title: FOXN1_MUT1


title: FOXN1_MUT4

status: Public on Oct 06 2021

type: SRA

city: Freiburg

first: Connor

middle: Patrick

last: O'Meara

address: Stuebeweg

country: Germany

institute: MPI

description:
Processed data files generated from multiple samples
processed data file:
log2.FOXN1.tabular.txt
n.counts.FOXN1.tabular.txt

library_source: transcriptomic

data_processing:
Reads were aligned to the reference genome with STAR 2.5.2b-1 (Dobin A. et al. Bioinformatics 2013) and the reference annotation from Ensembl (Zv10.85, http://www.ensembl.org/info/data/ftp/index.html)
Resulting alignments were quantified at the gene level with featureCounts version 1.6.0.1 (Liao Y, Smyth G.K., and Shi W., Bioinformatics 2014) and differential expression performed using DESeq2 version 2.11.40.1 (Love M.I., Huber W. and Anders S. Genome Biol 2014). All tools were used with default parameters unless otherwise stated.
Genome_build: z10.85
Supplementary_files_format_and_content: DESeq2 tables of differential gene expression analysis are provided (log2 fold-change and normalized counts)

molecule: total RNA

organism: Danio rerio

source_name: ENU mutagenesis forward genetic screen

growth_protocol: zebrafish embryos (5 d.p.f)

extract_protocol:
Individual zebrafish embryos (5 d.p.f) from an incross of heterozygous carriers were homogenized in 100 μL of Tri Reagent (Sigma, Cat#93289) and transferred to 2 mL deep 96 well plates containing an additional 400μL of Tri Reagent. The RNA-containing aqueous phase was stored at -80°C until genotyping was completed. DNA was extracted from the interphase and organic phase by phenol-chloroform according to the manufacturer’s instructions. Following genotyping, RNA was extracted from embryos homozygous mutants and sibling homozygous wt. DNA was removed from RNA extraction using TURBO DNA-free kit (Invitrogen, Cat#AM1907). RNA was quantified using Qubit RNA HS Assay Kit (ThermoScientific, Cat#Q32852) and the Qubit 4 Fluoromter (ThermoScientific, Q33226). RNA quality was checked by 18S/28S rRNA ratio using the Fragment Analyzer RNA Kit (ThermoScientific, Cat#DNF-471-0500) and the 5200 Fragment Analyzer System (ThermoScientific, Cat#M5310AA).
cDNA libraries were prepared from 1μg of mRNA following poly-A selection using TruSeq stranded mRNA Library Prep (Illumina, Cat#20020595) according to manufacturer’s instuctions. RNA-Seq was performed using mutant and wt sibling from each zebrafish line (n = 2 – 6). The libraries were sequenced in paired-end 75 bp mode at a depth of 25 million reads on an Illumina HiSeq 2500/3000 instrument.

tag: genotype

value: MUT

tag: strain background

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

tag: population

value: whole embryo

tag: surface phenotype

value: lymphoid development, defect in rag1 expression in thymus


title: WtSti23 BMDM RNA-seq

city: Bern

first: Philipp

last: Kirchner

address: Murtenstrasse 31

department: Pathology

country: Switzerland

institute: University of Bern

data_processing:
Illumina RTA3 was used for base calling
Paired-end clean reads were mapped to the mouse reference genome (GRCm38/mm10) using HISAT2 (v.2.0.5) software.
HTSeq (v.0.6.1) was used to count the read numbers mapped of each gene, including known and novel genes. Subsequently, RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between two conditions with three biological replicates per condition was performed using DESeq2 (v.1.22.2). The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with counts per gene per sample with Ensembl identifiers and gene names

organism: Mus musculus

source_name: bone marrow

growth_protocol: Macrophage precursors were isolated from bone marrow of wild type or mutant C57BL/6 mice, cultured and diferentiated to macrophages in MCSF-conditioned medium for 5 days.

extract_protocol:
RNA isolation was performed using the RNeasy Mini kit (QIAGEN,Cat No./ID: 74104).
Sequencing libraries were generated from 1ug input material using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB) following manufacturer’s instructions and sequenced on a NovaSeq 6000 platform (paired end 150 bp).

treatment_protocol: Macrophages were treated with the indicated cytokines for 36 h

tag: strain

tag: cell type

value: in vitro cultured bone marrow derived macrophages

tag: stimulation


title: KO1Sti03 BMDM RNA-seq


title: COL1_DMSO1_S1_ROW09

city: Rochester

first: Jason

last: Myers

state: NY

address: 601 Elmwood Ave.

country: USA

institute: University of Rochester

data_processing:
Data Formatting - bcltofastq-2.19.0
Data Cleaning - Trimmomatic-0.36, TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:15
Genome Alignment - STAR_2.5.2b, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1 - subread-1.5.0p3, featurecounts, -s 2 -t exon -g gene_name
Genome_build: GRCh38 + gencode25
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample

organism: Homo sapiens

source_name: 40 year old female

extract_protocol:
Fluidigm C1 HT scRNAseq protocol, no offline RNA extraction performed
Fluidigm C1 HT scRNAseq library construction protocol

tag: cell line

value: Invasive Ductal Carcinoma


title: COL1_DMSO1_S1_ROW08


title: WtSti22 BMDM RNA-seq


title: WtSti21 BMDM RNA-seq


title: KO1_a: Haspin KO1 stem cells rep1

city: Ioannina

first: Katerina

middle: Periklis

last: Soupsana

address: Dourouti

department: Medical School

country: Greece

institute: University of Ioannina

data_processing:
Chipster software was used.
Trimming was performed with Trimmomatic
The sequenced reads were aligned using TopHat2 (single end reads, library type: fr-firststrand) on mouse genome GRCm38.87
The aligned reads were counted by HTSeq (union, stranded-reverse)
Differential expression analysis was carried out by DeSeq2 (p value cutoff <0.05 and log2 fold >│1│)
Genome_build: mouse genome GRCm38.87
Supplementary_files_format_and_content: Counts file contains HTSeq output for every sample and Normilized data file contains DeSeq2 output for every pairwise comparison

source_name: E14 stem cells

growth_protocol: E14 stem cells were cultured under standard undifferentiated conditions (serum&LIF).

extract_protocol:
Total RNA was extracted using RNeasy protect mini kit (Qiagen) with on-column DNAse digestion.
Truseq stranded mRNA library kit (Illumina) was used

treatment_protocol: no treatment

tag: tissue

value: E14 stem cells

tag: developmental stage

value: Haspin knock out


title: COL1_DMSO1_S1_ROW07


title: 2012_WT2

description:
Processed data files generated from multiple samples
processed data file:
log2.TOP3A.tabular.txt
n.counts.TOP3A.tabular.txt

value: WT

value: normal lymphoid development in thymus


title: COL1_DMSO1_S1_ROW06


title: WtSti13 BMDM RNA-seq


title: Treatment with ascites from TG2 KO mice RNA-seq rep 2

city: Chicago

first: Daniela

middle: Elena

last: Matei

state: IL

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

data_processing:
Fastq files were pre-processed using TrimGalore (0.4.4) and cutadapt (1.14)
Trimmed reads were aligned to the ENSEMBL mouse genome version 95 GRCm38 using STAR (2.5.2)
HTSeq and EdgeR is used for generating raw count and differntial gene lists for RNAseq data
Genome_build: GRCm38
Supplementary_files_format_and_content: counts

source_name: surface epithelial cancer cell line

growth_protocol: 30000 ID8 cells were seeded in 6-wells in DMEM complete media.

extract_protocol:
RNA was purified with the RNeasy Qiagen Mini Kit. Genomic DNA was removed using RNase-free DNase Set and RNeasy Mini Elute Spin Columns . Then, mRNA was isolated with Ambion Dynabeads mRNA purification kit.
RNA libraries were prepared for sequencing using NEBNext Ultra II RNA Library Prep kit for Illumina.

treatment_protocol: Fortyeight hours after seeding, cells were treated with 20% ascites pooled from 5 mice in each group (or left untreated). Another treatment was applied after 3 days and cells were collected at the end of 5 days of treatment in 600 uL RLT buffer+beta-mercaptoethanol according to manufacturer's recommendation. Cell suspension was passed through a 18-gauge syringe needle and stored at -80 degrees until RNA isolation.

value: murine ovarian cancer cell

tag: passage

tag: genotype/variation

value: TG2 KO

tag: treatment

value: ascites


title: 2012_WT1


title: 2012_WT4


title: Untreated RNA-seq rep 1

growth_protocol: 30002 ID8 cells were seeded in 6-wells in DMEM complete media.

value: wild type

value: untreated


title: Treatment with ascites from WT mice RNA-seq rep 2


title: COL1_DMSO1_S1_ROW05


title: 2012_MUT3


title: WtSti11 BMDM RNA-seq


title: Treatment with ascites from WT mice RNA-seq rep 1


title: COL1_DMSO1_S1_ROW04


title: COL1_DMSO1_S1_ROW03


title: Treatment with ascites from TG2 KO mice RNA-seq rep 1


title: 2012_MUT2


title: WtSti03 BMDM RNA-seq


title: 2012_MUT1


title: 1810_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.LSM8.tabular.txt
n.counts.LSM8.tabular.txt


title: 2012_MUT4


title: 1810_WT3


title: Raji-4RH-chidamide_RNA-seq-2

city: Shanghai

first: Jiaying

last: Zhang

state: Shanghai

address: 320 Yue Yang Road

department: CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health

country: China

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

description:
R4c2
processed data file: gene_expression.txt

data_processing:
Clean data were aligned to hg38 by HISAT2 (2.0.5) with default parameters; aligned SAM files were handled using samtools (1.7).
Aligned reads were extracted by Htseq (0.9.1) with default parameters; FPKM were calculated by R script on its definition; differential genes were generated by R package Deseq2 (1.22.2).
Genome_build: hg38 (GRCh38) for RNA-seq
Supplementary_files_format_and_content: gene_expression.txt: Tab-delimited text file; FPKM were calculated by definition.

source_name: lymphoma cell

growth_protocol: Raji and Raji-4RH cells were cultured in RPMI 1640 with Glutamax-1 (Gibco, C11875500CP) supplemented with 10% heat-inactivated fetal bovine serum (FBS), HEPES (5mmol/l), penicillin and streptomycin (100IU/ml) and sodium pyruvate (1mmol/l).

extract_protocol:
After 24h treatment, cells were harvested by flow sorting and RNA was extracted with TRIzol Reagent (Invitrogen).
A total amount of 3µg RNA per sample was used as input material for the RNA sample preparation. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and sequenced with Illumina HiSeq X ten.

treatment_protocol: Raji and Raji-4RH cells were treated with DMSO or chidamide (3μM) for 24h at 5*10^5/2ml.

value: Rituximab resistant Burkitt's lymphoma cell line

tag: passages

value: 2-3 passages

value: Chidamide


title: COL1_DMSO1_S1_ROW01


title: Raji-4RH-chidamide_RNA-seq-1

description:
R4c1
processed data file: gene_expression.txt


title: Raji-4RH-con_RNA-seq-2

description:
R4con2
processed data file: gene_expression.txt

value: DMSO


title: Raji-4RH-con_RNA-seq-1

description:
R4con1
processed data file: gene_expression.txt


title: Small_tumor_rep3

city: Xiamen

first: Dawang

last: Zhou

state: Fujian

address: Xiang'an south rd, Xiang'an district

department: Life Science

institute: Xiamen University

description:
Tumor(7 month)
s6

data_processing:
Basecalls were performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence and low quality bases using cutadapt(v.1.18)
Clean reads were mapped to mm10 refernece genome using STAR (v.2.5.2b) .
Read counts were obtained by mapping the aligned reads to the transcripts of known genes from UCSC by using GenomicAlignments (v.1.20.1).
Differential expression analysis was performed with methods based on the negative binomial distribution in DESeq2 (v.1.24.0), using default parameters. Benjamini and Hochberg correction were used for significance tests and multiple comparisons.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts and FPKM values for each gene in each sample.

source_name: liver

growth_protocol: Multiple serial FFPE sections from liver tissues were deparaffinized and dissectioned using the arpha AVENIO Millisect System (Roche Diagnostics, Indianapolis, IN).

