title: 48hpf_sox17M_ATAC_rep1

description: Library name: 48hpf_sox17M_ATAC_rep1

value: hematovascular

tag: cell type


title: P3504_1048

status: Public on Feb 16 2026

type: SRA

city: Stockholm

first: Andreas

last: Liontos

state: Stockholm

address: Svante Arrheniusväg 20C

department: Molecular Biosciences-The Wenner Gren Institute

country: Sweden

institute: Stockholm University

description:
single cell library
Smart-Seq2

library_source: transcriptomic single cell

data_processing:
Sequencing was done with Illumina 2500 HiSeq Rapid mode using paired-end (2x125 bp) and single-end (1x50 bp). For downstream analysis, we used the one strand sequencing out of paired-end libraries and trimmed the reads to 50 bp
High quality transcriptomic libraries were obtained after filtering, for doublet cells included in our experiment as sequencing controls, for cells obtaining less than 40% uniquely mapped reads, for cells that had number of detected genes outside mean ± 2s.d range and for cells whose GFP  expression ratio was lower than the GFP ration determined in embryonic epithelial cells.
The following single cells were removed as known doublets in our analysis: "P7657_1067", "P7657_1189", "P2661_1003", "P4730_1029". The following single cells were removed because they had <40% uniquely mapped reads: "P2272_1042", "P2661_1042", "P3504_1071", "P3504_1082", "P4730_1040", "P7657_1022", "P7657_1024", "P7657_1025", "P7657_1032", "P7657_1070".
Assembly: Custom Mus Musculus (GRCm38) reference genome that contained GFP sequence and Ai14 cassette (RFP and WPRE sequences). The reference genome was created with the 10x Genomics "cell ranger mkref" and the mapping of the reads was done with the "cellranger count" function, using default settings.
Supplementary files format and content: raw count matrix and metadata files for the 464/478 single cells remaining after removal of doublet cells (4 cells removed) and removal of cells that failed uniquely map read filtering (10 cells removed) step.

molecule: total RNA

organism: Mus musculus

source_name: lung

extract_protocol:
For full-length (Smart-Seq2) library preparation (Picelli et al., 2014), the left lungs were used for enzymatic digestion and right lungs were treated as described above for histological analysis. Briefly, we cut the lungs in small pieces using a razor blade and digested with elastase (Worthington, LS002292) and DNase I 0.5 mg/ml (Sigma-Aldrich, DN25) in HBSS (Gibco, 14175), at 37oC for 1 hour with rotation. Equal volume of HBSS++ [HBSS (Gibco, 14175), supplemented with 2% 0.2µm filtered FCS (Gibco, 10500), 0.1 M HEPES (Sigma-Aldrich, H0887), antibiotics (Gibco, 15240096) and EGTA 2 mM] was added and the suspension was mixed gently. Then cells were centrifuged at 800g for 10 minutes at 4oC. Supernatant was removed with a serological pipette and cells were resuspended in HBSS++. Viability was tested using trypan blue (Sigma-Aldrich, T8154) (1:1 dilution) and presence of fluorescence positive cells was evaluated using a normal fluorescence microscope. Just before sorting, cells were passed through a 100 µm BD Filcon (BD Biosciences, 340610) in order to remove cell aggregates. For E16.5 lungs, after digestion, centrifuge and cell resuspension in HBSS++, cells were passed through a 100 µm BD Filcon (BD Biosciences, 340610) and counted. We resuspented the cells in the proper amount of HBSS++ in order to obtain 20x106 cells/ml cell concentration. 100 µl of cell suspension were stained with 0.5 µl of anti-EpCam-PE antibody (Biolegend, 118205) and 0.5 µl anti-CD45-APC antibody (Biolegend, 103112). Replicates of the above reactions were set in separate tubes; in order to prevent the formation of cell aggregates, which is typical when we centrifuge large amount of epithelial cells.
For cell-sorting, we used a BD FACSARIA III cell-sorter, using 100 µm nozzle, applying single-cell sorting purity setting. For E16.5 lungs, EpCampos CD45neg cells were sorted. Cells from all other stages were isolated according to GFP expression.
Cell sorting and single-cell library preparation were done according to Smart Seq2 protocol (Picelli et al., 2013; Picelli et al., 2014) with some modifications. Cells were sorted in 96-well plates (Piko PCR Plates 24-well, Thermo Scientific, SPL0240 and Plate Frame for 24-well PikoPCR Plates, Thermo Scientific, SFR0241).  Each well contained Triton-X100 (0.2%) (Sigma-Aldrich, T9284-100ML), ERCC RNA Spike-In Mix (1:400.000) (Life-Technologies, 4456740), Oligo-dT30 VN (1,25uM) AAGCAGTGGTATCAACGCAGAGTAC (30 x T) VN, dNTPs (2.5mM/each) (Thermo Scientific-Fermentas, R0192) and Rnase Inhibitor (1U/ul) (Clontech, 2313A) in 4 µl final volume. After sorting, strips were covered with Axygen PCR-tube caps (VWR, PCR-02-FCP-C), centrifuged and placed on dry ice until storage at -80oC for further use. For cell culture cells were sorted into HBSS++ buffer and kept on ice until they were placed in culture.
Smart Seq2 protocol is optimal for cell lines and/or large human cells (Picelli et al., 2014). Mouse primary pulmonary cells are smaller and they contain smaller amount of RNA, as a result high amount of primer concatamers were formed during cDNA library preparation, compromising its efficiency. Our optimized protocol contains 50% less Oligo-dT30 VN and cDNA synthesis was divided into two steps, the first was without TSO LNA and the second contained 1µM TSO LNA and additional 40 U of SuperScript II RT (Thermo-Fisher Scientific, 18064071). Reaction lasted 30 minutes at 42oC. Then enzyme was deactivated at 70oC for 15 minutes. For Pre-Amplification PCR, we used the KAPA HiFi Hotstart ReadyMix (2x) (KAPA Biosystems, KK2602) and the ISPCR-primer AAGCAGTGGTATCAACGCAGAGT. PCR included 21 cycles and the total volume increased to 50ul in order to reduce the concentration of the unused Oligo-dT30 VN and TSO-LNA primers.
Tagmentation and indexed library amplification were done with Nextera® XT DNA Library Preparation Kit (Illumina, FC-131-1096) and Nextera® XT Index Kit (96 indexes, 384 samples), (Illumina, FC-131-1002) according to the manufacturer protocol (with 2.5 x volume reduction in all reactions). The quantity of the used library for tagmentation was 50 pg of the 500-9000 bp fraction of the library, as indicated by its Bioanalyzer profile.

tag: tissue

value: lung

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

value: lung epithelial secretory cells

tag: genotype

value: WT

tag: developmental stage

tag: individual

tag: sorting date

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

value: single-end 50bp

tag: lane

tag: plate well

tag: internal number

tag: n primer

tag: s primer


title: HFD_fed_Mock_Female_3dpi-4

city: Ann Arbot

first: Raymond

last: Yung

state: Michigan

address: 109 Zina Pitcher Pl

country: USA

institute: University of Michigan

description: Library name: 13375-NN-162

library_source: transcriptomic

data_processing:
The reads were trimmed using Cutadapt v4.8. Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a  and assigned count estimates to genes with RSEM v1.3.3.
Assembly: GRCm38
Supplementary files format and content: counts

source_name: Cecum

growth_protocol: Young 4-6 weeks old male and female C57BL/6J mice housed at the University of Michigan were used in this study. Mice were either fed with high-fat diet (HFD) (42% Kcal from fat, Inotiv; TD.88137) or normal diet (ND) (13% Kcal from fat, LabDiet; 5L0D) for 12 weeks

extract_protocol:
Cecal samples were processed for RNA isolation using Direct-zol™ RNA Miniprep (Zymo Research). RNA samples were then submitted to University of Michigan Advanced Genomics Core for quality check, library preparation, sequencing and generating count files
Library prep and next-generation sequencing was carried out in the Advanced Genomics Core at the University of Michigan

treatment_protocol: Sixteen-eighteen weeks old mice were intraperitoneally (i.p.) injected with clindamycin (10mg/kg) (Sigma). After 24 hours, mice were inoculated with 103 VPI 10643 via oral gavage, while mock mice were given distilled water at the same time

value: Cecum

tag: diet

value: HFD

tag: Sex

value: Female

tag: treatment

value: Mock

tag: days post_infection


title: P3504_1049

description:
single cell library
Smart-Seq2

tag: tissue

tag: strain

tag: cell type

tag: genotype


title: hapo_newborn_cordblood_A1796

type: genomic

city: Chicago

first: Jami

middle: L

last: Josefson

state: Illinois

address: 225 E Chicago Avenue

institute: Ann & Robert H. Lurie Children's Hospital of Chicago

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

hyb_protocol: Genome-wide methylation profiling was conducted with the Infinium MethylationEPIC BeadChip version 1.0 (Illumina, Inc., San Diego, California) array, which interrogates > 850,000 CpG sites at singlenucleotide resolution

scan_protocol: BeadChips were scanned with an Illumina iScan

data_processing:
minfi package in R environment (version 1.40.0)
processed value definition: M values transformed from beta (HAPO_GA_illumina_methylation.xlsx linked to the Series record)

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: newborn cordblood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from whole blood that was stored at -80 C and was quantified with the Qubit Fluorometer (Thermo Fisher Scientific, Waltham, Massachusetts)

value: Male

value: cord clood

tag: developmental stage

value: newborn

value: whole blood cells


title: F1

city: Champaign

first: QIQI

last: XIE

state: IL

address: 2753-11 Hunters Pond Run, Champaign, IL 61820

institute: University of Illinois Urbana-Champaign

description: Library name: Sample 4

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer ’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq Xten platform and paired-end reads were generated.
Raw reads were filtered to remove low-quality reads and adaptors. Clean reads were mapped to the reference genome (Rattus norvegicus) using standard alignment software STAR.
Gene expression levels were quantified and calculated using featureCounts. Differential expression analysis was performed comparing the TBHP group and the TBHP+FGF21 group. Differentially expressed genes (DEGs) were identified based on the threshold of |logFC| > 1 and P < 0.05.
Assembly: http://ftp.ensembl.org/pub/release-105/fasta/rattus_norvegicus/
Supplementary files format and content: The file format is CSV. The content is a gene count matrix. The first column contains gene symbols. Columns F1, F2, and F3 represent TBHP plus FGF21 samples. Columns T1, T2, and T3 represent TBHP samples. Values represent raw read counts.

organism: Rattus norvegicus

source_name: Nucleus pulposus

growth_protocol: Nucleus pulposus cells (NPCs) were isolated from the caudal vertebrae of male Sprague-Dawley rats (120–150 g). The NP tissues were digested with 0.1 mg/mL collagenase II (Proteintech, China) for 20 minutes. Cells were cultured in DMEM/F12 medium supplemented with 15% fetal bovine serum (FBS) and 1% antibiotics at 37°C in a 5% CO2 atmosphere.

extract_protocol:
RNA concentration and purity was measured using NanoDrop 2000(Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNextR  UltraTM  Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3 ’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and  library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: The cells were divided into two groups to investigate the effect of FGF21 on senescence. The model group was treated with tert-butyl hydroperoxide (TBHP) to induce oxidative stress and senescence. The treatment group was co-treated with TBHP and recombinant rat FGF21. Total RNA was extracted after the treatment period.

value: Nucleus pulposus

tag: cell line

value: Primary Nucleus Pulposus Cells

value: Nucleus Pulposus Cells

value: Wild type Sprague-Dawley (SD) rat

value: treated with tert-butyl hydroperoxide (TBHP) and recombinant FGF21


title: HFD_fed_Mock_Female_3dpi-3

description: Library name: 13375-NN-161


title: ND_fed_Mock_Female_3dpi-1

description: Library name: 13375-NN-155

value: ND


title: hapo_newborn_cordblood_A1777


title: P3504_1035

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

value: lung epithelial secretory cells

value: WT

tag: individual

tag: sorting date

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date


title: RNA-seq of mouse cardiac tissue: AAV9_Ctrl_Sham_1

city: Changchun

first: BIng

last: Li

address: 130021, No. 1, Xinmin Street, Chaoyang District, Changchun, Jilin Province

country: China

institute: First Hospital of Jilin University

description:
Library name: AAV9_Ctrl_Sham_1
Transcriptome sequencing of mouse cardiac tissues performed by Novogene (Beijing, China). mRNA was enriched via oligo(dT) magnetic beads, randomly fragmented, and reverse transcribed into double-stranded cDNA. The cDNA was then subjected to end-repair, A-tailing, adapter ligation, and PCR amplification. Qualified libraries were sequenced on the Illumina platform. Raw sequencing data were processed via fastp to remove adapter sequences and low-quality reads, yielding clean reads.

