title: HSF01-Mock

city: Berlin

first: Fabian

last: Pott

state: Berlin

address: Charitéplatz 1

department: Institute for Virology

country: Germany

institute: Charité - Universitaetsmedizin Berlin

description:
CHIKV_vs_Mock_ExpressionBrowser_HSF.xlsx
CHIKV+C9_vs_Mock_ExpressionBrowser_HSF.xlsx
OASF_vs_HSF_ExpressionBrowser_Uninfected.xlsx

data_processing:
Transcriptomic analyses were performed using CLC Genomics Workbench (Qiagen, Aarhus)
Generated Fastq files were mapped against the hg19 human genome reference scaffold with annotated gene and mRNA tracks.
Normalised gene expression was calculated for individual transcripts from raw count data as reads per kilobase per million bases mapped (RPKM).
Differential Expression of Genes (DEG) analyses were performed and p-values calculated for each gene.
Genome_build: hg19
Supplementary_files_format_and_content: Excel sheet containing raw reads and RPKM values for each sample as well as statistical analysis (FDR-corrected p-value, Bonferroni correction).

source_name: Knee synovial fibroblast

growth_protocol: Primary human fibroblasts were obtained from synovial biopsies from donors suffering from osteoarthritis or a non-arthritic background, purified, and cultured in standard cell culture flask in Dulbecco’s modified Eagle’s medium - high glucose (DMEM, Sigma-Aldrich) supplemented with 20 % heat-inactivated fetal bovine serum (FBS, Sigma-Aldrich), 2mM L-Glutamine (Gibco), and 100 units/ml penicillin-streptomycin (Gibco).

extract_protocol:
Cells were lysed and RNA was extracted using the Promega Maxwell 16 with LEV simplyRNA Tissue Kits (OA-samples) or the Zymo Research Direct-Zol RNA MiniPrep Kit (HSF-samples).
RNA libraries were prepared for sequencing using NEBNext Ultra II Directional RNA kit (OA-samples) or Illumina TruSeq stranded mRNA kit (HSF-samples).

treatment_protocol: CHIKV particles produced by electroporation of in-vitro transcribed full-length genomic RNA into BHK-21 cells were pre-incubated with 1 µg/ml neutralizing antibody C9 for 1 h or left untreated before infection. Fibroblasts were infected at an MOI of 10 for 24 h with neutralized or untreated virus or mock-infected.

tag: state

value: healthy

tag: donor

value: HSF 1


title: HSF02-Mock

status: Public on Jun 19 2020

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: HSF 2


title: HSF01-C9

description: CHIKV+C9_vs_Mock_ExpressionBrowser_HSF.xlsx


title: HSF01-CHIKV

description:
CHIKV_vs_Mock_ExpressionBrowser_HSF.xlsx
OASF_vs_HSF_ExpressionBrowser_CHIKV-infected.xlsx


title: HSF02-C9


title: HSF02-CHIKV


title: Cord blood ID_361

type: genomic

city: Diepenbeek

first: Michelle

last: Plusquin

address: Campus Diepenbeek Agoralaan Gebouw D

country: Belgium

institute: Hasselt University

hyb_protocol: Bisulphite converted DNA (using the Zymo EZ DNA methylationTM kit - Zymo, Irvine, CA, USA) was hybridized to Illumina HumanMethylation 450K BeadChip arrays

scan_protocol: Arrays were scanned using an Illumina iScan

data_processing:
An in-house software written for the R statistical computing environment was used to preprocess the data as follows: removal of probes based on signal intensities and control probes, background subtraction and dye bias correction (for probes using the Infinium II design). Additionally, data were trimmed removing the outliers as defined by observations exceeding three interquartile ranges below the first quartile or above the fourth quartile. Sample failing quality control and with potential sex mismatch were removed.
normalized Average Beta in supplementary file

label: Cy3, Cy5

molecule: genomic DNA

source_name: cord blood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from buffy coats according to standard protocol

tag: tissue

value: cord blood

tag: birthweight


title: Cord blood ID_362


title: Cord blood ID_360


title: Cord blood ID_359


title: Cord blood ID_363


title: Cord blood ID_355


title: REH control (scrambled shRNA) RNA-seq

city: Birmingham

first: Yanfeng

last: Zhang

state: AL

address: Kaul Human Genetics Building 720 20th St S

department: Department of Genetics

country: USA

institute: University of Alabama at Birmingham

description: RNA sequencing analysis of control RHE

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using tophat2 with default parameters
Reads were demuxed based on their index sequence at the Genomic Services Laboratory at HudsonAlpha. After removal of adapter sequences, low-quality reads, and trimmed reads that were shorter than 20 bp by using cutadapt (v1.3.1), filtered reads were aligned with Tophat2 with default parameters. Mapped reads in BAM format were assembled with Cufflinks (v2.2.1). The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file

source_name: REH

growth_protocol: REH cells were cultured in RMPI-1640 medium, supplemented with 10% FBS (37℃, 95% humidity, 5%CO2).

extract_protocol:
RNA was isolated from cells using TRIzol Reagent (Invitrogen) according to the manufacturer’s protocol.
Indexed libraries were constructed from ~500ng total RNA using the NEBNext Ultra RNA Library Prep Kit for Illumina with the Poly(A) mRNA Magnetic Isolation Module (NEB). We confirmed the final cDNA library size range by gel electrophoresis on a 1.7% agarose gel. Samples were barcoded during library preparation and sequenced on a NextSeq (Illumina) instrument as 2x75 bp paired-end libraries at the HudsonAlpha Institute Sequencing Facility.

treatment_protocol: No treatment.

tag: cell type

value: REH pre-B lymphoblastic cells

tag: lentivirus

value: scrambled shRNA


title: Cord blood ID_357


title: Cord blood ID_358


title: Cord blood ID_356


title: RNA-seq TGFb-and-RA-med-dose-rep2-technicalrep3

city: Philadelphia

first: Eric

middle: M

last: Sanford

state: PA

address: 2135 Clymer St

institute: University of Pennsylvania

description:
RNA-seq-50-TGFb-and-RA-med-second-RNA-extraction
technical replicate, second library preparation from second RNA extraction from Qiazol lysate, of RNA-seq-18-TGFb-and-RA-med.  Publication sums this sample's gene counts with RNA-seq-48-TGFb-and-RA-med and uses the result as one sample.