extract_protocol:
Total RNA was isolated using a High Pure FFPE RNA Isolation Kit (Roche)
libraries were constructed using ABclonal Whole RNA-seq Lib Prep kit for illumina (RK20351). Briefly, about 500 ng of each RNA sample was hybridized with rRNA Probe Mix (H/M/R) to depleted ribosome RNA. rRNA-depleted RNA was purified with VAHTS RNA Clean Beads and Mg2+ makes it single-strand breaks. Then reverse transcription and end repair. End-prep DNA was ligased with RNA truncated adapter and purified with Agencourt AMPure XP beads. Purified products were amplificated by 15 cycles and purified with Agencourt AMPure XP beads again. Finally, the concentration of 30 μL DNA libraries was analyzed using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).

treatment_protocol: DEN was dissolved in 0.9% saline at 2.5 mg/mL. Male mice were injected intraperitoneally with 25 mg/kg body weight of DEN at the age of 14 days. Liver tissue samples were harvested at indicated time points.

tag: tumor stage

value: Small  glycogen stacked region

value: early


title: WtSti12 BMDM RNA-seq

value: in vitro cultured bone marrow derived macrophages


title: Untreated RNA-seq rep 2


title: WtSti01 BMDM RNA-seq


title: Raji-chidamide_RNA-seq-2

description:
Rc2
processed data file: gene_expression.txt

value: Raji

value: Rituximab sensitive Burkitt's lymphoma cell line


title: 1810_WT1

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: whole embryo


title: WtSti02 BMDM RNA-seq


title: Small_tumor_rep1

description:
Tumor(7 month)
s4


title: COL1_DMSO1_S1_ROW02

value: Invasive Ductal Carcinoma


title: 1810_MUT4

value: MUT

value: lymphoid development, defect in rag1 expression in thymus


title: Normal_rep3

description:
Normal adjacent tissue(7 month)
s3

value: Normal


title: 1810_WT2

value: WT

value: normal lymphoid development in thymus


title: 1810_MUT2


title: 1810_MUT3


title: Raji-con_RNA-seq-2

description:
Rcon2
processed data file: gene_expression.txt


title: Normal_rep2

description:
Normal adjacent tissue(7 month)
s2


title: Raji-con_RNA-seq-1

description:
Rcon1
processed data file: gene_expression.txt


title: Raji-chidamide_RNA-seq-1

description:
Rc1
processed data file: gene_expression.txt


title: Normal_rep1

description:
Normal adjacent tissue(7 month)
s1


title: 1810_MUT1


title: ONT-6hpirep1

status: Public on Oct 05 2021

city: Pittsburgh

first: Jeffrey

last: Gross

state: PA

department: Ophthalmology

institute: University of Pittsburgh School Of Medicine

description:
RGC_6hpi_TPM_totalCOUNTS.txt
F1_Gross_10_9_19_cDNA_S2

data_processing:
All processing of raw data was performed using the CLC Genomics Workbench (v20) Toolbox
Reads were trimmed using quality trim limit = 0.05, ambiguous trim = 2, and automatic read-through adapter trimming enabled (Trim Reads tool v2.4)
Reads were mapped to the zebrafish reference genome, GRCz11, and TPM expression values were caluclated using the RNA-seq Analysis tool (v2.2) in CLC Genomics Workbench
Genome_build: GRCz11
Supplementary_files_format_and_content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint

molecule: polyA RNA

source_name: retinal ganglion cell

growth_protocol: Animals were maintained under standard conditions at 28.5 C on a 14h light/10 h dark cycle. 3-5 month-old zebrafish were utilized

extract_protocol:
1000 GFP-positive cells from dissociated enuculeated isl2b:GFP adult fish eyes were FACS-sorted directly into buffer from the SMART-Seq HT Ultra Low Input RNA Kit from Takara Bio, Inc. cDNA synthesis, amplification, and purification was performed using the SMART-Seq HT Ultra Low Input RNA Kit.
Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina, following manufacterer's instructions

treatment_protocol: A subset of isl2b:GFP adult fish (5 replicates from each timepoint) went through optic nerve transection surgery and samples were collected at 6,12 and 24 hours post injury.

value: retinal ganglion cell

value: ONT-

tag: time point

tag: replicate


title: ONT-6hpirep3

description:
RGC_6hpi_TPM_totalCOUNTS.txt
D1_Gross_10_9_19_cDNA_S14


title: ONT-6hpirep2

description:
RGC_6hpi_TPM_totalCOUNTS.txt
B1_Gross_10_9_19_cDNA_S12


title: 3 lnc

type: RNA

city: Taipei

first: yu chin

last: Huang

address: No.1 Jen Ai road section 1

country: Taiwan

institute: NTU

hyb_protocol: Samples were hybridized with Clariom™ S Assay, human Arrays (Applied Biosystems) and scanned at the NHRI Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Applied Biosystems)

data_processing: The data were analyzed using Transcriptome Analysis Console (TAC) Software default analysis settings. Expression values were processed with Signal Space Transformation (SST) and Robust Multichip Average method, which included log2 transformation and quantile normalization.

label: biotin

source_name: HUVECs

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Plus cDNA Synthesis Kit (Applied Biosystems) and then fragmented and labeled with the WT Terminal Labeling Kit (Applied Biosystems).

growth_protocol: Cells from the fifth passage were incubated in EGMTM-2 Endothelial Cell Growth Medium-2 BulletKitTM

extract_protocol: Total RNAs extracted from the HUVECs infected with lentivirus expressing lnc-SLC151A-1 or EV were isolated by using NucleoZOL reagent (Machery-Nagel) and treated with DNase I following the manufacturer’s instructions. RNA was amplified (in vitro transcription) and biotin-labeled single-stranded cDNA was generated according to the manufacturer's instructions. Single-stranded cDNA was generated from the amplified cRNA with the GeneChip™ WT PLUS Reagent Kit and then fragmented and labeled with the GeneChip™ WT Terminal Labeling Kit.

treatment_protocol: HUVECs were transfected witha lnc-SLC15A1-1 expression plasmid (pcDNA3.1(+)-lnc-SLC15A1-1) or empty vector (EV) as a control by employing the TransIT-X2 delivery system

value: primary HUVECs

value: transfection with lnc-SLC15A1-1 overexpression vector


title: ONT+6hpirep2

description:
RGC_6hpi_TPM_totalCOUNTS.txt
H2_Gross_10_9_19_cDNA_S12

value: ONT+


title: 2 lnc


title: ONT+6hpirep1

description:
RGC_6hpi_TPM_totalCOUNTS.txt
B3_Gross_10_9_19_cDNA_S14


title: ONT+12hpirep3

description:
RGC_12hpi_TPM_totalCOUNTS.txt
E2_Gross_10_9_19_cDNA_S9


title: ONT+12hpirep2

description:
RGC_12hpi_TPM_totalCOUNTS.txt
H1_Gross_10_9_19_cDNA_S4


title: ONT-12hpirep2

description:
RGC_12hpi_TPM_totalCOUNTS.txt
E1_Gross_10_9_19_cDNA_S1


title: ONT+12hpirep1

description:
RGC_12hpi_TPM_totalCOUNTS.txt
G2_Gross_10_9_19_cDNA_S11


title: ONT-24hpirep3

description:
RGC_24hpi_TPM_totalCOUNTS.txt
F2_Gross_10_9_19_cDNA_S10


title: ONT+24hpirep3

description:
RGC_24hpi_TPM_totalCOUNTS.txt
C1_Gross_10_9_19_cDNA_S13


title: ONT-24hpirep2

description:
RGC_24hpi_TPM_totalCOUNTS.txt
G1_Gross_10_9_19_cDNA_S3


title: ONT+24hpirep2

description:
RGC_24hpi_TPM_totalCOUNTS.txt
B2_Gross_10_9_19_cDNA_S6


title: ONT+6hpirep3

description:
RGC_6hpi_TPM_totalCOUNTS.txt
D2_Gross_10_9_19_cDNA_S8


title: ONT+24hpirep1

description:
RGC_24hpi_TPM_totalCOUNTS.txt
C2_Gross_10_9_19_cDNA_S7


title: 1 EV

value: transfection with empty vector


title: 3 EV


title: KM12SM _parental_RNASeq_rep3

first: Huanlong

last: Qin

address: 301 Yan Chang Road

department: Gastrointestinal Surgery

institute: Shanghai Tenth People’s Hospital Affiliated to Tongji University

description:
wild-type cell line
untreated3

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome using STAR v2.7.3a with default parameters
Raw reads were counted using HTseq-count with  parameters -s no -m intersection-strict.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file with raw gene counts for every gene and every sample

source_name: CRC cell line

growth_protocol: Cells were routinely maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100U/ml penicillin and 100ug/ml streptomycin.

extract_protocol:
Cells were collected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colorectal cancer liver metastasis

tag: genotype

value: wild-type


title: KM12SM _HNF1Ako_RNASeq_rep1

description:
knocked-out cell line
HNF1Ako1

value: HNF1A knocked out


title: ONT-12hpirep3

description:
RGC_12hpi_TPM_totalCOUNTS.txt
A3_Gross_10_9_19_cDNA_S13


title: 2 EV


title: KM12SM _HNF1Ako_RNASeq_rep3

description:
knocked-out cell line
HNF1Ako3


title: ONT-24hpirep1

description:
RGC_24hpi_TPM_totalCOUNTS.txt
A1_Gross_10_9_19_cDNA_S11


title: DHT+ENZ#1

first: Junhao

last: Hu

address: Build 13, No.100 Kaike Road, Pudong District

institute: Interdisciplinary Research Center of Biology and Chemistry

data_processing:
Reads cleaning: raw FASTQ files were quality checked using FASTQC . Then fastp was used to quality trim FASTQ files by both read quality and length (Q30 > 20, length > 36)
Alignment: clean reads were aligned to reference genome GRCh38 using Hisat
Quantification: gene level expressions were counted with FeatureCounts
Enrichment analysis: differential expressed genes were tested by DESeq2 first. Gene set enrichment analysis (GSEA) were performed with clusterProfiler using  DESeq2-generated wald test results.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: LNCaP (DSMZ,  ACC256, male)

growth_protocol: LNCaP cells were cultured in RPMI1640 supplemented with 10% (v/v) FBS, 100   462 units/mL penicillin and 100 mg/mL streptomycin

extract_protocol:
RNA were extracted using TRIzol Reagent (15596018, Invitrogen)
RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep kit v2

treatment_protocol: LNCaP cells were treated with 10 μM ET516/ENZ/DMSO (DHT was added 2 hours after the compound)  for 12 hours

value: DHT+ENZ

value: LNCaP


title: DHT+ENZ#2


title: KM12SM _parental_RNASeq_rep2

description:
wild-type cell line
untreated2


title: DHT+ET516#1


title: KM12SM _parental_RNASeq_rep1

description:
wild-type cell line
untreated1


title: KM12SM _HNF1Ako_RNASeq_rep2

description:
knocked-out cell line
HNF1Ako2


title: 1 lnc


title: DHT#1

value: DHT


title: DHT+ET516#2


title: DHT#2


title: Small_tumor_rep2

description:
Tumor(7 month)
s5

value: Small  glycogen stacked region

value: early


title: DMSO#2

value: DMSO


title: DMSO#1


title: Control, Keren_6

city: Tel-Aviv

first: Chen

last: Varol

address: Tel-Aviv University

country: Israel

institute: The Research Center for Digestive Tract and Liver Diseases, Tel-Aviv Sourasky Medical Center and Sackler School of Medicine

data_processing:
Reads were trimmed using cutadapt
After trimming, the reads were mapped to the mous genome (GRCm38) using STAR 2.7.3a (using options alignEndsType EndToEnd and outFilterMismatchNoverLmax set to 0.04)
Counting proceeded over genes annotated in Ensembl release 92, using htseq-count (version 0.12.4)
Normalization and differential expression was performed using DESeq2 (Version 2_1.26.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed file include raw counts and DESeq2 normalized counts.

source_name: Commd10fl/fl mouse BM

growth_protocol: Animal experiments were performed with male adult mice (C57BL/6 background). Animals were maintained in specific pathogen-free animal facility, and experiments were performed according to protocols approved by the Animal Care Use Committee of the Sourasky Medical Center. Mice were housed with 12-h light cycles and a constant temperature of 22°C.