data_processing:
Raw sequencing data were processed using fastp to remove adaptor sequences and low-quality reads, generating clean reads; Q20, Q30, and GC content of clean reads were calculated.
Clean reads were aligned to the mouse reference genome (GRCm39/mm39), and gene expression levels were quantified.
Assembly: GRCm39/mm39 for mouse cardiac tissues.
Supplementary files format and content: GEO_gene_count.xls.csv

molecule: polyA RNA

source_name: Left ventricle

growth_protocol: C57BL/6J mice were raised under specific pathogen-free (SPF) conditions.

extract_protocol:
Total RNA was extracted using TRIzol reagent and treated with DNase I to remove genomic DNA.
mRNA was enriched from total RNA using Oligo(dT) magnetic beads, randomly fragmented, and reverse-transcribed into double-stranded cDNA. The cDNA was then subjected to end repair, A-tailing, adaptor ligation, and PCR amplification. Qualified libraries (verified by Qubit quantification and Agilent fragment analysis) were sequenced on an Illumina platform (conducted by Novogene, Beijing, China).

treatment_protocol: Mice were injected with AAV9 control or AAV9-Irx3 vector via tail vein, followed by sham or MI surgery.

value: Left ventricle

value: Cardiomyocytes

value: Wild type

value: Sham surgery + AAV9 control vector

tag: batch


title: 28hpf_sox17M_ATAC_rep2

city: Coventry

first: Andrew

last: Nelson

address: Gibbet Hill Road

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

description: Library name: 28hpf_sox17M_ATAC_rep2

library_source: genomic

data_processing:
ATAC-seq: Reads were trimmed from the 3’ end to a uniform 75 bp using seqtk so that mapping of reads was not impacted by sequencing read length. Adapter sequences were trimmed using Trimmomatic version 0.39 (Bolger et al. 2014). Data quality control and confirmation of adapter removal was performed using FastQC (Andrews 2010). Reads were aligned to the genome reference consortium zebrafish build 11 (GRCz11v97) using Bowtie2 (Langmead and Salzberg 2012) using “Very sensitive” and 2 kb maximum fragment length for paired-end alignments. Samtools (Li et al. 2009) was also used to filter out reads that mapped to the mitochondrial genome, duplicated reads and low-quality reads with a MAPQ score < 22.
Assembly: danRer11
Supplementary files format and content: ATAC-seq processed data are CPM normalised bigWig files of ATAC-seq profiles with biological replicates merged, produced using deepTools bamCoverage.

organism: Danio rerio

source_name: hematovascular

growth_protocol: Embyos were maintained in E3 embryo medium at 28.5 degrees celcius

extract_protocol:
Cell populations were isolated according to fluorescence profiles using a BD FACSAria Fusion flow cytometer.  ATAC-seq libraries were produced according to "Corces MR, Trevino AE, Hamilton EG, et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature methods 14: 959".
ATAC-seq libraries were produced according to "Corces MR, Trevino AE, Hamilton EG, et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature methods 14: 959".

value: hematovascular

value: AB

value: FACS isolated


title: HFD_fed_Mock_Female_3dpi-1

description: Library name: 13375-NN-159

value: Cecum

value: HFD

value: Female

value: Mock


title: hapo_newborn_cordblood_A1811

value: Male

value: cord clood

value: newborn

value: whole blood cells


title: P3504_1033

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

value: lung epithelial secretory cells

value: GFP^pos

tag: type of_sequencing

value: single-end 50bp

tag: lane

tag: plate well

tag: internal number

tag: n primer

tag: s primer


title: hapo_newborn_cordblood_A1775

tag: Sex

tag: tissue


title: HFD_fed_CDI_Male_3dpi-4

description: Library name: 13375-NN-153

tag: diet

tag: treatment

value: CDI

tag: days post_infection

tag: strain


title: ND_fed_Mock_Female_3dpi-3

description: Library name: 13375-NN-157

value: ND


title: P3504_1032

description:
single cell library
Smart-Seq2

tag: cell type

tag: genotype

value: WT

tag: developmental stage

tag: individual

tag: sorting date


title: P3504_1028

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing


title: P3504_1027

description:
single cell library
Smart-Seq2

tag: lane

tag: plate well

tag: internal number

tag: n primer


title: hapo_newborn_cordblood_A1802

tag: Sex

tag: tissue


title: P3504_1031

description:
single cell library
Smart-Seq2

tag: s primer


title: F2

description: Library name: Sample 5

value: Nucleus pulposus

tag: cell line

value: Primary Nucleus Pulposus Cells

value: Nucleus Pulposus Cells

value: Wild type Sprague-Dawley (SD) rat

tag: treatment

value: treated with tert-butyl hydroperoxide (TBHP) and recombinant FGF22


title: ND_fed_Mock_Female_3dpi-2

description: Library name: 13375-NN-156

value: Cecum

tag: diet

value: Female

value: Mock

tag: days post_infection

tag: strain


title: P3504_1030

description:
single cell library
Smart-Seq2

tag: cell type

tag: genotype

tag: developmental stage

tag: individual

tag: sorting date


title: P3504_1026

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane


title: T3

description: Library name: Sample 3

tag: tissue

value: treated with tert-butyl hydroperoxide (TBHP)


title: P3504_1025

description:
single cell library
Smart-Seq2

value: lung

tag: plate well

tag: internal number

tag: n primer

tag: s primer


title: P3504_1029

description:
single cell library
Smart-Seq2

value: Scgb1a1CREERT2; Rosa26R-fGFP


title: HFD_fed_CDI_Male_3dpi-2

description: Library name: 13375-NN-151

tag: diet

value: HFD

tag: Sex

value: Male

tag: treatment

tag: days post_infection


title: HFD_fed_CDI_Male_3dpi-5

description: Library name: 13375-NN-154

tag: strain


title: hapo_newborn_cordblood_A1762

value: cord clood

tag: developmental stage

value: newborn

tag: cell type

value: whole blood cells


title: P3504_1024

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

tag: genotype

value: WT

tag: individual

tag: sorting date

tag: isolation criteria

value: GFP^pos

value: single-end 50bp


title: T2

description: Library name: Sample 2

value: Nucleus pulposus

tag: cell line

value: Primary Nucleus Pulposus Cells

value: Nucleus Pulposus Cells

value: Wild type Sprague-Dawley (SD) rat


title: hapo_newborn_cordblood_A1774

value: Female

tag: tissue


title: T1

description: Library name: Sample 1

value: treated with tert-butyl hydroperoxide (TBHP)


title: hapo_newborn_cordblood_A1756


title: hapo_newborn_cordblood_A1773


title: HFD_fed_CDI_Male_3dpi-3

description: Library name: 13375-NN-152

value: Cecum

value: CDI


title: mediumH26

type: RNA

city: Hannover

first: Maximilian

last: Fuchs

address: Carl-Neuberg-Str. 1

department: IMTTS

country: Germany

institute: Hanover Medical School

hyb_protocol: cDNA were hybridized for 18 h at 48 °C with the array.

scan_protocol: Read out was performed with an with a GeneChip® Scanner 3000 7G

data_processing: Data procession and analysis was performed within R version 4.1.3. Raw CEL files were loaded using the “oligo” package and transformed using rma package

label: biotin

source_name: PCLS

label_protocol: 100 ng of total RNA was labeled with biotin using the flashtag™ HSR RNA labeling kit (ThermoFisher Scientific)

growth_protocol: PCLS were generated from fresh explant human lung tissue. Tissue slices were cultivated submerged in medium (DMEM/F12 supplemented with 1 % penicillin/streptomycin) at 37 °C, 5 % CO2 overnight.

extract_protocol: RNA including miRNA was isolated using the Mag MAX mirVana Total RNA Isolation Kit (ThermoFisher Scientific) with several modifications. All samples had acceptable RIN numbers (range 4.9-10, average 7.4)

treatment_protocol: PCLS were infected with 25,000 ffu/well in 250 µL of hPIV-3. 72 hours post infection, PCLS were snap frozen and subjected to RNA extraction

