title: PUM2sh#1 3

first: Johan

last: Auwerx

address: Station 15

department: SV IBI NCEM

institute: EPFL

description: RNA-Seq normalized counts.xlsx

data_processing:
The reads obtained were first trimmed out to remove adaptor sequences and then mapped using a TopHat2 against the human genome (GRCh37).
HTSeq-count was then used to obtain the counts of each gene.
Differential expressed genes in each condition were identified using R/Bioconductor package Deseq.
Genome_build: GRCh37
Supplementary_files_format_and_content: xlsx with normalized counts

source_name: HeLa

growth_protocol: DMEM plus L-glutamine and pyruvate with 10% inactivated FBS and penicillin and streptomycin

extract_protocol:
Total RNA from HeLa cells was extracted using TRIzol (Thermo Fisher Scientific) and purified by column using RNeasy Mini kit (Qiagen).
Total RNA sample was digested by DNaseІ (NEB) and purified by oligo-dT beads (Dynabeads mRNA purification kit, Invitrogen, 61006), then poly (A)-containing mRNA were fragmented into 130bp with First Strand buffer. First-strand cDNA was generated by N6 primer, FirstStrand Master Mix and Super Script II reverse transcription (Invitrogen, 18064022) (Reaction condition25°C for 10 min；42°C or 40 min；70°C for 15 min). Then Second Strand Master Mix was added to synthesize the second-strand cDNA (16°C for 1h). The cDNA was purified with Ampure XP Beads (Agencourt, A63880), combined with End Repair Mix, incubated at 20°C for 30min, purified, added with A-Tailing Mix and incubated at 37°C for 30 min. Then the samples were combined with Adenylate 3' Ends DNA, Adapter and Ligation Mix and incubated for the ligation reaction at 20°C for 20 min. Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix were performed to enrich the cDNA fragments. Then the PCR products were purified with Ampure XP Beads. The final library was quantitated in two ways: determining the average molecule length using the Agilent 2100 bioanalyzer (Agilent DNA 1000 Reagents), and quantifying the library by real-time quantitative PCR (QPCR) (TaqMan Probe). The libraries were amplified on cBot to generate the cluster on the flow cell (TruSeq PE Cluster Kit V3–cBot–HS, Illumina, PE-401-3001) and the amplified flow cell was sequenced pair end on the HiSeq 2000 System (TruSeq SBS KIT-HS V3，Illumina, TG-101-3001), with read length 50bp.

value: HeLa


title: Shammed, dorsal SCN, replicate 1, batch A

status: Public on Jan 01 2019

type: RNA

city: Rotterdam

first: Karl

last: Brand

address: Dr Molewaterplein 50

department: Bioinformatics

country: Netherlands

institute: Erasmus Medical Center

hyb_protocol: Each batch of biotin labelled cDNA samples was fragmented and combined with hybridisation cocktail including DMSO according to the manufacturers protocol (Nugen Technologies) and hybridised to Affymetrix GeneChip 430_2.0 arrays for 18 hrs. Post-hybridisation washing, scanning and image analysis were performed according to the Affymetrix fluidics protocol FS450_0004.

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Expression measures were exported using the MAS5.0 software suite (Affymetrix, Santa Clara, USA), and normalised per batch using the GeneChip Robust Multi-array Analysis method available as the BioConductor (v2.12) package, gcrma,v2.32.0, running in the R v3.0.2 environment.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Sham treated dorsal suprachiasmatic nuclei

label_protocol: Amplification and cDNA labelling with biotin was accomplished using the Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 respectively according to the manufacturers protocols (Nugen Technologies, San Carlos, USA). Efficiency of the amplification was assayed quantitatively by 260/280 nm estimation of cDNA concentration, where a yield of at least 5 μg cDNA was deemed sufficient for specific amplification of the RNA template. Amplification and labelling was achieved batch wise.

growth_protocol: Eight week old C57BL/6 mice were obtained from Harlan (Horst, The Netherlands) and individually housed with conventional chow (Special Diets Services, Witham, UK) and tap water (acidified with HCl to pH 2.9, to prevent bacterial growth) ad libitum.

extract_protocol: Isolated SCN sub-regions were lysed in Lysis Buffer (Qiagen, Hilden, Germany) and stored at -80° C until RNA purification. RNA was purified with on-column DNase treatment using the RNeasy Micro kit (Qiagen) according to the manufacturers instructions, except that 20 ng of 16S/23S bacterial ribosomal RNA (Roche, Woerden, The Netherlands) was used as carrier species and an additional elution was performed in the final step to maximise RNA yield. RNA was eluted with DEPC treated water, vacuum evaporated and immediately amplified.

treatment_protocol: 25 μm thick coronal cryosections mounted on 1mm PALM pen-membrane slides (Carl Zeiss AG, Oberkochen, Germany) were rapidly thawed, fixed for 30sec in 70% ethanol and stained with haematoxylin for 3min. Following staining, sections were rinsed in diethylpyrocarbonate (DEPC) treated water and dehydrated by several rinses in 100% ethanol. Laser catapult microdissection of ventral, dorsal and central SCN subregions was accomplished using the PALM Micolaser system (Carl Zeiss AG, Oberkochen, Germany ) on freshly prepared sections.

tag: treatment

value: 30m sham treatment

tag: tissue

value: dorsal shell SCN

tag: batch

value: batch A

tag: strain


title: Shammed, central SCN, replicate 4, batch B

source_name: Sham treated central suprachiasmatic nuclei

value: central middle SCN

value: batch B


title: Pulsed, ventral SCN, replicate 4, batch B

source_name: Light pulsed ventral suprachiasmatic nuclei

value: 30m light pulsed

value: ventral core SCN


title: Pulsed, dorsal SCN, replicate 3, batch B

source_name: Light pulsed dorsal suprachiasmatic nuclei


title: Pulsed, central SCN, replicate 1, batch A

source_name: Light pulsed central suprachiasmatic nuclei


title: Shammed, central SCN, replicate 1, batch A


title: SCR2

type: SRA

city: Lausanne

country: Switzerland

description: RNA-Seq normalized counts.xlsx

library_source: transcriptomic

organism: Homo sapiens

tag: cell line

value: control shRNA (SCR)


title: Shammed, ventral SCN, replicate 3, batch B

source_name: Sham treated ventral suprachiasmatic nuclei


title: Shammed, dorsal SCN, replicate 4, batch B


title: PUM2sh#1 2

description: RNA-Seq normalized counts.xlsx


title: SCR1

description: RNA-Seq normalized counts.xlsx


title: PUM2sh#1 1

description: RNA-Seq normalized counts.xlsx


title: SCR3

description: RNA-Seq normalized counts.xlsx


title: Tamoxifen (4-OHT)-rep1

city: Berlin

first: Matthias

last: Wirth

address: Hindenburgdamm 30

country: Germany

institute: Charité Berlin

description: 1: TAM

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie2
Differentially expressed features from count tables were determined via DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each sample.

source_name: Tamoxifen (4-OHT), PDAC

extract_protocol:
Cells were collected in RLT buffer and isolated via silica-based columns. Illumina TruSeq RNA Sample Prep Kit was used with 1 µg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tumor entity

value: pancreatic ductal adenocarcinoma

value: IMIM-PC1 (Instituto Municipal de Investigacion Medica-Pancreas Cancer 1)

tag: genotype

value: stably expressing the MYC-ER fusion protein

tag: agent

value: Tamoxifen (4-OHT)


title: Ctrl-rep1

description: 4: Ctrl

source_name: Ctrl, PDAC

value: Ctrl


title: Ctrl-rep3

description: 6: Ctrl


title: Tamoxifen (4-OHT)-rep3

description: 3: TAM


title: NG-10690_Axin57Mutated

first: Ron

last: Smits

address: Wytemaweg 80

institute: Erasmus MC

data_processing:
The reads were aligned using STAR version 2.5.3a (Dobin et al, 2013) against the UCSC hg38 reference genome, using GENCODE annotation.gtf version 26 (GENCODE 2012 Genome Research)
Read counts on GENCODE annotation were computed using the featureCounts version 1.5.2 using --largestOverlap --primary --fracOverlap 0.8
The differentially expressed genes were called using a generalized linear negative binomial model with controlling the effect of the RNA sample preparation date. The calculations were performed by the DESeq2 R package (Anders and Huber, Genome Biology 2010)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include Ensemble Gene Id  and read count

molecule: polyA RNA

source_name: SNU449 clones

growth_protocol: SNU449 cells were routinely cultured in DMEM with 10% FCS

extract_protocol:
Total RNA was isolated from 70-80% confluent plates with the Machery-NucleoSpin RNA II kit
Library was constructed and sequenced with an Illumina HiSeqTM2000 (GATC Biotech, Konstanz, Germany). Briefly, the mRNA was enriched using oligo-dT magnetic beads, followed by fragmentation (about 200 bp). Then first strand cDNA was synthesized using random hexamer-primers and the second strand was further synthesized in a reaction buffer including dNTPs, RNase H and DNA polymerase I. Double stranded cDNA was purified with magnetic beads. Then, the 3’-end single nucleotide A (adenine) was added and adapters were ligated to the fragments which were enriched by PCR amplification.

treatment_protocol: No specific treatment

value: SNU449 hepatocellular carcinoma cells

tag: axin1 protein status

value: wild type AXIN1


title: NG-10690_Axin20Mutated


title: Pulsed, ventral SCN, replicate 2, batch A


title: NG-10690_Axin2Ctr

value: homozygous p.R712*AXIN1


title: NG-10690_Axin3Ctr


title: NG-10690_Axin6Ctr


title: NG-10690_Axin14Mutated


title: Evec3

city: Wuhan

first: Zhao

middle: Lian

last: Zhong

address: Shizishan Street

country: China

institute: Huazhong Agriculture University

description: cultured cells

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the mm10 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: A549 cell line

growth_protocol: 12-well planted human A549 lung epithelial cells were cultured at 37 °C and 5 % CO2 in F12 media (Invitrogen) supplemented with 10 % fetal bovine serum.

extract_protocol:
Total RNA was extracted with RNeasy mini kit (Qiagen, Germany).
Following "TruSeq RNA Sample Preparation Guide".

treatment_protocol: Cells were transfected with 2μg miR340 expressing plasmids or empty vector for 24 hours

tag: transfection

value: empty vector


title: p3402

description: cultured cells


title: Evec2

description: cultured cells


title: Pulsed, ventral SCN, replicate 1, batch A


title: AR_siLINC00844_4_ETOH_R2

city: Macau

first: Edwin

last: Cheung

state: Macau

address: Taipa

department: Faculty of Health Sciences

country: Macau

institute: University of Macau

library_source: genomic

data_processing:
Raw data were aligned using bwa aligner to Hg19 genome downloaded from UCSC
MACS2 were used to call peak
Genome_build: Hg19
Supplementary_files_format_and_content: bw

molecule: genomic DNA

growth_protocol: LNCaP cells were maintained in hormone satrved condition (RPMI media without phenole red + 10% charcole dextran treated FBS) for 72 hours before treatment

extract_protocol:
Nuclear fraction was sonicated and chromatin bound AR was precipitated by antibody.
DNA library was constructed using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, catalogue # E7370L) according to manufacturer’s protocol.

treatment_protocol: LNCaP cells were consecutively transfected twice with with 5nM of dsiRNA every 24 hours and after 48 hours of last trasfection, cells were treated with 100nM of DHT or ETOH for 2 hours

value: LNCaP cells

value: ETOH

tag: chip antibody

value: AR Antibody (H-280) (SCBT, cat# sc-13062, lot# B2616)


title: 5074 vs. 6072

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: polarity(+)

hyb_protocol: Whole mouse genome 4x44k microarrays were done according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution and extended range (XDR)  using a DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware). Intra-array data were normalized with the GE2_1105_Oct12 extraction protocol and interarray normalization was done by the mean of trimmed positive non-flagged/non-control reporters.

label_protocol: RNA labeling was performed with the Quick-Amp Labeling Kit  (Agilent Technologies) according supplier's instructions.

growth_protocol: Animals were maintained in autoclaved microisolator cages and provided with sterile drinking water and chow ad libitum.

extract_protocol: Total RNA was isolated according the manufacturer´s protocol.

treatment_protocol: Tamoxifen (Sigma) was injected intraperitoneally into mice either as single dose or on three consecutive days (4 mg/25 g bodyweight, diluted in 200 µl corn oil) at the indicated time points to deplete Rspo3 expression

tag: background strain

value: Rspo3 ++

value: stomach

tag: stomach region

value: antrum

value: Rspo3 KO


title: Tamoxifen (4-OHT)-rep2

description: 2: TAM


title: AR_siLINC00844_4_DHT_R1

value: DHT


title: AR_siLINC00844_1_ETOH_R2


title: AR_siLINC00844_4_DHT_R2


title: AR_siLINC00844_1_DHT_R2


title: AR_siLINC00844_1_DHT_R1


title: Ctrl-rep2

description: 5: Ctrl

value: pancreatic ductal adenocarcinoma


title: NC_ETOH_R2

value: control


title: NC_ETOH_R1


title: NC_DHT_R2


title: NC_DHT_R1


title: p3403

description: cultured cells


title: Evec1

description: cultured cells


title: p3401

description: cultured cells


title: AR_siLINC00844_1_ETOH_R1


title: OrgBRAF2 BASE

city: BALTIMORE

first: hari

last: easwaran

state: MD

address: 1650 Orleans Street, CRB1, Room 530

department: Oncology

country: USA

institute: Johns Hopkins University

hyb_protocol: 825ng of each Cy3- labeled cRNA was hybridized to Agilent mouse GF 4x44K V2 microarray (G4846A) at 65ºC for 17 hours. Then, the arrays were scanned by an Agilent G2565 scanner.