extract_protocol:
For the isolation of BM cells, femurs and tibia of LysMDCommd10 and weight matched littermate Commd10fl/fl controls were carefully dissected and flashed with cold Dulbecco’s phosphate-buffered saline without calcium and magnesium (PBS−/−). Ly6Chi monocytes were defined as living CD45+CD11b+CD115+CD117-Ly6ChiLy6G- cells. Cell sorting was performed using the BD FACSAriaTM FUSION cell sorter (BD Bioscience). RNA was extracted using miRNeasy Mini Kit (Qiagen) according to the manufacture protocol.
Libraries were prepared using the INCPM-mRNA-seq. Briefly, the polyA fraction (mRNA) was purified from 500 ng of total input RNA followed by fragmentation and the generation of double-stranded cDNA. After Agencourt Ampure XP beads cleanup (Beckman Coulter), end repair, A base addition, adapter ligation and PCR amplification steps were performed. Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent). Sequencing was done on a Nextseq 75 cycles high output kit, allocating 20M reads per sample (Illumina; single read sequencing).

treatment_protocol: No treatment

tag: gender

value: Male

tag: age

value: 8 weeks old

value: Steady state

value: BM

value: Ly6Chi monocytes


title: ONT-12hpirep1

description:
RGC_12hpi_TPM_totalCOUNTS.txt
A2_Gross_10_9_19_cDNA_S5

value: retinal ganglion cell

value: ONT-


title: Control, Keren_5


title: Control, Keren_3


title: LysM, Keren_14

source_name: LysMDCommd10 mouse BM


title: LysM, Keren_11


title: LysM, Keren_13


title: LysM-12 COMMD10-

data_processing:
Reads were trimmed using cutadapt
After trimming, the reads were mapped to the mous genome (GRCm38) using STAR 2.7.3a (using options alignEndsType EndToEnd and outFilterMismatchNoverLmax set to 0.04)
Counting proceeded over genes annotated in Ensembl release 92, using htseq-count (version 0.12.4)
Normalization and differential expression was performed using DESeq2 (Version 1.26.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed file include raw counts and DESeq2 normalized counts.

source_name: LysMDCommd10 mouse liver

extract_protocol:
Isolation of hepatic non-parenchymal cells was performed as previously described (Ben Shlomo et al., 2019; Graubardt et al., 2017; Zigmond et al., 2014). In brief, mice were anesthetized and perfused livers were collected, cut into small fragments, and incubated with 5 mL digestion buffer composed of 5% fetal bovine serum (Biological Industries, Israel), 0.5 mg/mL collagenase VIII from Clostridium histolyticum (Sigma-Aldrich, USA), 0.1 mg/mL Deoxyribonuclease I from bovine pancreas (Sigma-Aldrich, USA) in Dulbecco’s phosphatebuffered saline with calcium and magnesium (PBS+/+, Biological Industries, Israel), in a shaker-incubator at 250 rpm, 37°C for 45 min. Samples were then subjected to three cycles of washing with Dulbecco’s phosphate-buffered saline without calcium and magnesium (PBS−/−) at 400 rpm, 4°C for 5 min from which the supernatant was kept, omitting the parenchymal cell pellet. Subsequently, the supernatant was centrifuged at 1,400 rpm, 4°C for 5 min and the cell pellet was lysed for erythrocytes by 2 min incubation with Ammonium-Chloride-Potassium (ACK) buffer composed of 0.15 M NH4Cl and 0.01 M KHCO3, and washed with PBS−/−. Cell sorting was performed using the BD FACSAriaTM FUSION cell sorter (BD Bioscience). RNA was extracted using miRNeasy Mini Kit (Qiagen) according to the manufacture protocol.
Libraries were prepared using the INCPM-mRNA-seq. Briefly, the polyA fraction (mRNA) was purified from 500 ng of total input RNA followed by fragmentation and the generation of double-stranded cDNA. After Agencourt Ampure XP beads cleanup (Beckman Coulter), end repair, A base addition, adapter ligation and PCR amplification steps were performed. Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent). Sequencing was done on a Nextseq 75 cycles high output kit, allocating 20M reads per sample (Illumina; single read sequencing).

treatment_protocol: Acetaminophen-induced liver injury (AILI) - mice were fasted overnight for 12 h prior to intraperitoneal (i.p.) administration of 300 mg/kg acetaminophen (APAP, Sigma-Aldrich, USA). Water was returned concomitantly with APAP administration and chow 2 h later

value: Acetaminophen-induced liver injury 24h

tag: genetic background

value: liver


title: C10-2 control COMMD10+

source_name: Commd10fl/fl mouse liver


title: LysM-13 COMMD10-


title: C10-3 control COMMD10+


title: LysM, Keren_12

tag: strain


title: C10-11 control COMMD10+

tag: cell type


title: 7K_Varol.Control2

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the human genome
Deduplication was carried out by flagging all reads that were mapped to the same gene and had the same UMI
Counting proceeded over genes (1000 bases of the 3’ UTR) using htseq-count
Normalization and differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes the normalized counts

source_name: KCs sorted from steady state livers

extract_protocol:
Isolation of hepatic non-parenchymal cells was performed as previously described (Ben Shlomo et al., 2019; Graubardt et al., 2017; Zigmond et al., 2014). In brief, mice were anesthetized and perfused livers were collected, cut into small fragments, and incubated with 5 mL digestion buffer composed of 5% fetal bovine serum (Biological Industries, Israel), 0.5 mg/mL collagenase VIII from Clostridium histolyticum (Sigma-Aldrich, USA), 0.1 mg/mL Deoxyribonuclease I from bovine pancreas (Sigma-Aldrich, USA) in Dulbecco’s phosphatebuffered saline with calcium and magnesium (PBS+/+, Biological Industries, Israel), in a shaker-incubator at 250 rpm, 37°C for 45 min. Samples were then subjected to three cycles of washing with Dulbecco’s phosphate-buffered saline without calcium and magnesium (PBS−/−) at 400 rpm, 4°C for 5 min from which the supernatant was kept, omitting the parenchymal cell pellet. Subsequently, the supernatant was centrifuged at 1,400 rpm, 4°C for 5 min and the cell pellet was lysed for erythrocytes by 2 min incubation with Ammonium-Chloride-Potassium (ACK) buffer composed of 0.15 M NH4Cl and 0.01 M KHCO3, and washed with PBS−/−. Cell sorting was performed using the BD FACSAriaTM FUSION cell sorter (BD Bioscience).
Bulk MARS-Seq protocol. In brief, mRNA was purified from ~10,000 cells of each sample using Dynabeads mRNA Direct purification kit (ThermoFisher), barcoded during reverse transcription and pooled. Following Agencourct Ampure XP beads cleanup (Beckman Coulter), the pooled samples underwent second strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR.  Libraries were quantified by Qubit and TapeStation as well as by qPCR for mouse ActB gene. Sequencing was done on a Nextseq 75 cycles high output kit (Illumina).
RNA-Seq (3') UMI appears in Read2

value: KCs


title: 3K_Varol.clec4f


title: LysM-6 COMMD10-


title: C10-10 control COMMD10+


title: 1K_Varol.Control1


title: 8K_Varol.Control2


title: 2K_Varol.Control1


title: E12.5 DFL WT Bolt et al., 2021_re-analyzed

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

institute: EPFL

description:
Capture Hi-C
GSM5034636

library_source: genomic

data_processing:
Library strategy: Capture HiC
All scripts are available on https://github.com/lldelisle/scriptsForAmandioEtAl2021
Raw reads were preprocessed with cutadapt version 1.16 (Martin 2011 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT --minimum-length=15 --pair-filter=any --quality-cutoff=30).
Then hicup version 0.6.1 (Dryden et al. 2014) with bowtie2 version 2.2.6 (Langmead et al. 2012) and samtools 1.2 (Danecek et al. 2021) were used with default parameters.
The bam file was converted to tabular file with a python script (see https://github.com/lldelisle/scriptsForAmandioEtAl2021 for more details).
The pairs  with both mates MAPQ30 and in the capture region (chr2:72402000-77000000) were then loaded to a 10kb resolution matrices with cooler version 0.7.4 (Abdennur and Mirny 2020).
The merge matrices were obtained using HiCExplorer hicSumMatrices tool version 3.6 (Ramirez et al. 2018, Wolff et al. 2018 and Wolff et al. 2020) and cooler balance.
Genome_build: mm10
Supplementary_files_format_and_content: validPairs_filtered.csort.txt: valid pairs in juicebox format: Each line is a pair: <readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2> str = strand (0 for forward, anything else for reverse). Only pairs with both mates MAPQ30 and in the capture region (chr2:72402000-77000000).
Supplementary_files_format_and_content: 10kb.cool: 10kb matrices ICEd normalized
Supplementary_files_format_and_content: merge_10kb.cool: 10kb matrices ICEd normalized of both replicates combined

molecule: genomic DNA

source_name: Distal forelimb

extract_protocol:
Micro-dissected E12.5 proximal and distal forelimb pairs and individual E9.5 trunks were isolated in PBS supplemented with 10% Fetal Calf Serum and dissociated into single cell by collagenase treatment (8ul of collagenase 50mg/ml (Sigma C9697) at 37º for approximately 10min). Samples were cross-linked with 1% formaldehyde (ThermoFisher 28908) for 10 minutes at room temperature, quenched with glycine and washed with PBS containing proteinase inhibitor. After discarding the supernatant cells were stored at -80º. Samples were genotyped by PCR to select for homozygous mutant or control tissues. Further processing was performed as described in (Yakushiji-Kaminatsui et al., 2018)
Following the Hi-C protocol, ligated DNA fragments were processed throught the Agilent SureSelectXT protocol to enrich for fragments coming from the probe region chr2:72240000-76840000 (mm9).

value: Distal forelimb

value: WT


title: E10.5 trunk Del(CBS1-5) ChIPM RAD21 rep2

description: ChIPmentation

data_processing:
Library strategy: ChIPmentation
All scripts are available on https://github.com/lldelisle/scriptsForAmandioEtAl2021
Adapters and bad quality bases were removed from the fastqs with cutadapt version 1.16 (Martin 2011 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q 30 -m 15).
Filtered reads were mapped to the mouse genome mm10 with bowtie2 version 2.3.5 (Langmead et al. 2012 with default options).
Only alignments with a mapping quality above 30 were kept (samtools version 1.9 Danecek et al. 2021).
PCR duplicates were removed with Picard version 2.19.0.
To decrease the importance of fragment length variation between libraries only the first read in pairs were kept and BAM was converted to BED.
Peak calling was run with a fixed fragment size of 200bp with macs2 callpeak version 2.1.1.20160309 ( --call-summits -f BED --nomodel --extsize 200 -B --keep-dup all).
In order to normalize all ChIP-M  despite different signal to noise ratios, we run MAnorm version 1.1.4 (Shao et al. 2012 with -w 100) between each sample and the second replicate of the wildtype. The M-A model coefficient was extracted and used to normalize each bedgraph from macs2 (see https://github.com/lldelisle/scriptsForAmandioEtAl2021 for all details).
Replicates were then averaged at each base using bedtools version 2.27.1 (Quinlan et al. 2010).
In parallel, the coverages from macs2 were normalized to the million tags. Then replicates were averaged.
Genome_build: mm10
Supplementary_files_format_and_content: bw: coverage normalized to the million tags
Supplementary_files_format_and_content: _MAnorm.bw: coverage normalized using MAnorm compared to the WT rep2
Supplementary_files_format_and_content: neqN.bw: average between N replicates of the coverage normalized to the million tags
Supplementary_files_format_and_content: MAnorm_neqN.bw: average between N replicates of the coverage normalized using MAnorm
Supplementary_files_format_and_content: narrowPeak: narrowPeak from macs2