tag: condition

value: medium


title: hapo_newborn_cordblood_A1771

value: Male


title: HFD_fed_CDI_Male_3dpi-1

description: Library name: 13375-NN-150

value: HFD


title: ND_fed_CDI_Male_3dpi-3

description: Library name: 13375-NN-147

value: ND


title: drug_controlH26


title: treated_100H26


title: P3504_1023

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane

tag: plate well

tag: internal number


title: ND_fed_CDI_Male_3dpi-5

description: Library name: 13375-NN-149

tag: diet

tag: Sex

tag: treatment

tag: days post_infection


title: hapo_newborn_cordblood_A1741

value: cord clood

tag: developmental stage

value: newborn

tag: cell type

value: whole blood cells


title: infectedH26

value: infected


title: ND_fed_CDI_Male_3dpi-4

description: Library name: 13375-NN-148

tag: strain


title: hapo_newborn_cordblood_A1745


title: ND_fed_CDI_Male_3dpi-2

description: Library name: 13375-NN-146


title: P3504_1022

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

tag: genotype

value: WT

tag: individual

tag: sorting date

tag: isolation criteria

value: GFP^pos

value: single-end 50bp

tag: n primer

tag: s primer


title: mediumH25

tag: condition


title: P3504_1021

description:
single cell library
Smart-Seq2

tag: tissue

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane


title: hapo_newborn_cordblood_A1715

tag: Sex


title: uv_infectedH26


title: P3504_1019

description:
single cell library
Smart-Seq2

tag: plate well

tag: internal number


title: P3504_1020

description:
single cell library
Smart-Seq2

tag: cell type

tag: developmental stage


title: ND_fed_CDI_Male_3dpi-1

description: Library name: 13375-NN-145

tag: diet

tag: treatment

tag: days post_infection

tag: strain


title: HFD_fed_Mock_Male_3dpi-4

description: Library name: 13375-NN-144

value: Mock


title: P3504_1018

description:
single cell library
Smart-Seq2

tag: genotype

tag: individual

tag: sorting date

tag: isolation criteria

tag: n primer


title: treated_10H26

tag: condition


title: hapo_newborn_cordblood_A1704

value: Female

tag: tissue


title: hapo_newborn_cordblood_A1730


title: HFD_fed_Mock_Male_3dpi-3

description: Library name: 13375-NN-143

value: Cecum


title: P3504_1017

description:
single cell library
Smart-Seq2

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane

tag: s primer


title: hapo_newborn_cordblood_A1703

tag: Sex

tag: developmental stage

tag: cell type


title: HFD_fed_Mock_Male_3dpi-2

description: Library name: 13375-NN-142

tag: diet

tag: treatment

tag: days post_infection


title: infectedH25


title: uv_infectedH25


title: hapo_newborn_cordblood_A1702


title: P3504_1016

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

tag: individual

tag: plate well

tag: internal number


title: ND_fed_Mock_Male_3dpi-4

description: Library name: 13375-NN-140

tag: tissue


title: P3504_1015

description:
single cell library
Smart-Seq2

tag: sorting date

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: n primer


title: hapo_newborn_cordblood_A1693


title: uv_infectedH24

tag: condition


title: P3504_1013

description:
single cell library
Smart-Seq2

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane

tag: s primer


title: HFD_fed_Mock_Male_3dpi-1

description: Library name: 13375-NN-141

tag: diet

tag: Sex

tag: treatment


title: ND_fed_Mock_Male_3dpi-3

description: Library name: 13375-NN-139

tag: days post_infection

tag: strain


title: drug_controlH24


title: infectedH24


title: mediumH24

value: medium


title: hapo_newborn_cordblood_A1674

value: Male

tag: developmental stage

tag: cell type


title: P3504_1012

description:
single cell library
Smart-Seq2

tag: tissue

tag: genotype

tag: individual

tag: plate well

tag: internal number


title: ND_fed_Mock_Male_3dpi-2

description: Library name: 13375-NN-138


title: hapo_newborn_cordblood_A1701


title: hapo_newborn_cordblood_A1667


title: P3504_1011

description:
single cell library
Smart-Seq2

tag: sorting date

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: n primer


title: ND_fed_Mock_Male_3dpi-1

description: Library name: 13375-NN-137


title: treated_100H24

tag: condition


title: treated_10H24


title: hapo_newborn_cordblood_A1655


title: mediumH17


title: hapo_newborn_cordblood_A1643


title: HFD_fed_CDI_Male_6dpi-5

description: Library name: 13375-NN-136

tag: diet

value: HFD

value: CDI


title: P3504_1010

description:
single cell library
Smart-Seq2

value: lung

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane

tag: s primer


title: P3504_1008

description:
single cell library
Smart-Seq2

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: developmental stage


title: uv_infectedH17


title: infectedH17


title: HFD_fed_CDI_Male_6dpi-4

description: Library name: 13375-NN-135

tag: tissue

tag: Sex

tag: treatment

tag: days post_infection


title: hapo_newborn_cordblood_A1641

value: cord clood

tag: cell type


title: P3504_1009

description:
single cell library
Smart-Seq2

tag: genotype

tag: individual

tag: sorting date

tag: plate well

tag: internal number


title: P3504_1007

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: n primer


title: HFD_fed_CDI_Male_6dpi-3

description: Library name: 13375-NN-134

tag: diet


title: HFD_fed_CDI_Male_6dpi-2

description: Library name: 13375-NN-133


title: drug_controlH17

tag: condition


title: hapo_newborn_cordblood_A1637

value: newborn


title: hapo_newborn_cordblood_A1632

value: whole blood cells


title: ND_fed_CDI_Male_6dpi-5

description: Library name: 13375-NN-131

value: ND

tag: strain


title: hapo_newborn_cordblood_A1622

tag: developmental stage


title: treated_10H17


title: P3504_1004

description:
single cell library
Smart-Seq2

tag: tissue

value: lung epithelial secretory cells

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane

tag: s primer


title: P3504_1006

description:
single cell library
Smart-Seq2

tag: cell type

tag: genotype

value: WT


title: HFD_fed_CDI_male_6dpi-1

description: Library name: 13375-NN-132

tag: Sex

tag: treatment

tag: days post_infection


title: P7657_1140

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: isolation criteria

value: GFP^pos

tag: plate well

tag: internal number


title: hapo_newborn_cordblood_A1624


title: treated_100H17

tag: condition


title: mediumH13


title: infectedH13

value: infected


title: P3504_1005

description:
single cell library
Smart-Seq2

tag: strain

tag: developmental stage

tag: ercc spike-in_lot_no

value: single-end 50bp

tag: n primer


title: hapo_newborn_cordblood_A1602

value: Female

tag: tissue


title: P3504_1002

description:
single cell library
Smart-Seq2

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane

tag: s primer


title: hapo_newborn_cordblood_A1603

tag: Sex

tag: cell type


title: ND_fed_CDI_Male_6dpi-4

description: Library name: 13375-NN-130

value: Cecum

tag: diet

tag: treatment

tag: days post_infection


title: ND_fed_CDI_Male_6dpi-2

description: Library name: 13375-NN-128


title: ND_fed_CDI_Male_6dpi-3

description: Library name: 13375-NN-129


title: hapo_newborn_cordblood_A1605


title: P3504_1003

description:
single cell library
Smart-Seq2

tag: genotype

tag: individual

tag: sorting date

tag: isolation criteria

tag: plate well


title: hapo_newborn_cordblood_A1583

tag: developmental stage


title: mediumH11

tag: condition

value: medium


title: treated_10H13


title: uv_infectedH11


title: hapo_newborn_cordblood_A1579

value: Male

tag: tissue


title: HFD_fed_Mock_Male_6dpi-3

description: Library name: 13375-NN-125

value: HFD

value: Mock

tag: strain


title: treated_100H13


title: P3504_1001

description:
single cell library
Smart-Seq2

value: lung

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: internal number

tag: n primer


title: ND_fed_CDI_Male_6dpi-1

description: Library name: 13375-NN-127

tag: diet

tag: Sex

value: CDI


title: P2661_1047

description:
single cell library
Smart-Seq2

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: cell type

tag: lane

tag: s primer


title: hapo_newborn_cordblood_A1584

value: cord clood

value: newborn


title: HFD_fed_Mock_Male_6dpi-4

description: Library name: 13375-NN-126

tag: treatment

tag: days post_infection


title: P2661_1046

description:
single cell library
Smart-Seq2

tag: genotype

tag: individual

tag: sorting date

tag: isolation criteria

tag: plate well


title: P2661_1042

description:
single cell library
Smart-Seq2

tag: tissue

tag: strain

tag: developmental stage

tag: ercc spike-in_lot_no


title: hapo_newborn_cordblood_A1575

value: whole blood cells


title: hapo_newborn_cordblood_A1568


title: treated_100H11

tag: condition


title: P2661_1045

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

tag: cdna library_preparation_date

tag: type of_sequencing

tag: internal number

tag: n primer


title: infectedH11


title: HFD_fed_Mock_Male_6dpi-1

description: Library name: 13375-NN-123

tag: diet

tag: Sex


title: HFD_fed_Mock_Male_6dpi-2

description: Library name: 13375-NN-124

tag: treatment

tag: days post_infection


title: hapo_newborn_cordblood_A1570

tag: cell type


title: treated_10H11


title: drug_controlH11


title: ND_fed_Mock_Male_6dpi-1

description: Library name: 13375-NN-119

value: ND


title: P2661_1039

description:
single cell library
Smart-Seq2

tag: genotype

value: WT

tag: individual

tag: sorting date

value: GFP^pos

tag: lane

tag: s primer


title: P2661_1038

description:
single cell library
Smart-Seq2

tag: tissue

tag: strain

tag: developmental stage

tag: isolation criteria

value: single-end 50bp

tag: plate well


title: P2661_1043

description:
single cell library
Smart-Seq2

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: internal number


title: P2661_1040

description:
single cell library
Smart-Seq2

tag: n primer


title: ND_fed_Mock_Male_6dpi-4

description: Library name: 13375-NN-122

tag: diet

tag: Sex

tag: treatment

tag: days post_infection


title: hapo_newborn_cordblood_A1563

value: Female

tag: cell type


title: hapo_newborn_cordblood_A1559


title: hapo_newborn_cordblood_A1523


title: ND_fed_Mock_Male_6dpi-3

description: Library name: 13375-NN-121

value: Cecum


title: Cortex specimen, glioblastoma patient 36

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

description: Gene expression profiling of cerebral cortex specimen with glioblastoma

hyb_protocol: For hybridization, 15 µg of fragmented cRNA were incubated with the chip (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array) in 200 µl of the hybrization solution in a Hybridization Oven 640 (Affymetrix) for 16 h at 45 °C. GeneChips were then washed and stained using the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual (Rev. 5).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing:
The signals were processed using Affymetrix GeneChip Operating Software (GCOS; v.1.4; Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 300.
The matrix table shows individual probe set intensities after scaling. The trimmed mean signal of each array was scaled to a target intensity of 300 with the Affymetrix GeneChip Operating Software (GCOS, v. 1.4., Affymetrix).

source_name: Cerebral cortex - glioblastoma

label_protocol: Biotinylated cRNA was prepared according to the protocol of the manufacturer (Affymetrix; GeneChip Expression Analysis Technical Manual; Rev. 5).

growth_protocol: Cerebral cortex specimens were taken in frame of surgery for glioblastoma from 12 patients.

extract_protocol: Total RNA was isolated from RNAlater stabilized brain tumor specimens with the RNeasy Minii kit according to the manufacturer`s instructions (Qiagen).

treatment_protocol: Patients were not treated.

tag: subject id

tag: gender

value: female

tag: age (years)

tag: dementia (likely due to ad)

value: No

value: Cerebral cortex - glioblastoma


title: hapo_newborn_cordblood_A1540

value: Male

tag: tissue

tag: developmental stage


title: ND_fed_Mock_Male_6dpi-2

description: Library name: 13375-NN-120

value: Mock

tag: strain


title: P2661_1037

description:
single cell library
Smart-Seq2

value: lung

tag: genotype

tag: individual

tag: sorting date

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: lane

tag: plate well

tag: s primer


title: Cortex specimen, glioblastoma patient 37


title: hapo_newborn_cordblood_A1514

tag: Sex


title: P2661_1033

description:
single cell library
Smart-Seq2

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: cell type

tag: cdna library_preparation_date

tag: type of_sequencing

tag: internal number

tag: n primer


title: HFD_fed_CDI_female_6dpi_5

description: Library name: 13375-NN-118

tag: tissue

tag: diet

value: HFD

tag: treatment

value: CDI

tag: days post_infection


title: Cortex specimen, glioblastoma patient 35

tag: subject id

tag: gender

tag: age (years)

tag: dementia (likely due to ad)


title: HFD_fed_CDI_female_6dpi_4

description: Library name: 13375-NN-117

tag: strain


title: hapo_newborn_cordblood_A1521

value: cord clood

tag: developmental stage

value: newborn

value: whole blood cells


title: P2661_1032

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

tag: genotype

value: WT

tag: individual

tag: sorting date

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: lane

tag: plate well

tag: s primer


title: HFD_fed_CDI_female_6dpi_3

description: Library name: 13375-NN-116

tag: tissue

tag: diet

tag: Sex


title: HFD_fed_CDI_female_6dpi_1

description: Library name: 13375-NN-114

tag: treatment

tag: days post_infection


title: Cortex specimen, glioblastoma patient 34

tag: subject id

tag: gender

tag: age (years)


title: Cortex specimen, glioblastoma patient 38

tag: dementia (likely due to ad)


title: hapo_newborn_cordblood_A1512

tag: developmental stage

tag: cell type


title: P2661_1029

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

tag: individual

tag: sorting date

value: GFP^pos

tag: cdna library_preparation_date

tag: type of_sequencing

value: single-end 50bp

tag: internal number

tag: n primer


title: P2661_1031

description:
single cell library
Smart-Seq2

tag: tissue

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: lane

tag: plate well

tag: s primer


title: Cortex specimen, glioblastoma patient 31

tag: subject id

tag: gender

tag: age (years)

tag: dementia (likely due to ad)


title: P2661_1028

description:
single cell library
Smart-Seq2

tag: strain

tag: cell type

tag: genotype

tag: developmental stage


title: Cortex specimen, glioblastoma patient 33

value: male


title: HFD_fed_CDI_female_6dpi_2

description: Library name: 13375-NN-115

value: Cecum

tag: diet

tag: Sex

value: Female

tag: treatment

tag: days post_infection


title: hapo_newborn_cordblood_A1511

tag: tissue


title: P2661_1030

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: internal number

tag: n primer


title: P2661_1027

description:
single cell library
Smart-Seq2

tag: strain

tag: lane

tag: plate well

tag: s primer


title: ND_fed_CDI_Female_6dpi-5

description: Library name: 13375-NN-113

tag: diet

value: ND


title: hapo_newborn_cordblood_A1503

tag: Sex

value: Male

tag: developmental stage

tag: cell type


title: hapo_newborn_cordblood_A1509

tag: tissue


title: hapo_newborn_cordblood_A1500


title: ND_fed_CDI_Female_6dpi-2

description: Library name: 13375-NN-110

tag: treatment

tag: days post_infection


title: Cortex specimen, glioblastoma patient 32

tag: subject id

tag: gender

value: female

tag: age (years)

tag: dementia (likely due to ad)

