title: MTgal4_shSv210_HP1_repeat

city: Pasadena

first: Maria

last: Ninova

state: CA

address: 1200 E California Blvd

department: Division of Biology and Biological Engineering

institute: Calfironia Institute of Technology

description: gDNA (ChIP)

data_processing:
RNA-seq reads aligning to rRNA were removed by mapping to Drosophila rRNA sequences using bowtie allowing 3 mismatches
Reads were mapped to the Drosophila genome allowing 2 mismatches and 1 mapping position or 0 mismatches and 10000 mapping positions for TE analysis
UCSC genome browser tracks were were generated from aligned reads (-v 2 -m 1) using BedTools and BigWig tools.
Genome_build: dm3
Supplementary_files_format_and_content: UCSC genome browser tracks (bigWig format) and tables showing RPKM normalized read counts, and raw read counts for 1kb gw.

source_name: adult fly ovaries gDNA (ChIP)

growth_protocol: Fly stocks were maintained at 24C on standard diet

extract_protocol:
Total RNA from ovary was isolated with Ribozol reagent, and rRNA was depleted with Ribo-Zero™ rRNA Removal Kit supplemented with Drosophila rRNA oligonucleotides according to the manufacturer's instruction. Ovaries were fixed using Paraformaldehyde (PFA) at a final concentration of 1% in PBS  for 10min at RT. Samples were quenched by 125mM glycine for 5 min at RT and washed 3 times in PBS. Ovaries were afterwards slightly dounced in Farnham Buffer (5mM HEPES pH8.0; 85mM KCl; 0.5% NP-40/Igepal; NaCl Protease Inhibitor Cocktail; NaF 10mM; Na3VO4 0.2mM) followed by strong douncing in RIPA Buffer (20mM Tris pH7.4; 150mM; 1% NP-40/Igepal; 0.5% Sodium Deoxycholate; 0.1% SDS; Protease Inhibitor Cocktail; NaF 10mM; Na3VO4 0.2mM). Lysates were sonicated using Bioruptor (Diagenode, 20 cycles of 30sec ON, 30sec OFF). Supernatants were pre-cleared for 2h at 4C using Dynabeads Protein G (Invitrogen) beads. 5% of samples were saved for inputs. The rest of the lysates were incubated with indicated antibodies pre-conjugated to protein G dynabeads (Invitrogen) for 2h to overnight at 4C. The beads were washed 5 times at 4C with LiCl IP wash buffer (10mM  Tris pH 7.4;  500mM  LiCL;  1%NP40/Igepal;  1%  Sodium  Deoxycholate) and once with TE. Protein was digested with proteinase K for 3hrs at 55C and reverse-crosslinked by incubation at 65C overnight. DNA was extracted by phenol:chloroform standard protocol.
RNA-seq libraries were made using the TruSeq RNA prep kit by Illumina (shW, shSv210-1, shSv210-2) or rthe NEBNext® Ultra™ Directional RNA Library Prep Kit. Libraries were sequenced on the Illumina HiSeq 2000 platform. ChIP-seq library construction was carried out using the NEBNext ChIP-Seq Library Prep Master Mix Set (E6240) with minor modifications. After adaptor ligation and PCR amplification, size selections were done on a 2% agarose gel to select the 200bp-400bp window size window. Libraries were sequenced on the Illumina HiSeq 2000 platform (SR 50bp).

treatment_protocol: Flies were fed with yeast for 2-3 days prior to dissection

value: adult fly ovaries

tag: chipantibody

value: C1A9, DSHB


title: MTgal4_shSv210_polII_repeat

status: Public on Dec 18 2019

type: SRA

country: USA

description: gDNA (ChIP)

library_source: genomic

molecule: genomic DNA

organism: Drosophila melanogaster

tag: tissue


title: MTgal4_shW_HP1_repeat

description: gDNA (ChIP)


title: MTgal4_shW_polII_repeat

description: gDNA (ChIP)


title: MTgal4_shSv210_H3K36_repeat

description: gDNA (ChIP)


title: MTgal4_shSv210_H3K4_repeat

description: gDNA (ChIP)


title: MTgal4_shW_H3K4_repeat

description: gDNA (ChIP)


title: MTgal4_shW_H3K36_repeat

description: gDNA (ChIP)


title: MTgal4_shSv210_H3K9_repeat

description: gDNA (ChIP)


title: MTgal4_shW_H3K9_repeat

description: gDNA (ChIP)


title: adult_day7_0

city: Oxford

first: Thomas

middle: J

last: Cahill

address: Sherrington Building, Sherrington Rd

department: Department of Physiology, Anatomy, & Genetics

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic

data_processing:
Reads were mapped to the mouse genome (Mm10) using TopHat15 v2.1.10, with Bowtie16 v.2.2.6
Cuffdiff used for pair-wise comparisons
DESeq2 was used to identify genes showing differential temporal regulation and STEM v.1.3.8 was used for temporal clustering
Genome_build: Mm10

molecule: total RNA

organism: Mus musculus

extract_protocol:
Single cell cardiac tissue suspensions were prepared by mincing hearts and gentle agitation in collagenase 500 units per ml in HBSS solution for 1 hour at 37degC. Samples were passed through a 70um filter, washed and resuspended in 2% FBS/PBS. Samples were incubated with FcR-block, and then labelled with anti-CD45 (Biolegend 103124, 1:200), anti-CD11b (Biolegend 101206, 1:100), anti-Ly6G (Biolegend 127636, 1:200), anti-F4/80 (Biolegend 123110, 1:100), anti-Ly6C (Biolegend 128026 1:800), anti-CD206 (Biolegend 141721, 1:100). Macrophages were identified as CD45+ CD11b+ Ly6G- F4/80+ cells
RNA extraction and DNAse treatment were carried out using the RNAqueous®-Micro Kit (Life Technologies, cat # AM1931). RNA integrity was checked with a RNA pico chip (Agilent Technologies, cat # 5067-1513) using the Agilent 2100 Bioanalyzer.
cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART-seqTMv4 ultra low input kit for RNA (Clontech laboratories, cat #’s 634888, 634889, 634890, 634891, 634892, 634893, and 634894). Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads (150 cycles) (Illumina, cat # FC-404-1002).

tag: strain

tag: development

value: Adult

tag: stage post injury

value: Day 7 post MI

value: Macrophages

value: FACS

tag: treatment

value: Myocardial infarction

tag: strand

value: reverse


title: adult_day7_2


title: adult_day7_1


title: P1_pre_0

value: Neonate P1

value: Baseline


title: adult_day4_2

value: Day 4 post MI


title: Cal-27 cells expreseses with empty vector

type: RNA

city: Taipei

first: Wei-Min

last: Chang

state: Not Applicable

address: 128 Academia Road, Section 2, Nankang,

country: Taiwan

institute: Academia Sinica

description: Gene expression data from CX-1 cells expressing control vector

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Homo sapiens

source_name: ATCC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cell were selected with antibiotics for two weeks.  Stably transduced cells were use for this experiment.

tag: genotype

value: Cal-27 cells expresses empty vector


title: adult_day4_0


title: HSC-2 cells expresses with shAKR1C1 vector

description: Gene expression data from CX-1 cells expressing RAB3C

source_name: JCRB

value: HSC-2 cells expresses shAKR1C1 vector


title: adult_day4_1


title: adult_day1_1

value: Day 1 post MI


title: HSC-2 cells expresses with shLuc control

value: HSC-2 cells expresses shLuc control vector


title: adult_day1_0


title: P1_day4_0


title: MTgal4_shW_input_repeat

description: gDNA

source_name: adult fly ovaries gDNA


title: Cal-27 cells expreseses with AKR1C1 vecotr

value: Cal-27 cells expresses AKR1C1 vector


title: MTgal4_shSv210_polII

description: gDNA (ChIP)


title: MTgal4_shW_polII

description: gDNA (ChIP)


title: MTgal4_shSv210_HP1

description: gDNA (ChIP)


title: MTgal4_shSv210_input_repeat

description: gDNA


title: MTgal4_shW_HP1

description: gDNA (ChIP)


title: adult_pre_2

source_name: BL D


title: adult_pre_0

source_name: BL A


title: MTgal4_shSv210_H3K36

description: gDNA (ChIP)


title: ROSA26-Input

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina bcl2fastq v2 software was used for basecalling.
Reads were aligned to the mouse genome (GRCm38.78) using bwa mem.
Duplicate reads and reads mapping to blacklist regions or the mitochondria were removed.
Peak-calling was performed using MACS2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: _peaks.narrowPeak: bed files of macs2 peaks.

source_name: MLL-AF9 I-BET resistant cells

growth_protocol: Cell lines were grown in RPMI-1640 supplemented with mouse IL-3 (10ng/ml), 20% FCS, streptomycin (100ug/ml), penicillin (100 units/ml) and glutamax (2nM), under standard culture conditions (5% CO2, 37°C). MLL-AF9 I-BET resistant cells were cultured with constant I-BET treatment (1000nM, 0.1% DMSO).

extract_protocol:
Lysate was isolated from formaldehyde cross-linked cells and sonicated to release the chromatin, then immunoprecipitated with antibody.
ThruPLEXTM-FD Prep Kit protocol (Rubicon Genomics).

treatment_protocol: Cell lines were removed from IBET and transduced with sgRNA targeting HBO1/ROSA26. Following 24 hours of transduction, sgRNA positive cells were selected with puromycin (5ug/ml) for a further 72 hours.

tag: strain/background

tag: cell type

value: haematopoietic progenitors

tag: condition

value: I-BET Resistant

tag: chip antibody


title: e12-2-H3K14Ac

value: Acetyl-Histone H3(K14) (D4B9, Cell Signalling Technologies, ref 10/2017)


title: e11-1-RNAPII

value: anti-RNA polymerase II (CTD4H8, Millipore, lot 2810725)


title: ROSA26-RNAPII


title: e11-1-H3K14Ac


title: ROSA26-H3K14Ac


title: e12-2-RNAPII


title: MTgal4_shW_H3K36

description: gDNA (ChIP)

value: adult fly ovaries


title: MTgal4_shW_H3K4

description: gDNA (ChIP)


title: MTgal4_shSv210_H3K9

description: gDNA (ChIP)


title: MTgal4_shSv210_input

description: gDNA


title: MTgal4_shSv210-2_RNAseq

description: total RNA

source_name: adult fly ovaries total RNA


title: MTgal4_shW_input

description: gDNA


title: MTgal4_shW_H3K9

description: gDNA (ChIP)


title: MTgal4_shSv210_H3K4

description: gDNA (ChIP)


title: MTgal4_shSv210-1_RNAseq

description: total RNA


title: e11_1_rep_3

description:
e11.1_3
PolyA RNA
processed data file: CPManno.txt

data_processing:
Illumina bcl2fastq v2 software was used for basecalling.
Reads were aligned to the mouse genome (GRCm38.78) using HISAT2.
Reads were assigned to genes using htseq-count. Differential expression was calculated using edgeR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: CPManno.txt: Tab-delimited text file includes CPM values for each Sample.

growth_protocol: Cell lines were grown in RPMI-1640 supplemented with mouse IL-3 (10ng/ml), 10% FCS, streptomycin (100ug/ml), penicillin (100 units/ml) and glutamax (2nM), under standard culture conditions (5% CO2, 37°C). MLL-AF9 I-BET resistant cells were cultured with constant I-BET treatment (1000nM, 0.1% DMSO).

