title: P_M_20_co14

city: ROMA

first: domenico

last: raimondo

state: RM

address: Viale Regina Elena 324

department: Molecular Medicine

institute: Sapienza University of Rome

hyb_protocol: standard protocol

scan_protocol: To quantify mRNA targets, each cartridge was scanned in 550 field-of-view by means of the automatic nCounter Digital Analyzer primers and 5 μL of TaqMan Pre Amp Master Mix (Applied Biosystems, Life Technology), amplified by 18 PCR cycles at 94°C for 15 seconds and 60°C for 4 minutes. After denaturation (94°C for 2 minutes, then on ice), the amplification product was hybridized for 18 hours at 65°C in the presence of both reporter and capture probes. The nCounter Prep Station was then used to purify and immobilize the resulting hybrid onto the internal surface of a cartridge.

data_processing: Raw count data were preprocessed with the NanoStringNorm R package, a set of tools for normalizing, running diagnostics, and visualizing NanoString nCounter data. Specifically, geometric mean-based scaling normalization was performed to account for technical assay variation, which involved choosing the geo.mean setting in the CodeCount R option. The background subtracted from each sample was calculated by setting mean.2sd in the background option. The method used to normalize for RNA content (i.e., pipetting fluctuations) entailed selecting the “housekeeping.geo.mean” setting in the SampleContent R option via all internal annotated housekeeping genes. All data were grouped in four classes based on cell sample subtype: naïve healthy donors (N-HDs), naïve patients (N-Ps), effector cells in healthy donors (Eff-HDs), and effector cells in patients (Eff-Ps). We did not consider genes that are not expressed in any sample, thereby excluding them from further analysis. This resulted in an analysis set of 401 unique genes and 26 samples.

label: NOT PROVIDED

source_name: decalcified and paraffin-embedded (FFDPE) biopsies

label_protocol: The nCounter® PanCancer Pathways Panel Kit contains fluorescent barcoded probes that are complementary to 770 genes from 13 cancer-associated canonical pathways to support the understanding of basic cancer biology, and 13 housekeeping genes (used as internal controls).

growth_protocol: not applicable

extract_protocol: Total RNA was extracted by RNeasy FFTE kit (Qiagen Germany) starting from a minimun of 4-micron-thick slides from FFPE tissues. The sections were scraped into the deparaffinization solution and total RNA was extracted and purified according to manufacturer’s instruction. RNA quantity and quality were assessed by NanoDrop2000 spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: Samples were stored at -80 °C until the assays were performed.

value: bone


title: 10 HTM.Low_3h [TRA00038862]

status: Public on Jun 07 2021

type: SRA

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

country: USA

institute: Joslin Diabetes Center

description: Mouse Hypothalamus RNA-seq by Illumina HiSeq 2500

library_source: transcriptomic

data_processing:
Reads were aligned to the mouse genome using STAR.
Reads were counted with featureCounts.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: CSV file contains read counts.

molecule: total RNA

organism: Mus musculus

extract_protocol:
Brain tissues were harvested, snap frozen in liquid nitrogen and kept at -80C. Total RNA was isolated from hypothalamus, hippocampus and nucleus accumbens.
Stranded cDNA libraries with unique index tags for each sample (48 multiplexed) were made using a directional RNA-seq kit (Wafergen).

tag: strain

tag: Sex

value: male

tag: age

value: 3 months

tag: time point

value: After 3 h of clamp

tag: dose

value: Low

tag: tissue

value: Hypothalamus


title: 9 HTM.Basal_3h [TRA00038429]

value: Basal


title: EOMES GATA6-/- Day 2

city: Charleston

first: Stephen

middle: A

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

library_source: genomic

data_processing:
FASTQC (v0.11.7) of raw sequencing file
Aligned reads to hg19 genome using Bowtie 2 (v.2.2.5)
Removed unaligned reads with Partek Flow software (v.9.0.20.0526)
Peaks identified by MACS2 (v2.1.1)
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph file generated by MACS2 (v2.1.1)

molecule: genomic DNA

organism: Homo sapiens

source_name: K3 Induced pluripotent stem cell

growth_protocol: Pluripotent stem cells were seeded on Geltrex-coated tissue culture plates. After 24 hours, the cells were subjected to hepatic differentiation. Briefly, iPSCs were supplemented with Activin A (100ng/ml), fibroblast growth factor 2 (FGF2 20ng/ml), and bone morphogenetic protein 4 (BMP4, 10ng/ml) for 2 days. Activin A (100ng/ml) alone was supplemented for a further 2 days to commit the culture to definitive endoderm.

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature. The cross-linking reaction was quenched by adding 125mM glycine and incubating at room temperature for 5 minutes. Chromatin was isolated from cell pellets using MNase enzymatic digestion following the manufacturers protocol (Magnetic CHIP kit, ThermoFisher/Pierce). Briefly, cell nuclei were isolated using a membrane lysis buffer. MNase was then added to the isolated nuclei at optimized concentrations and incubated at 37°C for 15 minutes. The enzymatic reaction was stopped with EDTA and digested chromatin was then extracted by brief sonication. Chromatin isolated from 4 individual differentiations were pooled for each condition. Pooled chromatin was incubated with primary antibodies overnight at 4°C. The following day, protein A/G magnetic beads were added to the sample-antibody mixture and incubated at 4°C for 2 hours. Beads were then washed three times in a low salt wash buffer, and once in a high salt wash buffer, before reverse cross-linking in elution buffer. Eluted samples were subjected to proteinase K digestion and the DNA isolated using DNA-binding columns.
CHIP DNA samples were submitted to Beijing Genomics Institute (BGI), who performed library preparation and sequencing on the BGISEQ-500 platform. 50bp single end reads were generated and provided as FASTQ files.

treatment_protocol: Doxycycline was supplemented to induce FOXA2-3xFLAG cDNA expression in the denoted samples

tag: cell type

value: K3 Induced pluripotent stem cell

tag: genotype

value: GATA6Ex4{delta}1/{delta}2;ind GATA6

tag: differentiation day

value: Day 2 - Mesendoderm

tag: doxycyline treatment

value: untreated

tag: chip antibody

value: EOMES (Cell Signaling - 66325)


title: P_M_16_va15

type: RNA

country: Italy

tag: gender


title: 8 NAC.High_3h [TRA00038412]

description: Mouse Nucleus accumbens RNA-seq by Illumina HiSeq 2500

source_name: High_Nucleus accumbens

value: High

value: Nucleus accumbens


title: flag.controlgRNA.rep10

city: Durham

first: Charles

last: Gersbach

address: 101 Science Drive

department: Biomedical Engineering

institute: Duke University

data_processing:
Sequences for TruSeq Illumina adapters were removed from the raw reads using Trimmomatic v0.32 (Bolger et al., 2014).
Single-end reads were mapped using Bowtie (v1.0.0 PMID: 19261174) against Mouse (mm10) genome with flags -v 2 -X 2000 --best --strata -m 1.
Duplicates were removed using Picard MarkDuplicates v1.130
Low mappability or blacklisted regions identified by the ENCODE project (Consortium, 2012) were filtered out from the final BAM files
Using the sequenced input controls, binding regions were identified using the callpeak function in MACS2 v2.1.0.20151222 (Zhang et al., 2008).
Signal files were generated with deeptools bamCoverage (v3.0.1 PMID:24799436) ignoring duplicates, extending reads 200bp and converting the read counts to RPKMs.
For the differential binding analysis, first, a union peakset was computed merging individual peak calls using bedtools2 v2.25.0 (Quinlan and Hall, 2010). Then, reads in peaks were estimated using featureCounts and the difference in binding was assessed with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig signal in RPMs

source_name: liver

extract_protocol:
On day of harvest, mice were euthanized by CO2 inhalation. Livers were harvested and immediately snap frozen using liquid N2.  Livers were then treated for chromatin extraction as described in Savic et al, 2013. Briefly, following fixation, livers were rocked at 4˚C in 10 ml Farnham Lysis Buffer for 10 minutes followed by centrifugation. Pellets were resuspended in 4 mL RIPA buffer. 1 mL RIPA and 1 mL RIPA containing resuspended liver was placed into a 15 mL tube with 800 mg of Diagenode sonication beads (Diagenode, C01020031). This tube was sonicated for 30 cycles of 30s on and 30s off using a Bioruptor Pico.
ChIP-seq libraries were prepared using a Kapa Hyper Prep kit.

treatment_protocol: Approximately 8 week old animals were injected with PBS or AAV.Cbh.gRNA (either control or targeted)

tag: grna target

value: non-targeting

tag: total viral genomes/mouse)

tag: antibody

value: anti-flag


title: VARI068 CRISPR RhoC KO replicate 2

city: Ann Arbor

first: Sofia

middle: D

last: Merajver

state: MI

address: 1500 E. Medical Ct. Dr., 7314 CC

department: Int Med-Hematology/Oncology

institute: University of Michigan

data_processing:
Read data in FASTQ format were quality assessed with FastQC/MultiQC (v.0.11.3) and contamination checked with fastq_screen (v.0.11.1)
Reads were adapter-trimmed using CutAdapt (v.1.8.1) and aligned to the GRCh37 hg19 human genome using Tophat/Bowtie2 (v.2.0.13/v.2.2.1, options –b2_very_sensitive and the default max intron length of 500000).
Raw read counts were extracted for each gene using HTSeq (v.0.6.0).
DESeq2 (v1.14.1), run within the R (v.3.3.3) Bioconductor package (Biobase v.2.34), was used to model differential expression in genes between modeled conditions. The main factors used in the model were cell line and CRISPR knockout status (cRhoC or WT). DESeq2 utilizes generalized linear models for each gene and infers a log2 fold change between conditions using maximum likelihood estimation and (by default) a Wald test for significance. Default parameters for DESeq2 were used, specifying a standardized normal prior on the non-intercept coefficients (betaPrior=TRUE).
Genes were annotated with NCBI Entrez GeneIDs and text descriptions.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts, normalized counts, differential expression measurements
Supplementary_files_format_and_content: kraken2 output

source_name: cell line

growth_protocol: Cell lines were incubated at 37°C. Normal growth media for each cell line was replaced with DMEM for 24 hrs prior to RNA extraction.

extract_protocol:
Extraction performed with RNeasy Plus Mini Kit (Qiagen) following normal protocols.
TruSeq stranded mRNA kit (Illumina), using 520ng of total RNA as input and 13 cycles of PCR.

tag: cell line

value: CRISPR RhoC KO


title: C2, biological replicate2

city: Beijing

first: Qing

last: Wei

address: NO.1 Beichen West Road, Chaoyang District

country: China

institute: Institute of Microbiology, Chinese Academy of Sciences

description: Gene expression data from Staphylococcus aureus grown till exponential phase

data_processing:
The raw paired end reads were trimmed and quality controlled by Trimmomatic with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT.
To identify DEGs (differential expression genes) between two different samples, the expression level for each transcript was calculated using the fragments per kilobase of read per million mapped reads (RPKM) method. The method Bowtie2 and RSEM were used for differential expression analysis
Genome_build: Staphylococcus aureus COL

organism: Staphylococcus aureus

source_name: Exponential phase bacterial culture of Staphylococcus aureus

growth_protocol: Bacterial cells were grown for 12 hr at 37C.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA-seq strand-specific libraries were prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA), using 5 μg of total RNA. Briefly, rRNA was removed by RiboZero rRNA removal kit (Epicenter), fragmented using fragmentation buffer. cDNA synthesis, end repair, A-base addition and ligation of the Illumina-indexed adaptors were performed according to Illumina’s protocol. Libraries were then size selected for cDNA target fragments of 200~300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles.

treatment_protocol: Bacterial cells were collected and kept on ice to extract RNA.

tag: treatment

value: liquid LB medium

tag: phase

value: Exponential phase

tag: genotype/variation

value: wild type


title: VARI068 wild type replicate 2

value: wild-type


title: P_F_7_bo16

value: female

value: bone


title: EOMES GATA6+/+ Day 2


title: P_M_19_de14

value: male


title: FOXA2 GATA6+/+ Day 2

value: K3 Induced pluripotent stem cell

value: FOXA2 (RnD - AF2400)


title: 13 HCA.Low_3h [TRA00038865]

description: Mouse Hippocampus RNA-seq by Illumina HiSeq 2500

tag: strain

tag: Sex

tag: age

value: 3 months

value: After 3 h of clamp

value: Low

value: Hippocampus


title: P_F_16_dr15

tag: tissue


title: 7 NAC.Low_3h [TRA00038411]

source_name: Low_Nucleus accumbens

tag: time point

tag: dose

value: Nucleus accumbens


title: SUM190 CRISPR RhoC KO replicate 4

tag: genotype


title: GATA6 GATA6+/+ Day 2

tag: cell type

tag: differentiation day

value: Day 2 - Mesendoderm

tag: doxycyline treatment

value: untreated

value: GATA6 (Cell Signaling - 5851)


title: SUM190 CRISPR RhoC KO replicate 3

value: CRISPR RhoC KO


title: 6 NAC.Basal_3h [TRA00038410]

source_name: Basal_Nucleus accumbens

value: Basal


title: P_F_6_bo15

tag: gender


title: FOXA2 GATA6+/+ Day 4

value: Day 4 - Definitive Endoderm

tag: chip antibody


title: SUM190 CRISPR RhoC KO replicate 2


title: P_M_16_ot14


title: RNA - Day 8 - R2 - GATA6+/+

data_processing:
FASTQC (v. 0.11.7) of raw sequencing files
Aligned reads to hg19 genome using STAR (v.2.6.1d)
Unaligned reads removed using Partek Flow software (v.9.0.20.0526)
Abundance measurements and counts per million normalization completed using Partek Flow software (v.9.0.20.0526)
Genome_build: hg19
Supplementary_files_format_and_content: Normalized reads .txt file generated using Partek Flow

growth_protocol: Pluripotent stem cells were seeded on Geltrex-coated tissue culture plates. After 24 hours, the cells were subjected to hepatic differentiation. Briefly, iPSCs were supplemented with Activin A (100ng/ml), fibroblast growth factor 2 (FGF2 20ng/ml), and bone morphogenetic protein 4 (BMP4, 10ng/ml) for 2 days. Activin A (100ng/ml) alone was supplemented for a further 3 days to form definitive endoderm. Subsequently, the definitive endoderm was specified towards a hepatic fate by supplementing the media with 3 days of BMP4 (20ng/ml) and FGF2 (10ng/ml).