value: No

value: Cerebral cortex - glioblastoma


title: ND_fed_CDI_Female_6dpi-3

description: Library name: 13375-NN-111


title: Cortex specimen, glioblastoma patient 30

value: Yes


title: P2661_1025

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: genotype

tag: individual

tag: sorting date

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: internal number


title: ND_fed_CDI_Female_6dpi-1

description: Library name: 13375-NN-109

tag: diet

tag: Sex

value: CDI

tag: strain


title: Cortex specimen, glioblastoma patient 29

tag: tissue


title: Cortex specimen, glioblastoma patient 27


title: P2661_1026

description:
single cell library
Smart-Seq2

tag: cell type

tag: developmental stage

tag: lane

tag: plate well

tag: n primer

tag: s primer


title: ND_fed_CDI_Female_6dpi-4

description: Library name: 13375-NN-112

tag: treatment

tag: days post_infection


title: hapo_newborn_cordblood_A1477

value: cord clood

value: newborn

value: whole blood cells


title: Cortex specimen, glioblastoma patient 28

tag: subject id

tag: gender

tag: age (years)

tag: dementia (likely due to ad)


title: hapo_newborn_cordblood_A1497


title: hapo_newborn_cordblood_A1495


title: hapo_newborn_cordblood_A1446


title: HFD_fed_Mock_female_6dpi-1

description: Library name: 13375-NN-105

value: HFD

value: Mock


title: HFD_fed_Mock_female_6dpi-2

description: Library name: 13375-NN-106


title: P2661_1021

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

tag: genotype

value: WT

tag: individual

tag: sorting date

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

value: single-end 50bp

tag: internal number


title: HFD_fed_Mock_female_6dpi-4

description: Library name: 13375-NN-108

tag: tissue

value: Cecum

tag: diet

tag: Sex

value: Female

tag: strain


title: P2661_1020

description:
single cell library
Smart-Seq2

tag: cell type

tag: developmental stage

tag: lane

tag: plate well

tag: n primer

tag: s primer


title: P2661_1024

description:
single cell library
Smart-Seq2

tag: genotype

tag: individual


title: Cortex specimen, glioblastoma patient 23

data_processing:
The signals were processed using Affymetrix GeneChip Operating Software (GCOS; v.1.4; Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 200.
The matrix table shows individual probe set intensities after scaling. The trimmed mean signal of each array was scaled to a target intensity of 200 with the Affymetrix GeneChip Operating Software (GCOS, v. 1.4., Affymetrix).

growth_protocol: Cerebral cortex specimens were taken in frame of surgery for glioblastoma from 16 patients.

tag: subject id

tag: gender

value: male

tag: age (years)

tag: dementia (likely due to ad)

value: No


title: P2661_1023

description:
single cell library
Smart-Seq2

tag: sorting date

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: internal number


title: Cortex specimen, glioblastoma patient 26

tag: tissue

value: Cerebral cortex - glioblastoma


title: Cortex specimen, glioblastoma patient 22

value: female


title: hapo_newborn_cordblood_A1443

tag: Sex

value: Male

tag: developmental stage

tag: cell type


title: HFD_fed_Mock_female_6dpi-3

description: Library name: 13375-NN-107

tag: diet

tag: treatment

tag: days post_infection

tag: strain


title: hapo_newborn_cordblood_A1450


title: P2661_1019

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: genotype

tag: individual

tag: lane

tag: plate well

tag: n primer

tag: s primer


title: hapo_newborn_cordblood_A1449

value: cord clood

value: newborn


title: Cortex specimen, glioblastoma patient 25

tag: subject id

tag: gender

tag: age (years)

tag: dementia (likely due to ad)


title: P2661_1022

description:
single cell library
Smart-Seq2

tag: tissue

tag: sorting date

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: internal number


title: ND_fed_Mock_Female_6dpi-3

description: Library name: 13375-NN-103

tag: diet

value: ND

tag: Sex

tag: treatment

tag: days post_infection

tag: strain


title: ND_fed_Mock_Female_6dpi-4

description: Library name: 13375-NN-104

value: Mock


title: P2661_1013

description:
single cell library
Smart-Seq2

tag: cell type

value: lung epithelial secretory cells

tag: genotype

tag: developmental stage

tag: individual

tag: lane

tag: plate well

tag: n primer

tag: s primer


title: ND_fed_Mock_Female_6dpi-2

description: Library name: 13375-NN-102

tag: tissue


title: Cortex specimen, glioblastoma patient 24

tag: subject id

tag: gender

tag: age (years)

tag: dementia (likely due to ad)


title: P2661_1011

description:
single cell library
Smart-Seq2

value: WT

tag: sorting date

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: internal number


title: Cortex specimen, glioblastoma patient 20


title: hapo_newborn_cordblood_A1418

tag: Sex

tag: developmental stage

tag: cell type

value: whole blood cells


title: ND_fed_Mock_Female_6dpi-1

description: Library name: 13375-NN-101

tag: diet

tag: treatment

tag: days post_infection

tag: strain


title: P2661_1010

description:
single cell library
Smart-Seq2

tag: tissue

tag: genotype

tag: individual

value: GFP^pos

value: single-end 50bp

tag: lane

tag: plate well

tag: n primer

tag: s primer


title: hapo_newborn_cordblood_A1437


title: hapo_newborn_cordblood_A1439

value: Female


title: Cortex specimen, glioblastoma patient 19

tag: subject id

tag: gender

tag: age (years)

tag: dementia (likely due to ad)


title: Cortex specimen, glioblastoma patient 17

value: male


title: Myc_ESC_DMSO_rep3

city: New York

first: UkJin

last: Lee

state: NY

address: 413 E 69th St

department: Sanford I. Weill Department of Medicine

institute: Weill Cornell Medicine

description:
Library name: Myc_ESC_DMSO_rep3
Weill Cornell Medicine Genomics Resources Core Facility

data_processing:
Adapters were trimmed from paired-end reads using cutadapt (v4.8) with the following options: -j 0 -e 0.15 -m 40.
Filtered reads were aligned to the mouse genome (mm10) and normalized using  Pipe4C pipeline (Krijger P.H.L., Methods, 2020, PMID: 31351925).
Reads were depth normalized to 1 million cis reads, excluding the top 3 fragments with the highest reads aligned. Smoothening was performed using only non-blind fragments, with sliding bin normalization. Bin sizes of 5 kb were used for Klf4, and 10 kb Tbx3, Myc, and Fosl2, with a bin shift size of 1/20 of the bin size. Visualization of the 4C-seq data was done in R using ggplot2.
Assembly: mm10
Supplementary files format and content: ".bigWig" for 4C-seq tracks.
Library strategy: 4C-Seq

source_name: RAD21-dTAG cell line (Bruce-4 derived)

growth_protocol: RAD21-dTAG cells were cultured at 37˚C on gelatinized plate in serum/2i/LIF medium. Cells were harvested by treating with Trypsin-EDTA for 3 min, washed with PBS, and centrifuged at 300 × g for 5 min at 4˚C. 2,000,000 cells per replicate were fixed with 1% w/v formaldehyde for 10 min at room temperature (RT) on a platform shaker, followed by quenching with 125 mM glycine for 5 minutes under the same conditions. Crosslinked cells were centrifuged at 500 × g for 5 min at 4˚C and were washed twice with ice-cold PBS. After the final wash and centrifuge, the pellet was snap-frozen before extraction.

extract_protocol:
The cell pellets were washed twice in PBS and resuspended in 300 μL of lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630, and 1X cOmplete EDTA-free protease inhibitor cocktail) and incubated on ice for 20 min. Following centrifugation at 500 × g for 5 min at 4˚C, the pellet was resuspended in 50 μL of 0.5% SDS and incubated at 65˚C for 10 min on a shaker at 1,250 rpm. SDS was quenched by adding 150 μL of ddH2O and 25 μL of 10% v/v Triton X-100 at 37˚C for 15 min on a shaker at 1,250 rpm.
To initiate the first digestion, 25 μL of NEBuffer DpnII and 10 µL of DpnII enzyme were added, and the samples were incubated overnight at 37˚C on a shaker at 750 rpm. The following morning, an additional 2 µL of DpnII was added, and the samples were incubated for 2 hr. Digestion efficiency was confirmed using gel electrophoresis. The enzyme was then inactivated by incubating at 65˚C for 20 min. Once the samples cooled down, 645 µL of ddH2O, 120 µL of 10X T4 DNA ligase reaction buffer, 120 µL of 10% v/v Triton X-100, 12 µL of 10 mg/mL BSA, 1 µL of 2000 U/µL T4 DNA ligase, and 60 µL of 10 mM ATP were added to the samples. The ligation reaction was incubated overnight at 16˚C in a water bath in a cold room. The following morning, 0.5 µL of 2000 U/µL T4 DNA ligase and 30 µL of 10 mM ATP were added, and the samples were incubated at RT with rotation until the ligation efficiency was verified using gel electrophoresis. After confirming successful ligation, 60 µL of 20 mg/mL Proteinase K and 120 µL of 10% v/v SDS were added, and the samples were incubated at 65˚C for 3 min. Then, 130 µL of 5 M NaCl was added, and the samples were incubated overnight at 65˚C on a shaker at 5,000 rpm for reverse crosslinking. The following morning, 10 µL of 10 mg/mL RNase A was added, and the samples were incubated at 37˚C for 1 h. DNA was purified using phenol-chloroform extraction and ethanol precipitation, and the pellet was dissolved in 100 µL of 10 mM Tris-HCl pH 8.0. The second digestion was performed by adding 20 µL of 10X Buffer B, 10 µL of 10 U/µL Csp6I, and 80 µL of ddH2O, and incubating overnight at 37˚C on a shaker at 700 rpm. After confirming digestion efficiency the next morning, a second ligation was performed by adding 2,204 µL of ddH2O, 300 µL of 10X T4 DNA ligase buffer, 1 µL of 2000 U/mL T4 DNA ligase, and 300 µL of 10 mM ATP. The reaction was incubated overnight at 16˚C in a water bath in a cold room. DNA was purified using phenol-chloroform extraction and ethanol precipitation, resulting in the 4C template. Primers for 4C libraries were designed around the transcription start site of each gene of interest according to previously described criteria.60 Libraries were generated from the 4C template using the inverse PCR strategy. Briefly, the first round of PCR was performed in quadruplicate per sample, with 150 ng of 4C template used for each reaction in the quadruplicate, employing Expand Long Template PCR system. The PCR products were pooled to increase the library complexity. A second round of PCR was performed using the initial PCR library as a template, with overlapping primers to add P5/P7 sequencing primers and sample-specific indexes. SPRIselect beads were used for DNA size selection throughout the protocol.

treatment_protocol: 0.05% v/v DMSO or 500 nM dTAG.

