in final analytical sample

tag: replicate

tag: replicate id

tag: generation of conflict exposure

tag: birth order


title: A-498, sgHIF2α, Rep1


title: A-498, sgHIF2α, Rep2


title: A-498, sgCtrl, Rep2

value: Infected with a ctrl giude RNA (sgCtrl)


title: A-498, EV, PT2399 72 h, Rep2

value: Infected with empty vector (EV), treated with PT2399 (2 uM) for 72 hours


title: A-498, sgCtrl, Rep1


title: A-498, EV, PT2399 72 h, Rep1


title: A-498, VHL, Veh 72 h, Rep3

value: Infected with pVHL protein (VHL), treatd with vehicle (Veh) for 72 hours


title: A-498, EV, PT2399 72 h, Rep3


title: A-498, sgCtrl, Rep3


title: genomic DNA from buccal swab 26

description:
3-4-F3-1-F
normal buccal swab

source_name: buccal swab 26

value: Female

tag: individual

tag: age

tag: nuclear family

tag: extended family

value: TRUE

value: FALSE

tag: serial number

tag: plate

tag: material deprivation

tag: socioeconomic status


title: A-498, VHL, Veh 72 h, Rep1

tag: cell line

tag: cell type

tag: treatment


title: 786-O, sgHIF2a, DNMT1i 9 d, Rep2

data_processing:
Raw sequencing reads were first aligned to the reference human transcriptome (hg19) using bowtie2 (v 2.3.4.3). Reads that failed to map to the human transcriptome were subsequently aligned to the reference ERV genome. Paired-end reads where both ends perfectly matching to at least one ERV reference sequence (PM), or those with no more than one mismatch across both reads (1MM), were preserved. Single ends from read pairs that met the following criteria were also kept for downstream analysis: (i) perfect match to an ERV reference sequence; (ii) not part of any paired-end PM or 1MM matches to any ERV reference sequence; (iii) no matches to the human transcriptome. Duplicated reads were identified and removed using PicardMarkDuplicates. Quantification was performed using HTSeq (v 0.11.0),and the final expression was defined as 2× number of paired-end matches (PM & 1MM) + number of single-end matches to the ERV reference database.The expression of each ERV was normalized by the library size of the corresponding sample as well as the length of the ERV. These normalized ERV counts were used in downstream analyses.
Assembly: hg19
Supplementary files format and content: An excel file, which contains normalized ERV counts for 3173 ERVs (defined by Vargiu et al, Retrovilogy, 2016) under all listed conditions

growth_protocol: 786-O cells were obtained from American Type Culture Collection and were cultured in DMEM (Gibco 11995073) supplemented with FBS (GeminiBio 100-106), 1% penicillin-streptomycin (Gibco 15140122)

extract_protocol:
786-O cells were homogenized with QIAshredder columns (Qiagen 79654), and total RNA was extracted from homogenized cell lysates using the RNeasy Mini Kit (Qiagen 74106) according to manufacturer’s protocol. The RNA was quantified on a NanoDrop spectrophotometer (Thermo Scientific ND-8000-GL).
Ribosomal RNA (rRNA)-depleted libraries were prepared using QIAseq FastSelect rRNA HMR reagents (Qiagen 334375) according to manufacturer’s protocol. Briefly, mRNA or non-coding RNA were enriched and then purified using KAPA pure beads and fragmented at 94°C for 8 min. 1st strand and 2nd strand were subsequently synthesized. cDNA fragments were end-repaired and adenylated at the 3′ ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment with 14 cycles of PCR post-adapter ligation on a Beckman Coulter Biomek i7. Finished dsDNA libraries were quantified by Qubit fluorometer and Agilent TapeStation 4200. Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance. The final pool was sequenced with paired-end 150 bp reads on an Illumina NovaSeq 6000 at the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

treatment_protocol: 786-O cells were first edited with a HIF2a sgRNA or a contrl sgRNA (sgCtrl), then treated with 0.5 uM GSK3685032 (DNMT1i) or vehicle (Veh) for 9 days.

value: Infected with a HIF2a giude RNA (sgCtrl), treated with 0.5 uM DNMT1i for 9 days


title: 786-O, sgHIF2a, DNMT1i 9 d, Rep1


title: 786-O, sgHIF2a, Veh 9 d, Rep2

value: Infected with a HIF2a giude RNA (sgCtrl), treated with vehicle for 9 days


title: 786-O, sgHIF2a, DNMT1i 9 d, Rep3


title: genomic DNA from buccal swab 35

description:
2-9-F2-M
normal buccal swab

source_name: buccal swab 35

tag: gender

tag: epithelial cell proportion

tag: generation

tag: passed methylation quality control

value: A

tag: slide

tag: violence trauma

tag: conflict exposed to

tag: arabic family food security scale


title: 786-O, sgHIF2a, Veh 9 d, Rep3


title: 786-O, sgHIF2a, Veh 9 d, Rep1


title: A-498, EV, Veh 72 h, Rep1

value: Infected with empty vector (EV), treated with vehicle (Veh) for 72 hours


title: 786-O, sgCtrl, DNMT1i 9 d, Rep2

value: Infected with a ctrl giude RNA (sgCtrl), treated with 0.5 uM DNMT1i for 9 days


title: 786-O, sgCtrl, DNMT1i 9 d, Rep1


title: 786-O, sgCtrl, DNMT1i 9 d, Rep3


title: 786-O, sgCtrl, Veh 9 d, Rep3

value: Infected with a ctrl giude RNA (sgCtrl), treated with vehicle for 9 days


title: 786-O, sgCtrl, Veh 9 d, Rep2


title: 786-O, sgCtrl, Veh 9 d, Rep1


title: A-498, EV, Veh 72 h, Rep3


title: A-498, VHL, Veh 72 h, Rep2


title: 786-O, sgHIF2α, Rep2

extract_protocol:
786-O cells were homogenized with QIAshredder columns (Qiagen 79654), and total RNA was extracted from homogenized cell lysates using the RNeasy Mini Kit (Qiagen 74106) according to manufacturer’s protocol. The RNA was quantified on a NanoDrop spectrophotometer (Thermo Scientific ND-8000-GL).
Ribosomal RNA (rRNA)-depleted libraries were prepared using KAPA RNA HyperPrep Kit with RiboErase (Roche) from 100 ng of total RNA according to manufacturer’s protocol. Briefly, mRNA or non-coding RNA were enriched and then purified using KAPA pure beads and fragmented at 94°C for 8 min. 1st strand and 2nd strand were subsequently synthesized. cDNA fragments were end-repaired and adenylated at the 3′ ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment with 14 cycles of PCR post-adapter ligation on a Beckman Coulter Biomek i7. Finished dsDNA libraries were quantified by Qubit fluorometer and Agilent TapeStation 4200. Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance. The final pool was sequenced with paired-end 150 bp reads on an Illumina NovaSeq 6000 at the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