extract_protocol:
Samples were collected and RNA extracted using QIAgen RNAeasy kits. Genomic DNA was removed using TurboDNAse. RNA clean up completed using QIAgen RNAeasy kit. Samples submitted to Beijing Genomics Institute (BGI), who performed library preparation and sequencing on the BGISEQ-500 platform. 50 million 50bp single end reads were generated and provided as FASTQ files.
Samples were submitted to Beijing Genomics Institute (BGI), who performed library preparation and sequencing on the BGISEQ-500 platform. 30 million 100bp paired end reads were generated and provided as FASTQ files.

treatment_protocol: Doxycycline was supplemented to induce GATA6-3xFLAG cDNA expression in the denoted samples

value: Day 8 - Hepatic Endoderm

tag: doxycyline


title: SUM190 CRISPR RhoC KO replicate 1

tag: cell line


title: 5 HCA.High_3h [TRA00038409]

value: High


title: VARI068 wild type replicate 1

value: wild-type


title: RNA - Day 6 - R2 - GATA6+/+

value: Day 6 - Pre-Hepatic Endoderm


title: LoVoS100A10

city: Tianjin

first: Zhang

middle: shi

last: wu

state: Tianjin

address: Tianjin Union Medical Center, JieYuan Street No.190, HongQiao District, Tianjin, China

department: Pathology

institute: Tianjin Union Medical Center

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from genome website directly
For a specific ChIP-seq binding site, individual reads mapping to the plus or minus strand and present significant enrich.
Strand cross-correlation of tag density providing a quick assessment of IP-seq data set quality and binding characteristics.
After mapping reads to the reference genome, we used the MACS2 version 2.1.0 (model-based analysis of ChIP-seq) (Zhang et al., 2008) peak finding algorithm to indentify regions of IP enrichment over background.
The interaction between transcript factor or chromatin histone modification and DNA were not random, while they shown some specific sequence preference. MEME (Timothy L. Bailey and Charles Elkan,1994) and DREME (Timothy L. Bailey,2011) were used to detect the sequence motif, which determined to detect long and short consensus sequence.
The position of peak summit around transcript start sites of genes can predict the interaction sites of protein and gene. PeakAnnotator was used to identify the nearest TSS of every peak and the distance distribution between peaks and TSS was shown.
Genome_build: ftp://ftp.ensembl.org/pub/release-94/fasta/homo_sapiens/dna/
Supplementary_files_format_and_content: tab-delimited text files include fold-enrichment values for each sample

source_name: colon cancer cell line

growth_protocol: PGCCs with daughter cells of LoVo and HCT116 all cultured in the T75, before ChIP, western blot of nuclear protien was performed to detect the expreesion of S100A10 in the nuclear.

extract_protocol:
Lysates were clarified from sonicated nuclei and S100A10-DNA complexes were isolated with antibody.
The purified DNA used for library construction with NEB Next Ultra ll DNA Library Prep Kit for llumina. Subsequently, pair-end sequencing of sample was performed on Illumina platform.

treatment_protocol: PGCCs with daughter cells of LoVo and HCT116 were treated by CoCl2 at 535.5 um for 48h

tag: treatment

value: treated with CoCl2

value: LoVo


title: LoVoInput

value: input


title: 3 HCA.Basal_3h [TRA00038407]

value: male

value: 3 months

value: After 3 h of clamp


title: FOXA2 GATA6-/-indFOXA2 Day 4

value: K3 Induced pluripotent stem cell

value: GATA6Ex4{delta}1/{delta}2;ind FOXA2

value: treated post day 1

value: FOXA2 (RnD - AF2400)


title: 4 HCA.Low_3h [TRA00038408]

value: Low

value: Hippocampus


title: SUM190 wild type replicate 4


title: HCT116Input


title: RNA - Day 6 - R1 - GATA6+/+

value: untreated


title: HCT116S100A10


title: SUM190 wild type replicate 3


title: RNA - Day 4 - R2 - GATA6Ex4∆1/∆2;ind GATA6 (+dox)

source_name: K3_GATA6Ex4∆1/∆2;ind GATA6

value: GATA6Ex4{deleta}1/{deleta}2;ind GATA6

value: Day 4 - Definitive Endoderm


title: SUM190 wild type replicate 2

value: wild-type


title: SUM190 wild type replicate 1


title: LNCaP METTL3 sh2 ENZ R2 RNA-Seq

city: Bern

first: Kellie

last: Cotter

state: Bern

address: Murtenstrasse 35

department: Dept for BioMedical Research

country: Switzerland

institute: University of Bern

description: Enzalutamide treated inducible METTL3 shRNA #2

data_processing:
Sequence reads were aligned to the human reference genome GRCh37 by STAR using the two-pass approach
Transcript quantification was performed using RSEM. Genes without >10 counts in at least 2 samples were discarded.
Counts were normalized using the median of ratios method from the DESeq2 package in R version 3.6.1.
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table containing log2 normalized counts data

source_name: LNCaP cell line

growth_protocol: Cells were maintained in RPMI medium, supplemented with 10% FBS, and 1% penicillin-streptomycin on poly-L-lysine coated plates.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit from Qiagen and genomic DNA was removed using the DNA-free kit from Ambion
Libraries were prepared using 1 ug of RNA and the NEBNext Ultra™ II RNA Library Prep Kit with rRNA depletion following the manufacturer’s instructions.

treatment_protocol: Cells were treated with 0.1% DMSO or 10 uM enzalutamide for 24 hours.

value: LNCaP

tag: shRNA

value: METTL3 shRNA 2

value: 10 uM enzalutamide


title: RNA - Day 4 - R1 - GATA6Ex4∆1/∆2;ind GATA6 (+dox)


title: SUM149 CRISPR RhoC KO replicate 4

value: CRISPR RhoC KO


title: 1 HTM.Basal_3h [TRA00038404]

value: male

value: Basal

value: Hypothalamus


title: RNA - Day 4 - R2 - GATA6Ex4∆1/∆2;ind GATA6 (-dox)

value: K3 Induced pluripotent stem cell


title: LNCaP METTL3 sh2 ENZ R1 RNA-Seq


title: RNA - Day 4 - R1 - GATA6Ex4∆1/∆2;ind GATA6 (-dox)


title: SUM149 CRISPR RhoC KO replicate 3


title: LNCaP METTL3 sh2 DMSO R3 RNA-Seq

description: Vehicle treated inducible METTL3 shRNA #2

value: 0.1% DMSO


title: RNA - Day 8 - R1 - GATA6+/+

value: Day 8 - Hepatic Endoderm


title: 127493 S10 27ac

city: Cologne

first: Alexander

last: Simonis

address: Kerpener Str. 62

country: Germany

institute: University Hospital of Cologne

data_processing:
We used the Genrich peak caller that calls peaks for multiple replicates collectively. This software first analyses the replicates separately, with p-values calculated for each. At each genomic position, the multiple replicates' p-values are then combined by Fisher's method. The combined p-values are converted to q-values, and peaks are called. In order to assess the differential coverage of binding sites we used the THOR software as described in (Allhoff, Sere et al., 2016).
Genome_build: The GRCh38 human reference genome was used to analyse peaks.
Supplementary_files_format_and_content: Raw fastq files where mapped and treated as described by Zhu at al. (PMID: 31500663).

source_name: monocyte-derived macrophages

growth_protocol: Blood samples were obtained from patients with proven SARS-CoV-2 infection. PBMCs (peripheral blood mononuclear cells) were purified by density gradient centrifugation (Ficoll Plus, GE Healthcare, Chicago, IL, USA). CD14+ cells were isolated from PBMCs by positive selection, using a monocyte isolation kit (Miltenyi Biotech, Bergisch Gladbach, Germany).

extract_protocol:
150.000 cells were washed twice with Wash Buffer (20mM MHEPES, 150mM NaCl, 0,5mM Spermidine) and bound to activated Concavalin A beads for 10 minutes at room temperature. Cell-bead suspension was then resuspended in antibody buffer (20mM MHEPES, 150mM NaCl, 0,5mM Spermidine, 0,05% Digitonin, 2mM EDTA) and incubated overnight at 4°C with H3K27ac (Active Motif #39133) and H3K4me3 (Active Motif #39159) antibodies (antibody dilution 1:50). Cell-bead suspension was then washed twice with Digitonin Buffer (20mM MHEPES, 150mM NaCl, 0,5mM Spermidine, 0,05% Digitonin) and incubated with 2.5 µl EpiCypher CUTANA pAG-MNase, for 10 minutes. After washing samples twice with Digitonin buffer, 1µl 100mM CaCl2 was added to samples which were incubated for 2 hours at 4°C, rotating. To stop the reaction, STOP buffer (340mM Nacl, 20mm EDTA, 4mM EGTA, 0,02%Digitonin, 50µg/ml RNase A, 50ug/ml Glycogen, yeast genomic DNA) was added in each tube. Samples were incubated at 37°C for 10 minutes at 500 rpm and after centrifugation, liquid was collected, DNA was purified using Zymo DNA clean concentrator kit and DNA was eluted in elution buffer.
For library preparation we used the TruSeq DNA nano kit and protocol from Illumina with 15 cycles of PCR. Libraries were validated and quantified (Agilent Tape Station 4200).
A pool of all libraries was quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System. Sequencing was done with NovaSeq sequencers (Illumina) and a PE100bp read length aiming at 10M reads/sample.

treatment_protocol: Cells were left untreated.

value: monocyte-derived macrophages

tag: antibody

value: k27ac (Active Motif #39133)

tag: age (ys)

tag: disease state

value: SARS-CoV-2 naïve individual


title: 127489 S8 27ac

value: SARS-CoV-2 convalescent patient


title: Cultured cell sample

city: Liverpool

first: Tony

last: Pang

state: NSW

address: 1 Campbell Street

department: South Western Sydney Clinical School

country: Australia

institute: University of New South Wales

description: Cult

data_processing:
demultiplex using cellranger mkfastq (3.1.0)
alignment, filtering, barcode counting, UMI counting with cellranger count (3.1.0) using a combined reference genome
QC cell filtering using Seurat (varying mitochondrial gene count, total feature count, gene counts)
Genome_build: Combined reference genome using GRCh38 human assembly (Ensembl release 93), GRCm38 mouse assembly (Ensembl release 93), modified firefly (photinus pyralis) luciferase transgene, luc+ from the PGL3 Basic plasmid (Promega Corporation, Madison, WI, USA) using cellranger mkref (3.1.0). Prefixes: GRCh38Luc = combined GRCh38 with luc+, mm10------ - GRCm38 mouse assembly
Supplementary_files_format_and_content: gene count / cell barcode matrix for each sample

source_name: Cells kept in tissue-culture condition

growth_protocol: Cultured cells grown in tissue culture conditions (37C, 5% CO2) in RPMI+20%FBS (AsPC-1 cells) and IMDM+10%FBS (cancer-associated human pancreatic stellate cells). These were grown separately and combined 1:1 into a single sample for cellular partitioning and library construction.