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit.
Libraries were prepared using QuantSeq 3’ mRNA-seq Library Prep kit (Lexigen).


title: MTgal4_shW_RNAseq

description: total RNA


title: ROSA26_rep_3

description:
ROSA26_3
PolyA RNA
processed data file: CPManno.txt


title: e12_2_rep_2

description:
e12.2_2
PolyA RNA
processed data file: CPManno.txt


title: e11_1_rep_2

description:
e11.1_2
PolyA RNA
processed data file: CPManno.txt


title: ROSA26_rep_2

description:
ROSA26_2
PolyA RNA
processed data file: CPManno.txt


title: e12_2_rep_1

description:
e12.2_1
PolyA RNA
processed data file: CPManno.txt


title: e11_1_rep_1

description:
e11.1_1
PolyA RNA
processed data file: CPManno.txt


title: ROSA26_rep_1

description:
ROSA26_1
PolyA RNA
processed data file: CPManno.txt


title: Adjacent non-tumor colon tissue CAM165

type: genomic

city: Basel

first: Faiza

last: Noreen

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

description:
CAM165
Paired with tumor PT165.

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27k BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: Quantile Normalization.

label: Cy5 and Cy3

source_name: Adjacent non-tumor colorectal tissue CAM165

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions.

tag: gender

value: female

value: adjacent non-tumor colorectal tissue

tag: colonic location

value: proximal


title: YAPTAZ KO2

city: Irvine

first: Hosung

last: Bae

address: 839 Health Sciences Road Sprague Hall, Room 150

institute: UC Irvine

description:
CCL19YT-KO2
We generated Yap/Taz∆FRC mouse by crossing the FRC-specific CCL19-Cre mouse and the double Yap (flox/flox) / Taz (flox/flox) mouse

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: YAPTAZ KO_FACS-sorted FRCs

growth_protocol: To explore roles of Yap in FRCs, we generated Yap/Taz∆FRC mouse by crossing the FRC-specific CCL19-Cre mouse and the double Yap(flox/flox) Taz(flox/flox) mouse. To determine role of Yap/Taz activation in FRCs, we generated Lats1/2i∆FRC-Pβ mouse by crossing the PDGFRβ-Cre-ERT2 mouse with Lats1 (flox/flox) Lats2 (flox/flox) mouse.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol:
All mice used were 7-week-old male C57BL/6 mice. For Lats1/2i∆FRC-Pβ mouse, 6-week-old male mice were injected with tamoxifen (2mg, four consecutive injections, i.p ) to induce cre recombination.
Skin-draining lymph nodes (inguinal, axillary and brachial) were isolated from C57BL/6 mice (n = 3-6), then were digested, enriched for CD45− stroma and sorted for CD45-/TER119-/CD31-/PDPN+ FRCs

tag: strain background

tag: genotype/variation

value: Yap/Taz deletion

value: skin-draining lymph nodes (inguinal, axillary and brachial)

value: Fibroblastic reticular cells (FRCs)


title: YAPTAZ KO3

description:
CCL19YT-KO3
We generated Yap/Taz∆FRC mouse by crossing the FRC-specific CCL19-Cre mouse and the double Yap (flox/flox) / Taz (flox/flox) mouse


title: Adjacent non-tumor colon tissue CAM64

description:
CAM64
Paired with tumor PT64.

source_name: Adjacent non-tumor colorectal tissue CAM64


title: YAPTAZ KO1

description:
CCL19YT-KO1
We generated Yap/Taz∆FRC mouse by crossing the FRC-specific CCL19-Cre mouse and the double Yap (flox/flox) / Taz (flox/flox) mouse


title: Adjacent non-tumor colon tissue CAM28

description:
CAM28
Paired with tumor PT28.

source_name: Adjacent non-tumor colorectal tissue CAM28


title: Adjacent non-tumor colon tissue CAM26

description:
CAM26
Paired with tumor PT26.

source_name: Adjacent non-tumor colorectal tissue CAM26


title: YAPTAZ WT4

description:
CCL19YT-WT4
We generated Yap/Taz∆FRC mouse by crossing the FRC-specific CCL19-Cre mouse and the double Yap (flox/flox) / Taz (flox/flox) mouse

source_name: YAPTAZ WT_FACS-sorted FRCs

value: wild type


title: Adjacent non-tumor colon tissue CAM41

description:
CAM41
Paired with tumor PT41.

source_name: Adjacent non-tumor colorectal tissue CAM41


title: Colon Adenocarcinoma PT165

description:
PT165
Paired with normal adjacent CAM165.

source_name: Colorectal adenocarcinoma PT165

value: colorectal adenocarcinoma


title: Adjacent non-tumor colon tissue CAM104

description:
CAM104
Paired with tumor PT104.

source_name: Adjacent non-tumor colorectal tissue CAM104


title: Adjacent non-tumor colon tissue CAM3

description:
CAM3
Paired with tumor PT3.

source_name: Adjacent non-tumor colorectal tissue CAM3


title: Adjacent non-tumor colon tissue CAM71

description:
CAM71
Paired with tumor PT71.

source_name: Adjacent non-tumor colorectal tissue CAM71


title: YAPTAZ WT2

description:
CCL19YT-WT2
We generated Yap/Taz∆FRC mouse by crossing the FRC-specific CCL19-Cre mouse and the double Yap (flox/flox) / Taz (flox/flox) mouse


title: Colon Adenocarcinoma PT104

description:
PT104
Paired with normal adjacent CAM104.

source_name: Colorectal adenocarcinoma PT104


title: BrafV637E_439967A03

hyb_protocol: NimbleGen Hybridization protocol

scan_protocol: Arrays were scanned on NimbleGen MS 200 Microarray Scanner

data_processing: NimbleScan was used to produce .ndf, .pos, and .pair files. Pair files were sacled using Tukey-bi-weight scaling using Ringo R package. Unique PROBE_ID with COUNT=1 from .pos file were used for further analysis.

source_name: DNA immunoprecipitated with monoclonal antibody against 5-methylcytidine

label_protocol: NimbleGen Dual-Color DNA Labeling Kits; untreated total DNA fraction was labeled with Cy3 and the methyled DNA fraction was labeled with Cy5.

value: BrafV637E+/- mice

value: small intestine

tag: type

value: hyperplastic (HP)

tag: Sex

tag: age

value: more than 55 weeks (>55w)

source_name: INPUT

value: none, input DNA


title: Colon Adenocarcinoma PT71

description:
PT71
Paired with normal adjacent CAM64.

source_name: Colorectal adenocarcinoma PT71

tag: tissue


title: YAPTAZ WT3

description:
CCL19YT-WT3
We generated Yap/Taz∆FRC mouse by crossing the FRC-specific CCL19-Cre mouse and the double Yap (flox/flox) / Taz (flox/flox) mouse


title: LATS1,2 KO3

description:
PBL1L2-KO3
We generated Lats1/2i∆FRC-Pβ mouse by crossing the PDGFRβ-Cre-ERT2 mouse with Lats1 (flox/flox) / Lats2 (flox/flox) mouse

source_name: LATS1,2 KO_FACS-sorted FRCs

value: Lats1,2 deletion


title: LATS1,2 KO2

description:
PBL1L2-KO2
We generated Lats1/2i∆FRC-Pβ mouse by crossing the PDGFRβ-Cre-ERT2 mouse with Lats1 (flox/flox) / Lats2 (flox/flox) mouse


title: Run2_shCTL_DMSO_3

city: Omaha

first: Holly

last: Feser Stessman

state: NE

address: 2500 California Plaza

department: Pharmacology & Neuroscience

institute: Creighton University

data_processing:
Fastq files processed as published in Trapnell, et al. (2012) Nat Protoc. ; 7(3): 562–578. PMID: 22383036. TopHat v2.1.0, Bowtie2 v2.2.6, Cufflinks v2.2.1.
Quality assesed by RSeQC (v.v3.0.1; tin.py)
Data visualization and mining were performed using cummeRbund for R (v3.5).
Genome_build: hg19 (ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz; downloaded 7 Sept 2018)
Supplementary_files_format_and_content: For each sample above, the following files have been included: raw file (*.fastq or *.fq.gz),differential expression analysis by run (*.tar.gz), and quality "TIN" scores (*.xls).

source_name: PANC-1 human pancreatic cancer cell line

growth_protocol: Cells were seeded into a 6-well plate at a density of 0.3 x 10^6 cells per well in 2 mL DMEM + 10% FBS and allowed to adhere overnight.

extract_protocol:
Cells were collected on ice, and RNA was extracted and purified using the RNeasy Plus Mini Kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 24 hours after seeding, cells were treated in 4 mL of medium and maintained at 37°C for the duration of the experiment.

tag: tissue origin

value: pancreas

tag: cell line

tag: passage

value: Scramble shRNA E64FC26 + Panobinostat


title: Colon Adenocarcinoma PT64

description:
PT64
Paired with normal adjacent CAM71.

source_name: Colorectal adenocarcinoma PT64


title: Run2_shCTL_DMSO_2

tag: treatment


title: LATS1,2 WT3

description:
PBL1L2-WT3
We generated Lats1/2i∆FRC-Pβ mouse by crossing the PDGFRβ-Cre-ERT2 mouse with Lats1 (flox/flox) / Lats2 (flox/flox) mouse

source_name: LATS1,2 WT_FACS-sorted FRCs


title: LATS1,2 WT2

description:
PBL1L2-WT2
We generated Lats1/2i∆FRC-Pβ mouse by crossing the PDGFRβ-Cre-ERT2 mouse with Lats1 (flox/flox) / Lats2 (flox/flox) mouse


title: Run2_shCTL_FC26_plus_Pano_3

value: Scramble shRNA DMSO


title: Run2_shCTL_DMSO_1


title: LATS1,2 WT4

description:
PBL1L2-WT4
We generated Lats1/2i∆FRC-Pβ mouse by crossing the PDGFRβ-Cre-ERT2 mouse with Lats1 (flox/flox) / Lats2 (flox/flox) mouse


title: Run2_shCTL_FC26_plus_Pano_2


title: Colon Adenocarcinoma PT28

description:
PT28
Paired with normal adjacent CAM28.

source_name: Colorectal adenocarcinoma PT28

value: female


title: LATS1,2 WT1

description:
PBL1L2-WT1
We generated Lats1/2i∆FRC-Pβ mouse by crossing the PDGFRβ-Cre-ERT2 mouse with Lats1 (flox/flox) / Lats2 (flox/flox) mouse


title: AsPC1_sgCont_rep3

city: Sendai

first: Mitsuyo

last: Matsumoto

address: 2-1 Seiryo-machi Aoba-ku

department: Biochemistry

country: Japan

institute: Tohoku university school of medicine

description:
RNAseq_all_counts_matrix_sgRNA.txt
RNAseq_AsPC1sgC.3

data_processing:
Alignment of reads to reference hg19 were performed using the RNASeqAnalysis plugin from the Ion torrent suite software. Files format of final downloaded data (raw data) from Ion Proton was BAM.
Read counts were performed using Htseq version 0.9.1 htseq-count (samtools view -F4 [raw_file(BAM)] | htseq-count -q -t exon -I gene_id - hg19.gtf).
Genome_build: hg19
Supplementary_files_format_and_content: txt (Matrix data containing read counts data of all sample)

growth_protocol: AsPC1 was cultured at 37°C in 5% CO2 in RPMI 1640 medium (Sigma Aldrich, MO, USA) with 20% fetal bovine serum (FBS, Sigma Aldrich), 0.1 mg/ml penicillin/streptomycin (P/S, GIBCO, NY, USA) and 10 mM HEPES (GIBCO).