data_processing:
RNA-seq analysis, align to transcriptome: STAR v2.7.1a
RNA-seq analysis, assign uniquely mapped reads to genes: HTSeq v0.6.1
RNA-seq analysis, GTF file used when assigning uniquely mapped reads to genes: hg38 GTF, Ensembl release 90
ATAC-seq analysis, align reads to hg38: bowtie2 v2.3.4.1
ATAC-seq analysis, filter out low quality alignments: samtools v1.1
ATAC-seq analysis, remove duplicate read pairs: picard 1.96
ATAC-seq analysis, call peaks: macs2  callpeak --nomodel --nolambda --keep-dup all --call-summits -B --SPMR --format BED -q 0.05  --shift 75 --extsize 150
Genome_build: hg38
Supplementary_files_format_and_content: HTSeq output containing gene counts; tab delimited text file containing ensembl gene ID and number of read counts within each gene
Supplementary_files_format_and_content: MACS2 peak file; narrowPeak output file from MACS2 peak calling
Supplementary_files_format_and_content: MACS2 bigWig output file; bigWig file showing normalized ATAC-seq signal, generated by MACS2 peak calling step

molecule: polyA RNA

source_name: MCF-7 cells

growth_protocol: We acquired one vial of MCF-7 cells from ATCC (lot 64125078), which we expanded in DMEM/F12 with 5% FBS and 1% penicillin/streptomycin. Prior to adding retinoic acid and TGF-β, the cells experienced a total of 13 passages and one freeze/thaw cycle. Because normal FBS can have significant amounts of retinoic acid (Napoli, 1986), we cultured the cells in a modified medium containing charcoal-stripped FBS, with each batch consisting of 50 ml charcoal-stripped FBS (Gemini, 100-119), 5 ml penicillin/streptomycin (Invitrogen, 15140-122), and 500 ml DMEM/F12 (Gibco, 10565018). We grew the MCF-7 cells in this charcoal-stripped FBS-containing medium for a total of 70 or 71 days prior to treating them with retinoic acid and TGF-β.

extract_protocol:
We extracted RNA from previously frozen MCF-7 cell Qiazol lysates using the Qiagen miRNeasy kit (217004)
For RNA-seq, we used the NEBNext Ultra II RNA Library Prep Kit for Illumina  (E7770) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490) and NEBNext  Multiplex Oligos for Illumina (E7600) to prepare individual libraries. For ATAC-seq,  we performed the Omni-ATAC  protocol (Corces et al., 2017) on 50,000 live MCF-7 cells, using Illumina Tagment DNA Enzyme  TDE1 (20034197) at the tagmentation step and double-sided bead purification at the endpoint  with Agencourt AMPure XP magnetic beads (A63880)

treatment_protocol: We treated cells for 72 hours in three doses of retinoic acid (50nM, 200 nM, and 400 nM), TGF-β (1.25 ng/ml, 5 ng/ml, 10 ng/ml), or both signals (50 nM retinoic acid + 1.25 ng/ml TGF-β, 200 nM RA + 5 ng/ml TGF-β, 400 nM RA + 10 ng/ml TGF-β). All conditions had the same 0.0125% concentration of ethanol. At 72 hours, we then trypsinized the cells in each well, removing 50,000 of them for immediate ATAC-seq library preparation and lysing the rest of them in Qiazol (storing immediately at -80°C) for subsequent RNA extraction and bulk RNA-seq library preparation.

tag: treatment (signal(s) given)

value: 200 nM retinoic acid and 5 ng/ul TGF-beta

tag: starting cell density

tag: cell line


title: RNA-seq RA-med-dose-rep2-technicalrep3

description:
RNA-seq-49-RA-med-second-RNA-extraction
technical replicate, second library preparation from second RNA extraction from Qiazol lysate, of RNA-seq-17-RA-med. Publication sums this sample's gene counts with RNA-seq-47-RA-med and uses the result as one sample.

value: 200 nM retinoic acid


title: RNA-seq RA-med-dose-rep2-technicalrep2

description:
RNA-seq-47-RA-med
technical replicate, second library preparation from same extracted RNA, of RNA-seq-17-RA-med


title: RNA-seq EtOH-nlDensity-dose-rep2-technicalrep2

description:
RNA-seq-46-EtOH-nlDensity
technical replicate, second library preparation from same extracted RNA, of RNA-seq-15-EtOH-nlDensity

value: ethanol control


title: RNA-seq TGFb-and-RA-med-dose-rep2-technicalrep2

description:
RNA-seq-48-TGFb-and-RA-med
technical replicate, second library preparation from same extracted RNA, of RNA-seq-18-TGFb-and-RA-med


title: RNA-seq RA-low-dose-rep3

value: 50 nM retinoic acid


title: REH XIST-KD (shRNA-XIST) RNA-seq

description: RNA sequencing analysis of shXIST RHE

value: shRNA-XIST


title: RNA-seq TGFb-and-RA-high-dose-rep3

value: 400 nM retinoic acid and 10 ng/ul TGF-beta


title: Cord blood ID_352


title: Cord blood ID_351


title: Cord blood ID_354


title: Cord blood ID_35


title: Cord blood ID_350


title: Cord blood ID_353


title: RNA-seq TGFb-med-dose-rep3

value: 5 ng/ul TGF-beta


title: RNA-seq EtOH-highDensity-dose-rep3


title: RNA-seq TGFb-low-dose-rep3

value: 1.25 ng/ul TGF-beta


title: RNA-seq TGFb-and-RA-low-dose-rep3

value: 50 nM retinoic acid and 1.25 ng/ul TGF-beta


title: RNA-seq TGFb-high-dose-rep3

value: 10 ng/ul TGF-beta


title: RNA-seq RA-high-dose-rep3

value: 400 nM retinoic acid


title: Cord blood ID_348


title: Cord blood ID_347


title: RNA-seq TGFb-and-RA-med-dose-rep3


title: RNA-seq RA-med-dose-rep3


title: RNA-seq EtOH-nlDensity-dose-rep3


title: Cord blood ID_346


title: Cord blood ID_376


title: Cord blood ID_344


title: Cord blood ID_343


title: Cord blood ID_349


title: Cord blood ID_342


title: Cord blood ID_341


title: RNA-seq RA-high-dose-rep2


title: RNA-seq RA-low-dose-rep2


title: RNA-seq EtOH-halfDensity-dose-rep3


title: Cord blood ID_340


title: Cord blood ID_34


title: Cord blood ID_339


title: RNA-seq EtOH-halfDensity-dose-rep2


title: Cord blood ID_337


title: Cord blood ID_336


title: RNA-seq TGFb-low-dose-rep2


title: RNA-seq TGFb-and-RA-med-dose-rep2

description:
RNA-seq-18-TGFb-and-RA-med
omit this sample from analysis due to high rRNA contamination; included only for completeness


title: RNA-seq RA-med-dose-rep2

description:
RNA-seq-17-RA-med
omit this sample from analysis due to high rRNA contamination; included only for completeness