extract_protocol:
Tumour samples were enzymatically and physically dissociated and dead cell depletion performed. Blood samples underwent red blood cell lysis, followed by mouse cell immunomagnetic depletion.
10x Chromium for 3' gene expression library construction, sequencing performed with Illumina NovaSeq 6000 with SP 100 cycle flow cell with read lengths 28,8,91bp

treatment_protocol: No treatments

tag: processing

value: Cultured cells

tag: strain


title: SUM149 CRISPR RhoC KO replicate 2


title: 127487 S7 27ac

value: female


title: 127485 S6 27ac


title: RNA - Day 4 - R2 - GATA6+/+

value: Day 4 - Definitive Endoderm

value: untreated


title: LNCaP METTL3 sh2 DMSO R1 RNA-Seq

value: LNCaP

value: METTL3 shRNA 2


title: RNA - Day 4 - R1 - GATA6+/+


title: LNCaP METTL3 sh1 ENZ R3 RNA-Seq

description: Enzalutamide treated inducible METTL3 shRNA #1

value: METTL3 shRNA 1

value: 10 uM enzalutamide


title: SUM149 wild type replicate 4

value: wild-type


title: 2 HTM.Low_3h [TRA00038405]

tag: Sex

value: male

tag: age

value: 3 months

tag: time point

value: After 3 h of clamp

value: Low

tag: tissue

value: Hypothalamus


title: LNCaP METTL3 sh2 DMSO R2 RNA-Seq

value: 0.1% DMSO


title: RNA - Day 2 - R2 - GATA6Ex4∆1/∆2;ind GATA6 (+dox)

value: K3 Induced pluripotent stem cell

tag: genotype

value: GATA6Ex4{deleta}1/{deleta}2;ind GATA6

tag: differentiation day

value: Day 2 - Mesendoderm

value: treated post day 1


title: 127495 S11 27ac

tag: cell type

value: monocyte-derived macrophages

value: k27ac (Active Motif #39133)

tag: gender

value: SARS-CoV-2 naïve individual


title: 127483 S5 27ac

value: female


title: SUM149 CRISPR RhoC KO replicate 1

value: CRISPR RhoC KO


title: LNCaP METTL3 sh1 ENZ R2 RNA-Seq

value: LNCaP

value: METTL3 shRNA 1

value: 10 uM enzalutamide


title: RNA - Day 2 - R1 - GATA6Ex4∆1/∆2;ind GATA6 (+dox)

tag: doxycyline


title: SUM149 wild type replicate 3

tag: cell line

value: wild-type


title: RNA - Day 2 - R2 - GATA6Ex4∆1/∆2;ind GATA6 (-dox)

value: untreated


title: LNCaP METTL3 sh1 ENZ R1 RNA-Seq

tag: treatment


title: SUM149 wild type replicate 2


title: SUM149 wild type replicate 1


title: 127477 S1 k27ac

value: male

value: SARS-CoV-2 convalescent patient


title: MDA231 CRISPR RhoC KO replicate 4


title: LNCaP METTL3 sh1 DMSO R3 RNA-Seq

description: Vehicle treated inducible METTL3 shRNA #1

tag: shRNA

value: 0.1% DMSO


title: LNCaP METTL3 sh1 DMSO R1 RNA-Seq


title: MDA231 CRISPR RhoC KO replicate 3


title: 127469 S8 me3

tag: antibody

value: (Active Motif #39159)


title: RNA - Day 2 - R2 - GATA6+/+

value: K3 Induced pluripotent stem cell


title: 127475 S11 me3

tag: age (ys)


title: 127473 S10 me3

value: k4me3 (Active Motif #39159)

tag: disease state


title: RNA - Day 2 - R1 - GATA6Ex4∆1/∆2;ind GATA6 (-dox)

value: GATA6Ex4{deleta}1/{deleta}2;ind GATA6

value: Day 2 - Mesendoderm


title: LNCaP METTL3 sh1 DMSO R2 RNA-Seq


title: H3K9me3 - Day 4 - GATA6 RES

data_processing:
FASTQC (v0.11.7) of raw sequencing file
Aligned reads to hg19 genome using Bowtie 2 (v.2.2.5)
Removed unaligned reads with Partek Flow software (v.9.0.20.0526)
bedGraph generation performed using HOMER software (v.4.10)
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files generated using the makeUCSCfile.pl script in HOMER using default settings

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature. The cross-linking reaction was quenched by adding 125mM glycine and incubating at room temperature for 5 minutes. Chromatin was isolated from cell pellets using MNase enzymatic digestion following the manufacturers protocol (Magnetic CHIP kit, ThermoFisher/Pierce). Briefly, cell nuclei were isolated using a membrane lysis buffer. MNase was then added to the isolated nuclei at optimized concentrations and incubated at 37°C for 15 minutes. The enzymatic reaction was stopped with EDTA and digested chromatin was then extracted by brief sonication. Chromatin isolated from 4 individual differentiations were pooled for each condition. Pooled chromatin was incubated with primary antibodies overnight at 4°C. The following day, protein A/G magnetic beads were added to the sample-antibody mixture and incubated at 4°C for 2 hours. Beads were then washed three times in a low salt wash buffer, and once in a high salt wash buffer, before reverse cross-linking in elution buffer. Eluted samples were subjected to proteinase K digestion and the DNA isolated using DNA-binding columns.
CHIP DNA samples were submitted to Beijing Genomics Institute (BGI), who performed library preparation and sequencing on the BGISEQ-500 platform.  50bp single end reads were generated and provided as FASTQ files.

value: Day 4 - Definitive Endoderm

tag: doxycyline treatment

value: treated post day 1

tag: chip antibody

value: H3K9me3 (Abcam; ab8898)


title: MDA231 wild type replicate 4


title: RNA - Day 0 - R1 - GATA6+/+

value: Day 0 - Pluripotent stem cells


title: RNA - Day 2 - R1 - GATA6+/+


title: 127467 S7 me3

value: monocyte-derived macrophages

value: female


title: MDA231 wild type replicate 3


title: LNCaP GFP sh ENZ R1 RNA-Seq

description: Enzalutamide treated control inducible shRNA

value: LNCaP

value: Non-targeting

value: 10 uM enzalutamide


title: 127481 S4 k27ac

value: k27ac (Active Motif #39133)

value: SARS-CoV-2 naïve individual


title: MDA231 CRISPR RhoC KO replicate 1

value: CRISPR RhoC KO


title: MDA231 wild type replicate 2

value: wild-type


title: 127465 S6 me3

value: (Active Motif #39159)

value: male

value: SARS-CoV-2 convalescent patient


title: H3K9me3 - Day 4 - GATA6 WT

value: K3 Induced pluripotent stem cell

value: untreated


title: 127461 S4 k4me3


title: LNCaP GFP sh ENZ R2 RNA-Seq


title: 127463 S5 me3

value: k4me3 (Active Motif #39159)


title: H3K9me3 - Day 4 - GATA6 KO

value: GATA6Ex4{deleta}1/{deleta}2;ind GATA6

value: Day 4 - Definitive Endoderm

value: H3K9me3 (Abcam; ab8898)


title: LNCaP GFP sh DMSO R3 RNA-Seq

description: Vehicle treated control inducible shRNA

value: 0.1% DMSO


title: MDA231 CRISPR RhoC KO replicate 2


title: LNCaP GFP sh ENZ R3 RNA-Seq

value: LNCaP


title: RNA - Day 0 - R2 - GATA6+/+

value: Day 0 - Pluripotent stem cells


title: LNCaP GFP sh DMSO R2 RNA-Seq

description: Vehicle treated control inducible shRNA

value: Non-targeting


title: MDA231 wild type replicate 1


title: H3K9me3 - Day 2 - GATA6 RES

value: Day 2 - Mesendoderm

value: treated post day 1


title: LNCaP GFP sh DMSO R1 RNA-Seq

description: Vehicle treated control inducible shRNA


title: H3K9me3 - Day 2 - GATA6 KO


title: LNCaP METTL3 sh2 200 DOX R3 Ribo-Seq

description: Doxycycline treated inducble METTL3 shRNA #2

data_processing:
Library strategy: Ribo-Seq
Sequence reads were aligned to the human reference genome GRCh37 by STAR using the two-pass approach
Ribo-Seq reads were alignes with the options –"winAnchorMultimapNmax 200  --seedSearchStartLmax 15 --outFilterMultimapNmax 20”, to improve mapping of short reads.
Transcript quantification was performed using RSEM. Genes without >10 counts in at least 2 samples were discarded.
Counts were normalized using the median of ratios method from the DESeq2 package in R version 3.6.1.
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table containing normalized counts data for 18 matched RNA-Seq samples for all three shRNAs with and without doxycycline.
Supplementary_files_format_and_content: Matrix table containing normalized counts data for matched RNA-Seq (12) and Ribo-Seq (10) samples for both METTL3 shRNAs with and without doxycycline.

extract_protocol:
Ribo-Seq: Ribsosome footprints were generated by digestion with RNAseI, followed by collection of ribosome-bound RNA fragments using MicroSpin S-400 columns. RNA fragments were purified using with the RNA Clean & Concentrator-25 kit from Zymo, and rRNA was removed using the NEBNext rRNA Depletion kit. 28-30 bp footprints were further purified on a 15% polyacrylamide TBE/Urea gel.
Ribo-Seq: Libraries were prepared with the purified footprints and the SMARTer Small RNA-Seq Kit from Takara following the manufacturer’s instructions.

treatment_protocol: Cells were pre-treated with 200 ng/ml doxycycline for 96 hours to stimulate shRNA induction. Post-induction cells (~15x10E6) were incubated with 100 ug/ml cycloheximide for 5 minutes at 37 °C, then trypsinized and pelleted. The pellet was resuspended in 425 ul of hypotonic buffer (5 mM Tris-HCl (pH 7.5), 2.5 mM MgCl2, 1.5 mM KCl and 1x Halt protease inhibitor cocktail), followed by the addition of 50 ug cycloheximide, 1 ul of 1M DTT, and 100 units of RNAse Inhibitor. The pellet was vortexed, 25 ul 10% Triton X-100 and 25 ul 10% sodium deoxycholate were added then followed by another vortex. The lysates were then cleared by spinning at 16,000 g for 8 minutes at 4 °C.

value: METTL3 shRNA 2

value: 200 ng/ml doxycycline 96 hours


title: MCF7 CRISPR RhoC KO replicate 4

value: CRISPR RhoC KO


title: H3K9me3 - Day 2 - GATA6 WT


title: MCF7 CRISPR RhoC KO replicate 3


title: MCF7 CRISPR RhoC KO replicate 2


title: LNCaP METTL3 sh2 200 DOX R1 Ribo-Seq


title: LNCaP METTL3 sh2 200 DOX R2 Ribo-Seq


title: 128217 R11 SP

data_processing:
Sequencing was done with NovaSeq6000 sequencers (Illumina, San Diego, CA, USA) with a PE100bp read length aiming at 50M reads/sample (RNA-Seq) or a SR50bp read length aiming at 5M reads/sample (small RNA).
Demultiplexing and FastQ file generation was performed using Illumina’s bcl2fastq2 software (v2.20.0).
Genome_build: Fastq files were adapter-trimmed with trimmomatic (v0.38) (Bolger, Lohse et al., 2014), removing sequences of length <18nt after trimming, then mapped against the hg38 human reference genome and the gene assembly v101 using STAR aligner (v2.6.1a) with the default settings.
Supplementary_files_format_and_content: The count matrix was generated using subread (v1.6.4) (Liao Y, Smyth GK, Shi W, 2014) and deferentially expressed genes (DEGs) were called with DeSeq2 (v1.20.0) with a padj. cutoff of 0.05. Overrepresented gene ontology biological processes and KEGG pathways were discovered using clusterprofiler (v3.17.0) (Yu, Wang et al., 2012) on up or down regulated DEGs (with padj<0.05 and a fold change of >2 for either up or down regulated). Volcano plots were generated with bioconductor package enchancedVolcano (v1.4.0) (https://github.com/kevinblighe/EnhancedVolcano) and heatmaps with the heatmap.2 or pheatmap sub-function of gplots (v3.1.0 and v1.0.12 respectevly) (https://github.com/talgalili/gplots and https://github.com/raivokolde/pheatmap respectevely).

growth_protocol: Blood samples were obtained from patients with proven SARS-CoV-2 infection. PBMCs (peripheral blood mononuclear cells) were purified by density gradient centrifugation (Ficoll Plus, GE Healthcare, Chicago, IL, USA). CD14+ cells were isolated from PBMCs by positive selection, using a monocyte isolation kit (Miltenyi Biotech, Bergisch Gladbach, Germany). 2.5×105 CD14+ cells were seeded into 24-well plates (TPP Techno Plastic Products AG, Trasadingen, Switzerland) and cultured for additional 5 days in Roswell Park Memorial Institute (RPMI) 1640 Medium (Thermo Fisher Scientific, Waltham, MA, USA) containing 10 % fetal bovine serum (Thermo Fisher Scientific) and 50 ng/ml M-CSF (Miltenyi Biotec) for macrophage differentiation at 37°C and 5 % CO2.

extract_protocol:
After 4h cells were washed, and total RNA were isolated with the mirVana™ Isolation Kit (Thermo Fisher Scientific) according to the manufacturer's instructions.
RNA-Seq library prep was performed with 100 ng total RNA input and the NEBNext Ultra RNA library prep protocol (New England Biolabs, Ipswich, MA, USA) according to standard procedures.
Libraries were validated and quantified (Tape Station 4200, Agilent Technologies, Santa Clara, CA, USA). All libraries were quantified by using the KAPA Library Quantification Kit (VWR International, Radnor, PA, USA) and the 7900HT Sequence Detection System (Applied Biosystems, Foster City, CA, USA).

treatment_protocol: Medium of differentiated macrophages was exchanged and macrophages were incubated for 2 h at 37 °C and 5 % CO2. After medium exchange lipopolysaccharide (LPS) (5 µg/ml) (Sigma-Aldrich, St. Louis, MO, USA), or SARS-CoV-2 proteins (1 µg/ml) were added for additional 4 h in order to prime the inflammasome process.

