title: LVshARID1A_Input

description: Input library from lentiviral shARID1A infected 12Z cells

data_processing:
Raw reads for IPs and inputs were trimmed with cutadapt and Trim Galore!
Trimmed reads were aligned to GRCh38.p12 reference genome via Bowtie2 with flag `--very-sensitive`. Aligned reads were sorted and indexed with samtools.
Only properly-paired read fragments were retained by samtools view with flag `-f 3` followed by sorting and indexing.
Library molecular complexity was then estimated from duplicate rates by ATACseqQC and preseqR, and libraries were subsampled to equivalent molecular complexity within an experimental design based on these estimates with samtools.
Picard MarkDuplicates was used to remove PCR duplicates, followed by sorting and indexing.
MACS2 was used to call broad peaks (FDR < 0.05) on each ChIP replicate against the input control with otherwise default settings.
A naïve overlapping peak set, as defined by ENCODE, was constructed by calling peaks on pooled replicates followed by bedtools intersect to select for peaks of at least 50% overlap with each biological replicate.
The resulting peaks were repeat-masked by ENCODE blacklist filtering and filtered for non-standard contigs.
Differential binding analysis was computed with csaw. Briefly, a consensus peak set was constructed for each differential experiment from the union of replicate-intersecting, filtered MACS2 peaks called in each condition. The replicate intersection criteria used here are less stringent than the naïve overlap; any partial intersect between ChIP replicates was accepted as a query region tested for differential binding. ChIP reads were counted in these query regions by csaw, then filtered for low abundance peaks with average logCPM > -3. When comparing ChIP libraries, any global differences in IP efficiency observed between the two conditions were considered a result of technical bias to ensure a highly conservative analysis. As such, we employed a non-linear loess-based normalization to the peak count matrix, as is implemented in csaw, to assume a symmetrical MA distribution. A design matrix was then constructed from one “condition” variable, without an intercept. The count matrix and loess offsets were then supplied to edgeR for estimating dispersions and fitting the quasi-likelihood generalized linear model for hypothesis testing. Nearby query regions were then merged up to 500 bp apart for a maximum merged region width of 5 kilobases, and the most significant probability was used to represent the merged region.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Tabular peak set files including blacklist-filtered ChIP replicate broadPeaks (FDR < 0.05 MACS2 output) and naïve replicate-overlapping broadPeaks. Non-thresholded differential binding results from csaw are also reported as a tab-separated values (TSV) file.

extract_protocol:
72 hours following lentiviral transduction, cells were treated with 1% formaldehyde in cell culture media for 15 min at room temp. Formaldehyde was quenched by the addition of 0.125 M Glycine, and cells were washed with PBS. 1x10^7 crosslinked cells were used per IP. Chromatin from crosslinked cells was fractionated by digestion with micrococcal nuclease using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling) per the manufacturers’ instructions. Nuclei were resuspended in nuclear lysis buffer (50 mM Tris-HCl [pH 8.0], 10 mM EDTA [pH 8.0], 1% SDS) and sonicated for 30 seconds. Protein G magnetic beads (Cell Signaling) were preconjugated with 5 ug mouse monoclonal anti-P300 (NM11) (sc-32244, Santa Cruz) overnight at 4C in wash buffer (1X PBS, 0.5% BSA, 0.02% Tween-20). Fractionated chromatin was diluted into IP buffer (0.01%SDS, 1.1% TrionX-100, 1.2 mM EDTA [pH 8.0], 16.7 mM Tris-HCl [pH 8.0], 167 mM NaCl) and incubated with preconjugated antibody/Dynabeads overnight at 4C. Samples were washed at 4C with high-salt buffer (0.1% SDS, 1% TritonX-100, 2 mM EDTA [pH 8.0], 20 mM Tris-HCl [pH 8.0], 0.5 M NaCl), low-salt buffer (0.1% SDS, 1% TritonX-100, 2 mM EDTA [pH 8.0], 20 mM Tris-HCl [pH 8.0], 150 mM NaCl), dialysis buffer (0.2% Sarcosyl, 2 mM EDTA [pH 8.0], 50mM Tris-HCl [pH 8.0]), IP wash buffer (0.25M LiCl, 1% NP-40, 1% Deoxycholate, 1 mM EDTA [pH 8.0], 10 mM Tris-HCl [pH 8.0]) and TE (10mM Tris-HCL [pH 8.0], 1mM EDTA [pH 8.0]). IP chromatin was eluted for 30 min at 37C with elution buffer (1% SDS, 0.1 M NaHCO3). Crosslinks were reversed with 0.4 mg/mL Proteinase K (ThermoFisher) and 0.2 M NaCl at 65C for 2 hrs. DNA was purified using the ChIP DNA Clean & Concentrator Kit (Zymo).
Libraries for Input and IP samples were prepared by the Van Andel Genomics Core from 10 ng of input and IP material when available, and all material when less than 10 ng available, using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems). Prior to PCR amplification, end repaired and A-tailed DNA fragments were ligated to Bioo Scientific NEXTflex Adapters (Bioo Scientific).

treatment_protocol: Cells were transduced with lentiviral particles which expressed shRNA targeting ARID1A (shARID1A) or non-targeting control (shNONtg) at 100 units per cell multiplicity of infection. Growth media was replaced 24 hours after transduction.


title: LBW male liver, biological rep2

status: Public on Nov 10 2020

type: RNA

city: London

first: Ousseynou

last: Sarr

state: United States

address: 1811 Creekside Street

department: Physiology & Pharmacology

country: Canada

institute: Western universitry

description:
22_TRT004D05D05_01
Gene expression data from young adult offspring fed a control diet

hyb_protocol: After fragmentation and labeling, 2.1 µg cDNA was hybridized onto Guinea Pig Gene 1.1 ST Array Plate (Thermo Fisher Scientific).

scan_protocol: GeneChips were scanned using the GeneTitan® Instrument (Thermo Fisher Scientific).

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) (version 4.0, Life Technologies) using Affymetrix default analysis settings and Summarization Method as normalization method.

label: biotin

molecule: total RNA

organism: Cavia porcellus

source_name: guinea pig liver at postnatal day 150

label_protocol: Sense-strand cDNA was synthesized from 100 ng of total RNA, and fragmentation and labeling were performed to produce ss-cDNA with the GeneChip® WT Terminal Labeling Kit according to manufacturer’s instructions (Thermo Fisher Scientific).

growth_protocol: Uterine artery ablation-induced low birth weight (LBW) and normal birth weight (NBW) male and female guinea pig offspring were fed a control diet from weaning until postnatal day 150.

extract_protocol: Trizol extraction of total RNA in livers was performed using the RNeasy Plus Universal Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: At postnatal day 150, offspring of each sex were fasted overnight, euthanized via CO2 inhalation in the morning (~ 10 am) of the following day and tissue collection conducted. The whole liver was removed and weighed immediately and the right lobe liver was frozen in liquid nitrogen and stored at −80 °C.

tag: strain

value: Dunkin Hartley

tag: gender

value: Male

tag: treatment

tag: age

value: postnatal day 150

tag: tissue

value: Liver


title: RNA-seq for CD127high monocytes D42

type: SRA

city: Beijing

first: Bin

last: Zhang

address: Zheng Yutong Building room D311

country: China

institute: Tsinghua University

description:
Expression_summary.txt
42P

library_source: transcriptomic

data_processing:
ATAC-seq paired-end reads were collected. Adapter sequences were trimmed from the ends of reads by Cutadapt (v1.14), and the reads that failed to pass the quality control (Q > 10) were discarded.
Tophat (v2.1.0) was used for RNA-seq single-end reads alignment with the following parameters: --min-segment-intron 50 --no-novel-indels --no-coverage-search.  Bowtie2 (v2.2.5) was used for ATAC-seq paired-end reads alignment with maximum 1000 bp fragment length and no more than one mismatch for each alignment seed with 15 bp in length.
Differentially expressed genes between CD127high and CD127low monocytes were identified by using DESeq2 (v1.27.9).
After alignment, the ATAC-seq peaks were called for CD127hgih and CD127low monocytes from three donors as significantly opened chromatin regions by using MACS2 (v2.1.1) (FDR < 0.05).
Differentially opened chromatin regions (OCR) between CD127high and CD127low monocytes were identified by using edgeR (v3.28.1).
Genome_build: hg38
Supplementary_files_format_and_content: Expression_summary.txt is the table containing the gene expression (FPKM) and statistical analysis result (p-value) by edgeR. Six .bed files are the ATAC-seq peaks called by MACS2 for each sample.

molecule: polyA RNA

organism: Homo sapiens

source_name: Buffy coat

extract_protocol: Buffy coat from healthy blood donor was diluted by PBS, and PBMC were isolated by Ficol gradient. CD14+ monocytes were isolated from PBMC with anti-CD14 magnetic beads (Miltenyi Biotec). CD14+ monocytes were treated with LPS for 6 h, and CD127high and CD127low monocytes were sorted by FACS. For ATAC-seq, cells were washed by PBS and 50000 cell were re-suspended in 50 μL of lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.5% NP-40) and nuclei were digested with Tn5 enzyme. DNA libraries were prepared for sequencing using TruePrepTM DNA Library Prep Kit V2 for Illumina protocols. Instrument Hiseq X ten.  For RNA-seq, RNA was extracted using TRIzol, and total RNA was polyA enriched. RNA libraries were prepared for sequencing using TruSeq mRNA-seq Sample Preparation Kit(Illunima). Instrument BGISEQ-500RS.

tag: cell type

value: Human CD14+ monocytes

tag: disease state

value: Healthy

tag: subtype

value: LPS


title: NBW male liver, biological rep3

description:
9_TRT011D02D02_01
Gene expression data from young adult offspring fed a control diet

value: normal birth weight (NBW)


title: kidney_No_ABMRh_60

city: Leuven

first: Jasper

last: Callemeyn

address: Herestraat 49

department: Microbiology, Immunology and Transplantation

country: Belgium

institute: KU Leuven University

description: Gene expression data from kidney allograft biopsy

hyb_protocol: Fragmented cRNA was hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays (Affymetrix). The arrays were washed and stained on an automated Fluidics Station (Affymetrix).

scan_protocol: Arrays were scanned on the GeneChip® Scanner 3000 7G System (Affymetrix)

data_processing: Resulting image files (.dat files) were generated using the GeneChip® Command Console® Software (AGCC), and intensity values for each probe cell (.cel file) were calculated.

label: Biotin

source_name: Kidney allograft biopsy

label_protocol: Extracted RNA was amplified and biotinylated to complementary RNA (cRNA) using the GeneChip® 3' IVT PLUS Reagent Kit (Affymetrix Inc., High Wycombe HP10 0HH, UK)

extract_protocol: Total RNA was isolated from the kidney allograft biopsy specimens -using the Allprep DNA/RNA/miRNA Universal Kit® (Qiagen Benelux BV) on a QIAcube instrument (Qiagen Benelux BV).

tag: phenotype

value: No ABMRh


title: kidney_No_ABMRh_62


title: RNA-seq for CD127low monocytes D41

description:
Expression_summary.txt
41N


title: LVshARID1A_P300_rep2

city: Grand Rapids

first: Ronald

middle: L.

last: Chandler

state: MI

department: Obstetrics, Gynecology and Reproductive Biology

country: USA

institute: Michigan State University

description: P300 ChIP (replicate 2) library from lentiviral shARID1A infected 12Z cells

library_source: genomic

molecule: genomic DNA

source_name: 12Z cell line

growth_protocol: 12Z cells were cultured in DMEM/F12 media supplemented with 10% FBS, 1% L-glutamine, and 1% Penicllin-Streptomycin.

tag: cell line

tag: genotype/variation


title: LVshARID1A_P300_rep1

description: P300 ChIP (replicate 1) library from lentiviral shARID1A infected 12Z cells


title: NBW male liver, biological rep4

description:
12_TRT001B02B02_01
Gene expression data from young adult offspring fed a control diet


title: kidney_No_ABMRh_83


title: RNA-seq for CD127low monocytes D23

description:
Expression_summary.txt
23N


title: LVshNONtg_Input

description: Input library from lentiviral non-targeting shRNA control (LVshNONtg) infected 12Z cells

value: Control


title: kidney_No_ABMRh_59


title: NBW male liver, biological rep2

description:
8_TRT010G01G01_01
Gene expression data from young adult offspring fed a control diet


title: RNA-seq for CD127high monocytes D41

description:
Expression_summary.txt
41P


title: kidney_No_ABMRh_58


title: RNA-seq for CD127high monocytes D23

description:
Expression_summary.txt
23P


title: RA_pbmc

description: Single cell RNA-seq

data_processing:
The Cell Ranger Software Suite (Version 3.1.0) was used to perform sample de-multiplexing, barcode processing and single-cell 5’ UMI counting with human GRCh38 as the reference genome. Specifically, splicing-aware aligner STAR was used in FASTQs alignment. Cell barcodes were then determined based on distribution of UMI count automatically. Finally, gene-barcode matrix for sample were generated for downstream analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Gene-barcode matrix for scRNA-seq dataset was saved as .h5 file.