extract_protocol:
The cells were harvested by centrifugation, and the total RNA was isolated using a RNeasy Plus Mini kit (QIAGEN) following the instruction manual. Five microgram of total RNA was treated using a GeneRead rRNA Depletion kit (Qiagen) for remove Ribosomal RNA (rRNA) and an RNeasy MiniElute kit (Qiagen) for cleanup. One hundred ng of rRNA-depleted RNA was incubated at 95 ºC for 10 min for fragmentation and was purified by Magnetic Beads Cleanup Module (Life Technologies).
The libraries were constructed using Ion Total RNA-seq kit for AB Libraly builer system (Thermo Fisher Scientific Inc.) and were barcoded with Ion Xpress RNA-seq BC primer ((Thermo Fisher Scientific Inc., 16 PCR cycles). Barcoded library fragment with the size range of 100-200 bp was selected with Agencourt AMPure XP beads (Beckman Coulter, Brea, CA). Templates were prepared using Ion PI Hi-Q Chef Kit (Thermo Fisher Scientific Inc.) on Ion Chef (Thermo Fisher Scientific Inc.). Sequencing was performed on an Ion Proton system by the P1 chip v3 (Thermo Fisher Scientific Inc.) using Hi-Q Sequensing kit (Thermo Fisher Scientific Inc.).

treatment_protocol: To knock-out BACH1 in AsPC-1, lentiviruses were prepared by using lentiCRISPR v2 (Addgene) with single guide RNAs (sgRNAs) targeting BACH1 (5' to 3':CCACTCAAGAATCGTAGGCCAGG ). The infected-AsPC-1 cells were selected by using medium supplemented with 10 μg/ml Puromycin (Sigma Aldrich).

value: Pancreatic ductal adenocarcinoma cell line AsPC-1

tag: genotype

value: control


title: Run2_shCTL_FC26_plus_Pano_1


title: Colon Adenocarcinoma PT26

description:
PT26
Paired with normal adjacent CAM26.

source_name: Colorectal adenocarcinoma PT26

value: proximal


title: BrafWT_4397902A01

value: wild type mice

value: wild type (WT)

value: male

value: monoclonal antibody against 5-methylcytidine


title: Run2_shATF3_FC26_plus_Pano_3

value: ATF3 shRNA E64FC65 + Panobinostat


title: AsPC1_sgCont_rep1

description:
RNAseq_all_counts_matrix_sgRNA.txt
RNAseq_AsPC1sgC.1


title: AsPC1_sgCont_rep2

description:
RNAseq_all_counts_matrix_sgRNA.txt
RNAseq_AsPC1sgC.2


title: Run2_shATF3_FC26_plus_Pano_2


title: BrafV637E_474571A03

value: BrafV637E+/- mice

value: small intestine

value: less than 13 weeks (<13w)


title: BrafV637E_439967A01

value: hyperplastic (HP)

value: more than 55 weeks (>55w)

value: none, input DNA


title: BrafV637E_474571A01


title: AsPC1_sgBACH1_rep3

description:
RNAseq_all_counts_matrix_sgRNA.txt
RNAseq_AsPC1sg2.3

value: BACH1 knock-out


title: adult_pre_1

source_name: BL B

tag: strain

tag: development

value: Adult

tag: stage post injury

value: Baseline

value: Macrophages

value: FACS

tag: strand

value: reverse


title: Run2_shATF3_DMSO_3

value: pancreas

value: ATF3 shRNA DMSO


title: AsPC1_sgBACH1_rep1

description:
RNAseq_all_counts_matrix_sgRNA.txt
RNAseq_AsPC1sg2.1

value: Pancreatic ductal adenocarcinoma cell line AsPC-1


title: BrafWT_439693A03

value: wild type mice

value: wild type (WT)

value: female

tag: chip antibody

value: monoclonal antibody against 5-methylcytidine


title: AsPC1_siCont_RNAseq_rep2

description:
RNAseq_count_all_matrix_siRNA.txt
Sample12

extract_protocol:
The cells were harvested by centrifugation, and the total RNA was isolated using a RNeasy Plus Mini kit (QIAGEN) following the instruction manual. Five microgram of total RNA was treated using a GeneRead rRNA Depletion kit (Qiagen) for remove Ribosomal RNA (rRNA) and an RNeasy MiniElute kit (Qiagen) for cleanup. One hundred ng of rRNA-depleted RNA was incubated at 95 ºC for 10 min for fragmentation and was purified by Magnetic Beads Cleanup Module (Life Technologies).
The libraries were constructed using Ion Total RNA-seq kit for AB Libraly builer system (Thermo Fisher Scientific Inc.) and were barcoded with Ion Xpress RNA-seq BC primer ((Thermo Fisher Scientific Inc., 16 PCR cycles). Barcoded library fragment with the size range of 100-200 bp was selected with Agencourt AMPure XP beads (Beckman Coulter, Brea, CA). Templates were prepared using Ion PI Hi-Q Chef Kit (Thermo Fisher Scientific Inc.) on Ion Chef (Thermo Fisher Scientific Inc.). Sequencing was performed on an Ion Proton system by the P1 chip v3 (Thermo Fisher Scientific Inc.) using Hi-Q Sequensing kit  (Thermo Fisher Scientific Inc.).

treatment_protocol: BACH1 specific siRNA (Stealth RNAiTMsiRNA Duplex Oligoribonucleotides, Invitrogen, CA, USA) was transfected using Lipofectamine RNAiMAX (Thermo Fisher Scientific Inc., MA, USA). 24 hours later, the cells were harvested for RNA isolation.

value: Pancreatic ductal adenocarcinoma cell line  AsPC-1

value: control


title: Run2_shATF3_DMSO_1


title: AsPC1_siCont_RNAseq_rep1

description:
RNAseq_count_all_matrix_siRNA.txt
Sample 11


title: Run2_shATF3_DMSO_2


title: Run1b_Pano_3

source_name: T98G human glioblastoma cancer cell line

value: glioblastoma

value: Panobinostat


title: LATS1,2 KO1

description:
PBL1L2-KO1
We generated Lats1/2i∆FRC-Pβ mouse by crossing the PDGFRβ-Cre-ERT2 mouse with Lats1 (flox/flox) / Lats2 (flox/flox) mouse

value: Lats1,2 deletion

value: skin-draining lymph nodes (inguinal, axillary and brachial)

tag: cell type

value: Fibroblastic reticular cells (FRCs)


title: Run1b_Pano_2


title: Run1b_Pano_1


title: Run1b_FC65_plus_Pano_3

value: E64FC65 + Panobinostat


title: AsPC1_siBACH1_RNAseq_rep3

description:
RNAseq_count_all_matrix_siRNA.txt
Sample 16

value: BACH1 knockdown


title: AsPC1_siBACH1_RNAseq_rep1

description:
RNAseq_count_all_matrix_siRNA.txt
Sample 14


title: Run1b_FC65_plus_Pano_1


title: Run2_shATF3_FC26_plus_Pano_1

value: ATF3 shRNA E64FC65 + Panobinostat


title: Run1b_FC65_3


title: Run1b_FC65_2


title: AsPC1_sgBACH1_rep2

description:
RNAseq_all_counts_matrix_sgRNA.txt
RNAseq_AsPC1sg2.2

value: BACH1 knock-out


title: AsPC1_siCont_RNAseq_rep3

description:
RNAseq_count_all_matrix_siRNA.txt
Sample 13


title: Tle4-/- mutant rep2

city: Shanghai

first: Guoping

last: Liu

address: 138 Yi Xue Yuan Road

country: China

institute: Fudan University

description:
Tle4-/- null mutant littermate
P0Cor5

data_processing:
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome (version:GRCm38.p4) using Hisat2 (version:2.0.4).
Stringtie (vetrsion: 1.3.0) was used to count the read numbers mapped to each gene, and standardrized the counts using TMM (Trimmed mean of M values)
edgeR was used to find the differential expression genes
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: P0 Cortex

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Cat#74106, QIAGEN) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cortex from P0 WT mice, and Tle4-/- mutant mice were dissected in ice-cold HBSS.These tissues were flash frozen in the nitrogen and then stored into -80 oC

value: a mixed genetic background of C57BL/6J, 129S6 and CD1

value: Cortex

tag: developmental stage

value: Postnatal day 0

value: Tle4-/- null


title: Tle4-/- mutant rep1

description:
Tle4-/- null mutant littermate
P0Cor4


title: Wild type rep3

description:
Wild type littermate
P0Cor3

value: Wild type


title: Run1b_FC65_1


title: Colon Adenocarcinoma PT41

description:
PT41
Paired with normal adjacent CAM41.

source_name: Colorectal adenocarcinoma PT41

tag: gender

value: female

value: colorectal adenocarcinoma

tag: colonic location

value: proximal


title: Wild type rep2

description:
Wild type littermate
P0Cor2


title: Run1b_DMSO_3

value: glioblastoma

value: DMSO


title: Run1b_DMSO_2


title: AsPC1_siBACH1_RNAseq_rep2

description:
RNAseq_count_all_matrix_siRNA.txt
Sample 15

value: Pancreatic ductal adenocarcinoma cell line  AsPC-1


title: Run1_Pano_3

value: pancreas

value: Panobinostat


title: Run1b_DMSO_1


title: Tle4-/- mutant rep3

description:
Tle4-/- null mutant littermate
P0Cor6


title: Run1b_FC65_plus_Pano_2

value: E64FC65 + Panobinostat


title: Run1_Pano_2


title: Run1_Pano_1


title: e12_2_rep_3

description:
e12.2_3
PolyA RNA
processed data file: CPManno.txt

source_name: MLL-AF9 I-BET resistant cells

tag: strain/background

value: haematopoietic progenitors

tag: condition

value: I-BET Resistant


title: Run1_FC65_plus_Pano_3


title: neonate_IFNL_3

city: Portland

first: Timothy

last: Nice

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Molecular Microbiology and Immunology

institute: Oregon Health & Science University

description:
JVW50featureCounts.exons.txt
RNA181119TN_JVW50-8_S26_L007_R1_001.fastq.gz

data_processing:
Reads were aligned to the mouse mm10 reference genome using STAR version 2.5.4b with default parameters.
Total read counts for annotated genes were determined using the featureCounts program.
Normalized abundance was determined using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: count matrix output from featureCounts program

source_name: IECs sorted from neonatal intestine

extract_protocol:
RNA was isolated from cells using the ZR Viral RNA Kit (Zymoresearch)
mRNA sequencing libraries were prepared using the TruSeq RNA Library Prep Kit (Illumina)