source_name: Embryonic trunk

extract_protocol:
ChIP-M experiments for CTCF and RAD21 were performed according to (Darbellay et al., 2019a). Briefly, trunk regions of E10.5 embryos (from below the post-occipital region) derived from trans-heterozygous crosses were individually dissociated into single cells with collagenase and fixed in 1% formaldehyde solution for 10 minutes at room temperature. The crosslinking reaction was stopped adding Glycine to a final concentration of 0,125 M and the cell pellet was washed three times with cold PBS with protease inhibitors (Complete mini EDTA –free proteinase inhibitor cocktail; Roche). Fixed samples were stored at -80C. Yolk sacs were used for genotyping. Samples from homozygous mutant embryos or control littermates were resuspended in sonication buffer (Tris HCl pH=8.0 50mM; EDTA 10 mM SDSS 0,25%; protease inhibitors) and the chromatin was sheared in a Covaris S200 sonicator to an average fragment size of 250-300 bp. The sonicated chromatin was diluted 2.5 times with dilution buffer (HEPES pH=7.3 20mM; EDTA 1mM; NP40 1%; NaCL 150mM; protease inhibitors). Antibodies against CTCF (Active Motif #61311; 4gr) or RAD21 (Abcam # ab992; 5ugr) were conjugated with Dynabeads Protein G (Thermofisher) magnetic beads. The bead-antibodies complexes were added to the diluted chromatin and incubated overnight at 4oC in a rotating platform. The day after, chromatin-antibody complexes were washed using a magnetic stand with RIPA buffer (Tris HCl pH=8.0 10mM; EDTA 1mM; Sodium Deoxycholate 0,1% TritonX-100 1%; NaCl 140mM; two washes); RIPA-High salt buffer (Tris HCl pH=8.0 10mM; EDTA 1mM;  Sodium Deoxycholate 0,1% TritonX-100 1%; NaCl 500mM; two washes), LiCl-buffer; (Tris HCl pH=8.0 10mM; EDTA 1mM;  LiCl 250mM; Sodium Deoxycholate 0,5% NP40 0,5%; two washes) and Tris HCl 10mm pH=8.0 (two washes). The chromatin was then tagmented for two minutes with the Tn5 transposase (Illumina). Tagmented chromatin was eluted, reverse crosslinked and purified using Qiagen Minielute columns. Libraries were quantified using the Kapa library quantification kit and PCR amplified using barcoded primers. ChIP-M libraries were pair-end sequenced in an NextSeq 500 sequencer (PE 2x 37-43bp).
Nextera library construction were done following the published ChIPmentation protocol (Schmidl, 2015)

value: Embryonic trunk

tag: chip-m antibody

value: RAD21 (Abcam #ab992)


title: E10.5 trunk Del(CBS2) ChIPM RAD21 rep1

description: ChIPmentation


title: E12.5 PFL WT Bolt et al., 2021_re-analyzed

description:
Capture Hi-C
GSM5034635

source_name: Proximal forelimb

value: Proximal forelimb


title: Control, Keren_2


title: E10.5 trunk Del(CBS1-4) ChIPM RAD21 rep2

description: ChIPmentation


title: E10.5 trunk Del(CBS1-4) ChIPM RAD21 rep1

description: ChIPmentation


title: E10.5 trunk Del(CBS1-5) ChIPM RAD21 rep1

description: ChIPmentation


title: E10.5 trunk Del(CBS1-3) ChIPM RAD21 rep2

description: ChIPmentation


title: E10.5 trunk Del(CBS1-3) ChIPM RAD21 rep1

description: ChIPmentation


title: LysM-5 COMMD10-


title: E10.5 trunk Del(CBS1) ChIPM RAD21 rep3

description: ChIPmentation


title: 6K_Varol.clec4f


title: E10.5 trunk Del(CBS1-2) ChIPM RAD21 rep1

description: ChIPmentation


title: E10.5 trunk Del(CBS1) ChIPM RAD21 rep2

description: ChIPmentation


title: 4K_Varol.clec4f


title: E10.5 trunk WT ChIPM RAD21 rep4

description: ChIPmentation


title: E10.5 trunk Del(CBS1) ChIPM RAD21 rep1

description: ChIPmentation


title: E10.5 trunk Del(CBS1-5) ChIPM CTCF rep1

description: ChIPmentation

value: CTCF (Active Motif #61311)


title: E10.5 trunk WT ChIPM RAD21 rep2

description: ChIPmentation


title: E10.5 trunk WT ChIPM RAD21 rep1

description: ChIPmentation


title: E10.5 trunk Del(CBS2) ChIPM CTCF rep1

description: ChIPmentation


title: E10.5 trunk Del(CBS1-4) ChIPM CTCF rep2

description: ChIPmentation


title: E10.5 trunk WT ChIPM RAD21 rep3

description: ChIPmentation


title: E10.5 trunk Del(CBS1-5) ChIPM CTCF rep2

description: ChIPmentation


title: E10.5 trunk Del(CBS1-4) ChIPM CTCF rep1

description: ChIPmentation


title: E10.5 trunk Del(CBS1-3) ChIPM CTCF rep2

description: ChIPmentation


title: E10.5 trunk Del(CBS1-2) ChIPM RAD21 rep2

description: ChIPmentation


title: E10.5 trunk Del(CBS1-3) ChIPM CTCF rep1

description: ChIPmentation


title: E10.5 trunk Del(CBS1) ChIPM CTCF rep2

description: ChIPmentation


title: E10.5 trunk Del(CBS1) ChIPM CTCF rep3

description: ChIPmentation


title: Embronic_day14_hindgut

first: Wei

last: Gu

address: 51 Rijing Road

department: Beigene Institute

institute: Beigene

data_processing:
Adapter removal and trimming: Cutadapt 1.42 with Python 2.7.12. Trimming with Trim Galore version: 0.4.4_dev, trimming mode: single-ended.
75-bp single-end reads were aligned to mouse reference genome Mm10 using Bowtie2 v2.3.4.3
Nonunique and duplicate reads were removed using SAMtools version 1.9
Bigwig files were generated using the bamCoverage module in deepTools v3.0.2 and normalized for 1x coverage using 10bp bins, smoothened over 30bp.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files

source_name: Intestine epithelium

growth_protocol: As described in Banerjee et al, Genes & Dev. 2018. 32: 1430-1442

extract_protocol:
Five to Thiry thousand cells were lysed and nuclei extracted in ATAC-Resuspension Buffer (RSB, 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) with 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. DNA was transposed by Nextera Tn5 Transposase (Illumina) for 30min at 37C and purified with QIAquick column (Qiagen)
NEBNext 2x MasterMix was used to pre-Amplify transposed DNA for 5 cycles and determine the required number of additional cycles by qPCR amplification. The final libraries were size selected (200bp to 800bp, including index) with AMpure beads
Libraries were sequenced on a NextSeq500 instrument (Ilumina)

treatment_protocol: Embryonic hindgut (distal to the cecum) was digested in 0.25% Trypsin-EDTA at 37°C for 30 minutes followed by neutralization with 5%FBS. Cells were incubated with APC-conjugated EpCAM antibody (BioLegend) and FACS-purified on an Aria II SORP flow cytometer (Becton-Dickinson).

tag: genotyping

value: wild type


title: Embronic_day16_hindgut


title: E10.5 trunk WT ChIPM CTCF rep2

description: ChIPmentation

tag: tissue


title: E10.5 trunk Del(CBS1) ChIPM CTCF rep1

description: ChIPmentation

tag: developmental stage


title: Embronic_day12_hindgut


title: E10.5 trunk Del(CBS1-2) ChIPM CTCF

description: ChIPmentation


title: E10.5 trunk WT ChIPM CTCF rep3

description: ChIPmentation


title: Postnatal_day1_hindgut


title: Glis2 KO rep3

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

description:
KO.d2441
mmwilson_IntCt.txt.gz
mmwilson_l2tpm.txt.gz

data_processing:
NextSeq 500 using v3 chemistry. Software: Control v4.0.0.19, RTA 2.11.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Paired-end RNAseq reads were used to quantify gene expression Salmon (version 1.2.1, Patro et al., 2017) using a transcriptome derived from the mm10 primary assembly and an ensembl v.100 annotation as a target. The mm10 genomic assembly was used as a selective alignment decoy.
Genome_build: mm10 with ensembl annotation v.100
Supplementary_files_format_and_content: mmwilson_IntCt.txt.gz is a tab separated text file of integer count data
Supplementary_files_format_and_content: mmwilson_l2tpm.txt.gz is a tab separated text file of log2 transcripts per million with a plus1 offset

source_name: mammary gland

growth_protocol: Mammary glands from 4 week old Glis2 wildtype or mutant females were dissociated using collagenase/hyaluronidase (STEMCELL Technologies) diluted (1:10) in DMEM/F-12 medium overnight at room temperature. The dissociated glands were spun down at 450 x g for 5 min and resuspended in ammonium chloride solution (STEMCELL Technologies) diluted (4:1) in HBSS buffer supplemented with 10 mM HEPES and 2 % FBS (HF buffer). The samples were spun down and resuspended in warm Trypsin-EDTA (Stem Cell Technologies) by pipetting for 3 min. Trypsin was inactivated by addition of HF buffer. The digested samples were spun down and further digested with dispase solution (STEMCELL Technologies) supplemented with 0.1 mg/mL DNase I for 1 min. Cell suspensions were diluted with HF buffer and filtered through a 40 mm cell strainer to collect single cells. To separate various cell populations, single cells were stained with a Live-Dead fixable violet dye and antibodies against TER-119, CD31, CD45 (PE/Cy7, Biolegend); CD24 (PE, Biolegend); CD49f (APC, Biolegend). Stained cells were sorted on a FACSAria II and FACS Fusion sorters.

extract_protocol:
Total RNA was extracted from cells sorted directly into TRIzol. After phenol-chloroform extraction, the aqueous phase was added to Buffer RLT + B-mercaptoethanol. The RNA solution was then loaded onto Qiagen RNeasy columns and purified using the Qiagen RNeasy Micro Kit. RNA was eluted in DEPC-treated water.
Purified RNA was quality and quantity-checked using an Agilent Femto Pulse. RNAseq libraries were prepared from 1ng of total RNA using the Takara SMARTer Stranded Total RNASeq Kit v2  PicoInput Mammalian kit with a 4 minute fragmentation and 15 cycles of PCR. Illumina libraries were validated using the Agilent Fragment Analyzer and quantified by qPCR

tag: glis2 genotype

value: KO


title: WT control rep2

description:
WT.d2437
mmwilson_IntCt.txt.gz
mmwilson_l2tpm.txt.gz


title: Glis2 KO rep1

description:
KO.d2439
mmwilson_IntCt.txt.gz
mmwilson_l2tpm.txt.gz


title: ASZ_cFOS_rep3

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

data_processing:
bowtie used for alignment.
duplicate fragments were removed using samtools
macs2 used for peak calling
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

extract_protocol:
ATAC-seq cell lysis and transposition with Tn5 was carried out based on published protocol by Buenrostro et. al (Nature Methods, 2013) with minor modifications for on-plate transposition. Briefly, 50,000 ASZ001 cells were plated per replicate in a 48-well plate, then serum starved for 24 hours. Wells were washed with cold PBS and lysed using 0.1% NP40 in resuspension buffer for 10 minutes at 25°C. Wells were washed again, then 100 µl of transposition mixture was added per well and incubated for 37°C for 30 min, shaking at 1000 RPM using a thermoshaker. DNA was purified using the Qiagen MinElute columns per manufacturer's instructions.
Libraries were generated using custom Nextera PCR primers and PCR conditions from published protocol by Buenrostro et. al (Nature Methods, 2013).

value: Dox

value: c-FOS

tag: cell line


title: WT control rep3

description:
WT.d2438
mmwilson_IntCt.txt.gz
mmwilson_l2tpm.txt.gz


title: ASZ_cFOS_control_rep4

tag: treatment

value: control


title: ASZ_cFOS_rep1


title: ASZ_cFOS_rep2


title: ASZ_cFOS_control_rep2


title: ASZ_cFOS_rep4


title: WT control rep1

description:
WT.d2436
mmwilson_IntCt.txt.gz
mmwilson_l2tpm.txt.gz


title: ASZ_RasTGFbKD_Input

data_processing:
bowtie2 used for alignment.
Duplicate fragments were removed using samtools1.8.
macs2 used for peak calling.
IDR analysis for generating reproducible peaks.
Genome_build: mm9
Supplementary_files_format_and_content: bed

source_name: ASZ001 murine BCC cell line

extract_protocol:
Six days after Dox + 4OHT induction, ASZ_RasV12_TGFβR1kd cells were crosslinked and chromatin immunoprecipitation for c-FOS was carried out as described in the methods section of the manuscript.
ChIP libraries were prepared for sequencing using standard Illumina protocols.

