title: Healthy 6 canine PBMC single-cell landscape

city: Jeju-si

first: Myung-Chul

last: Kim

state: Jeju-do

address: 102, Jejudaehak-ro, Jeju-si, Jeju-do

institute: Jeju National University

description:
Library name: Healthy 6
10x Genomics

data_processing:
Base calling and FASTQ generation were performed with bcl2fastq (Illumina) and cellranger mkfastq (Cell Ranger v8.0.0, 10x Genomics). Reads were aligned and quantified using cellranger count by using two canine genome references: CanFam3.1 (GCA_000002285.3) and GSD_1.0/CanFam4 (GCF_011100685.1). Genome references were constructed with cellranger mkref using filtered FASTA and GTF files containing only protein coding genes.
Assembly: GSD_1.0/CanFam4 (GCF_011100685.1)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Canis lupus familiaris

source_name: Blood, PBMC

extract_protocol:
Blood was collected via jugular venipuncture and processed immediately. Peripheral leukocytes or peripheral blood mononuclear cells were isolated by density gradient centrifugation using SepMate 15 tubes (Stemcell Technologies, Vancouver, Canada) and Ficoll Paque PLUS (GE Healthcare, Chicago, IL, USA). The PBMC fraction was washed twice with Dulbecco’s phosphate buffered saline (DPBS; Thermo Fisher Scientific, Waltham, MA, USA) containing 2% heat inactivated fetal bovine serum (FBS; Life Technologies, Pleasanton, CA, USA). A small aliquot of the suspension was cytospun onto glass slides and stained with Diff Quik to confirm cell composition. The remaining PBMCs were cryopreserved in a cytoprotective medium—either CryoStor CS10 (Stemcell Technologies) or Cellbanker 1 (Zenogen Pharma, Koriyama, Japan), and stored in liquid nitrogen until further analysis. Thawed PBMCs were washed and incubated on ice for 10 minutes with an anti dog Fc receptor blocking reagent (Invitrogen, eBioscience, San Diego, CA, USA). After washing with DPBS containing 2% FBS, cells were stained for 30 minutes at 37 °C, protected from light, with Fixable Viability Dye eFluor 780 (Invitrogen, eBioscience), anti dog CD45 FITC (clone YKIX 716.13; Bio Rad Laboratories, Hercules, CA, USA), and anti dog CD3 FITC (clone CA17.2A12; Bio Rad Laboratories). Live single cells were then sorted on a FACSAria III (BD Biosciences Pharmingen, San Diego, CA, USA), gating on CD45⁺CD3⁺ T cells and CD45⁺CD3⁻ non T leukocytes. Post sort viability and cell counts were assessed using a LUNA FL™ Automated Fluorescence Cell Counter (Logos Biosystems, Anyang, South Korea). Equal numbers of CD45⁺CD3⁺ and CD45⁺CD3⁻ cells from each dog were pooled and immediately processed for single cell library construction on the 10x Genomics Chromium platform in a single run.
Single cell libraries were prepared using the Chromium Next GEM Single Cell 5′ Kit v2 (10x Genomics) following the manufacturer’s protocol 38,39. Libraries were sequenced on an Illumina NovaSeq 6000 with 2 × 150 bp paired end reads.

value: Blood, PBMC

value: Primary cells

value: PBMC, mononuclear cells

value: Wild type

value: Batch 1


title: vASC+Capan-1_RFP_1

status: Public on Jan 12 2026

type: SRA

city: New York

first: Lingyi

last: Cai

state: New York

address: 2960 Broadway

country: USA

institute: Columbia University

description: Library name: J37

library_source: transcriptomic

data_processing:
For each sample, we performed gene expression quantification using RSEM (RNA-seq by Expectation Maximization) v1.3.1 with STAR (Spliced Transcripts Alignment to a Reference) v2.7.1a as the aligner (31,32). Paired-end sequencing reads in raw FASTQ format were processed with the “rsem-calculate-expression” function.
We used the DESeq2 (1.30.1) method to identify differentially expressed genes (DEGs). Genes with fewer than ten raw counts across all samples were excluded from the analysis. To create the DESeq2 object, we used the “DESeqDataSetFromMatrix” function, specifying the design to indicate the various experimental conditions. DEGs were estimated using the “lfcShrink” function with a “normal” estimator. We performed Gene Set Enrichment Analysis (GSEA) using the fgsea (v 1.16.0) R package with 50 broad hallmark gene sets and thousands of Gene Ontology (GO) sets. For comparison, we selected DEGs (adj p values < 0.05) and ranked them by fold change. From the ranked list, we chose the top 100 genes for further over-representation analysis. GO term over-representation analysis was conducted using the “enrichGO” function from the clusterProfiler (v3.18.1) package using the org.Hs.eg.db (v3.12.0) annotation database. In independent analyses, Qiagen Ingenuity Pathway Analysis (IPA) software was used to identify condition-dependent changes in signaling networks.
Assembly: GRCh38
Supplementary files format and content: Analyzed data are presented as TPM count in Microsoft Excel format (xlsx).

molecule: total RNA

organism: Homo sapiens

source_name: adipose stromal vascular fraction

growth_protocol: Cells were grown in DMEM with high glucose (Cytiva, #SH30243.01) supplemented with 20% FBS (Sigma, #F0926) and 1X Antibiotic/Antimycotic solution (Hyclone, #SV30079.01) and maintained at 37C with 5% CO2.

extract_protocol:
After 7-days growth media was aspirated and cells were washed with PBS. Trypsin (0.25%) was used to seperate cells into single cell suspension. Cells were then sorted based on RFP+ or GFP+ expression using FACS. RNA from cells was isolated using the RNeasy Plus Mini Kit (Qiagen, #74104).
RNA samples were submitted to Cancer Genomics Center at The University of Texas Health Science Center at Houston (CPRIT RP240610). For DNA depletion, the RNA samples were treated with DNase using RNeasy Mini Kit (#74104, Qiagen, Germany) and RNase-free DNase Set (#79254, Qiagen, Germany). The treated RNA samples were eluted in 10ul nuclease-free water. Total RNA was quality-checked using Agilent RNA 6000 Pico kit (#5067-1513) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA). RNA with DV200 greater than 66% was used for library preparation. Libraries were prepared with SMARTer Stranded Total RNA-Seq Kit v2 (#634418, Takara Bio, Japan) and Unique Dual Index Kit (#634752, Takara Bio, Japan) following the manufacturer’s instructions. The quality of the final libraries was examined using Agilent High Sensitive DNA Kit (#5067-4626) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA). The libraries were pooled evenly and went for the paired-end 75-cycle sequencing on an Illumina NextSeq 550 System (Illumina, Inc., USA) using High Output Kit v2.5 (#20024907, Illumina, Inc., USA).

treatment_protocol: For coculture experiments, vASC, vASC_LINC, vASC_SFRP4 and Capan-1 cells were plated at 300K:300K cells per well in 6-well plates in replicates and cultured for 7-days. Media was replensihed every 48-hours.

tag: tissue

value: adipose stromal vascular fraction

tag: cell line

value: vASC

tag: cell type

value: adipose stromal cells


title: CHLA90_RA_REP2

city: London

first: Sally

middle: Linda

last: George

address: 26 Oakleaf Avenue

country: United Kingdom

institute: The Institute of Cancer Research

description: Library name: GEO5504A16

library_source: genomic

data_processing:
nf-core/atacseq release 3.0
Assembly: GRCh38, Ensembl release 95
Supplementary files format and content: bigWig files generated by nfcore pipeline
Supplementary files format and content: broadPeak files

molecule: genomic DNA

growth_protocol: DMEM Glutamax 10% FBS

extract_protocol: OMNI-ATAC protocol

treatment_protocol: 72 hours treatement with either DMSO (vehicle) or 10uM retinoic acid

value: Neuroblastoma

tag: genotype

value: ATRX IFF

tag: treatment

value: 10uM Retinoic acid


title: Healthy 4 canine PBMC single-cell landscape

country: South Korea

description:
Library name: Healthy 4
10x Genomics

library_source: transcriptomic single cell

molecule: polyA RNA

tag: batch


title: Healthy 3 canine PBMC single-cell landscape

description:
Library name: Healthy 3
10x Genomics


title: AML Ly6Glo CD101- rep 1

city: Birmingham

first: Paran

last: Goel

state: Alabama

address: Department of Hematology and O, 701 20th Street South

institute: University of Alabama, Birming

description: Library name: AML_A_1

data_processing:
Raw ATAC-seq data were processed using the nf-core/atacseq pipeline (v 2.1.2)(PMID: 32055031), which follows best practices for chromatin accessibility data analysis. The pipeline performs adaptor trimming (Trim Galore!), read alignment to the mm10 genome (Bowtie2), duplicate marking (picard), and duplicate removal (SAMtools) before generating normalised bigWig files scaled to 1 million mapped reads (BEDTools, bedGraphToBigWig).
Assembly: mm10
Supplementary files format and content: bigwig

organism: Mus musculus

source_name: Bone Marrow

extract_protocol:
tdTOM+ neutrophil subpopulations (50000) were sorted from AML (Meis1-HoxA9 overexpression) mice and controls nad were washed once with cold phosphate-buffered saline (PBS) and resuspended with 50 µl cold ATAC-Resuspension Buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM Mg2Cl, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin, and protease inhibitor). After incubation on ice for 3 minutes, the cell nuclei were collected by centrifugation at 500 g for 5 mins at 4°C.
Tn5 transposition of nuclei pellets was carried out at 37°C for 30 min using the DNA Sample Preparation Kit from TruePrep Index Kit V2 for Illumina (Vazyme, TD501). The transposed DNA was purified using DNA purification columns (Zymo Research, D4003) and subjected to PCR amplification for library generation. ATAC-seq libraries were sequenced on the Illumina HiSeq 4000 platform for paired-end 150 cycles.

value: Bone Marrow

value: Neutrophil

value: paired-end


title: Healthy 2 canine PBMC single-cell landscape

description:
Library name: Healthy 2
10x Genomics


title: Cis_3

city: Woolloongabba

first: Qi

last: Ruan

state: QLD

address: 37 Kent Street

department: Frazer Institute

country: Australia

institute: The University of Queensland

description: Library name: Sample 3

data_processing:
The primary sequence data was generated using the Illumina bcl2fastq 2.20.0.422 pipeline.
The cleaned sequence reads were then aligned against the Homo sapiens genome (Build version HG38).
The STAR aligner (v2.5.3a) was used to map reads to the genomic sequences.
Counts are summarised at gene level using the featureCounts v1.5.3
Assembly: hg38
Supplementary files format and content: tab-delimited text file of the raw count matrix for each sample

source_name: human primary hepatic stellate cell

growth_protocol: Primary HSCs were maintained in DMEM with 2% FBS and antibiotics at humitified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA from primary HSCs was extracted and purified using RNeasy Plus Mini Kit (Qiagen, USA). Individual libraries were quantified by qPCR.
and all libraries were normalized to 2nM and pooled. Libraries were clustered through the Illumina cBot system using TruSeq PE Cluster Kit v3 reagents.