treatment_protocol: 786-O cells were infected with bicistronic vectors (pLX304-EV-IRES-GFP or pLX304-VHL-IRES-Tdtomato), GFP or Tdtomato positive cells were isolated by FACS. For the sorted cells that express pVHL and EV, cells express EV were treated with either 2 uM PT2399 (PT) or vehicle (Veh) for 72 hours, at the same time, cells that express pVHL were also treated with vehicle (Veh) for 72 h. Cells from the three conditions listed above were harvested at the end of 72 hours. 786-O cells that were edited with a HIF2a sgRNA or a contrl sgRNA (sgCtrl) were also collected.

value: Infected with a HIF2α giude RNA (sgHIF2α)


title: 786-O, sgCtrl, Rep3


title: 786-O, sgHIF2α, Rep1


title: 786-O, sgHIF2α, Rep3


title: 786-O, EV, PT2399 72 h, Rep2


title: 786-O, EV, PT2399 72 h, Rep3


title: 786-O, EV, PT2399 72 h, Rep1


title: 786-O, VHL, Veh 72 h, Rep3


title: 786-O, sgCtrl, Rep2


title: 786-O, VHL, Veh 72 h, Rep2


title: 786-O, EV, Veh 72 h, Rep3


title: 786-O, EV, Veh 72 h, Rep2


title: 786-O, sgCtrl, Rep1


title: OS-RC-2, PT2399 2 h, Rep2

library_source: other

data_processing:
*library strategy: PRO-Seq
Raw sequencing reads were first aligned to the reference human transcriptome (hg19) using bowtie2 (v 2.3.4.3). Reads that failed to map to the human transcriptome were subsequently aligned to the reference ERV genome. Paired-end reads where both ends perfectly matching to at least one ERV reference sequence (PM), or those with no more than one mismatch across both reads (1MM), were preserved. Single ends from read pairs that met the following criteria were also kept for downstream analysis: (i) perfect match to an ERV reference sequence; (ii) not part of any paired-end PM or 1MM matches to any ERV reference sequence; (iii) no matches to the human transcriptome. Duplicated reads were identified and removed using PicardMarkDuplicates. Quantification was performed using HTSeq (v 0.11.0),and the final expression was defined as 2× number of paired-end matches (PM & 1MM) + number of single-end matches to the ERV reference database.The expression of each ERV was normalized by the library size of the corresponding sample as well as the length of the ERV. These normalized ERV counts were used in downstream analyses.
Assembly: hg19
Supplementary files format and content: An excel file, which contains normalized ERV counts for 3173 ERVs (defined by Vargiu et al, Retrovilogy, 2016) under all conditions

molecule: other

growth_protocol: OS-RC-2 cells were obtained from RIKEN Bioresource Research Center Cell Bank and were cultured in RPMI-1640 (Gibco 11875119) supplemented with FBS (GeminiBio 100-106), 1% penicillin-streptomycin (Gibco 15140122)