title: RNA-seq EtOH-highDensity-dose-rep2


title: Cord blood ID_335


title: RNA-seq TGFb-med-dose-rep2


title: RNA-seq EtOH-nlDensity-dose-rep2


title: Cord blood ID_345


title: RNA-seq TGFb-and-RA-low-dose-rep2


title: Cord blood ID_334


title: Cord blood ID_332


title: Cord blood ID_33


title: Cord blood ID_330


title: RNA-seq TGFb-high-dose-rep2


title: Cord blood ID_329


title: RNA-seq TGFb-high-dose-rep1


title: RNA-seq TGFb-and-RA-med-dose-rep1


title: RNA-seq TGFb-and-RA-high-dose-rep2


title: Cord blood ID_326


title: Cord blood ID_338


title: Cord blood ID_324


title: RNA-seq RA-high-dose-rep1


title: RNA-seq EtOH-halfDensity-dose-rep1


title: Cord blood ID_322


title: RNA-seq EtOH-nlDensity-dose-rep1


title: Cord blood ID_321


title: RNA-seq RA-med-dose-rep1


title: Cord blood ID_331


title: Cord blood ID_320


title: Cord blood ID_32


title: RNA-seq TGFb-and-RA-high-dose-rep1


title: Cord blood ID_319


title: RNA-seq EtOH-highDensity-dose-rep1


title: RNA-seq RA-low-dose-rep1


title: RNA-seq TGFb-med-dose-rep1


title: RNA-seq TGFb-low-dose-rep1


title: RNA-seq TGFb-and-RA-low-dose-rep1


title: ATAC-seq TGFb-and-RA-high-dose-rep3

description:
35-TGFb-and-RA-high
tagmented DNA from 50,000 live cell nuclei

library_source: genomic


title: Cord blood ID_325


title: ATAC-seq EtOH-highDensity-dose-rep3

description:
34-EtOH-highDensity
tagmented DNA from 50,000 live cell nuclei


title: ATAC-seq TGFb-low-dose-rep3

description:
33-TGFb-low
tagmented DNA from 50,000 live cell nuclei


title: Cord blood ID_317


title: Cord blood ID_316


title: Cord blood ID_315


title: ATAC-seq RA-high-dose-rep3

description:
32-RA-high
tagmented DNA from 50,000 live cell nuclei


title: Cord blood ID_314


title: Cord blood ID_313


title: ATAC-seq TGFb-high-dose-rep3

description:
31-TGFb-high
tagmented DNA from 50,000 live cell nuclei


title: ATAC-seq TGFb-med-dose-rep3

description:
30-TGFb-med
tagmented DNA from 50,000 live cell nuclei


title: ATAC-seq TGFb-and-RA-low-dose-rep3

description:
29-TGFb-and-RA-low
tagmented DNA from 50,000 live cell nuclei


title: Cord blood ID_311


title: Cord blood ID_312


title: ATAC-seq TGFb-and-RA-med-dose-rep3

description:
28-TGFb-and-RA-med
tagmented DNA from 50,000 live cell nuclei


title: Cord blood ID_310


title: Cord blood ID_318


title: ATAC-seq EtOH-nlDensity-dose-rep3

description:
27-EtOH-nlDensity
tagmented DNA from 50,000 live cell nuclei


title: Cord blood ID_309


title: ATAC-seq RA-med-dose-rep3

description:
26-RA-med
tagmented DNA from 50,000 live cell nuclei


title: Cord blood ID_31


title: Cord blood ID_306


title: ATAC-seq EtOH-halfDensity-dose-rep3

description:
25-EtOH-halfDensity
tagmented DNA from 50,000 live cell nuclei


title: ATAC-seq RA-low-dose-rep3

description:
36-RA-low
tagmented DNA from 50,000 live cell nuclei


title: Cord blood ID_308


title: Cord blood ID_305


title: ATAC-seq RA-low-dose-rep2

description:
24-RA-low
tagmented DNA from 50,000 live cell nuclei


title: Cord blood ID_304


title: ATAC-seq RA-high-dose-rep2

description:
23-RA-high
tagmented DNA from 50,000 live cell nuclei


title: Cord blood ID_303


title: ATAC-seq TGFb-high-dose-rep2

description:
22-TGFb-high
tagmented DNA from 50,000 live cell nuclei


title: ATAC-seq TGFb-and-RA-high-dose-rep2

description:
21-TGFb-and-RA-high
tagmented DNA from 50,000 live cell nuclei


title: ATAC-seq EtOH-halfDensity-dose-rep2

description:
20-EtOH-halfDensity
tagmented DNA from 50,000 live cell nuclei


title: Cord blood ID_302


title: Cord blood ID_301


title: ATAC-seq TGFb-low-dose-rep2

description:
19-TGFb-low
tagmented DNA from 50,000 live cell nuclei


title: ATAC-seq TGFb-and-RA-med-dose-rep2

description:
18-TGFb-and-RA-med
tagmented DNA from 50,000 live cell nuclei


title: Cord blood ID_300


title: Cord blood ID_30


title: Cord blood ID_3


title: ATAC-seq RA-med-dose-rep2

description:
17-RA-med
tagmented DNA from 50,000 live cell nuclei


title: Cord blood ID_299


title: ATAC-seq EtOH-highDensity-dose-rep2

description:
14-EtOH-highDensity
tagmented DNA from 50,000 live cell nuclei


title: ATAC-seq TGFb-med-dose-rep2

description:
16-TGFb-med
tagmented DNA from 50,000 live cell nuclei


title: Cord blood ID_297


title: Cord blood ID_296


title: Cord blood ID_298


title: ATAC-seq TGFb-and-RA-low-dose-rep2

description:
13-TGFb-and-RA-low
tagmented DNA from 50,000 live cell nuclei


title: Cord blood ID_295


title: ATAC-seq RA-med-dose-rep1

description:
12-RA-med
tagmented DNA from 50,000 live cell nuclei


title: ATAC-seq TGFb-and-RA-high-dose-rep1

description:
11-TGFb-and-RA-high
tagmented DNA from 50,000 live cell nuclei


title: Cord blood ID_294


title: ATAC-seq TGFb-high-dose-rep1

description:
10-TGFb-high
tagmented DNA from 50,000 live cell nuclei


title: ATAC-seq TGFb-and-RA-med-dose-rep1

description:
09-TGFb-and-RA-med
tagmented DNA from 50,000 live cell nuclei


title: Cord blood ID_293


title: ATAC-seq TGFb-and-RA-low-dose-rep1

description:
08-TGFb-and-RA-low
tagmented DNA from 50,000 live cell nuclei


title: Cord blood ID_292


title: Cord blood ID_290


title: Cord blood ID_29


title: Cord blood ID_291


title: ATAC-seq EtOH-halfDensity-dose-rep1

description:
07-EtOH-halfDensity
tagmented DNA from 50,000 live cell nuclei


title: ATAC-seq EtOH-nlDensity-dose-rep1

description:
05-EtOH-nlDensity
tagmented DNA from 50,000 live cell nuclei


title: ATAC-seq RA-high-dose-rep1

description:
06-RA-high
tagmented DNA from 50,000 live cell nuclei


title: ATAC-seq EtOH-highDensity-dose-rep1

description:
04-EtOH-highDensity
tagmented DNA from 50,000 live cell nuclei


title: ATAC-seq RA-low-dose-rep1

description:
03-RA-low
tagmented DNA from 50,000 live cell nuclei


title: Cord blood ID_289


title: ATAC-seq EtOH-nlDensity-dose-rep2

description:
15-EtOH-nlDensity
tagmented DNA from 50,000 live cell nuclei


title: Cord blood ID_288


title: ATAC-seq TGFb-med-dose-rep1

description:
02-TGFb-med
tagmented DNA from 50,000 live cell nuclei


title: Cord blood ID_286


title: Cord blood ID_285


title: ATAC-seq TGFb-low-dose-rep1

description:
01-TGFb-low
tagmented DNA from 50,000 live cell nuclei


title: Cord blood ID_28


title: Cord blood ID_281


title: Cord blood ID_282


title: Cord blood ID_280


title: Cord blood ID_279


title: Cord blood ID_277