value: interferon lambda


title: neonate_PBS_4

description:
JVW50featureCounts.exons.txt
RNA181119TN_JVW50-10_S28_L007_R1_001.fastq.gz

value: PBS


title: neonate_IFNB_4

description:
JVW50featureCounts.exons.txt
RNA181119TN_JVW50-12_S30_L007_R1_001.fastq.gz

value: interferon beta


title: neonate_IFNB_3

description:
JVW50featureCounts.exons.txt
RNA181119TN_JVW50-9_S27_L007_R1_001.fastq.gz


title: neonate_PBS_3

description:
JVW50featureCounts.exons.txt
RNA181119TN_JVW50-7_S25_L007_R1_001.fastq.gz


title: neonate_IFNB_2

description:
JVW50featureCounts.exons.txt
RNA181119TN_JVW50-6_S24_L007_R1_001.fastq.gz


title: neonate_IFNL_4

description:
JVW50featureCounts.exons.txt
RNA181119TN_JVW50-11_S29_L007_R1_001.fastq.gz


title: Run1_FC65_plus_Pano_1


title: Run1_FC65_2


title: Run1_FC65_3


title: Wild type rep1

description:
Wild type littermate
P0Cor1

value: a mixed genetic background of C57BL/6J, 129S6 and CD1

tag: tissue

value: Cortex

value: Postnatal day 0


title: neonate_IFNL_1

description:
JVW50featureCounts.exons.txt
RNA181119TN_JVW50-2_S20_L007_R1_001.fastq.gz


title: neonate_IFNB_1

description:
JVW50featureCounts.exons.txt
RNA181119TN_JVW50-3_S21_L007_R1_001.fastq.gz


title: organoid_PBS_3

description:
TN170featureCounts.exons.txt
RNA160817TN_TN170-30_S32_L006_R1_001.fastq.gz

source_name: IEC organoid


title: Run1_DMSO_3

tag: tissue origin


title: Run1_DMSO_2

tag: cell line


title: neonate_PBS_1

description:
JVW50featureCounts.exons.txt
RNA181119TN_JVW50-1_S19_L007_R1_001.fastq.gz


title: Run1_FC65_1

tag: passage


title: Run1_DMSO_1

tag: treatment


title: organoid_IFNL_3

description:
TN170featureCounts.exons.txt
RNA160817TN_TN170-29_S31_L006_R1_001.fastq.gz


title: SW1990_INPUT

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using bwa version 0.7.10
bwa data (bam) were merged for each experiment
peaks were called using MACS2 version 2.1.0 with " macs2 callpeak -t  -c  -f BAM -g hs --SPMR -q 0.01 --keep-dup auto --nomodel --extsize (AsPC-1: 171, SW1990: 175, fragment size was calculated by "macs2 predictd") --bdg "
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using bam2bigwig.sh from BAM files

growth_protocol: SW1990 were cultured at 37°C in 5% CO2 in RPMI 1640 medium (Sigma Aldrich, MO, USA) with 10% fetal bovine serum (FBS, Sigma Aldrich), 0.1 mg/ml penicillin/streptomycin (P/S, GIBCO, NY, USA) and 10 mM HEPES (GIBCO). AsPC-1 was cultured at 37°C in 5% CO2 in RPMI1640 with 20% FBS, 0.1 mg/ml P/S and 10 mM HEPES.

extract_protocol:
Cells were fixed 1% formaldehyde, followed by quenching with 125mM of glycine. The cells were washed with ice-cold PBS and were lysed. The crosslinked chromatin was shared with a Bioruptor Sonicator (CosmoBio) and target protein-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared from ~10 ng of ChIP DNA with the use of Ovation Ultralow DR Multiplex System (Nugen). The DNA libraries were clonally amplified on a flow cell and sequenced on HiSeq2500 (HiSeq Control Software v2.2.38, Illumina) with 51-mer paired-end sequence. Image analysis and base calling were performed using Real-Time Analysis Software (v1.18.61, Illumina).

treatment_protocol: no treatment

value: Pancreatic ductal adenocarcinoma cell line SW1990


title: Run1_FC65_plus_Pano_2


title: organoid_IFNL_2

description:
TN170featureCounts.exons.txt
RNA160817TN_TN170-23_S28_L006_R1_001.fastq.gz


title: organoid_IFNB_2

description:
TN170featureCounts.exons.txt
RNA160817TN_TN170-22_S27_L006_R1_001.fastq.gz


title: organoid_IFNB_3

description:
TN170featureCounts.exons.txt
RNA160817TN_TN170-28_S30_L006_R1_001.fastq.gz


title: organoid_PBS_2

description:
TN170featureCounts.exons.txt
RNA160817TN_TN170-24_S29_L006_R1_001.fastq.gz


title: neonate_IFNL_2

description:
JVW50featureCounts.exons.txt
RNA181119TN_JVW50-5_S23_L007_R1_001.fastq.gz


title: neonate_PBS_2

description:
JVW50featureCounts.exons.txt
RNA181119TN_JVW50-4_S22_L007_R1_001.fastq.gz


title: AsPC1_BACH1_ChIPseq

value: Bach1 (House made (A1-6))


title: organoid_IFNL_1

description:
TN170featureCounts.exons.txt
RNA160817TN_TN170-17_S25_L006_R1_001.fastq.gz


title: organoid_IFNB_1

description:
TN170featureCounts.exons.txt
RNA160817TN_TN170-16_S24_L006_R1_001.fastq.gz


title: HCASMC H3K27ac ChIPseq_reanalyzed

city: Stanford

last: Quertermous

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

description:
IP DNA
H3K27ac_peak.bed
H3K27ac.bw
GSM1876036

data_processing:
ChIP was performed with approximately 4e6 HCAMSC cells using SRF antibody (sc-335). Two biological replicates GAII for 36bp paired-end sequencing. Quality control of ChIPseq data was performed using Fastqc, and then low-quality bases and adaptor contamination were trimmed by cutadapt. Filtered reads were mapped to hg19 using BWA mem algorithm. Duplicate reads were marked by Picard Markduplicate module and removed with unmapped reads by samtools view -f 2 -F 1804. macs2 callpeak was used for peaks calling with --broad parameters and input as control. The fastq files of TCF21 (SRR1573744&SRR1573745), H3K27ac ChIPseq (GSE72696) and ATACseq (GSE72696) were extracted from GEO database by fastq-dump. These samples have been included here so that the entire study can be downloaded from a single SRP.
Genome_build: hg19
Supplementary_files_format_and_content: bed with called peaks and bw

source_name: Cultured coronary artery smooth muscle cells

growth_protocol: Primary human coronary artery smooth muscle cells (HCASMCs) were purchased from Lonza (Lonza 0000317155) at passage 2 and were cultured in smooth muscle cell basal media along with hEGF, insulin, hFGF-B and fetal bovine serum (FBS) (Lonza # CC-3182) according to the manufacturer’s instructions. HCASMCs between passages 5-8 were used for all the experiments.

extract_protocol:
Briefly, approximately 4e6 HCASMC cells were fixed with 1 % formaldehyde and quenched by glycine. The cells were washed three times with PBS and then harvested in ChIP lysis buffer (50 mM Tris-HCl, pH 8, 5 mM EDTA, 0.5 % SDS). Crosslinked chromatin was sheared for 3x1 min by sonication (Branson SFX250 Sonifier) before extensive centrifugation. Four volumes of ChIP dilution buffer (20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 2 mM EDTA, 1 % Triton X-100) was added to the supernatant. The resulting lysate was then incubated with Dynabeads™ Protein G (Thermo Scientific, 10009D) and antibodies at 4°C overnight. Beads were washed once with buffer 1 (20 mM Tris pH 8, 2 mM EDTA, 150 mM NaCl, 1% Triton X100, 0.1% SDS), once with buffer 2 (10 mM Tris pH 8, 1 mM EDTA, 500 mM NaCl, 1% Triton X100, 0.1% SDS), once with buffer 3 (10 mM Tris pH 8, 1 mM EDTA, 250 mM LiCl, 1% NP40, 1% sodium deoxycholate monohydrate) and twice with TE buffer. DNA was eluted by ChIP elution buffer (0.1 M NaHCO3, 1 % SDS, 20 μg/ml proteinase K). The elution was incubated at 65 °C over-night and DNA was extracted with DNA purification kit (Zymo D4013). The purified DNA was assayed by quantitative PCR with ABI ViiA 7 and Power SYBR Green Master Mix (ABI 4368706).
Two biological replicates DNA was combined for library preparation. Libraries were prepared with KAPA Hyper Prep kit (KK8502).

value: Cultured HCASMC

tag: growth medium

value: Grown in serum

value: H3K27ac (Abcam ab4729)


title: organoid_PBS_1

description:
TN170featureCounts.exons.txt
RNA160817TN_TN170-18_TN170-21_S26_L006_R1_001.fastq.gz

tag: strain


title: IBET.D14.R2

description:
Pooled shRNA screen
processed data file: Pool1RawCounts.csv

data_processing:
Illumina bcl2fastq v2 software was used for basecalling.
Reads were demultiplexed using a custom in-house script.
Reads were aligned and analysed using edgeR from Bioconductor in R.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Pool1RawCounts.csv: Comma-separated text file of raw counts.
Supplementary_files_format_and_content: Pool1revcompbarcodes.txt: Tab-delimited text file containing the barcodes for each sample in the pool.
Supplementary_files_format_and_content: Pool1revcompshRNA.txt: Tab-delimited text file containing the sequences of each shRNA hairpin in the pool.

extract_protocol:
Genomic DNA was isolated with DNeasy Blood & Tissue Kit (Qiagen).
shRNA sequences were amplified by PCR with primers.

treatment_protocol: 4x10^6 cells were transduced with shRNA pool at multiplicity of infection of 0.3. Following 30 hours of transduction, hairpin positive cells were selected with puromycin.

value: I-BET resistant


title: LNCaP_ERN1_KO_2

city: Nijmegen

first: Suzan

last: Stelloo

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

data_processing:
Sequences were generated by the Illumina Hiseq 2500 genome analyzer (using 65bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA version 0.5.9. Reads with a BWA alignment quality score less than 20 were removed.
Peaks were called using DFilter (Kumar V et al. Nat Biotechnol 2013;31(7):615-22) and MACS peak caller version 1.4 (Zhang Y et al. Genome Biol 2008;9(9):R137). Only peaks called by both algorithms were used for the analysis. MACS was run with the default parameters, except p=10-5. DFilter was run with bs=50, ks=30, refine, nonzero.
Genome_build: hg19
Supplementary_files_format_and_content: Peaks called by both peak callers

source_name: LNCaP ERN1 Knockout

growth_protocol: LNCaP cells were cultured in RPMI-1640 supplemented with 10% FBS. Cells were hormone deprived three days before stimulation.

extract_protocol:
Chromatin immunoprecipitations (ChIP) were performed as described (Stelloo et al. Oncogene 2018) For each ChIP, 7.5μg of XBP1s antibody or 5μg of RNA polII Ser2 antibody prebound to protein A beads were used.  In brief, Nuclear lysates were incubated with 5ug of RNA polymerase Serine 2 phosphorylation antibody (Abcam, ab5095) and 50ul protein A beads. Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Kapa Biosystems kit,KK8234).