treatment_protocol: Primary HSCs were incubated in conditioned medium (CM) collected from Huh7 cells for 24 hours. CM from Huh7 cells in 1% FBS for 18 hours was collected as control and CM from Huh7 cells treated with 10uM cisplatin for 6 hours then replaced with 1% FBS for 18 hours was collected as cisplatin pretreated.

value: human primary hepatic stellate cell

value: cisplatin-pretreated


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0884_O

city: Chicago

first: Heather

last: Marlow

state: IL

address: 920 E 58th Street

department: Organismal Biology and Anatomy

institute: University of Chicago

description:
Library name: RP0884_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

data_processing:
Paired-end fastq sequencing reads were reformatted to the following STARSolo compatible read structure: Read1: mRNA fragment, Read2: Cell barcode (11nucleotides (nt) total, including a 4nt library barcode and 7nt well barcode), then UMI barcode (8nt). These fastq reads are provided for each half-plate library. For each demultiplexing pool of libraries, with unique cell barcodes, reads were demultiplexed and mapped with STARSolo (STAR version 2.7.10b), using a demultiplexing pool barcode file to match the cell barcode identifier (11nt bc) to the cell identifier (RPXXXX_WXXX format, column Well_ID) used in the study. STARSolo demultiplexing pooling barcode sheets are provided for each pool of libraries.
Assembly: Nematostella vectensis genome (jaNemVect1.1, GCF_932526225.1 accession reference) from the Darwin Tree of Life project with the calibration ERCC sequence and the KikGR transgene sequences added (fasta and gtf files are supplied as processed data files here)
Supplementary files format and content: tab-separated cell barcodes to cell identifiers for the multiple demultiplexing pools, each pool can be demultiplexed together with STARSolo using the corresponding "cellBarcodeToCellIdentifier_DemultiplexingPool" file provided.
Supplementary files format and content: count table RDS object (cells by genes UMI counts) for cells present in the global KikGR+ clustering (file matrix_totalKikGRClustering_RNAcounts.RDS), and raw count table RDS object for all cells (cells by genes prior to filtering) including empty wells, and tRNA, and calibration ERCC sequences (file matrix_rawCounts_unfiltered_withEmptyWells_withERCC). A cell metadata file with the matching Cell_identifier (Well_ID) and sample information (library, reporter driver, photoconversion treatment, sample, etc...) is also provided.

organism: Nematostella vectensis

source_name: body wall with mesenteries

growth_protocol: Animals kept in the dark in 12.5ppt artificial seawater at 18C, and fed 4X a week with freshli hatched Artemia nauplii

extract_protocol:
KikGR-positive (from drivers Elav>KikGR, FoxL2>KikGR, SoxC>KikGR) cells from dissociated sea anemone adults (Nematostella vectensis) amputated below the pharynx (body wall with mesenteries regions) were sorted using a FACS Aria into individual wells of a 384-well plate containing lysis buffer with polyT barcoded capture oligos (MARS-Seq protocol).
scRNA-Seq libraries were prepared using the published plate-based MARS-Seq scRNA-Seq protocol (2 libraries from each sorted 384well plate).

value: body wall with mesenteries

tag: genetic modification

value: FoxL2>KikGR stable transgene

tag: developmental stage

value: 6-8 weeks adults

value: FoxL2>KikGR heterozygote

tag: day post_kikgrphotoconversion


title: EP_snATAC-seq

city: Hangzhou

first: Saiyong

last: Zhu

state: Zhejiang

address: 866 Yuhangtang Rd.

department: Life Sciences Institute

country: China

institute: Zhejiang University

description:
Library name: Sample 2
10x Genomics

library_source: genomic single cell

data_processing:
Alignment to the genome and initial processing were performed using the 10x Genomics Cell Ranger ATAC v2.1.0 pipeline
Assembly: hg38
Supplementary files format and content: CellRanger output files: filtered_peak_bc_matrix.h5, fragments.tsv.gz, fragments.tsv.gz.tbi, singlecell.csv

source_name: MEL1 hESC line

growth_protocol: ePPs were cultured on feeder in EF6I medium: DMEM containing 1:50 B27, 50 ng/ml EGF, 10 ng/ml bFGF, 10 μM 616452, and 1 μM I-BET151 (APExBIO).  R6 medium: DMEM containing 1:50 B27, 0.05% BSA (Yeasen), 10 μM zinc sulfate (Vetec), 10 μg/ml heparin (Sigma), 10 μM 616452 (TargetMol), 1 μM T3 (Sigma), 0.2 μM LDN-193189 (Tocris), 0.2 μM Compound E (MedChem Express), 0.5 mM vitamin C, and 10 μM forskolin (TargetMol). R7 medium: DMEM containing 1:50 B27, 0.05% BSA, 10 μM zinc sulfate, 10 μg/ml heparin, 10 μM 616452, 1 μM T3, 1 mM N-acetyl cysteine (Sigma), 1 μM Trolox (Sigma), and 0.5 mM vitamin C.

extract_protocol:
DNA extraction were performed by LC-Bio Technology.
Libraries were constructed at LC-Bio Technology.

value: MEL1 hESC line

value: ePP-derived endocrine precursors


title: ePP_snATAC-seq

description:
Library name: Sample 1
10x Genomics

value: hPSC-derived expandable pancreatic progenitor cells


title: CHLA90_RA_REP3

description: Library name: GEO5504A24


title: Cis_1

description: Library name: Sample 1


title: AML Ly6Ghi CD101- rep 2

description: Library name: AML_B_2


title: hemocytes, WSSV uninfected

city: NanChang

first: 航

last: 胡

address: No. 999, Xue Fu Road

institute: 生命科学学院本部

description:
Library name: WT
DNBelabC4

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1(https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Scylla paramamosain (green mud crab) genome assembly ASM3559412v1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Scylla paramamosain

source_name: hemolymph

extract_protocol:
The isolated blood cells were washed twice with PBS
After quality inspection and counting of single-cell suspension, it is generally required that the cell viability is above 80%. Gel Beads in Emulsion (GEMs) were constructed for single cell separation according to the expected number of target cells. GEMs are collected after normal formation and are reverse-transcribed in the PCR instrument to realize labeling. For GEMs oil breaking treatment, the first strand cDNA was purified and enriched with magnetic beads, then cDNA amplification and quality inspection were carried out. The qualified cDNA was constructed by the second generation sequencing library, and the quantitative quality of the library was finally tested through the experimental processes of fragmentation, connecting sequencing joints, and sample Index PCR. The constructed library was sequenced using Novaseq Xplus/DNBSEQ-T7 high-throughput sequencing platform and PE150 sequencing mode.

treatment_protocol: WSSV infected

value: hemolymph

value: WSSV uninfected


title: tp_42_2

city: Shanghai

first: Wanxing

last: Xu

address: 227 South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

description:
NA25
32C_sample_count.txt

data_processing:
Adapter and quality trimming were performed by Trim galore v0.6.6. Filtered reads were mapped with STAR v2.6.1d to reference genome. The expression profile of each gene was obtained by StringTie v2.1.4.
Assembly: GCA_002759435.2, GCA_000182965.3
Supplementary files format and content: tab-delimited, raw count

organism: Candidozyma auris

extract_protocol:
Total RNA was extracted using TRIZOL (Invitrogen) according to the manufacturer’s directions and stored at -80 ̊C.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: YPD 42℃(4h20min)


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0870_O

description:
Library name: RP0870_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: AML Ly6Ghi CD101- rep 3

description: Library name: AML_B_3


title: tp_37_3

description:
NA23
32C_sample_count.txt

value: YPD 37℃(4h20min)


title: CHLA90_RA_REP1

description: Library name: GEO5504A8

value: Neuroblastoma

value: ATRX IFF

value: 10uM Retinoic acid


title: Healthy 5 canine PBMC single-cell landscape

description:
Library name: Healthy 5
10x Genomics

value: Blood, PBMC

value: Primary cells

value: PBMC, mononuclear cells

value: Wild type

value: Batch 1


title: CHLA90_DMSO_REP1

description: Library name: GEO5504A7

value: Vehicle DMSO


title: Healthy 1 canine PBMC single-cell landscape

description:
Library name: Healthy 1
10x Genomics


title: SKNMM_RA_REP2

description: Library name: GEO5504A14

source_name: SKNMM

value: SKNMM


title: SKNMM_RA_REP3

description: Library name: GEO5504A22


title: Adult body wall with mesenteries, Elav>KikGR-positive cells, library RP0881_O

description:
Library name: RP0881_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: body wall with mesenteries

value: Elav>KikGR stable transgene

value: 6-8 weeks adults

value: Elav>KikGR heterozygote


title: SKNMM_DMSO_REP1

description: Library name: GEO5504A5


title: AML Ly6Ghi CD101- rep 1

description: Library name: AML_B_1

value: Bone Marrow

value: Neutrophil

value: paired-end


title: E6_RA_REP3

description: Library name: GEO5103A24

source_name: SK-N-SH

value: SK-N-SH

value: Neuroblastoma

value: ATRX LoF


title: tp_30_42_30_2

description:
NA18
32C_sample_count.txt


title: SKNMM_DMSO_REP2

description: Library name: GEO5504A13

value: ATRX IFF


title: tp_42_3

description:
NA26
32C_sample_count.txt

value: YPD 42℃(4h20min)


title: CHLA90_DMSO_REP2

description: Library name: GEO5504A15


title: E6_DMSO_REP3

description: Library name: GEO5103A21


title: tp_30_42_10_2

description:
NA16
32C_sample_count.txt


title: ePP_scRNA-seq

description:
Library name: Sample 1
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
RNA extraction and sequencing were performed by LC-Bio Technology.
Libraries were constructed at LC-Bio Technology.