value: monocyte-derived macrophages

tag: stimulation

value: stimulated with S-protein

value: male

value: SARS-CoV-2 naïve individual


title: MCF7 CRISPR RhoC KO replicate 1


title: H3K9me2 - Day 4 - GATA6 RES

value: K3 Induced pluripotent stem cell

value: H3K9me2 (Abcam; ab1220)


title: 128211 R10 SP


title: 128213 R11 unst

value: unstimulated


title: MCF7 wild type replicate 4

value: wild-type


title: LNCaP METTL3 sh2 0 DOX R3 Ribo-Seq

description: Untreated inducble METTL3 shRNA #2

value: untreated


title: 128207 R10 unst


title: 128209 R10 LPS

value: stimulated with LPS


title: H3K9me2 - Day 4 - GATA6 KO

value: GATA6Ex4{deleta}1/{deleta}2;ind GATA6

value: Day 4 - Definitive Endoderm


title: MCF7 wild type replicate 3


title: 127457 S1 k4me3

value: k4me3 (Active Motif #39159)

value: SARS-CoV-2 convalescent patient


title: LNCaP METTL3 sh1 200 DOX R3 Ribo-Seq

description: Doxycycline treated inducble METTL3 shRNA #1

value: METTL3 shRNA 1


title: H3K9me2 - Day 4 - GATA6 WT


title: MCF7 wild type replicate 2


title: 128205 R8 SP


title: 128215 R11 LPS


title: H3K9me2 - Day 2 - GATA6 KO

value: Day 2 - Mesendoderm


title: MCF7 wild type replicate 1


title: H3K9me2 - Day 2 - GATA6 RES

value: treated post day 1


title: H3K9me3 - Day 0 - GATA6 WT

value: Day 0 - Pluripotent stem cells

value: H3K9me3 (Abcam; ab8898)


title: LNCaP METTL3 sh1 200 DOX R2 Ribo-Seq

value: 200 ng/ml doxycycline 96 hours


title: 128201 R8 unst

value: monocyte-derived macrophages

value: male


title: 128203 R8 LPS


title: LNCaP METTL3 sh2 0 DOX R1 Ribo-Seq

description: Untreated inducble METTL3 shRNA #2

value: METTL3 shRNA 2


title: H3K9me2 - Day 2 - GATA6 WT

value: K3 Induced pluripotent stem cell

value: H3K9me2 (Abcam; ab1220)


title: LNCaP METTL3 sh1 0 DOX R2 Ribo-Seq

description: Untreated inducble METTL3 shRNA #1

value: untreated


title: LNCaP METTL3 sh1 200 DOX R1 Ribo-Seq


title: MCF10A CRISPR RhoC KO replicate 4

value: CRISPR RhoC KO


title: LNCaP METTL3 sh2 200 DOX R4 RNA-Seq

data_processing:
Sequence reads were aligned to the human reference genome GRCh37 by STAR using the two-pass approach
Ribo-Seq reads were alignes with the options –"winAnchorMultimapNmax 200  --seedSearchStartLmax 15 --outFilterMultimapNmax 20”, to improve mapping of short reads.
Transcript quantification was performed using RSEM. Genes without >10 counts in at least 2 samples were discarded.
Counts were normalized using the median of ratios method from the DESeq2 package in R version 3.6.1.
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table containing normalized counts data for 18 matched RNA-Seq samples for all three shRNAs with and without doxycycline.
Supplementary_files_format_and_content: Matrix table containing normalized counts data for matched RNA-Seq (12) and Ribo-Seq (10) samples for both METTL3 shRNAs with and without doxycycline.

extract_protocol:
RNA-Seq: Total RNA was extracted from the above lysate using the RNA Clean & Concentrator-25 kit, and genomic DNA was removed using the DNA-free kit from Ambion.
RNA-Seq: Libraries were prepared using 1 ug of RNA and the NEBNext Ultra™ II RNA Library Prep Kit with rRNA depletion following the manufacturer’s instructions.


title: MCF10A CRISPR RhoC KO replicate 3


title: MCF10A CRISPR RhoC KO replicate 1


title: H3K9me2 - Day 0 - GATA6 WT


title: LNCaP METTL3 sh1 0 DOX R1 Ribo-Seq

description: Untreated inducble METTL3 shRNA #1


title: MCF10A CRISPR RhoC KO replicate 2


title: LNCaP METTL3 sh2 200 DOX R3 RNA-Seq


title: 128197 R7 LPS

value: stimulated with LPS

value: female


title: 128195 R7 unst

value: unstimulated


title: MCF10A wild type replicate 4

value: wild-type


title: 128193 R6 SP

value: stimulated with S-protein

value: SARS-CoV-2 convalescent patient


title: 128191 R6 LPS


title: H3K4me1 - Day 4 - GATA6 WT

value: Day 4 - Definitive Endoderm

value: H3K4me1 (Diagenode; C15410194)


title: MCF10A wild type replicate 3


title: LNCaP METTL3 sh2 200 DOX R2 RNA-Seq


title: 128199 R7 SP


title: H3K4me1 - Day 2 - GATA6 RES

value: GATA6Ex4{deleta}1/{deleta}2;ind GATA6

value: Day 2 - Mesendoderm

value: treated post day 1


title: MCF10A wild type replicate 2


title: H3K4me1 - Day 2 - GATA6 KO


title: LNCaP METTL3 sh2 200 DOX R1 RNA-Seq

value: 200 ng/ml doxycycline 96 hours


title: 128189 R6 unst

value: monocyte-derived macrophages

value: male


title: LNCaP METTL3 sh2 0 DOX R4 RNA-Seq

description: Untreated inducble METTL3 shRNA #2

value: METTL3 shRNA 2


title: H3K4me1 - Day 4 - GATA6 KO

value: K3 Induced pluripotent stem cell

value: untreated


title: H3K4me1 - Day 4 - GATA6 RES


title: H3K4me1 - Day 2 - GATA6 WT


title: ATAC - Day 4 - GATA6Ex4∆1/∆2;ind FOXA2 (++dox)

description:
sample batch 2
KO_GATA6_RES_FOXA2_Plus_Plus

data_processing:
FASTQC (v0.11.7) of raw sequencing file
Aligned reads to hg19 genome using Bowtie 2 (v.2.2.5)
Peaks identified using MACS2 software (v2.1.1)
Values normalized using Partek Flow (v.9.0.20.0526)
Genome_build: hg19
Supplementary_files_format_and_content: MACS2 output as BigWIG; normalized peak values by TMM and counts per million by Partek Flow

source_name: K3_GATA6Ex4∆1/∆2;ind FOXA2

extract_protocol:
Samples were submitted to Quick Biology. ATAC-seq protocol completed according to published methodology using Nextera Tn5 transposase
Quick Biology completed library prep using established Illimunia pipelines. 25 million paired-end reads were generated using the Illumina HiSeq 4000 platform and provided as FASTQ files.

treatment_protocol: Doxycycline was supplemented to induce GATA6-3xFLAG or FOXA2-3xFLAG cDNA expression in the denoted samples

value: GATA6Ex4{deleta}1/{deleta}2;ind FOXA2

value: treated post day 1 above endogenous level


title: MCF10A wild type replicate 1


title: 128185 R5 LPS

value: stimulated with LPS

value: female

value: SARS-CoV-2 naïve individual


title: ATAC - Day 4 - GATA6Ex4∆1/∆2;ind FOXA2 (+dox)

description:
sample batch 2
KO_GATA6_RES_FOXA2_Plus

value: treated post day 1 endogenous level


title: LNCaP METTL3 sh2 0 DOX R3 RNA-Seq

description: Untreated inducble METTL3 shRNA #2


title: LNCaP METTL3 sh2 0 DOX R1 RNA-Seq

description: Untreated inducble METTL3 shRNA #2


title: 128181 R4 SP

value: stimulated with S-protein


title: 128183 R5 unst

value: unstimulated


title: ATAC - Day 4 - GATA6Ex4∆1/∆2;ind FOXA2 (-dox)

description:
sample batch 2
KO_GATA6_RES_FOXA2_Minus

value: Day 4 - Definitive Endoderm


title: H3K4me1 - Day 0 - GATA6 WT

value: Day 0 - Pluripotent stem cells

value: H3K4me1 (Diagenode; C15410194)


title: 128179 R4 LPS


title: PBMC02.2-3

city: St Louis

first: David

last: Gutmann

state: MO

address: 660 S Euclid Ave

department: Neurology

institute: Washington University in St Louis

description:
total gene deletion (TGD) patient-derived line 3 experimental replicate 3
pbmc.1_GTCAACTCGG-TACACATCGC_S107

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read
RNA-seq reads were aligned to the Ensembl release 100 primary assembly with STAR version 2.7.3a
The raw gene count matrix was imported into Partek Flow software, version 8.0. Normalization size factors were calculated for all gene counts by CPM to adjust for differences in sequencing depth. Ribosomal genes and genes not expressed in the smallest group size minus samples greater than one count-per-million were excluded from further analysis.
Gene-specific analysis was then performed using the lognormal with shrinkage model (limma-trend method) to analyze for differential expression between the three groups of samples
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files containing normalized gene counts for each sample and also output from GSA differential analysis

source_name: hiPSC-derived neural progenitor cells

growth_protocol: For NPC differentiation, hiPSCs were passaged onto PLO/Laminin (Millipore Sigma)-coated plates using ReLeSR (STEMCELL Technologies), and seeded at 200,000 cells/cm2 in NPC induction medium (50% DMEM F12 [Gibco], 50% Neurobasal medium [Gibco], supplemented with N2, B27 [Fisher], 2 mM GlutaMAX [Gibco], 10 ng/mL hLIF, 4 μM CHIR99021, 3 μM SB431541, and 0.1 μM Compound E [all from STEMCELL Technologies]). Cells were maintained in this medium supplemented with 2 μM dorsomorphin for 3 days and without dorsomorphin (STEMCELL Technologies) for an additional 5 days. NPCs were subsequently incubated in NPC maturation medium (50% DMEM/F12, 50% Neurobasal medium supplemented with N2, B27, 2 mM GlutaMAX, 10 ng/mL hLIF, 3 μM CHIR99021 and 2 μM SB431541), and were passaged weekly following Accutase (STEMCELL Technologies) dissociation according to the manufacturer's instructions.

extract_protocol:
Total RNA was extracted from snap-frozen cell pellets of three independent passages using QIAGEN RNeasy Mini Kit according to manufacturer’s instructions.
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq by the Washington University GTAC core

treatment_protocol: CTL1 hiPSCs were infected with four independent CRLF3 shRNA lentiviral particles (sc-94066-V, Santa Cruz Biotechnology; shCRLF3 A: AAAGGCTTCGCACATTCAGTTGGACAGCT; shCRLF3 B: TACAGTCTGAGCAGTCGAAGAAATATAGC; shCRLF3 C: GACATTGAAGCCGTGACTCTAGGAACCAC; TL305215V, Origene) (MOI = 5) . Infected cultures were incubated with mTeSR Plus medium (05825, STEMCELL Technologies) containing 0.4 µg/mL puromycin (73342, STEMCELL Technologies) for selection, and the medium was replaced every other day until drug-resistant colonies formed (~14 days).