tag: cell line

value: RAD21-dTAG cell line (Bruce-4 derived)

value: Mouse embryonic stem cell

tag: viewpoint

value: Myc

value: DMSO


title: hapo_newborn_cordblood_A1414

tag: Sex

tag: developmental stage

tag: cell type


title: Cortex specimen, glioblastoma patient 21

value: female

value: No

value: Cerebral cortex - glioblastoma


title: hapo_newborn_cordblood_A1434

value: cord clood

value: newborn


title: hapo_newborn_cordblood_A1429


title: hapo_newborn_cordblood_A1420

value: Male


title: P2661_1009

description:
single cell library
Smart-Seq2

value: lung

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

value: lung epithelial secretory cells

tag: sorting date

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: internal number


title: Cortex specimen, glioblastoma patient 16

value: Yes

tag: tissue


title: Tbx3_ESC_DMSO_rep2

description:
Library name: Tbx3_ESC_DMSO_rep2
Weill Cornell Medicine Genomics Resources Core Facility

tag: genotype

tag: treatment


title: Cortex specimen, glioblastoma patient 18

tag: subject id

tag: gender

tag: age (years)


title: Tbx3_ESC_dTAG_rep2

description:
Library name: Tbx3_ESC_dTAG_rep2
Weill Cornell Medicine Genomics Resources Core Facility

tag: cell line

tag: viewpoint

value: dTAG


title: Myc_ESC_dTAG_rep2

description:
Library name: Myc_ESC_dTAG_rep2
Weill Cornell Medicine Genomics Resources Core Facility


title: P2661_1008

description:
single cell library
Smart-Seq2

value: WT

tag: developmental stage

tag: individual

value: GFP^pos

value: single-end 50bp

tag: lane

tag: plate well

tag: n primer

tag: s primer


title: hapo_newborn_cordblood_A1410

tag: Sex

tag: cell type

value: whole blood cells


title: P2661_1004

description:
single cell library
Smart-Seq2

tag: strain

tag: sorting date

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: internal number


title: hapo_newborn_cordblood_A1409

value: Female

tag: tissue


title: P2661_1003

description:
single cell library
Smart-Seq2

tag: genotype


title: Klf4_ESC_dTAG_rep2

description:
Library name: Klf4_ESC_dTAG_rep2
Weill Cornell Medicine Genomics Resources Core Facility

tag: cell line

value: RAD21-dTAG cell line (Bruce-4 derived)

value: Mouse embryonic stem cell

tag: viewpoint

tag: treatment


title: P2661_1006

description:
single cell library
Smart-Seq2

tag: developmental stage

tag: individual

tag: lane

tag: plate well


title: Cortex specimen, glioblastoma patient 12

tag: subject id

tag: gender

value: female

tag: age (years)

tag: dementia (likely due to ad)

value: No


title: hapo_newborn_cordblood_A1407

tag: Sex

value: cord clood

tag: cell type


title: Cortex specimen, glioblastoma patient 13

value: Cerebral cortex - glioblastoma


title: P2661_1005

description:
single cell library
Smart-Seq2

tag: strain

tag: sorting date

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: n primer

tag: s primer


title: Myc_EpiLC_dTAG_rep2

description:
Library name: Myc_EpiLC_dTAG_rep2
Weill Cornell Medicine Genomics Resources Core Facility

tag: cell line

value: Mouse epiblast-like cell

tag: genotype

tag: viewpoint

value: Myc

tag: treatment


title: Myc_EpiLC_DMSO_rep3

description:
Library name: Myc_EpiLC_DMSO_rep3
Weill Cornell Medicine Genomics Resources Core Facility

value: DMSO


title: hapo_newborn_cordblood_A1399

value: Male

tag: tissue

tag: developmental stage

value: newborn


title: Cortex specimen, glioblastoma patient 11

tag: subject id

tag: gender

value: male

tag: age (years)

tag: dementia (likely due to ad)


title: P2272_1047

description:
single cell library
Smart-Seq2

value: lung

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: cell type

value: lung epithelial secretory cells

value: WT

tag: individual

tag: sorting date

value: pair-end 125bp

tag: lane

tag: plate well

tag: internal number


title: hapo_newborn_cordblood_A1396

tag: Sex

value: whole blood cells


title: Cortex specimen, glioblastoma patient 14


title: Fosl2_ESC_dTAG_rep2

description:
Library name: Fosl2_ESC_dTAG_rep2
Weill Cornell Medicine Genomics Resources Core Facility

tag: cell line

value: RAD21-dTAG cell line (Bruce-4 derived)

value: Mouse embryonic stem cell

tag: genotype

value: dTAG


title: Cortex specimen, glioblastoma patient 15

value: No


title: Fosl2_ESC_DMSO_rep2

description:
Library name: Fosl2_ESC_DMSO_rep2
Weill Cornell Medicine Genomics Resources Core Facility

tag: viewpoint

tag: treatment


title: hapo_newborn_cordblood_A1395

tag: tissue

value: cord clood

tag: developmental stage


title: Klf4_ESC_DMSO_rep3

description:
Library name: Klf4_ESC_DMSO_rep3
Weill Cornell Medicine Genomics Resources Core Facility


title: P2272_1045

description:
single cell library
Smart-Seq2

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: n primer

tag: s primer


title: Cortex specimen, glioblastoma patient 8

data_processing:
The signals were processed using Affymetrix GeneChip Operating Software (GCOS; v.1.4; Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 200.
The matrix table presents individual probe set intensities after scaling. The trimmed mean signal of each array was scaled to a target intensity of 200 with the Affymetrix GeneChip Operating Software (GCOS, v. 1.4., Affymetrix)

growth_protocol: Cerebral cortex specimens were taken in frame of surgery for glioblastoma from 10 patients.

extract_protocol: Total RNA was isolated from RNAlater-stabilized brain specimens with the RNeasy Minii kit according to the manufacturer`s instructions (Qiagen).

tag: subject id

tag: gender

value: female

tag: age (years)

tag: dementia (likely due to ad)

value: Yes

value: Cerebral cortex - glioblastoma


title: P2272_1046

description:
single cell library
Smart-Seq2

tag: strain

tag: cell type

tag: individual

tag: sorting date

tag: lane

tag: plate well

tag: internal number


title: Cortex specimen, glioblastoma patient 9

tag: tissue


title: Cortex specimen, glioblastoma patient 10


title: hapo_newborn_cordblood_A1394

tag: Sex

value: Female

tag: developmental stage

value: newborn


title: P2272_1043

description:
single cell library
Smart-Seq2

value: lung

tag: genotype

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing


title: Fosl2_EpiLC_DMSO_rep2

description:
Library name: Fosl2_EpiLC_DMSO_rep2
Weill Cornell Medicine Genomics Resources Core Facility

tag: cell line

value: Mouse epiblast-like cell

tag: viewpoint

tag: treatment

value: DMSO


title: Fosl2_EpiLC_dTAG_rep2

description:
Library name: Fosl2_EpiLC_dTAG_rep2
Weill Cornell Medicine Genomics Resources Core Facility

tag: cell type


title: Cortex specimen, glioblastoma patient 7

tag: subject id

tag: gender

value: male

tag: age (years)

tag: dementia (likely due to ad)


title: G1_ESC_dTAG_rep6

description:
Library name: G1_ESC_dTAG_rep6
Weill Cornell Medicine Genomics Resources Core Facility

data_processing:
Paired-end reads were aligned to the mouse genome (mm10) using BWA-MEM algorithm from bwa (v0.7.17) with the following options: -5SP -T0.
Parse module of pairtools (v1.1.0) was used to filter high-quality valid read pairs with the with the following options: --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30. Dedup module of pairtools (v1.1.0) was used to remove PCR duplicates, followed by split module to generate ‘pairs’ file.
Juicer (v1.22.01)  was then used to generate a contact matrix in ‘hic’ format from ‘pairs’ file. For downstream analysis, ‘hic’ format was converted to ‘mcool’ format using HicConvertFormat of HiCExplorer (v3.0.1).
TAD, Compartment
Assembly: mm10
Supplementary files format and content: TAD, Compartment

growth_protocol: RAD21-dTAG cells were cultured at 37˚C on gelatinized plate in serum/2i/LIF medium. Cells were harvested by treating with Trypsin-EDTA for 3 min, washed with PBS, and centrifuged at 300 × g for 5 min at 4˚C. 2,000,000 cells per replicate were collected and centrifuged at 300 × g for 5 min. The pellet was frozen at -80˚C for 30 min, thawed at RT, and resuspended in 1 mL PBS. Freshly prepared 10 µL of 0.3 M DSG (Sigma-Aldrich, 80424) in DMSO was added, and the samples were incubated with rotation at RT for 10 min. Subsequently, 27 µL of 37% formaldehyde (Sigma-Aldrich, 252549) was added, and the samples were incubated at RT for an additional 10 min. After centrifugation at 3,000 × g for 5 min at 4˚C, the pellets were washed with 200 µL of 1X wash buffer from Dovetail Micro-C kit (Cantata Bio, 210006). ESCs were treated with N2B27 media + FGF2/ActivinA for EpiLC differentiation

extract_protocol:
The pellet was resuspended in 200 µL of MB1 buffer (50 mM NaCl, 10 mM Tris-HCl pH7.5, 5 mM MgCl2, 1 mM CaCl2, 0.2% v/v NP-40 alternative (MilliporeSigma, 492016), 1 X cOmplete EDTA-free protease inhibitor cocktail in ddH2O) and incubated on ice for 20 min. The samples were centrifuged at 1,750 × g for 5 min at 4˚C, and the pellets were washed with 200 µL of MB1 buffer.
The nuclei pellets were then resuspended in 200 µL of MB1 buffer, and 28 U of MNase (Worthinigton Biochemical Corporation, LS004798) was added. After brief vortexing, the samples were incubated at 37˚C for 20 min on a shaker at 1,000 rpm. The amount of MNase to use was determined based on a separate titration experiment. The samples were transferred onto ice and 1.6 µL of 500 mM EGTA was added to stop the digestion. The reaction was further incubated at 65˚C for 10 min for complete inactivation of MNase. The samples were centrifuged at 170 × g for 5 min at 4˚C, and the pellets were washed with 1 mL MB2 (50 mM NaCl, 10 mM Tris-HCl pH 7.6, 10 mM MgCl2 in ddH2O). The pellets were resuspended in 50 µL of 1X Nuclease Digestion Buffer from Dovetail Micro-C kit. To lyse the nuclei, 3 µL of 20% v/v SDS was added, and the samples were incubated at 22˚C for 15 min on a shaker at 1,250 rpm. The rest of the steps in Micro-C library preparation, including lysate quality control, proximity ligation, library preparation, ligation capture, and library amplification, were performed following Dovetail Micro-C kit user guide v1.2.

treatment_protocol: 0.05% v/v DMSO, 500 nM dTAG, or 20 µM A485.


title: P2661_1001

description:
single cell library
Smart-Seq2

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

value: lung epithelial secretory cells

value: WT

tag: individual

tag: sorting date

value: single-end 50bp

tag: lane

tag: plate well

tag: internal number

tag: n primer

tag: s primer


title: hapo_newborn_cordblood_A1390

tag: Sex

tag: tissue

tag: developmental stage

value: whole blood cells


title: G1_ESC_dTAG_rep4

description:
Library name: G1_ESC_dTAG_rep4
Weill Cornell Medicine Genomics Resources Core Facility

tag: cell line

value: RAD21-dTAG cell line (Bruce-4 derived)

value: Mouse embryonic stem cell

tag: genotype

tag: treatment

value: dTAG


title: hapo_newborn_cordblood_A1391

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

value: Male

value: cord clood

tag: cell type


title: Cortex specimen, glioblastoma patient 5

tag: subject id

tag: gender

value: female

tag: age (years)

value: No

value: Cerebral cortex - glioblastoma


title: hapo_newborn_cordblood_A1385

value: Female

value: newborn


title: Cortex specimen, glioblastoma patient 4

tag: dementia (likely due to ad)


title: G1_ESC_A485_rep6

description:
Library name: G1_ESC_A485_rep6
Weill Cornell Medicine Genomics Resources Core Facility


title: Cortex specimen, glioblastoma patient 6

description: Gene expression profiling of cerebral cortex specimen with glioblastoma


title: G1_ESC_A485_rep5

description:
Library name: G1_ESC_A485_rep5
Weill Cornell Medicine Genomics Resources Core Facility


title: P2272_1042

description:
single cell library
Smart-Seq2

value: lung

tag: strain

tag: individual

tag: sorting date

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

value: pair-end 125bp


title: Cortex specimen, glioblastoma patient 3

tag: tissue


title: G1_ESC_dTAG_rep5

description:
Library name: G1_ESC_dTAG_rep5
Weill Cornell Medicine Genomics Resources Core Facility


title: P2272_1038

description:
single cell library
Smart-Seq2

value: Scgb1a1CREERT2; Rosa26R-fGFP

value: lung epithelial secretory cells

tag: developmental stage

tag: lane

tag: plate well

tag: internal number

tag: n primer

tag: s primer


title: hapo_newborn_cordblood_A1389

tag: Sex

tag: cell type


title: hapo_newborn_cordblood_A1375


title: G1_ESC_A485_rep4

description:
Library name: G1_ESC_A485_rep4
Weill Cornell Medicine Genomics Resources Core Facility

tag: cell line

tag: genotype

tag: treatment


title: Cortex specimen, glioblastoma patient 1

tag: subject id

tag: gender

tag: age (years)

tag: dementia (likely due to ad)