value: MEL1 hESC line

value: hPSC-derived expandable pancreatic progenitor cells


title: tp_30_42_30_1

description:
NA17
32C_sample_count.txt


title: Adult body wall with mesenteries, Elav>KikGR-positive cells, library RP0856_O

description:
Library name: RP0856_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: tp_37_2

description:
NA22
32C_sample_count.txt

value: YPD 37℃(4h20min)


title: p53_RA_REP3

description: Library name: GEO5103A19

value: ATRX WT

value: 10uM Retinoic acid


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0886_O

description:
Library name: RP0886_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: body wall with mesenteries

value: FoxL2>KikGR stable transgene

value: FoxL2>KikGR heterozygote


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0885_O

description:
Library name: RP0885_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: 6-8 weeks adults


title: tp_42_1

description:
NA24
32C_sample_count.txt


title: tp_30_2

description:
NA28
32C_sample_count.txt

value: YPD 30℃(4h20min)


title: tp_30_1

description:
NA27
32C_sample_count.txt


title: SKNMM_RA_REP1

description: Library name: GEO5504A6

value: SKNMM


title: tp_30_3

description:
NA29
32C_sample_count.txt


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0872_E

description:
Library name: RP0872_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: p53_DMSO_REP3

description: Library name: GEO5103A18

value: Vehicle DMSO


title: sfu1_1

description:
NA166
iron_gene_sample_count.xls

source_name: BJCA001 SFU1 KO

value: BJCA001 SFU1 KO

value: SFU1 KO


title: E6_RA_REP2

description: Library name: GEO5103A16

value: SK-N-SH

value: Neuroblastoma

value: ATRX LoF


title: Adult body wall with mesenteries, Elav>KikGR-positive cells, library RP0856_E

description:
Library name: RP0856_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: Elav>KikGR stable transgene

value: Elav>KikGR heterozygote


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0868_O

description:
Library name: RP0868_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0872_O

description:
Library name: RP0872_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0882_E

description:
Library name: RP0882_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: Adult body wall with mesenteries, Elav>KikGR-positive cells, library RP0875_O

description:
Library name: RP0875_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: sc_N-his_1

description:
NA90
32C_sample_count.txt

value: YPD(5h)+SC - his+3AT(5h)


title: sc_N-as_2

description:
NA88
32C_sample_count.txt


title: sfu1_3

description:
NA168
iron_gene_sample_count.xls


title: sc_N-as_3

description:
NA89
32C_sample_count.txt


title: E6_DMSO_REP2

description: Library name: GEO5103A14


title: Adult body wall with mesenteries, Elav>KikGR-positive cells, library RP0875_E

description:
Library name: RP0875_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: sc_N-aa_3

description:
NA83
32C_sample_count.txt

value: YPD(5h)+SC - AA(5h)


title: E6_RA_REP1

description: Library name: GEO5103A7

value: 10uM Retinoic acid


title: p53_DMSO_REP2

description: Library name: GEO5103A9

value: ATRX WT


title: E6_DMSO_REP1

description: Library name: GEO5103A5


title: sef1_3

description:
NA171
iron_gene_sample_count.xls

source_name: BJCA001 SEF1 KO

value: BJCA001 SEF1 KO

value: SEF1 KO


title: hemocytes, WSSV infected

description:
Library name: WSSV
DNBelabC4

value: hemolymph

value: WSSV infected


title: sc_N-aa_N-as_3

description:
NA86
32C_sample_count.txt


title: p53_RA_REP1

description: Library name: GEO5103A4


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0870_E

description:
Library name: RP0870_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: body wall with mesenteries

value: FoxL2>KikGR stable transgene

value: 6-8 weeks adults

value: FoxL2>KikGR heterozygote


title: sc_N-aa_N-as_2

description:
NA85
32C_sample_count.txt


title: tp_37_1

description:
NA21
32C_sample_count.txt

value: YPD 37℃(4h20min)


title: sc_N-aa_N-as_1

description:
NA84
32C_sample_count.txt


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0884_E

description:
Library name: RP0884_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: sfu1_2

description:
NA167
iron_gene_sample_count.xls

value: BJCA001 SFU1 KO

value: SFU1 KO


title: rapamycin_2

description:
NA49
32C_sample_count.txt

value: YPD (4h53min)-YPD +Rapmycin  (1h)


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0883_E

description:
Library name: RP0883_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: tp_30_42_60_2

description:
NA20
32C_sample_count.txt


title: rapamycin_c_1

description:
NA45
32C_sample_count.txt

value: YPD (4h53min)-YPD +DMSO (1h)


title: sef1_1

description:
NA169
iron_gene_sample_count.xls


title: Adult body wall with mesenteries, Elav>KikGR-positive cells, library RP0849_E

description:
Library name: RP0849_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: Elav>KikGR stable transgene

value: Elav>KikGR heterozygote


title: tp_30_42_10_1

description:
NA15
32C_sample_count.txt


title: p53_RA_REP2

description: Library name: GEO5103A11

value: SK-N-SH

value: Neuroblastoma

value: 10uM Retinoic acid


title: alkaline_3

description:
NA80
32C_sample_count.txt


title: WSU-DLCL2 (Hi-C)

city: Ann Arbor

first: Russell

middle: James Hubbard

last: Ryan

state: MI

address: 4306 Rogel Cancer Center, 1500 E Medical Center Dr.

department: Department of Pathology

institute: University of Michigan Medical School

description: Library name: HIC_WSU_DLCL2

data_processing:
Hi-C sequencing data was processed using the Arima-SV-Pipeline (v1.3), comprising HiCUP (v0.8.0) to calculate quality control metrics and perform read alignment and filtering, hic_breakfinder to call rearrangement breakpoints, and Juicer Tools (v1.6) to produce multi-resolution Hi-C matrices from mapped and filtered read pairs. FFPE samples were processed using default pipeline parameters for the Arima-HiC+ for FFPE restriction enzyme chemistry. Alignment was performed against the GRCh38 human reference genome.
Assembly: GRCh38
Supplementary files format and content: Genome-wide Hi-C matrices in .hic file format

extract_protocol:
FFPE tissue from 2-5 unstained slides cut at 5-10µm were processed using the Arima HiC+ for FFPE kit (Product Number A311038, Arima Genomics, Carlsbad, CA) as per manufacturer protocols to produce Illumina-compatible sequencing libraries. Briefly, 5µm unstained FFPE tissue sections were first de-waxed and rehydrated, and then subjected to Hi-C sample preparation using Arima HiC+ for FFPE kit.  For generation of FFPE cell blocks, 10 million cells from each cell line in standard growth conditions were harvested, washed in PBS, and fixed in 3.7% formaldehyde in phosphate-buffered saline (“10% neutral-buffered formalin”) at room temperature for 20 min, then washed 2x in PBS. Cells were then processed by the standard cell block preparation method of the University of Michigan Cytology Laboratory: cells were pelleted at 0.8 x g for 5 minutes, resuspended in warmed (50°C) HistoGel (Epredia, HG4000012) and incubated at 4°C for 30 min. The HistoGel pellet was then fixed for an additional 6 hrs at room temperature in 10% neutral-buffered formalin prior to submission for standard FFPE tissue processing and embedding. After verifying cellularity with an H&E slide, ten x 10-micron sections were cut from each block for FFPE Hi-C processing as described above.
Following Hi-C sample preparation,  Illumina-compatible sequencing libraries were constructed by shearing the proximally ligated DNA and then size selecting DNA fragments using SPRI beads. The size-selected DNA fragments containing proximity ligation junctions were then enriched using Enrichment Beads (provided in the Arima HiC+ for FFPE kit) and converted to Illumina-compatible sequencing libraries. The resulting Hi-C libraries underwent standard quality control (qPCR and BioAnalyzer).


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0883_O

description:
Library name: RP0883_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: sef1_2

description:
NA170
iron_gene_sample_count.xls

value: BJCA001 SEF1 KO

value: SEF1 KO


title: sc_N-his_3

description:
NA92
32C_sample_count.txt

value: YPD(5h)+SC - his+3AT(5h)


title: sc_N-as_1

description:
NA87
32C_sample_count.txt


title: sc_N-aa_1

description:
NA81
32C_sample_count.txt

value: YPD(5h)+SC - AA(5h)


title: sc_N-his_2

description:
NA91
32C_sample_count.txt


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0867_E

description:
Library name: RP0867_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: body wall with mesenteries

value: FoxL2>KikGR stable transgene


title: sc_N-aa_2

description:
NA82
32C_sample_count.txt


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0878_O

description:
Library name: RP0878_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: 6-8 weeks adults

value: FoxL2>KikGR heterozygote


title: ANBL6 (Hi-C)

description: Library name: HIC_ANBL6


title: oxygen_6p_3

description:
NA152
32C_sample_count.txt

value: YPD 30°C (OD0.15 6h hypoxia solid medium


title: rapamycin_3

description:
NA50
32C_sample_count.txt


title: oxygen_6p_2

description:
NA151
32C_sample_count.txt


title: TOE1_RNAi_2

city: Shenzhen

first: Yi

address: Shenzhen Campus of Sun Yat-sen University, Guangming New District, Shenzhen

institute: Sun Yat-sen University School of Medicine

description:
Library name: Sample5
Forty-eight hours post-TOE1_RNAi_2 transfection, cellular samples were harvested and submitted for RNA-seq

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
Assembly: hg38
Supplementary files format and content: The table includes the FPKM values for each sample gene.

source_name: cell line

growth_protocol: We obtained HepG2 cell from Hunan Fenghui Biotechnology Co., Ltd. Cells were maintained in high-glucose DMEM supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin-streptomycin-amphotericin B, under standard culture conditions (37°C, 5% CO2).