value: hiPSC-derived neural progenitor cells

tag: mutation

value: 17q11.2 locus 1.4Mb microdeletion


title: LNCaP METTL3 sh1 200 DOX R4 RNA-Seq

value: METTL3 shRNA 1

value: 200 ng/ml doxycycline 96 hours


title: LNCaP METTL3 sh1 200 DOX R3 RNA-Seq


title: ATAC - Day 4B - GATA6+/+

description:
sample batch 2
WT_GATA6_Day_4B

value: K3 Induced pluripotent stem cell


title: PBMC02.2-1

description:
total gene deletion (TGD) patient-derived line 3 experimental replicate 1
pbmc.4_CAATTGCTAC-ACGTCCTTGC_S42


title: PBMC02.2-2

description:
total gene deletion (TGD) patient-derived line 3 experimental replicate 2
pbmc.3_AGAGGAATCG-ATATGGCAGA_S30


title: LNCaP METTL3 sh1 200 DOX R2 RNA-Seq


title: 128187 R5 SP

value: monocyte-derived macrophages


title: PBMC03.3-3

description:
atypical TGD (aTGD) patient-derived line 1 experimental replicate 3
pb03_cl3_npcs_no_5_rna.AGCAGACATT-GAACACGCCT.HFCTWDSXY_AGCAGACATT-GAACACGCCT

value: 17q11.2 locus 0.9Mb atypical microdeletion


title: 128177 R4 unst


title: ATAC - Day 8 - GATA6+/+

description:
sample batch 1
WT_GATA6_Day_8

value: Day 8 - Hepatic Endoderm

value: untreated


title: 128175 R1 SP

value: male

value: SARS-CoV-2 convalescent patient


title: PBMC03.3-2

description:
atypical TGD (aTGD) patient-derived line 1 experimental replicate 2
pb03_cl3_npcs_no_4_rna.TGACCTGCTG-ATCTGACGGA.HFCTWDSXY_TGACCTGCTG-ATCTGACGGA


title: LNCaP METTL3 sh1 200 DOX R1 RNA-Seq


title: LNCaP METTL3 sh2 0 DOX R2 RNA-Seq

description: Untreated inducble METTL3 shRNA #2

value: METTL3 shRNA 2


title: 128173 R1 LPS

value: stimulated with LPS


title: LNCaP METTL3 sh1 0 DOX R4 RNA-Seq

description: Untreated inducble METTL3 shRNA #1


title: 128171 R1 unst

value: unstimulated


title: ATAC - Day 4 - GATA6Ex4∆1/∆2;ind GATA6 (+dox)

description:
sample batch 1
KO_GATA6_RES_GATA6_Plus_Day_4

value: GATA6Ex4{deleta}1/{deleta}2;ind GATA6

value: Day 4 - Definitive Endoderm

value: treated post day 1


title: PBMC03.3-1

description:
atypical TGD (aTGD) patient-derived line 1 experimental replicate 1
pb03_cl3_npcs_no_1_rna.CGCCAGAATC-ACACGAACAA.HFCTWDSXY_CGCCAGAATC-ACACGAACAA

value: hiPSC-derived neural progenitor cells


title: F08-002.1-3

description:
control line 2 - experimental replicate 3
f08_002.1_3_AAGACATGCG-ACGCAACACA_S7


title: ATAC - Day 4 - GATA6Ex4∆1/∆2;ind GATA6 (-dox)

description:
sample batch 1
KO_GATA6_RES_GATA6_Minus_Day_4


title: LNCaP METTL3 sh1 0 DOX R3 RNA-Seq

description: Untreated inducble METTL3 shRNA #1


title: ATAC - Day 4A - GATA6+/+

description:
sample batch 1
WT_GATA6_Day_4A


title: LNCaP METTL3 sh1 0 DOX R2 RNA-Seq

description: Untreated inducble METTL3 shRNA #1


title: 182444_EM_rash

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

institute: Yale University

data_processing:
Base calls were converted to FASTQs using Illumina’s bcl2fastq conversion software and reads were aligned to the human hg19 genome using STAR 2.7 alignment software via the Broad Institute’s dropseq_workflow pipeline (https://github.com/klarman-cell-observatory/cumulus/blob/master/workflows/drop-seq/dropseq_workflow.wdl), which also converts reads to cell-by-gene sparse count matrices.
The output was loaded into Seurat v3.1.5 for analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data for each sample is a cell-by-gene sparse count matrix, in text format and gzip compressed.

source_name: skin

extract_protocol:
Single cell suspensions were obtained from fresh human skin biopsies obtained with a Biopsy puncher using the Whole Skin Dissociation Kit (Miltenyi Biotec, San Diego, CA, 130-101-540), placed in MACS Tissue Storage Solution (Miltenyi Biotec, 130-100-008) and stored for less than 48 hrs at 4o Celsius. The tissue was washed in DMEM media (ThermoFisher Scientific, 11960).  After the enzymatic digestions, the sample was placed in the MACS Dissociator (Miltenyi Biotec, 130-093-235) and program h-skin-01 was used to isolate cells.  The cells were then washed in DMEM, filtered with a 70um filter, pelleted and resuspended in DMEM.
Single cell suspensions from skin were first counted, their viability assessed using trypan blue (Sigma, St Louis, MO) and adjusted to 50,000/ml in RPMI 1640 medium supplemented with 2 nM L-glutamine, 5 mM 462 HEPES, 100 U/ml penicillin, 100 μg/ml streptomycin, 0.5 mM sodium pyruvate, 0.05 mM 463 nonessential amino acids, and 5% human AB serum (Gemini Bio-Products). We used the Seq-Well platform. Briefly, 10,000 single cells (200 µl of cell suspensions) were loaded into a Seq-Well array preloaded with barcoded capture beads (ChemGenes). After washing excess beads and cells, the arrays were sealed with a polycarbonate membrane and incubated for 30 minutes at 37ºC. Each cell sequestered in a nanowell with a barcoded capture bead was subject to lysis followed by transcript hybridization. The beads recovered from the entire array are washed then mixed with reverse transcriptase master mix. The resulting cDNA was amplified using KAPA HiFi PCR Mastermix (Kapa Biosystems KK2602) with 2,000 beads per 50 μL reaction volume. Generated libraries were then pooled and purified using Agencourt AMPure XP beads (Beckman Coulter, A63881) by a 0.6X SPRI followed by a 0.7X SPRI and quantified using nanodrop. Library quality was assessed using a bioanalyzer 2100 (Agilent Technologies). Single-cell barcoded paired-end sequencing libraries were produced from cDNA with the Nextera XT DNA sample Prep Kit.

tag: Sex

value: M

tag: age

tag: ethnicity

value: Not Hispanic or Latino

tag: disease stage

value: Acute/Recent onset


title: 182298_EM_rash

value: F


title: ATAC - Day 2 - GATA6Ex4∆1/∆2;ind GATA6 (+dox)

description:
sample batch 1
KO_GATA6_RES_GATA6_Plus_Day_2

tag: cell type

value: K3 Induced pluripotent stem cell

tag: genotype

tag: differentiation day

value: Day 2 - Mesendoderm


title: ATAC - Day 6 - GATA6+/+

description:
sample batch 1
WT_GATA6_Day_6

value: Day 6 - Pre-Hepatic Endoderm

tag: doxycyline


title: LNCaP METTL3 sh1 0 DOX R1 RNA-Seq

description: Untreated inducble METTL3 shRNA #1

value: METTL3 shRNA 1

tag: treatment

value: untreated


title: 182298_unaffected_skin


title: LNCaP GFP sh 200 DOX R2 RNA-Seq

description: Doxycycline treated control inducible shRNA

tag: shRNA

value: Non-targeting

value: 200 ng/ml doxycycline 96 hours


title: ATAC - Day 0 - GATA6+/+

description:
sample batch 1
WT_GATA6_Day_0

value: Day 0 - Pluripotent stem cells


title: ATAC - Day 2 - GATA6+/+

description:
sample batch 1
WT_GATA6_Day_2


title: 182296_unaffected_skin


title: ATAC - Day 2 - GATA6Ex4∆1/∆2;ind GATA6 (-dox)

description:
sample batch 1
KO_GATA6_RES_GATA6_Minus_Day_2


title: NF14.1-3

description:
total gene deletion (TGD) patient-derived line 2 experimental replicate 3
14.1_3_CAGCCTTGAG-ATGGCTGGAC_S53

value: 17q11.2 locus 1.4Mb microdeletion


title: F08-002.1-1

description:
control line 2 - experimental replicate 1
f08_002.1_1_CACAGGACTC-GCCATATGTG_S45


title: 182296_EM_rash


title: F08-002.1-2

description:
control line 2 - experimental replicate 2
f08_002.1_2_GTAATGCGGC-TACCAAGCTA_S100


title: LNCaP GFP sh 200 DOX R1 RNA-Seq


title: LNCaP GFP sh 0 DOX R3 RNA-Seq

description: Untreated control inducible shRNA


title: 182288_EM_rash


title: NF-6.1-3

description:
total gene deletion (TGD) patient-derived line 1 experimental replicate 3
6.1_4_AATCGTGCGG-TAACGCAGTC_S18


title: NF14.1-1

description:
total gene deletion (TGD) patient-derived line 2 experimental replicate 1
14.1_1_TCCGTACTTG-TGGATGGATA_S115


title: LNCaP GFP sh 0 DOX R2 RNA-Seq

description: Untreated control inducible shRNA


title: NF-6.1-2

description:
total gene deletion (TGD) patient-derived line 1 experimental replicate 2
6.1_3_CGGCATATAC-TAGTGAATCG_S89


title: LNCaP GFP sh 0 DOX R1 RNA-Seq

description: Untreated control inducible shRNA


title: NF-6.1-1

description:
total gene deletion (TGD) patient-derived line 1 experimental replicate 1
6.1_1_TCACGAACGT-ACACACACGC_S112


title: NF14.1-2

description:
total gene deletion (TGD) patient-derived line 2 experimental replicate 2
14.1_2_GCTATGACCT-ATCCGACACA_S96


title: CrePos.NTC.rep3

data_processing:
Sequences for TruSeq Illumina adapters were removed from the raw reads using Trimmomatic v0.32 (Bolger et al., 2014).
Reads were aligned against the latest mouse reference genome (GRCm38) using the aligner STAR v2.4.1a following the proposed 2-pass strategy, removing alignments containing non-canonical splice junctions (--outFilterIntronMotifs RemoveNoncanonical)
Aligned reads were assigned to genes in the GENCODE vM13 comprehensive gene annotation using the featureCounts command in the subread package with default settings (v1.4.6-p4)
Differential expression analysis was performed using DESeq2 (v1.22.0) running on R (v3.5.1). Briefly, raw counts were imported and filtered to remove genes with low or no expression, that is, keeping genes having two or more counts per million (CPMs) in two or more samples.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files with raw gene counts

molecule: polyA RNA

source_name: CD4+ Th0 cells

extract_protocol:
72 hours post transduction, transduced cells were FACS purified using an SH800 and fluorescent antibody targeting Thy1.1 present in the gRNA cassette. Cell pellets were processed using Qiagen RNeasy RNA extraction kit. RNA-seq libraries were built from rRNA depleted mRNA
Library preparation was performed using the Illumina TruSeq stranded mRNA prep kit (20020595)

treatment_protocol: Spleens and lymphnodes from approximately 8 week old animals were processed to FACS purify naïve CD4+ T cells. After 24hrs of activation in vitro (anti-CD3/anti-CD28) Tcells were transduced with retrovirus containing gRNA expression cassette (either targeting foxp3 or a non-targeting control)

tag: strain

tag: grna target

value: non-targeting

value: CD4+ Th0 cells


title: LNCaP GFP sh 200 DOX R3 RNA-Seq


title: CrePos.NTC.rep2


title: shCRLF3_2

description:
lentiviral CRLF3 knockdown - clone 2
bjff_1_3g2_npc_shcrlf3.AGACAGACGT-TATCAGTGCA.HFF7CDSXY_AGACAGACGT-TATCAGTGCA

value: CRLF3 silencing


title: CrePos.NTC.rep1


title: shCRLF3_3

description:
lentiviral CRLF3 knockdown - clone 3
bjff_4_3g2_npc_shcrlf3.AGAAGGAACA-TGGTAGATGC.HFF7CDSXY_AGAAGGAACA-TGGTAGATGC

value: hiPSC-derived neural progenitor cells


title: shCRLF3_1

description:
lentiviral CRLF3 knockdown - clone 1
bjff_1_1c2_npc_shcrlf3.AGCCATTGCG-ATCCTGCCAG.HFF7CDSXY_AGCCATTGCG-ATCCTGCCAG


title: BJFF 3

description:
control line 1 - experimental replicate 3
ctl-3.GTACCGGATA-AGTGAAGCGC.GTACCGGATA-AGTGAAGCGC_S61


title: BJFF 2

description:
control line 1 - experimental replicate 2
ctl-2.AAGGACCGCA-ATGAGAGAGA.AAGGACCGCA-ATGAGAGAGA_S5


title: CrePos.g5.rep3


title: CrePos.g5.rep2


title: BJFF 1

description:
control line 1 - experimental replicate 1
ctl-1.TCTCTAGCGC-CTGCTTGACG.TCTCTAGCGC-CTGCTTGACG_S76


title: CrePos.g5.rep1


title: AP_d

city: Saint Louis

first: Kristen

middle: L

last: Kroll

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
Raw reads were trimmed with cutadapt to remove low quality bases
Trimmed reads were aligned to hg38 using STAR_2.5.4b with gencode v27 annotation
Aligned reads were quantified using featureCounts 1.6.3 from the subreads package
Genome_build: hg38
Supplementary_files_format_and_content: gene counts text file

source_name: Neural Progenitor Cells generated from iPSCs, further matured for 15 days as a cortical neuroids

extract_protocol:
After 15 days of cortical neuroid differentiation total RNA was collected from the AP, UM, and Unrelated Control Male (UC-M) and Unrelated Control Female (UC-F) lines, using NucleoSpin RNA II kit (Takara) per the manufacturer’s instructions  . RNA was quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific) and the Agilent Bioanalyzer 2100 was used to assess RNA integrity, with only samples with an RNA Integrity Number of >8 used for the sequencing analysis.
RNA-seq library preparation (Ribo-zero) and Illumina sequencing were performed by the Genome Technology Access Center at Washington University.

value: Cortical neuroid

tag: individual

value: Affected Proband (boy)


title: CreNeg.NTC.rep1


title: AP_c


title: AP_b


title: CreNeg.g5.rep3


title: AP_a


title: 20977: Peripheral Blood Mononuclear Cells, Healthy control 6

first: Laiyuan

last: Wang

state: Beijing

address: Xicheng District, No.167 Beilishi Road

department: Department of Epidemiology

institute: Department of Epidemiology, State Key Laboratory of Cardiovascular Disease

description: Gene expression

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: Peripheral Blood Mononuclear Cells

label_protocol: rRNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Overnight fasting blood samples were drawn by venipuncture from all patients and stored at -80 ℃ prior to use. PBMCs were isolated from the middle white monolayer by density gradient centrifugation using lymphocyte separation medium (TBD, Tianjin, China).