extract_protocol:
Cells (Human or Drosophila) were washed with RT PBS, trypsinized for 1-2 min at 37°C, quenched with ice-cold DMEM +10% FBS and transferred to 50 ml conical tubes. After harvesting, cells were always kept on ice. 5×106 to 1×107 cells per condition were collected by centrifugation at 300×g for 4 min at 4°C. The supernatant was removed, and the cell pellets were gently resuspended in 10 ml ice-cold PBS, followed by centrifugation at 300×g for 4 min at 4°C. The supernatant was removed, and the cells were resuspended in 250 ml wash buffer [10 mM Tris-HCl pH 8.0, 10 mM KCl, 250 mM Sucrose, 5 mM MgCl2, 1 mM EGTA, 10% (v/v) glycerol, 0.5 mM DTT (Thermo Fisher Scientific 707265ML), 0.2 ml/ml RNase inhibitor (Invitrogen AM2696) and 1× protease inhibitor (Thermo Fisher Scientific A32965)]. The cell pellets were gently pipetted using wide bore filtered pipette tips (Thermo Fisher Scientific 2079GPK) to create a single-cell suspensions. The cell suspension was passed through a cell strainer once (Falcon 352235) to avoid cell clumps. 10 ml permeabilization buffer [10 mM Tris-HCl pH 8.0, 10 mM KCl, 250 mM Sucrose, 5 mM MgCl2, 1 mM EGTA, 10% (v/v) glycerol, 0.1 % (v/v) IGEPAL CA-630, 0.05% (v/v) Tween-20, 0.5 mM DTT, 0.2 ul/ml RNase inhibitor and 1× protease inhibitor] was slowly (over 5-10 seconds) added to the single-cell suspension along the wall of the conical tube. The samples were then incubated on ice for 5 min before centrifugation at 400×g for 4 min at 4°C. The supernatant was removed by gently inverting the tubes after which 1 ml of ice-cold wash buffer was added to each of the pellets to dilute out the residual permeabilization buffer followed by gently pipetting 2-3 times to achieve a single cell suspension. Next an additional 9 ml of ice-cold wash buffer was added to each tube and the samples were pelleted by centrifugation at 400×g for 4 min at 4°C. This wash procedure (1 ml wash buffer followed by 9 ml wash buffer) was repeated an additional 2 times. After the washes, the cell pellets were resuspended in 250 ul freezing buffer [50 mM Tris-HCl, pH 8.0, 40% (v/v) glycerol, 5 mM MgCl2, 1.1 mM EDTA, 0.5 mM DTT, 1 ul/ml RNase inhibitor] and transferred to 1.5 ml low binding tubes (Thermo Fisher Scientific Pl90410). 250 ul freezing buffer/tube was also added to the 50 ml conical tubes, followed by gentle pipetting, to collect any residual cells, which were then pooled with the first resuspension (bringing the total volume to 500 ul, which was further resuspended by gentle pipetting). Trypan blue-stained cell number was determined using a hemocytomer after which the cells were diluted using freezing buffer to the concentration of 1×106 cell/100 ul. Aliquots of 5×106 permeabilized cells per 1.5 ml low binding tube were flash frozen in liquid nitrogen and stored at -80°C prior to use. To conduct nuclear run-ons and library preparation, aliquots of frozen permeabilized cells were thawed on ice, pipetted gently, and recounted using a Luna II automated cell counter (Logos Biosystems). For each sample, 1×106 permeabilized Human cells were used for nuclear run-ons, with 5×104 permeabilized Drosophila S2 cells added to each sample for normalization. Nuclear run-on assays and library preparation were performed as described in (Reimer et al, Mol Cell, 2021) with modifications. Briefly, nascent RNA was labeled by a run-on assay in which an equal volume of 2× nuclear run-on buffer [10 mM Tris-HCl, pH 8.0, 300 mM KCl, 1% sarkosyl, 10 mM MgCl2, 1 mM DTT, 20 uM/ea biotin-11-NTPs (Perkin Elmer NEL543001EA), 0.8 U/ul RNase inhibitor)] was added into permeabilized cell mixture and incubated for 5 min at 37°C. RNA was purified by the Total RNA Purification Kit (Norgen Biotek Corp 17200) per manufacturer’s instructions, eluted in 100 ul H2O, and fragmented by base hydrolysis by adding 25 ul 5× fragmentation solution (375 mM Tris-HCl, pH 8.3, 562.5 mM KCl, 22.5 mM MgCl2) followed by incubation for 5 min at 94°C. Fragmentation was stopped by adding 125 ul ice-cold 0.1 M EDTA. To enrich for biotin-labeled nascent RNA, 10 ml of streptavidin C1 magnetic beads (Invitrogen 65001) were washed, rendered RNase free per manufacturer’s instructions, and resuspended in 50 ml binding buffer (10 mM Tris-HCl pH 7.4, 300 mM NaCl, 0.1% Triton X-100) before being added to the fragmented RNA. The samples were rotated end-to-end for 20 min at RT. The streptavidin magnetic beads were then washed twice with high salt buffer (50 mM Tris-HCl pH 7.4, 2 M NaCl, 0.5% Triton X-100), twice with binding buffer (listed above), and twice with low salt buffer (5 mM Tris-HCl pH 7.4, 0.1% Triton X-100). The beads were next resuspended in 500 ml TRIzol Reagent (Invitrogen 15596026) and incubated at 65°C for 5 min to elute RNA from the beads. This elution step was repeated once and the first and second eluates for a given sample were pooled. The RNA was subsequently purified by adding 2.75× volumes of 100% ethanol to the 400 ul solution recovered from aqueous phase of TRIzol in the presence of 20 ug of Ultrapure glycogen (Invitrogen 10814010). The pelleted RNA was subsequently washed per manufacturer’s instructions and resuspended in 5 ul of 10 uM App-VRA3_6N 3’ end adapter prepared using the 5' DNA Adenylation Kit (New England Biolabs M2611A) and ligated using T4 RNA ligase 2, truncated KQ (New England Biolabs M0373) per manufacturer’s instructions with 15% (w/v) PEG-8000 in final solution and incubated overnight at 16°C. 180 ml of betaine binding buffer [1.42g of betaine (Sigma-Aldrich 61962) in 10 ml with binding buffer] was mixed with ligations and incubated for 5 min at 65°C and then for 2 min on ice. Capture on Streptavidin beads was again performed as above to enrich for ligated nascent RNAs except for the addition of a final wash with 1× MDE buffer (New England Biolabs B0608S) after the washes with high salt buffer, binding buffer, and low salt buffer. To prepare nascent RNA for 5’ end adapter ligation, the 5’ ends of the RNA were first decapped by mRNA decapping enzyme (New England Biolabs M0608S) for 1 h at 37°C. The beads were washed once in high, once with low salt buffer, and then once in 1× T4 PNK reaction buffer. The samples were then treated with T4 polynucleotide kinase (New England Biolabs M0201) for 1 h at 37°C for 5’-hydroxyl repairs, followed by one wash with high salt buffer, one wash with low salt buffer, and one wash with 0.25× T4 RNA ligase reaction buffer prior to resuspension in 5 ml of 10 pmol 5' RNA adapter VRA5_6N. Next T4 RNA ligase 1 (New England Biolabs M0204L) was used to ligate the 5’ RNA adapter per manufacturer’s instructions with 15% (w/v) PEG-8000 in final solution and incubated overnight at 16°C. Following the 5’ end ligation, beads were washed twice with high salt buffer, twice with binding buffer, and twice with low salt buffer, then once with 0.25× SuperScript IV reaction buffer. Reverse transcription was performed using SuperScript IV Reverse Transcriptase (Invitrogen 18090010) and the cDNA was eluted from the beads by heating the samples twice for 30 seconds at 95°C.
The eluted cDNA was initially amplified for 5-cycles of "preCR" [NEBNext Ultra II Q5 master mix (New England Biolabs M0544S) with Illumina TruSeq PCR primers RP-1 and RPI-X for indexing] following the manufacturer's suggested PCR cycling protocol for library construction]. A portion of preCR was serially diluted and for test amplification to determine optimal amplification of final libraries. Libraries were amplified by 3 additional cycles of PCR (8 cycles in total). The amplified library was purified using the ProNex Size-Selective Purification System (Promega) and sequenced using the Illumina NovaSeq platform.

treatment_protocol: OS-RC-2 cells were treated with either 2 uM PT2399 (PT) or vehicle (Veh) for 2 hours and cells from the two conditions listed above were harvested at the end of 2 hours.