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

treatment_protocol: TOE1 expression was knocked down using TOE1-targeted siRNA (TOE1, NM_025077.4; siRNA sequence: 5′-GGAAGAGUUUGCUGAACCA-3′, designated as siTOE1). For transfection, 200 nM siRNA was used per 60-mm dish. Transfection was performed using Lipo8000 (Beyotime, C0533) following the supplier's standardized protocol.

value: HepG2 cell line

value: human liver cancer cell


title: p53_DMSO_REP1

description: Library name: GEO5103A1

value: ATRX WT

value: Vehicle DMSO


title: oxygen_6_3

description:
NA149
32C_sample_count.txt

value: YPD 30°C (OD0.15 6h）hypoxia


title: Adult body wall with mesenteries, Elav>KikGR-positive cells, library RP0881_E

description:
Library name: RP0881_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: Elav>KikGR stable transgene

value: Elav>KikGR heterozygote


title: rapamycin_c_2

description:
NA46
32C_sample_count.txt

value: YPD (4h53min)-YPD +DMSO (1h)


title: UoCB6 (Hi-C)

description: Library name: HIC_UOCB6


title: TOE1_RNAi_1

description:
Library name: Sample4
Forty-eight hours post-TOE1_RNAi_1 transfection, cellular samples were harvested and submitted for RNA-seq


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0867_O

description:
Library name: RP0867_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0886_E

description:
Library name: RP0886_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: rapamycin_c_3

description:
NA47
32C_sample_count.txt


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0868_E

description:
Library name: RP0868_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: alkaline_2

description:
NA79
32C_sample_count.txt


title: rapamycin_1

description:
NA48
32C_sample_count.txt

value: YPD (4h53min)-YPD +Rapmycin  (1h)


title: oxygen_4_3

description:
NA146
32C_sample_count.txt

value: YPD 30°C (OD0.15 4h）hypoxia


title: NC_3

description:
Library name: Sample3
Forty-eight hours post-NC_3 transfection, cellular samples were harvested and submitted for RNA-seq


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0882_O

description:
Library name: RP0882_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: NC_2

description:
Library name: Sample2
Forty-eight hours post-NC_2 transfection, cellular samples were harvested and submitted for RNA-seq


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0878_E

description:
Library name: RP0878_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: NC_1

description:
Library name: Sample1
Forty-eight hours post-NC_1 transfection, cellular samples were harvested and submitted for RNA-seq


title: alkaline_1

description:
NA78
32C_sample_count.txt


title: oxygen_3p_3

description:
NA143
32C_sample_count.txt

value: YPD 30°C (OD0.15 3h hypoxia solid medium


title: SU-DHL6 (Hi-C)

description: Library name: HIC_SU_DHL6


title: oxygen_3p_1

description:
NA141
32C_sample_count.txt


title: acidic_2

description:
NA76
32C_sample_count.txt


title: TOE1_RNAi_3

description:
Library name: Sample6
Forty-eight hours post-TOE1_RNAi_3 transfection, cellular samples were harvested and submitted for RNA-seq


title: oxygen_2_2

description:
NA139
32C_sample_count.txt

value: YPD 30°C (OD0.15 2h）hypoxia


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0833_O

description:
Library name: RP0833_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: body wall with mesenteries

value: SoxC>KikGR stable transgene

value: SoxC>KikGR heterozygote

value: DMSO 1%


title: oxygen_4_1

description:
NA144
32C_sample_count.txt


title: oxygen_6_2

description:
NA148
32C_sample_count.txt


title: acidic_1

description:
NA75
32C_sample_count.txt


title: Adult body wall with mesenteries, Elav>KikGR-positive cells, library RP0799_O

description:
Library name: RP0799_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: 6-8 weeks adults


title: oxygen_2_1

description:
NA138
32C_sample_count.txt


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0836_E

description:
Library name: RP0836_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: UNT1

city: Chandigarh

first: Arnab

last: Pal

state: Chandigarh UT

address: Sector 12

department: Biochemistry

country: India

institute: Post Graduate Institute of Medical Education and Research

description:
Library name: Sample5
replicate 1 of untreated Cal27 cells
counts column = UNT1

data_processing:
BCL files were converted into per-read FASTQ format using bcl2fastq Conversion Software v2.20 (Illumina).
Quality of 100-bp paired-end reads was assessed using FastQC v0.11.7. Only quality-passed reads were retained for downstream analysis.
Genome index was created using: Human genome FASTA file: hg19.genome.fa; Gene annotation file: Homo_sapiens.GRCh37.87.gtf
Paired-end reads were aligned to the GRCh37 human reference genome using STAR aligner (v2.6). Transcript information was incorporated during alignment. Output: Aligned and sorted BAM files (sorted by chromosomal position) for each sample.
HTSeq-count (v0.6.1) was used to quantify gene-level expression. Output: Raw read counts per gene per sample.
Raw counts were normalized for RNA composition bias using: Trimmed Mean of M-values (TMM) method via EdgeR. Output: TMM-normalized CPM (Counts Per Million) values.
Assembly: GRCh38
Supplementary files format and content: Gene count matrix (.txt)

growth_protocol: Cal27 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, maintained at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted using ureLink® RNA Mini Kit (Invitrogen™, # 12183018A). The quality and quantity of isolated RNA was checked using NanoDrop™ spectrophotometer (Thermofisher scientific), Qubit™ 4 Fluorometer (Invitrogen, #Q33226) and Agilent 2100 Bioanalyzer System.
RNA was extracted and used to prepare sequencing libraries with the TruSeq Stranded Total RNA Library Prep Kit (Illumina, #20020597) on a Biomek i7 automated workstation (Beckman Coulter).

treatment_protocol: Cells were transduced with lentiviral particles carrying either the GFP control vector or the Cornulin (CRNN) overexpression construct. Lentiviral transduction was carried out in the presence of polybrene (8 µg/ml), and cells were harvested after 48 hours. Untreated Cal27 cells were used as controls.

value: epithelial cell

value: WT

value: untreated


title: GFP2

description:
Library name: Sample4
replicate 2 of GFP vector control Cal27 cells
counts column = GFP2

value: GFP Expressing

value: GFP vector


title: oxygen_0_1

description:
NA132
32C_sample_count.txt

value: YPD 30°C (OD0.15 0h）hypoxia


title: acidic_3

description:
NA77
32C_sample_count.txt


title: RCK8 (Hi-C)

description: Library name: HIC_RCK8


title: oxygen_4_2

description:
NA145
32C_sample_count.txt


title: oxygen_6p_1

description:
NA150
32C_sample_count.txt

value: YPD 30°C (OD0.15 6h hypoxia solid medium


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0885_E

description:
Library name: RP0885_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: FoxL2>KikGR stable transgene

value: FoxL2>KikGR heterozygote


title: sodium_2_3

description:
NA116
32C_sample_count.txt

value: YPD+1M NaCl (6h)


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0803_O

description:
Library name: RP0803_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0843_O

description:
Library name: RP0843_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: sodium_2_2

description:
NA115
32C_sample_count.txt


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0803_E

description:
Library name: RP0803_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: oxygen_6_1

description:
NA147
32C_sample_count.txt

value: YPD 30°C (OD0.15 6h）hypoxia


title: sodium_2_1

description:
NA114
32C_sample_count.txt


title: UNT2

description:
Library name: Sample6
replicate 2 of untreated Cal27 cells
counts column = UNT2


title: Adult body wall with mesenteries, Elav>KikGR-positive cells, library RP0849_O

description:
Library name: RP0849_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: Elav>KikGR stable transgene

value: Elav>KikGR heterozygote


title: oxygen_2_3

description:
NA140
32C_sample_count.txt

value: YPD 30°C (OD0.15 2h）hypoxia


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0843_E

description:
Library name: RP0843_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: body wall with mesenteries

value: SoxC>KikGR stable transgene

value: SoxC>KikGR heterozygote


title: methylm_1

description:
NA60
32C_sample_count.txt


title: methylm_2

description:
NA61
32C_sample_count.txt


title: oxygen_3p_2

description:
NA142
32C_sample_count.txt

value: YPD 30°C (OD0.15 3h hypoxia solid medium


title: diff4d_GATA1s_1D5_2, H3K18la , replica 2

city: Memphis

first: Rashid

last: Mehmood

state: Tennessee

address: 324 NIGHT SAIL DR N APT 112, UNIT # 04-112

department: Hematology

institute: St Jude Children's Research Hospital

description:
Library name: diff24h_GATA1s_1D5_H3K18la_2
CUT&RUN

data_processing:
raw reads were processed using the community driven nfcore cutandrun version 3.1 pipeline
Assembly: hg38
Supplementary files format and content: .bigWig
Library strategy: CUT&Run

growth_protocol: Expansion condition: SFEM II containing 3 U/mL EPO, 50 ng/mL hSCF, 1 μM dexamethasone and 1 μg/mL doxycycline; Differentiation condition: IMDM containing 2% FBS, 3% human AB serum, 3 U/mL EPO, 10 μg/mL insulin, 3 U/mL heperin, 1mg/mL human holo-transferrin, 50 ng/mL hSCF and 1 μg/mL doxycline.

extract_protocol:
CUT&RUN DNA was purified from HUDEP1 clones expressing either the full-length GATA1 (GATA1FL) or the short isoform (GATA1s_1D5 and GATA1s_1KI9) under expansion or differentiation (on day 4 or 24 hours) conditions, respectively. The CUT&RUN process was conducted using CUTANA™ ChIC/CUT&RUN Kit (REF#14-1048).
CUT&RUN libraries were constructed according to the CUTANA™ CUT&RUN Library Prep Kit (REF#14-1001 and 14-1002) protocol.

value: erythroid progenitor cell line

value: differentiation


title: l_zinc_3

description:
NA122
32C_sample_count.txt

value: YPD+50μM TPEN(6h)


title: Adult body wall with mesenteries, Elav>KikGR-positive cells, library RP0795_O

description:
Library name: RP0795_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: 6-8 weeks adults

value: DMSO 1%


title: oxygen_0_p_1

description:
NA135
32C_sample_count.txt

value: YPD 30°C (OD0.15 0h hypoxia solid medium


title: l_zinc_c_3

description:
NA125
32C_sample_count.txt

value: YPD+50μM TPEN+1mM ZnCl2(6h)


title: Adult body wall with mesenteries, Elav>KikGR-positive cells, library RP0805_O

description:
Library name: RP0805_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: oxygen_0_p_2

description:
NA136
32C_sample_count.txt


title: diff4d_GATA1s_1D5_1, H3K27la , replica 1

description:
Library name: diff24h_GATA1s_1D5_H3K27la_1
CUT&RUN


title: Adult body wall with mesenteries, Elav>KikGR-positive cells, library RP0799_E

description:
Library name: RP0799_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: l_zinc_2

description:
NA121
32C_sample_count.txt


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0771_E

description:
Library name: RP0771_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: FoxL2>KikGR stable transgene

value: FoxL2>KikGR heterozygote


title: GFP1

description:
Library name: Sample3
replicate 1 of GFP vector control Cal27 cells
counts column = GFP1

value: epithelial cell

value: GFP Expressing

value: GFP vector


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0836_O

description:
Library name: RP0836_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: oxygen_0_3

description:
NA134
32C_sample_count.txt

value: YPD 30°C (OD0.15 0h）hypoxia


title: l_iron_2_c_3

description:
NA104
32C_sample_count.txt

value: YPD (5h20min)


title: l_iron_2_c_2

description:
NA103
32C_sample_count.txt


title: l_iron_2_c_1

description:
NA102
32C_sample_count.txt


title: oxygen_0_p_3

description:
NA137
32C_sample_count.txt


title: CRNN2

description:
Library name: Sample2
replicate 2 of Cornulin overexpression Cal27 cells
counts column = CRNN2

value: Cornulin overexpression


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0763_E

description:
Library name: RP0763_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: body wall with mesenteries