tag: chip antibody


title: ASZ_RasTGFbKD_Fos_rep2

value: Rabbit anti-c-FOS mAb (9F6) (CST)


title: ASZ_cFOS_control_rep1


title: ASZ_cFOS_control_rep3


title: E10.5 trunk WT ChIPM CTCF rep1

description: ChIPmentation


title: D55-POU5F1-rep1

city: Bar Harbor

first: Christopher

last: Baker

state: ME

address: 600 Main St

institute: The Jackson Laboratory

description:
POU5F1normcounts.tsv
chip61

data_processing:
Bulk RNA reads were aligned to transcriptome (mm10 or modified to include known D2 SNPs, R78-REL1505) using bowtie v.1.0.0. ChIP and ATAC reads were aligned to genome using hisat2 v.2.0.5.
Allele specific gene counts were performed using EMASE. For ChIP and ATAC, peaks were called using MACS v.1.4.2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt files representing ensembl gene id along with normalized read counts for each sample. tab-delimited txt files representing the position of identified ChIP peaks in mm10 coordinates along with normalized read counts. Expression libraries for single cell RNAseq gene-cell: matrices are provided in the format produced by CellRanger. MULTI-seq Libraries for single cell RNAseq: barcode-cell matrices are provided in CSV format. The columns in the matrix Byers_EB_lipidhash_deMULTIplex_matrix.csv.gz represent individual embryoid body samples identified by unique lipid-modified oligos.

source_name: embryonic stem cell

growth_protocol: Mouse embryonic stem cells were derived and maintained in naive conditions following protocol from Czechanski et al. 2014 (Nature Protocols). Culture conditions to transition ESCs to EpiLCs followed Buecker et al. 2014 (Cell Stem Cell). Spontaneous differentiation of ESCs to EBs was achieved by first transitioning through EpiLC state for 48 hours followed by seeding cells on AggreWell400 Plates (STEMCELL Technologies) in EB medium ensuring 750 cells/EB. Aggregates were allowed to form for 48 hours and then filtered to remove unincorporated cells. Collected EBs were then plated on 100mm Corning Ultra-low attachment culture dishes and continued growth with rotation on BellyButton rotator for another 48 hours.

extract_protocol:
A single cell suspension of ESCs and EpiLCs were harvested at a concentration of 1 million cells/mL; 1 million cells were lysed and RNA extracted using RNeasy (Qiagen) RNA extraction kit; 100,000 cells were used for transposition reaction. For ChIP, 10 million cells were harvested and nuclei isolated using hypotonic lysis. Chromatin was fragmented using Covaris followed by dialysis and immunoprecipitation against protein targets was performed. For single cell RNAseq, single cell suspension was achieved for EB cultures and 500,000 cells for each individual sample was labeled with unique Multiseq LMO barcode. Labelled samples were pooled at 3,000 cells per sample and 40,000 cells were loaded onto a single lane of a 10X Chromium microfluidic chip. Cells were lysed in droplets using 10X Chromium instrument and reverse transcription was performed in droplet and library construction performed according to 10X Chromium v3 chemistry.
Libraries were constructed using the KAPA mRNA HyperPrep Kit for ESC and EpiLC bulk RNA samples. Modified Illumina Nextera adapters were used to construct ATAC libraries. ChIP-seq librariers were constructed using KAPA HyperPrep Kit. Single cell RNA-seq library preparation was performed using 10X Chromium v3.

value: naive esc

tag: mouse strain

value: POU5F1 (Cell Signaling Tech Oct-4A rabbit mAb, 5677S)


title: D29-POU5F1-rep1

description:
POU5F1normcounts.tsv
chip60


title: B51-POU5F1-rep2

description:
POU5F1normcounts.tsv
chip59


title: Glis2 KO rep2

description:
KO.d2440
mmwilson_IntCt.txt.gz
mmwilson_l2tpm.txt.gz


title: D55-P300-rep2

description:
p300normcounts.tsv
chip57


title: CPB2_3_input

city: Lanzhou

first: Zhang

middle: Juan

last: li

address: No. 1 Yingmen Village

institute: Gansu Agricultural University

data_processing:
Illumina Novaseq™ 6000 used for basecalling
fastp softwarewere used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter
 used HISAT2to map reads to the reference genomesus scrofa(11.1)
Mapped reads of IP and input libraries were provided for R package exomePeak
HOMER  were used for de novo and known motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker .
StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
Genome_build: genomesus scrofa(11.1)
Supplementary_files_format_and_content: txt file for genes_fpkm_expression

organism: Sus scrofa

extract_protocol:
Using 90% DMEM/HIGH GLUCOSE (HyClone, Logan, Utah, USA) and 10% fetal bovine serum (FBS) (HyClone), penicillin (100 U/mL), and 1% streptomycin (100 μg/mL) at an atmosphere of 95% O2, and 37℃under 5% CO2. Medium was changed every 2d and cells were passaged by trypsinization at 80-90% confluency
Total RNA was isolated using TRIzol (Invitrogen) reagent
Extract total RNA, establish IP library and input library respectively, and use Illumina Novaseq™ 6000 for paired-end sequencing

treatment_protocol: CPB2 treat porcine small intestinal epithelial cells  with 24h

value: 20ug/ml CPB2

tag: antibody


title: B41-POU5F1-rep1

description:
POU5F1normcounts.tsv
chip58


title: B41-P300-rep1

description:
p300normcounts.tsv
chip54


title: D29-TRIM28-input


title: B51-P300-rep2

description:
p300normcounts.tsv
chip55


title: D55-TRIM28-rep3

description:
TRIM28normcounts.tsv
chip52


title: D29-P300-rep1

description:
p300normcounts.tsv
chip56


title: CPB2_2_input

source_name: porcine small intestinal epithelial cells


title: ASZ_RasTGFbKD_Fos_rep1


title: Control3_input

value: porcine small intestinal epithelial cells


title: D29-TRIM28-rep1

description:
TRIM28normcounts.tsv
chip50


title: DAC203-TRIM28-rep2

description:
TRIM28normcounts.tsv
chip51


title: CPB2_1_input


title: B51-TRIM28-rep3

description:
TRIM28normcounts.tsv
chip46


title: Control1_input


title: B41-TRIM28-rep1

description:
TRIM28normcounts.tsv
chip44


title: CPB2_3_IP


title: B44-TRIM28-rep2

description:
TRIM28normcounts.tsv
chip45


title: CPB2_2_IP


title: CPB2_1_IP


title: Control2_input


title: BXD74-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA44

source_name: epiblast-like stem cell

value: esc transitioned to formative EpiLC

value: bxd


title: Control3_IP


title: BXD81-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA45


title: Control2_IP


title: BXD124-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA43


title: BXD69-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA42


title: Control1_IP


title: BXD87-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA38


title: BXD73-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA39


title: BXD99-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA37


title: B41-TRIM28-input


title: BXD71-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA41


title: BXD48-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA36


title: BXD83-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA34


title: BXD63-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA35


title: BXD64-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA33


title: BXD86-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA40


title: BXD43-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA31


title: BXD67-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA32


title: BXD61-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA30


title: BXD125-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA27


title: BXD161-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA29


title: BXD154-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA28


title: BXD98-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA26


title: BXD95-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA25


title: BXD90-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA24


title: P_60

city: Greifswald

first: Sabine

last: Ameling

address: Felix-Hausdorff.Str 8

department: Interfakultäres Institut für Genetik und Funktionelle Genomforschung

institute: Universitätsmedizin Greifswald

description: patient

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip System Confocal Scanner 3000.

data_processing: Expression raw data were transferred to Rosetta Resolver 7.2 (Rosetta Inpharmatics LLC) and Rosetta extraction algorithm was performed. For further analyses probe sets exhibiting p<0.05 were used. The pipeline calculates expression summaries using MAS5 via Affymetrix Power Tools from scans using both the perfect-match (PM) and mis-match (MM) probes. It returns only sequence-level results. The resulting P-values may be used as a guideline to decide expression presence or absence. This pipeline combines the expression values for individual profiles using an arithmetic average and computes the error of the result. P-value is the geometric mean of the profile-level P-values. Results are computed from sequence-level data using group processing. All profiles in the experiment definition are normalized together.

source_name: HEMB

label_protocol: Two round T7 RNA polymerase mediated linear amplification was performed with 14-25ng RNA starting amount according to the Affymetrix manufacturers Two Cycle Target Labelling protocol

extract_protocol: Column based RNA extraction (Qiagen) was performed following the manufacturers instructions for total RNA isolation from fibrous tissues, including purifications step using Charge Switch Total RNA Cell Kit. RNA integrity was checked using RNA 6000 Pico LabChip on a Bioanalyzer 2100 (Agilent)

tag: condition

value: DCM with LV systolic dysfunction (LVEF < 45 percent) and symptoms of HF


title: BXD84-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA22


title: BXD75-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA21


title: BXD85-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA23


title: BXD68-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA20


title: BXD66-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA19


title: P_62

description: patient


title: P_24

description: patient


title: P_63

description: patient


title: BXD65-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA18


title: P_61

description: patient


title: P_58

description: patient


title: P_59

description: patient


title: P_49

description: patient


title: P_41

description: patient


title: P_55

description: patient


title: P_28

description: patient


title: BXD62-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA17


title: BXD55-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA16


title: P_57

description: patient


title: P_20

description: patient


title: BXD49-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA15


title: BXD45-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA14


title: BXD44-RNA-EpiLC

description:
epilc_counts.norm.tsv.gz
RNA13


title: KO Colon  (ScRNAseq)

data_processing:
Unique molecular identifiers (UMIs) that barcode each individual mRNA molecule within a cell during reverse transcription were used to remove PCR duplicates.
Cells expressing fewer than 1000 or greater than 5500 genes were filtered out to exclude non-cells or cell aggregates. Cells expressing greater than 25 percent mitochondrial related genes were also removed.
Seurat standard pipeline was used for normalization and scaling while regressing out mitochondrial and cell cycle variation.
The Slingshot algorithm was used to order and project cells into principal curves on a diffusion map projection representing distinct trajectories with the arc length along each principal curve representing pseudotime, denoting a biological development process.
For each dataset, differentially expressed genes that were upregulated in each cluster compared to the rest of the cells were identified using Suerat’s implementation of the model-based analysis of single cell transcriptomics (MAST) algorithm.
To identify cell types, genes with a Bonferroni-adjusted P<0.001 and log fold change of at least 0.25 were taken into consideration.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx

extract_protocol:
Cells washed with 0.4% BSA in PBS and processed with 10X genomics single cell droplet sample preparation workflow at the Genomics Core facility at Weill Cornell Medicine
Beads-in-Emulsion (GEMs) were transferred and GEMs-RT was undertaken in droplets by PCR incubation. After purification of first-strand cDNA from the post GEM-RT reaction mixture, barcoded and full-length cDNAs were amplified via PCR to for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. TruSeq Read 1 (read 1 primer sequence) was added during GEM incubation.  A sample index and TruSeq Read 2 (read 2 primer sequence) were added via End Repair, A-tailing, Adaptor Ligation, and PCR

treatment_protocol: Live Epcam+, CD45-, and CD31- epithelial cells sorted by SONY MA900. Genotypes include Vil-CreER;Satb2f/f and Satb2f/f control mice

tag: genotype

value: Satb2 Knock out

value: Colon


title: P_53

description: patient


title: P_50

description: patient


title: P_51

description: patient


title: P_48

description: patient


title: WT Colon  (ScRNAseq)


title: P_46

description: patient


title: P_42

description: patient


title: 82 Luminal#4

description:
Luminal#4
82

data_processing:
Quality control:QC was carried out by MIT BMC/BCC in house pipeline including sequencing error rate estimation, sequencing reads complexity estimation, fastqc report, and sample contamination estimation.  Hierarchical clustering and heatmap creation were carried out by TIBCO Spotfire 7.11.1.0.12 basing on log2(fpkm+1) values of the expressed coding genes to observe sample relationship and to detect outliers.
For breast tumors, reads were mapped to the human genome (USCS GRCh38/hg38 build) and transcript abundance was determined using STAR v. 2.7.2b. Molecular subtyping, PAM50 and Claudin-low, was performed using the Genefu v.2.20.0 R package.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text file of integer count data