treatment_protocol: Cells were treated with vehicle, 10nM R1881 for 24 hours or 10nM Thapsigargin (Tg) for 3 hours.

value: LNCaP prostate cancer cells

tag: genotype

value: ERN1 Knockout

value: Tg

value: XBP1s (Biolegend, 619502)


title: IBET.D14.R1

value: haematopoietic progenitors


title: LNCaP_px330_2

source_name: LNCaP wildtype

value: wildtype


title: LNCaP_ERN1_KO_1


title: XBP1s_Tg_2


title: IBET.D10.R2


title: LNCaP_px330_1


title: IBET.D10.R1


title: IBET.D8.R1


title: XBP1s_Tg_1


title: AsPC1_INPUT

value: Pancreatic ductal adenocarcinoma cell line  AsPC-1


title: SW1990_BACH1_ChIPseq


title: XBP1s_veh_3

value: veh


title: IBET.D4.R2


title: XBP1s_veh_2


title: IBET.D2.R2


title: IBET.D4.R1


title: XBP1s_R1881_1


title: IBET.D2.R1


title: DMSO.D14.R2

source_name: MLL-AF9 I-BET sensitive cells

value: I-BET sensitive


title: XBP1s_veh_1


title: DMSO.D14.R1


title: MTgal4_shSmt3_H3K9_IP_2

description: gDNA (ChIP)

source_name: adult fly ovaries gDNA (ChIP)

value: adult fly ovaries

tag: chipantibody


title: HCASMC ATACseq_reanalyzed

description:
ATAC_peaks.bed
ATAC_NC1.bw
GSM1876021


title: DMSO.D10.R2


title: MTgal4_shSmt3_H3K9_Input_2

description: gDNA

source_name: adult fly ovaries gDNA


title: IBET.D8.R2


title: XBP1s_veh_4


title: MTgal4_shW_H3K9_Input_2(MTgal4_shSUMO ctrl)

description: gDNA


title: DMSO.D10.R1


title: MTgal4_shSmt3_H3K9_Input_1

description: gDNA


title: MTgal4_shSmt3_H3K9_IP_1

description: gDNA (ChIP)


title: DMSO.D8.R1


title: DMSO.D8.R2


title: DMSO.D4.R1


title: MTgal4_shW_H3K9_Input_1(MTgal4_shSUMO ctrl)

description: gDNA


title: DMSO.D4.R2


title: MTgal4_shW_H3K9_IP_1(MTgal4_shSUMO ctrl)

description: gDNA (ChIP)


title: XBP1s_R1881_2


title: DMSO.D2.R1


title: MTgal4_shSmt3_RNAseq_2

description: total RNA

source_name: adult fly ovaries total RNA


title: MTgal4_shW_RNAseq_2(MTgal4_shSUMO ctrl)

description: total RNA


title: MTgal4_shSmt3_RNAseq_1

description: total RNA


title: Sample_Flexors_Mouse_3

city: New York

first: Christopher

middle: L

last: Mendias

state: NY

address: 535 E 70th St

institute: Hospital for Special Surgery

description:
Mouse tendons edgeR.txt
Mouse tendons counts.txt

data_processing:
Quality assessment and fold change calculations were performed in edgeR
Sequencing data was quality checked using FastQC, aligned to the reference genome (mm10) with the HiSAT2 software package
Differential expression based on counts per million mapped reads was performed using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: edgeR

source_name: Forepaw flexor tendon

extract_protocol:
RNA was purified with a miRNeasy Micro Kit (Qiagen) supplemented with DNase I (Qiagen). RNA concentration was determined using a NanoDrop 2000 (Thermo Fisher). RNA was delivered to Weill Cornell Epigenomics Core Facility for RNA sequencing analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Forepaw flexor tendon


title: MTgal4_shW_RNAseq_1(MTgal4_shSUMO ctrl)

description: total RNA

data_processing:
RNA-seq reads aligning to rRNA were removed by mapping to Drosophila rRNA sequences using bowtie allowing 3 mismatches
Reads were mapped to the Drosophila genome allowing 2 mismatches and 1 mapping position or 0 mismatches and 10000 mapping positions for TE analysis
UCSC genome browser tracks were were generated from aligned reads (-v 2 -m 1) using BedTools and BigWig tools.
Genome_build: dm3
Supplementary_files_format_and_content: UCSC genome browser tracks (bigWig format) and tables showing RPKM normalized read counts, and raw read counts for 1kb gw.

extract_protocol:
Total RNA from ovary was isolated with Ribozol reagent, and rRNA was depleted with Ribo-Zero™ rRNA Removal Kit supplemented with Drosophila rRNA oligonucleotides according to the manufacturer's instruction. Ovaries were fixed using Paraformaldehyde (PFA) at a final concentration of 1% in PBS  for 10min at RT. Samples were quenched by 125mM glycine for 5 min at RT and washed 3 times in PBS. Ovaries were afterwards slightly dounced in Farnham Buffer (5mM HEPES pH8.0; 85mM KCl; 0.5% NP-40/Igepal; NaCl Protease Inhibitor Cocktail; NaF 10mM; Na3VO4 0.2mM) followed by strong douncing in RIPA Buffer (20mM Tris pH7.4; 150mM; 1% NP-40/Igepal; 0.5% Sodium Deoxycholate; 0.1% SDS; Protease Inhibitor Cocktail; NaF 10mM; Na3VO4 0.2mM). Lysates were sonicated using Bioruptor (Diagenode, 20 cycles of 30sec ON, 30sec OFF). Supernatants were pre-cleared for 2h at 4C using Dynabeads Protein G (Invitrogen) beads. 5% of samples were saved for inputs. The rest of the lysates were incubated with indicated antibodies pre-conjugated to protein G dynabeads (Invitrogen) for 2h to overnight at 4C. The beads were washed 5 times at 4C with LiCl IP wash buffer (10mM  Tris pH 7.4;  500mM  LiCL;  1%NP40/Igepal;  1%  Sodium  Deoxycholate) and once with TE. Protein was digested with proteinase K for 3hrs at 55C and reverse-crosslinked by incubation at 65C overnight. DNA was extracted by phenol:chloroform standard protocol.
RNA-seq libraries were made using the TruSeq RNA prep kit by Illumina (shW, shSv210-1, shSv210-2) or rthe NEBNext® Ultra™ Directional RNA Library Prep Kit. Libraries were sequenced on the Illumina HiSeq 2000 platform. ChIP-seq library construction was carried out using the NEBNext ChIP-Seq Library Prep Master Mix Set (E6240) with minor modifications. After adaptor ligation and PCR amplification, size selections were done on a 2% agarose gel to select the 200bp-400bp window size window. Libraries were sequenced on the Illumina HiSeq 2000 platform (SR 50bp).


title: Sample_Flexors_Mouse_2


title: MTgal4_shW_H3K9_IP_2(MTgal4_shSUMO ctrl)

description: gDNA (ChIP)


title: MTgal4_shSv210-2_RNA-seq2-2

description: total RNA


title: Sample_Achilles_Mouse_4

source_name: Achilles tendon

value: Achilles tendon


title: Sample_Achilles_Mouse_3


title: MTgal4_shW_RNA-seq2-1

description: total RNA


title: MTgal4_shW_RNA-seq2-2

description: total RNA


title: Sample_Achilles_Mouse_1


title: Sample_Supra_Mouse_4

source_name: Supraspinatus tendon

value: Supraspinatus tendon


title: Sample_Supra_Mouse_3


title: YAPTAZ WT1

description:
CCL19YT-WT1
We generated Yap/Taz∆FRC mouse by crossing the FRC-specific CCL19-Cre mouse and the double Yap (flox/flox) / Taz (flox/flox) mouse

source_name: YAPTAZ WT_FACS-sorted FRCs

tag: strain background

tag: genotype/variation

value: wild type

value: skin-draining lymph nodes (inguinal, axillary and brachial)

value: Fibroblastic reticular cells (FRCs)


title: Sample_Flexors_Mouse_4


title: obese_diabetic_3

city: Odense

first: Jan

middle: Wilhelm

last: Kornfeld

address: Campusbej 50

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: SupplementaryData5_RNA-Seq[HS_T2D--OBESE--LEAN]_masked.xlsx

data_processing:
alignment of reads to the genome using Tophat2 (2.0.10)
transcript assembly using Cufflinks (2.1.1)
Differential expression analysis using DESeq2 (1.10.1)
upload to QuickNGS
annotation using the biomaRt package (2.16.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: xlsx spreadsheet containing results of the gene-level differential expression testing comparing the obese diabetic and the obese non-diabetic group with the lean group. Includes amongst others ENSEMBL gene id, biotype, GO anotation, fold change,.

source_name: liver

extract_protocol:
All samples were taken in the fasted state and frozen immediately in liquid nitrogen before storage at -80 °C. Total RNA was isolated using peqGOLD TriFast (PEQLAB Biotechnologie).
Following initial quality checks, 1ug of total RNA of each sample was depleted for cytoplasmic and mitochondrial rRNA with Ribo-Zero Gold and strand-specific library preparation was performed using TruSeq RNA Gold Kit from Illumina. All libraries were sequenced in parallel on a HiSeq 4000 for 2 x 76 PE sequencing.

value: liver

value: obese diabetic


title: Sample_Supra_Mouse_2


title: Sample_Supra_Mouse_1


title: obese_diabetic_2


title: obese_nonDiabetic_4

value: obese non-diabetic


title: obese_diabetic_1


title: obese_nonDiabetic_1


title: obese_nonDiabetic_2


title: Sample_Flexors_Mouse_1


title: obese_nonDiabetic_3


title: lean_4

value: lean non-diabetic


title: Sample_Patellar_Mouse_2

source_name: Patellar tendon

value: Patellar tendon


title: MTgal4_shSv210-2_RNA-seq2-1

description: total RNA


title: Sample_Patellar_Mouse_3


title: Sample_Patellar_Mouse_4


title: obese_diabetic_4


title: Sample_Achilles_Mouse_2


title: lean_3


title: Sample_Patellar_Mouse_1


title: MethylC_E85_head_Kmt2b_KO_5mC_rep2

city: Beijing

first: Wei

last: Xie

address: Haidian District

department: School of Life Science

institute: Tsinghua University

description: processed data file: MethylC_E85_head_Kmt2b_KO_mCG.bed.gz

data_processing:
Library strategy: TELP
STEM-seq datasets were trimmed adaptors by Trim galore and then aligned to the mm9 reference genome though BSSeeker2 with the parameters: --bt2-p 8 --XS 0.2,3 --a CCCCCC --m 4. Multiple mapped and duplicated reads were also removed.
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files for STAR ChIP-seq contains the RPKM value in 100bp bin across the mm9 genome. For STEM-seq, the bed files contains reads count for each CpG site. The txt file of RNA-seq contains quantile normalized FPKM for each sample and the .hic files generated by Juicer v0.7.5 contain validpairs.

source_name: embryo

growth_protocol: To obtain E8.5 brain tissue, embryos were firstly collected and removed amniotic membrane in PBS buffer, and then directly made a cut near their neck region. The head part was collected as brain tissues.