value: Treated with 2 uM PT2399 for 2 hours


title: OS-RC-2, PT2399 2 h, Rep1


title: 786-O, VHL, Veh 72 h, Rep1


title: RCC4 FLAG-HIF2α, FLAG, Rep2, ChIP

library_source: genomic

data_processing:
For peak calling and data analysis, all samples were processed through the computational pipeline developed at the Dana-Farber Cancer Institute Center for Functional Cancer Epigenetics (CFCE) using primarily open-source programs. Sequence tags were aligned with Burrows-Wheeler Aligner (BWA) to build hg19 and uniquely mapped, non-redundant reads were retained. These reads were used to generate binding sites with Model-Based Analysis of ChIP-Seq 2 (MACS v2.1.1.20160309), with a q-value (FDR) threshold of 0.0195. We evaluated multiple quality control criteria based on alignment information and peak quality: (i) sequence quality score (ii) uniquely mappable reads (reads that could only map to one location in the genome) (iii) uniquely mappable locations (locations that could only be mapped by at least one read) (iv) peak overlap with Velcro regions, a comprehensive set of locations – also called consensus signal artifact regions – in the genome that have anomalous, unstructured high signal or read counts in next-generation sequencing experiments independent of cell line and of type of experiment (v) number of total peaks (each sample had >3,000 peaks, passing the minimum requirement of 1000) (vi) high-confidence peaks (the number of peaks that were tenfold enriched over background) (vii) percentage overlap with known DHS sites derived from the ENCODE Project (samples meet the minimum threshold 80%) and (viii) peak conservation (a measure of sequence similarity across species based on the hypothesis that conserved sequences are more likely to be functional). All samples in this study passed quality control criteria. For differential binding analyses, differential peak analysis was performed using the CoBRA pipeline. Differential peaks were identified by DEseq2 with adjusted p ≤ 0.05. A total number of reads in each sample was applied to the size factor in DEseq2, which can normalize the sequencing depth between samples. To identify overlapped ERV and HIF2α peak location, HIF2α bed file was extended by 1 kb, 5 kb, 10 kb for each peak region using BEDOPS tool. The extended HIF2α bed files were intersected with ERV reference bed file using BedTools intersect command. Final Lists contain overlapped genomic locations of ERV and extended HIF2α peaks
Assembly: hg19
Supplementary files format and content: An excel file, which contains HIF2α binding sites in the genome based on anti-HIF2α ChIP Seq in 786-O sgCtrl cells and the distance of these peaks with 3173 ERVs.

growth_protocol: 786-O cells were obtained from American Type Culture Collection. RCC4 cells were provided by Dr. Peter Ratcliffe (University of Oxford and Francis Crick Institute). OS-RC-2 were obtained from RIKEN Bioresource Research Center Cell Bank. 786-O and RCC4 cells were cultured in DMEM (Gibco 11995073). OS-RC-2 were cultured in RPMI-1640 (Gibco 11875119). All media were supplemented with FBS (GeminiBio 100-106), 1% penicillin-streptomycin (Gibco 15140122)

extract_protocol:
For ChIP sample preparation, 1×107 adherent cells were washed with PBS, trypsinized, transferred to Eppendorf tubes and collected by centrifugation at 300×g for 5 min at RT. Cell pellets were washed once with RT PBS-complete [PBS supplemented with 1× protease inhibitor (Sigma PIC0006) and 5mM sodium butyrate], resuspended in 2 mM of disuccinimidyl glutarate (DSG, Thermo Fisher Scientific 20593) diluted in PBS, and then agitated at 850 rpm on a Fisherbrand Isotemp Heat/Cool Programmable Thermal Mixer II (Thermo Fisher Scientific) at RT for 45 min. The cell pellets were collected by centrifugation at 300×g for 5 min at RT. The supernatant was removed, and the cell pellets were resuspended in freshly made 1% formaldehyde (Thermo Fisher Scientific 28908) diluted in PBS followed by agitation at 850 rpm on a Fisherbrand Isotemp Heat/Cool Programmable Thermal Mixer II for 10 min at RT. The crosslinking was quenched by adding glycine to a final concentration of 0.125 M with agitation at 850 rpm on a Fisherbrand Isotemp Heat/Cool Programmable Thermal Mixer II for 5 min at RT. The cell pellets were collected by centrifugation at 300×g for 5 min at 4°C. Cell pellets were washed once with ice-cold PBS-complete. Crosslinked cells were then pelleted, snapfrozen and stored at -80°C.
Aliquots of frozen pellets were thawed on ice, resuspended in 500 ulof 1% SDS lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% SDS, 1× protease inhibitor, 5 mM sodium butyrate) and lysed on ice for 10-15 min. The lysates were transferred to 1 ml Adaptive Forced Acoustics (AFA) fiber milliTUBEs (Covaris 520135) and sonicated at the following settings: 140 peak incident power, 5% duty factor and 200 cycles per burst) using Covaris E220 sonicator. Sonication lasted for 10 min. Post sonication, the lysates were transferred to Eppendorf tubes and cleared by centrifugation at 17,000×g for 15 min at 4°C.
To determine the amount of precleared chromatin to be used for ChIP-Seq experiments, 10 ulof the lysates were aliquoted (INPUT) and 90 ulof TE was added to make 100 ulsolution. 1 ulRNase A (Invitrogen AM2696) was added to the samples and incubated for 30 min at 37°C, then 5 ulProteinase K (20 mg/ml, Thermo Fisher Scientific EO0492) was directly added to the mixture and incubated at 65°C for 16 h with constant agitation at 850 rpm on a Fisherbrand Isotemp Heat/cool Programmable Thermal Mixer II at the indicated temperatures. Next the chromatin was purified using PCR Purification Kit (Qiagen 28104). Briefly, 500 ulPB buffer was added to each 100 ulsample and the mixture was mixed and loaded onto the purification column. The purified chromatin was eluted using 32 ulEB buffer. Chromatin (INPUT) concentration was determined using a Qubit High Sensitivity Kit (Life Technologies A33231) on a Qubit 4 Fluorometer (Invitrogen Q33239). 40 ug chromatin (INPUT) was immunoprecipitated with 5 ug of FLAG antibody (Sigma-Aldrich F1804) or 10 ulHIF2α antibody (a gift from Dr. David R. Mole).
Antibody-bead conjugation was done by first taking 30 ulof protein G beads (Life Technologies 10004D) per sample and washing them three times with 500 ulice-cold 0.5% BSA diluted in PBS. The beads were then resuspended in 500 ulice-cold 0.5% BSA diluted in PBS with the desired number of antibodies and rotated end-to-end for 4-6 h at 4°C, followed by two additional washed with ice-cold 0.5% BSA diluted in PBS to remove unbound antibodies. Lysates containing the desired amount of chromatin/protein were diluted 10-fold using ChIP dilution buffer (20 mM Tris-HCl pH 8.0, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 1× protease inhibitor, 5 mM sodium butyrate), added to pre-washed antibody-bead conjugates and then rotated end-to-end overnight at 4°C. The next day, the bead-bound chromatin-antibody complexes were washed twice with RIPA 0 buffer (10 mM Tris-HCl pH 7.4, 1 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate), twice with RIPA 0.3 buffer (10 mM Tris-HCl pH 7.4, 1 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate, 0.3 M NaCl), twice with LiCl buffer (10 mM Tris-HCl pH 7.4, 1 mM EDTA pH 8.0, 0.5% NP40, 0.5% sodium deoxycholate, 0.25 M LiCl), and then eluted with 100 ulpre-warmed (37°C) ChIP elution buffer (1% SDS, 0.1 M NaHCO3 in H2O). 1 ulRNase A was added to the samples and incubated for 30 min at 37°C, then 5 ulProteinase K was added to the samples and incubated at 65°C for 16 h. For RNase A and Proteinase K incubation, the samples were constantly agitated at 850 rpm on Fisherbrand Isotemp Heat/cool Programmable Thermal Mixer II. The supernatant was purified using a MinElute PCR Purification Kit (Qiagen 28004), eluted in 12 ulH2O, and quantified using a Qubit High Sensitivity Kit (Invitrogen Q33230).
A 5 ulsample was used for ChIP-seq library preparation with a Swift DNA Library Prep Kit (Swift Biosciences 1002). 75 bp paired-end reads were sequenced on a NextSeq instrument (Illumina).