source_name: Tumor

extract_protocol:
total RNA was extracted from frozen sections of breast tumor samples using the  Nucleospin RNA set for Nucleozol kit according to the manufacturer’s protocol (Macherey-Nagel).
For breast tumor extracts, libraries were prepared using a modified version of the Takara SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian kit (Hendricks et al., in preparation). In brief, 100 ng of RNA at 10 ng/μL was sonicated using RL230 Covaris sonicator (Covaris Inc) and resulting material was confirmed using a Fragment Analyzer (Agilent). 10 ng of each sonicated sample was prepared using the pico input kit as for FFPE samples using a 1:8 volume reduction on the STP MosquitoHV. Final libraries were validated by Fragment Analyzer and qPCR prior to sequencing

value: Breast tumor

tag: type

value: Lum

tag: claudin

value: Others

tag: tumor type

value: Luminal


title: 81 Luminal#3

description:
Luminal#3
81


title: 83 Luminal#5

description:
Luminal#5
83


title: 80 Luminal#2

description:
Luminal#2
80


title: P_56

description: patient


title: 79 Luminal#1

description:
Luminal#1
79


title: P_54

description: patient


title: P_52

description: patient


title: 78 TNBC#62

description:
TNBC#62
78

value: IM

value: TNBC


title: P_44

description: patient


title: 77 TNBC#61

description:
TNBC#61
77

value: UNS


title: P_40

description: patient


title: P_38

description: patient


title: P_34

description: patient


title: 76 TNBC#60

description:
TNBC#60
76


title: 75 TNBC#59

description:
TNBC#59
75


title: P_19

description: patient


title: 74 TNBC#58

description:
TNBC#58
74

value: LAR


title: P_39

description: patient


title: P_31

description: patient


title: 73 TNBC#57

description:
TNBC#57
73

value: M


title: 72 TNBC#56

description:
TNBC#56
72

value: Claudin


title: P_37

description: patient


title: P_36

description: patient


title: P_45

description: patient


title: P_43

description: patient


title: P_47

description: patient


title: P_35

description: patient


title: P_32

description: patient


title: 69 TNBC#53

description:
TNBC#53
69


title: P_30

description: patient


title: 67 TNBC#51

description:
TNBC#51
67


title: 66 TNBC#50

description:
TNBC#50
66


title: 65 TNBC#49

description:
TNBC#49
65

value: MSL


title: 71 TNBC#55

description:
TNBC#55
71


title: 64 TNBC#48

description:
TNBC#48
64


title: 70 TNBC#54

description:
TNBC#54
70


title: 63 TNBC#47

description:
TNBC#47
63


title: 61 TNBC#45

description:
TNBC#45
61


title: 60 TNBC#44

description:
TNBC#44
60


title: P_27

description: patient


title: 58 TNBC#42

description:
TNBC#42
58


title: 62 TNBC#46

description:
TNBC#46
62


title: P_25

description: patient


title: P_18

description: patient


title: 57 TNBC#41

description:
TNBC#41
57


title: P_23

description: patient


title: P_21

description: patient


title: p27plusmacromet

city: Seattle

first: Cyrus

middle: M

last: Ghajar

state: WA

address: 1100 Fairview Ave. N.

department: Public Health Sciences Division/Translational Research Program

institute: Fred Hutchinson Cancer Research Center

data_processing:
Illumina HiSeq2500 used for basecalling
CellRanger software package (3.1.0) used for alignment, filtering, barcode reading and data visualization
Genome_build: GRCh38 3.0.0
Supplementary_files_format_and_content: raw feature bc matrix: barcode, feature, and matrix file (of the number of UMIs associated with a feature (row) and a barcode (column))

source_name: mVenus-p27+ (quiescent) cells recovered from metastatic lesions

extract_protocol:
The brain was removed and placed in ice cold Hank's Balanced Salt Solution (HBSS) in a 10 cm dish. Fresh brain tissues were dissected under an Axiozoom fluorescent stereoscope (Zeiss) to distinguish tdTomato+ metastatic lesions from apparently uninvolved brain. The metastatic and uninvolved brain tissue were separated and minced using a razor blade, then enzymatically dissociated with papain (2 mg/ml) (Worthington Biochemical Corporation) and 0.06 mg/ml DNase I (Worthington Biochemical Corporation) in HBSS. A single cell suspension was obtained by incubating samples at 37oC for 30 minutes with agitation every 5 minutes. The cell mixture was filtered through a 70 μm cell strainer to remove unlysed tissue fragments and single cells were pelleted at 500 x g for eight minutes. The cell pellet was resuspended immediately in 1 ml fresh RBC lysis buffer (Biolegend) to remove red blood cells. Lysis was neutralized by adding 1-3 volumes of HBSS and 10% FBS, then cells were pelleted and resuspended in 10 ml 30% Percoll (GE Healthcare). The sample was centrifuged at 700 x g using a swinging bucket rotor for 10 minutes to remove myelin (breaks set to 0, acceleration set to 1). The cell pellet was resuspended in 200 μl of 2% FBS/HBSS and filtered through a 40 μm cell strainer before flow sorting.
Single-cell libraries were prepared using the Chromium 3′ v2 platform (10X Genomics) following the manufacturer’s protocol 7. Briefly, single cells were partitioned into gel beads in emulsion in the 10X Chromium Controller instrument followed by cell lysis and barcoded reverse transcription of RNA, amplification, shearing and 5′ adapter and sample index attachment. Cells from the three groups indicated above were loaded separately onto the Chromium Chip A for indexing before libraries were combined for paired-end sequencing on the Illumina HiSeq2500 (PE1 54 bp and PE2 66 bp).

treatment_protocol: TdTomato-mVenus-p27K- T4-2 breast cancer cells (5 x 105 cells in 100 µl PBS) were injected via ultrasound-guided injection into the left ventricle of four 6-8-week-old female NOD-SCID mice.Animals were euthanized one-month post-injection and perfused with 25 mL cold DEPC-treated PBS (Sigma) via the left ventricle.

tag: host strain

value: 6-8-week-old female NOD-SCID

value: triple negative TdTomato-mVenus-p27K- T4-2 human breast cancer cell line

value: mouse brain

tag: cell population


title: P27plusandnegativedtc

source_name: micromet-derived DTCs including both mVenus-p27+ and p27- cells from uninvolved brain

tag: cell type

value: mVenus-p27+ and p27- cells


title: 56 TNBC#40

description:
TNBC#40
56


title: P_22

description: patient

value: DCM with LV systolic dysfunction (LVEF < 45 percent) and symptoms of HF


title: p27minusmacromet

source_name: mVenus-p27- cells from metastatic lesions


title: P_16

description: patient


title: P_15

description: patient


title: P_Co11

description: Control

value: control


title: P_11

description: patient


title: P_Co12

description: Control


title: P_Co13

description: Control


title: YS5_s4012 H3.3K27M_5

first: Yusuke

last: Tomita

state: Illinois

address: 225 E Chicago Ave Box 18

department: Pediatrics

data_processing:
FASTQ files were aligned to the mm10 genome using RNA-STAR 2.7 .
Aligned reads were counted using HTSeq-count with the Ensembl mm10 transcriptome GTF file as the feature with the following HTSeq-count parameters: stranded = no, mode = union, minimum alignment quality = 10, map nonunique or ambiguous reads = none.
HTSeq-count files were imported into R (https://www.r-project.org/https://www.r-project.org/), genes with < 10 reads base mean were removed, and differential expression analysis was performed with the DESeq2 package using the DESeqDataSetFromHTSeqCount function with default settings. DESeq2 analyses were run comparing the H3.3K27M tumors and the H3.3WT tumors.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table in Excel format containing DESeq2 output and DESeq2 normalized abundance measurements for each sample

growth_protocol: RCAS-PDGFB, and -H3.3K27M or -H3.3WT were injected to postnatal day 3 Olig2-Tv-a-Cre; p53 fl/fl mice, and all the mice were euthanized at the indicated endpoint.

extract_protocol:
Purified RNA was obtained by using Qiagen Rneasy extraction kit and protocol
TruSeq mRNA-Seq Library Prep
HiSeq 4000  sequencing, 50bp, Single Reads

value: RNA derived from tumor

tag: strain

value: untreated


title: 55 TNBC#39

description:
TNBC#39
55

tag: tissue

value: Breast tumor


title: 59 TNBC#43

description:
TNBC#43
59

value: Others


title: P_13

description: patient


title: P_Co18

description: Control


title: 54 TNBC#38

description:
TNBC#38
54


title: P_Co10

description: Control


title: YS4_s3987 H3.3K27M_4


title: 53 TNBC#37

description:
TNBC#37
53


title: YS3_s3409 H3.3K27M_3


title: 52 TNBC#36

description:
TNBC#36
52


title: P_Co4

description: Control


title: 51 TNBC#35

description:
TNBC#35
51


title: P_Co14

description: Control


title: YS1_s3202 H3.3K27M_1


title: YS2_s3209 H3.3K27M_2


title: YS10_s4112 H3.3WT_5


title: YS8_s4013 H3.3WT_3


title: P_Co19

description: Control


title: 49 TNBC#33

description:
TNBC#33
49


title: 48 TNBC#32

description:
TNBC#32
48


title: 47 TNBC#31

description:
TNBC#31
47

value: IM


title: 46 TNBC#30

description:
TNBC#30
46

value: TNBC


title: YS7_s3895 H3.3WT_2


title: PaK_711F H3.3K27M_5

growth_protocol: RCAS-PDGFA, and -H3.3K27M or -H3.3WT were injected to postnatal day 3 Olig2-Tv-a-Cre; p53 fl/fl mice, and all the mice were euthanized at the indicated endpoint.


title: 45 TNBC#29

description:
TNBC#29
45

value: UNS


title: YS6_s3605 H3.3WT_1


title: PaK_503F H3.3K27M_3


title: PaK_299M H3.3K27M_2


title: PaK_710F H3.3K27M_4


title: PaK_9770M H3.3K27M_1


title: 43 TNBC#27

description:
TNBC#27
43


title: 42 TNBC#26

description:
TNBC#26
42


title: 41 TNBC#25

description:
TNBC#25
41


title: 50 TNBC#34

description:
TNBC#34
50


title: PaH_1082F H3.3WT_5


title: 39 TNBC#23

description:
TNBC#23
39

value: LAR


title: YS9_s4014 H3.3WT_4


title: PaH_741F H3.3WT_4


title: 40 TNBC#24

description:
TNBC#24
40


title: PaH_740F H3.3WT_3


title: 38 TNBC#22

description:
TNBC#22
38


title: PaH_738M H3.3WT_2


title: S20-1211-4 H3.3K27M_7

growth_protocol: RCAS-PDGFA, -H3.3K27M or -H3.3WT, and -Cre were injected to postnatal day 3 Nestin Tv-a; p53 fl/fl mice, and all the mice were euthanized at the indicated endpoint.


title: 37 TNBC#21

description:
TNBC#21
37


title: 35 TNBC#19

description:
TNBC#19
35

value: M


title: 44 TNBC#28

description:
TNBC#28
44

value: Claudin


title: S21-0210-3 H3.3K27M_6


title: 33 TNBC#17

description:
TNBC#17
33


title: 34 TNBC#18

description:
TNBC#18
34


title: 32 TNBC#16

description:
TNBC#16
32


title: S20-0814-5 H3.3K27M_3


title: 30 TNBC#14

description:
TNBC#14
30


title: S20-0308-3 H3.3K27M_2


title: 31 TNBC#15

description:
TNBC#15
31


title: 29 TNBC#13

description:
TNBC#13
29


title: S19-0903-2 H3.3K27M_1


title: 28 TNBC#12

description:
TNBC#12
28


title: S20-0935-5 H3.3WT_9


title: WT Ileum  (ScRNAseq)

value: wild type

value: Ileum


title: 27 TNBC#11

description:
TNBC#11
27


title: S20-0714-7 H3.3WT_7


title: S20-1051-1 H3.3WT_8


title: S20-0814-2 H3.3WT_6


title: 25 TNBC#9

description:
TNBC#9
25


title: PaH_505M H3.3WT_1


title: 36 TNBC#20

description:
TNBC#20
36


title: 24 TNBC#8

description:
TNBC#8
24


title: 26 TNBC#10

description:
TNBC#10
26


title: S20-1051-5 H3.3WT_3


title: S21-0210-2 H3.3K27M_5


title: S20-0308-10 H3.3WT_4


title: S21-0210-4 H3.3K27M_4


title: S20-0308-8 H3.3WT_2


title: 22 TNBC#6

description:
TNBC#6
22


title: 21 TNBC#5

description:
TNBC#5
21


title: 20 TNBC#4

description:
TNBC#4
20


title: S19-0619-4 H3.3WT_1


title: 18 TNBC#2

description:
TNBC#2
18


title: E12.5 PFL Del(CBS1-3) cHiC

description: Capture Hi-C

tag: developmental stage

value: Proximal forelimb


title: E12.5 PFL Del(CBS1) cHiC

description: Capture Hi-C


title: E12.5 PFL Del(CBS1-5) cHiC

description: Capture Hi-C


title: E12.5 DFL Del(CBS1-5) cHiC

description: Capture Hi-C

value: Distal forelimb


title: RK_transduced_stim_C

city: Vancouver

first: Stuart

middle: E

last: Turvey

state: British Columbia

address: A5-122 950 W 28th Avenue

country: Canada

institute: The University of British Columbia

data_processing:
RNA was sequenced on the Illumina NextSeq 500 with Paired End 42bp x 42bp reads
Read sequences were aligned to the Homo sapiens reference sequence (UCSC hg19) using STAR aligner (version STAR_2.5.0b)
Assembly of transcripts and measurement of abundance was done using Cufflinks (Version 2.2.1)
TMM analysis using EdgeR was used for raw count normalization
Genome_build: Homo sapiens (UCSC hg19)
Supplementary_files_format_and_content: Raw counts and normalized counts are presented as .csv matrix files

source_name: SV40-transformed skin fibroblasts

growth_protocol: Patient-derived skin fibroblasts were immortalized by transfection with a plasmid expresing SV40 large T antigen. Cells were then infected with HOIL1-WT or HOIL1-R/K lentiviral particles and subsequently propagated in complete DMEM.