value: Yes


title: P2272_1040

description:
single cell library
Smart-Seq2

tag: strain

value: WT

tag: individual

tag: sorting date

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing


title: P2272_1041

description:
single cell library
Smart-Seq2

tag: tissue

tag: developmental stage

tag: lane

tag: plate well

tag: internal number

tag: n primer

tag: s primer


title: P2272_1036

description:
single cell library
Smart-Seq2

tag: cell type

tag: genotype


title: G1_EpiLC_dTAG_rep4

description:
Library name: G1_EpiLC_dTAG_rep4
Weill Cornell Medicine Genomics Resources Core Facility

tag: cell line

value: RAD21-dTAG cell line (Bruce-4 derived)

value: Mouse epiblast-like cell

tag: treatment


title: hapo_newborn_cordblood_A1381

tag: Sex

value: whole blood cells


title: P2272_1037

description:
single cell library
Smart-Seq2

tag: strain

tag: individual

tag: sorting date


title: CCseq_MJ1438B_sae2Dxrs2-11_6h_rep1

city: Brighton

first: Jon

middle: Alexander

last: Harper

address: School of Life Sciences, John Maynard Smith Building, University of Sussex, Falmer

department: Genome Damage and Stability Centre

institute: University of Sussex

description: Library name: MATa/alpha ho::LYS2/’, lys2/’, ura3/’, arg4-nsp/’, leu2::hisG/’, his4X::LEU2/’, nuc1::LEU2/’, xrs2-11/’, sae2∆::KanMX6/’ rep2

data_processing:
FASTQ reads were aligned to the reference genome (SacCer3H4L2; which includes the HIS4::LEU2 and leu2::hisG loci inserted into the Cer3 S. cerevisiae genome build as described in Gittens 2019) via Bowtie2, using TermMapper as previously described in Gittens 2019 (https://github.com/Neale-Lab/terminalMapper) Assembly: SacCer3H4L2 which includes the HIS4::LEU2 and leu2::hisG loci inserted into the Cer3 R64 S. cerevisiae genome build Supplementary files format and content: Sparse table of positions (Pos) of read frequencies of 5' ends of Read 1 molecules mapping to the top (Watson) and bottom (Crick) strand of each chromosome (Chrom) of the reference genome Library strategy: CC-seq
Assembly: SacCer3H4L2 which includes the HIS4::LEU2 and leu2::hisG loci inserted into the Cer3 R64 S. cerevisiae genome build
Supplementary files format and content: FASTQ paired reads

organism: Saccharomyces cerevisiae

growth_protocol: For meiosis induction, a single colony was inoculated in 4mL of YPD medium (1% yeast extract, 2% peptone, 2% glucose supplemented with 0.5 mM adenine and 0.4 mM uracil) and incubated at 30 °C, 250 rpm for a day to reach saturation, then diluted to OD600 of 0.2 in a volume of 200 mL of either YPA (1% yeast extract, 2% peptone, 1% potassium acetate) or SPS (0.5% yeast extract, 1% peptone, 0.67% Yeast Nitrogen Base without amino acids, 1% potassium acetate, 0.05M Potassium Hydrogen phthalate, 0.001% Antifoam 204) pre-sporulation medium. Cultures were incubated at 30 °C, 250 rpm for 14–16 hours, then washed and resuspended in 200 mL pre-warmed SPM sporulation medium (2% potassium acetate supplemented with diluted amino acids) and incubated at 30°C, 250rpm for the duration of the time course.

extract_protocol:
Protein-DNA Covalent-Complex Mapping (CC-seq) in yeast followed a method previously described (Gittens 2019). Briefly, meiotic cell samples are chilled and frozen at -20˚C for at least 8 hours, then thawed and spheroplasted (in 1 M sorbitol, 50 mM NaHPO4, 10 mM EDTA, 30 min at 37˚C), fixed in 70% ice-cold ethanol, collected by centrifugation, dried briefly, then lysed in STE (2% SDS, 0.5 M Tris, 10 mM EDTA). Genomic DNA was extracted via Phenol/Chloroform/IAA extraction (25:24:1 ratio) at room temperature, with aqueous material carefully collected, precipitated with ethanol, washed, dried, then resuspended in 1xTE buffer (10 mM Tris/1 mM EDTA). Total genomic DNA was sonicated to <500 bp average length using a Covaris M220 before equilibrating to a final concentration of 0.3 M NaCl, 0.1% TritonX100, 0.05% Sarkosyl. Covalent complexes were enriched on silica columns (Qiagen) via centrifugation, washed with TEN solution (10 mM Tris / 1 mM EDTA / 0.3 M NaCl), before eluted with TES buffer (10 mM Tris / 1 mM EDTA / 1% SDS). Samples were treated with Proteinase K at 50˚C, and purified by ethanol precipitation.
DNA ends were filled and repaired using NEB Ultra II end-repair module (NEB #E7645), with adapters ligated sequentially to the sonicated, then blocked, ends with recombinant TDP2 treatment in between these steps to remove the 5-phosphotyrosyl-linked Spo11 peptide. Ampure bead cleanups were used to facilitate sequential reactions. PCR-amplified libraries were quantified on a Bioanalyser and appropriately diluted and multiplexed for deep sequencing (Illumina MiSeq 2x75 bp).

treatment_protocol: 50 mL of culture was taken at t = 6 hours. Samples were centrifuged at 3000 x g for 5 minutes, supernatant discarded and pellet frozen at -20 °C until use.

value: Meiotic

value: 6 hour


title: CCseq_MJ1439A_sae2Dxrs2KF_6h_rep1

description: Library name: MATa/alpha ho::LYS2/’, lys2/’, ura3/’, arg4-nsp/’, leu2::hisG/’, his4X::LEU2/’, nuc1::LEU2/’, xrs2 K846A/F847A::KANMX6/’, sae2∆::KanMX6/’ tep1


title: CCseq_MJ1439B_sae2Dxrs2KF_6h_rep1

description: Library name: MATa/alpha ho::LYS2/’, lys2/’, ura3/’, arg4-nsp/’, leu2::hisG/’, his4X::LEU2/’, nuc1::LEU2/’, xrs2 K846A/F847A::KANMX6/’, sae2∆::KanMX6/’ rep2


title: hapo_newborn_cordblood_A1374

value: Male

value: cord clood


title: hapo_newborn_cordblood_A1368


title: P2272_1035

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date


title: hapo_newborn_cordblood_A1370

tag: tissue

tag: developmental stage


title: Cortex specimen, glioblastoma patient 2

tag: subject id

tag: gender

value: female

tag: age (years)

tag: dementia (likely due to ad)

value: No

value: Cerebral cortex - glioblastoma


title: P2272_1033

description:
single cell library
Smart-Seq2

value: lung

tag: cell type

tag: type of_sequencing

tag: lane

tag: plate well

tag: internal number

tag: n primer

tag: s primer


title: G1_EpiLC_dTAG_rep3

description:
Library name: G1_EpiLC_dTAG_rep3
Weill Cornell Medicine Genomics Resources Core Facility

tag: cell line

tag: genotype

tag: treatment

value: dTAG


title: hapo_newborn_cordblood_A1356

tag: Sex

value: newborn


title: G1_EpiLC_dTAG_rep2

description:
Library name: G1_EpiLC_dTAG_rep2
Weill Cornell Medicine Genomics Resources Core Facility


title: CCseq_MJ1438A_sae2Dxrs2-11_6h_rep1

description: Library name: MATa/alpha ho::LYS2/’, lys2/’, ura3/’, arg4-nsp/’, leu2::hisG/’, his4X::LEU2/’, nuc1::LEU2/’, xrs2-11/’, sae2∆::KanMX6/’ rep1

tag: tissue


title: hapo_newborn_cordblood_A1365

tag: developmental stage


title: hapo_newborn_cordblood_A1340


title: CCseq_LLR22_sae2Dndt80DSPO11-GBDtel1D_6h_rep1

description: Library name: MATa/alpha ho::LYS2, lys2, ura3, arg4-nsp, leu2::hisG, gal4::natMX, spo11::URA3, trp1::pREC8-GAL4BD-SPO11-TRP1, sae2::KanMX4, tel1::HpHMX4,ndt80∆::LEU2


title: P2272_1027

description:
single cell library
Smart-Seq2

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: individual

tag: sorting date

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

value: pair-end 125bp


title: G1_EpiLC_DMSO_rep4

description:
Library name: G1_EpiLC_DMSO_rep4
Weill Cornell Medicine Genomics Resources Core Facility

tag: cell type

value: DMSO


title: P2272_1028

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

value: WT

tag: type of_sequencing

tag: lane

tag: plate well


title: P2272_1031

description:
single cell library
Smart-Seq2

tag: internal number

tag: n primer

tag: s primer


title: G1_EpiLC_DMSO_rep3

description:
Library name: G1_EpiLC_DMSO_rep3
Weill Cornell Medicine Genomics Resources Core Facility

tag: cell line

value: RAD21-dTAG cell line (Bruce-4 derived)

value: Mouse epiblast-like cell

tag: genotype

tag: treatment


title: CCseq_LLR22_sae2Dndt80DSPO11-GBDtel1D_6h_rep2

description: Library name: MATa/alpha ho::LYS2, lys2, ura3, arg4-nsp, leu2::hisG, gal4::natMX, spo11::URA3, trp1::pREC8-GAL4BD-SPO11-TRP1, sae2::KanMX4, tel1::HpHMX4,ndt80∆::LEU4

tag: tissue

value: Meiotic

value: 6 hour


title: hapo_newborn_cordblood_A1334

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

tag: Sex

value: Male

value: cord clood

tag: developmental stage

value: whole blood cells


title: P2272_1029

description:
single cell library
Smart-Seq2

tag: strain

tag: individual

tag: sorting date


title: P2272_1025

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date


title: G1_EpiLC_DMSO_rep2

description:
Library name: G1_EpiLC_DMSO_rep2
Weill Cornell Medicine Genomics Resources Core Facility

tag: cell type


title: CCseq_MJ1099_sae2Dndt80Dtel1kd_6h_rep1

description: Library name: MATa/alpha ho::LYS2/’, lys2/’, ura3/’, arg4-nsp/’, leu2::hisG/’, his4X::LEU2/’, nuc1::LEU2/’, sae2∆::KanMX4/’, ndt80∆::LEU2/’, tel1-D2612A, N2617A, D2631A/’


title: CCseq_LLR19_sae2Dndt80DSPO11-GBD_6h_rep2

description: Library name: MATa/alpha ho::LYS2, lys2, ura3, arg4-nsp, leu2::hisG, gal4::natMX, spo11::URA3, trp1::pREC8-GAL4BD-SPO11-TRP1, sae2::KanMX4,  ndt80∆::LEU4


title: hapo_newborn_cordblood_A1333


title: hapo_newborn_cordblood_A1322


title: CCseq_LLR19_sae2Dndt80DSPO11-GBD_6h_rep1

description: Library name: MATa/alpha ho::LYS2, lys2, ura3, arg4-nsp, leu2::hisG, gal4::natMX, spo11::URA3, trp1::pREC8-GAL4BD-SPO11-TRP1, sae2::KanMX4,  ndt80∆::LEU2


title: P2272_1024

description:
single cell library
Smart-Seq2

tag: type of_sequencing

tag: lane

tag: plate well


title: G1_EpiLC_dTAG_rep1

description:
Library name: G1_EpiLC_dTAG_rep1
Weill Cornell Medicine Genomics Resources Core Facility


title: P2272_1026

description:
single cell library
Smart-Seq2

tag: internal number

tag: n primer

tag: s primer


title: P2272_1023

description:
single cell library
Smart-Seq2

tag: genotype


title: OVSAHO, STAT3 siRNA + IFNγ, Rep3

city: Rochester

first: Esther

last: Rodman

state: Minnesota

address: 200 1st St SW

institute: Mayo Clinic

description:
Library name: OVSAHO_STAT3_siRNA_IFNY_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

data_processing:
Reads were aligned using STAR (version 2.7.3a) and featureCounts (version 2.8.2) was used to assign mapped reads. Any gene with an RPKM < 1 in all samples were considered to be lowly expressed and removed from further analysis.
Assembly: hg38
Supplementary files format and content: .xlsx table file including raw counts and RPKM values for each sample

source_name: cell line

growth_protocol: MDAH and OVSAHO cells were maintained in phenol red free RPMI (#11835050, Gibco), containing 10% (v/v) FBS (#900-308, Gemini Bioproducts) and 1% (v/v) antibiotic/antimycotic (#15240-062, Gibco)

extract_protocol:
Total RNA was isolated using the Qiagen miRNeasy mini kit (#217004, Qiagen)
LibTruSeqStrmRNAv2(TSMRN)

treatment_protocol: MDAH and OVSAHO cells were plated at a density of 100,000 cells per well in 6 well plates and after 24 hours were transfected with 5 nM non-targeting (control), STAT1, or STAT3 siRNA with the addition of 5 nM Dharmafect Reagent 1 (Dharmacon) following the manufacture’s guidelines. Following 72 hours of transfection, siRNA containing media was removed and cells were treated with 30 ng/mL IL6, 10 ng/mL IFNγ, or vehicle (PBS) for 2 hours.