source_name: PBMC

extract_protocol: Peripheral blood of RA patient were diluted by PBS, and PBMC were isolated by Ficol gradient. PBMC were frozen in FBS with 10% DMSO for preservation. For library construction, cells were thawed and resuspened, and the single-cell capturing and downstream library constructions were performed using the Chromium Single Cell 5’ library preparation kit according to the manufacturer’s protocol (10x Genomics). Full-length cDNA along with cell-barcode identifiers were PCR-amplified and were further prepared as sequencing library.  Instrument BGI MGISEQ2000.

value: Human PBMC

value: Rheumatoid arthritis


title: NBW male liver, biological rep1

description:
7_TRT009B03B03_01
Gene expression data from young adult offspring fed a control diet


title: LVshNONtg_P300_rep2

description: P300 ChIP (replicate 2) library from lentiviral non-targeting shRNA control (LVshNONtg) infected 12Z cells


title: CD14_mono_LPS

description: Single cell RNA-seq

extract_protocol: Buffy coat from healthy blood donor was diluted by PBS, and PBMC were isolated by Ficol gradient. CD14+ monocytes were isolated from PBMC with anti-CD14 magnetic beads (Miltenyi Biotec). CD14+ monocytes were treated with LPS for 6 h, and were collected and frozen in FBS with 10% DMSO for preservation. For library construction, cells were thawed and resuspened, and the single-cell capturing and downstream library constructions were performed using the Chromium Single Cell 5’ library preparation kit according to the manufacturer’s protocol (10x Genomics). Full-length cDNA along with cell-barcode identifiers were PCR-amplified and were further prepared as sequencing library.  Instrument BGI MGISEQ2000.


title: kidney_DSAnegABMRh_6

value: DSAnegABMRh


title: kidney_No_ABMRh_57


title: 3281

city: Stanford

first: Molly

last: Uyeda

state: CA

address: 265 Campus Drive

institute: Stanford University

data_processing: Transcript reads were quantified using salmon-0.11.3 with indexes made with the following parameters (Ensembl cDNA on human GRCh38 --perfectHash --type quasi -k 31) Transcript abundances were then aggregated to the gene level with tximport

source_name: bone marrow aspirates

growth_protocol: thawed and incubated for 2h in X-VIVO15 supplemented 5% human AB serum with IL-3 (20 ng/mL, Peprotech) and G-CSF (20 ng/ml, Peprotech) at 10^6 cells/ml.

extract_protocol:
50,000 pAML cells were lysed in Trizol-LS
RNAqueous Micro Total RNA Isolation Kit (Thermo Fisher) including on-column DNAse digestion
KAPA mRNA HyperPrep Kit (KAPA Biosystems)

tag: condition

value: pediatric AML


title: 3209


title: LVshNONtg_P300_rep1

description: P300 ChIP (replicate 1) library from lentiviral non-targeting shRNA control (LVshNONtg) infected 12Z cells


title: 3082


title: kidney_DSAnegABMRh_5


title: 1355


title: 1563


title: kidney_DSAposABMRh_9

value: DSAposABMRh


title: 882


title: 794


title: kidney_No_ABMRh_55


title: kidney_No_ABMRh_56


title: iPS-cytoplasmic-3

city: Lund

first: Olof

last: Gidlof

address: Solvegatan 19

country: Sweden

institute: Lund University

description: Cytoplasmic RNA

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Probe summarization and data normalization was performed using the Robust Multi-array Average algorithm and signals were log2 transformed.

source_name: iPS-derived cardiomyocytes

label_protocol: cRNA synthesis and hybridization was performed using the GeneChip WT Pico Kit with 10 ng of RNA/sample as input and following the manufacturers recommendations

growth_protocol: Human iPS-derived cardiomyocytes, human primary microvascular endothelial cells and human primary cardiac fibroblasts were cultured in accordance with the manufacturers' instructions.

extract_protocol: RNA was isolated using the miRNEasy mini kit (Qiagen) or the Nuclear and Cytoplasmic RNA Purification Kit (Norgen) according to the manufacturers' instructions

value: iPS-derived cardiomyocytes


title: iPS-cytoplasmic-2

description: Cytoplasmic RNA


title: kidney_No_ABMRh_54


title: kidney_No_ABMRh_52


title: HCF-nuclear-2

description: Nuclear RNA

source_name: Human cardiac fibroblasts

value: Human cardiac fibroblasts


title: 728


title: kidney_No_ABMRh_51


title: iPS-cytoplasmic-1

description: Cytoplasmic RNA


title: Biopsy-Total-4

description: Total RNA

source_name: Left ventricular biopsy

value: Left ventricular biopsy


title: HCF-nuclear-1

description: Nuclear RNA


title: 683


title: 646


title: HCF-cytoplasmic-3

description: Cytoplasmic RNA


title: kidney_No_ABMRh_49


title: HCF-nuclear-3

description: Nuclear RNA


title: 351


title: HCMVEC-total-2

description: Total RNA

source_name: Human cardiac microvascular endothelial cells


title: kidney_No_ABMRh_50


title: HCMVEC-total-3

description: Total RNA

value: Human cardiac microvascular endothelial cells


title: HCF-total-1

description: Total RNA


title: kidney_No_ABMRh_48


title: HCF-total-3

description: Total RNA


title: iPS-total-3

description: Total RNA


title: Biopsy-Total-5

description: Total RNA


title: HCF-total-2

description: Total RNA


title: HCMVEC-total-1

description: Total RNA


title: Biopsy-Total-3

description: Total RNA


title: HCF-cytoplasmic-2

description: Cytoplasmic RNA


title: kidney_No_ABMRh_47


title: 263


title: Biopsy-Nuclear-PCM1neg-5

description: Nuclear RNA


title: kidney_DSAnegABMRh_4


title: iPS-total-1

description: Total RNA


title: Biopsy-Nuclear-PCM1pos-5

description: Nuclear RNA


title: iPS-total-2

description: Total RNA


title: 3514


title: Schwann cell like cells (SCLCs)

city: 遵义

first: hutaotao

middle: taotao

last: hu

address: Zunyi City

institute: ZunyiMedicalUniversity

description: a sample from human amniotic mesenchymal stem cells (hAMSCs)

data_processing:
Using Illumina hiseq pe150 or novaseq pe150 sequencing strategy, it is recommended to measure 50000-100000 reads per cell, that is, 15-30m data per cell. There is a certain saturation in sequencing. Increasing the amount of sequencing data can improve the detection rate of genes.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Schwann cell like cells (SCLCs)

extract_protocol:
10x Genomics® Cell Preparation Guide describes best practices and general protocols for washing, counting and concentrating cells from both abundant and limited cell suspensions (greater than or less than 100000 total cells, respectively) in preparation for use in 10x Genomics Single Cell Protocols.
The cell suspension was loaded into Chromium microfluidic chips with 3’ (v2 or v3, depends on project) chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2(v2 or v3, depends on project) reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina (HiSeq 2000 or NovaSeq , depends on project) according to the manufacturer’s instructions (Illumina).

value: Schwann cell like cells (SCLCs)


title: Biopsy-Nuclear-PCM1pos-4

description: Nuclear RNA


title: Biopsy-Nuclear-PCM1neg-3

description: Nuclear RNA


title: kidney_No_ABMRh_46


title: Biopsy-Nuclear-PCM1neg-4

description: Nuclear RNA


title: human amniotic mesenchymal stem cells (hAMSCs)

description: a sample from human amniotic

value: 20-30 years old

tag: mode of delivery

value: Cesarean section


title: kidney_No_ABMRh_45


title: HCF-cytoplasmic-1

description: Total RNA


title: Biopsy-Nuclear-PCM1pos-3

description: Nuclear RNA


title: HCMVEC-nuclear-3

description: Nuclear RNA


title: HCMVEC-nuclear-2

description: Nuclear RNA


title: HCMVEC-nuclear-1

description: Nuclear RNA


title: HCMVEC-cytoplasmic-3

description: Cytoplasmic RNA


title: kidney_No_ABMRh_42


title: kidney_No_ABMRh_43


title: kidney_DSAposABMRh_8


title: kidney_No_ABMRh_41


title: kidney_No_ABMRh_40


title: FRCs Cycle 1 2

city: Rotterdam

first: Gerben

last: Schaaf

address: Wytemaweg 80

country: Netherlands

institute: Erasmus MC

data_processing:
Hybridized products were sequentially amplified, linearized and end-blocked according to the Illumina Single Read Multiplex Sequencing user guide
After hybridization of the sequencing primer, sequencing-by-synthesis was performed using the HiSeq 2500 with a single read 50-cycle protocol followed by dual index sequencing
Illumina adapter sequences have been trimmed off the reads, which were subsequently mapped against the GRCm38 mouse reference using HiSat2 (version 2.1.0) (Kim et al., 2015)
Gene expression values were called using htseq-count (version 0.9.1) (Anders et al., 2015) and Ensembl release 91 gene and transcript annotation
Normalization and expression value generation was done using DESeq2 (rlog)
Genome_build: GRCm38
Supplementary_files_format_and_content: htseq-count

organism: Mus musculus

source_name: Skeletal muscle

growth_protocol: Reserve cell populations were passaged twice after isolation in proliferation conditions before harvesting. Samples were harvested using RLT buffer (QIAGEN, Germantown, MD).

extract_protocol:
RNA was extracted using the RNeasy minikit with DNase treatment (QIAGEN, Germantown, MD)
Triplicate RNA-Seq libraries were prepared according to the Illumina TruSeq stranded mRNA protoco

value: Myoblasts

value: FVB/N

tag: cell population

value: FRCs Cycle 1


title: SRCs Cycle 3 3

value: SRCs Cycle 3


title: HCMVEC-cytoplasmic-2

description: Cytoplasmic RNA


title: HCMVEC-cytoplasmic-1

description: Cytoplasmic RNA


title: kidney_DSAposABMRh_7


title: iPS-nuclear-1

description: Nuclear RNA


title: Input no dox H3K9me3/H3K36me3

city: Stuttgart

first: Albert

last: Jeltsch

address: Allmandring 31

department: Institute of Biochemistry and Technical Biochemistry

country: Germany

institute: University Stuttgart

data_processing:
Data were submitted in FASTQ format and all data processing steps were performed on the European Galaxy platform (usegalaxy.eu)
The quality of the reads was checked using the FastQC tool
Reads were mapped on human genome 19 (hg19/GRCh37) using bowtie2 in default settings. When necessary (re-sequencing), BAM- files were merged using the Merge BAM Files tool.
Coverage files (bigwig) were generated using bamCoverage from DeepTools (25 bp bins) with RPKM normalization. Re-calibration of bigWig files was performed as described in the supplement section to obtain a scaling factor for. BamCoverage was repeated in RPKM mode (25 bp bins) implying this scaling factor.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: bigWig

source_name: HEK293 cell line

extract_protocol:
For ZnF(3xHA)-ChIP, chromatin was crosslinked with 1% formaldehyde, sheared using a probe sonicator (100 - 1000 bp fragment size) and preciptated with an antibody. In case of nChIP experiments, chromatin was fragmented by Mnase digest and precipitated with an antibody.
Libraries for all samples (except H3K27ac) were constructed by the Max Planck-Genome-centre Cologne. In case of H3K27ac, libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer's protocol.

treatment_protocol: For induction of the ZnF-3AC construct, cell culture medium was supplemented with 1 µg/ml doxycyclin (Sigma-Aldrich) for three days.

tag: antibody

value: Input

tag: antibody vendor/amount


title: SRCs Cycle 3 1


title: SRCs Cycle 3 2


title: iPS-nuclear-2

description: Nuclear RNA


title: H3K36me3 3d dox


title: H3K36me3 no dox


title: FRCs Cycle 1 1


title: H3K36me3 5d off


title: Parental 1

value: Parental


title: iPS-nuclear-3

description: Nuclear RNA


title: FRCs Cycle 1 3


title: H3K9me3 no dox


title: kidney_No_ABMRh_53

value: No ABMRh


title: kidney_No_ABMRh_39


title: Parental 2


title: H3K27ac 5d off

tag: additional treatment

value: All used buffers were supplemented with 100 nM Trichostatin A (Sigma Aldrich) during harvesting of cells and nucleosome preparation.