extract_protocol:
RNA was extracted with a RNeasy Mini Plus Kit (Qiagen)
RNA samples were prepared following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England BioLabs)

treatment_protocol: Stimulated with 10ng/mL IL-1b for 4h

value: SV40-transformed skin fibroblasts

tag: genotype/variation

value: infected with HOIL1-R/K lentiviral particles

tag: unstim or stim

value: Stimulated

tag: replicate number


title: S20-1021-8 H3.3WT_5

institute: Northwestern University

value: RNA derived from tumor

tag: treatment


title: E12.5 DFL Del(CBS1) cHiC

description: Capture Hi-C


title: 17 TNBC#1

description:
TNBC#1
17


title: RK_transduced_stim_B


title: RK_transduced_stim_A


title: 23 TNBC#7

description:
TNBC#7
23


title: E9.5 trunk Del(CBS1-5) cHiC rep1

description: Capture Hi-C

value: Embryonic trunk


title: E9.5 trunk Del(CBS1-5) cHiC rep2

description: Capture Hi-C


title: E9.5 trunk Del(CBS1-3) cHiC rep2

description: Capture Hi-C


title: RK_transduced_unstim_C

value: Unstimulated


title: E9.5 trunk Del(CBS1-3) cHiC rep1

description: Capture Hi-C


title: WT_transduced_stim_C

value: infected with HOIL1-WT lentiviral particles


title: RK_transduced_unstim_B


title: RK_transduced_unstim_A


title: WT_transduced_stim_A


title: WT_transduced_unstim_C


title: WT_transduced_stim_B


title: WT_transduced_unstim_B


title: E9.5 trunk Del(CBS1) cHiC rep2

description: Capture Hi-C


title: E9.5 trunk Del(CBS1) cHiC rep1

description: Capture Hi-C


title: 19 TNBC#3

description:
TNBC#3
19

value: Breast tumor

value: Others


title: E12.5 PFL Del(CBS1-5) RNAseq rep2

data_processing:
Raw RNA-seq reads were processed with cutadapt version 1.16 (Martin 2011 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -q 30 -m 15) to remove TruSeq adapters and bad quality bases.
Filtered reads were mapped on the mouse genome mm10 with STAR version 2.7.0.e (Dobin et al. 2013) with ENCODE parameters with a custom gtf file (https://doi.org/10.5281/zenodo.4596489) based on Ensembl version 102.
FPKM values were evaluated by cufflinks version 2.2.1 (Tranell et al. 2010 Roberts et al. 2011 with options --max-bundle-length 10000000 --multi-read-correct --library-type "fr-firststrand" -b mm10.fa  --no-effective-length-correction -M MTmouse.gtf -G).
All counts were merged in a single file. Same for FPKM and multiple entries with the same gene_id were summed.
Strand specific coverage were obtained with bedtools version 2.27.1 on a filtered BAM with only uniquely mapped reads.
Genome_build: mm10
Supplementary_files_format_and_content: AllCufflinks_Simplified.txt: table with all FPKM values
Supplementary_files_format_and_content: AllHTSeqCounts_subset.txt: gene counts obtained by STAR from autosomal genes.
Supplementary_files_format_and_content: _Uniq_fwd.bw: forward strand coverage
Supplementary_files_format_and_content: _Uniq_rev.bw: reverse strand coverage

extract_protocol:
Micro-dissected individual pairs of either control or mutant E12.5 proximal and distal forelimbs were stored at -80˚C in RNAlater stabilization reagent (Ambion) before further sample processing. Total RNA was extracted from tissues using Qiagen RNeasy Plus Micro Kit (Qiagen) after disruption and homogenization according to manufacture instructions. RNA quality was assessed using an Agilent 2100 Bioanalyser.
The sequencing libraries were prepared according to TruSeq Stranded mRNA Illumina protocol, with polyA selection. RNA-seq libraries were sequenced on an Illumina HiSeq 4000 sequencer, as single-end reads (read length 50 bp).


title: E9.5 trunk WT cHiC rep2

description: Capture Hi-C

value: WT


title: E12.5 DFL Del(CBS1-5) RNAseq rep3


title: WT_transduced_unstim_A


title: E12.5 PFL Del(CBS1-5) RNAseq rep1


title: Untransduced_stim_A


title: E12.5 PFL Del(CBS1-5) RNAseq rep3


title: E9.5 trunk WT cHiC rep1

description: Capture Hi-C


title: E12.5 DFL Del(CBS1-3) cHiC

description: Capture Hi-C


title: E12.5 DFL Del(CBS1-5) RNAseq rep2


title: E12.5 PFL Del(CBS1-4) RNAseq rep3


title: Untransduced_unstim_B


title: Untransduced_unstim_C


title: E12.5 PFL Del(CBS1-4) RNAseq rep1


title: Untransduced_unstim_A


title: E12.5 DFL Del(CBS1-4) RNAseq rep3


title: E12.5 DFL Del(CBS1-4) RNAseq rep2


title: E12.5 PFL Del(CBS1-4) RNAseq rep2


title: E12.5 DFL Del(CBS1-5) RNAseq rep1


title: Untransduced_stim_C


title: Untransduced_stim_B


title: E12.5 DFL Del(CBS1-4) RNAseq rep1


title: E12.5 PFL Del(CBS1-3) RNAseq rep2


title: E12.5 PFL Del(CBS1-3) RNAseq rep3


title: Tumor Sample 5

city: Teliyarganj, Prayagraj

first: VIVEK

last: KUMAR

state: Uttar Pradesh

address: Department of Biotechnology, MNNIT Allahabad

department: Biotechnology

country: India

institute: Motilal Nehru National Institute of Technology Allahabad

data_processing:
Adaptor clipping and quality trimming was done using Trimomatic (v0.35)
Low quality data (reads with more than 10% quality threshold (QV) < 20 phred score) were removed using Trimomatic (V0.35).
High quality read were mapped to Hg19(GRCh37) using BWA-Mem with default parameters. Further alignment files were processed by samtools (V1.6) and alignment files were converted to BAM file.
Samtools (v1.6) was used to remove duplicated reads
During post alignment preocessing, differential methylated regions were directly performed on BAM files using diffReps (v1.55.6) with sliding window of 1kb, step size of 100bp and reads falling into region were counted. G-test was performed on log fold change value to calculate p-Value and q-Values.
Methylated genomic intervals were annotated using the tool region_analysis (v 1.0)
miRNA proximal promoter region was identified from miRstart, microTSS and TransmiR v2.0, further manually screened in identified DMRs for their hypo and hypermethylation status
Genome_build: Hg19(GRCh37)
Supplementary_files_format_and_content: These are the alignment files in binary formate with methylation call

source_name: Cancerous Ovary Tissue

extract_protocol:
Ovarian tissue samples were extracted, washed in PBS, and homogenized in SET buffer. Further homozenate was treated with protenase K and 10% SDS followed by overnight incubation at 37 ºC. Next, phase sepration and precipitation in 3M sodium acetate and chilled absolute ethanol. further precipitate was subjected to centrifugation, supernatant was discarded and pellet was retained and air dried overnight and resuspended in 150 µl of TE Buffer and stored in 4 ºC till further use.   Total 1µg of genomic DNA was used to prepare MeDIP seq library using  Illumina TruSeq Nano DNA Library Prep Kit and MagMeDIP Kit (Diagenode, USA; Cat. No. C02010020).
DNA libraries were prepared for sequencing following standard Illumina protocol

tag: disease state

value: ovarian cancer

tag: cancer stage

value: IA

value: Cancerous Ovary

tag: age


title: Tumor Sample 2

value: IIIC


title: Tumor Sample 1


title: Tumor Sample 4

value: IV


title: Normal Sample 2

source_name: Normal Ovary Tissue

value: control

value: Normal Ovary


title: Tumor Sample 6

value: II


title: E12.5 DFL Del(CBS1-3) RNAseq rep3

source_name: Distal forelimb

value: Distal forelimb

tag: genotype


title: Normal Sample 1


title: E12.5 PFL Del(CBS1-3) RNAseq rep1

value: Proximal forelimb


title: E12.5 DFL Del(CBS1-3) RNAseq rep2


title: E12.5 PFL Del(CBS1-2) RNAseq rep2


title: E12 brain ChIP CTCF

description: ChIP

data_processing:
All scripts are available on https://github.com/lldelisle/scriptsForAmandioEtAl2021
TrueSeq adapters were removed from single-reads fastqs with cutadapt version 1.16 (Martin 2011 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -q 30 -m 15).
Filtered reads were mapped to the mouse genome mm10 with bowtie2 version 2.3.5 (Langmead et al. 2012 with default options). Only alignments with a mapping quality above 30 were kept (samtools version 1.9 Danecek et al. 2021).
Peak calling was run with a fixed fragment size of 200bp with macs2 callpeak version 2.1.1.20160309 (--call-summits --nomodel --extsize 200 -B).
Finally the coverage were normalized to the million unique tags.
Genome_build: mm10
Supplementary_files_format_and_content: bw: normalized coverage track
Supplementary_files_format_and_content: narrowPeak: narrowPeak from macs2

source_name: Brain

extract_protocol:
For the posterior trunk sample, the portion corresponding to the tailbud, presomitic mesoderm, and 2-3 somite pairs, excluding as much as possible the region of the evaginating hindlimb buds, was micro-dissected from approximately thirty E9.75-E10 embryos. For the brain sample, a pool of six micro-dissected telencephalons from E12.5 embryos was used. CTCF ChIP-seq experiments were performed as described in (Rodríguez-Carballo et al 2017).
Libraries were prepared as described in Rodríguez-Carballo et al., 2017

value: Brain

tag: chip antibody

value: CTCF (Active Motif #61311)


title: E12.5 PFL Del(CBS1-2) RNAseq rep3

source_name: Proximal forelimb


title: E12 PFL ChIP CTCF_re-analyzed

description:
ChIP
GSM2713708


title: E12.5 DFL Del(CBS1-2) RNAseq rep3


title: BXD161-ATAC-ESC

value: naive esc

tag: mouse strain

value: bxd


title: E12.5 DFL Del(CBS1-2) RNAseq rep2


title: BXD124-ATAC-ESC


title: Tumor Sample 3


title: BXD95-ATAC-ESC


title: BXD83-ATAC-ESC


title: E12.5 PFL Del(CBS1) RNAseq rep3


title: BXD67-ATAC-ESC


title: E12.5 PFL Del(CBS1) RNAseq rep2


title: BXD98-ATAC-ESC


title: E12 DFL ChIP CTCF_re-analyzed

description:
ChIP
GSM2713707


title: E12.5 DFL Del(CBS1-3) RNAseq rep1


title: E12.5 DFL Del(CBS1) RNAseq rep3


title: E12.5 PFL Del(CBS1-2) RNAseq rep1


title: BXD62-ATAC-ESC


title: E12.5 PFL Del(CBS1) RNAseq rep1


title: DA6

city: Columbus

first: Jose

middle: P

last: Guirao-Abad

state: OH

address: 2255 Kenny Rd

department: Emergency Medicine

institute: Ohio State University

description: Mutant lacking the spfA gene

data_processing:
A poly(A) RNA-Seq was carried out in the Genomics, Epigenomics and Sequencing Core (GESC) at the University of Cincinnati using a NextSeq 550 system (Illumina). After adapter trimming and quality control, fastq files of each sample were merged before data analysis
Gene expression analysis was carried out using the A. fumigatus Af293 reference genome and annotation tracks from FungiDB (release 51) in CLC Genomics Workbench (QIAgen). Expression values were estimated as transcripts per million (TPM).
Differential expression for RNA-Seq was calculated between the control and mutant strains using TMM as the normalization method.
Downstream analysis was performed using FungiDB and FungiFun2
Genome_build: Af293
Supplementary_files_format_and_content: Matrix table with expression values in TPM, fold change (∆spfA vs Parental strain), statistical analysis and enrichment analysis for every gene and every sample

organism: Aspergillus fumigatus

source_name: ∆spfA (772) rep3

growth_protocol: Cultures containing 50 mL of liquid YG were inoculated with 1 x 106 conidia/mL and incubated for 16 h at 37°C and 200 rpm.