treatment_protocol: 786-O cells were underwent CRISPR-based gene editing with a HIF2α sgRNA or a control sgRNA (sgCtrl) and were then treated with 0.5 uM GSK3685032 (DNMT1i) or vehicle (Veh) for 9 days. We performed anti-HIF2α ChIP-Seq using the cells listed above. In addition, we also performed ChIP-Seq using an anti-FLAG antibody and ccRCC cells (786-O, OS-RC-2, and RCC4) cells in which CRISPR/Cas9 was used to append a FLAG-HA epitope tag to the N-terminus of HIF2α expressed from the endogenous HIF2α locus.

value: FLAG-HA epitope tag coding sequence was inserted at the 5’ end of the endogenous HIF2α open reading frame by CRISPR-HDR (FLAG-HIF2α)


title: OS-RC-2, Veh 2 h, Rep3

value: ccRCC

value: Treated with vehicle (Veh) for 2 hours


title: RCC4 FLAG-HIF2α, FLAG, Rep1, ChIP


title: OS-RC-2, Veh 2 h, Rep2


title: RCC4 sgAAVS1, FLAG, Rep2, ChIP

value: Infected with a ctrl guide RNA (sgAAVS1)


title: OS-RC-2, Veh 2 h, Rep1


title: OS-RC-2 FLAG-HIF2α, FLAG, Rep1, ChIP


title: RCC4 sgAAVS1, FLAG, Rep1, ChIP


title: OS-RC-2 FLAG-HIF2α, FLAG, Rep2, ChIP


title: OS-RC-2 sgAAVS1, FLAG, Rep1, ChIP


title: 786-O FLAG-HIF2α, FLAG, Rep2, ChIP


title: OS-RC-2 sgAAVS1, FLAG, Rep2, ChIP


title: 786-O FLAG-HIF2α, FLAG, Rep1, ChIP


title: 786-O sgCtrl, HIF2α, DNMT1i 9 days, Rep2, ChIP

value: Infected with a ctrl guide RNA (sgCtrl), treated with 0.5 uM DNMT1i for 9 days


title: 786-O sgHIF2α, HIF2α, DNMT1i 9 days, ChIP

value: Infected with a HIF2α guide RNA (sgHIF2α), treated with 0.5 uM DNMT1i for 9 days


title: 786-O sgHIF2α, HIF2α, Veh 9 days, ChIP

value: Infected with a HIF2α guide RNA (sgHIF2α), treated with vehicle (Veh) for 9 days


title: 786-O sgAAVS1, FLAG, Rep1, ChIP


title: 786-O sgCtrl, HIF2α, DNMT1i 9 days, Rep1, ChIP


title: 786-O sgCtrl, HIF2α, Veh 9 days, Rep2, ChIP

value: Infected with a ctrl guide RNA (sgCtrl), treated with vehicle (Veh) for 9 days


title: FVB.129P2-Pde6b + Tyr c-ch/AntJ  LEPR mutant male mice replicate 1

status: Public on Feb 19 2025

city: LITTLE ROCK

first: Melanie

last: MacNicol

state: Arkansas

address: 4301 W Markham St

department: Neuroscience

institute: UAMS

data_processing:
10x Genomics Cell Ranger 7.1 mkfastq wrapper and was used to perform sample demultiplexing and generate fastq files
The reads were aligned with 10x Genomics CellRanger 3.1.0 to the University of California, Santa Cruz (UCSC) mm10 reference transcriptome using STAR and transcript counts were generated
Cells with unique feature counts over more the 75th percentile plus 1.5 times the interquartile range (IQR) or less 200 unique features, total gene counts more than more the 75th percentile plus 1.5 times the IQR or less than 1000 counts, and/or mitochondrial feature percentage more the 75th percentile plus 1.5 times the IQR or less than the 25th percentile minus 1.5 times the IQR were filtered out of the data. Next, the 2000 highest variable features were selected.
The data were then scaled by a linear transformation and variation associated with cell death and cell cycling where regressed out of the scaled data using mitochondrial feature percentage and cell cycle scoring values. Counts were normalized using the SCTransform and PCA was performed on the scaled data. A Uniform Manifold Approximation and Projection (UMAP) was used to visualize and explore the clustering results.
Seurat’s FindNeighbors and FindClusters functions were optimized to label clusters based on the visual clustering in the projections. Seurat FindAllMarkers function was used to identify gene markers that define cluster cell types.
Differential expression analysis was performed using the FindMarkers to compare similar cell types across the genders. The MAST test, a GLM-framework that treats cellular detection rate as a covariate, was used to determine statistically different transcription
Assembly: GRCm38 / mm10
Supplementary files format and content: Hierarchical Data Format (H5) containing the barcodes, gene annotation, and gene counts for each sample

source_name: Pituitary

growth_protocol: The FVB hybrid strain of mice was FVB.129P2-Pde6b + Tyr c-ch/AntJ.  We began the study with 6-month-old mice, because our previous studies had shown that the phenotype associated with the loss of LEPR in somatotropes was most evident after this age.   Mice were housed at 28.4°C (thermoneutrality) on a 11 h light (07:00 start) and 13 h dark (18:00 start) cycle.