extract_protocol:
The DNA extraction follows STEM-seq protocol.
The STEM-seq libraries were generated following the protocol as described previously(Zhang et al., 2018).

value: head


title: MethylC_E85_head_Kmt2b_KO_5mC_rep1


title: lean_2


title: MethylC_E85_head_Kmt2b_WT_5mC_rep1

description: processed data file: MethylC_E85_head_Kmt2b_WT_mCG.bed.gz

value: WT


title: MethylC_E65Epi_Kmt2b_KO_5mC_rep3

description: processed data file: MethylC_E65Epi_Kmt2b_KO_mCG.bed.gz

data_processing:
STAR ChIP-seq datasets were mapped to the mouse mm9 reference genome using Bowtie2 (version 2.2.2) with the parameter:–t –q –N 1 –L 25. Multiple mapped reads and PCR duplicates were removed. After validating the reproducibility, replicates were pooled for downstream analysis.
RNA-seq datasets were mapped to the mouse mm9 reference genome by Tophat 2.0.11. Gene expression was then calculated according to refFlat database by cufflinks 2.0.2.
STEM-seq datasets were trimmed adaptors by Trim galore and then aligned to the mm9 reference genome though BSSeeker2 with the parameters: --bt2-p 8 --XS 0.2,3 --a CCCCCC --m 4. Multiple mapped and duplicated reads were also removed.
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files for STAR ChIP-seq contains the RPKM value in 100bp bin across the mm9 genome. For STEM-seq, the bed files contains reads count for each CpG site. The txt file of RNA-seq contains quantile normalized FPKM for each sample.

growth_protocol: Tissues of post-implantation embryos were collected as described previously (Zhang, et al., 2018).

value: epiblast


title: MethylC_E65Epi_Kmt2b_KO_5mC_rep2


title: MethylC_E65Epi_Kmt2b_KO_5mC_rep1


title: TGFb and JQ1 treated at 72 hrs Replicate 2

city: Cambridge

first: Ju

last: Wang

state: MA

address: 610 Main Street

department: Inflammation & Immunology

institute: Pfizer Inc

data_processing:
40 M 2x150 paired end reads were generated from an Illumina HiSeq 4000 Platform
Following raw reads were filtered: reads containing adaptors, reads containing N>10% (N represents the base connot be determined); reads containing low quality (Qscore<=5) bases which is over 50% of the total reads.
QuickRNASeq pipeline was used in reads mapping and counting: STAR 2.5.2.a was used for mapping; featureCounts subread-1.5.1 was used for counting; RSeQC was used for read QC; VarScan.v2.4.0 was used for SNP calling.
Genome_build: Genome fasta file is GRCh38.primary.genome.fa. Gene annotation file is GRCh38.gencode v25 annotation file. Gtf file is GRCh38.gencode.v25.gtf;  Bed file is GRCh38.gencode.v25.bed
Supplementary_files_format_and_content: Processed data is a tab delimited text file contains gene name as row, and the fpkm for that gene from each sample is the column.

source_name: primary hepatic stellate cells

growth_protocol: Primary hepatic stellate cells (passage number < 3) were cultured with Stellate cell media (Sciencell, Carlsbad, CA) at 37 deg Celsius with 5% CO2.

extract_protocol:
RNA extraction was performed with QIAzol (custom method using Qiagen cat# 79306). The yield and quality of the isolated RNA was assessed using Qubit Fluorometer Qubit 2.0 fluorometer (Thermo Fisher Scientific?Waltham, MA, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), respectively.
1 ug of RNA was used for cDNA library construction using an NEBNext® Ultra Directional RNA Library Prep Kit for Illumina® (cat# E7420S, New England Biolabs, Ipswich, MA, USA) according to the manufacturer's protocol. The resulting 250-350 bp insert libraries were quantified using a Qubit 2.0 fluorometer (Thermo Fisher Scientific?Waltham, MA, USA) and quantitative PCR. Size distribution was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Qualified libraries were sequenced on an Illumina HiSeq 4000 Platform (Illumina, San Diego, CA , USA) using a paired-end 150 run (2×150 bases). 40 M clean reads were generated from each library.

treatment_protocol: Cells were treated with recombinant human TGF-b1, recombinant human TGFb-1 and JQ1 or 0.1% DMSO (control for untreated). Cells were washed with PBS and lysed usingRLT-Plus buffer (Qiagen, Hilden, Germany) with 1% 2-mercaptoethanol (Sigma-Aldrich, St. Louis, MO) at given time points. Cell lysates were collected and snap frozen on dry ice and stored at -80 celcius until RNA extraction.

tag: cell type

value: primary hepatic stellate cells

value: recombinant human TGFb1 and JQ1

tag: time point (hr)


title: TGFb and JQ1 treated at 48 hrs Replicate 1


title: TGFb and JQ1 treated at 48 hrs Replicate 2


title: ChIP_Mes_H3K27ac_rep1

description: processed data file: Mes_H3K27ac.bed.gz

extract_protocol:
The DNA extraction follows STAR ChIP-seq protocol.
The STAR ChIP-seq libraries were generated following the protocol as described previously(Zhang et al., 2016).

value: mesoderm

tag: chip antibody

value: H3K27ac(Active Motif,Cat.39133)


title: TGFb and JQ1 treated at 48 hrs Replicate 3


title: TGFb and JQ1 treated at 24 hrs Replicate 3


title: DMSO.D2.R2

value: haematopoietic progenitors

value: I-BET sensitive


title: ChIP_PS_H3K27ac_rep1

description: processed data file: PS_H3K27ac.bed.gz

value: primitive streak


title: MethylC_E85_head_Kmt2b_WT_5mC_rep2


title: HiC_E65Epi_Kmt2b_KO_rep2_part3

description: processed data file: E65Epi_Kmt2b_KO_rep2.hic

data_processing:
Library strategy: sisHi-C
sisHi-C datasets were mapped, processed and iteratively corrected using HiC-Pro (v2.7.8), The validpair produced by HiC-Pro was used for .hic file generation with Juicer v0.7.5. Replicates were pooled for downstream analysis.
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files for STAR ChIP-seq contains the RPKM value in 100bp bin across the mm9 genome. For STEM-seq, the bed files contains reads count for each CpG site. The txt file of RNA-seq contains quantile normalized FPKM for each sample and the .hic files generated by Juicer v0.7.5 contain validpairs.

extract_protocol:
The DNA extraction follows sisHi-C protocol.
The sisHi-C libraries were generated following the protocol as described previously(Du et al., 2017).


title: ChIP_Ect_H3K27ac_rep1

description: processed data file: Ect_H3K27ac.bed.gz

value: ectoderm


title: HiC_E65Epi_Kmt2b_KO_rep2_part2


title: TGFb and JQ1 treated at 24 hrs Replicate 2


title: HiC_E65Epi_Kmt2b_WT_rep2

description: processed data file: E65Epi_Kmt2b_WT_rep2.hic


title: TGFb and JQ1 treated at 72 hrs Replicate 3


title: ChIP_End_H3K27me3_rep1

description: processed data file: End_H3K27me3.bed.gz

value: endoderm


title: ChIP_Mes_H3K27me3_rep2

description: processed data file: Mes_H3K27me3.bed.gz


title: HiC_E65Epi_Kmt2b_WT_rep5


title: HiC_E65Epi_Kmt2b_WT_rep3


title: HiC_E65Epi_Kmt2b_KO_rep3


title: HiC_E65Epi_Kmt2b_WT_rep4


title: TGFb and JQ1 treated at 72 hrs Replicate 1

value: liver


title: TGFb treated at 72 hrs Replicate 3

value: recombinant human TGFb1


title: HiC_E65Epi_Kmt2b_KO_rep2_part1


title: TGFb and JQ1 treated at 24 hrs Replicate 1


title: ChIP_Mes_H3K27me3_rep1


title: ChIP_E65Epi_Tet1/2_DKO_H3K4me3_rep2

description: processed data file: E65Epi_Tet1/2_DKO_H3K4me3.bed.gz

data_processing:
Library strategy: TELP
STAR ChIP-seq datasets were mapped to the mouse mm9 reference genome using Bowtie2 (version 2.2.2) with the parameter:–t –q –N 1 –L 25. Multiple mapped reads and PCR duplicates were removed. After validating the reproducibility, replicates were pooled for downstream analysis.
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files for STAR ChIP-seq contains the RPKM value in 100bp bin across the mm9 genome. For STEM-seq, the bed files contains reads count for each CpG site. The txt file of RNA-seq contains quantile normalized FPKM for each sample and the .hic files generated by Juicer v0.7.5 contain validpairs.

tag: chip-antibody

value: H3K4me3(home made)


title: ChIP_E85_head_Kmt2b_WT_H3K4me3_rep2

description: processed data file: E85_head_Kmt2b_WT_H3K4me3.bed.gz


title: Colon Adenocarcinoma PT3

description:
PT3
Paired with normal adjacent CAM3.

data_processing: Quantile Normalization.

source_name: Colorectal adenocarcinoma PT3

extract_protocol: Genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions.

tag: gender

value: female

value: colorectal adenocarcinoma

tag: colonic location

value: proximal


title: ChIP_PS_H3K27me3_rep2

description: processed data file: PS_H3K27me3.bed.gz

tag: tissue

value: WT


title: ChIP_E65Epi_H3

description: processed data file: E65Epi_H3.bed.gz

value: epiblast

value: H3(abcam, Cat.ab1791)


title: TGFb treated at 72 hrs Replicate 1

value: primary hepatic stellate cells


title: ChIP_PS_H3K27me3_rep1

description: processed data file: PS_H3K27me3.bed.gz


title: Sample_Flexors_Rat_4

description:
Rat tendons edgeR.txt
Rat tendons counts.txt

data_processing:
Quality assessment and fold change calculations were performed in edgeR
Sequencing data was quality checked using FastQC, aligned to the reference genome (rn6) with the HiSAT2 software package
Differential expression based on counts per million mapped reads was performed using edgeR
Genome_build: rn6
Supplementary_files_format_and_content: edgeR

organism: Rattus norvegicus

value: Sprague Dawley

value: Forepaw flexor tendon


title: RNA_E85_head_Tet1/2_DKO_rep2

description: processed data file: Tet12.RNA.FPKM.txt.gz

data_processing:
RNA-seq datasets were mapped to the mouse mm9 reference genome by Tophat 2.0.11. Gene expression was then calculated according to refFlat database by cufflinks 2.0.2.
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files for STAR ChIP-seq contains the RPKM value in 100bp bin across the mm9 genome. For STEM-seq, the bed files contains reads count for each CpG site. The txt file of RNA-seq contains quantile normalized FPKM for each sample and the .hic files generated by Juicer v0.7.5 contain validpairs.

extract_protocol:
The RNA extraction follows smart-seq2 protocol.
The RNA-seq libraries were generated following the Smart-seq2 protocol with minor modification (Picelli et al., 2014).