scan_protocol: Arrays were scanned by an Agilent G2565 scanner.

data_processing: Expression data were analyzed in the R/Bioconductor environment using the limma package, and quantile normalized.

source_name: BRAF(2) organoid in BASE for 48hr

label_protocol: Labeled cRNA was generated through in vitro transcription by T7 RNA polymerase in presence of labeled by Cyainine-3 labeled CTP (Perkin Elmer).

growth_protocol: Male mice from each genotype around the age of 40 days were euthanized by Carbon Dioxide. The first 2.5cm of proximal colon is collected from the mice. The colon crypts were isolated and the culture was established as described previously. Organoids were plated within Matrigel(Corning #356231). Culture media was made of 50% of Wnt3a conditioned media, 20% of R-Spondin conditioned media, 20% of Advanced DMEM/F12(ThermoFisher #12634010) with B27® (ThermoFisher #17504044), 10% of Noggin conditioned media and EGF. The conditioned media for Wnt3a, R-Spondin and Noggin were made as described previously.

extract_protocol: DNA/RNA was extract using Allprep kit mini or micro (Qiagen)

tag: culture

value: organoid


title: AR_siLINC00844_4_ETOH_R1


title: OrgBRAF3_Base ENSW

source_name: BRAF(3) grown in base media organoid in ENSW for 48hr


title: OrgBRAF2 ENSW

source_name: BRAF(2) organoid in ENSW for 48hr


title: OrgBRAF2_EV BASE

source_name: BRAF(2) empty vector organoid in BASE for 48hr


title: OrgWT BASE

source_name: wt organoid in BASE for 48hr


title: OrgBRAF1 ENSW

source_name: BRAF(1) organoid in ENSW for 48hr


title: OrgBRAF2_EV ENSW

source_name: BRAF(2) empty vector organoid in ENSW for 48hr


title: OrgBRAF1 BASE

source_name: BRAF(1) organoid in BASE for 48hr


title: OrgBRAF1_Base ENSW

source_name: BRAF(1) grown in base media organoid in ENSW for 48hr


title: OrgBRAF3 ENSW

source_name: BRAF(3) organoid in ENSW for 48hr


title: OrgBRAF3 BASE

source_name: BRAF(3) organoid in BASE for 48hr


title: OrgBRAF3_Base BASE

source_name: BRAF(3) grown in base media organoid in BASE for 48hr


title: OrgBRAF2_Base BASE

source_name: BRAF(2) grown in base media organoid in BASE for 48hr


title: OrgBRAF1_Base BASE

source_name: BRAF(1) grown in base media organoid in BASE for 48hr


title: OrgBRAF2_Base ENSW

source_name: BRAF(2) grown in base media organoid in ENSW for 48hr


title: OrgWT ENSW

source_name: wt organoid in ENSW for 48hr


title: OrgBRAF3_EV ENSW

source_name: BRAF(3) empty vector organoid in ENSW for 48hr


title: OrgBRAF3_EV BASE

source_name: BRAF(3) empty vector organoid in BASE for 48hr


title: OrgBRAF1_EV BASE

source_name: BRAF(1) empty vector organoid in BASE for 48hr


title: grl_T1_vs_B1

city: New York

first: Mo

last: Chen

state: New York

address: 630 W168th Street

institute: Columbia University

hyb_protocol: The corresponding Cy3- and Cy5- labeled cDNAs were combined and hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven. In general, control samples are labeled with Cy3 and experimental samples are labeled with Cy5.

scan_protocol: Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using Agilent’s DNA microarray scanner (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities and ratios (including background subtraction and normalization), rejects outliers and calculates statistical confidences (p-values).

source_name: primary odontoblast

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 and Cy5 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: age

value: 2 week

value: Dental Pulp

tag: cell type

value: primary odontoblast

source_name: calvarial osteoblast

value: calvaria bone

value: calvarial osteoblast


title: DSChypox2

city: West Haven

first: Kalle

middle: T

last: Rytkönen

state: CT

address: 840 West Campus Drive

department: EEB, Systems Biology institute

institute: Yale University

data_processing:
Basecalls performed using CASAVA version 1.4
mRNA-seq reads were aligned to the human (GRCh37.69) cDNA builds using Tophat2 version 2.0.5
Number of times reads overlapped with known features (gene counts) was counted using HTSeq
Transcripts per million (TPM) values were calculated according to Wagner et al (2012) Theor. Biosci.
Genome_build: GRCh37.69
Supplementary_files_format_and_content: ESFhypox_DSChypox_HTseqcounts_TPMs.txt is a tab limited text file that contains the HTseq read counts and transcripts per million (TPM) values for 4 samples

source_name: decidual stromal cells

extract_protocol:
Cell cultures were treated with trypsin and detached from flasks, and RNA was isolated using the RNeasy Mini RNA extraction kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: in vitro decidualized endometrial stromal fibroblast (ATCC:CRL-4003) grown in culture


title: grl_T3_vs_B3


title: OrgBRAF1_EV ENSW

source_name: BRAF(1) empty vector organoid in ENSW for 48hr


title: grl_T4_vs_B4


title: grl_T2_vs_B2


title: DSChypox1


title: GFP- and anti-KLF4 shRNA-transduced [KLF4KD] Bio rep.3  Tech rep  b

city: EVRY

first: Nicolas

last: Fortunel

address: 2 rue Gaston Cremieux

department: IRCM/SCSR

country: France

institute: CEA

data_processing:
Base Calling: Basecalls performed using CASAVA version 1.4
Read Quality: Quality of raw reads was assessed using FastQC quality control version 0.11.3  http://www.bioinformatics.babraham.ac.uk/projects/fastqc
Mapping: Primary assembly Homo sapiens genome sequence (release GRCh38.p3) and transcriptome annotations (Ensembl release 81) were downloaded from the GENCODE website2 (files GRCh38.primary_assembly.genome.fa  and gencode.v23.primary_assembly.annotation.gtf respectively). Raw read data (fastq files) were mapped to these sequences using STAR
Merging: For each biological replicate the 3 technical replicates were merged
Normalization: For the quality control representations, the effective library sizes were first computed using function estimateSizeFactors from package DESeq24. The raw count values were then transformed using a regularized log (function rlogTransformation from package DESeq2 with parameter blind=TRUE).
Gene filtering: Genes that did not have more than one count per million counts in at least 2 samples were filtered out. Genes were also filtered if their Ensembl description was either empty, “Uncharacterized protein” or an open reading frame.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw and normalized counts

source_name: skin, epidermis

growth_protocol: Human skin tissue from adult healthy donors was collected in the context of breast reduction surgery, after informed consent. Epidermal keratinocytes were extracted after enzymatic treatment. Frozen banked samples of human epidermal holoclone keratinocytes were studied as a model of skin keratinocyte precursor cells. Mass cultures of holoclone cells (keratinocyte precursor cells) were performed in a serum-containing medium, in the presence of a feeder-layer of human dermal fibroblasts growth-arrested by γ irradiation (60 Gy). Cultures were performed in plastic devices coated with type I collagen. Medium was renewed 3 times a week, and sub-cultured every week. Numbers of population doublings achieved by cultures were calculated after each passage, as follows: PD = (log N/N0)/log 2, where N0 represents the number of plated cells, and N the number of cells obtained after 1 week of growth.

extract_protocol:
Total RNA from these 9 samples was extracted with RNeasy Mini and Micro kits (Qiagen) followed by quality control using capillary electrophoresis (RNA 6000 Nano chips, Agilent).
Libraries were prepared according to Illumina's instructions with theTruSeq RNA Library Prep Kit v2. Briefly, total RNA (1µg) was purified and fragmented before first strand and second strand cDNA synthesis. Then ends are repaired and 3’ends adenylated before adapters ligation and PCR amplification. Libraries were then validated, normalized, and sequenced on Illumina HiSeq 1000 as short-insert paired-end libraries with read lengths 100 bp.

treatment_protocol: Lentiviral vectors were used for stable gene knock-down in holoclone cells (keratinocyte precursor cells). Transduction was performed on cultured cells at 50 population doublings after initial clonal derivation and at 20 % confluence. Cells were incubated overnight with lentiviral particles in the presence of hexadimethrine bromide. After 3 days, keratinocytes at 80 % confluence were collected and analyzed by flow cytometry. Transduced cells were sorted according to their GFP fluorescence.

value: holoclone cells, keratinocyte precursor cells

tag: biological samples

value: adult skin biopsies (breast surgery)

tag: culture history

value: 58 population doublings post-initial clonal isolation


title: ESFhypox1

source_name: endometrial stromal fibroblasts

value: endometrial stromal fibroblast (ATCC:CRL-4003) grown in culture


title: GFP- and anti-KLF4 shRNA-transduced [KLF4KD] Bio rep.3  Tech rep  c


title: ExVitroSpermatogonial stem cell_24h_Captopril 2

city: Nanjing

first: Xiaoyan

last: Huang

address: No.101, longmian Avenue

department: Department of Histology and Embryology

institute: State Key Laboratory of Reproductive Medicine, Nanjing Medical University

description: Gene expression in 24hr in 0.01M captopril treated spermatogonial stem cells

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by quantile normalization.

source_name: Spermatogonial stem cell_24h_Captopril

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: Briefly, dissociated testis cells were cultured on a 0.2% (w/v) gelatin-coated tissue culture plate (2 × 105 cells/3.8 cm2) overnight. The plates were washed twice with PBS before use. The floating cells were passaged to secondary plates. These cells were then passaged two or three times before they were transferred to medium containing MEFs.

extract_protocol: Total RNAs were extracted from 3 independent mouse SSCs with captopril and 3 SSCs without captopril (NC) by the Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion) according to the manufacter’s protocol. The quality of RNA was determined by 1% formaldehyde denaturing gel electrophoresis.

treatment_protocol: 4-5 days after SSCs passage, 0.01M captopril was added to SSCs culture for 24 hours. SSCs cultured  with 0.01M ddH2O served as Negative control.

value: ex vitro Spermatogonial stem cell

tag: treatment

value: 24hr in 0.01M captopril


title: GFP-transduced [KLF4WT] Bio rep.2  Tech rep  b

value: 54 population doublings post-initial clonal isolation


title: GFP- and anti-KLF4 shRNA-transduced [KLF4KD] Bio rep.3  Tech rep  a


title: GFP- and anti-KLF4 shRNA-transduced [KLF4KD] Bio rep.1  Tech rep  a

value: 56 population doublings post-initial clonal isolation


title: GFP- and anti-KLF4 shRNA-transduced [KLF4KD] Bio rep.2  Tech rep  c

value: 57 population doublings post-initial clonal isolation


title: GFP- and anti-KLF4 shRNA-transduced [KLF4KD] Bio rep.2  Tech rep  b


title: GFP-transduced [KLF4WT] Bio rep.2  Tech rep  a


title: GFP-transduced [KLF4WT] Bio rep.3  Tech rep  b

value: 55 population doublings post-initial clonal isolation


title: GFP-transduced [KLF4WT] Bio rep.3  Tech rep  c


title: GFP- and anti-KLF4 shRNA-transduced [KLF4KD] Bio rep.2  Tech rep  a


title: ESFhypox2


title: GFP-transduced [KLF4WT] Bio rep.3  Tech rep  a


title: Non-transduced [KLF4WT] Bio rep.3  Tech rep  a

value: 52 population doublings post-initial clonal isolation


title: ExVitroSpermatogonial stem cell_24h_sterile water 3

description: Gene expression in 24hr in 0.01M sterile water treated spermatogonial stem cells

value: 24hr in 0.01M sterile water


title: Non-transduced [KLF4WT] Bio rep.3  Tech rep  c


title: GFP-transduced [KLF4WT] Bio rep.1  Tech rep  a

value: 53 population doublings post-initial clonal isolation


title: ExVitroSpermatogonial stem cell_24h_Captopril 4


title: Non-transduced [KLF4WT] Bio rep.3  Tech rep  b


title: GFP- and anti-KLF4 shRNA-transduced [KLF4KD] Bio rep.1  Tech rep  c


title: ExVitroSpermatogonial stem cell_24h_sterile water 2


title: Non-transduced [KLF4WT] Bio rep.1  Tech rep c

value: 50 population doublings post-initial clonal isolation


title: Non-transduced [KLF4WT] Bio rep.2  Tech rep b

value: 51 population doublings post-initial clonal isolation


title: Non-transduced [KLF4WT] Bio rep.2  Tech rep a


title: ExVitroSpermatogonial stem cell_24h_Captopril 3


title: Non-transduced [KLF4WT] Bio rep.2  Tech rep c


title: ExVitroSpermatogonial stem cell_24h_sterile water 4


title: Non-transduced [KLF4WT] Bio rep.1  Tech rep a


title: Non-transduced [KLF4WT] Bio rep.1  Tech rep b


title: GFP- and anti-KLF4 shRNA-transduced [KLF4KD] Bio rep.1  Tech rep  b


title: GFP-transduced [KLF4WT] Bio rep.1  Tech rep  c


title: GFP-transduced [KLF4WT] Bio rep.1  Tech rep  b


title: Btz810

city: Cologne

first: Thorsten

last: Hoppe

address: Joseph-Stelzmann-Str. 26

department: Institut für Genetik

institute: CECAD Cologne and Institute for Genetics

data_processing:
Illumina Casava software used for basecalling
RNA-Seq data were processed through the QuickNGS analysis pipeline
Sequenced reads mapped to C elegans
Fragment Per Kilobase of exon per Million (FPKM) were calculated using a Cufflinks
Genome_build: caenorhabditis_elegans
Supplementary_files_format_and_content: tab-delimited file include FPKM values for each Sample