title: Cord blood ID_276


title: LTL331_CR_Cell

city: Vancouver

first: Yuzhuo

last: Wang

state: BC

address: 2660 Oak Street

department: Vancouver Prostate Centre

country: Canada

institute: University of British Columbia

data_processing:
Libraries were pooled and sequenced on the NextSeq 500, with the aim of at least 20M reads per library
Fastq files were mapped to the database combining human and mouse reference genome ( GRCh38, GRCm38, and Ensembl gene annotation release 90 ) using splice-aware mapper STAR 2.6.0a, and extract those reads only mapped to human or mouse genome for downstream analysis.
Gene expressions were estimated by htseq-count 0.10.0 (counting mode: intersection-strict), and normalization was done with DESeq2 1.16.1.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include log2RPKM values for each Sample

source_name: LTL331_CR_Cell, conditionally reprogrammed cell line derived from LTL331

growth_protocol: Primary CR cells were cultured in F medium containing the following reagents: DMEM/F12 (3:1 (v/v), Thermo Fisher), 5% fetal bovine serum (Thermo Fisher), 0.4 μg/mL hydrocortisone (Sigma-Aldrich), 5 μg/mL insulin (Sigma-Aldrich), 8.4 ng/mL cholera toxin (Sigma-Aldrich), 10 ng/mL epidermal growth factor (Sigma-Aldrich), 24 μg/mL adenine (Sigma-Aldrich), and 10 μM Y-27632.

extract_protocol:
Total RNA was extracted via homogenization on the Precellys (1x30sec, 6000rpm, in the Maxwell kit homogenization buffer), followed by the Maxwell RSC Simply RNA Tissue kit (Promega), following the manufacturer's instructions
RNA libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit, with 200ng total RNA used as input (this kit includes a poly A enrichment step)

value: conditionally reprogrammed cell derived from prostate cancer PDX


title: LTL331_CR_Tumor

source_name: LTL331_CR_Tumor, xenograft tumor derived from LTL331_CR_Cell

growth_protocol: For primary cell xenografting, 1 x 107 cells were mixed with rat tail collagen (5 mg/ml, house made) at a 1:1 ratio in a final volume of 100 μl before grafting under the mouse renal capsule.

value: xenograft tumor derived from conditionally reprogrammed cell


title: Cord blood ID_274


title: LTL331R

source_name: LTL331R, LTL331 castration relapsed tumor

growth_protocol: Castration relapsed LTL331 PDX tissues were cut into pieces (1 × 3 × 3 mm3) and grafted into the sub-renal capsule site of castrated male nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice.

value: xenograft subline derived from prosate cancer PDX


title: Cord blood ID_275

value: cord blood


title: LTL331

source_name: LTL331, patient-derived xenograft

growth_protocol: Patient prostate cancer tissues were cut into pieces (1 × 3 × 3 mm3) and grafted into the sub-renal capsule site of male nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice supplemented with testosterone.

value: prostate cancer PDX


title: Cord blood ID_272


title: Cord blood ID_273


title: Cord blood ID_271


title: 1.0 µM GNE-781 6h_PER403R2

city: BOSTON

first: Chevaun

last: Morrison-Smith

state: MA

address: 77 AVENUE LOUIS PASTEUR, NRB 652

department: Pathology

institute: Brigham and Women's Hospital

data_processing:
Single-end (75 bp) reads were trimmed and verified for quality with Trim Galore! (v.0.3.7, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Trimmed reads were aligned with STAR (v.2.7.1a, Pubmed:23104886) to the human genome (GRCh38 primary assembly) with Gencode (v.30) annotations and to the External RNA Control Consortium (ERCC92, Pubmed:16179916) spike-in sequences in a single pass using default settings for gene counting (--quantMode GeneCounts)
Transcripts with < 1 million reads mapped in all samples (74%) were removed before differential expression (DE) analysis.
ERCC-invariant sequences were used with RUVg with k=1 (v.1.8.0 [Pubmed:25150836] under R 3.3.3 [R Core Team (2017).
The resulting weight matrix was incorporated into the edgeR (v.3.16.5, Pubmed:22287627) design matrix. Given a group size of 2, genes were deemed to be differentially expressed with adjusted p-value < 0.05 and fold change > 3.
Genome_build: GRCh38
Supplementary_files_format_and_content: TDF for IGV viewing, and tab delimited text files with raw counts or CPM data

source_name: RNA from PER-403 cells

growth_protocol: TC-797 and PER-403 cells were maintained as monolayer cultures in DMEM supplemented with 10% FBS and 1% pen–strep.

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini plus kit. Genomic DNA was removed through rigorous DNase treatment with the Invitrogen TURBO DNA-free kit (Fisher Scientific; AM1907)
ERCC ExFold RNA spike-in controls (Invitrogen; 4456739) were added according to manufacturer’s instructions to 1 µg of purified RNA from each sample to enable fold change quantification in treated samples relative to vehicle condition.  Ribosomal rRNA (rRNA) was depleted using the NEBNext rRNA Depletion Kit (NEB; E6350L) according to manufacturer’s instructions. Sequencing libraries were generated using the NEBNext Ultra II Directional RNA library kit (NEB; E7760S). Libraries were single-end 75 bp sequenced on an Illumina Nextseq 500

treatment_protocol: Cells were treated for 6h with the indicated compounds

tag: treatment


title: Cord blood ID_270


title: 1.0 µM NEO2734_PER403R2


title: Cord blood ID_283


title: 0.5 µM OTX-015 6h_PER403R2


title: DMSO 6h_PER403R2


title: 62.5 nM OTX-015 + 62.5 nM GNE-781 6h_PER403R2


title: Cord blood ID_268


title: Cord blood ID_27


title: 1.0 µM NEO2734_PER403R1


title: 0.5 µM OTX-015 6h_PER403R1


title: 1.0 µM GNE-781 6h_PER403R1


title: Cord blood ID_267


title: Cord blood ID_269


title: Cord blood ID_266


title: Cord blood ID_265


title: DMSO 6h_PER403R1


title: 1.0 µM NEO2734 _797R2

source_name: RNA from TC-797 cells


title: Cord blood ID_263


title: 1.0 µM GNE-781 6h_797R2


title: Cord blood ID_261


title: 0.5 µM OTX-015 6h_797R2


title: 62.5 nM OTX-015 + 62.5 nM GNE-781 6h_797R2


title: Cord blood ID_260


title: 1.0 µM NEO2734_797R1


title: DMSO 6h_797R2


title: Cord blood ID_26


title: Cord blood ID_259


title: 1.0 µM GNE-781 6h_797R1


title: Cord blood ID_257


title: Cord blood ID_258


title: 0.5 µM OTX-015 6h_797R1


title: ARID1A KO_undiff_scRNA-seq

city: Indianapolis

first: Lei

last: Yang

state: Indiana

address: 1044 W. Walnut St.