tag: diagnosis

value: Healthy control

tag: tissue

value: whole blood

tag: gender

value: male

value: Peripheral Blood Mononuclear Cells


title: 20905: Peripheral Blood Mononuclear Cells, Healthy control 4

description: Gene expression


title: 20753: Peripheral Blood Mononuclear Cells, Healthy control 3

description: Gene expression


title: 20663: Peripheral Blood Mononuclear Cells, Healthy control 2

description: Gene expression


title: UM_d

value: Unaffected Mother


title: CreNeg.g5.rep1


title: CreNeg.NTC.rep2


title: CreNeg.g5.rep2


title: UM_c


title: 20984: Peripheral Blood Mononuclear Cells, Healthy control 7

description: Gene expression


title: 20970: Peripheral Blood Mononuclear Cells, Healthy control 5

description: Gene expression


title: mmCD4.CREpos.NTC.K27ac.rep3

data_processing:
Sequences for TruSeq Illumina adapters were removed from the raw reads using Trimmomatic v0.32 (Bolger et al., 2014).
Paired-end reads were mapped using Bowtie (v1.0.0 PMID: 19261174) against Mouse (mm10) genome with flags -v 2 -X 2000 --best --strata -m 1.
Duplicates were removed using Picard MarkDuplicates v1.130
Low mappability or blacklisted regions identified by the ENCODE project (Consortium, 2012) were filtered out from the final BAM files
Using the sequenced input controls, binding regions were identified using the callpeak function in MACS2 v2.1.0.20151222 (Zhang et al., 2008).
Signal files were generated with deeptools bamCoverage (v3.0.1 PMID:24799436) ignoring duplicates, extending reads 200bp and converting the read counts to RPKMs.
For the differential binding analysis, first, a union peakset was computed merging individual peak calls using bedtools2 v2.25.0 (Quinlan and Hall, 2010). Then, reads in peaks were estimated using featureCounts and the difference in binding was assessed with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig signal in RPMs

extract_protocol:
72 hours post transduction, transduced cells were sort purified using an SH800 and fluorescent antibody targeting Thy1.1 present in the gRNA cassette. Cells were crosslinked for 10 minutes at RT with 1% formaldehyde before nuclei were processed for ChIP as described in Savic et al, 2013. Briefly, following fixation, cells were incubated with 1mL Farnham Lysis Buffer for 10 minutes followed by centrifugation. Pellets were resuspended in 100µL RIPA buffer and sonicated in a 1.5mL tube for 30 cycles of 30s on and 30s off using a Bioruptor Pico.
ChIP-seq libraries were prepared using a Kapa Hyper Prep kit.

treatment_protocol: Spleens and lymphnodes from approximately 8 week old animals were processed to MACS purify naïve CD4+ T cells. After 24hrs of activation in vitro (anti-CD3/anti-CD28) Tcells were transduced with retrovirus containing gRNA expression cassette (either targeting Foxp3 or a non-targeting control)

tag: chip antibody


title: 16638: Peripheral Blood Mononuclear Cells,CAD patient 22

description: Gene expression

value: coronary artery disease


title: Subject 192567 Unaffected Skin (scBCR)

data_processing:
Base calls were converted to fastq sequences and demultiplexed using the cellranger v3.1.0 mkfastq function and aligned to the GCRhg38 genome supplied by 10X Genomics.
Sparse count matrices, barcode assignments and feature calls were made using the cellranger count subcommand.
Reconstructed V(D)J sequences from single cell sequencing were extracted using the cellranger vdj function from fastq reads.
V(D)J germline genes were re-assigned using IgBLAST v.1.6.1 also using the September 12, 2018 version of the IMGT gene database.
Following V(D)J annotation, non-functional sequences were removed from further analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: Output files from Cell Ranger (10X Genomics) were archived and compressed into a tar.gz file, one per sample. Each compressed archive contains the tab-delimited text files filtered_contig_annotations.csv & filtered_contig.fasta.

extract_protocol:
PBMCs and skin infiltrating cells were isolated by Ficoll-Paque PLUS (GE Healthcare) gradient centrifugation. Red blood cells (RBCs) were lysed using ACK buffer (ThermoFisher A1049201). Single cell suspensions were obtained from fresh human skin biopsies obtained with a Biopsy puncher using the Whole Skin Dissociation Kit (Miltenyi Biotec, San Diego, CA, 130-101-540), placed in MACS Tissue Storage Solution (Miltenyi Biotec, 130-100-008) and stored for less than 48 hrs at 4o Celsius.
Single cell preparations were loaded into the Chromium Controller (10x Genomics) for emulsion generation and libraries were prepared using the Chromium Single-cell 5′ Reagent Kit for version 1 chemistry per the manufacturer’s protocol. Libraries were sequenced on the NovaSeq 6000 with 2 x150 paired end reads.

tag: Sex

value: F

value: Not Hispanic or Latino

value: Acute/Recent onset


title: Subject 192566 Unaffected Skin (scBCR)

value: M

tag: age


title: UM_b


title: 17329: Peripheral Blood Mononuclear Cells,CAD patient 24

description: Gene expression


title: 20162: Peripheral Blood Mononuclear Cells, Healthy control 1

description: Gene expression


title: mmCD4.CREpos.NTC.K27ac.rep2


title: 16571: Peripheral Blood Mononuclear Cells,CAD patient 21

description: Gene expression


title: 15413: Peripheral Blood Mononuclear Cells,CAD patient 19

description: Gene expression


title: Subject 192566 EM Lesion (scBCR)

tag: ethnicity


title: Subject 192567 EM Lesion (scBCR)

tag: disease stage


title: 16707: Peripheral Blood Mononuclear Cells,CAD patient 23

description: Gene expression

tag: cell type


title: UM_a


title: Subject 192566 PBMC (scBCR)

source_name: PBMC


title: Subject 192565 Unaffected Lesion (scBCR)


title: UC_M_c

value: unrelated male


title: Subject 192565 EM Lesion (scBCR)


title: mmCD4.CREpos.NTC.K27ac.rep1

value: non-targeting


title: mmCD4.CREpos.g5.K27ac.rep3

value: CD4+ Th0 cells


title: UC_M_d


title: mmCD4.CREpos.g5.K27ac.rep2


title: mmCD4.CREpos.g5.K27ac.rep1


title: 15190: Peripheral Blood Mononuclear Cells,CAD patient 16

description: Gene expression


title: 16206: Peripheral Blood Mononuclear Cells,CAD patient 20

description: Gene expression


title: mmCD4.CREneg.g5.K27ac.rep3


title: Subject 192564 Unaffected Skin (scBCR)


title: UC_F_d

value: unrelated female


title: Subject 192564 EM Lesion (scBCR)


title: mmCD4.CREneg.g5.K27ac.rep2


title: Subject 192563 EM Lesion (scBCR)


title: UC_F_c


title: mmCD4.CREneg.g5.K27ac.rep1


title: Subject 192561 Unaffected Skin (scBCR)


title: UC_M_b


title: UC_F_b


title: ATAC_Control_2

city: Rome

first: Matteo

last: Pallocca

address: Via Fermo Ognibene

institute: Italian National Cancer Institute "Regina Elena"

data_processing:
BaseSpace Illumina Cloud Environment was used for basecalling and demultiplexing.
Reads were mapped with Bowtie vv. 2.2.3
Peaks were called with MACS2, with parameters --nomodel --shift -100 --extsize 200
Genome_build: mm9
Supplementary_files_format_and_content: bigWig enrichment files generated with MACS2 bdgcmp command

source_name: VkCHE mice

extract_protocol:
To profile open chromatin, we used the ATAC-seq protocol developed by (Buenrostro et al., 2013) with minor modifications. Malignants and control Bone Marrow aspirates, were isolated for PCs by magnetic cell separation using human CD138 positive selection kit (Miltenyi-Biotec- Germany) and Macs separator (Macs Miltenyi-biotec- Germany. To perform the analysis 50,000 cells were washed once with 1X PBS and centrifuged at 500g for 5 minutes at 4°C. For flash-frozen cell pellets were removed from -80°C and immediately re-suspended in ice-cold cell lysis buffer. Nuclear morphological evaluation was performed by Trypan blue coloration, before starting the tagmentation. Pellets were re-suspended in transposase 25 μl reaction buffer containing 2,5 μl of Tn5 transposase and 12.5 μl of TD buffer (Nextera DNA Sample preparation kit from Illumina) on ice. Samples were incubated at 37°C for 30 min. The samples were purified with MiniElute PCR Purification Kit (Qiagen).
To amplify transposed DNA fragments we used NEBNext High-Fidelyty 2x PCR Master Mix (New England Labs) and the Customized Nextera PCR Primers (see Table 3). Libraries were purified using Agencourt Ampure XP (Beckman) magnetic beads (1:1 ratio) to remove remaining adapters and double purified (1:0,5 and 1:1,8-05) for right side selection. Libraries were controlled using a High Sensitivity DNA Kit Bioanalyzer (Agilent Technologies).

tag: genotype/variation

value: Control


title: Subject 192561 EM Lesion (scBCR)


title: 14425: Peripheral Blood Mononuclear Cells,CAD patient 15

description: Gene expression


title: UC_M_a

value: Cortical neuroid


title: UC_F_a


title: ATAC_Control_1


title: 14304: Peripheral Blood Mononuclear Cells,CAD patient 13

description: Gene expression


title: 13070: Peripheral Blood Mononuclear Cells,CAD patient 11

description: Gene expression


title: ATAC_vkCHE_5

value: Che-1 silencing


title: 14186: Peripheral Blood Mononuclear Cells,CAD patient 12

description: Gene expression


title: ATAC_vkCHE_4


title: ATAC_vkCHE_3


title: ATAC_vkCHE_2


title: Mouse primary tumour

description: MsPrim

source_name: Orthotopic pancreatic cancer model

tag: processing

value: Dissociated cells from tumour

value: Primary tumour


title: 12878: Peripheral Blood Mononuclear Cells,CAD patient 8

description: Gene expression

value: whole blood

value: male


title: 12879: Peripheral Blood Mononuclear Cells,CAD patient 9

description: Gene expression

value: Peripheral Blood Mononuclear Cells


title: ATAC_vkCHE_1


title: M11_dHS3_H3K27me3_ChIP-Seq

city: Busan

first: AeRi

last: Kim

address: 2, Busandaehak-ro 63beon-gil, Geumjeong-gu

country: South Korea

institute: Pusan national university

data_processing:
ChIP-seq raw reads were filtered to remove input read ends with poor quality values (quality score 20) and then aligned to the human chromosome 11 (hg19 genome assembly)  using Bowtie2. Aligned BAM files were filtered by Minimum MAPQ quality score 20 and sorted by chromosomal coordinates. Potential PCR duplicates were removed from BAM files. Bigwig files generated from BAM files using BamCoverage
Genome_build: human chromosome 11 (hg19)
Supplementary_files_format_and_content: bigwig

growth_protocol: MEL/ch11 cells were cultured in DMEM medium containing 10% FBS.

extract_protocol:
Nuclei were digested with 100 units of MNase at 37°C for 15 min. Mono or di-nucleosomes sized chromatin was incubated with antibodies for 3 h at 4°C and recovered with protein A agarose beads.
ChIP DNA (10 ng for H3K27ac and 1 ng for H3K27me3) was processed using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) with manufacturer’s instructions. The ends of ChIP DNA were repaired by NEBNext Ultra II End Prep enzyme mix and ligated with NEBNext adaptors. Adaptor-ligated DNA was selected at 175-200 bp size using NEBNext sample purification bead and amplified using the adaptor primers (7 cycles for H3K27ac and 10-11 cycles for H3K27me3). The fragments are purified using NEBNext sample purification beads.

treatment_protocol: For transcriptional activation of the β-globin gene, MEL/ch11 cells were induced at a concentration of 1.5x10^5 cells/ml with 5 mM HMBA for 72 h.

tag: cell line

value: erythroleukemia cells

tag: genotype

value: LCR HS2 deletion

value: H3K27me3 (Millipore, 07-449)


title: M11_dHS3_H3K27ac_ChIP-Seq

value: H3K27ac (Abcam, ab4729)


title: Mouse blood sample

description: MsBlood

value: Enriched cells (mouse immunomagnetic depletion) from blood

value: Blood sample


title: 13033: Peripheral Blood Mononuclear Cells,CAD patient 10

description: Gene expression

value: coronary artery disease


title: Mouse secondary tumour

description: MsSec

value: Secondary tumour


title: vkche_2

data_processing:
BaseSpace Illumina Cloud Environment was used for basecalling and demultiplexing.
RNA-seq was analyzed via the web pipeline RAP, which employs the Tuxedo suite for mapping (Tophat) and transcripts reconstruction (Cufflinks, Cuffdiff)
For spikein-normalized data, HTSeq count were normalized using spikein raw counts as scaling factors.
Genome_build: mm9
Supplementary_files_format_and_content: all genes spikein-normalized differential expression
Supplementary_files_format_and_content: spikein raw count table

extract_protocol:
total RNA was extracted using Qiazol (Invitrogen), purified from genomic DNA contamination through a DNase I (Qiagen) digestion step and further enriched by Qiagen RNeasy columns for gene expression profiling (Qiagen). Quantity and integrity of the extracted RNA were assessed by NanoDrop Spectrophotometer (NanoDrop Technologies) and by Agilent 2100 Bioanalyzer (Agilent Technologies), respectively.
RNA libraries for sequencing were generated in triplicate according to the Illumina TruSeq Stranded Total RNA kit with an initial ribosomal depletion step using Ribo Zero Gold (Illumina, Inc., San Diego, CA, US). Starting material was 500ng of total RNA.