value: head


title: RNA_E85_head_Tet1/2_DKO_rep1


title: ChIP_Ect_H3K27me3_rep2

description: processed data file: Ect_H3K27me3.bed.gz


title: RNA_E85_head_Tet1/2_WT_rep2


title: Sample_Flexors_Rat_3


title: lean_1

tag: condition

value: lean non-diabetic


title: Sample_Flexors_Rat_2


title: TGFb treated at 48hrs Replicate 3


title: RNA_E85_head_Tet1/2_WT_rep1


title: TGFb treated at 48hrs Replicate 1


title: RNA_E65Epi_Tet1/2_DKO_rep2


title: Sample_Achilles_Rat_4

value: Achilles tendon


title: TGFb treated at 24 hrs Replicate 2


title: ChIP_Ect_H3K27me3_rep1

value: ectoderm


title: ChIP_E65VE_H3K27me3_rep2

description: processed data file: E65VE_H3K27me3.bed.gz

value: visceral endoderm


title: ChIP_E65VE_H3K27me3_rep1


title: Sample_Flexors_Rat_1


title: TGFb treated at 72 hrs Replicate 2

value: liver


title: Sample_Achilles_Rat_3


title: ChIP_E65Epi_H3K27me3_rep2

description: processed data file: E65Epi_H3K27me3.bed.gz


title: ChIP_E65VE_H3

description: processed data file: E65VE_H3.bed.gz


title: RNA_E65Epi_Tet1/2_DKO_rep1


title: Sample_Achilles_Rat_2


title: ChIP_E65Epi_H3K27me3_rep1


title: TGFb treated at 24 hrs Replicate 1

value: recombinant human TGFb1


title: RNA_E95_head_Kmt2b_KO

description: processed data file: Kmt2b.RNA.FPKM.txt.gz

growth_protocol: To obtain E9.5 brain tissue, embryos were firstly collected and removed amniotic membrane in PBS buffer, and then directly made a cut near their neck region. The head part was collected as brain tissues.


title: Sample_Achilles_Rat_1


title: RNA_E95_head_Kmt2b_WT_rep3


title: TGFb treated at 24 hrs Replicate 3


title: Untreated at 72hrs Replicate 3

value: untreated


title: TGFb treated at 48hrs Replicate 2


title: ChIP_End_H3K4me3_rep2

description: processed data file: End_H3K4me3.bed.gz

value: endoderm

value: H3K4me3(home made)


title: ChIP_End_H3K4me3_rep1

description: processed data file: End_H3K4me3.bed.gz


title: Sample_Supra_Rat_4

value: Supraspinatus tendon


title: Sample_Supra_Rat_3


title: Untreated at 72hrs Replicate 1


title: RNA_E95_head_Kmt2b_WT_rep2

value: WT


title: Sample_Supra_Rat_2


title: Untreated at 72hrs Replicate 2


title: RNA_E95_head_Kmt2b_WT_rep1


title: Untreated at 48hrs Replicate 2


title: Untreated at 48hrs Replicate 3


title: ChIP_PS_H3K4me3_rep2

description: processed data file: PS_H3K4me3.bed.gz

value: primitive streak


title: RNA_E85_head_Kmt2b_WT_rep3


title: Untreated at 48hrs Replicate 1


title: Sample_Supra_Rat_1


title: ChIP_Mes_H3K4me3_rep2

description: processed data file: Mes_H3K4me3.bed.gz

value: mesoderm


title: RNA_E85_head_Kmt2b_WT_rep2


title: ChIP_PS_H3K4me3_rep1

description: processed data file: PS_H3K4me3.bed.gz


title: ChIP_Mes_H3K4me3_rep1

description: processed data file: Mes_H3K4me3.bed.gz


title: Sample_Patellar_Rat_4

value: Patellar tendon


title: HiC_E65Epi_Kmt2b_KO_rep1_part2


title: Sample_Patellar_Rat_3

value: Sprague Dawley


title: ChIP_Ect_H3K4me3_rep2

description: processed data file: Ect_H3K4me3.bed.gz


title: Untreated at 24hrs Replicate 3

value: primary hepatic stellate cells


title: HiC_E65Epi_Kmt2b_KO_rep1_part1


title: ChIP_E65VE_H3K4me3_rep2

description: processed data file: E65VE_H3K4me3.bed.gz


title: Sample_Patellar_Rat_1


title: HiC_E65Epi_Kmt2b_WT_rep1_part2


title: Sample_Patellar_Rat_2


title: HiC_E65Epi_Kmt2b_WT_rep1_part1


title: Untreated at 0hrs Replicate 3


title: Untreated at 24hrs Replicate 1


title: ChIP_Ect_H3K4me3_rep1

description: processed data file: Ect_H3K4me3.bed.gz


title: ChIP_E65VE_H3K4me3_rep1


title: ChIP_E65Epi_Tet1/2_KO_H3K4me3_rep1

description: processed data file: E65Epi_Tet12_KO_H3K4me3.bed.gz

value: epiblast


title: ChIP_E65Epi_H3K4me3_rep2

description: processed data file: E65Epi_H3K4me3.bed.gz


title: ChIP_E85_head_Kmt2b_WT_H3K4me3_rep1

description: processed data file: E85_brain_Kmt2b_WT_H3K4me3.bed.gz

value: brain

value: H3K4me4(home made)


title: ChIP_E65Epi_H3K4me3_rep1


title: Untreated at 0hrs Replicate 2


title: d0

city: Palo Alto

first: Sayed

last: Nazish

address: 300 Pasteur Dr

institute: stanford

description: Ampli-seq

data_processing:
Torrent Suite Software 5.12，ampliSeqRNA plugin
Genome_build: hg19
Supplementary_files_format_and_content: csv file with RPM value

source_name: human fibroblast

growth_protocol: EGM2 medium

extract_protocol:
QIAGEN RNeasy Mini Kit
Libraries prepared from 10ng RNA using the Ion AmpliSeq Transcriptome Human Gene Expression Kit. Sequencing data was un-stranded, ERCC spike-in (Ambion) used for data normalization.
Depth of reads= 5 million/sample

treatment_protocol: 30 ng/ml Poly I:C

value: fibroblast

tag: agent

value: no treatment

tag: time point


title: d4

description: Ampli-seq

value: 30 ng/ml Poly I:C

value: 4 days


title: d6

description: Ampli-seq

value: 6 days


title: IEC-S4-KO-Lif_1

city: Suzhou

first: Yanan

middle: S

last: Zhang

state: Jiangsu

address: 199 Renai Road

department: Institutes of Biology and Medical Sciences

institute: Soochow University

description: IECs.GeneExpression.FPKM.xlsx

data_processing:
Bowtie2 was used to map clean reads to reference gene. Bowtie2 parameters forPE reads:-q--phred64--sensitive--dpad0--gbar99999999--mp1,1--np1--score-minL,0,-0.1-I1-X1000--no-mixed--no-discordant -p  16-k 200  Bowtie2 parameters forSE reads:-q--phred64--sensitive--dpad0--gbar99999999--mp1,1--np1--score-minL,0,-0.1-p16-k 200
HISAT was used to map clean reads to reference genome.HISAT parameters forPE reads:-p8--phred64--sensitive--no-discordant--no-mixed-I1-X1000  HISTAparameters forSE reads:-p8--phred64--sensitive-I1-X 1000
FPKM method is used in calculated expression level.
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs

source_name: Intestinal epithelial cells

growth_protocol: IECs were isolated from colon of wild type (WT) and Stat4-/- mice, and plated on Matrigel-coated 12-well plates in F12/DMEM medium, supplemented with 5% FBS, insulin mix, 100U/ml of both penicillin and streptomycin. The IECs were allowed to attach for 24 hours, at which time all unattached material was removed and the cells were supplied with fresh culture medium as described above.

extract_protocol:
IECs were collected, flash frozen on dry ice, 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

treatment_protocol: IECs were treated with 20ng/ml of LIF at different time points.

value: colon

tag: treatment

value: LIF

value: intestinal epithelial cell (IEC)


title: d2

description: Ampli-seq

value: 2 days


title: ChIP_E85_head_Kmt2b_KO_H3K4me3_rep2

description: processed data file: E85_brain_Kmt2b_KO_H3K4me3.bed.gz

value: H3K4me3(home made)


title: ChIP_E85_head_Kmt2b_KO_H3K4me3_rep1


title: ChIP_E65Epi_Kmt2b_KO_H3K4me3_rep3

description: processed data file: E65Epi_Kmt2b_KO_H3K4me3.bed.gz


title: Untreated at 24hrs Replicate 2

value: liver

value: untreated


title: IEC-S4-KO-control_1

description: IECs.GeneExpression.FPKM.xlsx

value: control


title: IEC-WT-Lif_1

description: IECs.GeneExpression.FPKM.xlsx

value: wild type


title: ChIP_E65Epi_Kmt2b_KO_H3K4me3_rep1

value: epiblast


title: ChIP_E65Epi_Kmt2b_KO_H3K4me3_rep2


title: IEC-WT-control_1

description: IECs.GeneExpression.FPKM.xlsx


title: Untreated at 0hrs Replicate 1

value: primary hepatic stellate cells


title: muscle

description: Tissue_Profiling_DIETERICH_gene_exp.diff.gz

data_processing:
barcode and adapter removal using flexbar 3.4.0
computational rRNA depletion by filtering reads that map to known rRNAs in mice using Bowtie2 2.2.9
alignment of non-rRNA reads to the mm10 reference genome using STAR 2.6.0c
transcript assembly using cufflinks followed by cuffmerge
differential expression analysis using cuffdiff (Cufflinks suite 2.2.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab separated values with results of the gene-level differential expression testing comparing all samples. Includes locus, FPKM values, log2FC as well as test statistics. For a complete description see https://cole-trapnell-lab.github.io/cufflinks/cuffdiff/

source_name: skeletal muscle

extract_protocol:
All tissues were dissected, washed with PBS and weighed. They were snap-frozen in liquid nitrogen and stored at -80C. Total RNA was isolated using peqGOLD TriFast (PEQLAB Biotechnologie).
Following initial quality checks, 1ug of total RNA of each sample was depleted for rRNA using NEBNext® rRNA depletion Kit (human/mouse/rat). Library preparation was performed with NEBNext UltraTM Directional RNA Library Prep Kit for Illumina (New England Biolabs) Gold. All libraries were sequenced in parallel on a HiSeq 2000 for 2 x 101 PE sequencing.