department: Department of Pediatrics

institute: Indiana University School of Medicine

data_processing:
CellRanger 2.1.0 was utilized to process the raw sequence data generated. The filtered gene-cell barcode matrices generated by CellRanger were used for further analysis.
Seurat was used for data normalization, data scaling, graph-based clustering, cluster marker genes idenfificationa.
The CCA function from Seurat was used for integrative analysis of the WT and KO samples.
Genome_build: hg38
Supplementary_files_format_and_content: genes.tsv, matrix.mtx and barcodes.tsv in each tar.gz file

source_name: hESCs H9 cells

growth_protocol: For the undifferentiated samples, H9 hESCs were routinely cultured in mTesR medium in a matrigel-coated 6-well plate). For the differentiated samples, H9 hESCs were routinely cultured in mTesR medium (a matrigel-coated 6-well plate). When cells density were 100%, medium were changed to chemically defined medium for cardiac differentiation induction.

extract_protocol:
H9 hESCs and differentiated hESCs were dissociated by Corning™ 0.25% Trypsin (Corning™ 25053CI) to single cells. Single cell 3’ RNA-seq experiments were conducted using the Chromium single cell system (10x Genomics, Inc) and Illumina sequencers at the Center of Molecular Genetics (CMG) of Indiana University School of Medicine. Cell suspension was first inspected on the Countess II FL (Thermo Fisher Scientific) and under microscope for cell number, cell viability, and cell size. Depending on the quality of the initial cell suspension, the single cell preparation included centrifugation, re-suspension, and filtration to remove cell debris, dead cells and cell aggregates. Single cell capture and library preparation were carried out according to the Chromium Single cell 3’ Reagent kits V2 User Guide (10X Genomics PN-120267, PN-1000009, PN-120262). Appropriate number of cells were loaded on a multiple-channel micro-fluidics chip of the Chromium Single Cell Instrument (10x Genomics) with a targeted cell recovery of 10,000. Single cell gel beads in emulsion containing barcoded oligonucleotides and reverse transcriptase reagents were generated with the v2 single cell reagent kit (10X Genomics). Following cell capture and cell lysis, cDNA was synthesized and amplified. Illumina sequencing libraries were then prepared with the amplified cDNA. The resulting libraries were assessed with an Agilent TapeStation or Bioanalyzer 2100. The final libraries of the undifferentiated samples were sequenced using a custom program on Illumina NextSeq 500/550; and the libraries of the differentiated samples were sequenced on Illumina NovaSeq 6000. 26 bp of cell barcode and UMI sequences, and 91 or 98 bp RNA reads were generated with Illumina NextSeq500/550 or NovaSeq 6000.
Single cell 3’ RNA-seq experiments were conducted using the Chromium single cell system (10x Genomics, Inc) and Illumina sequencers at the Center of Molecular Genetics (CMG) of Indiana University School of Medicine. Cell suspension was first inspected on the Countess II FL (Thermo Fisher Scientific) and under microscope for cell number, cell viability, and cell size. Depending on the quality of the initial cell suspension, the single cell preparation included centrifugation, re-suspension, and filtration to remove cell debris, dead cells and cell aggregates. Single cell capture and library preparation were carried out according to the Chromium Single cell 3’ Reagent kits V2 User Guide (10X Genomics PN-120267, PN-1000009, PN-120262). Appropriate number of cells were loaded on a multiple-channel micro-fluidics chip of the Chromium Single Cell Instrument (10x Genomics) with a targeted cell recovery of 10,000. Single cell gel beads in emulsion containing barcoded oligonucleotides and reverse transcriptase reagents were generated with the v2 single cell reagent kit (10X Genomics). Following cell capture and cell lysis, cDNA was synthesized and amplified. Illumina sequencing libraries were then prepared with the amplified cDNA. The resulting libraries were assessed with an Agilent TapeStation or Bioanalyzer 2100.

treatment_protocol: Cells were dissociated by Corning™ 0.25% Trypsin (Corning™ 25053CI) to single cells.

tag: cell type source

value: hESCs H9 cells

tag: passage

tag: status

value: undifferenciated

tag: genotype/variation

value: ARID1A KO


title: DMSO 6h_797R1


title: WT_undiff_scRNA-seq

value: wild type


title: 62.5 nM OTX-015 + 62.5 nM GNE-781 6h_797R1


title: Cord blood ID_255


title: Cord blood ID_264


title: Cord blood ID_254


title: 62.5 nM OTX-015 + 62.5 nM GNE-781 6h_PER403R1


title: Cord blood ID_252


title: Cord blood ID_253


title: ARID1A_ChIPSeq

data_processing:
Base calling and quality scoring were performed in Illumina NextSeq
The reads were mapped to the human genome (UCSC hg38) using Bowtie2 (v2.3.2), PICARD (v2.10.7) function MarkDuplicates was used to identify duplicate reads
MACS2 (v 2.1.2) were used to call peaks using Input as control at FDR cut off of less than 1e-2
The signal at each base was normalized by per 10 million reads
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig file showing the normalized read signal, narrowpeak file showing the peaks

growth_protocol: H9 hESCs were routinely cultured in mTesR medium (typically 1× 106 - 1×107 cells in a matrigel-coated P10 plate).

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.

treatment_protocol: Briefly, hESCs were fixed with methanol-free formaldehyde provided by truChIP™ Chromatin Shearing Kit (Covaris, PN 520154). Chromatin of cell lysis was sheared using truChIP™ Chromatin Shearing Kit according its manual by ME220 Focused-ultrasonicator (Covaris). The sheared chromatin was then incubated with anti-ARID1A antibody and purified by using EZ-Magna ChIP™ A/G Chromatin Immunoprecipitation Kit (Millipore, 17-10086). Chromatin DNAs quality was assessed by 2100 Bioanalyzer (Agilent Technologies)

tag: antibody

value: 04-080 Sigma-Aldrich, Anti-BAF250a/ARID1a Antibody, clone PSG3


title: 1% Input

value: input


title: Cord blood ID_262


title: Mother_TOF02_d60_4.8

first: Silke

last: Sperling

address: Lindenberger Weg 80

department: Cardiovascular Genetics

institute: Experimental and Clinical Research Center (ECRC), Charité / MDC for Molecular Medicine

description: Sequenced with NextSeq 500 (2x76bp)

data_processing:
Basecalls performed using CASAVA version 1.8.0
Mapping using STAR v2.4.2a with basic 2-pass mapping and the GENCODE gene/transcript annotation set v22
TPM expression values were calculated using RSEM v1.2.31 with GENCODE v22 annotations for a strand-specific protocol
Differentially expression was calculated for autosomal protein-coding genes with TPM>1 in at least one sample using EdgeR v3.16.5. Genes were defined as significantly differentially expressed if the adjusted p-value was below 0.05 using Benjamini-Hochberg correction as well as a fold change greater or equal to two.
Genome_build: GRCh38
Supplementary_files_format_and_content: RSEM gene count file including expected count, TPM and FPKM
Supplementary_files_format_and_content: RSEM transcript count file including expected count, TPM and FPKM

source_name: CM d60

extract_protocol:
mRNA was isolated using Direct-zol RNA Kits (Zymo Reasearch) and purified with Dynabeads Oligo(dT)25 (Thermo Fisher Scientific) to get the poly(A) RNA.
RNA libraries were prepared with the ScriptSeq v2 RNA-Seq Library Preparation Kit (Illumina).