value: SoxC>KikGR stable transgene

value: SoxC>KikGR heterozygote


title: oxygen_0_2

description:
NA133
32C_sample_count.txt


title: diff4d_GATA1FL_1, H3K18la , replica 1

description:
Library name: diff24h_GATA1FL_H3K18la_1
CUT&RUN

value: erythroid progenitor cell line

value: differentiation


title: CRNN1

description:
Library name: Sample1
replicate 1 of Cornulin overexpression Cal27 cells
counts column = CRNN1


title: tp_30_42_60_1

description:
NA19
32C_sample_count.txt


title: hydrox_1

description:
NA57
32C_sample_count.txt

value: YPD (2h)+ 20mM HU(4h)


title: methylm_3

description:
NA62
32C_sample_count.txt


title: hap43_2

description:
NA173
iron_gene_sample_count.xls

source_name: BJCA001 HAP43 KO

value: BJCA001 HAP43 KO

value: HAP43 KO rep2_1.fq.gz


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0813_O

description:
Library name: RP0813_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: 6-8 weeks adults

value: DMSO 1%


title: diff4d_GATA1FL_1, H3K27la , replica 1

description:
Library name: diff24h_GATA1FL_H3K27la_1
CUT&RUN


title: l_zinc_1

description:
NA120
32C_sample_count.txt

value: YPD+50μM TPEN(6h)


title: hap43_1

description:
NA172
iron_gene_sample_count.xls

value: HAP43 KO rep1_1.fq.gz


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0833_E

description:
Library name: RP0833_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: hydrop_2

description:
NA55
32C_sample_count.txt


title: diff24h_GATA1s_1D5_1, IgG , replica 1

description:
Library name: diff24h_GATA1s_1D5_IgG
CUT&RUN


title: l_iron_2_3

description:
NA107
32C_sample_count.txt

value: YPD+500μM BPS  (5h20min)


title: l_zinc_c_2

description:
NA124
32C_sample_count.txt

value: YPD+50μM TPEN+1mM ZnCl2(6h)


title: l_iron_2_2

description:
NA106
32C_sample_count.txt


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0771_O

description:
Library name: RP0771_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: FoxL2>KikGR stable transgene

value: FoxL2>KikGR heterozygote


title: hydrop_c_1

description:
NA51
32C_sample_count.txt


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0776_O

description:
Library name: RP0776_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: diff4d_GATA1s_1D5_1, H3K27ac , replica 1

description:
Library name: diff24h_GATA1s_1D5_H3K27ac_1
CUT&RUN


title: diff4d_GATA1s_1D5_2, H3K27la , replica 2

description:
Library name: diff24h_GATA1s_1D5_H3K27la_2
CUT&RUN


title: diff4d_GATA1FL_2, H3K18la , replica 2

description:
Library name: diff24h_GATA1FL_H3K18la_2
CUT&RUN


title: h_zinc_2

description:
NA127
32C_sample_count.txt

value: YPD+5mM ZnCl2(6h)


title: diff4d_GATA1FL_1, H3K27ac , replica 1

description:
Library name: diff24h_GATA1FL_H3K27ac_1
CUT&RUN


title: diff4d_GATA1s_1D5_1, H3K18la , replica 1

description:
Library name: diff24h_GATA1s_1D5_H3K18la_1
CUT&RUN


title: l_iron_2_1

description:
NA105
32C_sample_count.txt


title: l_zinc_c_1

description:
NA123
32C_sample_count.txt


title: diff4d_GATA1FL_2, H3K27la , replica 2

description:
Library name: diff24h_GATA1FL_H3K27la_2
CUT&RUN


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0774_E

description:
Library name: RP0774_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: body wall with mesenteries


title: hap43_3

description:
NA174
iron_gene_sample_count.xls

value: HAP43 KO rep3_1.fq.gz


title: hydrox_2

description:
NA58
32C_sample_count.txt


title: diff24h_GATA1FL_1, IgG , replica 1

description:
Library name: diff24h_GATA1FL_IgG
CUT&RUN


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0763_O

description:
Library name: RP0763_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: SoxC>KikGR stable transgene

value: SoxC>KikGR heterozygote


title: hydrop_c_2

description:
NA52
32C_sample_count.txt


title: hydrox_3

description:
NA59
32C_sample_count.txt


title: diff4d_GATA1s_1KI9_3, H3K27ac, replica 3

description:
Library name: diff4d_GATA1s_1KI9_H3K27ac_3
CUT&RUN

value: erythroid progenitor cell line

value: differentiation


title: diff4d_GATA1s_1KI9_2, H3K27ac, replica 2

description:
Library name: diff4d_GATA1s_1KI9_H3K27ac_2
CUT&RUN


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0801_E

description:
Library name: RP0801_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: h_zinc_c_1

description:
NA129
32C_sample_count.txt


title: hydrop_c_3

description:
NA53
32C_sample_count.txt


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0837_O

description:
Library name: RP0837_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: Adult body wall with mesenteries, Elav>KikGR-positive cells, library RP0795_E

description:
Library name: RP0795_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: Elav>KikGR stable transgene

value: Elav>KikGR heterozygote


title: h_iron_3

description:
NA98
32C_sample_count.txt


title: hydrop_3

description:
NA56
32C_sample_count.txt


title: h_zinc_c_2

description:
NA130
32C_sample_count.txt


title: diff4d_GATA1s_1KI9_1, H3K4me3, replica 1

description:
Library name: diff4d_GATA1s_1KI9_H3K4me3_1
CUT&RUN


title: hydrop_1

description:
NA54
32C_sample_count.txt


title: h_zinc_c_3

description:
NA131
32C_sample_count.txt


title: h_iron_c_3

description:
NA101
32C_sample_count.txt


title: h_zinc_3

description:
NA128
32C_sample_count.txt


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0809_O

description:
Library name: RP0809_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: 6-8 weeks adults


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0767_O

description:
Library name: RP0767_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: DMSO 1%


title: diff4d_GATA1s_1KI9_2, H3K4me3, replica 2

description:
Library name: diff4d_GATA1s_1KI9_H3K4me3_2
CUT&RUN


title: diff4d_GATA1s_1KI9_3, H3K4me3, replica 3

description:
Library name: diff4d_GATA1s_1KI9_H3K4me3_3
CUT&RUN


title: diff4d_GATA1s_1KI9_1, H3K27ac, replica 1

description:
Library name: diff4d_GATA1s_1KI9_H3K27ac_1
CUT&RUN


title: h_zinc_1

description:
NA126
32C_sample_count.txt


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0813_E

description:
Library name: RP0813_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: h_iron_c_1

description:
NA99
32C_sample_count.txt


title: h_iron_c_2

description:
NA100
32C_sample_count.txt


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0809_E

description:
Library name: RP0809_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0801_O

description:
Library name: RP0801_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: h_iron_2

description:
NA97
32C_sample_count.txt


title: diff4d_GATA1s_1KI9_2, GATA1 , replica 2

description:
Library name: diff4d_GATA1s_1KI9_GATA1_2
CUT&RUN


title: h_iron_1

description:
NA96
32C_sample_count.txt


title: diff4d_GATA1s_1KI9_3, GATA1 , replica 3

description:
Library name: diff4d_GATA1s_1KI9_GATA1_3
CUT&RUN


title: glycerol_c_3

description:
NA68
32C_sample_count.txt


title: diff4d_GATA1s_1KI9_1, IgG, replica 1

description:
Library name: diff4d_GATA1s_1KI9_IgG_1
CUT&RUN


title: glycerol_3

description:
NA74
32C_sample_count.txt


title: glycerol_2

description:
NA73
32C_sample_count.txt


title: glcNAC_1

description:
NA63
32C_sample_count.txt

value: SC+50mM GlcNAC(5h)


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0815_E

description:
Library name: RP0815_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: glycerol_c_1

description:
NA66
32C_sample_count.txt


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0838_E

description:
Library name: RP0838_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: diff4d_GATA1s_1D5_2, H3K27ac, replica 2

description:
Library name: diff4d_GATA1s_1D5_H3K27ac_2
CUT&RUN


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0776_E

description:
Library name: RP0776_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: diff4d_GATA1s_1KI9_1, GATA1 , replica 1

description:
Library name: diff4d_GATA1s_1KI9_GATA1_1
CUT&RUN


title: glycerol_c_2

description:
NA67
32C_sample_count.txt


title: diff4d_GATA1s_1D5_1, H3K27ac, replica 1

description:
Library name: diff4d_GATA1s_1D5_H3K27ac_1
CUT&RUN


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0815_O

description:
Library name: RP0815_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: glcNAC_c_1

description:
NA69
32C_sample_count.txt

value: SC+50mM Glucose(5h)


title: glcNAC_c_3

description:
NA71
32C_sample_count.txt


title: glycerol_1

description:
NA72
32C_sample_count.txt


title: diff4d_GATA1s_1D5_3, H3K4me3, replica 3

description:
Library name: diff4d_GATA1s_1D5_H3K4me3_3
CUT&RUN


title: glcNAC_2

description:
NA64
32C_sample_count.txt


title: diff4d_GATA1s_1D5_3, H3K27ac, replica 3

description:
Library name: diff4d_GATA1s_1D5_H3K27ac_3
CUT&RUN


title: sc_c_2

description:
NA94
32C_sample_count.txt


title: glcNAC_3

description:
NA65
32C_sample_count.txt


title: glcNAC_c_2

description:
NA70
32C_sample_count.txt


title: Adult body wall with mesenteries, Elav>KikGR-positive cells, library RP0805_E

description:
Library name: RP0805_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: sc_c_1

description:
NA93
32C_sample_count.txt


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0837_E

description:
Library name: RP0837_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: sc_c_3

description:
NA95
32C_sample_count.txt


title: diff4d_GATA1s_1D5_2, H3K4me3, replica 2

description:
Library name: diff4d_GATA1s_1D5_H3K4me3_2
CUT&RUN


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0767_E

description:
Library name: RP0767_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0838_O

description:
Library name: RP0838_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: copper_2_c_3

description:
NA119
32C_sample_count.txt


title: diff4d_GATA1s_1D5_1, H3K4me3, replica 1

description:
Library name: diff4d_GATA1s_1D5_H3K4me3_1
CUT&RUN


title: h_copper_2_2

description:
NA112
32C_sample_count.txt

value: YPD + 5mM CuSO4(6h)


title: copper_2_c_1

description:
NA117
32C_sample_count.txt


title: h_copper_2_1

description:
NA111
32C_sample_count.txt


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0774_O

description:
Library name: RP0774_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: diff4d_GATA1s_1D5_2, GATA1 , replica 2

description:
Library name: diff4d_GATA1s_1D5_GATA1_2
CUT&RUN


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0773_E

description:
Library name: RP0773_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: calcofw_1