value: bone marrow


title: vkche_3


title: vkche_1


title: M11_dHS2_2nd_H3K27me3_ChIP-Seq


title: M11_dHS2_H3K27ac_ChIP-Seq


title: M11_dHS2_H3K27me3_ChIP-Seq


title: Control_3

value: control


title: M11_Con_H3K27me3_R2_ChIP-Seq


title: 12545: Peripheral Blood Mononuclear Cells,CAD patient 7

description: Gene expression


title: Control_2


title: M11_Con_H3K27ac_ChIP-Seq


title: M11_Con_H3K27me3_R1_ChIP-Seq


title: Control_1


title: 11777: Peripheral Blood Mononuclear Cells,CAD patient 6

description: Gene expression


title: 11657: Peripheral Blood Mononuclear Cells,CAD patient 5

description: Gene expression


title: 11061: Peripheral Blood Mononuclear Cells,CAD patient 4

description: Gene expression


title: M24 VMH_nonstressRep3

status: Public on Jun 06 2021

city: oxford

first: Haifei

last: Shi

state: OH

address: 700 E High Street

department: Biology

institute: Miami University

data_processing:
trimming of any low-quality reads with Phred quality score of Q30 was performed in CLC genomics workbench 10.0
After QC and adaptor read-through trimming, deconvoluting likely PCR based duplicates using UMIs, 98% of the reads mapped to the Rattus norvegicus (Ensembl, Rnor_6.0) genome
Assessment of sample variability was confirmed using Principal Component Analysis in CLC Genomics Workbench 10.0. Potential outliers were confirmed by notes obtained during my punches and discarded.
differential expression gene analysis was performed in CLC Genomics Workbench 10.0 using a bootstrapped receiver operating characteristic (bROC) approach with a Gini coefficient of CONF ≥ 0.95 cut-off for DE of identified genes between nonstress and stress groups
Genome_build: Ensembl, Rnor_6.0) genome.
Supplementary_files_format_and_content: Differential Expression analyses: Stress vs. Nonstress groups for each of the 9 brain regions from females and for each of the 9 brain regions from males

organism: Rattus norvegicus

source_name: brain punches

extract_protocol:
Brain punches were vortexed for 10-20 seconds and total RNA was isolated following manufacturer’s instructions using Maxwell® 16 LEV simplyRNA Tissue kit (Promega, Madison, WI). 100 ng of total RNA was subjected to ribosomal RNA (rRNA) removal using Low Input Ribominus Eukaryote System v2 (Ambion # A15027). Concentration, purity, and integrity of all RNA samples were assessed using a Nanodrop and RNA 6000 pico chip on the Agilent 2100 Bioanalyzer.
An RNA-sequencing library was prepared from the rRNA-depleted RNA using Nextflex Rapid Directional qRNA-Seq Kit (Bioo Scientific, TX, USA).
final pooling and sequencing (Illumina 150bp Paired End HiSeq3000, Center for Genome Research and Biocomputing at Oregon State University, Corvallis, Oregon, USA)

value: Sprague Dawley

tag: postnatal day (pd)

tag: group

value: nonstress

tag: brain region

value: ventromedial hypothalamic nucleus


title: 10984: Peripheral Blood Mononuclear Cells,CAD patient 3

description: Gene expression


title: 10959: Peripheral Blood Mononuclear Cells,CAD patient 2

description: Gene expression


title: M24 CA1_nonstressRep3

tag: strain

value: Cornu Ammonis area 1 of the hippocampus


title: M24 OFC_nonstressRep3

value: orbitofrontal cortex of the prefrontal lobe


title: M24 DG_nonstressRep3

value: male

value: dentate Gyrus of the hippocampus


title: 10092: Peripheral Blood Mononuclear Cells,CAD patient 1

description: Gene expression

tag: diagnosis

value: whole blood

value: Peripheral Blood Mononuclear Cells


title: M24 ARC_nonstressRep2

value: arcuate nucleus of the hypothalamus


title: M17 PVN_nonstressRep2

value: paraventricular nucleus of the hypothalamus


title: M17 CA1_nonstressRep2


title: M17 ARC_nonstressRep2


title: 15381: Peripheral Blood Mononuclear Cells,CAD patient 17

description: Gene expression

tag: tissue


title: M12 ARC_stressRep3

value: stress


title: M11 CA1_stressRep3


title: M12 PVN_stressRep3


title: M11 VMH_stressRep3


title: M11 PVN_stressRep2


title: M11 OFC_stressRep3


title: M11 ARC_stressRep2


title: M24 PVN_nonstressRep3


title: M9 CEA_nonstressRep3

value: central nucleus of the amygdala


title: M9 ARC_nonstressRep1


title: 14378: Peripheral Blood Mononuclear Cells,CAD patient 14

description: Gene expression

value: coronary artery disease

tag: gender


title: M2 PVN_stressRep1


title: M2 DG_stressRep3

value: Dentate Gyrus of the hippocampus


title: M9 PVN_nonstressRep1


title: M2 OFC_stressRep2


title: M2 CEA_stressRep3


title: M2 VMH_stressRep2


title: M2 CA3_stressRep3

value: Cornu Ammonis area 3 of the hippocampus


title: F22 PVN_stressRep3

value: female


title: M2 CA1_stressRep2

value: Sprague Dawley


title: M2 BLA_stressRep3

value: basolateral amygdala


title: M2 ARC_stressRep1


title: F18 ARC_stressRep2


title: F18 PVN_stressRep2


title: F17 PVN_stressRep1


title: F7 ARC_nonstressRep3

value: nonstress


title: F7 PVN_nonstressRep3


title: F17 ARC_stressRep1


title: BGB-Tram-D11-2

city: LOS ANGELES

first: Sixue

last: Liu

state: California

address: 10833 Le Conte Avenue

department: Medicine

institute: UCLA

data_processing:
Library strategy: RNA-based TCR-seq
Raw reads were analyzed from the QIAGEN GeneGlobe Data Analysis Center to estimate the abundance of reads of unique CDR3 sequence and generate TCR clonotype calls
R package tcR was used to perform all the statistical analysis for TCR repertoires
Genome_build: GRCh38
Supplementary_files_format_and_content: raw count matrix of TCR clones

source_name: Nras mutated syngeneic mouse model

extract_protocol:
QIAGEN All Prep DNA/RNA Mini Kit and Ambion mirVana miRNA Isolation Kit
QIAGEN QIAseq Immune Repertoire RNA Library Kit

value: Nras mutated murine melanoma cell line

tag: treatment

tag: rna population

value: Transcripts of T cell receptor alpha, beta, gamma, and delta genes (CDR3 region)


title: BGB-Tram-D4-3


title: BGB-Tram-D11-3


title: BGB-Tram-D11-1


title: BGB-Tram-D4-2


title: F2 VMH_nonstressRep3

tag: Sex

value: ventromedial hypothalamic nucleus


title: F3 ARC_nonstressRep2


title: WT_D5_dEN_Rep4

first: Hua-Jun

last: Wu

address: 8 science park road, zhongguancun life science park

department: School of Basic Medical Sciences

institute: Peking University Health Science Center

data_processing:
Raw sequence reads of capture Hi-C (cHi-C) were mapped to the hg19 version of the human genome using BWA (v0.7.17) with parameters (mem -A 1 -B 4 -E 50 -L 0). Mapped reads were further processed by HiCExplorer (v3.5.1) to remove duplicated reads and reads from dangling ends, self-circle, self-ligation and same fragments. The replicates of the same samples were compared, and confirmed to have high consistency (Pearson correlation coefficient: 0.83-0.99), then were merged to construct contact matrices of 2 kb resolution. Normalization was performed to ensure that all samples have the same number of total contacts, followed by KR normalization. The relative contact difference between two cHi-C maps was calculated by subtracting one from the other after scaling one sample to the other by using the total number of contacts in each sample.
Genome_build: hg19
Supplementary_files_format_and_content: hd5 containing raw Hi-C matrix; SOX17_TAD_ProbeFile.bed is the probe list used for all capture Hi-C libraries

source_name: Human induced pluripotent stem cell (hiPSC)

growth_protocol: ZIP13K2 cultures were treated with Accutase (Sigma-Aldrich, A6964) supplemented by 10 µM Y-27632 (Tocris, 1254) to obtain single cells. To quench and wash the cells, equal volumes of mTeSR1 (Stemcell Technologies) were added and cells spun down for 5 min. at 300 x g, 21°C. After resuspension in mTeSR1 supplemented by 10 µM Y-27632, cells were counted and seeded according to the manufacturer’s instructions on Matrigel (Corning) pre-coated culture plates / dishes. Media change using the STEMdiff Trilineage Endoderm Differentiation media (Stemcell Technologies) was performed on a daily base after washing the cultures with equal volumes of DPBS (Thermo Fischer Scientific, 14190250) according to the manufacturer’s instructions.

extract_protocol: cHi-C libraries were prepared from wild type or homozygous SOX17∆5’CTCF iPSC or dEN cells. Undifferentiated or day 5 differentiated ZIP13K224 cells were grown to a final count of 4-5 million, treated with Accutase (Sigma-Aldrich, A6964), resuspended and washed in DPBS. Cell lysis, NlaIII (NEB R0125) digestion, ligation and de-crosslinking was performed according to the Franke et al. protocol25. Adaptors were added to DNA and amplified according to Agilent instructions for Illumina sequencing. The library was hybridized to the custom-designed sure-select beads and indexed for sequencing of 200x106 fragments per sample (100 bp paired-end) following the Agilent instructions. Capture Hi-C experiments were performed as biological duplicates.

tag: perturbation

value: Wildtype

tag: differentiation days

value: day 5


title: F2 OFC_nonstressRep3

value: orbitofrontal cortex of the prefrontal lobe


title: BGB-Tram-D4-1


title: 15399: Peripheral Blood Mononuclear Cells,CAD patient 18

description: Gene expression

value: whole blood

value: male

tag: cell type

value: Peripheral Blood Mononuclear Cells


title: WT_D5_dEN_Rep3


title: F22 ARC_stressRep3

value: stress

value: arcuate nucleus of the hypothalamus


title: BGB-D11-3


title: F2 CEA_nonstressRep3

value: central nucleus of the amygdala


title: F2 CA1_nonstressRep3

value: Cornu Ammonis area 1 of the hippocampus


title: WT_D5_dEN_Rep2


title: F3 PVN_nonstressRep2

value: female

value: paraventricular nucleus of the hypothalamus


title: F2 BLA_nonsressRep3

value: Sprague Dawley

value: basolateral amygdala


title: M24 CEA_nonstressRep2

value: nonstress


title: BGB-D11-2

value: Nras mutated murine melanoma cell line

value: Transcripts of T cell receptor alpha, beta, gamma, and delta genes (CDR3 region)


title: M24 BLA_nonstressRep3


title: F2 PVN_nonstressRep1


title: WT_D0_iPS_Rep4

value: Wildtype

value: day 0


title: BGB-D4-2


title: BGB-D11-1


title: BGB-D4-1


title: F2 ARC_nonstressRep1


title: WT_D5_dEN_Rep1

value: day 5


title: M24 CA3_nonstressRep3

value: Cornu Ammonis area 3 of the hippocampus


title: WT_D0_iPS_Rep1


title: BGB-D4-3


title: M17 VMH_nonstressRep2

value: male

value: ventromedial hypothalamic nucleus


title: M17 CA3_nonstressRep2


title: M17 BLA_nonstressRep2


title: M17 OFC_nonstressRep2

value: orbitofrontal cortex of the prefrontal lobe


title: WT_D0_iPS_Rep3


title: M12 VMH_stressRep1

value: stress


title: M12 OFC_stressRep1


title: M17 DG_nonstressRep2

value: Dentate Gyrus of the hippocampus


title: Tram-D11-3

value: Trametinib


title: Tram-D11-2


title: WT_D0_iPS_Rep2


title: M17 CEA_nonstressRep1

value: central nucleus of the amygdala


title: M12 DG_stressRep2


title: KO_D5_dEN_Rep3

description:
SOX17 upstream TIR boundary CTCF knockout
SOX17_TAD_ProbeFile.bed


title: M12 CEA_stressRep2


title: Tram-D4-3


title: M12 BLA_stressRep2


title: KO_D5_dEN_Rep2


title: M12 CA3_stressRep2


title: M12 CA1_stressRep1

value: Cornu Ammonis area 1 of the hippocampus


title: M11 CEA_stressRep1

value: Sprague Dawley


title: M11 BLA_stressRep1

value: basolateral amygdala


title: KO_D0_iPS_Rep3


title: KO_D0_iPS_Rep4


title: KO_D5_dEN_Rep4


title: M11 CA3_stressRep1


title: V-D11-2

value: no


title: KO_D0_iPS_Rep1


title: F22 VMH_stressRep3

value: female


title: M11 DG_stressRep1


title: Tram-D4-1

value: Nras mutated murine melanoma cell line

value: Transcripts of T cell receptor alpha, beta, gamma, and delta genes (CDR3 region)