title: H3K9me3 5d off


title: H3K9me3 3d dox


title: Input no dox H3K27ac


title: kidney_No_ABMRh_38


title: Transgenic3

city: Urbana

first: Sushant

last: Bangru

state: Illinois

address: 600 S Mathews Avenue

department: Biochemistry

institute: University of Illinois, Urbana-Champaign

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina)
Adaptors were trimmed from the reads using trimmomatic
Reads were mapped to the genome using STAR_2.4.2a
TPM values generated from counts obtained from HTseq and DESeq2
FPKM values were generated and compared between sets of samples using CuffDiff_2.2.1
Gene Ontology was determined using DAVID_6.8
GRCm38 vM10 mm10 (mus musculus)
Supplementary_files_format_and_content: csv file containing average TPM values for all 4 conditions for all mouse genes in mm10 gene build

source_name: Mouse peritoneal macrophages

extract_protocol:
RNA was extracted using Trizol based standard methods
RNA libraries were prepared for sequencing using standard Illumina protocols for “TruSeq Stranded mRNAseq Sample Prep kit”

treatment_protocol: Mouse PM were harvested 5 days after aged 3% thioglycolate injection. 4–5 × 106 cells were plated in 60mm culture dishes and cultured overnight in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS). For lipidomic and transcriptomic analyses, the media was replaced by DMEM-1% FBS supplemented with Hi-TBAR oxLDL (50 μg/ml, Alfa Aesar J65261) for 48h. Cells were harvested with cold 1× PBS and immediately frozen and stored at −80 °C.

value: peritoneal macrophages

tag: strain

tag: genotype

value: LDAH overexpression


title: Transgenic2


title: kidney_DSAposABMRh_6

value: DSAposABMRh


title: H3K27ac 3d dox


title: Input no dox H3K4me3/H3K27me3


title: H3K27ac no dox


title: Transgenic1


title: H3K27me3 5d off

value: Active Motif #39155 (5 µg)


title: Control4

value: LDAH ApoE control


title: Transgenic4


title: H3K27me3 11d off


title: H3K27me3 3d dox


title: H3K27me3 8d off


title: H3K4me3 5d off


title: H3K27me3 no dox


title: H3K4me3 11d off


title: H3K4me3 8d off


title: H3K4me3 no dox


title: H3K4me3 3d dox


title: kidney_No_ABMRh_37


title: Control1


title: Control2


title: KO3

value: LDAH KO


title: KO4


title: Control3


title: KO2


title: Lats1/2 mutant eye tumor, Rep#2

city: Worcester

first: Julie

last: Zhu

state: MA

address: 364 Plantation Street

department: Molecular Cellular and Cancer Biology

institute: UMass Medical School

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for the first and last 10 bases, then mapped to mm10 using tophat2/2.0.9 with parameters --b2-very-sensitive
Differential expressed genes were determined by cufflinks/2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include related cuffdiff output files:
gene_exp.diff: Gene-level differential expression. Tests differences in the summed FPKM of transcripts sharing each gene_id
genes.count_tracking.txt: Gene counts. Tracks the summed counts of transcripts sharing each gene_id
genes.fpkm_tracking.txt: Gene FPKMs. Tracks the summed FPKM of transcripts sharing each gene_id
genes.read_group_tracking.txt: Gene read group tracking. Tracks the summed expression and counts of transcripts sharing each gene_id in each replicate

source_name: mouse eye tumor tissue

extract_protocol:
Wild type uveal tissue or Lats1/2-mutated eye tumor tissue were freshly isolated, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used
RNA libraries were prepared for sequencing using standard Illumina protocols

value: eye tumor

tag: developmental stage

value: adult

value: AAV5-Cre;Lats1/2 fl/fl


title: Lats1/2 mutant eye tumor, Rep#3


title: Wild type_eye, Rep#2

source_name: mouse uveal eye tissue

value: eye

value: wild type


title: 5d_off_Rep1_RNA-seq

description:
processed data file: Gene_FPKM_tracking.txt
processed data file: 5d_off_Rep1+2_merged_RNA-seq_CPM.bigwig

data_processing:
Data were submitted in FASTQ format and all data processing steps were performed on the European Galaxy platform (usegalaxy.eu).
The quality of the reads was checked using the FastQC tool.
Reads were mapped on human genome 19 (hg19/GRCh37) using the gapped-read mapper TopHat under default settings.
Transcripts were assembled with Cufflinks using the reference annotation for genes from UCSC. Transcripts were merged using the Cuffmerge tool (default settings) and expression levels of genes were calculated in FPKM using the Cuffdiff tool (default settings).
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: Gene_FPKM_tracking.txt: Tab-delimited text file includes FPKM values.

extract_protocol:
RNA was purified from frozen cell using the RNeasy® Plus Mini Kit (Qiagen) according to the manufacturer’s protocol and eluted in RNase-free water. The concentration was measured using NanoDrop 1000 (Thermo Fisher Scientific).
Per sample, 100 ng of RNA were processed using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB) according to manufacturer’s protocol. Indexing and barcoding of samples was performed using the NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) (NEB). The barcoded libraries were pooled (250 ng each) and sequenced at the Max Planck-Genome-Centre Cologne.

treatment_protocol: For induction of the ZnF-3AC construct, cell culture medium was supplemented with 1 µg/ml doxycycline (Sigma-Aldirch) for three days.

value: Catalytic domain of DNMT3A fused to a zinc finger (ZnF-3AC) under control of dox promoter

tag: treatment

value: Doxycycline for 3 days, 5 days after dox removal


title: 5d_off_Rep2_RNA-seq


title: Lats1/2 mutant eye tumor, Rep#1

tag: tissue


title: KO1

tag: cell type


title: Wild type_eye, Rep#1


title: no_dox_Rep2_RNA-seq

description:
processed data file: Gene_FPKM_tracking.txt
processed data file: no_dox_Rep1+2_merged_RNA-seq_CPM.bigwig

value: Before doxycycline


title: WT4

value: LDAH WT


title: 3d_dox_Rep2_RNA-seq

description:
processed data file: Gene_FPKM_tracking.txt
processed data file: 3d_dox_Rep1+2_merged_RNA-seq_CPM.bigwig

value: Doxycycline for 3 days


title: WT3


title: no_dox_Rep1_RNA-seq


title: 3AC 3d dox Rep2 MBD2 seq

data_processing:
Data were submitted in FASTQ format and all data processing steps were performed on the European Galaxy platform (usegalaxy.eu)
The quality of the reads was checked using the FastQC tool
Reads were mapped on human genome 19 (hg19/GRCh37) using bowtie2 in default settings
Reproducibility of replicates was confirmed and BAM-files of corresponding replicates were merged using the Merge BAM Files tool
Coverage files (bigwig) were generated using bamCoverage from DeepTools (25 bp bins) with RPKM normalization. Re-calibration of bigWig files was performed as follows: signals in CpG islands (CGIs) (obtained from UCSC Table Browser) were determined via multiBigwigSummary tool for each time point. The 1000 highest methylated CGIs at "no dox" were selected, the means in these CGIs were calculated for each time point and the ratios were used as scaling factor. BamCoverage was repeated in RPKM mode (25 bp bins) implying this scaling factor.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: bigWig

extract_protocol:
Genomic DNA (gDNA) from frozen HEK293 pellets was isolated using the QIAmp DNA Mini Kit (Qiagen) according to manufacturer's protocol. gDNA was sonicated with a EpiShear probe sonicator (Active Motif) to obtain fragment sizes between 200 and 1000 bps. For pulldown, 1 µg of sheared gDNA was used with 8.75 µg GST-MBD2 in PB150 Buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 0.5 % Igepal CA-630, 2 mM DTT) and samples were incubated overnight at 4°C. The next day, 50 µl of Gluthathione Agarose beads (Macherey-Nagel) were washed three times with PB150 and the pulldown sample was added subsequently. After 2 h rotation at 4°C, DNA-GST-MBD2-beads complexes were washed three times with PB500 buffer (50 mM Tris-HCl pH 8.0, 500 mM NaCl, 1 mM EDTA, 0.5 % Igepal CA-630, 2 mM DTT) for 5 min. DNA was eluted twice with 150 µL PB2000 buffer at room temperature for 15 min. After pooling of elution fractions, the precipitated DNA was purified using the ChIP DNA Purification Kit (Active Motif) as described in the manufacturer's protocol.
Libraries for all ZnF-3AC related samples were constructed by the Max Planck-Genome-centre Cologne. In case of 3AC, libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer's protocol.

treatment_protocol: For induction of the ZnF-3AC construct, cell culture medium was supplemented with 1 µg/ml doxycyclin (Sigma-Aldirch) for three days

tag: binding protein


title: WT2


title: 258

value: pediatric AML


title: kidney_DSAnegABMRh_3

value: DSAnegABMRh


title: kidney_No_ABMRh_36

value: No ABMRh


title: kidney_No_ABMRh_32


title: 3d_dox_Rep1_RNA-seq


title: kidney_No_ABMRh_31


title: kidney_No_ABMRh_26


title: kidney_No_ABMRh_29


title: WT1

value: peritoneal macrophages


title: kidney_No_ABMRh_33


title: kidney_No_ABMRh_30


title: kidney_No_ABMRh_25


title: 3AC 3d dox Rep1 MBD2 seq


title: kidney_No_ABMRh_44


title: kidney_No_ABMRh_35


title: FLB_E9_24somites_delCS3840_RNA-seq

city: Geneva

first: Eddie

last: Rodríguez-Carballo

address: 4, Boulevard d'Yvoy

department: Department of Genetics and Evolution

country: Switzerland

institute: Université de Genève

description: Forelimb buds mouse E9.5 del(CS38-40) 24 somites RNA-seq

data_processing:
Analysis was performed on our local galaxy server.
Strand specific coverage was performed on uniquely mapped reads (tag NH:i:1) with bedtools version 2.27.1
Bedgraphs were normalized to the number of million uniquely mapped reads using using awk.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized bedgraph of the forward or reverse strand unique read coverage.

source_name: forelimb buds

extract_protocol:
RNA was extracted using the it RNAeasy (Microkit, QIAGEN).
Truseq Stranded mRNA

treatment_protocol: Micro-dissected forelimb buds from either E9.5 wild type or del(CS38-40) embryos. Tissues were dissected and placed in RNAlater (invitrogen) and kept at -80ªC until further use. The rest of the embryo was stained with DAPI and somites were counted to classify the embryonic timing.

tag: embryonic day


title: Rat_HCC03

city: Shanghai

first: Shengli

last: Li

address: 650 Xinsongjiang Road

institute: Shanghai Jiao Tong University School of Medicine

hyb_protocol: target cRNA was prepared and hybridized (45 °C, 16 h) to GeneChip rat 230A arrays according to the manufacturer's directions (Affymetrix).

scan_protocol: Hybridized arrays were washed and stained using the GeneChip fluidics station 400 and scanned using the Agilent GeneArray scanner.

data_processing: Signals were analyzed using Microarray Suite 5.0 software (Affymetrix). The signals were normlized by RMA methods.

organism: Rattus norvegicus

source_name: Hepatocarcinoma stage_liver

label_protocol: standard Affymetrix protocol

growth_protocol: The rats were acclimatized to standard laboratory conditions (temperature 22–25°C, relative humidity 50–60%, and 12-hour photoperiods (lights on 07:00–19:00 h)) and were housed in stainless steel wire-mesh cages (3 rats per cage). During the entire period of study, the rats were supplied with a semipurified basal diet and water ad libitum

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA)

treatment_protocol: After 1 week on a basal diet, rats belonging to the DEN group were injected intraperitoneally with a dosage of 70 mg/kg of DEN once per week for 10 weeks. Animals that belonged to the control group were injected with distilled water. The rats were sacrificed with 1.5% (g/ml) pentobarbital sodium (30 mg/kg) by intraperitoneal injection at different time points. At the end of the 5th (hepatitis group), 13/14th (cirrhosis group) and 23/24th (carcinoma group) weeks after DEN-treatment, 12 rats were sacrificed at each of these time points.