description:
NA39
32C_sample_count.txt

value: YPD (5h20min)-YPD+40μg/ml CFW (60min)


title: calcofw_2

description:
NA40
32C_sample_count.txt


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0812_O

description:
Library name: RP0812_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: FoxL2>KikGR stable transgene


title: h_copper_2_3

description:
NA113
32C_sample_count.txt


title: Adult body wall with mesenteries, Elav>KikGR-positive cells, library RP0804_O

description:
Library name: RP0804_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0789_E

description:
Library name: RP0789_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: diff4d_GATA1FL_3, H3K27ac, replica 3

description:
Library name: diff4d_GATA1FL_H3K27ac_3
CUT&RUN


title: copper_2_c_2

description:
NA118
32C_sample_count.txt


title: calcofw_3

description:
NA41
32C_sample_count.txt


title: diff4d_GATA1s_1D5_1, IgG, replica 1

description:
Library name: diff4d_GATA1s_1D5_IgG_1
CUT&RUN


title: calcium_40m_2

description:
NA36
32C_sample_count.txt

value: YPD (5h20min)-YPD+200mM CaCl2(40min)


title: calcofw_c_2

description:
NA43
32C_sample_count.txt


title: diff4d_GATA1FL_1, H3K27ac, replica 1

description:
Library name: diff4d_GATA1FL_H3K27ac_1
CUT&RUN


title: diff4d_GATA1FL_3, H3K4me3 , replica 3

description:
Library name: diff4d_GATA1FL_H3K4me3_3
CUT&RUN


title: calcofw_c_1

description:
NA42
32C_sample_count.txt


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0777_E

description:
Library name: RP0777_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: diff4d_GATA1FL_2, H3K27ac, replica 2

description:
Library name: diff4d_GATA1FL_H3K27ac_2
CUT&RUN


title: calcium_40m_1

description:
NA35
32C_sample_count.txt


title: diff4d_GATA1s_1D5_1, GATA1 , replica 1

description:
Library name: diff4d_GATA1s_1D5_GATA1_1
CUT&RUN


title: Adult body wall with mesenteries, Elav>KikGR-positive cells, library RP0782_E

description:
Library name: RP0782_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0806_O

description:
Library name: RP0806_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: FoxL2>KikGR heterozygote


title: calcium_c_3

description:
NA32
32C_sample_count.txt

value: YPD (5h20min)


title: calcofw_c_3

description:
NA44
32C_sample_count.txt


title: calcium_c_2

description:
NA31
32C_sample_count.txt


title: diff4d_GATA1FL_2, H3K4me3 , replica 2

description:
Library name: diff4d_GATA1FL_H3K4me3_2
CUT&RUN


title: calcium_c_1

description:
NA30
32C_sample_count.txt


title: diff4d_GATA1s_1D5_2, IgG, replica 2

description:
Library name: diff4d_GATA1s_1D5_IgG_2
CUT&RUN


title: calcium_60m_2

description:
NA38
32C_sample_count.txt

value: YPD (5h20min)-YPD+200mM CaCl2(60min)


title: diff4d_GATA1s_1D5_3, GATA1 , replica 3

description:
Library name: diff4d_GATA1s_1D5_GATA1_3
CUT&RUN


title: calcium_60m_1

description:
NA37
32C_sample_count.txt


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0762_E

description:
Library name: RP0762_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: body wall with mesenteries

value: SoxC>KikGR stable transgene


title: Adult body wall with mesenteries, Elav>KikGR-positive cells, library RP0796_E

description:
Library name: RP0796_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: l_copper_2_1

description:
NA108
32C_sample_count.txt

value: YPD +500μM BCS(6h)


title: 680_KO_8_3

description:
FRAS220043251-1r
680k_ph8_vs_ph7_gene_counts.tsv

source_name: BJCA001 RIM101 KO

value: BJCA001 RIM101 KO

value: pH8 KO3


title: diff4d_GATA1FL_3, GATA1 , replica 3

description:
Library name: diff4d_GATA1FL_GATA1_3
CUT&RUN

value: erythroid progenitor cell line

value: differentiation


title: 680_KO_8_1

description:
FRAS220043249-1r
680k_ph8_vs_ph7_gene_counts.tsv

value: pH8 KO1


title: l_copper_2_3

description:
NA110
32C_sample_count.txt


title: diff4d_GATA1FL_2, GATA1 , replica 2

description:
Library name: diff4d_GATA1FL_GATA1_2
CUT&RUN


title: 680_KO_8_2

description:
FRAS220043250-1r
680k_ph8_vs_ph7_gene_counts.tsv

value: pH8 KO2


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0766_O

description:
Library name: RP0766_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: 6-8 weeks adults

value: DMSO 1%


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0800_O

description:
Library name: RP0800_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)


title: 680_KO_7_1

description:
NA12
680k_ph8_vs_ph7_gene_counts.tsv

value: pH7 KO1


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0773_O

description:
Library name: RP0773_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: SoxC>KikGR heterozygote


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0770_E

description:
Library name: RP0770_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: FoxL2>KikGR stable transgene


title: 680_WT_8_2

description:
NA10
680_ph8_vs_ph7_gene_counts.tsv

value: pH8 WT2


title: diff4d_GATA1FL_1, IgG , replica 1

description:
Library name: diff4d_GATA1FL_IgG_1
CUT&RUN


title: diff4d_GATA1FL_1, H3K4me3 , replica 1

description:
Library name: diff4d_GATA1FL_H3K4me3_1
CUT&RUN


title: l_copper_2_2

description:
NA109
32C_sample_count.txt


title: calcium_20m_2

description:
NA34
32C_sample_count.txt

value: YPD (5h20min)-YPD+200mM CaCl2(20min)


title: calcium_20m_1

description:
NA33
32C_sample_count.txt


title: 680_WT_7_1

description:
NA6
680_ph8_vs_ph7_gene_counts.tsv

value: pH7 WT1


title: GATA1s_1KI9_2, H3K27ac, replica 2

description:
Library name: GATA1s_1KI9_H3K27ac_2
CUT&RUN

value: expansion


title: 680_WT_8_1

description:
NA9
680_ph8_vs_ph7_gene_counts.tsv

value: pH8 WT1


title: GATA1s_1KI9_1, H3K27ac, replica 1

description:
Library name: GATA1s_1KI9_H3K27ac_1
CUT&RUN


title: 680_WT_8_3

description:
NA11
680_ph8_vs_ph7_gene_counts.tsv

value: pH8 WT3


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0777_O

description:
Library name: RP0777_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: body wall with mesenteries

value: SoxC>KikGR stable transgene


title: 680_KO_7_3

description:
NA14
680k_ph8_vs_ph7_gene_counts.tsv

value: BJCA001 RIM101 KO

value: pH7 KO3


title: GATA1s_1KI9_3, H3K27ac, replica 3

description:
Library name: GATA1s_1KI9_H3K27ac_3
CUT&RUN

value: erythroid progenitor cell line


title: DMN+, batch 2, partially methylated Lambda DNA, input  [k_L0]

first: Yang

last: Li

institute: The University of Chicago

description:
Library name: DMN+, Lambda sample 2, input_k_L0
k_region_counts_L.tsv

data_processing:
*library strategy: DEMETER-assisted 5-Methylcytosine Nicking sequencing (DMN-seq)
After trimming the TruSeq sequencing adapters from the 3′ ends of read 1 and read 2 via the Cutadapt (v4.9) tool, low-quality, short reads or reads without 3 consecutive A from the beginning were filtered out. The clean reads were then aligned to the spike-in sequences (the 164 bp and 200 bp synthetic dsDNA spike-ins in Supplementary Table 1 and GenBank J02459.1 for λ-DNA) and reference genomes (mouse reference mm10 for mESC samples) via HISAT2 (v2.2.1). The sorted mapped reads in the mESC samples were then processed to remove PCR duplicates via the Picard tool. Finally, the number of signals was calculated by counting the number of starts of reads at each genomic site.
Assembly: Lambda DNA
Supplementary files format and content: The processed data were given in a tsv with start, end, id, quality, strand and CIGAR mapping string for each signal point.

organism: Lambdavirus lambda

source_name: Phage

extract_protocol:
Lambda DNA-only samples were prepared by fragmenting
Lambda DNA-only samples were prepared by fragmenting 200 ng -DNA using NEBNext dsDNA Fragmentase, followed by purification and spike-in with 1% each of 200 bp and 164 bp dsDNA oligos. Samples underwent end-repair/dA-tailing, adapter ligation using either methylated NEBNext  customized phosphorothioate-modified DME adaptors, and subsequent purification with AMPure XP beads. The DME adaptor-ligated samples were then subjected to DME enzyme treatment, multiple exonuclease digestions to enrich for 5-phosphorylated fragments, and TACS ligation for library preparation. Finally, libraries were PCR-amplified, purified, quality-checked, and sequenced using the Illumina NextSeq 1000/2000 platform.The UBS-seq sample was subjected to UBS-1 conditions and desulphonated via DNA Methylation-Gold Kit (Zymo Research) following the UBS-seq procedure.

value: Phage

value: partially methylated Lambda DNA, input


title: Adult body wall with mesenteries, Elav>KikGR-positive cells, library RP0782_O

description:
Library name: RP0782_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: Elav>KikGR stable transgene

value: 6-8 weeks adults

value: Elav>KikGR heterozygote

value: DMSO 1%


title: DMN+, batch 1, partially methylated Lambda DNA, treated  [c_A2]

description: Library name: DMN+, Lambda sample 1, treated_c_A2


title: GATA1s_1KI9_2, H3K4me3, replica 2

description:
Library name: GATA1s_1KI9_H3K4me3_2
CUT&RUN


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0766_E

description:
Library name: RP0766_E
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: FoxL2>KikGR stable transgene

value: FoxL2>KikGR heterozygote


title: Ucn3_ATACs_3_Father

city: Cambridge

first: Brandon

last: Logeman

state: MA

address: 16 Divinity

institute: Harvard University

description: Library name: Ucn3_ATAC_3_Father

data_processing:
Illumina sequencing reads were aligned to mm10 using the 10x Genomics CellRanger pipeline with default parameters.
Assembly: mm10
Supplementary files format and content: RNAseq files exist as Feature Barcode Market Exchange Matrices (MEX) files. ATACseq files exist as indexed Fragment files.

source_name: brain

extract_protocol:
For all samples, the preoptic area of the hypothalamus was dissected and snap frozen in liquid nitrogen. Tissue samples from five animals per sample were pooled and Dounce homogenized before isolating GFP-expressing nuclei via FANS.
Library construction was performed according to 10x Genomics protocols.