value: cardiomyocytes

tag: differentiation stage


title: Cord blood ID_251


title: Mother_TOF02_d60_4.6

description: Sequenced with NextSeq 500 (2x76bp)


title: Mother_TOF02_d60_4.3

description: Sequenced with NextSeq 500 (2x76bp)


title: Father_TOF01_d60_2.4

description: Sequenced with NextSeq 500 (2x76bp)


title: Cord blood ID_25


title: Father_TOF01_d60_2.1

description: Sequenced with NextSeq 500 (2x76bp)


title: Father_TOF01_d60_2.2

description: Sequenced with NextSeq 500 (2x76bp)


title: Cord blood ID_256


title: TOF01_d60_1.5

description: Sequenced with NextSeq 500 (2x76bp)


title: TOF01_d60_1.3

description: Sequenced with NextSeq 500 (2x76bp)


title: Cord blood ID_249


title: TOF01_d60_1.2

description: Sequenced with NextSeq 500 (2x76bp)


title: Cord blood ID_247


title: TOF01_d15_1.2

description: Sequenced with NextSeq 500 (2x76bp)

source_name: CM d15


title: TOF01_d15_1.5

description: Sequenced with NextSeq 500 (2x76bp)


title: Father_TOF01_d15_2.1

description: Sequenced with NextSeq 500 (2x76bp)


title: Cord blood ID_246


title: OA04-CHIKV

description:
CHIKV_vs_Mock_ExpressionBrowser_OASF.xlsx
OASF_vs_HSF_ExpressionBrowser_CHIKV-infected.xlsx

value: osteoarthritic

value: OASF 4


title: OA04-C9

description: CHIKV+C9_vs_Mock_ExpressionBrowser_OASF.xlsx


title: Cord blood ID_250


title: HNC-85

type: RNA

city: Heidelberg

first: Omics IT & Data Management

last: Core Facility

address: Im Neuenheimer Feld 280

department: Omics IT & Data Management Core Facility

institute: German Cancer Research Center (DKFZ)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Microarray scanning was done using an iScan + array scanner and iScan Control Software 3.3.28

data_processing: Data extraction was done for all beads individually. The values of the beads of the probe were averaged to produce a unique expression measure per probe. Data normalization was performed using the 'limma' package, applying the 'neqc' function for normexp background correction and quantile normalization. The background was estimated by the function using the detection p-value.

label: biotin

source_name: biopsy HNC

label_protocol: Biotin-labeled cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit

extract_protocol: RNA and was extracted using the AllPrep DNA/RNA/Protein Mini Kit (Qiagen) with a modification to include small RNAs/miRNAs. Quality control was performed using Qubit RNA broad range assay kit (Thermo Fisher) and RNA screentape for Tapestation System (Agilent)

tag: subsite

value: oropharynx

tag: Sex

value: female

tag: age (years)

tag: smoker

value: yes

tag: alcohol

value: no

tag: hpv infection

tag: t status

tag: n status

tag: pathological grading

tag: therapy

value: SRT

tag: r status

tag: pfs event

tag: pfs months

tag: dss event

tag: dss months

tag: tumor cell content


title: Cord blood ID_245

tag: tissue

tag: birthweight


title: Father_TOF01_d15_2.2

description: Sequenced with NextSeq 500 (2x76bp)

tag: cell type

tag: differentiation stage


title: HNC-82

tag: subsite

value: nasal cavity

tag: Sex

value: male

tag: age (years)

tag: smoker

value: SRCT


title: HNC-86

tag: alcohol

tag: hpv infection

tag: t status

tag: n status

value: S


title: HNC-79

tag: pathological grading

tag: therapy

tag: r status

tag: pfs event


title: HNC-83

tag: pfs months

tag: dss event

tag: dss months

tag: tumor cell content


title: OA04-Mock

description:
CHIKV_vs_Mock_ExpressionBrowser_OASF.xlsx
CHIKV+C9_vs_Mock_ExpressionBrowser_OASF.xlsx
OASF_vs_HSF_ExpressionBrowser_Uninfected.xlsx

tag: state

tag: donor


title: TG LA 3

first: Jasmeet

middle: S

last: Reyat

address: Vincent Drive

country: United Kingdom

institute: University of Birmingham

data_processing:
De-multiplexing perfeormed using Bcl2Fastq v2.20.4.422 tool (Illumina)
Sequences then trimmed and a quality control check was carried out using Cutadapt
FASTQ files were aligned on HISAT2 (version 2.1.0) using Ensembl Mus Musculus reference GRCm38.91. Aligned reads were counted using Htseq version 0.9.1. Required transformations through different RNA-Seq analysis steps were done using Samtools version 1.4.
Differential expression was obtained using DEseq2 in R. Ensemble IDs were transformed to gene symbols using BioTools.
Genome_build: GRCm38.91
Supplementary_files_format_and_content: tab-delimited text files include BaseMean values for each Sample

organism: Mus musculus

source_name: left atrial tissue

extract_protocol:
Left atrias were removed, snap forzen using liquid nitrogen, and RNA was harvested using RNeasy Micro Kit (Cat#74004).
RNA was enriched for the Poly(A) RNA fraction by using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). Subsequent Next Generation SequencingGS cDNA library preparation was carried out using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions. The size of the resulting library was checked (Agilent Bioanalyzer High Sensitivity DNA Analysis Kit) and quantified by qPCR (NEBNext Library quant Kit for Illumina, NEB).