value: Sprague-Dawley

tag: age

tag: Sex

value: male

tag: sample group

value: Hepatocarcinoma stage

value: liver


title: Rat_HCC02

value: adult


title: kidney_No_ABMRh_28

tag: phenotype


title: kidney_No_ABMRh_27


title: kidney_No_ABMRh_34


title: FLB_E9_24somites_wt_RNA-seq

description: Forelimb buds mouse E9.5 wt 24 somites RNA-seq


title: FLB_E9_20somites_delCS3840_RNA-seq

description: Forelimb buds mouse E9.5 del(CS38-40) 20 somites RNA-seq


title: FLB_E9_20somites_wt_RNA-seq

description: Forelimb buds mouse E9.5 wt 20 somites RNA-seq


title: Parental 3

value: Myoblasts

value: FVB/N

value: Parental


title: Rat_HCC01


title: E9_FLB_wt_Hoxd9

description: Forelimb bud mouse E9_wt_Hoxd9 viewpoint

data_processing:
Library strategy: 4C-seq
Analyses were performed using the facilities of the Scientific IT and Application Support Center of EPFL.  De-multiplexing, mapping and 4C-analysis were performed through on a local version of HTSstation (David et al, 2014 and http://htsstation.epfl.ch/). Reads were mapped to the inv(T-DOM) mm10-based genome or the wild-type mm10 (GRCm38) mouse genome assembly with bowtie2 version 2.2.1 (Langmead et al, 2012) with parameters “--end-to-end --sensitive -k 20”.
segtofrag files were obtain after mapping the 4C on mm10 (or mm10_invTDOM) and performing the 4C-analysis of the local version of HTSstation (David et al, 2014 and http://htsstation.epfl.ch).
4C figures were made using a running mean algorithm with a window size of eleven fragments. Normalisation is done by dividing the fragment scores by the mean of fragments scores falling into a region defined as +/-5Mb around the centre of the bait coordinates, such as to see only changes in contact distribution and to minimize PCR complexity bias in each sample.
The segToFrag were smoothed on 11 fragments after the removing 0, 1kb, 2kb, 3kb each side of the viewpoint.  4Cin (Irastorza-Azcarate et al., 2018) was applied 5 times for each of  the 4 preprocessing steps.  The 20 virtual Hi-C obtained were then averaged and analysed for clustering.
all scripts are available at https://github.com/lldelisle/scriptsForRodriguezCarballoEtAl2020
Genome_build: mm10 or mm10_invTDOM
Supplementary_files_format_and_content: Smoothed/normalized data (bedGraph), one per viewpoint, per tissue.   Segtofrag are scores of each fragment once mapped on the wild-type or mutant genome.   AllVhic.tar.gz contains all virtual Hi-C as text files as output from 4Cin (20 per tissue-stage).  Cool files are matrices summarizing all vitual Hi-C: *__all.cool is the average of all models and *__cluster*.cool is the average of all models in the same cluster.

source_name: Whole forelimb bud

extract_protocol:
Micro-dissected proximal segments of E12.5 and E9 forelimbs either from wild type or mutant embryos. Tissues were dissected, dissociated with collagenase (Sigma Aldrich/Fluka) and filtered through a 35 micron mesh to isolate single cells. Cells were fixed with 2% formaldehyde (in PBS/10%FBS) for 10 min at room temperature and the reaction was quenched on ice with glycine. Cells were further lysed with 10 mM Tris pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EDTA, 1x Protease inhibitor cocktail to isolate nuclei and stored at -80°C. Nuclei from pools of 10-12 pairs of proximal limbs or 90 to 150 were digested with NlaIII (New England Biolabs) and ligated with T4 DNA ligase HC (Promega) in diluted conditions to promote intramolecular ligation. Samples were digested again with DpnII (New England Biolabs) and ligated with T4 DNA ligase HC (Promega) in diluted conditions.
These templates were amplified using Expand long template (Roche) and inversed PCR primers flanked with adaptors allowing multiplexing. The illumina adaptors used were 5'-AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCT-3' for the inverse-forward primers located at the NlaII site and 5'-CAAGCAGAAGACGGCATACGA-3' for the inverse-reverse primers located at the DpnII site. Barcodes (4bp) were added between the illumina adaptor and the specific NlaIII primers when the same viewpoints were multiplexed in the same run. Specific primer information for each viewpoint is displayed in the related publication (Rodríguez-Carballo et al, 2020).

value: Whole forelimb bud

value: wild-type


title: ZnF-3AC 8d off Rep3 MBD2 seq

tag: cell line


title: ZnF-3AC 11d off Rep2 MBD2 seq


title: ZnF-3AC 11d off Rep1 MBD2 seq


title: ZnF-3AC 11d off Rep3 MBD2 seq


title: ZnF-3AC 8d off Rep2 MBD2 seq


title: ZnF-3AC 8d off Rep1 MBD2 seq


title: E9_FLB_wt_Hoxd4

description: Forelimb bud mouse E9_wt_Hoxd4 viewpoint


title: kidney_No_ABMRh_24

description: Gene expression data from kidney allograft biopsy

source_name: Kidney allograft biopsy


title: kidney_No_ABMRh_23


title: E9_FLB_wt_Hoxd13

description: Forelimb bud mouse E9_wt_Hoxd13 viewpoint


title: Rat_LC02

source_name: Cirrhosis stage_liver

value: Cirrhosis stage


title: kidney_No_ABMRh_21


title: kidney_No_ABMRh_20


title: Rat_LH03

source_name: Hepatitis stage_liver

value: Hepatitis stage


title: Rat_LC01


title: E9_FLB_wt_Hoxd11

description: Forelimb bud mouse E9_wt_Hoxd11 viewpoint


title: ZnF-3AC 5d off Rep3 MBD2 seq


title: Rat_LC03


title: Rat_LH01


title: E9_FLB_wt_CTCF-37154

description: Forelimb bud mouse E9_wt_CTCF-37154 viewpoint


title: ZnF-3AC 5d off Rep1 MBD2 seq


title: LVshARID1A_Input

description: Input library from lentiviral shARID1A infected 12Z cells

data_processing:
Raw reads for IPs and inputs were trimmed with cutadapt and Trim Galore!
Trimmed reads were aligned to GRCh38.p12 reference genome via Bowtie2 with flag `--very-sensitive`. Aligned reads were sorted and indexed with samtools.
Only properly-paired read fragments were retained by samtools view with flag `-f 3` followed by sorting and indexing.
Library molecular complexity was then estimated from duplicate rates by ATACseqQC and preseqR, and libraries were subsampled to equivalent molecular complexity within an experimental design based on these estimates with samtools.
Picard MarkDuplicates was used to remove PCR duplicates, followed by sorting and indexing.
MACS2 was used to call narrow peaks (FDR < 0.05) on each ChIP replicate against the input control with flags `--nomodel --extsize 146` to bypass model building.
A naïve overlapping peak set, as defined by ENCODE, was constructed by calling peaks on pooled replicates followed by bedtools intersect to select for peaks of at least 50% overlap with each biological replicate.
The resulting peaks were repeat-masked by ENCODE blacklist filtering and filtered for non-standard contigs.
Differential ChIP analysis was computed with csaw. Briefly, a consensus peak set was constructed for each differential experiment from the union of replicate-intersecting, filtered MACS2 peaks called in each condition. The replicate intersection criteria used here are less stringent than the naïve overlap; any partial intersect between ChIP replicates was accepted as a query region tested for differential binding. ChIP reads were counted in these query regions by csaw, then filtered for low abundance peaks with average logCPM > -3. When comparing ChIP libraries, any global differences in IP efficiency observed between the two conditions were considered a result of technical bias to ensure a highly conservative analysis. As such, we employed a non-linear loess-based normalization to the peak count matrix, as is implemented in csaw, to assume a symmetrical MA distribution. A design matrix was then constructed from one “condition” variable, without an intercept. The count matrix and loess offsets were then supplied to edgeR for estimating dispersions and fitting the quasi-likelihood generalized linear model for hypothesis testing. Nearby query regions were then merged up to 500 bp apart for a maximum merged region width of 5 kilobases, and the most significant probability was used to represent the merged region.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Tabular peak set files including blacklist-filtered ChIP replicate narrowPeaks (FDR < 0.05 MACS2 output) and naïve replicate-overlapping narrowPeaks. Non-thresholded differential ChIP results from csaw are also reported as a tab-separated values (TSV) file.

source_name: 12Z cell line

extract_protocol:
72 hours following lentiviral transduction, cells were treated with 1% formaldehyde in cell culture media for 15 min at room temp. Formaldehyde was quenched by the addition of 0.125 M Glycine, and cells were washed with PBS. 1x10^7 crosslinked cells were used per IP. Chromatin from crosslinked cells was fractionated by digestion with micrococcal nuclease using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling) per the manufacturers’ instructions. IPs were performed using the SimpleChIP Enzymatic Chromatin IP Kit per the manufacturers’ instructions. 4 ug H3K4me1 (abcam, ab8895) antibody was used per IP sample. DNA was purified using the ChIP DNA Clean & Concentrator Kit (Zymo).
Libraries for Input and IP samples were prepared by the Van Andel Genomics Core from 10 ng of input and IP material when available, and all material when less than 10ng available, using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems, Wilmington, MA USA). Prior to PCR amplification, end-repaired and A-tailed DNA fragments were ligated to IDT for Illumina unique dual adapters (IDT DNA Inc, Coralville, IA, USA) at a concentration of 3uM. Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Individually indexed libraries were pooled and 50 bp, paired end sequencing was performed on an Illumina NovaSeq6000 sequencer using an SP, 100 cycle sequencing kit (Illumina Inc., San Diego, CA, USA). Each library was sequenced to minimum read depth of 100M reads per input, 50M reads per IP. Base calling was done by Illumina RTA3 and output was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.

treatment_protocol: Cells were transduced with lentiviral particles which expressed shRNA targeting ARID1A (shARID1A) or non-targeting control (shNONtg) at 100 units per cell multiplicity of infection. Growth media was replaced 24 hours after trandsuction.

tag: genotype/variation


title: E9_FLB_wt_ELCR2

description: Forelimb bud mouse E9_wt_ELCR2 viewpoint


title: ZnF-3AC 5d off Rep2 MBD2 seq


title: Rat_Control03

source_name: Normal control_liver

value: Normal control


title: kidney_No_ABMRh_18


title: ZnF-3AC 3d dox Rep3 MBD2 seq


title: LVshARID1A_H3K4me1_rep1

description: H3K4me1 ChIP (replicate 1) library from lentiviral shARID1A infected 12Z cells


title: kidney_DSAposABMRh_5

value: DSAposABMRh


title: kidney_No_ABMRh_15


title: kidney_No_ABMRh_16


title: E9_FLB_wt_CS93

description: Forelimb bud mouse E9_wt_CS93 viewpoint


title: kidney_No_ABMRh_14


title: Rat_Control02


title: ZnF-3AC 3d dox Rep2 MBD2 seq


title: LVshARID1A_H3K4me1_rep2

description: H3K4me1 ChIP (replicate 2) library from lentiviral shARID1A infected 12Z cells


title: kidney_No_ABMRh_19


title: kidney_No_ABMRh_13


title: kidney_No_ABMRh_17


title: kidney_No_ABMRh_22


title: Rat_LH02


title: ZnF-3AC no dox Rep3 MBD2 seq


title: Rat_Control01


title: ZnF-3AC 3d dox Rep1 MBD2 seq


title: E9_FLB_wt_CTCF-37141

description: Forelimb bud mouse E9_wt_CTCF-37141 viewpoint


title: E9_FLB_wt_CS65

description: Forelimb bud mouse E9_wt_CS65 viewpoint


title: kidney_DSAposABMRh_4


title: kidney_No_ABMRh_12


title: E9_FLB_wt_CS40

description: Forelimb bud mouse E9_wt_CS40 viewpoint


title: LVshNONtg_Input

description: Input library from lentiviral non-targeting shRNA control (LVshNONtg) infected 12Z cells

value: shNONtg (control)


title: E9_FLB_invTDOM_Hoxd9

description: Forelimb bud mouse E9_invTDOM_Hoxd9 viewpoint

value: HoxDinv(T-DOM)


title: LVshNONtg_H3K4me1_rep1

description: H3K4me1 ChIP (replicate 1) library from lentiviral non-targeting shRNA control (LVshNONtg) infected 12Z cells


title: LVshNONtg_H3K4me1_rep2

description: H3K4me1 ChIP (replicate 2) library from lentiviral non-targeting shRNA control (LVshNONtg) infected 12Z cells


title: E9_FLB_invTDOM_Hoxd4

description: Forelimb bud mouse E9_invTDOM_Hoxd4 viewpoint


title: kidney_DSAposABMRh_3


title: ZnF-3AC no dox Rep1 MBD2 seq


title: siARID1A_1uMA485_H3K27ac_rep2_CUTNRUN

description: H3K27ac CUT&RUN library (replicate 2) from 12Z cells after 72 hours treatment with ARID1A siRNA (siARID1A) and 48 hours treatment with 1 uM A-485.