extract_protocol:
biomass was grounded under liquid nitrogen and the RNA extracted using a Direct-zol RNA MiniPrep kit (Zymo Research).
Library preparation was performed using NEBNext Ultra II Directional RNA Library Prep kit for RNA-seq.

value: spfA knockout mutant

value: Untreated

value: {delta}akuB::pyrG+, {delta}spfA::six


title: BXD43-ATAC-ESC


title: DA5

description: Mutant lacking the spfA gene

source_name: ∆spfA (772) rep2


title: E12.5 DFL Del(CBS1-2) RNAseq rep1


title: DA4

description: Mutant lacking the spfA gene

source_name: ∆spfA(772) rep1


title: BXD68-ATAC-ESC

source_name: embryonic stem cell


title: BXD71-ATAC-ESC


title: DA1

description: Mutant Deficient for Nonhomologous End Joining

value: Parental strain


title: E12.5 DFL Del(CBS1) RNAseq rep2


title: BXD86-ATAC-ESC


title: BXD73-ATAC-ESC


title: E12.5 PFL WT RNAseq rep3

value: WT


title: LysM-4 K.O 10x scRNA-seq

data_processing:
cellranger-3.0.2 was run for bcl2fastq, Read filter and count
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: 10x run of mouse monocytes

extract_protocol:
Isolation of hepatic non-parenchymal cells was performed as previously described (Ben Shlomo et al., 2019; Graubardt et al., 2017; Zigmond et al., 2014). In brief, mice were anesthetized and perfused livers were collected, cut into small fragments, and incubated with 5 mL digestion buffer composed of 5% fetal bovine serum (Biological Industries, Israel), 0.5 mg/mL collagenase VIII from Clostridium histolyticum (Sigma-Aldrich, USA), 0.1 mg/mL Deoxyribonuclease I from bovine pancreas (Sigma-Aldrich, USA) in Dulbecco’s phosphatebuffered saline with calcium and magnesium (PBS+/+, Biological Industries, Israel), in a shaker-incubator at 250 rpm, 37°C for 45 min. Samples were then subjected to three cycles of washing with Dulbecco’s phosphate-buffered saline without calcium and magnesium (PBS−/−) at 400 rpm, 4°C for 5 min from which the supernatant was kept, omitting the parenchymal cell pellet. Subsequently, the supernatant was centrifuged at 1,400 rpm, 4°C for 5 min and the cell pellet was lysed for erythrocytes by 2 min incubation with Ammonium-Chloride-Potassium (ACK) buffer composed of 0.15 M NH4Cl and 0.01 M KHCO3, and washed with PBS−/−. Cell sorting was performed using the BD FACSAriaTM FUSION cell sorter (BD Bioscience).
10x genomics according to the manufacturer protocol

value: LysMDCommd10 C57BL/6

tag: organ

value: Liver

value: monocytes

value: Acetaminophen-induced liver injury

tag: mouse age

value: 8 weeks


title: DA2


title: c10-1 Control 10x scRNA-seq

value: Commd10fl/fl C57BL/6


title: E12.5 DFL Del(CBS1) RNAseq rep1

value: Distal forelimb


title: E12.5 PFL WT RNAseq rep2

value: Proximal forelimb


title: WT Colon Organoid rep 3

data_processing:
Adapter and low quality bases trimming (Q<20) using Trim Galore! with default parameters
Paired end alignment using STAR with defaut parameters
Generation of counts relative to genes using featureCounts with defaut paramets (unstranded mode)
Generation of normalized read counts and differential expression genes with normal shrinkage mode by DEseq2 package in Rstudio
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized gene counts table

source_name: 3D cultured mouse Organoids

growth_protocol: Crypts were collected from mice intestine by EDTA method and embedded in materigel with large intestine culture medium. After one passage, organoids were differentiated and collected for RNA extraction. Genotypes include Vil-CreER;Satb2f/f and Satb2f/f control mice, after 30 days of tamoxifen injection.

extract_protocol:
Qiagen Mini RNA extract kit
NEBNext® Ultra™ RNA Library Prep Kit for Illumina, following manufacturer's protocol.
Library construction performed by Novogene.co.  Non-directional eukaryotic mRNA library

treatment_protocol: Materigel was removed by Cell recovery solution, pellet organoids were resuspended in RLT lysis buffer (Qigen Kit)

tag: genotyping

value: Wild Type

tag: intestine part

value: Colon


title: E12.5 PFL WT RNAseq rep1

tag: strain


title: E12.5 DFL WT RNAseq rep3

tag: tissue


title: BXD48-ATAC-ESC

tag: cell type

value: naive esc


title: WT Colon Organoid rep 2


title: E12.5 DFL WT RNAseq rep2

tag: developmental stage


title: BXD49-ATAC-ESC

value: bxd


title: DA3


title: BXD61-ATAC-ESC


title: E12.5 DFL WT RNAseq rep1


title: BXD69-ATAC-ESC


title: SATB2 KO colonic epithelium input rep 2

description: Input

data_processing:
All reads were trimmed with trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), and subjected to quality control with FastQC before and after adapter trimming.
Bowtie2 (Langmead and Salzberg, 2012) was used to align the two independent ChIP-Seq analyses to the mouse (mm10) genome with default parameters.
Aligned ChIP-Seq data in SAM format were transformed to BAM files and non-uniquely mapped reads were filtered-out.
Duplicate alignments were then marked and removed using Sambamba.
The merge function in samtools was used to merge the BAM files of different replicates and filter out non-uniquely mapped reads.
Deeptools bamCoverage (duplicate reads ignored, RPKM normalized) was used to generate bigWig files from BAM files.
Genome_build: Mouse mm10
Supplementary_files_format_and_content: Bigwig files for visualization of TFs genomic binding peaks.

source_name: Intestine epithelium

extract_protocol:
50 µl of pelleted cross-linked cells were resuspended in 350 µl sarkosyl lysis buffer (0.25% sarkosyl, 1 mM DTT and protease inhibitor in RIPA buffer) and sonicated at 15% amplification by a tip sonicator (Qsonica, Q125) to obtain 200bp to 800bp chromatin fragments. Diluted lysates were incubated with TFs antibodies at 4°C overnight and were additionally incubated with 30 µl protein A/G magnetic beads. ChIPed DNA was purified with a MinElute purification kit.
Libraries were prepared using the ThruPLEX DNA-Seq Kit
Exactly followed the protocol from Takara bio, R400428 or R400427 (Same protocol with R400428, different index system). All final libraries were size selected (200-800 bp) by AMPure XP beads (Beckman, A63880) and loaded for sequencing.

treatment_protocol: Epithilal tissues were collected by the EDTA method 30 days after tamoxifen injection and cross-linked with 2mM DSG and 1% formaldehye.


title: KO Colon Organoid rep 3

value: Satb2 Knock out


title: BXD64-ATAC-ESC


title: c10-3 Control 10x scRNA-seq


title: BXD65-ATAC-ESC


title: KO Colon Organoid rep 2


title: WT Colon Organoid rep 1


title: WT Ileum Organoid rep 3

value: Ileum


title: BXD55-ATAC-ESC


title: WT Ileum Organoid rep 2


title: KO Colon Organoid rep 1


title: SATB2 KO colonic epithelium input rep 1

description: Input


title: Wild type colonic epithelium input rep 2

description: Input


title: Wild type colonic epithelium input rep 1

description: Input


title: HNF4A_ChIP in HNF4A KO colonic epithelium

description: HNF4A_ChIP (Negative Control)


title: BXD63-ATAC-ESC


title: BXD75-ATAC-ESC


title: BXD85-ATAC-ESC


title: HNF4A_ChIP in SATB2 KO colonic epithelium rep 2


title: BXD99-ATAC-ESC


title: HNF4A_ChIP in SATB2 KO colonic epithelium rep 1


title: DTR_GFP(-)_IgG

data_processing:
Reads were trimmed with trim_galore.
Paired-end reads were then mapped to the mm10 genome using Bowtie2 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
Only uniquely mapped reads were retained with samtools
Peaks were called from macs2 with pooled reads and with both replicate samples by merge broad and narrow peak files.
only peaks ±2 Kb outside TSSs were permitted, using ‘distal peaks’ as enhancer peaks
Genome_build: Mouse mm10

extract_protocol:
10x5 cells were attached to Concanavalin A conjugated magnetic beads, permeabilized, and incubated with anti-SATB2 or isotype control antibodies at 4C for overnight. pAG-MNase (1:1000) was added in digitonin buffer to bind with antibodies. Finally, targeted chromatins were digested and released into the supernatant. DNA was purified with a MinElute purification kit.
Libraries were prepared using the ThruPLEX DNA-Seq Kit
Exactly followed the protocol from Takara bio (R400665). All final libraries were size selected (200-800 bp) by AMPure XP beads (Beckman, A63880) and loaded for sequencing.

treatment_protocol: EDTA stripped Lgr5DTRGFP colonic epithelia were dissociated into single cells with TrypLE. Single cells incubated with anti-EPCAM-APC antibody for 30mins on ice. Epcam+ and GFP+ double postive cells were collected as stem cells. Epcam+ and GFP- cells were sorted as differentiated cells. Mutipule mice cells were combined as one sample.

tag: gfp signal

value: Negative

value: differentiated cells


title: DTR_GFP(+)_IgG

value: Positive

value: stem cells


title: BXD44-ATAC-ESC


title: HNF4A_ChIP in wild type colonic epithelium rep 2


title: BXD154-ATAC-ESC


title: DTR_GFP(-)_SATB2


title: DTR_GFP(+)_SATB2


title: ASZ_RasV12_TGFbR1-kd_rep2

data_processing:
bowtie used for alignment.
duplicate fragments were removed using samtools
macs2 used for peak calling
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: ASZ_ RasV12_TGFbR1-kd/Dox-4OHT

growth_protocol: ASZ001 cells were cultured in 154CF medium (Life Technologies) supplemented with 2% chelated FBS and 0.05 mM CaCl2.

extract_protocol:
ATAC-seq cell lysis and transposition with Tn5 was carried out based on published protocol by Buenrostro et. al (Nature Methods, 2013) with minor modifications for on-plate transposition. Briefly, 50,000 ASZ001 cells were plated per replicate in a 48-well plate, then serum starved for 24 hours. Wells were washed with cold PBS and lysed using 0.1% NP40 in resuspension buffer for 10 minutes at 25°C. Wells were washed again, then 100 µl of transposition mixture was added per well and incubated for 37°C for 30 min, shaking at 1000 RPM using a thermoshaker. DNA was purified using the Qiagen MinElute columns per manufacturer's instructions.
Libraries were generated using custom Nextera PCR primers and PCR conditions from published protocol by Buenrostro et. al (Nature Methods, 2013).

value: 6 days Dox/4OHT

tag: cell line


title: CDX2_ChIP in SATB2 KO colonic epithelium rep 2