tag: strain

tag: tissue

value: Left atria

tag: age

value: 12 weeks

tag: genotype


title: WT LA 3

value: wild type


title: Cord blood ID_248

value: cord blood

tag: birthweight


title: OA03-C9

value: OASF 3


title: HNC-78

tag: subsite

value: oral cavity

tag: Sex

tag: age (years)

tag: smoker

tag: alcohol

tag: hpv infection

tag: t status


title: TG LA 2


title: Cord blood ID_243


title: WT LA 2


title: Cord blood ID_244


title: HNC-84

tag: n status

tag: pathological grading

tag: therapy

tag: r status

tag: pfs event

tag: pfs months

tag: dss event


title: Cord blood ID_242

tag: tissue


title: OA03-CHIKV

tag: state

value: osteoarthritic

tag: donor


title: HNC-80

tag: subsite

tag: dss months

tag: tumor cell content


title: WT LA 1

tag: strain

tag: age

tag: genotype


title: OA03-Mock


title: HNC-77

tag: Sex

tag: age (years)

tag: smoker

tag: alcohol

tag: hpv infection

tag: t status


title: OA02-CHIKV

value: OASF 2


title: HNC-75

value: larynx

tag: n status

tag: pathological grading

tag: therapy

tag: r status

tag: pfs event

tag: pfs months


title: HNC-76

tag: subsite

tag: dss event

tag: dss months


title: TG LA 1

tag: strain

tag: tissue

tag: age


title: Cord blood ID_24

tag: birthweight


title: OA02-C9

tag: state

tag: donor


title: Cord blood ID_239


title: OA02-Mock


title: Cord blood ID_237


title: Mouse, adult, male, knockout 76

first: Kelly

middle: Anne

last: Hyndman

state: Al

address: 1918 University BLVD

department: Medicine

description: single nuclear sequencing

data_processing:
Count matrices were generated with Cell Ranger v3.0.2 (10X Genomics) and saved as a filtered_feature_bc_matrix (Filtered feature-barcode matrices containing only cellular barcodes in MEX format)
The filtered_feature_bc_matrix was imported into Seurat (V3.1.4) and Seurat objects created, filtered using min.cells = 3, min.features = 500, and percent.mt<2.  The counts were then SCTRansformed with Seurat.
Seurat objects of the 4 samples were combined and used for downstream analyses of clustering and differential gene expression determination.
Genome_build: mm10_3.0.0
Supplementary_files_format_and_content: CellRanger output files from filtered_feature_bc_matrix.  For each sample (66, 67, 76, 77) there are barcodes.tsv, genes.tsv, and matrix.mtx files.

source_name: kidney

extract_protocol:
The left kidney was excised, decapsulated, cut into 5 mm cubes and snap frozen. Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (cOmplete™ ULTRA tab; Sigma-Aldrich) and RNase inhibitors: RNAsin Plus (5 ml/ml, Promega, Madison, WI) and SUPERaseIN (5 ml/ml , ThermoFisher The frozen kidney cubes were placed in a sterile petri dish with 1 ml of Nuclei EZ lysis buffer (plus protease and RNase inhibitors) and quickly minced.  The tissue was then homogenized with RNase-free, disposable pellet pestles and tubes (Fisher #12-141-368), and a hand held, Bel-Art™ Micro-Tube homogenizer (Wayne, NJ).  The homogenate was filtered through a 200 micron strainer (all strainers were purchase from pluriSelect Life Science), and homogenized again with a fresh tube and pestle.  The homogenate was moved to a sterile, RNase-free 15 ml tube with an additional 2 ml of Nuclei EZ lysis buffer (plus protease and RNase inhibitors).  After a 5 min incubation on ice, the homogenate was filtered through a 40 micron strainer.  The subsequent homogenate was centrifuged at 500 g for 5 min at 4°C.  The pellet was resuspending in Nuclei EZ lysis buffer (plus 1 ml/ml of SUPERaseIN and RNAsin), incubated on ice for 5 min and centrifuged again.  The pellet was resuspended in 2 ml of 1X Dulbecco’s Phosphate-buffered saline + 1% bovine serum albumin, filtered through a 5 micron strainer, and nuclei immediately counted with a hemocytometer. At least 5000 nuclei from each sample were placed into oil droplets with the 10X Genomics Chormium™ Single Cell B Chip kit, and cDNA libraries made using 10x Chorminum™ Single cell 3’ library and gel bead kit (version 3, 10X Genomics).
cDNA libraries made using 10x Chorminum™ Single cell 3’ library and gel bead kit (version 3, 10X Genomics).

treatment_protocol: All mice were provided 2 mg/ml doxycycline in 2% sucrose water for 7 days, followed by 7-day washout before kidney excision.  Mice positive for PAX8-rtTA/LC-1 Cre would knock down HDAC1 and HDAC2.

tag: Sex

value: Male

tag: genotype

value: kidney, epithelial, HDAC1 and HDAC2 knockdown

value: kidney


title: Mouse, adult, female, knockout 66

description: single nuclear sequencing

value: Female


title: Mouse, adult, male, control 77

description: single nuclear sequencing

value: Control


title: Cord blood ID_238


title: Mouse, adult, female, control 67

description: single nuclear sequencing


title: OA01-C9

value: OASF 1


title: OA01-Mock


title: Cord blood ID_236


title: 30mNMJ_rep7

city: Basel

first: Anastasiya

last: Boersch

address: Klingelbergstrasse 50 / 70

department: Biozentrum

country: Switzerland

institute: University of Basel

description:
average insert size: 103
standard deviation: 60.8733
direction: random
nmj_counts.txt
nmj_tpms.txt

data_processing:
RNA-seq reads were subjected to 3’ adapter and poly(A)/poly(T) tail trimming using Cutadapt v1.9.1 from Martin et al., EMBnet.journal, 2011. The following 3’ adapter sequence was utilized for generating RNA-Seq libraries and subsequently trimmed: Read1 5’-CTGTCTCTTATACACATCTCCGAGCCCACGAGAC-3’.
Reads shorter than 20 nucleotides were discarded.
The kallisto v0.43.1 software from Bray et al., Nature Biotechnology, 2016 was used for building transcriptome index and aligning filtered reads. The default options of kallisto were utilized for building transcriptome index. For aligning filtered reads we used options “--single”, “-l”, “-s” and “--pseudobam”.
Mapped reads were assigned to transcripts in a weighted manner: if a read was uniquely mapped to a transcript, then the transcript’s read count was incremented by 1; if a read was mapped to n different transcripts, each transcript’s read count was incremented by 1/n.
The expression of each transcript was estimated in transcripts per million (TPM) units by dividing its read count by the transcript length and normalizing to the library size. The expression of a gene was obtained by summing up the normalized expression of the transcripts associated with it. For every gene, read counts of transcripts associated with this gene were also summed up and further used for the differential expression analysis.
Genome_build: As the reference mouse transcriptome, we considered sequences of protein coding transcripts with the support level 1-3 based on genome assembly GRCm38 (release 92) and transcript annotations from Ensembl database (see Hubbard et al., Nucleic Acids Research, 2002).
Supplementary_files_format_and_content: tab-delimited text files include raw counts and TPM values at the gene level for each sample

source_name: Tibialis anterior muscle, synaptic region

growth_protocol: Mice were singly caged throughout the treatment period.

extract_protocol:
The SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) was used for the library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Male, C57BL/6JRj mice were singly caged and fed an AIN93M diet for either 2-3 months (10 months group) or 16 months (30 months group).