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Synchronized worms were grown on 20°C until day 1 of adulthood. Food source: E. coli OP50

extract_protocol:
The RNA isolation followed the standard procedures using Trizol reagent (Invitrogen). RNA was subsequently purified using the RNeasy kit (Qiagen).
Illumina RNASeq library Protocol
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Synchronized L4 worms were placed on stress plates (200uM fluphenazine, 200uM cantharidin, 10uM bortezomib or 25uM bortezomib) and collected the next day. For rpn-6 RNAi treatment, synchronized L3 worms were placed on RNAi plates and collected at day 1. For starvation, synchronized worms were placed on empty plates 15h prior collection. Control worms were not treated.

value: wildtype (N2)

value: bortezomib 10uM

tag: tissue

value: whole organism


title: Btz710

tag: strain


title: Btz625

value: bortezomib 25uM


title: Btz425


title: Control7

value: non (control)


title: Rpn6RNAi6

value: rpn-6 RNAi


title: Rpn6RNAi5


title: Btz325


title: Canta3

value: cantharidin


title: Canta9


title: Flu2

value: fluphenazine


title: Control6


title: Starv15h3

value: 15h starvation


title: Canta1


title: Btz910


title: Flu4


title: Starv15h2


title: Starv15h1


title: Control4


title: Rpn6RNAi4


title: Mouse kideny control 3

city: Edmonton

first: R. Todd

last: Alexander

state: Alberta

department: Paediatrics

country: Canada

institute: The University of Alberta

description: control renal gene expression

hyb_protocol: AS per genome quebec

scan_protocol: AS per genome quebec

data_processing: Scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters to create background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: kidney control

label_protocol: AS per genome quebec

extract_protocol: RNA was etracted with Trizol then an RNA miniplus column

treatment_protocol: Please refer to Dimke et al Am J Physiol Renal Physiol. 2013 Mar 15;304(6):F761-9. for specific details, however, 3 month old male mice were given standaard chow or 1mg/g body weight cinacalcet for 5 days then euthanized and kidneys extracted and snap frozen

tag: gender

value: male

value: 12 weeks

value: standard chow


title: Mouse kidney control 1

description: control renal gene expression


title: Mouse kidney cinacalcet 4

description: Cinacalcet treated gene expression

source_name: kidney cinacalcet treated

value: cinacalcet HCl (1mg/g body weight)


title: Mouse kidney cinacalcet 2

description: Cinacalcet treated gene expression


title: Mouse kidney control 4

description: control renal gene expression


title: Flu9


title: Mouse kidney cinacalcet 1

description: Cinacalcet treated gene expression


title: Mouse kidney control 2

description: control renal gene expression


title: GMPs_control_water_rep2

city: Philadelphia

first: Lehn

middle: K

last: Weaver

state: PA

address: 3615 Civic Center Boulevard

department: Pediatric Rheumatology

institute: The University of Pennsylvania / The Children's Hospital of Philadelphia

hyb_protocol: 2 ?g of fragmented and labeled SPIA cDNA was hybridized to an Affymetrix Mouse Gene 2.0ST Array for 17 hours at 50C and 60rpm.

scan_protocol: Arrays were washed on an Affymetrix GeneChip Fluidics Station 450 using fluidics protocol FS450_0002 and scanned on Affymetrix GeneChip Scanner 3000.

data_processing: Normalization of the individual microarray chips was performed with robust multichip averaging using Transcriptome Analysis Console software. The microarray dataset was filtered using Partek Genomics Suite software to include probesets with annotations to gene names in the Refseq and ENSEMBL databases. The gene list was filtered on transcripts that had an absolute value fold difference >1.5 between myeloid progenitors from antibiotic-treated mice and control mice using GenePattern modules from the Broad Institute. Differentially expressed genes (DEGs) were identified by two-way ANOVA and corrected for multiple testing using the Benjamini-Hochberg procedure to calculate a false discovery rate (FDR) of <0.2 using Partek Genomics Suite software.

source_name: GMPs, bone marrow, control mouse

label_protocol: NuGen Ovation Pico WTA System V2 (PN: 3302) was used to generate single stranded SPIA cDNA from 2.6 ng of total RNA. 5 ?g of SPIA cDNA was fragmented and labeled using the NuGen Encore Biotin Module (PN: 4200).

growth_protocol: Mice were treated with antibiotic or control water for three weeks prior to sorting bone marrow myeloid progenitors.  Antibiotic-treated mice received a combination of four antibiotics (ampicillin, metronidazole, neomycin, and vancomycin, 1 g/L/antibiotic) ad libitum.  Sucrose (2%) was added to antibiotic and control water to encourage drinking.  Antibiotic and control water was changed twice weekly.  Myeloid progenitors were sorted as CMPs (Lin-c-Kit+CD105- CD16/32midCD115-), GMPs (Lin-c-Kit+CD105-CD16/32highCD115-), MDPs (Lin-cKit+CD105-CD115+Ly6C-), and cMoPs (Lin-c-Kit+CD105-CD115+Ly6C+). The lineage panel included antibodies against B220, CD4, CD5, CD8a, CD11b, CD11c, CD90.2, CD49b, Ly6G, NK1.1, Sca-1, and Ter119.

extract_protocol: Bone marrow CMPs, GMPs, and cMoPs were sorted from antibiotic-treated and control mice directly into lysis buffer and frozen at -80°C prior to RNA extraction.  The Qiagen RNeasy Micro kit was used to isolate RNA from each sample per the manufacturer’s instructions.

treatment_protocol: As defined in the growth protocol.

tag: myeloid progenitor

value: Granulocyte Monocyte Progenitor (GMP)


title: Mouse kidney cinacalcet 3

description: Cinacalcet treated gene expression


title: GMPs_control_water_rep1


title: cMoPs_control_water_rep2

source_name: cMoPs, bone marrow, control mouse

value: committed Monocyte Progenitor (cMoP)


title: GMPs_antibiotic_water_rep3

source_name: GMPs, bone marrow, antibiotic-treated mouse


title: CMPs_antibiotic_water_rep3

source_name: CMPs, bone marrow, antibiotic-treated mouse

value: Common Myeloid Progenitor (CMP)


title: GMPs_antibiotic_water_rep1


title: cMoPs_antibiotic_water_rep2

source_name: cMoPs, bone marrow, antibiotic-treated mouse


title: Empty vector3 control organoids cultured 14 months and further grown in full medium for 3 weeks

description:
BRAF3_EV_14m
Exome analysis
processed data file: Exon_seq_results.xlsx

data_processing:
Library strategy: Exome-seq
Potential somatic single nucleotide variants (SNVs) and small insertion/deletions in BrafCA-IND & BrafEV-12m/14m samples were identified using Varscan (v2.3.9) (Koboldt et al., 2012), and the matched BrafEV samples were used as normal control. From the result, somatic mutations were identified based on the following major criteria: (1) high mapping quality bases (read mapping quality ≥30); (2) mutations should not be significantly enriched within 5 bp of the 5′ or 3′ ends of the read; (3) there should be a significant allele frequency change (somatic_p_value <0.05); (4) the variant reads in BrafEV samples should be less than 2, and the variant reads in BrafCA-IND and BrafEV-12m/14m samples should be larger than 5. ANNOVAR was used to annotate confident variant results (Yang and Wang, 2015).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Exon_seq_results.xlsx: Potential somatic single nucleotide variants (SNVs) and small insertion/deletions in Braf_Base and BrafEV-12m/14m samples were identified using Varscan (v2.3.9), and the matched BrafEV samples were used as normal control. As shown in Exon_seq_results.xlsx, the identified somatic single nucleotide variants (SNVs) and small insertion/deletions in BRAF1_Base/BRAF2_Base/BRAF3_Base/BRAF1_EV_12m/BRAF3_EV_14m were listed. We only presented the Missense mutations, Nonsense mutations, and Frameshift mutations. The p-value were calculated by Varscan to represent the significance of allele frequency change. Also, when the mutations hit the frequent mutated genes in COSMIC cancer database, we also annotated them.

source_name: organoid culture

growth_protocol: Male mice from each genotype around the age of 40 days were euthanized by Carbon Dioxide. The first 2.5cm of proximal colon is collected from the mice. The colon crypts were isolated and the culture was established as described previously. Organoids were plated within Matrigel (Corning #356231). Culture media was made of 50% of Wnt3a conditioned media, 20% of R-Spondin conditioned media, 20% of Advanced DMEM/F12 (ThermoFisher #12634010) with B27® (ThermoFisher #17504044), 10% of Noggin conditioned media and EGF. The conditioned media for Wnt3a, R-Spondin and Noggin were made as described previously. A total of 0.5 million cells were injected subcutaneously in NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) (JAX™) with Matrigel. Injection sites were examined every week for tumor growth.

extract_protocol:
DNA was extracted from cells and xenograft tissues was extract using Allprep kit mini or micro (Qiagen).
Fragmented genomic DNA was used for Illumina TruSeq library construction. Paired-end sequencing, resulting in 100 or 150 bases from each end of the DNA fragments for the exome or targeted sequencing libraries, respectively, was performed using Illumina HiSeq 2000/2500 instrumentation.

tag: strain/background

tag: genotype/variation

value: Control

value: Male

value: Proximal colon-derived cultured organoid

tag: culture time

value: 14 months

tag: culture medium

value: Full for 3 weeks


title: Ezh2 KO Adrenal, biological replicate 4

city: Aubiere

first: Pierre

last: Val

address: 24 avenue des Landais

institute: CNRS

description:
KO4_EZH2
Mice are on an uncontrolled mixed genetic background essentially composed of C57BL/6 and SV129.
Gene expression

hyb_protocol: Following fragmentation, CDNA were hybridized for 17h at 45C on GeneChip Mouse Gene 2.0 ST from Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: RMA normalisation was performed with R and the BioConductor package.

source_name: Ezh2 conditional KO

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 500 ng of total RNA (following the GeneChip® WT PLUS Reagent Kit Affymetrix).

extract_protocol: Total RNA were extracted from whole adrenal glands using RNA II nucleotide extraction kit from Macherey Nagel. RNA quality was assessed by Agilent Bioanalyzer chips.

value: sf1:Cre; Ezh2 Fl/Fl

value: Whole adrenal gland

value: Female

value: 2 months


title: Ezh2 KO Adrenal, biological replicate 3

description:
KO3_EZH2
Mice are on an uncontrolled mixed genetic background essentially composed of C57BL/6 and SV129.
Gene expression


title: CMPs_control_water_rep1

source_name: CMPs, bone marrow, control mouse


title: CMPs_control_water_rep2


title: WT Adrenal, biological replicate 3

description:
Ctrl4_EZH2
Mice are on an uncontrolled mixed genetic background essentially composed of C57BL/6 and SV129.
Gene expression

source_name: WT Mouse adrenal

value: WT


title: Empty vector1 control organoids cultured 2 months and further grown in full medium for 3 weeks

description:
BRAF1_EV_2m
Exome analysis
processed data file: Exon_seq_results.xlsx


title: Empty vector3 control organoids cultured 2 months and further grown in full medium for 3 weeks

description:
BRAF3_EV_2m
Exome analysis
processed data file: Exon_seq_results.xlsx


title: GMPs_antibiotic_water_rep2


title: CMPs_control_water_rep3


title: cMoPs_control_water_rep1


title: cMoPs_antibiotic_water_rep1


title: CMPs_antibiotic_water_rep2


title: Ezh2 KO Adrenal, biological replicate 1

description:
KO1_EZH2
Mice are on an uncontrolled mixed genetic background essentially composed of C57BL/6 and SV129.
Gene expression


title: WT Adrenal, biological replicate 1

description:
Ctrl2_EZH2
Mice are on an uncontrolled mixed genetic background essentially composed of C57BL/6 and SV129.
Gene expression


title: Ezh2 KO Adrenal, biological replicate 2

description:
KO2_EZH2
Mice are on an uncontrolled mixed genetic background essentially composed of C57BL/6 and SV129.
Gene expression


title: ChIPseq_H2AK119Ub_TX1072_Hdac3KO_24h_Dox_Rep1

city: Paris

first: Aurélie

last: Bousard

address: 26, rue d'Ulm

institute: Institut Curie

data_processing:
Adapters and low quality bases (<Q20) have been removed with TrimGalore (v0.4.0) (Krueger) and Cutadapt (1.8.2) (Martin et al, 2011).
An ‘N-masked” genome has been generated with SNPSplit (0.3.2) {Krueger, 2016 #2319} which is a version of the mouse reference genome mm10 where all the polymorphic sites for the hybrid strain Mus musculus CAST/EiJ and Mus musculus C57BL/6 are masked by ambiguity nucleobase ‘N’. For all samples, reads were then mapped to the ‘N-masked” genome with Bowtie2 (2.2.5) (Langmead B and Salzberg S, 2012) with options [KOend-to-end -N1 -q]
Duplicates were discarded with Picard MarkDuplicates (1.65) with options [REMOVE_DUPLICATES=true] (DePristo et al., 2011) and reads mapped on blacklisted regions from Encode Consortium (Dunham et al., 2012) were discarded.
SNPSplit (0.3.2) {Krueger, 2016 #2319} was then used to generate allele-specific BAM files by separating the alignment into two distinct alleles (CAST and B6) based on SNPs information downloaded on Sanger {Keane, 2011 #1133}.
Bigwig files were created with bedtools genomeCoverageBed (2.25.0) (Quinlan and Hall, 2010), using a scale factor calculated on the total library (10.000.000/total reads) for both allele specific bigwigs, and loaded on UCSC genome browser (Kent et al., 2002).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

growth_protocol: TX1072 based ESC lines were plated at a density of 1.8mln/T75 flask. After 24hrs of culture in DMEM/15%FCS+LIF+2i cell the medium was supplemented with doxycycline (1ug/ml). Cells were then collected at regular intervals.