extract_protocol:
Six (6) pituitaries per sex/diet/transgenic were collected for single-cell RNA-sequencing (scRNA-seq) analyses. Individual pituitary cell suspensions were then pooled within treatment groups (2-3 pituitaries/pool) for counting. Cell concentration within each pool was adjusted to optimally target 10,000 cells according to 10X Genomics guidelines and samples were then submitted to the UAMS Cancer Institute Genomics Core facility. Visual examination under a microscope (EVOS M7000, Thermo Fisher Scientific) was used to detected cell debris or aggregates, which were removed by passing cell suspensions through a Flowmi™ _(SP BEL-ART, catalog # 136800040) cell strainer (40 microns).  Following centrifugation at 250 g for 10 min, cells were re-suspended in 1X PBS (Ca2+/Mg2+-free) containing 0.04% (w/v) BSA. Cell concentration and viability were detected with ReadyProbes™ _Cell Viability Imaging Kit, Blue/Green (Thermo Fisher Scientific, catalog # R37609), and manually counted.
Single-cell 3′ library generation was performed using a 10x Genomics Chromium Controller and Chromium next GEM Single Cell 3’ Reagent Kits v 3.1 (Dual index). Libraries were sequenced on the Illumina NovaSeq 6000 platform with paired-end mode (read1: 28 cycles, read 2: 90 cycles, i7: 10 cycles, i5: 10 cycles) to generate a minimum of 20,000 read pairs per cell.

treatment_protocol: The deletion mutant mice were produced by crossing females bearing one allele of Cre-recombinase driven by the rat GH promoter and two alleles of floxed LEPR-exon 1 with males bearing floxed LEPR-exon 1.  Half of the progeny carry the Cre-recombinase and ablated LEPR in somatotropes and the other half bear only floxed LEPR exon 1 (littermate controls).

tag: tissue

value: Pituitary

tag: genotype

value: FVB.129P2-Pde6b + Tyr c-ch/AntJ; Tg(Gh1-cre)bKnmn (+/-); Leprtm1Rck (fl/fl)

value: LEPR mutant


title: A-498, EV, Veh 72 h, Rep2


title: 786-O, EV, Veh 72 h, Rep1


title: FVB.129P2-Pde6b + Tyr c-ch/AntJ control male mice replicate 2

value: FVB.129P2-Pde6b + Tyr c-ch/AntJ; Leprtm1Rck (fl/fl)


title: FVB.129P2-Pde6b + Tyr c-ch/AntJ control male mice replicate 1


title: 786-O sgCtrl, HIF2α, Veh 9 days, Rep1, ChIP


title: OS-RC-2, PT2399 2 h, Rep3


title: FVB.129P2-Pde6b + Tyr c-ch/AntJ  LEPR mutant male mice replicate 2


title: FVB.129P2-Pde6b + Tyr c-ch/AntJ  LEPR mutant female mice replicate 2


title: blood, time point 2, e28

status: Public on Feb 18 2025

city: Sao Paulo

first: Sintia

last: Belangero

address: Rua Botucatu

department: Morphology and Genetics

country: Brazil

institute: UNIFESP

description: Library name: e28_w1

data_processing:
To quantify gene expression, we downloaded the transcript list (manifest file) provided by Illumina. We then converted the target coordinates from the hg19 reference genome to the hg38 reference genome using the liftOver tool. Each target was assigned a unique GENCODE ID by comparing its coordinates with genes annotated by GENCODE [version 38] using the bedtools intersect tool [default parameters]. To guarantee precise GENCODE ID assignment, a manual verification was performed. Other coding genes that overlapped with the targets in the GENCODE annotated transcripts were removed. Kallisto was used to initiate the quantification of target expression. We generated a transcript index based on this new transcript list (excluding overlapping genes) using the command “kallisto index -i”. Kallisto was then executed for each sample individually (single end mode). The analysis considered the average read length calculated for each sample and a standard deviation of 0.0000001. To quantify gene-level expression, the tximport tool was employed.
Assembly: hg38
Supplementary files format and content: raw read counts after tximport

source_name: blood

extract_protocol:
Blood samples were collected in PAXgene RNA tubes (PreAnalytix, Switzerland), and leukocyte RNA was extracted from whole blood using the PAXgene Blood RNA Kit (Qiagen, Germany). RNA quality and quantity were assessed with the NanoDropTM 1000 Spectrophotometer (Thermo Fisher Scientific) and the Qubit 2.0 fluorometer with the Qubit RNA BR Assay Kit (Thermo Fisher Scientific), respectively. DNA contamination was verified on a 1.5% agarose gel, and RNA integrity was evaluated using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Kit (Agilent).
Gene expression was measured using next-generation sequencing with the TruSeq® Targeted RNA Expression protocol (Illumina). Genes were selected based on four previous studies, two of them in the Brazilian High Risk Cohort for Mental Conditions (BHRCS). Briefly, 55 genes exhibited differential expression in the blood of BHRCS individuals who transitioned from low to high psychiatric symptoms over a 3- year follow-up period, indicating the onset of symptoms (10.1038/s41398-020-0772-3). Conversely, four genes were differentially expressed in individuals who showed a reduction in psychiatric symptoms, suggesting remission (10.1038/s41398-020-0772-3). Additionally, three genes displayed differential expression in the blood of BHRCS participants with major depressive disorder (10.1016/j.jpsychires.2017.03.015). Furthermore, we included 20 genes known to be differentially expressed in the brains of individuals with autism spectrum disorders, schizophrenia, bipolar disorder, depression, or general mental health conditions (10.1126/science.aad6469), as well as 6 endogenous control genes for blood samples for normalization procedures (10.1186/1755-8794-2-49). A total of 100 ng of RNA was reverse transcribed into cDNA using ProtoScript II Reverse Transcriptase (New England Biolabs). Libraries were prepared using the TruSeq Targeted RNA Expression Kit and the TruSeq® Targeted RNA Custom Oligonucleotide Pool (Illumina). Libraries were pooled and sequenced on the NextSeq 500 instrument (Illumina) using the MidOutput v2 kit (150 cycles) and 100 single end reads.