value: skeletal muscle

value: wt

tag: diet

value: NCD


title: ChIP_End_H3K27ac_rep2

description: processed data file: End_H3K27ac.bed.gz

value: endoderm

value: WT

value: H3K27ac(Active Motif,Cat.39133)


title: BAT

source_name: interscapular brown adipose tissue

tag: strain

value: interscapular brown adipose tissue


title: ChIP_End_H3K27ac_rep1

description: processed data file: End_H3K27ac.bed.gz

tag: genotype


title: SCAT

source_name: subcutaneous adipose tissue

value: subcutaneous adipose tissue


title: ChIP_Mes_H3K27ac_rep2

description: processed data file: Mes_H3K27ac.bed.gz

value: mesoderm


title: cortex

source_name: cortex

value: cortex


title: Healthy Control 4

city: Wuhan

first: Guohua

last: Zhen

state: Hubei

address: Jiefang Street No.1095

department: Tongji Medical College, Tongji Hospital

institute: Huazhong University of Science and Technology

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm. Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

source_name: healthy

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

value: Bronchial epithelial brushings

tag: diagnosis

value: healthy

tag: age

value: 26 years

tag: Sex

value: Male


title: Healthy Control 3

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

value: 22 years


title: Healthy Control 1

value: 49 years

value: Female


title: ChIP_PS_H3K27ac_rep2

description: processed data file: PS_H3K27ac.bed.gz

value: primitive streak


title: Patient 4 Th2 low

source_name: asthma

value: asthma

value: 18 years


title: Healthy Control 2

value: 23 years


title: Patient 3 Th2 low

value: 35 years


title: VAT

source_name: visceral adipose tissue

value: visceral adipose tissue

value: wt

value: NCD


title: ChIP_Ect_H3K27ac_rep2

description: processed data file: Ect_H3K27ac.bed.gz

value: ectoderm

value: WT

value: H3K27ac(Active Motif,Cat.39133)


title: Patient 2 Th2 low

value: Bronchial epithelial brushings

value: 57 years


title: 254706910106_b3 - 9_GRTT1-EtOH_3 vs 12_GRTT1-DEX_3

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Discover TT1 donwstream targets

hyb_protocol: 12_GRTT1-DEX_3 Cy5 / 9_GRTT1-EtOH_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  .

growth_protocol: silique and seed - Media: soil Hygrometry: Green house condition Temperature: around 22 Light: long days

treatment_protocol: Name:DEX treatment - time course study - compound addition,cycloheximide and dex:time 1hour . Siliques have been first treated with cycloheximide, an inhibitor of protein synthesis, to prevent indirect transcriptional effects of the inducible TT1 transcription factor. RNA profiling experiments (CATMA microarrays) will be then conducted before and after DEX induction of TT1.

tag: ecotype background

value: columbia

tag: genotype/variation

value: mutant

tag: dev.stage (boyes et al. plant cell 2001)

value: wild type


title: 254706910106_b1 - 8_GRTT1-EtOH_2 vs 11_GRTT1-DEX_2

description: Discover TT1 donwstream targets

hyb_protocol: 11_GRTT1-DEX_2 Cy5 / 8_GRTT1-EtOH_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910105_b4 - 10_GRTT1-DEX_1 vs 7_GRTT1-EtOH_1

description: Discover TT1 donwstream targets

hyb_protocol: 7_GRTT1-EtOH_1 Cy5 / 10_GRTT1-DEX_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910106_b4 - 12_GRTT1-DEX_3 vs 9_GRTT1-EtOH_3

description: Discover TT1 donwstream targets

hyb_protocol: 9_GRTT1-EtOH_3 Cy5 / 12_GRTT1-DEX_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910106_b2 - 11_GRTT1-DEX_2 vs 8_GRTT1-EtOH_2

description: Discover TT1 donwstream targets

hyb_protocol: 8_GRTT1-EtOH_2 Cy5 / 11_GRTT1-DEX_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910105_b3 - 7_GRTT1-EtOH_1 vs 10_GRTT1-DEX_1

description: Discover TT1 donwstream targets

hyb_protocol: 10_GRTT1-DEX_1 Cy5 / 7_GRTT1-EtOH_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910105_b2 - 6_Col0-DEX_3 vs 3_Col0-EtOH_3

description: Discover TT1 donwstream targets

hyb_protocol: 3_Col0-EtOH_3 Cy5 / 6_Col0-DEX_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: boyes:8 silique


title: ChIP_E65VE_H3K27ac_rep2

description: processed data file: E65VE_H3K27ac.bed.gz

value: visceral endoderm

tag: chip antibody


title: kidney

source_name: kidney

value: kidney


title: liver

value: liver


title: ChIP_E65Epi_H3K27ac_rep2

description: processed data file: E65Epi_H3K27ac.bed.gz

value: epiblast


title: ChIP_E65VE_H3K27ac_rep1


title: Patient 1 Th2 low

value: asthma

value: 45 years

value: Female


title: patient 4 Th2 high

value: 46 years


title: CCl4+EV rep-2

city: Columbus

first: David

last: Brigstock

state: OH

address: 700 Children's Drive

institute: Nationwide Children's Hospital

description:
CCl4_E_2
processed data file: CCl4_vs_Oil_3511_DEGs.xlsx

data_processing:
Quality of libraries was determined via Agilent 4200 Tapestation using a High Sensitivity D1000 ScreenTape Assay kit, and quantified by KAPA qPCR (KAPA BioSystems).
Approximately 60-80 million paired-end 150 bp sequence reads were generated for each library on the Illumina HiSeq 4000 platform.
Each sample was aligned to the GRCm38.p3 assembly of the Mus musculus reference from NCBI (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.23/) using version 2.6.0c of the RNA-Seq aligner STAR (http://bioinformatics.oxfordjournals.org/content/early/2012/10/25/bioinformatics.bts635).
Features were identified from the GFF file that came with the assembly from Gencode (Release M19).
Feature coverage counts were calculated using featureCounts (http://bioinf.wehi.edu.au/featureCounts/).
Differentially expressed features were calculated using DESeq2 (http://genomebiology.com/2014/15/12/550).
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: CCl4_vs_Oil_3511_DEGs.xlsx: Excel spreadsheet containing normalized read counts and differential expression data for each comparison.

source_name: liver tissue

extract_protocol:
Tissues were lysed in Trizol and a miRNeasy mini kit was used for RNA extraction with on-column DNase I treatment.
RNA-seq libraries (n = 3 per group) were prepared using the TruSeq Stranded protocol (Illumina, San Diego CA).

treatment_protocol: Cut the liver tissue, save at -80C before RNA extraction.

value: Swiss Webster

value: Male

value: Liver


title: CCl4+EV rep-3

description:
CCl4_E_3
processed data file: CCl4_vs_Oil_3511_DEGs.xlsx


title: HFD_wt_1

description: SupplementaryData1_RNA-Seq[HFD--CD].xlsx

data_processing:
barcode and adapter removal using flexbar 3.4.0
computational rRNA depletion by filtering reads that map to known rRNAs in mice using Bowtie2 2.2.9
alignment of non-rRNA reads to the mm10 reference genome using STAR 2.6.0c
transcript assembly using cufflinks followed by cuffmerge
differential expression analysis using cuffdiff (Cufflinks suite 2.2.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: xlsx spreadsheet containing results of the transcript-level differential expression testing comparing two levels. Includes locus, FPKM values, log2FC as well as test statistics. For a complete description see https://cole-trapnell-lab.github.io/cufflinks/cuffdiff/

extract_protocol:
All tissues were dissected, washed with PBS and weighed. They were snap-frozen in liquid nitrogen and stored at -80C. Total RNA was isolated using peqGOLD TriFast (PEQLAB Biotechnologie).
Following initial quality checks, 1ug of total RNA of each sample was depleted for cytoplasmic and mitochondrial rRNA with Ribo-Zero and strand-specific library preparation was performed using TruSeq RNA Gold Kit from Illumina. All libraries were sequenced in parallel on a HiSeq 2000 for 2 x 100 PE sequencing.

treatment_protocol: Diet-induced obesity (DIO) was achieved by feeding a high-fat diet (HFD, D12492 (I) mod; Sniff) containing 22 kJ% carbohydrates, 24 kJ% protein and 54 kJ% fat from starting at 6-7-weeks-of-age. NCD (D12450B* mod LS; Sniff): containing 62 kJ% carbohydrates, 27 kJ% protein and 11 kJ% fat.

value: wt

value: HFD


title: H2009 RUVBL2 PCRmutant +dox rep3

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Reads were mapped to amplicon sequence using bwa (v.0.7.15)
Extracted mismatched reads and pielup was generated using samtools
Computed the perbase composition from pileup using pileup2base
Calculated per base error rate
Supplementary_files_format_and_content: tab-separated file & perbase composition from mismatched reads

growth_protocol: H2009 cells lentivirally transduced with doxycycline-inducible PCR mutated RUVBL1 or RUVBL2 cDNAs were grown to confluency

extract_protocol:
Cells harvested via trypsinization and then genomic DNA was isolated using Qiagen Blood & Cell Culture DNA Mini Kit
RUVBL1 or RUVBL2 cDNAs were amplified via nested-PCR with primers containing a unique barcode for each sample. Adapators and sequencing barcodes were added using the KAPA Hyper Prep Kit
DNAsequencing using MiSeq

treatment_protocol: For + dox samples: Cells were treated with doxycycline to induce PCR-mutated RUVBL1 or RUVBL2 alleles, and then a toxic dose (500 nM) of the RUVBL1/RUVBL2 inhibitor Compound B was added. Cells were kept in Compound B + doxycycline for ~1 month until resistant cells emerged. For - dox samples: these are the parental, untreated cells used in the +dox experiments.

tag: cell type

value: non-small cell lung cancer cell line

tag: cell line

value: RUVBL2 PCRmutant

value: dox


title: HFD_wt_3

tag: tissue


title: patient 2 Th2 high

value: Bronchial epithelial brushings

value: 20 years


title: patient 1 Th2 high

value: 28 years


title: HFD_wt_2

value: liver


title: ChIP_E65Epi_H3K27ac_rep1

value: epiblast

value: WT

value: H3K27ac(Active Motif,Cat.39133)


title: ChIP_End_H3K27me3_rep2

description: processed data file: End_H3K27me3.bed.gz

value: endoderm


title: patient 3 Th2 high

value: asthma

value: 29 years

value: Female


title: ChIP_E55Epi_H3K27me3_rep2

description: processed data file: E55Epi_H3K27me3.bed.gz


title: H2009 RUVBL2 PCRmutant +dox rep2


title: NCD_wt_3

value: NCD


title: NCD_wt_2

value: wt


title: H2009 RUVBL2 PCRmutant +dox rep1


title: CCl4+EV rep-1

description:
CCl4_E_1
processed data file: CCl4_vs_Oil_3511_DEGs.xlsx

value: Swiss Webster

value: Male

value: Liver


title: CCl4 rep-2

description:
CCl4_2
processed data file: CCl4_vs_Oil_3511_DEGs.xlsx


title: ChIP_E55Epi_H3K27me3_rep1


title: 254706910094_b4 - 5_Col0-DEX_2 vs 2_Col0-EtOH_2

description: Discover TT1 donwstream targets

hyb_protocol: 2_Col0-EtOH_2 Cy5 / 5_Col0-DEX_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: columbia

value: wild type

value: boyes:8 silique

value: mutant


title: CCl4 rep-3

description:
CCl4_3
processed data file: CCl4_vs_Oil_3511_DEGs.xlsx


title: 254706910094_b3 - 2_Col0-EtOH_2 vs 5_Col0-DEX_2

description: Discover TT1 donwstream targets

hyb_protocol: 5_Col0-DEX_2 Cy5 / 2_Col0-EtOH_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910094_b1 - 1_Col0-EtOH_1 vs 4_Col0-DEX_1

description: Discover TT1 donwstream targets

hyb_protocol: 4_Col0-DEX_1 Cy5 / 1_Col0-EtOH_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910105_b1 - 3_Col0-EtOH_3 vs 6_Col0-DEX_3

description: Discover TT1 donwstream targets

hyb_protocol: 6_Col0-DEX_3 Cy5 / 3_Col0-EtOH_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.