extract_protocol:
Cells were isolated in PBS supplemented with 10% Fetal Calf Serum. ATAC experiments were performed according to Buenrostros et al., (2013) protocol and using a homemade transposome from Picelli et al., (2014). 7-8 embryos at 10-12s were dissected in cold PBS for each genotype and cells were mechanically dissociated. Cells were lysed before transposition using 1µL of transposome and purified using a Qiagen MinElute Kit with 10µL of Elution Buffer. Transposed DNA was amplified by PCR as previously described and quantified by qPCR using 5µL of PCR products. The number of additionnal cycles is determined by plotting linear Rn versus cycle and correspond to the one-third of the maximum fluorescence intensity. The remaining 45µL of PCR products are runned with the additional number of cycles. The final product is purified with Qiagen PCR Cleanup Kit and eluted in 20µL Elution Buffer.
Cells were collected using Accutase (Thermo Fisher Scientific), washed twice in ice-cold PBS and counted. Typically, 3.5mln cells were used per immunoprecipitation (IP). A fraction of cells was always used for RNA/FISH verification of Xist induction. Cell pellet was resuspended in 90ul (per 10mln cells) of Lysis Buffer (50mM Tris-HCl, pH7.5; 150mM NaCl;
0.1% sodium deoxycholate;
1% Triton X-100;
5mM CaCl2; Protease Inhibitor Cocktail; 5mM sodium butyrate). After lysing cells on ice for 10min we added 62ul (per 10mln cells) of Lysis Buffer with MNase (500ul buffer + 0.5ul MNase). Chromatin was digested for exactly 10min at 37°C and reaction was stopped by the addition of 20mM EGTA. To remove uindigested debris the lysates were centrifuged at 13000rpm for 5min at 4°C. Supernatant was transferred to a fresh tube, an equal volume of STOP Buffer (50mM Tris-HCl, pH7.5; 150mM NaCl;
0.1% sodium deoxycholate;
1% Triton X-100;
30mM EGTA;
30mM EDTA; Protease Inhibitor Cocktail; 5mM sodium butyrate) was added, samples were stored on ice. 5ul of lysate was digested in 45ul of ProtK Digestion Buffer (20mM HEPES; 1mM EDTA; 0.5% SDS) for 30min at 56°C. 50ul of AMPure XP beads were added to the digested lysate together with 60ul of 20% PEG8000 1.25M NaCl. After mixing the samples were incubated for 15min at RT. Beads were separated on a magnet and washed twice with 80% Ethanol for 30sec. DNA was eluted in 12ul of Low-EDTA TE and DNA concentration was measured using Qubit DNA High-Sensitivity kit. These measurements were used to normalise lysate concentration between samples. DNA isolated in this step was used as the input sample. The volume of each undigested lysate was adjusted for equal concentration and to obtain 1mL per IP using a 1:1 mix of Lysis Buffer and STOP Buffer. We have washed twice anti-mouse Dynabeads (50ul/IP) and Protein-A Dynabeads (10ul/IP) in Blocking Buffer (0.5% BSA; 0.5% Tween in PBS). Beads were then resuspended in Blocking buffer and coated with antibodies for 4hrs at 4°C (anti-mouse Dynabeads: H3K9ac[1ug/IP], H3K4me3[2.5ug/IP], H3K27ac[1ug/IP]; Protein-A dynabeads: H3K4me1[0.4ug/IP], H3K27me3[1ug/IP], H2AK119Ub[0.4ug/IP], H4ac[2ug/IP]). Once coated beads were magnet-separated and resuspended in 1mL of concentration-adjusted lysate. Samples were left rotating overnight at 4°C. Following day beads were magnet-separated and washed quickly with ice-cold washing buffers. anti-H3K4me3 IP was washed 8 times with Low Salt Buffer (0.1% SDS;
1% TritonX-100;
2 mM EDTA;
20 mM Tris-HCl, pH 8.1; 150 mM NaCl;
0.1% sodium deoxycholate). All remaining IPs were washed 4-times with Low Salt Buffer, 2-times with High Salt Buffer (0.1% SDS;
1% TritonX-100;
2 mM EDTA;
20 mM Tris-HCl, pH 8.1; 360 mM NaCl;
0.1% sodium deoxycholate) and 2-times with LiCl buffer (0.25 M LiCl;
1% NP40;1.1% sodium deoxycholate; 1 mM EDTA; 10 mM Tris-HCl pH 8.1). Prior to elution all samples were rinsed once in TE. ChIP-DNA was eluted in ProtK-Digestion buffer for 15min at 56 °C. Beads were separated and the supernatant was further digested for another 2hrs at 56 °C. DNA was isolated using AMPure XP beads as described for the input sample. For each nChIPseq, 0.5ul of each sample was used for qPCR validation of enrichment at control regions. 0.5ul of input samples were also used to verify the digestion efficiency using D1000 tapestation.

value: CAST / C57BL/6

tag: cell line

tag: genotype

tag: condition

value: 24h Dox

tag: replicate

tag: assay

value: ChIP-seq

tag: target

tag: antibody


title: WT Adrenal, biological replicate 2

description:
Ctrl3_EZH2
Mice are on an uncontrolled mixed genetic background essentially composed of C57BL/6 and SV129.
Gene expression

tag: age


title: Empty vector1 control organoids cultured 12 months and further grown in full medium for 3 weeks

description:
BRAF1_EV_12m
Exome analysis
processed data file: Exon_seq_results.xlsx

value: 12 months


title: cMoPs_antibiotic_water_rep3


title: ChIPseq_H2AK119Ub_TX1072_Hdac3KO_0h_Dox_Rep1

value: 0h Dox


title: ChIPseq_H2AK119Ub_TX1072_Hdac3KO_0h_Dox_Rep2


title: ChIPseq_H3K27me3_TX1072_Hdac3KO_24h_Dox_Rep2


title: ChIPseq_H3K27me3_TX1072_Hdac3KO_24h_Dox_Rep1


title: ChIPseq_H3K27me3_TX1072_Hdac3KO_0h_Dox_Rep1


title: EtOH4: gavaged with ethanol（1g/kg bw）

city: Beijing

first: LI

middle: Yong

last: Ning

address: 7 Panjiayuan Nanli

institute: China National Center for Food Safety Risk Assessment

data_processing:
Illumina HiSeq sequencer and software used for sequencing and basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome of mm10 using HISTA. Transcript assembly were performed using Cufflink. DEG analyses were performed using Cuffdiff.
Genome_build: GRCm38（mm10）
Supplementary_files_format_and_content: tab-delimited text files include p-value or q-value for each Sample.

source_name: Liver

growth_protocol: 20-30g C57 male mice, 12 mice per group

extract_protocol:
Liver were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kitwas 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: Four groups of mice were gavaged with  0.5% CMC, 1g/kg bw ethanol, 2500 mg/kg bw DEHP and  DEHP（2500 mg/kg bw） +ethanol（1g/kg bw）, respectively.

value: liver

tag: Sex

value: male


title: EtOH5: gavaged with ethanol（1g/kg bw）

tag: tissue


title: DEHP4: gavaged with DEHP（2500 mg/kg bw）

tag: strain


title: DEHP3: gavaged with DEHP（2500 mg/kg bw）


title: DEHP2: gavaged with DEHP（2500 mg/kg bw）


title: EtOH1: gavaged with ethanol（1g/kg bw）


title: EtOH3: gavaged with ethanol（1g/kg bw）


title: EtOH6: gavaged with ethanol（1g/kg bw）


title: DEHP1: gavaged with DEHP（2500 mg/kg bw）


title: DEHP6: gavaged with DEHP（2500 mg/kg bw）


title: DEHP5: gavaged with DEHP（2500 mg/kg bw）


title: DE3: gavaged with DEHP（2500 mg/kg bw） +ethanol（1g/kg bw）


title: DE5: gavaged with DEHP（2500 mg/kg bw） +ethanol（1g/kg bw）


title: DE4: gavaged with DEHP（2500 mg/kg bw） +ethanol（1g/kg bw）


title: DE6: gavaged with DEHP（2500 mg/kg bw） +ethanol（1g/kg bw）


title: DE2: gavaged with DEHP（2500 mg/kg bw） +ethanol（1g/kg bw）


title: DE1: gavaged with DEHP（2500 mg/kg bw） +ethanol（1g/kg bw）


title: CT4: gavaged with 0.5% CMC


title: CT2: gavaged with 0.5% CMC


title: CT3: gavaged with 0.5% CMC


title: CT5: gavaged with 0.5% CMC


title: CMPs_antibiotic_water_rep1

value: Common Myeloid Progenitor (CMP)


title: ChIPseq_H3K27me3_TX1072_Hdac3KO_0h_Dox_Rep2


title: CT1: gavaged with 0.5% CMC


title: CT6: gavaged with 0.5% CMC


title: BRAF1_EV_2m [BiSulfite-seq]

description:
Control organoids grown in full medium
BRAF1_EV_12m_Vs_BRAF1_EV_2m_Hyper.txt, BRAF1_EV_12m_Vs_BRAF1_EV_2m_Hypo.txt

data_processing:
The quality of the read sequence was examined using the quality control package “FastQC v0.11.7”. The sequence reads were then subjected to adaptor removal and quality trimming using Trim Galore v0.4.4_dev, which comes with additional functionality for the MspI-digested RRBS libraries. Alignment of the sequenced reads was performed using Bismark v0.14.3, and the identified methylation sites were analyzed using the Bismark processing report (Krueger and Andrews, 2011). Guidance from the “M-Bias Plot” was used to further trim the biased methylation sites and the reads were realigned using Bismark (Hansen et al., 2012). For the downstream analysis, “Methylkit” package version 1.7.4 in R platform was used (Akalin et al., 2012). A minimum read coverage of 4 and a minimum quality of 20 was used to call a methylation status of the base. The mouse genome, gene annotations and locations of CpG islands were obtained from the UCSC Genome Browser with the assembly GRCm38/mm10. Differentially methylated regions (DMRs) were identified by using tiling windows of 200 base pairs, minimum average methylation difference of 20 percent and a q-value threshold of 0.01. DMRs were associated with the annotated genomic intervals using the package “Genomation v1.13.0” (Akalin et al., 2015). Statistical significance of the overlap between two groups of methylated genes of various samples were calculated using the website http://nemates.org/MA/progs/overlap_stats.html.
Genome_build: mm10

source_name: Emty vector control organoids cultured 2 months and further grown in full medium for 3 weeks

extract_protocol:
DNA/RNA was extract using Allprep kit mini or micro (Qiagen)
RRBS was performed as previously reported (Petkovich et al., 2017). RRBS library was constructed following exactly the same protocol. Sequencing libraries were sequenced on the Illumina HiSeq 2500 platform using 50bp single-end sequencing with v4 reagents (Bauer Core Facility, Harvard University). Since RRBS libraries generate low complexity libraries, the samples were spiked with ∼10% phiX.
Ligation reactions were set up by adding 4.8 µl of T4 Ligation buffer, 1.6 µl of T4 DNA Ligase (New England Biolabs), and 3.2 of µl TruSeq Nano DNA LT adapter from Illumina that was diluted 1:20, and 6.4 µl of nuclease-free water to the DNA samples. We used 4–6 different indexed adaptors per library.