tag: tissue

value: cell line

tag: cell line

value: OVSAHO

value: High grade serous ovarian cancer

tag: treatment

value: STAT3 siRNA + IFNγ


title: OVSAHO, STAT3 siRNA + IFNγ, Rep2

description:
Library name: OVSAHO_STAT3_siRNA_IFNY_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: G1_EpiLC_DMSO_rep1

description:
Library name: G1_EpiLC_DMSO_rep1
Weill Cornell Medicine Genomics Resources Core Facility


title: P2272_1022

description:
single cell library
Smart-Seq2

value: lung

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: developmental stage


title: hapo_newborn_cordblood_A1318

tag: Sex

value: newborn


title: P2272_1021

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: isolation criteria

value: GFP^pos

value: pair-end 125bp


title: hapo_newborn_cordblood_A1290

tag: cell type


title: OVSAHO, STAT3 siRNA + Veh, Rep3

description:
Library name: OVSAHO_STAT3_siRNA_Veh_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: WT

value: STAT3 siRNA + Veh


title: P2272_1020

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing


title: hapo_newborn_cordblood_A1287


title: hapo_newborn_cordblood_A1310

value: Female


title: OVSAHO, STAT3 siRNA + Veh, Rep2

description:
Library name: OVSAHO_STAT3_siRNA_Veh_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: H3K4me3_EpiLC_rep2

description:
Library name: H3K4me3_EpiLC_rep2
Weill Cornell Medicine Genomics Resources Core Facility

data_processing:
Adapters were trimmed off from paired-end reads using bbduk.sh (v2.4.5) with the following option: ktrim=r ref=adapters rcomp=t tpe=t tbo=t hdist=1 mink=11.
Filtered reads were aligned to the mouse genome (mm10) using bowtie2 (v2.4.5) with the options --local --sensitive-local --no-unal.
PCR duplicates were removed using MarkDuplicates module from picard (v2.27.4) with the following option: --VALIDATION_STRINGENCY=LENIENT.
Bedtools (v2.30.0) was used to remove reads overlapping with blacklist region and convert data to ‘bedgraph’ format. BedGraphToBigWig module from kentUtil was used to convert data to ‘bigWig’ format. Peaks were called with macs2 callpeak with ‘--call-summits’ option.
Assembly: mm10
Supplementary files format and content: ".bigWig" for ChIP-exo tracks. ".bed" for narrow peaks.

growth_protocol: Bruce-4 cells were cultured at 37˚C on gelatinized plate in serum/2i/LIF medium. Cells were harvested by treating with Trypsin-EDTA for 3 min, washed with PBS, and centrifuged at 300 × g for 5 min at 4˚C. 10,000,000 cells per replicate were fixed with 1% w/v formaldehyde for 10 min at room temperature (RT) on a platform shaker, followed by quenching with 125 mM glycine for 5 minutes under the same conditions. Crosslinked cells were centrifuged at 500 × g for 5 min at 4˚C and were washed twice with ice-cold PBS. After the final wash and centrifuge, the pellet was snap-frozen before extraction.

extract_protocol:
Briefly, Bruce-4 cells were crosslinked in 1 % w/v formaldehyde at room temperature for 10 min and quenched with 125 mM glycine for 5 min at room temperature. Crosslinked cells were centrifuged at 1250rcf for 5 min at 4 ˚C and were washed twice with ice-cold PBS before snap-freezing. The cells were used for Rad21 ChIP (10 x 106), H3K27ac ChIP (15 x 106) and H3K4me3 ChIP (15 x 106). 5% of 1% fixed human MelI ESCs were added as a spike-in. For the Rad21 ChIP the cells were lysed in 1 ml cold cell lysis buffer (10 mM Tris pH 8.0, 10 mM NaCl and 0.2 % NP-40/Igepal (Sigma, I8896-50ML)) supplemented with protease inhibitors (Roche, 4693132001) for 20 min on ice. Nuclei were pelleted at 800g for 5 min, resuspended in 300 ul nuclear lysis buffer (50 mM Tris pH 8.0, 0.5% SDS and 10 mM EDTA) containing protease inhibitors and incubated on ice for 20 min as previously described.93  For the H3K27ac and H3K4me3 ChIP, cells were lysed in 300 ul lysis buffer (10 mM Tris pH 8, 1 mM EDTA and 0.5% SDS (Sigma, 05030-500ml-F) supplemented with protease inhibitors and incubated on ice for 20 min. The cells were sonicated in a Bioruptor device (30 s on/off; high setting) and spun down at the maximum speed for 15 min at 4 ˚C. The supernatants were precleared under rotation for 1h at 4 ˚C with protein G Dynabeads (Invitrogen, 10004D) pre-blocked with BSA-protein (Sigma, 9048-46-8).
Next, the supernatants were diluted five times with dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris pH 8 and 167 mM NaCl) and incubated overnight with the respective antibody with rotation at 4 °C. Protein G Dynabeads preblocked with BSA protein were added the following day and incubated for 3-4h at 4 ˚C. The beads were immobilized on a magnet and washed twice with low-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl and 20 mM Tris pH 8), twice in high-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl and 20 mM Tris pH 8), twice in LiCl buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholic acid (sodium salt), 1 mM EDTA and 10 mM Tris pH 8) and once in TE buffer. DNA elution from the beads was done by incubating with 125 ul elution buffer (1% SDS and 10 mM NaHCO3) for 30 min at 65 ˚C 2000 rpm in a thermomixer. The supernatants and the inputs were reverse crosslinked by incubation overnight at 65 ˚C with X amount of proteinase K. After treatment with RNase A for 30 min at 37 ˚C, the DNA was purified using a kit for DNA cleaning and concentration (Zymo, zd4014). The immunoprecipitated DNA was used of library preparation using the KAPA Hyper prep kit (KAPA Biosystems, 7962347001).

value: RAD21-dTAG cell line (Bruce-4 derived)

value: Mouse epiblast-like cell

tag: antibody

value: Rabbit monoclonal to H3 (trimethyl K4) MilliporeSigma Cat# 04-745


title: Histone-Input_EpiLC

description:
Library name: Histone-Input_EpiLC_rep1
Weill Cornell Medicine Genomics Resources Core Facility


title: H3K4me3_ESC_rep2

description:
Library name: H3K4me3_ESC_rep2
Weill Cornell Medicine Genomics Resources Core Facility

value: Mouse embryonic stem cell


title: hapo_newborn_cordblood_A1297

value: Male

value: cord clood

value: whole blood cells


title: Histone-Input_ESC

description:
Library name: Histone-Input_ESC_rep1
Weill Cornell Medicine Genomics Resources Core Facility


title: H3K4me3_ESC_rep1

description:
Library name: H3K4me3_ESC_rep1
Weill Cornell Medicine Genomics Resources Core Facility


title: hapo_newborn_cordblood_A1281


title: H3K4me3_EpiLC_rep1

description:
Library name: H3K4me3_EpiLC_rep1
Weill Cornell Medicine Genomics Resources Core Facility


title: P2272_1019

description:
single cell library
Smart-Seq2

tag: lane

tag: plate well

tag: internal number

tag: n primer


title: P2272_1017

description:
single cell library
Smart-Seq2

tag: tissue

tag: genotype

tag: s primer


title: OVSAHO, STAT3 siRNA + Veh, Rep1

description:
Library name: OVSAHO_STAT3_siRNA_Veh_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: cell line

tag: cell line

value: OVSAHO

value: High grade serous ovarian cancer

tag: treatment


title: H3K27ac_ESC_rep1

description:
Library name: H3K27ac_ESC_rep1
Weill Cornell Medicine Genomics Resources Core Facility

value: Rabbit polyclonal to H3 (acetyl K27) Abcam Cat# ab4927


title: H3K27ac_EpiLC_rep2

description:
Library name: H3K27ac_EpiLC_rep2
Weill Cornell Medicine Genomics Resources Core Facility


title: hapo_newborn_cordblood_A1284

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

tag: Sex

tag: developmental stage

value: newborn


title: OVSAHO, STAT3 siRNA + IL6, Rep2

description:
Library name: OVSAHO_STAT3_siRNA_IL6_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: STAT3 siRNA + IL6


title: P2272_1018

description:
single cell library
Smart-Seq2

value: lung

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

value: WT

tag: individual

tag: sorting date

tag: isolation criteria

value: GFP^pos

value: pair-end 125bp


title: HA-Input_ESC-DMSO

description:
Library name: HA-Input_ESC-DMSO
Weill Cornell Medicine Genomics Resources Core Facility

value: RAD21-dTAG cell line (Bruce-4 derived)

tag: cell type

value: DMSO


title: hapo_newborn_cordblood_A1282


title: H3K27ac_EpiLC_rep1

description:
Library name: H3K27ac_EpiLC_rep1
Weill Cornell Medicine Genomics Resources Core Facility

value: Mouse epiblast-like cell

tag: antibody


title: OVSAHO, STAT3 siRNA + IL6, Rep3

description:
Library name: OVSAHO_STAT3_siRNA_IL6_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: H3K27ac_ESC_rep2

description:
Library name: H3K27ac_ESC_rep2
Weill Cornell Medicine Genomics Resources Core Facility

value: Mouse embryonic stem cell


title: OVSAHO, STAT3 siRNA + IL6, Rep1

description:
Library name: OVSAHO_STAT3_siRNA_IL6_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: P2272_1016

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane


title: hapo_newborn_cordblood_A1261

value: Male

tag: tissue

value: cord clood

value: whole blood cells


title: OVSAHO, STAT1 siRNA + IFNγ, Rep3

description:
Library name: OVSAHO_STAT1_siRNA_IFNY_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: cell line

value: OVSAHO

value: High grade serous ovarian cancer

tag: genotype

value: STAT1 siRNA + IFNγ


title: P2272_1014

description:
single cell library
Smart-Seq2

value: lung

tag: plate well

tag: internal number

tag: n primer

tag: s primer


title: HA_ESC-DMSO_rep2

description:
Library name: HA_ESC-DMSO_rep2
Weill Cornell Medicine Genomics Resources Core Facility

tag: cell line

tag: treatment

value: Mouse monoclonal to HA Tag Cell Signaling Technology Cat# 3724


title: P2272_1015

description:
single cell library
Smart-Seq2

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

value: WT

tag: developmental stage

tag: individual


title: HA-Input_EpiLC

description:
Library name: HA-Input_EpiLC
Weill Cornell Medicine Genomics Resources Core Facility

tag: cell type


title: OVSAHO, STAT1 siRNA + IFNγ, Rep1

description:
Library name: OVSAHO_STAT1_siRNA_IFNY_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: P2272_1013

description:
single cell library
Smart-Seq2

tag: sorting date

tag: isolation criteria

value: GFP^pos

value: pair-end 125bp


title: hapo_newborn_cordblood_A1255

tag: Sex

value: Female

value: newborn


title: hapo_newborn_cordblood_A1256


title: hapo_newborn_cordblood_A1252


title: OVSAHO, STAT1 siRNA + IFNγ, Rep2

description:
Library name: OVSAHO_STAT1_siRNA_IFNY_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: hapo_newborn_cordblood_A1247


title: HA_EpiLC_rep2

description:
Library name: HA_EpiLC_rep2
Weill Cornell Medicine Genomics Resources Core Facility

value: RAD21-dTAG cell line (Bruce-4 derived)