value: brain

tag: sample group


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0789_O

description:
Library name: RP0789_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: SoxC>KikGR heterozygote


title: DMN+, batch 1, partially methylated Lambda DNA, input  [c_I]

description: Library name: DMN+, Lambda sample 1, input_c_I


title: 680_KO_7_2

description:
NA13
680k_ph8_vs_ph7_gene_counts.tsv

value: pH7 KO2


title: GATA1s_1KI9_3, GATA1 , replica 3

description:
Library name: GATA1s_1KI9_GATA1_3
CUT&RUN

value: expansion


title: 1b.1.046.epi

city: St Louis

first: Margaret

middle: L

last: Axelrod

state: MO

address: 660 South Euclid Avenue, Campus Box 8118

department: Pathology and Immunology

institute: Washington University in St. Louis

description: Library name: 1b.1.046.epi

data_processing:
Sequencing (fastq) files were initially processed through the proprietary GeoMx NGS Pipeline. The raw reads were trimmed, paired-end reads were merged, and then these reads were aligned to the corresponding identification barcodes based on their tag sequence identifiers, which correspond to genes in the transcriptome. The number of tags were counted to determine number of transcripts, corresponding to level of RNA expression. PCR duplicates were removed by sorting the unique molecular identifiers. Data was normalized using Q3 normalization. Low quality reads (low percent aligned reads, low percent stitched reads, low nuclei count) were excluded from analysis.
Assembly: hg38
Supplementary files format and content: Raw linear counts are included as the processed data file

source_name: Cervix

extract_protocol:
ROIs were segregated using a nuclear counterstain and anti-cytokeratin immunofluorescence probes (clone AE1/AE3, Novus NBP2-33200) to separate RNA captured from tumor epithelium (cytokeratin-positive) from RNA in the adjacent SIME (cytokeratin negative). Aspirates from 93 ROIs were collected (25 benign cervix, 21 Silva A, 22 Silva B, and 25 Silva C)
Library preparation was performed according to the manufacturer’s instructions. During the library preparation process, the photocleaved oligonucleotides with tag sequence identifiers, unique molecular identifiers, and sequencing primer reads were PCR amplified. Unique dual indexes and flow cell sequences were added. Library concentration was quantified by Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Libraries were sequenced on the Illumina NovaSeq X Plus (Illumina, Inc., San Diego, CA, USA), targeting 1.5 billion reads per library.

value: Cervix

value: epi

tag: silva pattern

value: B

tag: risk

value: High

tag: caseid


title: 1b.1.046.stroma

description: Library name: 1b.1.046.stroma

value: stroma


title: Adult body wall with mesenteries, FoxL2>KikGR-positive cells, library RP0770_O

description:
Library name: RP0770_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: body wall with mesenteries


title: 1b.1.045.epi

description: Library name: 1b.1.045.epi


title: GATA1s_1KI9_2, GATA1 , replica 2

description:
Library name: GATA1s_1KI9_GATA1_2
CUT&RUN

value: erythroid progenitor cell line


title: 1b.1.044.epi

description: Library name: 1b.1.044.epi

value: normal

value: Normal


title: 680_WT_7_2

description:
NA7
680_ph8_vs_ph7_gene_counts.tsv

value: pH7 WT2


title: Adult body wall with mesenteries, Elav>KikGR-positive cells, library RP0796_O

description:
Library name: RP0796_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: Elav>KikGR stable transgene

value: 6-8 weeks adults

value: Elav>KikGR heterozygote

value: DMSO 1%


title: GATA1s_1KI9_3, H3K4me3, replica 3

description:
Library name: GATA1s_1KI9_H3K4me3_3
CUT&RUN


title: Ucn3_ATACs_2_Father

description: Library name: Ucn3_ATAC_2_Father

value: brain


title: GATA1s_1KI9_2, IgG, replica 2

description:
Library name: GATA1s_1KI9_IgG_2
CUT&RUN


title: 680_WT_7_3

description:
NA8
680_ph8_vs_ph7_gene_counts.tsv

value: pH7 WT3


title: diff4d_GATA1FL_2, IgG , replica 2

description:
Library name: diff4d_GATA1FL_IgG_2
CUT&RUN

value: differentiation


title: DMN+, batch 2, partially methylated Lambda DNA, treated  [k_L1-1]

description:
Library name: DMN+, Lambda sample 2, treated_k_L1-1
k_region_counts_L.tsv

value: Phage


title: 1b.1.042.stroma

description: Library name: 1b.1.042.stroma

value: Cervix


title: diff4d_GATA1FL_1, GATA1 , replica 1

description:
Library name: diff4d_GATA1FL_GATA1_1
CUT&RUN


title: DMN+, batch 2, partially methylated Lambda DNA, treated  [k_L2]

description:
Library name: DMN+, Lambda sample 2, treated_k_L2
k_region_counts_L.tsv


title: UBS-seq, batch 1, partially methylated Lambda DNA [f_B]

description: Library name: UBS-seq, lambda sample 1_f_B

data_processing:
After trimming the TruSeq sequencing adapters from the 3′ ends of read 1 and read 2 via the Cutadapt (v4.9) tool, low-quality, short reads or reads without 3 consecutive A from the beginning were filtered out. The clean reads were then aligned to the spike-in sequences (the 164 bp and 200 bp synthetic dsDNA spike-ins in Supplementary Table 1 and GenBank J02459.1 for λ-DNA) and reference genomes (mouse reference mm10 for mESC samples) via HISAT2 (v2.2.1). The sorted mapped reads in the mESC samples were then processed to remove PCR duplicates via the Picard tool. Finally, the number of signals was calculated by counting the number of starts of reads at each genomic site.
Assembly: Lambda DNA
Supplementary files format and content: The processed data were given in a tsv with start, end, id, quality, strand and CIGAR mapping string for each signal point.

value: partially methylated Lambda DNA


title: DMN+, batch 1, partially methylated Lambda DNA, treated  [c_A1]

description: Library name: DMN+, Lambda sample 1, treated_c_A1


title: DMN+, batch 2, partially methylated Lambda DNA, treated  [k_L1-2]

description:
Library name: DMN+, Lambda sample 2, treated_k_L1-2
k_region_counts_L.tsv


title: 1b.1.042.epi

description: Library name: 1b.1.042.epi

value: epi


title: Ucn3_ATACs_2_VirginFemale

description: Library name: Ucn3_ATAC_2_VirginFemale


title: DMN+, batch 2, partially methylated Lambda DNA, treated  [k_L1-3]

description:
Library name: DMN+, Lambda sample 2, treated_k_L1-3
k_region_counts_L.tsv


title: Adult body wall with mesenteries, SoxC>KikGR-positive cells, library RP0762_O

description:
Library name: RP0762_O
MARS-Seq scRNA-Seq library, reformatted with the following structure: Read1: mRNA fragment, Read2: cell identifier barcode (11nt, combining 4nt of plate barcode and 7nt of well barcode), then UMI barcode (8nt)