tag: organoids

value: control

tag: medium

value: full


title: BRAF3_EV_2m [BiSulfite-seq]

description:
Control organoids grown in full medium
BRAF3_EV_14m_Vs_BRAF3_EV_2m_Hyper.txt, BRAF3_EV_14m_Vs_BRAF3_EV_2m_Hypo.txt


title: BRAF3_EV_14m [BiSulfite-seq]

description:
aged organoids grown in full medium for 14 months
BRAF3_EV_14m_Vs_BRAF3_EV_2m_Hyper.txt, BRAF3_EV_14m_Vs_BRAF3_EV_2m_Hypo.txt

value: aged


title: BRAF3_Base [BiSulfite-seq]

description:
BrafV600E organoids grown in Base medium
BRAF3_Base_Vs_BRAF3_EV_Hyper.txt, BRAF3_Base_Vs_BRAF3_EV_Hypo.txt

source_name: BRAF3 organoids cultured 5 months and further grown  in Base medium for 3 weeks

value: 5  months

value: Base


title: BRAF1_EV [BiSulfite-seq]

description:
Control organoids grown in full medium
BRAF1_Base_Vs_BRAF1_EV_Hyper.txt, BRAF1_Base_Vs_BRAF1_EV_Hypo.txt

source_name: Emty vector control organoids cultured 5 months and further grown in full medium for 3 weeks


title: BRAF1_Base [BiSulfite-seq]

description:
BrafV600E organoids grown in Base medium
BRAF1_Base_Vs_BRAF1_EV_Hyper.txt, BRAF1_Base_Vs_BRAF1_EV_Hypo.txt


title: BRAF1_EV_12m [BiSulfite-seq]

description:
aged organoids grown in full medium for 12 months
BRAF1_EV_12m_Vs_BRAF1_EV_2m_Hyper.txt, BRAF1_EV_12m_Vs_BRAF1_EV_2m_Hypo.txt

source_name: Emty vector control organoids cultured 12 months and further grown in full medium for 3 weeks


title: untreated B16F10 3D spheroid, 3rd replicate

city: Epalinges

first: Tatiana

last: Petrova

state: VD

address: 155, Chemin des Boveresses

institute: University of Lausanne

data_processing:
Target transcript sequences were obtained from ENSEMBLE (GRCm38.p6), and the abundance of transcripts were quantified using kallisto (0.44.0) with default parameters.
Kallisto's transcript-level estimates were summarized at the gene-level using tximport (1.8.0) from Bioconductor.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited text file providing gene-by-sample matrix of estimated counts.

source_name: B16F10 3D spheroids

growth_protocol: 500 B16F10 cells were plated in 50 µl of 7 mg/ml Matrigel (Corning, 356231)

extract_protocol:
RNA was extracted using QIAGEN RNeasy Plus Mini Kit following the manufacturer's instructions
Illumina TruSeq, 500 ng of total RNA

treatment_protocol: 100 ng/ml BMP2 or PBS for 10 days

tag: batch


title: untreated B16F10 3D spheroid, 1st replicate


title: ChIPseq_H2AK119Ub_TX1072_WT_24h_Dox_Rep2

data_processing:
Adapters and low quality bases (<Q20) have been removed with TrimGalore (v0.4.0) (Krueger) and Cutadapt (1.8.2) (Martin et al, 2011).
An ‘N-masked” genome has been generated with SNPSplit (0.3.2) {Krueger, 2016 #2319} which is a version of the mouse reference genome mm10 where all the polymorphic sites for the hybrid strain Mus musculus CAST/EiJ and Mus musculus C57BL/6 are masked by ambiguity nucleobase ‘N’. For all samples, reads were then mapped to the ‘N-masked” genome with Bowtie2 (2.2.5) (Langmead B and Salzberg S, 2012) with options [KOend-to-end -N1 -q].
Duplicates were discarded with Picard MarkDuplicates (1.65) with options [REMOVE_DUPLICATES=true] (DePristo et al., 2011) and reads mapped on blacklisted regions from Encode Consortium (Dunham et al., 2012) were discarded.
SNPSplit (0.3.2) {Krueger, 2016 #2319} was then used to generate allele-specific BAM files by separating the alignment into two distinct alleles (CAST and B6) based on SNPs information downloaded on Sanger {Keane, 2011 #1133}.
Bigwig files were created with bedtools genomeCoverageBed (2.25.0) (Quinlan and Hall, 2010), using a scale factor calculated on the total library (10.000.000/total reads) for both allele specific bigwigs, and loaded on UCSC genome browser (Kent et al., 2002).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

growth_protocol: TX1072 (mouse, female, [Mus musculus castaneus X C57BL/6] embryonic stem cells) cells have been previously derived in the lab {Schulz, 2014 #1419}. Hdac3-/-clones have been derived from the TX1072 line by CRISPR/Cas9 targeting. Cells were cultured on gelatin-coated plates in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% foetal bovine serum, 2-mercaptoethanol (0.1mM), LIF(1000u/mL) and 2i (PD0325901 [0.4 mM], CHIR99021 [3 mM]) {Ying, 2008 #767}.

extract_protocol:
Cells were collected using Accutase (Thermo Fisher Scientific), washed twice in ice-cold PBS and counted. Typically, 3.5mln cells were used per immunoprecipitation (IP). A fraction of cells was always used for RNA/FISH verification of Xist induction. Cell pellet was resuspended in 90ul (per 10mln cells) of Lysis Buffer (50mM Tris-HCl, pH7.5; 150mM NaCl;
0.1% sodium deoxycholate;
1% Triton X-100;
5mM CaCl2; Protease Inhibitor Cocktail; 5mM sodium butyrate). After lysing cells on ice for 10min we added 62ul (per 10mln cells) of Lysis Buffer with MNase (500ul buffer + 0.5ul MNase). Chromatin was digested for exactly 10min at 37°C and reaction was stopped by the addition of 20mM EGTA. To remove uindigested debris the lysates were centrifuged at 13000rpm for 5min at 4°C. Supernatant was transferred to a fresh tube, an equal volume of STOP Buffer (50mM Tris-HCl, pH7.5; 150mM NaCl;
0.1% sodium deoxycholate;
1% Triton X-100;
30mM EGTA;
30mM EDTA; Protease Inhibitor Cocktail; 5mM sodium butyrate) was added, samples were stored on ice.  5ul of lysate was digested in 45ul of ProtK Digestion Buffer (20mM HEPES; 1mM EDTA; 0.5% SDS) for 30min at 56°C. 50ul of AMPure XP beads were added to the digested lysate together with 60ul of 20% PEG8000 1.25M NaCl. After mixing the samples were incubated for 15min at RT. Beads were separated on a magnet and washed twice with 80% Ethanol for 30sec. DNA was eluted in 12ul of Low-EDTA TE and DNA concentration was measured using Qubit DNA High-Sensitivity kit. These measurements were used to normalise lysate concentration between samples. DNA isolated in this step was used as the input sample. The volume of each undigested lysate was adjusted for equal concentration and to obtain 1mL per IP using a 1:1 mix of Lysis Buffer and STOP Buffer.  We have washed twice anti-mouse Dynabeads (50ul/IP) and Protein-A Dynabeads (10ul/IP) in Blocking Buffer (0.5% BSA; 0.5% Tween in PBS). Beads were then resuspended in Blocking buffer and coated with antibodies for 4hrs at 4°C (anti-mouse Dynabeads: H3K9ac[1ug/IP], H3K4me3[2.5ug/IP], H3K27ac[1ug/IP]; Protein-A dynabeads: H3K4me1[0.4ug/IP], H3K27me3[1ug/IP], H2AK119Ub[0.4ug/IP], H4ac[2ug/IP]). Once coated beads were magnet-separated and resuspended in 1mL of concentration-adjusted lysate. Samples were left rotating overnight at 4°C.  Following day beads were magnet-separated and washed quickly with ice-cold washing buffers. anti-H3K4me3 IP was washed 8 times with Low Salt Buffer (0.1% SDS;
1% TritonX-100;
2 mM EDTA;
20 mM Tris-HCl, pH 8.1; 150 mM NaCl;
0.1% sodium deoxycholate). All remaining IPs were washed 4-times with Low Salt Buffer, 2-times with High Salt Buffer (0.1% SDS;
1% TritonX-100;
2 mM EDTA;
20 mM Tris-HCl, pH 8.1; 360 mM NaCl;
0.1% sodium deoxycholate) and 2-times with LiCl buffer (0.25 M LiCl;
1% NP40;1.1% sodium deoxycholate; 1 mM EDTA; 10 mM Tris-HCl pH 8.1). Prior to elution all samples were rinsed once in TE. ChIP-DNA was eluted in ProtK-Digestion buffer for 15min at 56 °C. Beads were separated and the supernatant was further digested for another 2hrs at 56 °C. DNA was isolated using AMPure XP beads as described for the input sample.  For each nChIPseq, 0.5ul of each sample was used for qPCR validation of enrichment at control regions. 0.5ul of input samples were also used to verify the digestion efficiency using D1000 tapestation.
Library preparation was done using Ovation® Ultralow Library System V2 following suppliers protocol. Amplified libraries were size-selected for dinucleotide fraction (350-600bp fragments) using agarose gel-separation and MinElute Gel Extraction Kit (Qiagen). Sample quality was inspected using D1000 tapestation. Samples were sequenced with Illumina HiSeq 2500 using PE100 mode.

treatment_protocol: TX1072 based ESC lines were plated at a density of 1.8mln/T75 flask. After 24hrs of culture in DMEM/15%FCS+LIF+2i cell the medium was supplemented with doxycycline (1ug/ml). Cells were then collected at regular intervals.

tag: strain background

tag: genotype/variation

value: ChIPseq


title: ChIPseq_H3K27me3_TX1072_WT_24h_Dox_Rep2


title: old transgenic 3

city: Sydney

first: Lars

middle: M

last: Ittner

state: NSW

address: Research Dirve

country: Australia

institute: Macquarie University

description:
20161109_old_wt_tg.csv
20161109_RNASeq_FPKM1_Log2FC058_sorted_ALL young old.xlsx
Sample 6

data_processing:
Sequencing was subsequently performed on the Illumina HiSeq 2500 platform following the HiSeq 2500 System User Guide Document #15035786 v01 HCS 2.2.70 protocol and using HCS version 2.2 for sequencing control. All samples generated >3 billion base pair reads of 100bp paired-ends reads which corresponds to 50x coverage. The HISAT2, StringTie and Ballgown pipeline was used for analysis as previously described (Pertea et al. 2016)
Reads were mapped against the mm10 Mus musculus reference genome using HISAT2 version 2.0.4 with the “–dta” option and sorted using samtools version 0.0.19. The subsequent sorted alignment data was compared to the GRCm38.85 assembly release to estimate transcript abundance and table counts using StringTie version 1.3.0 with options “-B –f 0.1 –m 200 –g 50”
Output from StringTie was used for differential expression analysis in Ballgown version 2.2.0 on the RStudio platform using R version 3.4.2. FPKM for between group comparison was performed using the stattest() function in Ballgown.
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs and Log2FC

source_name: old transgenic

growth_protocol: Mice were maintained on a pure C57Bl/6J background and held in littermate groups on a 12-hour light/dark cycle with access to standard chow and water ad libitum.

extract_protocol:
RNA extraction was performed using Maxwell 16 LEV simplyRNA tissue kits (Promega)
library construction performed using TruSeq Stranded Total RNA with Ribo-Zero Gold sample prep kit & TruSeq rapid SBS kit

treatment_protocol: No treatment

value: transgenic (TAU58/2)

value: 10 months

value: cortex


title: old control 3

description:
20161109_old_wt_tg.csv
20161109_RNASeq_FPKM1_Log2FC058_sorted_ALL young old.xlsx
Sample 4

source_name: old control

value: non-transgenic


title: young transgenic 2

description:
20161109_young_wt_tg.csv
20161109_RNASeq_FPKM1_Log2FC058_sorted_ALL young old.xlsx
Sample 8

source_name: young transgenic

value: 3 months


title: old control 1

description:
20161109_old_wt_tg.csv
20161109_RNASeq_FPKM1_Log2FC058_sorted_ALL young old.xlsx
Sample 2


title: young control 2

description:
20161109_young_wt_tg.csv
20161109_RNASeq_FPKM1_Log2FC058_sorted_ALL young old.xlsx
Sample 11

source_name: young control


title: young control 1

description:
20161109_young_wt_tg.csv
20161109_RNASeq_FPKM1_Log2FC058_sorted_ALL young old.xlsx
Sample 9


title: young control 3

description:
20161109_young_wt_tg.csv
20161109_RNASeq_FPKM1_Log2FC058_sorted_ALL young old.xlsx
Sample 12


title: old transgenic 1

description:
20161109_old_wt_tg.csv
20161109_RNASeq_FPKM1_Log2FC058_sorted_ALL young old.xlsx
Sample 1


title: Bmp2-treated B16F10 3D spheroid, 2nd replicate


title: BRAF3_EV [BiSulfite-seq]

description:
Control organoids grown in full medium
BRAF3_Base_Vs_BRAF3_EV_Hyper.txt, BRAF3_Base_Vs_BRAF3_EV_Hypo.txt

tag: culture time


title: young transgenic 1

description:
20161109_young_wt_tg.csv
20161109_RNASeq_FPKM1_Log2FC058_sorted_ALL young old.xlsx
Sample 7


title: ChIPseq_H3K4me3_TX1072_WT_24h_Dox_Rep2

value: CAST / C57BL/6

tag: cell line

value: WT

value: 24h Dox


title: young transgenic 3

description:
20161109_young_wt_tg.csv
20161109_RNASeq_FPKM1_Log2FC058_sorted_ALL young old.xlsx
Sample 10

tag: genotype


title: EtOH2: gavaged with ethanol（1g/kg bw）

value: liver


title: old transgenic 2

description:
20161109_old_wt_tg.csv
20161109_RNASeq_FPKM1_Log2FC058_sorted_ALL young old.xlsx
Sample 5