value: Mouse epiblast-like cell

tag: antibody


title: HA_ESC-DMSO_rep1

description:
Library name: HA_ESC-DMSO_rep1
Weill Cornell Medicine Genomics Resources Core Facility

value: Mouse embryonic stem cell

value: DMSO


title: P2272_1012

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane


title: OVSAHO, STAT1 siRNA + Veh, Rep2

description:
Library name: OVSAHO_STAT1_siRNA_Veh_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

tag: tissue

value: cell line

tag: genotype

value: STAT1 siRNA + Veh


title: OVSAHO, STAT1 siRNA + Veh, Rep3

description:
Library name: OVSAHO_STAT1_siRNA_Veh_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: OVSAHO

value: High grade serous ovarian cancer


title: P2272_1011

description:
single cell library
Smart-Seq2

value: lung

tag: plate well

tag: internal number

tag: n primer

tag: s primer


title: P2272_1010

description:
single cell library
Smart-Seq2

tag: strain

tag: developmental stage


title: OVSAHO, STAT1 siRNA + Veh, Rep1

description:
Library name: OVSAHO_STAT1_siRNA_Veh_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

tag: cell line

tag: cell type

tag: treatment


title: hapo_newborn_cordblood_A1225

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

tag: Sex

value: cord clood

value: whole blood cells


title: HA_EpiLC_rep1

description:
Library name: HA_EpiLC_rep1
Weill Cornell Medicine Genomics Resources Core Facility

tag: antibody

value: Mouse monoclonal to HA Tag Cell Signaling Technology Cat# 3724


title: hapo_newborn_cordblood_A1224


title: P2272_1009

description:
single cell library
Smart-Seq2

value: Scgb1a1CREERT2; Rosa26R-fGFP

value: WT

tag: individual

tag: sorting date

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no


title: OVSAHO, STAT3 siRNA + IFNγ, Rep1

description:
Library name: OVSAHO_STAT3_siRNA_IFNY_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

tag: tissue

value: STAT3 siRNA + IFNγ


title: hapo_newborn_cordblood_A1213

value: Female

value: newborn


title: OVSAHO, STAT1 siRNA + IL6, Rep3

description:
Library name: OVSAHO_STAT1_siRNA_IL6_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

tag: genotype

value: STAT1 siRNA + IL6


title: P2272_1008

description:
single cell library
Smart-Seq2

tag: cdna library_preparation_date

tag: type of_sequencing

value: pair-end 125bp

tag: lane

tag: plate well


title: OVSAHO, STAT1 siRNA + IL6, Rep1

description:
Library name: OVSAHO_STAT1_siRNA_IL6_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: RAD21_ESC-dTAG_rep1

description:
Library name: RAD21_ESC-dTAG_rep1
Weill Cornell Medicine Genomics Resources Core Facility

value: RAD21-dTAG cell line (Bruce-4 derived)

value: Mouse embryonic stem cell

value: dTAG

value: Rabit polyclonal to Rad21 Abcam Cat# ab992


title: P2272_1007

description:
single cell library
Smart-Seq2

tag: strain

value: lung epithelial secretory cells

tag: internal number

tag: n primer

tag: s primer


title: OVSAHO, Control siRNA + IFNγ, Rep3

description:
Library name: OVSAHO_Con_siRNA_IFNY_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: cell line

tag: cell line

value: OVSAHO

tag: cell type

value: High grade serous ovarian cancer

tag: treatment

value: Control siRNA + IFNγ


title: RAD21_ESC-dTAG_rep2

description:
Library name: RAD21_ESC-dTAG_rep2
Weill Cornell Medicine Genomics Resources Core Facility

tag: antibody


title: OVSAHO, STAT1 siRNA + IL6, Rep2

description:
Library name: OVSAHO_STAT1_siRNA_IL6_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: RAD21_ESC-DMSO_rep1

description:
Library name: RAD21_ESC-DMSO_rep1
Weill Cornell Medicine Genomics Resources Core Facility

value: DMSO


title: OVSAHO, Control siRNA + IFNγ, Rep2

description:
Library name: OVSAHO_Con_siRNA_IFNY_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: WT


title: hapo_newborn_cordblood_A1209

tag: Sex

value: Male

value: cord clood

tag: developmental stage

value: whole blood cells


title: P2272_1006

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: individual

tag: sorting date

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no


title: RAD21_EpiLC_rep2

description:
Library name: RAD21_EpiLC_rep2
Weill Cornell Medicine Genomics Resources Core Facility

value: RAD21-dTAG cell line (Bruce-4 derived)

value: Mouse epiblast-like cell

tag: genotype


title: OVSAHO, Control siRNA + IFNγ, Rep1

description:
Library name: OVSAHO_Con_siRNA_IFNY_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

tag: tissue


title: P2272_1004

description:
single cell library
Smart-Seq2

tag: cdna library_preparation_date

tag: type of_sequencing

value: pair-end 125bp

tag: lane

tag: plate well


title: RAD21_ESC-DMSO_rep2

description:
Library name: RAD21_ESC-DMSO_rep2
Weill Cornell Medicine Genomics Resources Core Facility

value: Mouse embryonic stem cell

value: Rabit polyclonal to Rad21 Abcam Cat# ab992


title: P2272_1003

description:
single cell library
Smart-Seq2

tag: strain

value: lung epithelial secretory cells

tag: internal number

tag: n primer

tag: s primer


title: RAD21_EpiLC_rep1

description:
Library name: RAD21_EpiLC_rep1
Weill Cornell Medicine Genomics Resources Core Facility

tag: cell line

tag: cell type

tag: treatment

tag: antibody


title: hapo_newborn_cordblood_A1196

tag: Sex

value: Female

tag: developmental stage

value: newborn


title: hapo_newborn_cordblood_A1273


title: P2272_1005

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: isolation criteria

tag: ercc spike-in_lot_no


title: RAD21-Input_ESC-dTAG

description:
Library name: RAD21-Input_ESC-dTAG
Weill Cornell Medicine Genomics Resources Core Facility

tag: genotype

value: dTAG


title: hapo_newborn_cordblood_A1186

tag: tissue


title: hapo_newborn_cordblood_A1202


title: RAD21-Input_ESC-DMSO

description:
Library name: RAD21-Input_ESC-DMSO
Weill Cornell Medicine Genomics Resources Core Facility

value: DMSO


title: hapo_newborn_cordblood_A1185

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: P2272_1002

description:
single cell library
Smart-Seq2

value: WT

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane

tag: plate well


title: OVSAHO, Control siRNA + Veh, Rep3

description:
Library name: OVSAHO_Con_siRNA_Veh_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: cell line

value: OVSAHO

value: High grade serous ovarian cancer

value: Control siRNA + Veh


title: P2272_1001

description:
single cell library
Smart-Seq2

value: lung

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: internal number

tag: n primer

tag: s primer


title: hapo_newborn_cordblood_A1195

value: cord clood

tag: cell type

value: whole blood cells


title: hapo_newborn_cordblood_A1182

tag: Sex


title: hapo_newborn_cordblood_A1190

value: Male

tag: developmental stage


title: OVSAHO, Control siRNA + Veh, Rep2

description:
Library name: OVSAHO_Con_siRNA_Veh_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

tag: cell line

tag: treatment


title: OVSAHO, Control siRNA + IL6, Rep2

description:
Library name: OVSAHO_Con_siRNA_IL6_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: Control siRNA + IL6


title: P88

city: Valencia

first: Patricia

last: Diaz-Gimeno

state: Valencia

address: EDIFICIO BIOPOLO - LA FE, Avenida Fernando Abril Martorell, 106 - Torre A, Planta 1ª

department: Genomics and Systems Reproductive Medicine

country: Spain

institute: IIS La Fe / IVIRMA Global Research Alliance

description: Library name: P88

data_processing:
Raw data were evaluated using FastQC. STAR was employed to align high-quality data using GRCh37/hg19 as a reference. Gene counts obtained using featureCounts.
Assembly: GRCh37/hg19
Supplementary files format and content: csv file includes raw counts for each sample

source_name: Endometrium

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
Samples were sequenced using the AmpliSeq for Illumina® Transcriptome Human Gene Expression Panel23 in a NextSeq 500/550 system.

value: Endometrium

value: In Vitro Fertilization


title: OVSAHO, Control siRNA + Veh, Rep1

description:
Library name: OVSAHO_Con_siRNA_Veh_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: hapo_newborn_cordblood_A1180


title: Mut-2

city: LA

first: Peixian

last: Dong

state: California

address: 1450 Biggy St, NRT 5514, LA. CA

institute: USC

description: Library name: Normalized read count N275D_P2

data_processing:
CLC Genomics Workbench v11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized read out for each Sample

source_name: Spleen

extract_protocol:
RNA was harvested using Rneasy Plus mini kit (Qiagen). 1ug of total RNA was usedfor the construction of sequencing libraries.
RNAseq PolyA Selection + NEBNext Ultra II Directional

value: Spleen

value: Th17 cell

value: Mut


title: OVSAHO, Control siRNA + IL6, Rep3

description:
Library name: OVSAHO_Con_siRNA_IL6_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: RAD21-Input_EpiLC

description:
Library name: RAD21-Input_EpiLC
Weill Cornell Medicine Genomics Resources Core Facility

value: RAD21-dTAG cell line (Bruce-4 derived)

value: Mouse epiblast-like cell

tag: antibody


title: Mut-3

description: Library name: Normalized read count N275D_P3


title: OVSAHO, Control siRNA + IL6, Rep1

description:
Library name: OVSAHO_Con_siRNA_IL6_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: cell line

value: WT


title: hapo_newborn_cordblood_A1181

value: newborn


title: P87

description: Library name: P87


title: P86

description: Library name: P86


title: WT-3

description: Library name: Normalized read count WT_P3


title: WT-2

description: Library name: Normalized read count WT_P2


title: P85

description: Library name: P85


title: Mut-1

description: Library name: Normalized read count N275D_P1


title: hapo_newborn_cordblood_A1179


title: P81

description: Library name: P81


title: MDAH, STAT3 siRNA + Veh, Rep3

description:
Library name: MDAH_STAT3_siRNA_Veh_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: Endometrioid ovarian cancer

value: STAT3 siRNA + Veh


title: MDAH, STAT3 siRNA + IFNγ, Rep2

description:
Library name: MDAH_STAT3_siRNA_IFNY_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: STAT3 siRNA + IFNγ


title: hapo_newborn_cordblood_A1161

value: cord clood


title: P83

description: Library name: P83


title: P82

description: Library name: P82


title: P80

description: Library name: P80


title: MDAH, STAT3 siRNA + Veh, Rep2

description:
Library name: MDAH_STAT3_siRNA_Veh_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: hapo_newborn_cordblood_D0872

value: whole blood cells


title: MDAH, STAT3 siRNA + IFNγ, Rep3

description:
Library name: MDAH_STAT3_siRNA_IFNY_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: G1_ESC_A485_Micro-C_rep2

description:
Library name: G1_ESC_A485_rep2
Weill Cornell Medicine Genomics Resources Core Facility
G1_ESC_A485_pool.hic
G1_ESC_A485_pool.mcool
G1_ESC_A485_compartment.bedgraph

growth_protocol: RAD21-dTAG cells were cultured at 37˚C on gelatinized plate in serum/2i/LIF medium. Cells were harvested by treating with Trypsin-EDTA for 3 min, washed with PBS, and centrifuged at 300 × g for 5 min at 4˚C. 2,000,000 cells per replicate were collected and centrifuged at 300 × g for 5 min. The pellet was frozen at -80˚C for 30 min, thawed at RT, and resuspended in 1 mL PBS. Freshly prepared 10 µL of 0.3 M DSG (Sigma-Aldrich, 80424) in DMSO was added, and the samples were incubated with rotation at RT for 10 min. Subsequently, 27 µL of 37% formaldehyde (Sigma-Aldrich, 252549) was added, and the samples were incubated at RT for an additional 10 min. After centrifugation at 3,000 × g for 5 min at 4˚C, the pellets were washed with 200 µL of 1X wash buffer from Dovetail Micro-C kit (Cantata Bio, 210006).

value: Mouse embryonic stem cell