value: SoxC>KikGR stable transgene

value: SoxC>KikGR heterozygote


title: GATA1s_1D5_3, H3K27ac, replica 3

description:
Library name: GATA1s_1D5_H3K27ac_3
CUT&RUN

value: erythroid progenitor cell line

value: expansion


title: Ucn3_ATACs_2_VirginMale

description: Library name: Ucn3_ATAC_2_VirginMale


title: GATA1s_1KI9_1, GATA1 , replica 1

description:
Library name: GATA1s_1KI9_GATA1_1
CUT&RUN


title: GATA1s_1D5_2, H3K27ac, replica 2

description:
Library name: GATA1s_1D5_H3K27ac_2
CUT&RUN


title: 1b.1.043.epi

description: Library name: 1b.1.043.epi

value: normal

value: Normal


title: Ucn3_ATACs_3_Mother

description: Library name: Ucn3_ATAC_3_Mother


title: 1b.1.038.epi

description: Library name: 1b.1.038.epi


title: 1b.1.037.stroma

description: Library name: 1b.1.037.stroma

value: stroma


title: Ucn3_ATACs_3_VirginMale

description: Library name: Ucn3_ATAC_3_VirginMale


title: GATA1s_1D5_2, H3K4me3, replica 2

description:
Library name: GATA1s_1D5_H3K4me3_2
CUT&RUN


title: 1b.1.045.stroma

description: Library name: 1b.1.045.stroma

value: B

value: High


title: 1b.1.044.stroma

description: Library name: 1b.1.044.stroma


title: Ucn3_ATACs_1_Mother

description: Library name: Ucn3_ATAC_1_Mother


title: GATA1s_1KI9_1, H3K4me3, replica 1

description:
Library name: GATA1s_1KI9_H3K4me3_1
CUT&RUN


title: 1b.1.041.epi

description: Library name: 1b.1.041.epi


title: 1b.1.037.epi

description: Library name: 1b.1.037.epi


title: GATA1s_1KI9_1, IgG, replica 1

description:
Library name: GATA1s_1KI9_IgG_1
CUT&RUN


title: 1b.1.043.stroma

description: Library name: 1b.1.043.stroma


title: 1b.1.041.stroma

description: Library name: 1b.1.041.stroma


title: 1b.1.036.stroma

description: Library name: 1b.1.036.stroma


title: 1b.1.038.stroma

description: Library name: 1b.1.038.stroma


title: Ucn3_ATACs_3_VirginFemale

description: Library name: Ucn3_ATAC_3_VirginFemale


title: 1b.1.040.epi

description: Library name: 1b.1.040.epi


title: 1b.1.039.epi

description: Library name: 1b.1.039.epi


title: 1b.1.039.stroma

description: Library name: 1b.1.039.stroma


title: 1b.1.034.epi

description: Library name: 1b.1.034.epi

value: C


title: Ucn3_ATACs_1_Father

description: Library name: Ucn3_ATAC_1_Father

value: brain


title: GATA1s_1D5_2, GATA1 , replica 2

description:
Library name: GATA1s_1D5_GATA1_2
CUT&RUN


title: Ucn3_ATACs_2_Mother

description: Library name: Ucn3_ATAC_2_Mother


title: Gal_ATACs_1_VirginMale

description: Library name: Gal_ATAC_1_VirginMale


title: GATA1s_1D5_3, H3K4me3, replica 3

description:
Library name: GATA1s_1D5_H3K4me3_3
CUT&RUN


title: GATA1s_1D5_1, H3K4me3, replica 1

description:
Library name: GATA1s_1D5_H3K4me3_1
CUT&RUN


title: Ucn3_ATACs_1_VirginFemale

description: Library name: Ucn3_ATAC_1_VirginFemale


title: 1b.1.031.stroma

description: Library name: 1b.1.031.stroma


title: 1b.1.032.epi

description: Library name: 1b.1.032.epi


title: 1b.1.040.stroma

description: Library name: 1b.1.040.stroma


title: Ucn3_ATACs_1_VirginMale

description: Library name: Ucn3_ATAC_1_VirginMale


title: 1b.1.036.epi

description: Library name: 1b.1.036.epi


title: Gal_ATACs_1_Father

description: Library name: Gal_ATAC_1_Father


title: Brs3_ATACs_2_Mother

description: Library name: Brs3_ATAC_2_Mother


title: GATA1s_1D5_1, H3K27ac, replica 1

description:
Library name: GATA1s_1D5_H3K27ac_1
CUT&RUN


title: Gal_ATACs_1_Mother

description: Library name: Gal_ATAC_1_Mother


title: 1b.1.035.stroma

description: Library name: 1b.1.035.stroma


title: 1b.1.035.epi

description: Library name: 1b.1.035.epi


title: 1b.1.033.epi

description: Library name: 1b.1.033.epi


title: GATA1s_1D5_3, GATA1 , replica 3

description:
Library name: GATA1s_1D5_GATA1_3
CUT&RUN


title: Brs3_ATACs_2_Father

description: Library name: Brs3_ATAC_2_Father


title: GATA1s_1D5_2, IgG, replica 2

description:
Library name: GATA1s_1D5_IgG_2
CUT&RUN


title: GATA1s_1D5_1, GATA1 , replica 1

description:
Library name: GATA1s_1D5_GATA1_1
CUT&RUN


title: 1b.1.031.epi

description: Library name: 1b.1.031.epi


title: Brs3_ATACs_2_VirginFemale

description: Library name: Brs3_ATAC_2_VirginFemale


title: Gal_ATACs_1_VirginFemale

description: Library name: Gal_ATAC_1_VirginFemale


title: GATA1FL_2, H3K27ac, replica 2

description:
Library name: GATA1FL_H3K27ac_2
CUT&RUN


title: 1b.1.027.stroma

description: Library name: 1b.1.027.stroma


title: GATA1s_1D5_1, IgG, replica 1

description:
Library name: GATA1s_1D5_IgG_1
CUT&RUN


title: 1b.1.030.epi

description: Library name: 1b.1.030.epi


title: GATA1FL_3, H3K27ac, replica 3

description:
Library name: GATA1FL_H3K27ac_3
CUT&RUN


title: 1b.1.030.stroma

description: Library name: 1b.1.030.stroma


title: GATA1FL_3, H3K4me3 , replica 3

description:
Library name: GATA1FL_H3K4me3_3
CUT&RUN


title: 1b.1.034.stroma

description: Library name: 1b.1.034.stroma


title: 1b.1.028.stroma

description: Library name: 1b.1.028.stroma


title: Brs3_ATACs_1_Mother

description: Library name: Brs3_ATAC_1_Mother


title: 1b.1.029.epi

description: Library name: 1b.1.029.epi


title: 1b.1.026.stroma

description: Library name: 1b.1.026.stroma


title: 1b.1.028.epi

description: Library name: 1b.1.028.epi


title: Brs3_ATACs_2_VirginMale

description: Library name: Brs3_ATAC_2_VirginMale


title: 1b.1.033.stroma

description: Library name: 1b.1.033.stroma


title: 1b.1.032.stroma

description: Library name: 1b.1.032.stroma


title: 1b.1.024.stroma

description: Library name: 1b.1.024.stroma


title: 1b.1.027.epi

description: Library name: 1b.1.027.epi


title: 1b.1.026.epi

description: Library name: 1b.1.026.epi


title: Brs3_ATACs_1_Father

description: Library name: Brs3_ATAC_1_Father


title: 1b.1.029.stroma

description: Library name: 1b.1.029.stroma


title: GATA1FL_1, H3K27ac, replica 1

description:
Library name: GATA1FL_H3K27ac_1
CUT&RUN


title: GATA1FL_1, H3K4me3 , replica 1

description:
Library name: GATA1FL_H3K4me3_1
CUT&RUN


title: GATA1FL_3, GATA1 , replica 3

description:
Library name: GATA1FL_GATA1_3
CUT&RUN


title: 1b.1.025.epi

description: Library name: 1b.1.025.epi


title: Brs3_ATACs_1_VirginFemale

description: Library name: Brs3_ATAC_1_VirginFemale


title: Brs3_ATACs_1_VirginMale

description: Library name: Brs3_ATAC_1_VirginMale


title: Ucn3_RNAs_3_Father

description: Library name: Ucn3_RNA_3_Father

molecule: nuclear RNA


title: GATA1FL_2, H3K4me3 , replica 2

description:
Library name: GATA1FL_H3K4me3_2
CUT&RUN


title: 1b.1.025.stroma

description: Library name: 1b.1.025.stroma


title: 1b.1.024.epi

description: Library name: 1b.1.024.epi


title: 1b.1.023.epi

description: Library name: 1b.1.023.epi


title: GATA1FL_2, GATA1 , replica 2

description:
Library name: GATA1FL_GATA1_2
CUT&RUN


title: Ucn3_RNAs_3_Mother

description: Library name: Ucn3_RNA_3_Mother


title: 1b.1.023.stroma

description: Library name: 1b.1.023.stroma


title: 1b.1.022.stroma

description: Library name: 1b.1.022.stroma


title: 1b.1.020.epi

description: Library name: 1b.1.020.epi


title: 1b.1.022.epi

description: Library name: 1b.1.022.epi


title: 1b.1.019.stroma

description: Library name: 1b.1.019.stroma


title: GATA1FL_2, IgG , replica 2

description:
Library name: GATA1FL_IgG_2
CUT&RUN


title: Ucn3_RNAs_3_VirginFemale

description: Library name: Ucn3_RNA_3_VirginFemale


title: GATA1FL_1, GATA1 , replica 1

description:
Library name: GATA1FL_GATA1_1
CUT&RUN


title: 1b.1.020.stroma

description: Library name: 1b.1.020.stroma


title: 1b.1.021.epi

description: Library name: 1b.1.021.epi


title: A549 cells (input), rep 2

city: Calgary

first: Alex

last: Gao

state: Alberta

address: 3330 Hospital Dr NW

department: Physiology and Pharmacology

country: Canada

institute: University of Calgary

description: Library name: Sample 26

data_processing:
Demultiplexing was performed using bcl2fastq conversion software (v2.18.0.12) and read quality was assessed using FastQC (v0.10.1).
Good-quality reads were mapped to GRCh38 reference genome using bowtie2 (v2.4.4) and the resultant BAM files were sorted and indexed using samtools (v) prior to peak calling using MACS2 (v2.2.7.1). MACS-identified peaks for GR and RELA were assessed by DiffBind R package (v3.2) to calculate differential binding in response to each treatment compared to no stimulation.
Due to the variability between the Ad-IκBαΔN ChIP samples in the number of reads that were successfully mapped to the reference genome, BAM files were normalized to account for such differences before the post-normalization “.bigwig” files were used for graphical representation in heatmaps and data summarization.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes peak names, locations, binding intensity, and behaviour upon combination treatment
Supplementary files format and content: bigwig

growth_protocol: The human pulmonary type II cell line, A549, was grown under standard culture condition using Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 2mM L-glutamine. Cells were incubated at 37°C in 5% CO2 and were grown to confluence either in 100mm, or 6/12/24-well plates, as appropriate. Prior to experiments, cells were incubated overnight in basal media that was serum- and additive-free.

extract_protocol:
Protein-DNA cross-linking was performed by adding methanol-free formaldehyde to 1% in the culture medium and incubating for 10 min at room temperature. Formaldehyde was then quenched at room temperature for 5 min with 125mM glycine prior to washing cells for 5 min with ice-cold PBS and scraping into ice-cold lysis buffer (5mM PIPES pH 8.0, 1mM EDTA, 85mM KCl, 5% glycerol, 0.5% NP-40) supplemented with protease inhibitor cocktail (PIC). Cell suspensions were incubated at 4°C for 3 h with continuous agitation. Nuclei were collected by centrifugation (600 g, 5 min, 4°C) and resuspended in ice-cold nuclei lysis buffer (NLB) (1xPBS containing 1mM EDTA, 5% glycerol, 0.5% sodium deoxycholate, 0.1% SDS, 1% NP-40) supplemented with PIC. Samples were sonicated at 4°C using a Bioruptor set for 28 – 30 high-power bursts with 30 s on-off cycles. Lysates were cleared by centrifugation (maximum speed for 15 min at 4°C) and supernatants used for immunoprecipitation. Protein G magnetic Dynabeads were preincubated with primary antibody (2.5µl/sample) overnight at 4 °C in NLB supplemented with PIC and 5 mg/ml BSA. After washing twice with ice-cold NLB plus PIC, the Dynabeads were incubated with cleared lysates overnight at 4°C in NLB supplemented with PIC and BSA. Beads were given 4 washes with ice-cold NLB containing 500mM NaCl, followed by 4 washes with ice-cold LiCl buffer (20mM Tris at pH 8.0, 1 mM EDTA, 250mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate). Crosslinks were reversed by incubation in TE buffer (10mM Tris-HCl,1mM EDTA, pH 8.0) supplemented with 0.7% SDS and 0.2 mg/ml proteinase K for 3h at 55 °C, then 16 h at 65°C. DNA was purified with a ChIP DNA Clean & Concentrator kit.
ChIP-seq libraries were prepared using the NEB Ultra II kit.

treatment_protocol: Budesonide was dissolved in DMSO as a 10mM stock. Unless specifically indicated, budesonide was used at 300nM on cells, representing a concentration that was maximally effective/near maximal on a 2×GRE reporter and gene expression in A549 cells. Final DMSO concentrations on cells were ≤ 0.1%. Recombinant human IL1B was dissolved in phosphate-buffered saline (PBS) containing 0.1% bovine serum albumin (BSA). IL1B was previously found to be maximally or near maximally effective on NF-κB reporters and gene expression at 1ng/ml and this concentration was used in all experiments unless specifically indicated. Following overnight incubation in serum free medium, cells were changed to fresh serum free medium and either not stimulated (NS) or treated with, IL1B, budesonide (Bud) or IL1B plus budesonide (I+B) for the indicated times prior to harvesting for RNA extraction. Data are from two independent experiments.

value: lung carcinoma epithelial cells

value: WT

tag: condition

tag: chip antibody


title: 1b.1.018.stroma

description: Library name: 1b.1.018.stroma


title: 1b.1.021.stroma

description: Library name: 1b.1.021.stroma


title: Ucn3_RNAs_3_VirginMale

description: Library name: Ucn3_RNA_3_VirginMale


title: 1b.1.017.stroma

description: Library name: 1b.1.017.stroma