title: ChIPseq_H4ac_TX1072_WT_24h_Dox_Rep2

tag: condition


title: ChIPseq_H3K27ac_TX1072_WT_24h_Dox_Rep2

tag: replicate


title: ChIPseq_H3K9ac_TX1072_WT_24h_Dox_Rep2

tag: assay


title: Bmp2-treated B16F10 3D spheroid, 3rd replicate


title: old control 2

description:
20161109_old_wt_tg.csv
20161109_RNASeq_FPKM1_Log2FC058_sorted_ALL young old.xlsx
Sample 3


title: Bmp2-treated B16F10 3D spheroid, 1st replicate


title: ChIPseq_H2AK119Ub_TX1072_WT_24h_Dox_Rep1

tag: target


title: ChIPseq_Input_TX1072_WT_24h_Dox_Rep2

value: Input


title: ChIPseq_H3K4me1_TX1072_WT_24h_Dox_Rep2

tag: antibody


title: ChIPseq_H3K27me3_TX1072_WT_24h_Dox_Rep1


title: ChIPseq_H3K4me3_TX1072_WT_24h_Dox_Rep1


title: ChIPseq_H3K4me1_TX1072_WT_24h_Dox_Rep1


title: ChIPseq_H4ac_TX1072_WT_24h_Dox_Rep1


title: ChIPseq_H2AK119Ub_TX1072_WT_12h_Dox_Rep2

value: 12h Dox


title: ChIPseq_H3K27ac_TX1072_WT_24h_Dox_Rep1


title: ChIPseq_Input_TX1072_WT_24h_Dox_Rep1


title: ChIPseq_H3K27me3_TX1072_WT_12h_Dox_Rep2


title: ChIPseq_H3K9ac_TX1072_WT_24h_Dox_Rep1


title: ChIPseq_H3K4me3_TX1072_WT_12h_Dox_Rep2


title: ChIPseq_H4ac_TX1072_WT_12h_Dox_Rep2


title: ChIPseq_H3K4me1_TX1072_WT_12h_Dox_Rep2


title: ChIPseq_Input_TX1072_WT_12h_Dox_Rep2


title: ChIPseq_H3K9ac_TX1072_WT_12h_Dox_Rep2


title: ChIPseq_H3K27me3_TX1072_WT_8h_Dox_Rep1

value: 8h Dox


title: ChIPseq_H2AK119Ub_TX1072_WT_12h_Dox_Rep1


title: ChIPseq_H3K27ac_TX1072_WT_12h_Dox_Rep2


title: untreated B16F10 3D spheroid, 2nd replicate


title: ChIPseq_H3K4me3_TX1072_WT_12h_Dox_Rep1


title: ChIPseq_H4ac_TX1072_WT_12h_Dox_Rep1


title: ChIPseq_H3K27ac_TX1072_WT_12h_Dox_Rep1


title: ChIPseq_H3K9ac_TX1072_WT_12h_Dox_Rep1


title: ChIPseq_H3K4me1_TX1072_WT_12h_Dox_Rep1


title: ChIPseq_H3K27me3_TX1072_WT_8h_Dox_Rep2


title: ChIPseq_H2AK119Ub_TX1072_WT_8h_Dox_Rep2


title: ChIPseq_Input_TX1072_WT_12h_Dox_Rep1


title: ChIPseq_H2AK119Ub_TX1072_WT_8h_Dox_Rep1


title: ChIPseq_H3K4me3_TX1072_WT_8h_Dox_Rep1


title: ChIPseq_H3K27ac_TX1072_WT_8h_Dox_Rep1


title: ChIPseq_H4ac_TX1072_WT_8h_Dox_Rep1


title: ChIPseq_H3K4me1_TX1072_WT_8h_Dox_Rep1


title: ChIPseq_Input_TX1072_WT_8h_Dox_Rep2


title: ChIPseq_H3K4me3_TX1072_WT_8h_Dox_Rep2


title: ChIPseq_H3K27ac_TX1072_WT_8h_Dox_Rep2


title: ChIPseq_H3K4me3_TX1072_WT_4h_Dox_Rep2

value: 4h Dox


title: ChIPseq_H3K27me3_TX1072_WT_4h_Dox_Rep2


title: ChIPseq_H4ac_TX1072_WT_4h_Dox_Rep2


title: ChIPseq_H3K27me3_TX1072_WT_12h_Dox_Rep1


title: ChIPseq_H3K9ac_TX1072_WT_8h_Dox_Rep1


title: ChIPseq_H3K4me1_TX1072_WT_8h_Dox_Rep2


title: ChIPseq_H4ac_TX1072_WT_8h_Dox_Rep2


title: ChIPseq_H3K9ac_TX1072_WT_8h_Dox_Rep2


title: ChIPseq_H3K4me1_TX1072_WT_4h_Dox_Rep2


title: ChIPseq_Input_TX1072_WT_8h_Dox_Rep1


title: ChIPseq_H3K9ac_TX1072_WT_4h_Dox_Rep2


title: ChIPseq_H2AK119Ub_TX1072_WT_4h_Dox_Rep2


title: ChIPseq_H3K27ac_TX1072_WT_4h_Dox_Rep2


title: ChIPseq_H3K27me3_TX1072_WT_4h_Dox_Rep1


title: ChIPseq_H3K4me1_TX1072_WT_4h_Dox_Rep1


title: ChIPseq_H3K4me3_TX1072_WT_4h_Dox_Rep1


title: ChIPseq_Input_TX1072_WT_4h_Dox_Rep2


title: ChIPseq_H2AK119Ub_TX1072_WT_4h_Dox_Rep1


title: ChIPseq_H4ac_TX1072_WT_4h_Dox_Rep1


title: ChIPseq_H3K9ac_TX1072_WT_4h_Dox_Rep1


title: ChIPseq_H3K27ac_TX1072_WT_4h_Dox_Rep1


title: ChIPseq_H3K4me1_TX1072_WT_0h_Dox_Rep1

value: 0h Dox


title: ChIPseq_H4ac_TX1072_WT_0h_Dox_Rep2


title: ChIPseq_H3K9ac_TX1072_WT_0h_Dox_Rep2


title: ChIPseq_H4ac_TX1072_WT_0h_Dox_Rep1


title: ChIPseq_Input_TX1072_WT_0h_Dox_Rep2


title: ChIPseq_H2AK119Ub_TX1072_WT_0h_Dox_Rep1


title: ChIPseq_H3K27ac_TX1072_WT_0h_Dox_Rep2


title: ChIPseq_H3K4me1_TX1072_WT_0h_Dox_Rep2


title: ChIPseq_H2AK119Ub_TX1072_WT_0h_Dox_Rep2


title: ChIPseq_H3K9ac_TX1072_WT_0h_Dox_Rep1


title: ChIPseq_H3K4me3_TX1072_WT_0h_Dox_Rep1


title: ChIPseq_Input_TX1072_Hdac3KO_8h_Dox_Rep2


title: ChIPseq_Input_TX1072_WT_0h_Dox_Rep1


title: ChIPseq_H3K27ac_TX1072_Hdac3KO_24h_Dox_Rep2


title: ChIPseq_H3K27me3_TX1072_WT_0h_Dox_Rep1


title: ChIPseq_H4ac_TX1072_Hdac3KO_8h_Dox_Rep2


title: ChIPseq_H3K27me3_TX1072_WT_0h_Dox_Rep2


title: ChIPseq_Input_TX1072_WT_4h_Dox_Rep1


title: ChIPseq_Input_TX1072_Hdac3KO_24h_Dox_Rep2


title: ChIPseq_H3K27ac_TX1072_Hdac3KO_0h_Dox_Rep2


title: ChIPseq_H3K4me3_TX1072_WT_0h_Dox_Rep2


title: ChIPseq_H3K27ac_TX1072_WT_0h_Dox_Rep1


title: ChIPseq_H3K27ac_TX1072_Hdac3KO_8h_Dox_Rep2


title: ChIPseq_H4ac_TX1072_Hdac3KO_24h_Dox_Rep1


title: ChIPseq_Input_TX1072_Hdac3KO_0h_Dox_Rep2


title: ChIPseq_H3K27ac_TX1072_Hdac3KO_24h_Dox_Rep1


title: ChIPseq_H2AK119Ub_TX1072_Hdac3KO_24h_Dox_Rep2

value: ChIP-seq


title: ChIPseq_Input_TX1072_Hdac3KO_24h_Dox_Rep1


title: ChIPseq_H4ac_TX1072_Hdac3KO_8h_Dox_Rep1


title: ChIPseq_Input_TX1072_Hdac3KO_8h_Dox_Rep1


title: ChIPseq_H4ac_TX1072_Hdac3KO_0h_Dox_Rep1


title: RNAseq_TX1072_Hdac3KO_0h_Dox_Rep1

data_processing:
Reads were first mapped on rRNA with Tophat (2.1.0) (Trapnell et al., 2009), with options [-g 1 KOno-coverage-search KOlibrary-type fr-secondstrand]. Paired unmapped reads were then used to reconstruct fastq files with bedTools bamToFastq (2.25.0) (Quinlan and Hall, 2010). Those files were then mapped with Tophat (2.1.0) (Trapnell et al., 2009), with options [-p 8 -g 1 -x 1 -N 3 KOread-edit-dist 3 KOno-coverage-search KOlibrary-type fr-secondstrand], with refFlat annotation.
Reads covering exons of each gene were then counted with featureCounts (1.5.1) with options [-C -p -s 1 -T 8] (Liao et al., 2014).
D-scores were then calculated for genes with minimum 10 allelic reads.
Genome_build: mm10
Supplementary_files_format_and_content: Count table per gene including : BL6 counts, CAST counts, d-score, total counts

growth_protocol: TX1072 (mouse, female, [Mus musculus castaneus X C57BL/6] embryonic stem cells) cells have been previously derived in the lab (Schulz et al, 2014). Hdac3KO clones have been derived from the TX1072 line by CRISPR/Cas9 targeting. Cells were cultured on gelatin-coated plates in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% foetal bovine serum, 2-mercaptoethanol (0.1mM), LIF(1000u/mL) and 2i (PD0325901 [0.4 mM], CHIR99021 [3 mM]) (Ying et al., 2008).

extract_protocol:
RNA was extracted according to the manufacturer’s recommendations using RNeasy Mini Kit (Qiagen) with on-column DNAse digestion (Qiagen). For cDNA synthesis 1.1ug RNA was reverse transcribed using Superscript III Reverse Transcriptase (Thermo Fisher Scientific).
RNA was prepared as described above and quality of samples were verified by Tapestation. Only samples with RIN score above 9 were processed. 100 ng of RNA was used for library preparation using Ovation® Mouse RNAseq System that uses mouse-specific InDA-C depletion of rRNA. Manufacturers recommendations were followed. Libraries were sequenced using HiSeq2500 at PE100 settings.


title: ChIPseq_H3K27ac_TX1072_Hdac3KO_0h_Dox_Rep1


title: RNAseq_TX1072_WT_24h_Dox_Rep2


title: ChIPseq_H3K27ac_TX1072_Hdac3KO_8h_Dox_Rep1


title: RNAseq_TX1072_WT_0h_Dox_Rep2


title: ChIPseq_Input_TX1072_Hdac3KO_0h_Dox_Rep1


title: RNAseq_TX1072_Hdac3KO_24h_Dox_Rep1


title: ChIPseq_H3K27me3_TXY_Xist_D2_Dox_Rep1

data_processing:
Adapters and low quality bases (<Q20) have been removed with TrimGalore (v0.4.0) (Krueger) and Cutadapt (1.8.2) (Martin et al, 2011).
Reads were then mapped to mm10 genome with Bowtie2 (2.2.5) (Langmead B and Salzberg S, 2012) with options [--end-to-end -N1 -q].
Reads mapped with low quality (<q10) were removed with Samtools (Li et al., 2009)
Duplicates were discarded with Picard MarkDuplicates (1.65) with options [REMOVE_DUPLICATES=true] (DePristo et al., 2011) and reads mapped on blacklisted regions from Encode Consortium (Dunham et al., 2012) were discarded.
Bigwig files were created with bedtools genomeCoverageBed (2.25.0) (Quinlan and Hall, 2010)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

growth_protocol: TXY:Xist and TXY:XistΔA (mouse, male embryonic stem cells) were obtained from the Wutz team {Wutz, 2002 #1960}. These lines were cultured on gelatin-coated plates in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% foetal bovine serum, 2-mercaptoethanol (50mM) and LIF (1000u/mL). All cells were incubated at 37°C with 8% CO2.