data_processing:
Library strategy: CUT&RUN
Raw reads for H3K27ac and IgG CUT&RUN libraries were trimmed with cutadapt and Trim Galore!
Trimmed reads were aligned to GRCh38.p12 reference genome via Bowtie2 with flag `--very-sensitive`. Aligned reads were sorted and indexed with samtools.
Only properly-paired read fragments were retained by samtools view with flag `-f 3` followed by sorting and indexing.
Library molecular complexity was then estimated from duplicate rates by ATACseqQC and preseqR, and libraries were subsampled to equivalent molecular complexity within an experimental design based on these estimates with samtools.
Picard MarkDuplicates was used to remove PCR duplicates, followed by sorting and indexing.
MACS2 was used to call narrow peaks (FDR < 0.05) on each H3K27ac CUT&RUN replicate against the respective IgG CUT&RUN control with flags `--nomodel --extsize 146` to bypass model building.
A naïve overlapping peak set, as defined by ENCODE, was constructed by calling peaks on pooled replicates followed by bedtools intersect to select for peaks of at least 50% overlap with each biological replicate.
The resulting peaks were repeat-masked by ENCODE blacklist filtering and filtered for non-standard contigs.
Differential H3K27ac CUT&RUN analysis was computed with csaw. In order to promote similarity between the differential H3K27ac CUT&RUN and ChIP-seq experiments, we used the same consensus peak set as defined by our differential H3K27ac ChIP-seq experiment for the CUT&RUN analysis here. H3K27ac CUT&RUN reads were counted in these query regions by csaw, then filtered for low abundance peaks with average logCPM > -3. When comparing CUT&RUN libraries, any global differences in CUT&RUN reaction efficiency observed between two conditions were considered a result of technical bias to ensure a highly conservative analysis. As such, we employed a non-linear loess-based normalization to the peak count matrix, as is implemented in csaw, to assume a symmetrical MA distribution. A design matrix was then constructed from one “condition” variable, without an intercept. The count matrix and loess offsets were then supplied to edgeR for estimating dispersions and fitting the quasi-likelihood generalized linear model for hypothesis testing. Nearby query regions were then merged up to 500 bp apart for a maximum merged region width of 5 kilobases, and the most significant probability was used to represent the merged region.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Tabular peak set files including blacklist-filtered CUT&RUN replicate narrowPeaks (FDR < 0.05 MACS2 output) and naïve replicate-overlapping narrowPeaks. Non-thresholded differential CUT&RUN results from csaw are also reported as a tab-separated values (TSV) file.

extract_protocol:
72 hours following siRNA transfection, 5*10^5 12Z cells were harvested and resuspended in Wash Buffer (20 mM HEPES-NaOH pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1X protease inhibitor cocktail) and washed twice by centrifuge at 600 g for 3 min, and then added to the concanavalin A bead suspension and mixed on a tube rotator for 10 min at room temp. Cell/bead conjugates were resuspended in 500 mL of Antibody Buffer (Wash Buffer with 0.05% Digitonin and 2 mM EDTA) containing 5 ug of H3K27ac antibody (Active Motif, cat# 39133) or Rabbit IgG (Cell Signaling, cat#2729) and incubated in a tube nutator overnight at 4° C. The following day, cells were washed in Digitonin Buffer (Wash Buffer with 0.05% Digitonin) three times, resuspended in 250 mL of Digitonin Buffer and 12.5 mL of CUTANA pAG-MNase (EpiCypher, cat# 15-1016) was added. Cells were mixed on a nutator at room temp for 1 hr, followed by two washes in Digitonin Buffer and one wash with Low-Salt Rinse Buffer (20 mM HEPES-NaOH pH 7.5, 0.5 mM Spermidine, 1X protease inhibitor cocktail). Tubes were chilled on ice, 1 mL of Calcium Incubation Buffer (3.5 mM HEPES-NaOH pH 7.5, 10 mM CaCl2, 0.05% Digitonin) was added, and tubes were nutated at 4° C. After 2.5 min, beads were bound to magnet, supernatant was removed and 250 mL of EGTA-STOP Buffer (170 mM NaCl, 20 mM EGTA, 0.05% Digitonin, 20 μg/mL RNase A, 20 μg/mL Glycogen, 0.8 pg/ml S. cerevisiae fragmented nucleosomal DNA) was added. Beads were nutated at 37° C for 30 min, followed by centrifuge at 16,000 g for 5 min at 4° C. DNA was purified using the NucleoSpin Gel and PCR Clean-up Kit (Takara, cat# 740609.50).
Libraries for CUT&RUN samples were prepared by the Van Andel Genomics Core from 0.5-1 ng of IP material, using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems, Wilmington, MA USA). Prior to PCR amplification, end-repaired and A-tailed DNA fragments were ligated to Bioo Scientific NEXTflex Adapters (Bioo Scientific, Austin, TX, USA) at a concentration of 500nM. Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Individually indexed libraries were pooled and 50 bp, paired end sequencing was performed on an Illumina NovaSeq6000 sequencer using an S1, 100 cycle sequencing kit (Illumina Inc., San Diego, CA, USA) Each library was sequenced to an average depth of 75M reads. Base calling was done by Illumina RTA3 and output was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.

treatment_protocol: Cells were transfected in the absence of antibiotic with 50 nM siRNA (Dharmacon, ON-TARGETplus) via RNAiMax (ThermoFisher) lipofectamine reagent in OptiMEM (Gibco). 24 hours following transfection, growth media was replaced with the addition of 0.1% DMSO (vehicle) or 1 uM A-485. 48 hours following transfection, growth media was replaced again with 0.5% FBS and inclusion of drug or vehicle treatment.

value: siARID1A + A-485 (1 uM)


title: siARID1A_1uMA485_IgG_CUTNRUN

description: IgG CUT&RUN library from 12Z cells after 72 hours treatment with ARID1A siRNA (siARID1A) and 48 hours treatment with 1 uM A-485.


title: Input DNA no dox


title: siARID1A_siP300_vehicle_IgG_CUTNRUN

description: IgG CUT&RUN library from 12Z cells after 72 hours treatment with ARID1A and P300 siRNAs (siARID1A+siP300) and 48 hours treatment with 0.1% DMSO (vehicle).

value: siARID1A + siP300


title: ZnF-3AC no dox Rep2 MBD2 seq


title: siARID1A_1uMA485_H3K27ac_rep1_CUTNRUN

description: H3K27ac CUT&RUN library (replicate 1) from 12Z cells after 72 hours treatment with ARID1A siRNA (siARID1A) and 48 hours treatment with 1 uM A-485.


title: E9_FLB_invTDOM_ELCR2

description: Forelimb bud mouse E9_invTDOM_ELCR2 viewpoint


title: E9_FLB_invTDOM_CTCF-37154

description: Forelimb bud mouse E9_invTDOM_CTCF-37154 viewpoint


title: shlacZ_3

city: Cheonan

first: Ita

middle: Novita

last: Sari

state: Chungcheongnam-do

address: Bongjeong-ro 25, Dongnam-gu

department: Soonchunhyang Institute of Medi-Bio Science

country: South Korea

institute: Soonchunhyang University

data_processing:
Mean expression of each groups were obtained by measuring the average of 3 samples in each group
Data were devided from either shAMD1 to shLacZ or sLacZ to shAMD1 to obtain the fold change number

source_name: Primary BC CML cells

growth_protocol: Primary BC CML cells were obtained from mouse bone marrow from each samples, then cells were grown in ex-vivo media containing 50ng/ml murine SCF and 20ng/ml murine TPO

extract_protocol:
Cells from mouse bone marrow were sorted, and total RNA were extracted using Qiagen Rneasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BC CML infected cells

value: Bone marrow


title: E9_FLB_invTDOM_CTCF-37141

description: Forelimb bud mouse E9_invTDOM_CTCF-37141 viewpoint


title: siARID1A_siP300_vehicle_H3K27ac_rep2_CUTNRUN

description: H3K27ac CUT&RUN library (replicate 2) from 12Z cells after 72 hours treatment with ARID1A and P300 siRNAs (siARID1A+siP300) and 48 hours treatment with 0.1% DMSO (vehicle).


title: macrophages from non-tumor bearing mice

city: New York

first: Xiaojing

last: Ma

address: 1300 York Ave.

institute: Weill Cornell Medicine

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the mouse GRCm38 reference genome using STAR v2.5.2b.
Transcript abundances was estimated in Fragments Per Kilobase of exon per Million mapped reads (FPKM) by using Cufflinks v2.1.1 package.
Genome_build: GRCm38
Supplementary_files_format_and_content: excel file storing expression FPKM values

source_name: Peritoneum

extract_protocol:
Macrophages (CD45+CD11b+F4/80+) were sorted from peritoneal washes of mice with Becton-Dickinson Influx, and then lysed in  Buffer RLT Plus. Total RNAs were extracted with the RNeasy Plus Mini Kit (QIAGEN, 74134)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Peritoneal macrophages were isolated from naïve or tumor bearing mice 5 weeks after tumor implantation

value: C57BL/6 mice

value: Macrophages

tag: tumor cell line

value: no


title: macrophages from WT ID8 tumor bearing mice

value: ID8 (WT)


title: siARID1A_siP300_vehicle_H3K27ac_rep1_CUTNRUN

description: H3K27ac CUT&RUN library (replicate 1) from 12Z cells after 72 hours treatment with ARID1A and P300 siRNAs (siARID1A+siP300) and 48 hours treatment with 0.1% DMSO (vehicle).


title: macrophages from UBR5 KO ID8 tumor bearing mice


title: shlacZ_2


title: E9_FLB_invTDOM_CS93

description: Forelimb bud mouse E9_invTDOM_CS93 viewpoint


title: E9_FLB_invTDOM_CS40

description: Forelimb bud mouse E9_invTDOM_CS40 viewpoint


title: kidney_No_ABMRh_7

description: Gene expression data from kidney allograft biopsy

data_processing: Resulting image files (.dat files) were generated using the GeneChip® Command Console® Software (AGCC), and intensity values for each probe cell (.cel file) were calculated.

extract_protocol: Total RNA was isolated from the kidney allograft biopsy specimens -using the Allprep DNA/RNA/miRNA Universal Kit® (Qiagen Benelux BV) on a QIAcube instrument (Qiagen Benelux BV).

value: No ABMRh


title: kidney_No_ABMRh_9


title: kidney_No_ABMRh_10


title: kidney_DSAnegABMRh_2

value: DSAnegABMRh


title: kidney_DSAnegABMRh_1


title: E9_FLB_invCS3840_Hoxd9

description: Forelimb bud mouse E9_invCS3840_Hoxd9 viewpoint

value: Whole forelimb bud


title: kidney_No_ABMRh_8


title: siARID1A_vehicle_IgG_CUTNRUN

description: IgG CUT&RUN library from 12Z cells after 72 hours treatment with ARID1A siRNA (siARID1A) and 48 hours treatment with 0.1% DMSO (vehicle).


title: siARID1A_vehicle_H3K27ac_rep1_CUTNRUN

description: H3K27ac CUT&RUN library (replicate 1) from 12Z cells after 72 hours treatment with ARID1A siRNA (siARID1A) and 48 hours treatment with 0.1% DMSO (vehicle).


title: E9_FLB_invTDOM_Hoxd11

description: Forelimb bud mouse E9_invTDOM_Hoxd11 viewpoint


title: siARID1A_vehicle_H3K27ac_rep2_CUTNRUN

description: H3K27ac CUT&RUN library (replicate 2) from 12Z cells after 72 hours treatment with ARID1A siRNA (siARID1A) and 48 hours treatment with 0.1% DMSO (vehicle).


title: E9_FLB_invTDOM_CS65

description: Forelimb bud mouse E9_invTDOM_CS65 viewpoint


title: kidney_No_ABMRh_6


title: shlacZ_1


title: shAMD1_3


title: siNONtg_vehicle_IgG_CUTNRUN

description: IgG CUT&RUN library from 12Z cells after 72 hours treatment with non-targeting siRNA control (siNONtg) and 48 hours treatment with 0.1% DMSO (vehicle).

value: Control


title: shAMD1_1


title: E9_FLB_invCS3840_Hoxd4

description: Forelimb bud mouse E9_invCS3840_Hoxd4 viewpoint


title: shAMD1_2


title: siNONtg_vehicle_H3K27ac_rep2_CUTNRUN

description: H3K27ac CUT&RUN library (replicate 2) from 12Z cells after 72 hours treatment with non-targeting siRNA control (siNONtg) and 48 hours treatment with 0.1% DMSO (vehicle).