title: V-D4-3


title: M9 VMH_nonstressRep1

value: nonstress


title: M9 OFC_nonstressRep1


title: V-D11-1


title: KO_D5_dEN_Rep1

value: day 5


title: Tram-D4-2


title: Tram-D11-1


title: F22 CA1_stressRep3


title: M9 CA1_nonstressRep1


title: D5_CTCFbKO_DDSOX17+S_CXCR4+_Rep3

data_processing:
Gene counts are quantified by using RSEM default parameters with REFSEQ annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Gene quantification files (*.genes.results) are generated using RSEM

growth_protocol: ZIP13K2 cultures were treated with Accutase (Sigma-Aldrich, A6964) supplemented by 10 µM Y-27632 (Tocris, 1254) to obtain single cells. To quench and wash the cells, equal volumes of mTeSR1 (Stemcell Technologies) were added and cells spun down for 5 min. at 300 x g, 21°C. After resuspension in mTeSR1 supplemented by 10 µM Y-27632, cells were counted and seeded according to the manufacturer’s instructions on Matrigel (Corning) pre-coated culture plates / dishes. Media change using the STEMdiff Trilineage Endoderm Differentiation media (Stemcell Technologies) was performed on a daily base after washing the cultures with equal volumes of DPBS (Thermo Fischer Scientific, 14190250) according to the manufacturer’s instructions. Triplicates of either undifferentiated or differentiated ZIP13K226 cultures were treated with Accutase® (Sigma-Aldrich, A6964) and differentiated cultures were further quenched with FACS-buffer containing 5 mM EDTA (ThermoFischer Scientific, 15575020) 10% Fetal bovine serum (FBS) (ThermoFischer Scientific, 26140079) in DPBS (Thermo Fischer Scientific, 14190250). In order to enrich for CXCR4- or CXCR4+ cell fractions of differentiated cultures, cells were stained for anti-Human CRCX4 (CD184) PE (as described under 21. FACS) and compared to Isotype and unstained control sorted for either CXCR4- or CXCR4+ on the Aria II (Beckton Dickinson).

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
RNA isolation including on-column DNase digest of enriched cell populations was performed using the RNeasy Mini Kit (Qiagen, 74104) according to the manufacturer’s instructions.

treatment_protocol: PB-CAG-DD-3xFLAG-hSOX17-GS-TagBFP-BGHpA rescue construct was generated by Gibson Assembly® (NEB, E2621L) of BstBI /BamHI double-digested PB-CAG-BGHpA (Addgene Plasmid #92161) and EcoRI digested synthetically generated pUC19 DD-3xFLAG-SOX17-GS-TagBFP (Genewiz). Both, PB-CAG-DD-3xFLAG-hSOX17-GS-TagBFP-BGHpA and pNF21a-Piggy-BAC-Transposase vector were co-transfected into SOX17∆5’CTCF#8.2 mTeSR1 (Stemcell Technologies) maintained human induced pluripotent stem cells of the ZIP13K224 cell line harboring the SOX17 boundary 2 deletion. Transfection was conducted by the use of equimolar plasmid ratios in combination with Lipofectamine Stem Transfection Reagent (Thermo Fischer Scientific, STEM00003) according to the manufacturer’s instructions. Transfected or untransfected cells were treated with mTeSR1 (Stemcell Technologies) containing 250 µg/ml m Hygromycin B (Carl Roth, 1287.1) for 2 weeks. TagBFP negative surviving cells were FACS-sorted on the FACS Aria Fusion (Beckton Dickinson) and seeded in low density (5-10x105/10 cm) using mTeSR1 supplemented with 10 µM Y-27632 (Tocris, 1254) to derive a polygenic /polyclonal SOX17 rescue cell line. To stabilize ectopic SOX17-TagBFP protein, undifferentiated iPSC or day 2 dEN onwards differentiating cells were treated with 1 µM final Shield-1 (Takara, 632189) back to back with untreated controls before sample collection for downstream analysis.

value: Day 5

value: SOX17(∆5'CTCF) + transgenic rescue element(SOX17)

value: 1 uM Shield-1 treated

tag: cxcr4 status


title: F22 OFC_stressRep3

value: orbitofrontal cortex of the prefrontal lobe


title: M9 DG_nonstressRep1

value: male


title: KO_D0_iPS_Rep2

value: day 0


title: F7 CEA_nonstressRep2


title: D5_CTCFbKO_DDSOX17+S_CXCR4-_Rep3


title: F18 BLA_stressRep3

value: stress


title: V-D4-2


title: M9 BLA_nonstressRep1


title: V-D4-1


title: M9 CA3_nonstressRep1

value: Cornu Ammonis area 3 of the hippocampus


title: D5_CTCFbKO_DDSOX17-S_CXCR4-_Rep3


title: CTCF bait_NSC_Rep1

city: London

first: Suzana

last: Hadjur

address: 72 Huntley street

department: Cancer biology

country: United Kingdom

institute: Ucl

data_processing:
Library strategy: UMI-4C
UMI-4C raw data were processed using the ‘umi4cPackage’ (v0.0.0.9000) pipeline from the Tanay Lab
To briefly summarize the pipeline
raw reads are parsed through the UMI-4C pipeline, those reads containing the bait and padding sequence are retained and demultiplexed if required
The retained reads are split based on a perfect match to the restriction enzyme sequence to create a segmented fastq file. The first 10 bases of read 2 are extracted and attached to the segments derived from each read pair. Segments are aligned to the mm10 genome using bowtie2.
UMI filtering is used to determine the number of molecules supporting each ligation event, this information is stored in an adj table
The resulting UMI-4C tracks are then imported into R where the molecule counts per ligated fragment can be visualized / interrogated
Genome_build: mm10
Supplementary_files_format_and_content: The final tracks after processing through the umi4cPackage pipeline, converted to a readable text file. Contains the number of molecules supporting each ligation event

source_name: ES-derived Neural stem cells

growth_protocol: Mouse embryonic stem cells (ESC) were cultured in naïve (2i) conditions and neural stem cells were cultured in EGF/FGF media.

extract_protocol:
cell were fixed and extracted nuclei were processed so to capture DNA fragments in close proximity.
Libraries were constructed according to the UMI-4C protocol. Please see methods section of manuscript for further information.
UMI-4C libraries were pooled and sequenced  on a HiSeq 2500 platform.

treatment_protocol: untreated

value: ES-derived Neural stem cells

tag: cell culture

value: EGF-FGF grown

tag: umi-4c bait


title: F3 CEA_nonstressRep1

value: Sprague Dawley

value: central nucleus of the amygdala


title: D5_CTCFbKO_DDSOX17-S_CXCR4+_Rep3

tag: cell line


title: CTCF bait_ESC_Rep2

source_name: Embryonic stem cells

value: Embryonic stem cells

value: 2i-LIF grown


title: F3 DG_nonstressRep3

tag: postnatal day (pd)

value: female

value: Dentate Gyrus of the hippocampus


title: ES FCS_Rep 3_SA1 3p KD

data_processing:
ES FCS RNA-seq data were processed using the RNA-seq Nextflow pipeline (v19.01.0), with the following parameters –aligner hisat2 –genome mm10, with –reverse_stranded specified for paired-end samples.
FeatureCounts output was parsed through edgeR (v3.16.5) and DESeq2 (v1.14.1) to generate normalized expression counts
The normalized counts for RNAseq Rep1 were calculated in edgeR. Very lowly expressed genes were removed (rowSum cpm <2 across SCR and SA1SP replicates), normalization factors were calculated using calcNormFactors and dispersions estimated using estimateDisp. The edgeR volcano plot statistics were calculated using the exactTest and topTags functions
To generate the normalized counts for all ES FCS RNAseq experiments for GSEA, the FeatureCounts output for all ES FCS experiments was combined into a single table and read it into DESeq2. A DESeq2 object was built using the function DESeqDataSetFromMatrix and estimation of size factors and dispersions were calculated using the DEseq function. Normalized counts were calculated using the ‘counts’ function. Very lowly expressed genes (rowSum normalized count <10 across all samples) were removed
The ES2i raw reads were parsed into VAST-TOOLS to calculate splicing statistics, therefore there is no processed data for them as the raw reads were used. VAST-TOOLS output reported in publication
Genome_build: mm10
Supplementary_files_format_and_content: ES_FCS_Rep1_SA1_SP_KD_Analysis.txt contains the EdgeR normalized counts  ES FCS Rep1
ES_FCS_All_Reps_Analysis.txt  contains the DESeq2 normalized counts for all ES_FCS experiments

growth_protocol: Mouse embryonic stem cells (ESC) were cultured in serum (FCS) or naïve (2i) conditions.

extract_protocol:
Total RNA was first depleted of rRNA (ES FCS) or enriched for PolyA (ES 2i). Two rounds of rRNA depletion were done.
RNA-seq libraries were prepared using NEBNext Ultra directional RNAseq kit with 8-10 cycles of PCR.

treatment_protocol: ESCs were treated for 24hrs with siRNA pools to Stag1 (SA1) including, SmartPool (SP), 5' or 3’ end of Stag1 (5p and 3p) and two sets of control siRNAs, scrambled (SCR) and Luciferase (Luc).

value: serum-grown

value: 3p siRNA

tag: rna prep

value: rRNA depletion


title: CTCF bait_ESC_Rep1


title: ES FCS_Rep 3_SCR

value: scramble control siRNA


title: F3 CA3_nonstressRep3

tag: group

value: nonstress

tag: brain region


title: ES FCS_Rep 3_SA1 SATS KD

value: SATS siRNA


title: F18 CA3_stressRep3

tag: strain


title: Nanog bait 2_NSC_Rep1

value: Nanog bait 2


title: D5_CTCFbKO_DDSOX17+S_CXCR4+_Rep2

value: Day 5

value: SOX17(∆5'CTCF) + transgenic rescue element(SOX17)

value: 1 uM Shield-1 treated


title: Nanog bait 2_ESC_Rep3


title: F3 BLA_nonstressRep2

value: basolateral amygdala


title: D5_CTCFbKO_DDSOX17+S_CXCR4-_Rep2


title: Nanog bait 2_ESC_Rep2


title: ES FCS_Rep 3_SA1 SP KD

value: SP siRNA


title: ES FCS_Rep 3_Luciferase CTL

value: luciferase control siRNA


title: ES FCS_Rep 3_SA1 5p KD

value: Embryonic stem cells

value: 5p siRNA


title: ES FCS_Rep 2_SA1 3p KD


title: Nanog bait 2_ESC_Rep1

value: 2i-LIF grown


title: Nanog bait 1_NSC_Rep3

value: ES-derived Neural stem cells

value: EGF-FGF grown

value: Nanog bait 1


title: D5_CTCFbKO_DDSOX17-S_CXCR4+_Rep2


title: D5_CTCFbKO_DDSOX17-S_CXCR4-_Rep2


title: F7 BLA_nonstressRep1

value: Sprague Dawley

value: female


title: ES FCS_Rep 2_SA1 5p KD

value: serum-grown

value: rRNA depletion


title: F18 OFC_stressRep2

value: stress

value: orbitofrontal cortex of the prefrontal lobe


title: Nanog bait 1_NSC_Rep2


title: ES FCS_Rep 2_SA1 SATS KD

value: SATS siRNA


title: D5_CTCFbKO_DDSOX17-S_CXCR4-_Rep1

description: SOX17 upstream TIR boundary CTCF knockout

value: Day 5

value: SOX17(∆5'CTCF) + transgenic rescue element(SOX17)


title: D5_CTCFbKO_DDSOX17-S_CXCR4+_Rep1


title: Nanog bait 1_NSC_Rep1


title: Nanog bait 1_ESC_Rep4


title: ES FCS_Rep 2_SA1 SP KD

value: SP siRNA


title: F18 CA1_stressRep2

value: Cornu Ammonis area 1 of the hippocampus


title: D5_CTCFbKO_DDSOX17+S_CXCR4+_Rep1

value: 1 uM Shield-1 treated


title: ES FCS_Rep 2_SCR

value: Embryonic stem cells

value: scramble control siRNA


title: Nanog bait 1_ESC_Rep3

value: 2i-LIF grown


title: F18 VMH_stressRep2

value: ventromedial hypothalamic nucleus


title: D5_CTCFbKO_DDSOX17+S_CXCR4-_Rep1


title: F17 VMH_stressRep1


title: D0_CTCFbKO_DDSOX17_Rep2

value: Day 0


title: D0_CTCFbKO_DDSOX17_Rep3


title: F17 OFC_stressRep1

value: Sprague Dawley


title: D0_CTCFbKO_DDSOX17_Rep1


title: Nanog bait 1_ESC_Rep2

value: Nanog bait 1