extract_protocol:
Cells were collected using Accutase (Thermo Fisher Scientific), washed twice in ice-cold PBS and counted. Typically, 3.5mln cells were used per immunoprecipitation (IP). A fraction of cells was always used for RNA/FISH verification of Xist induction. Cell pellet was resuspended in 90ul (per 10mln cells) of Lysis Buffer (50mM Tris-HCl, pH7.5; 150mM NaCl; 0.1% sodium deoxycholate; 1% Triton X-100; 5mM CaCl2; Protease Inhibitor Cocktail; 5mM sodium butyrate). After lysing cells on ice for 10min we added 62ul (per 10mln cells) of Lysis Buffer with MNase (500ul buffer + 0.5ul MNase). Chromatin was digested for exactly 10min at 37°C and reaction was stopped by the addition of 20mM EGTA. To remove undigested debris the lysates were centrifuged at 13000rpm for 5min at 4°C. Supernatant was transferred to a fresh tube, an equal volume of STOP Buffer (50mM Tris-HCl, pH7.5; 150mM NaCl; 0.1% sodium deoxycholate; 1% Triton X-100; 30mM EGTA; 30mM EDTA; Protease Inhibitor Cocktail; 5mM sodium butyrate) was added, samples were stored on ice. 5ul of lysate was digested in 45ul of ProtK Digestion Buffer (20mM HEPES; 1mM EDTA; 0.5% SDS) for 30min at 56°C. 50ul of AMPure XP beads were added to the digested lysate together with 60ul of 20% PEG8000 1.25M NaCl. After mixing the samples were incubated for 15min at RT. Beads were separated on a magnet and washed twice with 80% Ethanol for 30sec. DNA was eluted in 12ul of Low-EDTA TE and DNA concentration was measured using Qubit DNA High-Sensitivity kit. These measurements were used to normalise lysate concentration between samples. DNA isolated in this step was used as the input sample. The volume of each undigested lysate was adjusted for equal concentration and to obtain 1mL per IP using a 1:1 mix of Lysis Buffer and STOP Buffer. We have washed twice anti-mouse Dynabeads (50ul/IP) and Protein-A Dynabeads (10ul/IP) in Blocking Buffer (0.5% BSA; 0.5% Tween in PBS). Beads were then resuspended in Blocking buffer and coated with antibodies for 4hrs at 4°C (anti-mouse Dynabeads: H3K9ac [1ug/IP], H3K4me3 [2.5ug/IP], H3K27ac [1ug/IP]; Protein-A dynabeads: H3K4me1 [0.4ug/IP], H3K27me3 [1ug/IP], H2AK119Ub [0.4ug/IP], H4ac [2ug/IP]). Once coated beads were magnet-separated and resuspended in 1mL of concentration-adjusted lysate. Samples were left rotating overnight at 4°C. Following day beads were magnet-separated and washed quickly with ice-cold washing buffers. anti-H3K4me3 IP was washed 8 times with Low Salt Buffer (0.1% SDS; 1% TritonX-100; 2 mM EDTA; 20 mM Tris-HCl, pH 8.1; 150 mM NaCl; 0.1% sodium deoxycholate). All remaining IPs were washed 4-times with Low Salt Buffer, 2-times with High Salt Buffer (0.1% SDS; 1% TritonX-100; 2 mM EDTA; 20 mM Tris-HCl, pH 8.1; 360 mM NaCl; 0.1% sodium deoxycholate) and 2-times with LiCl buffer (0.25 M LiCl; 1% NP40; 1.1% sodium deoxycholate; 1 mM EDTA; 10 mM Tris-HCl pH 8.1). Prior to elution all samples were rinsed once in TE. ChIP-DNA was eluted in ProtK-Digestion buffer for 15min at 56 °C. Beads were separated and the supernatant was further digested for another 2hrs at 56 °C. DNA was isolated using AMPure XP beads as described for the input sample. For each nChIPseq, 0.5ul of each sample was used for qPCR validation of enrichment at control regions. 0.5ul of input samples were also used to verify the digestion efficiency using D1000 tapestation.
Library preparation was done using Ovation Ultralow Library System V2 following suppliers protocol. Amplified libraries were size-selected for dinucleotide fraction (350-600bp fragments) using agarose gel-separation and MinElute Gel Extraction Kit (Qiagen). Sample quality was inspected using D1000 tapestation. Samples were sequenced with HiSeq2500 using PE100 mode.

treatment_protocol: For TXY based ESC lines we have plated them at a density of 1mln/T75. After 24hrs of culture in DMEM/15%FCS+LIF cells were washed twice with PBS and medium was changed to DMEM/10%FCS-LIF with our without doxycycline (1.5ug/ml). Cells were collected after 48hrs of differentiation.

value: TXY

value: XistWT

tag: chip antibody


title: RNAseq_TX1072_Hdac3KO_24h_Dox_Rep2


title: RNAseq_TX1072_WT_24h_Dox_Rep1


title: RNAseq_TX1072_WT_0h_Dox_Rep1


title: RNAseq_TX1072_Hdac3KO_0h_Dox_Rep2


title: ChIPseq_H2AK119Ub_TXY_Xist_D2_Dox_Rep2


title: ChIPseq_H2AK119Ub_TXY_Xist_D2_noDox_Rep2


title: ChIPseq_H3K27me3_TXY_Xist_D2_noDox_Rep1


title: ChIPseq_H3K27me3_TXY_Xist_D2_noDox_Rep2


title: ChIPseq_H3K27ac_TXY_Xist_D2_Dox_Rep2


title: ChIPseq_H3K27me3_TXY_Xist_D2_Dox_Rep2


title: ChIPseq_H3K27ac_TXY_Xist_D2_Dox_Rep1


title: ChIPseq_H2AK119Ub_TXY_Xist_D2_Dox_Rep1


title: ChIPseq_input_TXY_Xist_D2_noDox_Rep1

value: input


title: ChIPseq_H2AK119Ub_TXY_Xist_D2_noDox_Rep1


title: ChIPseq_H2AK119Ub_TXY_XistdeltaA_D2_Dox_Rep2

value: Xist{delta}A


title: ChIPseq_H3K27ac_TXY_Xist_D2_noDox_Rep1


title: ChIPseq_H3K27me3_TXY_XistdeltaA_D2_Dox_Rep2


title: ChIPseq_H2AK119Ub_TXY_XistdeltaA_D2_Dox_Rep1


title: ChIPseq_H2AK119Ub_TXY_XistdeltaA_D2_noDox_Rep2


title: ChIPseq_H3K27ac_TXY_Xist_D2_noDox_Rep2


title: ChIPseq_H3K27ac_TXY_XistdeltaA_D2_noDox_Rep1


title: ChIPseq_H3K27ac_TXY_XistdeltaA_D2_Dox_Rep2


title: ChIPseq_input_TXY_XistdeltaA_D2_noDox_Rep1


title: BRAF3_EV

description:
Normalized_methylationProfile.txt
BRAF3_EV

data_processing:
Reads were aligned to the mm10 mouse reference genome using bowtie2 (Langmead and Salzberg, 2012) and duplicated reads were removed. For identifying differential methylated CpG-island promoters, the data was normalized using TMM normalization (Trimmed Mean of M-values)(Robinson and Oshlack, 2010). After normalization, the sum of MBD-seq counts for each promoter region with CpG-islands and without CpG-island was computed. Promoters with CpG-islands are defined as any promoter TSS regions within 500bp from an annotated CpG-island (downloaded from UCSC).
Genome_build: mm10
Supplementary_files_format_and_content: Text file containing normalized data binned in 200 bp windows

source_name: Empty vector control organoids cultured 5 months and further grown in full medium for 3 weeks before microarray

extract_protocol:
DNA/RNA was extract using Allprep kit mini or micro (Qiagen)
For genome-wide DNA methylation analysis, we carried out MBD-seq, but with significant modifications at the SKCCC Experimental and Computational Genomics Core at the Johns Hopkins University. Briefly, 100 ~ 200 ng of genomic DNA was sonicated to an average size of 200 ~ 400 bp and subsequently methylated DNA fragments were enriched using modified MBD polypeptides immobilized on protein A magnetic beads (NEB, EpiMark Methylated DNA Enrichment Kit) according to the manufacturer’s protocol. Then, the enriched DNA fragments were eluted and prepared as barcoded next generation sequencing libraries using the ThruPlex DNA library preparation kit (Rubicon Genomics) according to the supplied protocols. The libraries were then sequenced by massively-parallel 50-bp single-end sequencing on an Illumina HiSeq 2500 in rapid run mode.
Enriched DNA fragments were eluted and prepared as barcoded next generation sequencing libraries using the ThruPlex DNA library preparation kit (Rubicon Genomics) according to the supplied protocols.

tag: culture

value: organoid


title: BRAF3_5mo

description:
Normalized_methylationProfile.txt
BRAF3_5mo

source_name: BRAF3 organoids cultured 5 months and further grown in full medium for 3 weeks before microarray


title: ChIPseq_H2AK119Ub_TXY_XistdeltaA_D2_noDox_Rep1


title: ChIPseq_H3K27me3_TXY_XistdeltaA_D2_noDox_Rep1


title: ChIPseq_H3K27ac_TXY_XistdeltaA_D2_noDox_Rep2


title: ChIPseq_H3K27me3_TXY_XistdeltaA_D2_Dox_Rep1


title: ChIPseq_H3K27ac_TXY_XistdeltaA_D2_Dox_Rep1


title: BRAF3_Base

description:
Normalized_methylationProfile.txt
BRAF3_Base

source_name: BRAF3 organoids cultured 5 months and further grown in Base medium for 3 weeks before microarray


title: RNAP-ser5 Taf5l-KO

city: Melbourne

first: Partha

last: Das

state: Victoria

address: 211 Wellington Road

department: Anatomy & Developmental Biology

institute: Monash University

data_processing:
The 50bp single end reads were mapped to the mm9 mouse genome assembly using Bowtie 2 (v2.3.2).
BigWig tracks were generated using the ‘bamCoverage’ program from the DeepTools software suite (v2.5.3), with reads extended to 300bp and tracks normalized using the  RPKM (Reads Per Kilobase per Million mapped reads) algorithm.
Peak calling was done with the MACS2 program (v2.1.1.20160309). For most ChIP-seq datasets default MACS2 settings were used. For the TAF5L-FB and TAF6L-FB datasets MACS2 was run with the “--nomodel” option and a fragment size of 300bp due to low numbers of peaks identified with the default settings with model generation.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig tracks were generated using the ‘bamCoverage’ program from the DeepTools software suite (v2.5.3). Peak files were generated using the MACS2 program (v2.1.1.20160309), and are in its '.xls' peak file format.

source_name: Embryonic Stem Cell

growth_protocol: Mouse ESCs (mESCs) were cultured in mouse ESC media that contains DMEM, supplemented with 15% fetal calf serum, 0.1mM b-mercaptoethanol, 2mM L-glutamine, 0.1mM NEAA, 1% of nucleoside mix , 1000 U/ml LIF/ESGRO, and 50U/ml Penicillin/Streptomycin. mESCs were cultured at 37ºC, 5% CO2.

extract_protocol:
Chromatin Immunoprecipitation (ChIP) was performed as described previously (Kim et al., 2009; Das et al., 2014). For bioChIP reactions, streptavidin beads (Dynabeads MyOne Streptavidin T1- Invitrogen) were used for the precipitation of chromatin, and 2% SDS was applied for first washing step. All other steps were same as conventional ChIP protocol.
2-10 ng of purified ChIP DNA was used to prepare sequencing libraries, using NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB) and NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

treatment_protocol: mESCs were crosslinked with 37% formaldehyde solution to a final concentration of 1% for 8 min at room temperature with gentle shaking; the reaction was quenched by adding 2.5M glycine to a final concentration of 0.125M (Das et al., 2014; Das et al.,2015)

value: 3e8-5, Chromotek

value: Taf5l KO


title: RNAP-ser5 Taf6l-KO

value: Taf6l KO


title: RNAP Taf5l-KO

value: 1c7-5, Chromotek


title: RNAP-ser5 Wild-type

value: WT


title: RNAP Taf6l-KO


title: Input Wild-type


title: RNAP Wild-type


title: RNAP-ser2 Wild-type

value: 3e10-5, Chromotek


title: RNAP-ser2 Taf6l-KO


title: RNAP-ser2 Taf5l-KO


title: ChIPseq_H3K27me3_TXY_XistdeltaA_D2_noDox_Rep2


title: H3K4me3 Taf5l-KO

value: ab1012, Abcam


title: H3K4me3 Taf6l-KO


title: H3K9ac Taf5l-KO

value: ab4441, Abcam


title: H3K9ac Wild-type


title: H3K9ac Taf6l-KO


title: Oct4 Wild-type

value: N-19:sc-8628, Santa Cruz


title: Oct4 Taf6l-KO


title: Myc Taf5l-KO

value: 9402, Cell signaling


title: Oct4 Taf5l-KO


title: Myc Taf6l-KO


title: Myc Wild-type


title: Chip BirA

value: RPN1231, GE healthcare


title: Input TAF5L-FB A5

description:
TAF5L Flag-Biotin (FB) tagged mESC line
-


title: Input BirA


title: Input TAF6L-FB 9

description:
TAF6L Flag-Biotin (FB) tagged mESC line
-


title: Chip TAF5L-FB A5

description:
TAF5L Flag-Biotin (FB) tagged mESC line
TAF5L-FB_A5_peaks.txt


title: H3K4me3 Wild-type


title: Fabry 3

city: bethesda

first: antony

middle: cyril

last: cougnoux

state: md

address: BG 10-CRC RM 1-3288 10 CENTER DR

department: nichd

institute: nih

data_processing:
RNA-STAR 2.5.1 to
Quantitation by subread featureCounts against RefSeq genes
Data was processed using subread featureCounts to quantitate count data, then differential expression was tested using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts, LogFC

source_name: microglia

extract_protocol:
FACS sorted cells were spun and stored in Trizol (ThermoScientific) prior isolation using RNAesasy Micro kit (Quiagen)
Clontech RNA-Seq Pico kit

tag: cell type

value: FACS isolated microglia Cx3cr1+CD45+

tag: source

value: Fabry


title: ML4 2

tag: strain

value: Mucolipidosis


title: Vehicle3

city: Palo Alto

first: Nathalie

last: Khoury

state: CA California

address: 3801 Miranda Avenue Blvd. 100 VAPA D3-111 - Neurology

institute: Stanford University

data_processing:
Paired-ends reads generated from sequencing on the Illumina Hiseq2500 were trimmed off the adaptor sequences using a custom script.
Trimmed reads were aligned to the mouse genome reference GRCm38 using the STAR aligner
Transcriptome for each sample was assembled using Cufflinks, which also provided transcripts abundance in fragments per kilobase of exon per million fragments mapped (FPKM)
Transcripts assemblies were merged using Cuffmerge.
Genes were annotated according to the ENSEMBL classification, and genes that were not annotated as protein coding genes, lincRNA or antisense RNA were filtered out.Differential gene expression analysis was performed using Cuffdiff.
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel file including FPKM values and statistic for each Sample

extract_protocol:
RNA was isolated using a combination of TRIzol and chloroform reagents followed by on column RNA extraction using the RNeasy Qiagen kit
500ng was used as an input material to generate the library following the TruSeq Stranded Total RNA Sample Preparation guide (15031048-E) with RiboZero Gold

treatment_protocol: Mice were subject to a single intraperitoneal injection of vehicle or resveratrol (10mg/kg), two weeks after the mice were sacrificied and their cortex was collected. RNA was then isolated from the right cortex and sent for library preperation and sequencing.