title: siNONtg_vehicle_H3K27ac_rep1_CUTNRUN

description: H3K27ac CUT&RUN library (replicate 1) from 12Z cells after 72 hours treatment with non-targeting siRNA control (siNONtg) and 48 hours treatment with 0.1% DMSO (vehicle).


title: E9_FLB_invCS3840_Hoxd13

description: Forelimb bud mouse E9_invCS3840_Hoxd13 viewpoint


title: E9_FLB_invCS3840_Hoxd11

description: Forelimb bud mouse E9_invCS3840_Hoxd11 viewpoint


title: siARID1A_siP300_vehicle_rep3_RNA

description: RNA library from 12Z cells after 72 hours treatment with ARID1A and P300 siRNAs (siARID1A+siP300) and 48 hours treatment with 0.1% DMSO (vehicle).

data_processing:
Raw reads were trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned GRCh38.p12 genome assembly, indexed to GENCODE (v28) GFF3 annotation via STAR aligner with flag ‘--quantMode GeneCounts’ for feature counting.
STAR sample gene counts were concatenated for Stranded-Reverse (libtype), corresponding to column 4 of STAR output ReadsPerGene.out.tab file.
Low count genes were filtered prior to DESeq2 count normalization (at least 1 count per sample on average) and subsequent differential-expression analysis comparisons. Calculated differential-expression probabilities were corrected for multiple testing by independent hypothesis weighting (IHW) for downstream analysis.
Genome_build: GRCh38.p12 indexed to GENCODE (v28) GFF3 annotation
Supplementary_files_format_and_content: Comma-separated values (CSV) and tab-separated values (TSV) tabular text files including gene counts (STAR output), a concatenated and symbol-converted raw counts table, DESeq2 linear normalized counts table, DESeq2 regularized-logarithm (rlog) counts table, and non-thresholded DESeq2 differential expression analysis.

extract_protocol:
72 hours following siRNA transfection and 48 hours following drug or vehicle treatment, RNA was extracted using the Quick-RNA Miniprep Kit (Zymo Research).
Directional mRNA-seq libraries were constructed from 500 ng of total RNA supplied to the KAPA mRNA HyperPrep kit (v4.17) (Kapa Biosystems). RNA was sheared to 300-400 bp. cDNA fragments were ligated to IDT for Illumina unique dual adapters (IDT DNA Inc.).

treatment_protocol: Cells were transfected in the absence of antibiotic with 50 nM siRNA (Dharmacon, ON-TARGETplus) via RNAiMax (ThermoFisher) lipofectamine reagent in OptiMEM (Gibco). 24 hours following transfection, growth media was replaced with the addition of 0.1% DMSO (vehicle) or 100 nM A-485. 48 hours following transfection, growth media was replaced again with 0.5% FBS and inclusion of drug or vehicle treatment.


title: E9_FLB_invCS3840_ELCR2

description: Forelimb bud mouse E9_invCS3840_ELCR2 viewpoint


title: p20097-s099_RVf12_4dpi

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were aligned using STAR v2.7.3.(Dobin et al.)
The STAR index was built by combining genome sequences for Macaca mulatta (Mmul10 Ensembl release 100), SARS-CoV2 (strain MN985325.1 - NCBI) and ERCC sequences. The gffread utility (https://github.com/gpertea/gffread) was used to convert gff3 file for SARS-CoV2 and the resulting gtf file for SARS-CoV2 was edited to include exon entries which had the same coordinates as CDS to get counts with STAR. The combined genomic and gtf files were used for generating the STAR index.
Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count(Sandler et al., 2014).
DESeq2 was used for normalization(Love et al.), producing a normalized read count table
Genome_build: Macaca mulatta Mmul10 Ensembl release 100
Genome_build: SARS-CoV2 (strain MN985325.1 - NCBI)
Supplementary_files_format_and_content: tab delimited text file containing raw or normalized read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: bronchoalveolar lavages

extract_protocol:
50,000 cells were lysed directly into 700 ul of QIAzol reagent.  RNA was isolated using RNeasy Mini or Micro kits (Qiagen) with on-column DNase digestion. RNA quality was assessed using an Agilent Bioanalyzer
total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the NexteraXT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled at equimolar concentrations, and sequenced on an Illumina NovaSeq6000 at 100SR, yielding 20-25 million reads per sample.

treatment_protocol: RMs were infected with 1.1x106 plaque forming units (PFU) SARS-CoV-2 via both the intranasal (1 mL) and intratracheal (1 mL) routes concurrently. Four RMs were administered 4 mg Baricitinib starting at day 2 post-infection (DPI) for 8-9 consecutive days. Baricitinib was supplied as a powder that was folded into food items (i.e. honey, yogurt, etc.) or distilled water, which was delivered either orally or as a gavage when animals were being anesthetically accessed, respectively.

tag: animalid

tag: day post infection


title: p20097-s098_RVf12_2dpi


title: p20097-s097_RVf12_-5dpi


title: kidney_No_ABMRh_4


title: kidney_DSAposABMRh_2


title: E9_FLB_invCS3840_CTCF-37154

description: Forelimb bud mouse E9_invCS3840_CTCF-37154 viewpoint

tag: strain


title: kidney_No_ABMRh_3


title: Input_K2R

first: Diego

last: Mourão

state: NY

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
filter with "ShortRead" package fastq file for reads with quality score > 300 and "N" < 10
Use "Rsubread" package to align filtered files to hg19 human genome assembly and generate "BAM" files
Use package "Rsamtools" to sort and index "BAM" files
Use "MACS2" peak calling as : macs2 callpeak -t BAM/Huh7_WT_Exp1_BRD4_CellSignaling_S1_R1_Filtered_sorted.bam -c BAM/Huh7_WT_Exp1_Input__S2_R1_Filtered_sorted.bam -f BAM -n WT_1 --outdir newmacs2 -g hs --broad --nomodel --extsize 75
Use package "GenomicRanges" to merge overlaping peaks present in at least 2 samples among "Empty1", "Empty2", "WT1" and "WT2", not present in the blacklist hg19BlackList_ENCFF001TDO.bed
Use package "DESeq2" to determine differential binding
Genome_build: hg19
Supplementary_files_format_and_content: BED files, Bigwig files

growth_protocol: Huh-7 cells, Huh-7 YFV-C and Huh-7 YFV-C K4RK8R cells were grown at 37˚C and 5% CO2

extract_protocol:
Cells were fixed with 1% formaldehyde (methanol-free) for 10 minutes. The formaldehyde was quenched for 5 minutes by addition of glycine to a final concentration of 0.125M. Cells were washed twice with ice cold PBS. Chromatin was sonicated to an average size of 200-600bp
DNA was blunt-ended, an “A”-overhang was added and Illumina Paired-End adaptors were ligated to the DNA fragments. ChIP-Seq library amplification was performed using Illumina primers 1.0 and 2.0.

treatment_protocol: 48 hours with 10ug/ml doxycycline.

value: Human hepatoma cell line Huh-7

tag: chip antibody

value: 10µg/ml of doxycycline for 48h to induce YFV mutant capsid protein


title: kidney_No_ABMRh_5


title: E9_FLB_invCS3840_CTCF-37141

description: Forelimb bud mouse E9_invCS3840_CTCF-37141 viewpoint

tag: genotype


title: kidney_No_ABMRh_2

description: Gene expression data from kidney allograft biopsy


title: kidney_DSAposABMRh_1

value: DSAposABMRh


title: p20097-s094_RHz12_4dpi

tag: treatment

value: Untreated


title: siARID1A_A485_rep3_RNA

description: RNA library from 12Z cells after 72 hours treatment with ARID1A siRNA (siARID1A) and 48 hours treatment with 100 nM A-485.


title: Input_Empty

value: 10µg/ml of doxycycline for 48h to induce HA-Flag fusion protein


title: siARID1A_siP300_vehicle_rep1_RNA


title: p20097-s093_RHz12_2dpi


title: E9_FLB_invCS3840_CS93

description: Forelimb bud mouse E9_invCS3840_CS93 viewpoint

tag: tissue


title: siARID1A_A485_rep2_RNA


title: p20097-s092_RHz12_-5dpi


title: Huh7_WT_2

value: rabbit monoclonal anti-BRD4 antibody (Cell Signaling, #134403S)

value: 10µg/ml of doxycycline for 48h to induce YFV capsid  protein


title: siARID1A_A485_rep1_RNA


title: siARID1A_siP300_vehicle_rep2_RNA

value: siARID1A + siP300


title: Huh7_Empty_2


title: kidney_No_ABMRh_1


title: p20097-s089_7_141_4dpi


title: Input_WT


title: Huh7_K2R_1


title: E9_FLB_invCS3840_CS40

description: Forelimb bud mouse E9_invCS3840_CS40 viewpoint


title: siARID1A_vehicle_rep3_RNA

description: RNA library from 12Z cells after 72 hours treatment with ARID1A siRNA (siARID1A) and 48 hours treatment with 0.1% DMSO (vehicle).


title: p20097-s088_7_141_2dpi


title: E9_FLB_delCS3840_Hoxd9

description: Forelimb bud mouse E9_delCS3840_Hoxd9 viewpoint


title: E9_FLB_delCS3840_Hoxd4

description: Forelimb bud mouse E9_delCS3840_Hoxd4 viewpoint


title: Huh7_WT_1


title: p20097-s084_RQv9_4dpi


title: siARID1A_vehicle_rep2_RNA


title: p20097-s087_7_141_-5dpi


title: E9_FLB_invCS3840_CS65

description: Forelimb bud mouse E9_invCS3840_CS65 viewpoint


title: siARID1A_vehicle_rep1_RNA


title: Huh7_Empty_1


title: siP300_vehicle_rep3_RNA

description: RNA library from 12Z cells after 72 hours treatment with P300 siRNA (siP300) and 48 hours treatment with 0.1% DMSO (vehicle).


title: siP300_vehicle_rep2_RNA


title: E9_FLB_delCS3840_ELCR2

description: Forelimb bud mouse E9_delCS3840_ELCR2 viewpoint


title: p20097-s083_RQv9_2dpi


title: ZnF(3xHA)-ChIP

tag: antibody

value: 3x HA-tag

tag: antibody vendor/amount


title: E9_FLB_delCS3840_CTCF-37154

description: Forelimb bud mouse E9_delCS3840_CTCF-37154 viewpoint

tag: embryonic day


title: Input ZnF(3xHA)-ChIP

value: Input


title: DOX39

city: Oxford

first: Eshita

last: Sharma

state: Oxfordshire

address: Roosevelt Drive, Headington

department: Bioinformatics

country: United Kingdom

institute: Wellcome Trust Centre for Human Genetics

description:
counts.txt
TIM6297A26

data_processing:
Real time Analysis (RTA):  HiSeq 4000 - RTA v2.7.7, Application Version: HD 3.4.0.38
Base-calling: bcl2fastq v2.17.1.14
Alignment: Reads in gzipped fastq format were aligned using Hisat2 version-2.0.4 with default parameters to the Rat genome Rnor_6.0, Ensembl release 81.
Read counts (abundance measurement): Reads mapping uniquely to genes annotated in ENSEMBL release 81 were counted using featureCounts implemented in subread-v1.5.0
Normalized Counts: Read counts were normalized to counts per million (CPM) and Transcripts per Million (TPM) by dividing each gene-count by total reads mapped (uniquely mapped to exonic regions) per million and using ENSEMBL annotated read-lengths
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: exon_counts.txt: Gene expression counts using reads aligning to annotated exon features of 32546 genes
Supplementary_files_format_and_content: tpm_normalized_counts.txt: The above count table normalized to transcripts per million
Supplementary_files_format_and_content: QC_Table.xlsx: Contains two excel sheets with Sheet 1 = sample information with information regarding sequencing depth and mapping QC metrics
Supplementary_files_format_and_content: QC_Table.xlsx: Sheet2= Contains description of column headers of cell metadata in Sheet 1
Supplementary_files_format_and_content: Text

source_name: heart

extract_protocol:
RNA was extracted with RNeasy® Fibrous Tissue Mini kit (Qiagen, Manchester, UK) using ~30 mg of snap-frozen heart tissue from the saline and DOX high group of cohort 1
Input material was normalised to equal input of 100 ng prior to library preparation. Polyadenylated transcript enrichment and strand specific library preparation was completed using NEBNext Ultra II mRNA kit (NEB) following manufacturer’s instructions.