value: blood

tag: Sex

value: Female

tag: time

tag: batch


title: FVB.129P2-Pde6b + Tyr c-ch/AntJ LEPR mutant female mice replicate 1


title: blood, time point 2, e1021

description: Library name: e1021_w1

value: Male


title: blood, time point 1, e1021

description: Library name: e1021_w0


title: FVB.129P2-Pde6b + Tyr c-ch/AntJ control female mice replicate 1


title: blood, time point 2, e1370

description: Library name: e1370_w1


title: 786-O sgAAVS1, FLAG, Rep2, ChIP


title: blood, time point 1, e1370

description: Library name: e1370_w0


title: blood, time point 1, e2089

description: Library name: e2089_w0


title: blood, time point 2, e721

description: Library name: e721_w1


title: blood, time point 1, e721

description: Library name: e721_w0


title: blood, time point 2, e2089

description: Library name: e2089_w1


title: blood, time point 1, e1060

description: Library name: e1060_w0


title: blood, time point 2, e1656

description: Library name: e1656_w1


title: blood, time point 1, e1656

description: Library name: e1656_w0


title: FVB.129P2-Pde6b + Tyr c-ch/AntJ control female mice replicate 2


title: blood, time point 2, e1060

description: Library name: e1060_w1


title: blood, time point 2, e876

description: Library name: e876_w1


title: blood, time point 1, e28

description: Library name: e28_w0


title: blood, time point 1, e18

description: Library name: e18_w0


title: blood, time point 1, e876

description: Library name: e876_w0


title: blood, time point 2, e2023

description: Library name: e2023_w1


title: blood, time point 1, e2023

description: Library name: e2023_w0


title: blood, time point 1, e733

description: Library name: e733_w0


title: blood, time point 2, e733

description: Library name: e733_w1


title: blood, time point 1, e1317

description: Library name: e1317_w0


title: blood, time point 2, e1317

description: Library name: e1317_w1


title: blood, time point 2, e37

description: Library name: e37_w1


title: blood, time point 2, e18

description: Library name: e18_w1


title: blood, time point 1, e37

description: Library name: e37_w0


title: blood, time point 2, e2064

description: Library name: e2064_w1


title: blood, time point 1, e2064

description: Library name: e2064_w0


title: blood, time point 1, e1509

description: Library name: e1509_w0


title: blood, time point 2, e1225

description: Library name: e1225_w1


title: blood, time point 2, e1509

description: Library name: e1509_w1


title: blood, time point 2, e379

description: Library name: e379_w1


title: blood, time point 2, e529

description: Library name: e529_w1


title: blood, time point 1, e1225

description: Library name: e1225_w0


title: blood, time point 1, e379

description: Library name: e379_w0


title: blood, time point 2, e2310

description: Library name: e2310_w1


title: blood, time point 1, e2310

description: Library name: e2310_w0


title: blood, time point 2, e504

description: Library name: e504_w1


title: blood, time point 1, e504

description: Library name: e504_w0


title: blood, time point 1, e185

description: Library name: e185_w0


title: blood, time point 2, e42

description: Library name: e42_w1


title: blood, time point 2, e925

description: Library name: e925_w1


title: blood, time point 1, e42

description: Library name: e42_w0


title: blood, time point 2, e406

description: Library name: e406_w1


title: blood, time point 1, e925

description: Library name: e925_w0


title: blood, time point 2, e1921

description: Library name: e1921_w1


title: blood, time point 1, e2450

description: Library name: e2450_w0


title: blood, time point 2, e2017

description: Library name: e2017_w1


title: blood, time point 1, e749

description: Library name: e749_w0


title: blood, time point 1, e2017

description: Library name: e2017_w0


title: blood, time point 1, e1764

description: Library name: e1764_w0


title: blood, time point 2, e133

description: Library name: e133_w1


title: blood, time point 1, e133

description: Library name: e133_w0


title: blood, time point 2, e1999

description: Library name: e1999_w1


title: blood, time point 1, e1921

description: Library name: e1921_w0


title: blood, time point 2, e1764

description: Library name: e1764_w1


title: blood, time point 1, e529

description: Library name: e529_w0


title: blood, time point 1, e2265

description: Library name: e2265_w0


title: blood, time point 1, e1999

description: Library name: e1999_w0


title: blood, time point 2, e1718

description: Library name: e1718_w1


title: blood, time point 2, e2265

description: Library name: e2265_w1


title: blood, time point 1, e1907

description: Library name: e1907_w0


title: blood, time point 2, e1907

description: Library name: e1907_w1


title: blood, time point 2, e185

description: Library name: e185_w1


title: blood, time point 1, e474

description: Library name: e474_w0


title: blood, time point 2, e474

description: Library name: e474_w1


title: blood, time point 1, e1406

description: Library name: e1406_w0


title: blood, time point 1, e1390

description: Library name: e1390_w0


title: blood, time point 1, e406

description: Library name: e406_w0


title: blood, time point 2, e2450

description: Library name: e2450_w1


title: blood, time point 2, e1406

description: Library name: e1406_w1


title: blood, time point 2, e1390

description: Library name: e1390_w1


title: blood, time point 2, e1399

description: Library name: e1399_w1


title: blood, time point 2, e749

description: Library name: e749_w1


title: blood, time point 1, e1399

description: Library name: e1399_w0


title: blood, time point 2, e1592

description: Library name: e1592_w1


title: blood, time point 1, e1592

description: Library name: e1592_w0


title: blood, time point 2, e855

description: Library name: e855_w1


title: blood, time point 1, e855

description: Library name: e855_w0


title: blood, time point 1, e431

description: Library name: e431_w0


title: blood, time point 2, e643

description: Library name: e643_w1


title: blood, time point 2, e573

description: Library name: e573_w1


title: blood, time point 1, e1718

description: Library name: e1718_w0


title: blood, time point 1, e521

description: Library name: e521_w0


title: blood, time point 2, e521