tag: age at sacrifice

value: 10 week-old

tag: treatment, dose, route

value: Vehicle, single injection of 10mg/kg, intraperitoneal

tag: tissue

value: Cortex


title: Resveratrol1

value: Resveratrol, single injection of 10mg/kg, intraperitoneal


title: Chip TAF5L-FB A6

description:
TAF5L Flag-Biotin (FB) tagged mESC line
TAF5L-FB_A6_peaks.txt

tag: genotype/variation


title: ML4 1


title: Resveratrol3


title: Vehicle2


title: Vehicle1


title: Input TAF5L-FB A6


title: Chip TAF6L-FB 15

description:
TAF6L Flag-Biotin (FB) tagged mESC line
TAF6L-FB_15_peaks.txt


title: Input TAF6L-FB 15


title: Chip TAF6L-FB 9

description:
TAF6L Flag-Biotin (FB) tagged mESC line
TAF6L-FB_9_peaks.txt


title: Resveratrol2


title: Fabry 1


title: Control 1

value: littermate control


title: Control 2


title: csPIMT-/-, 6 months old (5 mice)

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Reads were aligned to mm10 using STARversion 020201 and default parameters
Gene counting was performed using htseq-count version 0.6.1p1 and default parameters
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Counts

growth_protocol: Mice were housed in animal house and maintained on a 12-h light-dark cycle. They received food and water ad libitum.

extract_protocol:
RNA was extracted with Trizol reagent. RNA quality and quantity were first determined with the Agilent Bioanalyzer 2100, accepting RNA integrity numbers (RIN) of >7 and quantities of 100 nanograms or more per sample.  Samples were enriched for mRNA using oligo-dT columns.
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocols

treatment_protocol: No treatment. RNA was isoltaed from the heart of 2 and 6 month old csPIMTfl/fl and csPIMT-/- mice.

tag: age

value: 6 month old

tag: gender

value: pooled male and female

value: KO

value: heart


title: ML4 3


title: csPIMT-/-, 2 months old (5 mice)

value: 2 month old

tag: genotype


title: PIMT fl/fl, 6 months old (5 mice)

value: WT


title: KRT5-traced transformed bladder cells [CTB057]

first: Tomasz

middle: Boguslaw

last: Owczarek

state: NY

address: 1130 St. Nicolas Av.

department: Hematology and Oncology

description:
CTB057
RIN: 9.7
processed data files:
raw_counts_unfiltered.txt.gz
raw_counts.filtered_4_counts.txt.gz
regularized_log_transform.filtered_4_counts.txt.gz
DKO_Dataset1_DEG.xlsx

data_processing:
RNA-seq pipeline description:
Libraries are sequenced using Illumina HiSeq2500 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.
Single-end (101 bp) reads were aligned to the mouse reference genome GRCm38 using the STAR Aligner (version STAR_2.4.2a_modified).
Exon read counts from Gencode GRCm38 GTF (gencode.vM8.annotation.gtf) were calculated using the SubRead package’s featureCounts command. Differential expression analysis was conducted with DESeq2 on raw feature counts after excluding features with less than four counts across all samples. The Biomart R package was used to map mouse mgi gene symbols from Ensembl IDs.
For PCA, raw feature counts (excluding features with less than four counts across all samples) were regularized log transformed.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: raw_counts_unfiltered.txt.gz: Raw counts.
Supplementary_files_format_and_content: raw_counts.filtered_4_counts.txt.gz: Filtered counts.
Supplementary_files_format_and_content: regularized_log_transform.filtered_4_counts.txt.gz: Filtered and transferred counts.
Supplementary_files_format_and_content: DKO_Dataset1_DEG.xlsx: Differentially expressed genes.

source_name: urothelial cells

extract_protocol:
RNA was extracted using the MagMAX-96 RNA isolation kit (Ambion). Quality control was performed with Agilent Bioanalyser 2100.
We use poly-A pull-down to enrich mRNAs from total RNA samples (5ng-200ng per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2500 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.

treatment_protocol: All mice were treated for 4 consecutive days with 100mg/kg/day of tamoxifen by oral gavage at 2 month of age. For analysis of normal KRT8- and KRT5-traced cells, mice were dissected 7 days post tamoxifen treatment. For analysis of transformed (combinatorial loss of p53 and PTEN) KRT8- and KRT5-traced cells, mice were dissected 3 months post tamoxifen treatment.

tag: strain/background

value: outbreed

value: KRT5-CreERT2, p53flox/flox, Ptenflox/flox, Rosa26YFP/+

value: 5 months

tag: Sex

value: Female

value: bladder

value: YFP-sorted urothelial cells


title: PIMT fl/fl, 2 months old (5 mice)


title: Fabry 2

value: FACS isolated microglia Cx3cr1+CD45+

value: Fabry


title: KRT5-traced transformed bladder cells [CTB054]

description:
CTB054
RIN: 9.6
processed data files:
raw_counts_unfiltered.txt.gz
raw_counts.filtered_4_counts.txt.gz
regularized_log_transform.filtered_4_counts.txt.gz
DKO_Dataset1_DEG.xlsx

value: Male


title: KRT5-traced transformed bladder cells [CTB055]

description:
CTB055
RIN: 10
processed data files:
raw_counts_unfiltered.txt.gz
raw_counts.filtered_4_counts.txt.gz
regularized_log_transform.filtered_4_counts.txt.gz
DKO_Dataset1_DEG.xlsx


title: KRT8-traced transformed bladder cells [CTB051]

description:
CTB051
RIN: 9.3
processed data files:
raw_counts_unfiltered.txt.gz
raw_counts.filtered_4_counts.txt.gz
regularized_log_transform.filtered_4_counts.txt.gz
DKO_Dataset1_DEG.xlsx

value: KRT8-CreERT2, p53flox/flox, Ptenflox/flox, Rosa26YFP/+


title: KRT5-traced normal bladder cells [CTB041]

description:
CTB041
RIN: 10
processed data files:
raw_counts_unfiltered.txt.gz
raw_counts.filtered_4_counts.txt.gz
regularized_log_transform.filtered_4_counts.txt.gz
DKO_Dataset1_DEG.xlsx

value: KRT5-CreERT2, Rosa26YFP/LacZ

value: 2 months


title: KRT8-traced transformed bladder cells [CTB052]

description:
CTB052
RIN: 9.5
processed data files:
raw_counts_unfiltered.txt.gz
raw_counts.filtered_4_counts.txt.gz
regularized_log_transform.filtered_4_counts.txt.gz
DKO_Dataset1_DEG.xlsx


title: KRT8-traced transformed bladder cells [CTB053]

description:
CTB053
RIN: 9.5
processed data files:
raw_counts_unfiltered.txt.gz
raw_counts.filtered_4_counts.txt.gz
regularized_log_transform.filtered_4_counts.txt.gz
DKO_Dataset1_DEG.xlsx


title: KRT5-traced normal bladder cells [CTB039]

description:
CTB039
RIN: 10
processed data files:
raw_counts_unfiltered.txt.gz
raw_counts.filtered_4_counts.txt.gz
regularized_log_transform.filtered_4_counts.txt.gz
DKO_Dataset1_DEG.xlsx


title: KRT5-traced normal bladder cells [CTB040]

description:
CTB040
RIN: 10
processed data files:
raw_counts_unfiltered.txt.gz
raw_counts.filtered_4_counts.txt.gz
regularized_log_transform.filtered_4_counts.txt.gz
DKO_Dataset1_DEG.xlsx


title: KRT5-traced normal bladder cells [CTB038]

description:
CTB038
RIN: 9.9
processed data files:
raw_counts_unfiltered.txt.gz
raw_counts.filtered_4_counts.txt.gz
regularized_log_transform.filtered_4_counts.txt.gz
DKO_Dataset1_DEG.xlsx


title: KRT8-traced transformed bladder cells [CTB050]

description:
CTB050
RIN: 9.5
processed data files:
raw_counts_unfiltered.txt.gz
raw_counts.filtered_4_counts.txt.gz
regularized_log_transform.filtered_4_counts.txt.gz
DKO_Dataset1_DEG.xlsx


title: KRT8-traced normal bladder cells [CTB033]

description:
CTB033
RIN: 9.7
processed data files:
raw_counts_unfiltered.txt.gz
raw_counts.filtered_4_counts.txt.gz
regularized_log_transform.filtered_4_counts.txt.gz
DKO_Dataset1_DEG.xlsx

value: KRT8-CreERT2, Rosa26YFP/LacZ


title: KRT8-traced normal bladder cells [CTB031]

description:
CTB031
RIN: 9.5
processed data files:
raw_counts_unfiltered.txt.gz
raw_counts.filtered_4_counts.txt.gz
regularized_log_transform.filtered_4_counts.txt.gz
DKO_Dataset1_DEG.xlsx


title: KD2B_8

city: Amsterdam

first: Kat

last: Moore

address: Plesmanlaan 125

institute: Sanquin Research

description:
B9
The cell line is derived from an erythroblast culture started from fetal liver of F1 mice (FVB/n x C57BL/6) both heterozygous for the Trp53 deletion described in [Clarke AR, Purdie CA, Harrison DJ, et al. Thymocyte apoptosis induced by p53-dependent and independent pathways. Nature. 1993; 362(6423):849-852].
Tis7 knockdown 2 rep B, time point 8.
shRNA sequence (5'-3'): CCGGCAGTACCACTTGCAGACAAATCTCGAGATTTGTCTGCAAGTGGTACTGTTTTTG
processed data file: Tis_rawcounts.txt

data_processing:
Raw fastq aligned to genome using Splice Transcripts Alignment to a Reference (STAR) v2.4, with parameters --quantMode GeneCounts --outFilterMultimapNmax 20 and -sjDBGTFfile with an Ensembl gtf file accessed on 17-Sept-2017.
Resulting raw (unnormalized) read counts were analyzed with DESeq2 using Wald test for pairwise comparisons and a likelihood ratio test to model the time course experiment.
Genome_build: mm10/GRCm38.p5
Supplementary_files_format_and_content: Tis_rawcounts.txt: Tab-delimited text file includes raw read counts.

source_name: Erythroblasts, KD2

growth_protocol: Murine erythroblasts, isolated from p53-/- mouse fetal livers, were cultured in Stempro supplemented with L-glutamine and Pen/Strep (Thermo Fisher), 0.5 U/ml erythropoietin (Epo, Jansen-Cilag), 1% stem cell factor (supernatant) and 1 nM dexamethasone (Sigma).

extract_protocol:
RNeasy Plus Kit (Qiagen).
Performed by Novogene, Co., LTD. Oligo(dt) bead isolation followed by cDNA synthesis with random hexamers and second strand synthesis using Illumina brand buffer, dNTPs, RNase H and DNA pol I. The final cDNA library was completed after a series of terminal repair, A-tailing, adapter ligation, size selection and PCR enrichment.

treatment_protocol: For stress induction, erythroblasts were treated with 2.5 µg/ml Tunicamycin (Sigma) for 0, 4 and 8 hours.

value: Erythroblasts

tag: tissue origin

value: fetal liver

tag: shRNA type

value: anti-Tis7 2

tag: tunicamycin exposure (hours)

tag: replicate

value: B


title: KRT8-traced normal bladder cells [CTB030]

city: New York

institute: Columbia University

description:
CTB030
RIN: 9.4
processed data files:
raw_counts_unfiltered.txt.gz
raw_counts.filtered_4_counts.txt.gz
regularized_log_transform.filtered_4_counts.txt.gz
DKO_Dataset1_DEG.xlsx

value: outbreed


title: Control 3

value: littermate control


title: KRT8-traced normal bladder cells [CTB032]

description:
CTB032
RIN: 9.5
processed data files:
raw_counts_unfiltered.txt.gz
raw_counts.filtered_4_counts.txt.gz
regularized_log_transform.filtered_4_counts.txt.gz
DKO_Dataset1_DEG.xlsx