tag: group

value: high DOX

value: male

value: Wistar

value: heart

tag: conditions

value: 5 weekly iv injections of 3mg/kg doxorubicin


title: p20097-s079_RLf10_4dpi


title: E9_FLB_delCS3840_CTCF-37141

description: Forelimb bud mouse E9_delCS3840_CTCF-37141 viewpoint

value: Whole forelimb bud


title: siNONtg_A485_rep3_RNA

description: RNA library from 12Z cells after 72 hours treatment with non-targeting siRNA control (siNONtg) and 48 hours treatment with 100 nM A-485.


title: p20097-s078_RLf10_2dpi


title: DOX38

description:
counts.txt
TIM6297A25

tag: Sex


title: E9_FLB_delCS3840_CS93

description: Forelimb bud mouse E9_delCS3840_CS93 viewpoint


title: E9_FLB_delCS3840_Hoxd11

description: Forelimb bud mouse E9_delCS3840_Hoxd11 viewpoint


title: DOX33

description:
counts.txt
TIM6297A24


title: p20097-s077_RLf10_-5dpi


title: DOX32

description:
counts.txt
TIM6297A23


title: p20097-s074_5_215_4dpi


title: E9_FLB_delCS3840_CS65

description: Forelimb bud mouse E9_delCS3840_CS65 viewpoint


title: E12_PFL_wt_Hoxd9

description: Proximal forelimb mouse E12.5_wt_Hoxd9 viewpoint

source_name: Proximal Forelimbs

value: Proximal Forelimbs

value: wild-type


title: p20097-s082_RQv9_-5dpi


title: siNONtg_vehicle_rep3_RNA

description: RNA library from 12Z cells after 72 hours treatment with non-targeting siRNA control (siNONtg) and 48 hours treatment with 0.1% DMSO (vehicle).

value: Control


title: DOX31

description:
counts.txt
TIM6297A22


title: p20097-s072_5_215_-5dpi


title: DOX30

description:
counts.txt
TIM6297A21


title: siNONtg_vehicle_rep2_RNA


title: E12_PFL_wt_Hoxd11

description: Proximal forelimb mouse E12.5_wt_Hoxd11 viewpoint


title: p20097-s073_5_215_2dpi


title: p20097-s069_RAt11_4dpi


title: siNONtg_vehicle_rep1_RNA


title: siP300_vehicle_rep1_RNA


title: DOX37

description:
counts.txt
TIM6297A10

value: saline control

value: 5 weekly iv injections of saline


title: DOX36

description:
counts.txt
TIM6297A9


title: E12_PFL_wt_CS38

description: Proximal forelimb mouse E12.5_wt_CS38 viewpoint


title: p20097-s068_RAt11_2dpi


title: SimpleChIP_LVshARID1A_H3K27ac_rep2

description: H3K27ac ChIP (replicate 2) library from lentiviral shARID1A infected 12Z cells

data_processing:
Raw reads for IPs and inputs were trimmed with cutadapt and Trim Galore!
Trimmed reads were aligned to GRCh38.p12 reference genome via Bowtie2 with flag `--very-sensitive`. Aligned reads were sorted and indexed with samtools.
Library molecular complexity was then estimated from duplicate rates by ATACseqQC and preseqR, and libraries were subsampled to equivalent molecular complexity within an experimental design based on these estimates with samtools.
Picard MarkDuplicates was used to remove PCR duplicates, followed by sorting and indexing.
MACS2 was used to call narrow peaks (FDR < 0.05) on each ChIP replicate against the input control with flags `--nomodel --extsize 146` to bypass model building.
A naïve overlapping peak set, as defined by ENCODE, was constructed by calling peaks on pooled replicates followed by bedtools intersect to select for peaks of at least 50% overlap with each biological replicate.
The resulting peaks were repeat-masked by ENCODE blacklist filtering and filtered for non-standard contigs.
Differential abundance analysis was computed with csaw. Briefly, a consensus peak set was constructed for each differential experiment from the union of replicate-intersecting, filtered MACS2 peaks called in each condition. The replicate intersection criteria used here are less stringent than the naïve overlap; any partial intersect between ChIP replicates was accepted as a query region tested for differential abundance. ChIP reads were counted in these query regions by csaw, then filtered for low abundance peaks with average logCPM > -3. When comparing ChIP libraries, any global differences in IP efficiency observed between the two conditions were considered a result of technical bias to ensure a highly conservative analysis. As such, we employed a non-linear loess-based normalization to the peak count matrix, as is implemented in csaw, to assume a symmetrical MA distribution. A design matrix was then constructed from one “condition” variable, without an intercept. The count matrix and loess offsets were then supplied to edgeR for estimating dispersions and fitting the quasi-likelihood generalized linear model for hypothesis testing. Nearby query regions were then merged up to 500 bp apart for a maximum merged region width of 5 kilobases, and the most significant probability was used to represent the merged region.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Tabular peak set files including blacklist-filtered ChIP replicate narrowPeaks (FDR < 0.05 MACS2 output) and naïve replicate-overlapping narrowPeaks. Non-thresholded differential abundance results from csaw are also reported as a tab-separated values (TSV) file.

extract_protocol:
72 hours following lentiviral transduction, cells were treated with 1% formaldehyde in cell culture media for 15 min at room temp. Formaldehyde was quenched by the addition of 0.125 M Glycine, and cells were washed with PBS. 1x10^7 crosslinked cells were used per IP. Chromatin from crosslinked cells was fractionated by digestion with micrococcal nuclease using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling) per the manufacturers’ instructions. IPs were performed using the SimpleChIP Enzymatic Chromatin IP Kit per the manufacturers’ instructions, with the addition of 5 mM sodium butyrate included in Buffer A and ChIP Buffer. Antibodies used were 10 ug H3K27ac (Active Motif, 39133) or 5 ug H3K18ac (ab1191, Abcam) antibody. DNA was purified using the ChIP DNA Clean & Concentrator Kit (Zymo).
Libraries for Input and IP samples were prepared by the Van Andel Genomics Core from 10 ng of input and IP material when available, and all material when less than 10 ng available, using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems). Prior to PCR amplification, end repaired and A-tailed DNA fragments were ligated to Bioo Scientific NEXTflex Adapters (Bioo Scientific).


title: siNONtg_A485_rep2_RNA


title: DOX35

description:
counts.txt
TIM6297A8


title: E12_PFL_wt_CS65

description: Proximal forelimb mouse E12.5_wt_CS65 viewpoint


title: siNONtg_A485_rep1_RNA


title: p20097-s067_RAt11_-5dpi


title: E12_PFL_invTDOMdelBd_Hoxd9

description: Proximal forelimb mouse E12.5_invTDOMdelBd_Hoxd9 viewpoint

value: HoxDinv(T-DOM)del(Bd)


title: DOX34

description:
counts.txt
TIM6297A7


title: E12_PFL_wt_Hoxd4

description: Proximal forelimb mouse E12.5_wt_Hoxd4 viewpoint


title: SimpleChIP_LVshARID1A_H3K27ac_rep1

description: H3K27ac ChIP (replicate 1) library from lentiviral shARID1A infected 12Z cells


title: E12_PFL_invTDOMdelBd_Hoxd4

description: Proximal forelimb mouse E12.5_invTDOMdelBd_Hoxd4 viewpoint


title: SimpleChIP_LVshARID1A_H3K18ac_rep2

description: H3K18ac ChIP (replicate 2) library from lentiviral shARID1A infected 12Z cells


title: p20097-s064_06_112_4dpi

value: Untreated


title: p20097-s063_06_112_2dpi


title: DOX10

description:
counts.txt
TIM6297A6


title: E12_PFL_invTDOMdelBd_Hoxd11

description: Proximal forelimb mouse E12.5_invTDOMdelBd_Hoxd11 viewpoint


title: SimpleChIP_LVshARID1A_H3K18ac_rep1

description: H3K18ac ChIP (replicate 1) library from lentiviral shARID1A infected 12Z cells


title: p20097-s062_06_112_-5dpi


title: E12_PFL_invTDOMdelBd_CTCF-37141

description: Proximal forelimb mouse E12.5_invTDOMdelBd_CTCF-37141 viewpoint


title: p20084-s008_RHz12_BAL_Day4_GEX

data_processing:
Cell Ranger software was used to perform demultiplexing of cellular transcript data
Cell Ranger v3.1 (10X Genomics) was used to perform  mapping and annotation of UMIs and abundance estimation of transcripts for downstream data analysis.
Cell Ranger was used to create a single cell reference with the Macaca mulatta (Mmul10 Ensembl release 100)
Genome_build: Macaca mulatta Mmul10 Ensembl release 100
Supplementary_files_format_and_content: CSV files are generated from CellrangerV3.1 containing per cell transcript counts.

extract_protocol:
single-cell suspensions of 100,000 BAL-derived cells, and approximately 30,000 cells were loaded onto 10X Chromium Controller in the BSL3. Single cells were partitioned into droplets (Gel Beads in Emulsion: GEMs) using Chromium NextGEM Single Cell 5’ Library & Gel Bead kits on the 10X Chromium Controller(Zheng et al., 2017).
The resulting cDNA was amplified and libraries were prepared for transcriptomic analysis according to manufacturer instructions. Gene expression libraries were sequenced as paired-end 26x91 reads on an Illumina NovaSeq6000 targeting a depth of 50,000 reads per cell

treatment_protocol: RMs were infected with 1.1x106 plaque forming units (PFU) SARS-CoV-2 via both the intranasal (1 mL) and intratracheal (1 mL) routes concurrently. Two RMs were administered 4 mg Baricitinib starting at day 2 post-infection (DPI) for 8-9 consecutive days. Baricitinib was supplied as a powder that was folded into food items (i.e. honey, yogurt, etc.) or distilled water, which was delivered either orally or as a gavage when animals were being anesthetically accessed, respectively.


title: SimpleChIP_LVshNONtg_H3K27ac_rep2

description: H3K27ac ChIP (replicate 2) library from lentiviral non-targeting shRNA control (LVshNONtg) infected 12Z cells


title: DOX9

description:
counts.txt
TIM6297A5


title: DOX7

description:
counts.txt
TIM6297A3


title: kidney_No_ABMRh_11

description: Gene expression data from kidney allograft biopsy

tag: phenotype

value: No ABMRh


title: DOX8

description:
counts.txt
TIM6297A4


title: E12_PFL_invTDOMdelBd_CS38

description: Proximal forelimb mouse E12.5_invTDOMdelBd_CS38 viewpoint


title: SimpleChIP_LVshNONtg_H3K27ac_rep1

description: H3K27ac ChIP (replicate 1) library from lentiviral non-targeting shRNA control (LVshNONtg) infected 12Z cells

tag: cell line


title: p20084_s004_RHz12_BAL_GEX


title: DOX6

description:
counts.txt
TIM6297A2


title: SimpleChIP_LVshNONtg_H3K18ac_rep2

description: H3K18ac ChIP (replicate 2) library from lentiviral non-targeting shRNA control (LVshNONtg) infected 12Z cells

tag: genotype/variation


title: p20084_s003_RVf12_BAL_GEX


title: E12_PFL_invTDOM_Hoxd4

description: Proximal forelimb mouse E12.5_invTDOM_Hoxd4 viewpoint

value: HoxDinv(T-DOM)


title: E12_PFL_invTDOM_Hoxd9

description: Proximal forelimb mouse E12.5_invTDOM_Hoxd9 viewpoint


title: SimpleChIP_LVshNONtg_H3K18ac_rep1

description: H3K18ac ChIP (replicate 1) library from lentiviral non-targeting shRNA control (LVshNONtg) infected 12Z cells


title: E12_PFL_invTDOM_Hoxd11

description: Proximal forelimb mouse E12.5_invTDOM_Hoxd11 viewpoint


title: E12_PFL_invTDOMdelBd_CTCF-37157

description: Proximal forelimb mouse E12.5_invTDOMdelBd_CTCF-37157 viewpoint


title: p20075-s012_RQv9_BAL_Day4_GEX


title: WT_P300_Input

description: Input library from wild-type 12Z cells

data_processing:
Raw reads for IPs and input were trimmed with cutadapt and Trim Galore!
Trimmed reads were aligned to GRCh38.p12 reference genome via Bowtie2 with flag `--very-sensitive`. Aligned reads were sorted and indexed with samtools.
Picard MarkDuplicates was used to remove PCR duplicates, followed by sorting and indexing.
MACS2 was used to call broad peaks (FDR < 0.05) on each ChIP replicate against the input control with otherwise default settings.
A naïve overlapping peak set, as defined by ENCODE, was constructed by calling peaks on pooled replicates followed by bedtools intersect to select for peaks of at least 50% overlap with each biological replicate.
The resulting peaks were repeat-masked by ENCODE blacklist filtering and filtered for non-standard contigs.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Tabular peak set files including blacklist-filtered ChIP replicate broadPeaks (FDR < 0.05 MACS2 output) and naïve replicate-overlapping broadPeaks.