description: Library name: e521_w1


title: blood, time point 2, e902

description: Library name: e902_w1


title: blood, time point 2, e2492

description: Library name: e2492_w1


title: blood, time point 1, e2492

description: Library name: e2492_w0


title: blood, time point 1, e902

description: Library name: e902_w0


title: blood, time point 1, e646

description: Library name: e646_w0


title: blood, time point 2, e171

description: Library name: e171_w1


title: blood, time point 1, e171

description: Library name: e171_w0


title: blood, time point 1, e1052

description: Library name: e1052_w0


title: blood, time point 2, e1052

description: Library name: e1052_w1


title: blood, time point 2, e1112

description: Library name: e1112_w1


title: blood, time point 2, e2354

description: Library name: e2354_w1


title: blood, time point 1, e1112

description: Library name: e1112_w0


title: blood, time point 2, e1579

description: Library name: e1579_w1


title: blood, time point 1, e2354

description: Library name: e2354_w0


title: blood, time point 2, e485

description: Library name: e485_w1


title: blood, time point 1, e1579

description: Library name: e1579_w0


title: blood, time point 2, e1437

description: Library name: e1437_w1


title: blood, time point 1, e643

description: Library name: e643_w0


title: blood, time point 2, e2396

description: Library name: e2396_w1


title: blood, time point 2, e431

description: Library name: e431_w1


title: blood, time point 1, e485

description: Library name: e485_w0


title: blood, time point 1, e2396

description: Library name: e2396_w0


title: blood, time point 1, e573

description: Library name: e573_w0


title: blood, time point 1, e1437

description: Library name: e1437_w0


title: blood, time point 1, e11

description: Library name: e11_w0


title: blood, time point 2, e1347

description: Library name: e1347_w1


title: blood, time point 1, e1928

description: Library name: e1928_w0


title: blood, time point 2, e873

description: Library name: e873_w1


title: blood, time point 1, e1347

description: Library name: e1347_w0


title: blood, time point 1, e873

description: Library name: e873_w0


title: blood, time point 2, e646

description: Library name: e646_w1


title: blood, time point 1, e1278

description: Library name: e1278_w0


title: blood, time point 2, e126

description: Library name: e126_w1


title: blood, time point 1, e126

description: Library name: e126_w0


title: blood, time point 1, e1583

description: Library name: e1583_w0


title: blood, time point 2, e1583

description: Library name: e1583_w1


title: blood, time point 2, e1829

description: Library name: e1829_w1


title: blood, time point 2, e1312

description: Library name: e1312_w1


title: blood, time point 1, e1312

description: Library name: e1312_w0


title: blood, time point 1, e1829

description: Library name: e1829_w0


title: blood, time point 2, e1355

description: Library name: e1355_w1


title: blood, time point 1, e351

description: Library name: e351_w0


title: blood, time point 2, e351

description: Library name: e351_w1


title: blood, time point 2, e899

description: Library name: e899_w1


title: blood, time point 2, e68

description: Library name: e68_w1


title: blood, time point 1, e1291

description: Library name: e1291_w0


title: blood, time point 1, e68

description: Library name: e68_w0


title: blood, time point 1, e1737

description: Library name: e1737_w0


title: blood, time point 2, e1278

description: Library name: e1278_w1


title: blood, time point 2, e1291

description: Library name: e1291_w1


title: blood, time point 2, e11

description: Library name: e11_w1


title: blood, time point 2, e1928

description: Library name: e1928_w1


title: blood, time point 2, e1496

description: Library name: e1496_w1


title: blood, time point 1, e1537

description: Library name: e1537_w0


title: blood, time point 2, e653

description: Library name: e653_w1


title: blood, time point 1, e899

description: Library name: e899_w0


title: blood, time point 2, e1537

description: Library name: e1537_w1


title: blood, time point 1, e1496

description: Library name: e1496_w0


title: blood, time point 2, e1784

description: Library name: e1784_w1


title: blood, time point 1, e1355

description: Library name: e1355_w0


title: blood, time point 1, e1784

description: Library name: e1784_w0


title: blood, time point 2, e48

description: Library name: e48_w1


title: blood, time point 1, e348

description: Library name: e348_w0


title: blood, time point 2, e384

description: Library name: e384_w1


title: blood, time point 2, e348

description: Library name: e348_w1


title: blood, time point 1, e1722

description: Library name: e1722_w0


title: blood, time point 2, e1737

description: Library name: e1737_w1


title: blood, time point 1, e48

description: Library name: e48_w0


title: blood, time point 2, e1727

description: Library name: e1727_w1


title: blood, time point 2, e1554

description: Library name: e1554_w1


title: blood, time point 1, e1554

description: Library name: e1554_w0


title: blood, time point 1, e1160

description: Library name: e1160_w0


title: blood, time point 1, e1079

description: Library name: e1079_w0


title: blood, time point 2, e1160

description: Library name: e1160_w1


title: blood, time point 2, e1887

description: Library name: e1887_w1


title: blood, time point 1, e2251

description: Library name: e2251_w0


title: blood, time point 1, e1887

description: Library name: e1887_w0


title: blood, time point 1, e1727

description: Library name: e1727_w0


title: blood, time point 2, e2251

description: Library name: e2251_w1


title: blood, time point 1, e1367

description: Library name: e1367_w0


title: blood, time point 2, e711

description: Library name: e711_w1


title: blood, time point 1, e653

description: Library name: e653_w0


title: blood, time point 1, e279

description: Library name: e279_w0


title: blood, time point 2, e1367

description: Library name: e1367_w1


title: blood, time point 1, e711

description: Library name: e711_w0


title: blood, time point 2, e2079

description: Library name: e2079_w1


title: blood, time point 1, e2079

description: Library name: e2079_w0


title: blood, time point 2, e293

description: Library name: e293_w1