extract_protocol:
Cells were treated with 1% formaldehyde in cell culture media for 15 min at room temp. Formaldehyde was quenched by the addition of 0.125 M Glycine, and cells were washed with PBS. 1x10^7 crosslinked cells were used per IP. Chromatin from crosslinked cells was fractionated by digestion with micrococcal nuclease using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling) per the manufacturers’ instructions. Nuclei were resuspended in nuclear lysis buffer (50 mM Tris-HCl [pH 8.0], 10 mM EDTA [pH 8.0], 1% SDS) and sonicated for 30 seconds. Protein G magnetic beads (Cell Signaling) were preconjugated with 5 ug mouse monoclonal anti-P300 (NM11) (sc-32244, Santa Cruz) overnight at 4C in wash buffer (1X PBS, 0.5% BSA, 0.02% Tween-20). Fractionated chromatin was diluted into IP buffer (0.01%SDS, 1.1% TrionX-100, 1.2 mM EDTA [pH 8.0], 16.7 mM Tris-HCl [pH 8.0], 167 mM NaCl) and incubated with preconjugated antibody/Dynabeads overnight at 4C. Samples were washed at 4C with high-salt buffer (0.1% SDS, 1% TritonX-100, 2 mM EDTA [pH 8.0], 20 mM Tris-HCl [pH 8.0], 0.5 M NaCl), low-salt buffer (0.1% SDS, 1% TritonX-100, 2 mM EDTA [pH 8.0], 20 mM Tris-HCl [pH 8.0], 150 mM NaCl), dialysis buffer (0.2% Sarcosyl, 2 mM EDTA [pH 8.0], 50mM Tris-HCl [pH 8.0]), IP wash buffer (0.25M LiCl, 1% NP-40, 1% Deoxycholate, 1 mM EDTA [pH 8.0], 10 mM Tris-HCl [pH 8.0]) and TE (10mM Tris-HCL [pH 8.0], 1mM EDTA [pH 8.0]). IP chromatin was eluted for 30 min at 37C with elution buffer (1% SDS, 0.1 M NaHCO3). Crosslinks were reversed with 0.4 mg/mL Proteinase K (ThermoFisher) and 0.2 M NaCl at 65C for 2 hrs. DNA was purified using the ChIP DNA Clean & Concentrator Kit (Zymo).
Libraries for Input and IP samples were prepared by the Van Andel Genomics Core from 10 ng of input and IP material when available, and all material when less than 10 ng available, using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems). Prior to PCR amplification, end repaired and A-tailed DNA fragments were ligated to Bioo Scientific NEXTflex Adapters (Bioo Scientific).

value: Wild-type


title: E12_PFL_invTDOM_CTCF-37157

description: Proximal forelimb mouse E12.5_invTDOM_CTCF-37157 viewpoint


title: HK6

city: Bodø

first: Jorge

last: Fernandes

address: Universitetsalleen 11

department: Faculty of Biosciences and Aquaculture

country: Norway

institute: Nord University

data_processing:
Raw data was demultiplexed with bcl2fastq (v2.20.0.422)
Raw fastq files were trimmed adapters using cutadapt (v1.12) and filtered low-quality reads using FASTX-Toolkit (0.0.14); Quality control of raw and clean reads were performed using FastQC (v0.11.5).
Clean reads were mapped to Atlantic salmon genome assembly ICSASG_v2 (GCF_000233375.1) using STAR with version 020201
Read counts were extracted from alignment file "ReadsPerGene.out.tab", and all samples were merged into one matrix
Differential gene expression analysis was performed using DESeq2 (v1.20.0), and plot visualization was achieved using R packages ggplot2 (v3.2.1) and pheatmap (v1.0.12).
Genome_build: ICSASG_v2
Supplementary_files_format_and_content: Tab-delimited matrix containing read counts of each individual samples

organism: Salmo salar

source_name: head kidney

growth_protocol: Atlantic salmon post smolts of about 70 g were purchased from a commercial producer (Sundsfjord Smolt, Nygårdsjøen, Norway) and maintained at the Research Station of Nord University, Bodø, Norway. Fish were fed a commercial feed (Ewos Micro, Ewos AS, Bergen, Norway) to satiation, and reared in a flow-through sea water system (temperature: 7-8°C, dissolved oxygen saturation: 87-92 %, 24-h light cycle). The fish (average 550g) were starved for 24 h and were killed with an overdose of MS-222. Head kidney (HK) and distal intestine (DI) samples were then collected. Immune cells from head kidney and distal intestine were isolated and grown at 12°C in Leibovitz’s L-15 Medium. The osmolality of cell culture media was adjusted to 380 mOsm by adding a solution consisting of 5% (v/v) 0.41 M NaCl, 0.33 M NaHCO3 and 0.66 (w/v) D-glucose.

extract_protocol:
Total RNA was extracted from adherent cells from HK or DI (< 500,000 cells) using the PicoPure RNA isolation kit (Thermo Fisher Scientific) according to the manufacturer’s protocol. The quality and quantity of total RNA were assessed using Agilent RNA high sensitivity screen tape kits and Bioanalyzer 2200 TapeStation system (Agilent Technologies, Santa Clara, CA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra II Directional RNA library preparation kit with poly (A) mRNA magnetic isolation module (NEB #E7490; New England BioLabs®, Herts, UK), according to the manufacturer’s protocol. For the first and second strand cDNA synthesis, 50 ng of total RNA having high RNA integrity number (RIN > 8) was enriched with Oligo(dT)-conjugated magnetic beads and fragmented to ~200 nt. Thereafter, the resulting cDNA were end-repaired for adaptor ligation. The ligated cDNAs were amplified on a thermal cycler for 14 cycles. The PCR products were purified using AMPure XP beads (Beckman Coulter Inc., Brea, CA, United States) to avoid contamination from residual adapter dimers and unwanted (smaller) fragments. After library preparation, the quality and quantity of individual libraries were assessed using Agilent DNA high sensitivity screen tape kits and Bioanalyzer 2200 TapeStation system.

treatment_protocol: The fish were starved for 24 h and were sacrificed with an overdose of MS-222 (80 mg/L). Head kidney and distal intestine samples were then collected. Immune cells from DI and HK were extracted and grown at 12°C in Leibovitz’s L-15 Medium (L-15). The isolated DI or HK leukocytes were allowed to adhere on a petri dish with 2 mL L-15+ for 2 days at 12°C. After removing the supernatant containing non-adherent cells, the cells adherent on petri dish were detached by washing three times with 1.5 mL ice-cold PBS supplemented with 5 mM EDTA. The cells were centrifuged (500 × g, 5 min, 4°C) and re-suspended with 2 mL L-15+.

tag: cell type

value: adherent cells from head kidney


title: HK4


title: E12_PFL_invTDOM_CTCF-37141

description: Proximal forelimb mouse E12.5_invTDOM_CTCF-37141 viewpoint


title: WT_P300_rep1

description: P300 ChIP (replicate 1) library from wild-type 12Z cells


title: HK5


title: p20075-s010_5-215_BAL_Day4_GEX

tag: animalid


title: WT_P300_rep2

description: P300 ChIP (replicate 2) library from wild-type 12Z cells


title: HK3


title: DOX5

description:
counts.txt
TIM6297A1


title: HK2


title: p20075-s011_RLf10_BAL_Day4_GEX

tag: day post infection


title: p20075-s005_5-215_BAL_GEX


title: E12_PFL_invTDOM_CS38

description: Proximal forelimb mouse E12.5_invTDOM_CS38 viewpoint

tag: strain


title: E12_PFL_delCTCFs_Hoxd9

description: Proximal forelimb mouse E12.5_delCTCFs_Hoxd9 viewpoint


title: p20084-s006_RVf12_BAL_Day4_GEX


title: HK1


title: p20075-s004_RLf10_BAL_GEX


title: CB2_UT_B

city: Faridabad

first: Suchitra

last: GOPINATH

address: NCR Biotech Science Cluster, 3rd Milestone,

country: India

institute: Translational Health Science and Technology Institute

data_processing:
qc is performed using softwareFastQc
read alignment was perfomed using STAR
read count generation was perfomred using htseq
differential expression analysis was perfomed using DESeq2 R package
Genome_build: hg38 souced from ensembl database
Supplementary_files_format_and_content: read count file containing raw read counts for each of the samples
Supplementary_files_format_and_content: diffeentially expressed gene list for different compaisons performed

source_name: mesenchymal stem cells

growth_protocol: Mesenchymal stem cells derived from umbilical cord blood were grown in αMEM (Hyclone, cat- SH30568.FS) with 20%FBS, 2mM Sodium pyruvate and 4mM L-glutamine. For propogation, 1 ml of Mesenpro from Mesenpro RS kit (cat no- 12746012) was added to the growth medium. For mesenchymal stem cells derived from umbilical cord tissue, cells were grown in αMEM with 20% FBS

extract_protocol:
Cells were washed in PBS on ice and RNA was extracted with Trizol (Invitrogen). RNA purification was done using the Direct-zol TM RNA MiniPrep kit (catalog # R2050, Zymo Research).
After QC procedures inclusive of agarose gel electrophoresis and ensuring RIN values of all samples were 9.8 or 10, mRNA was enriched using oligo(dT) beads. The mRNA was then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) was added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library was ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment. Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then are diluted to 1 ng/ul before checking insert size on an Agilent 2100 and further quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity >2 nM). Libraries were fed into Illumina machines after pooling according to activity and expected data volume if library quality is up to standard.

treatment_protocol: For inducing myogenic differentiation, mesenchymal stem cells from umbilical cord blood and cord tissue were plated on tissue culture plates coated with 0.01% Collagen Type 1 (Merck cat # C8919) and 20 ug/ml Laminin (Merck, cat # L2020) in M1 medium (DMEM, 5% horse serum, 0.1 µM dexamethasone, and 50 µM hydrocortisone) for 7 days. Medium was changed every other day.

value: umbilical cord tissue derived mesenchymal stem cells

tag: differentiation state

value: differentiated to myogenic cell type

tag: passages

value: 4 to 6


title: E12_PFL_delCTCFs_Hoxd4

description: Proximal forelimb mouse E12.5_delCTCFs_Hoxd4 viewpoint

tag: genotype


title: CB1_UT_B

value: umbilical cord blood derived mesenchymal stem cells


title: E12_PFL_delCTCFs_Hoxd11

description: Proximal forelimb mouse E12.5_delCTCFs_Hoxd11 viewpoint

tag: tissue


title: DI5

source_name: distal intestine

value: adherent cells from distal intestine


title: CB1_UT_A


title: p20075-s006_RQv9_BAL_GEX

tag: treatment


title: CONTUTD2_B

value: undifferentiated


title: DI6


title: E12_PFL_delCTCFs_CS65

description: Proximal forelimb mouse E12.5_delCTCFs_CS65 viewpoint

value: Proximal Forelimbs


title: DI4


title: E12_PFL_delCTCFs_CS38

description: Proximal forelimb mouse E12.5_delCTCFs_CS38 viewpoint


title: CB2_UT_A


title: DI3


title: M2_TCR_day10_LCMV_armstrong

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

description: Day 10 LCMV armstrong

data_processing:
Reads were aligned to mouse reference genome mm10
Single cell TCR data were filtered to select the best TCR alpha and beta chain at the clonal level, based on full length, productive CDR3 regions and expression level
Genome_build: mm10
Supplementary_files_format_and_content: Matrix files were generated using Cell Ranger (10x Genomics).

extract_protocol:
Chromium single cell 5' kit V2 from 10x genomics
Chromium single cell 5' kit V2 from 10x genomics for single cell gene expression (GEX) and single cell TCR library

treatment_protocol: Activated antigen specific CD4 T cells (CD4+CD44+GP66+) were sorted from five C57BL/6J mice at day 10 post acute LCMV armstrong infection and were loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 5’ v2 and v3 Reagent Kit (10x Genomics) according to manufacturer’s protocol. Libraries were loaded onto an Illumina NextSeq with the NextSeq 500/550 High Output Kit v2 (150 cycles)

value: C57BL/6 mice

tag: infection

value: LCMV armstrong

value: spleen


title: CONTUTD1_B


title: CONTUTD1_A


title: CONTUTD2_A


title: DI2