value: Tibialis anterior muscle

value: post natal month 30


title: OA01-CHIKV

source_name: Knee synovial fibroblast


title: HNC-72

value: oropharynx

value: male

tag: age (years)

tag: smoker

value: yes

tag: alcohol

tag: hpv infection

value: no

tag: t status

tag: n status

value: SRCT

tag: tumor cell content


title: Cord blood ID_233

source_name: cord blood

value: cord blood


title: HNC-74

tag: subsite

value: oral cavity

tag: pathological grading

tag: therapy

value: S

tag: r status

tag: pfs event

tag: pfs months

tag: dss event


title: HNC-70

tag: dss months


title: HNC-73

tag: Sex

value: SRT


title: HNC-68

value: larynx


title: HNC-71


title: Cord blood ID_234

tag: tissue

tag: birthweight


title: TET2_6_TET2i_Bisulfite_Padlock_seq

city: Grand Rapids

first: Lee

last: Marshall

state: MI

address: 333 Bostwick Ave NE

department: Center for Neurodegenerative Science

institute: Van Andel Research Institute

description: 72 hrs Dharmacon TET2 siGENOME SMARTpool

data_processing:
Libraries sequenced on the HiSeq 2500 platform (Illumina) using custom sequencing primers.
Adapter sequences were removed from fastq files using TrimGalore (v0.4.4).
The remaining sequencing reads were then aligned to the target reference genome (GRCh37/hg19) indexed by Bismark (v0.17.0).
DNA methylation calls were counted using Bismark (v0.17.0).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Each txt file contains the following information in order: chromosome #, genomic coordinate, strand, unmethylation count, methylation count, CHH/CHG/CG context of cytosine, exact sequence of the previous context

growth_protocol: SH-SY5Y cells were cultured in 10 % FBS (Gibco) RPMI (Thermo Fisher Scientific)

extract_protocol:
After 72 h post-transfection, genomic DNA was extracted from the SH-SY5Y cells by standard phenol-chloroform extraction methods.
Libraries were prepared using a targeted bisulfite sequencing approach known as bisulfite padlock probes sequencing. Padlock probes were designed to human brain enhancers and promoters (NIH Roadmap ChromHmm) and synthesized using a programmable microfluidic platform (Custom Array, Inc.). Genomic DNA was bisulfite converted and purified using the EZ DNA Methylation-Lightning Kit (Zymo Research). The bisulfite-converted DNA (200 ng) was then hybridized to the padlock probes (1.5 ng). PfuTurbo Cx (Agilent Technologies) was used to extend across the target regions and circularization was completed using Ampligase (Epicentre). Non-circularized DNA was digested using an exonuclease cocktail and the remaining circularized DNA was amplified using a common linker sequence in the padlock probe. Libraries were PCR amplified, pooled in equimolar amounts, purified by QIAquick Gel Extraction kit (Qiagen) and quantified by qPCR (Kapa Biosystems) on a ViiA 7 Real-time PCR system (Applied Biosystems). Next-generation sequencing of the libraries was performed on an Illumina HiSeq 2500 machine on HiOutput mode.

treatment_protocol: SH-SY5Y cell were transfected with 100 nM of either human TET2 siGENOME SMARTpool siRNA or a non-targeting siGENOME Control#2 siRNA (Dharmacon), using X-tremeGENE siRNA Transfection Reagent (Sigma-Aldrich) according the manufacturer’s instructions

tag: cell line

tag: sirna

tag: transfection hours

tag: replicate

value: Biological Sample


title: 30mNMJ_rep8

description:
average insert size: 101
standard deviation: 60.0558
direction: random
nmj_counts.txt
nmj_tpms.txt

tag: strain

tag: age

tag: genotype

value: wild type


title: TET2_8_TET2i_Bisulfite_Padlock_seq


title: 30mNMJ_rep5

description:
average insert size: 129
standard deviation: 54.272
direction: random
nmj_counts.txt
nmj_tpms.txt


title: 30mNMJ_rep6

description:
average insert size: 108
standard deviation: 60.1948
direction: random
nmj_counts.txt
nmj_tpms.txt


title: 30mNMJ_rep4

description:
average insert size: 106
standard deviation: 58.8786
direction: random
nmj_counts.txt
nmj_tpms.txt


title: TET2_7_TET2i_Bisulfite_Padlock_seq


title: 30mNMJ_rep3

description:
average insert size: 108
standard deviation: 60.3656
direction: random
nmj_counts.txt
nmj_tpms.txt


title: TET2_5_TET2i_Bisulfite_Padlock_seq


title: TET2_4R_TET2i_Bisulfite_Padlock_seq

value: Technical Replicate


title: Cord blood ID_232


title: Cord blood ID_230


title: TET2_4_TET2i_Bisulfite_Padlock_seq


title: Cord blood ID_231


title: HNC-66

tag: subsite

value: female

tag: age (years)

tag: smoker

tag: alcohol

tag: hpv infection

tag: t status

tag: n status

tag: pathological grading

tag: tumor cell content


title: HNC-67

tag: Sex

tag: therapy

tag: r status

tag: pfs event

tag: pfs months

tag: dss event

tag: dss months


title: HNC-65


title: 30mNMJ_rep2

description:
average insert size: 102
standard deviation: 58.4528
direction: random
nmj_counts.txt
nmj_tpms.txt

tag: strain

tag: tissue

tag: age

tag: genotype


title: Cord blood ID_23

tag: birthweight


title: HNC-63

tag: subsite

tag: age (years)

tag: smoker

tag: alcohol

tag: hpv infection


title: HNC-64

tag: Sex

tag: t status

tag: n status

tag: pathological grading

tag: tumor cell content


title: HNC-69

tag: therapy

tag: r status

tag: pfs event

tag: pfs months

tag: dss event


title: Cord blood ID_229

tag: tissue


title: 30mNMJ_rep1

description:
average insert size: 119
standard deviation: 68.8755
direction: random
nmj_counts.txt
nmj_tpms.txt

tag: strain

tag: age

tag: genotype


title: 30mxNMJ_rep8

description:
average insert size: 87
standard deviation: 56.7758
direction: random
nmj_counts.txt
nmj_tpms.txt

source_name: Tibialis anterior muscle, extra-synaptic region


title: Cord blood ID_227

tag: birthweight


title: TET2_3_TET2i_Bisulfite_Padlock_seq

tag: cell line

tag: sirna

tag: transfection hours

tag: replicate


title: TET2_2_TET2i_Bisulfite_Padlock_seq


title: 30mxNMJ_rep7

description:
average insert size: 92
standard deviation: 57.5472
direction: random
nmj_counts.txt
nmj_tpms.txt


title: TET2_1_TET2i_Bisulfite_Padlock_seq


title: 30mxNMJ_rep5

description:
average insert size: 130
standard deviation: 68.2822
direction: random
nmj_counts.txt
nmj_tpms.txt


title: 30mxNMJ_rep6

description:
average insert size: 96
standard deviation: 57.7912
direction: random
nmj_counts.txt
nmj_tpms.txt


title: NT_8_TET2i_Bisulfite_Padlock_seq

description: 72 hrs Dharmacon non-targeting siGENOME Control#2

value: non-targeting


title: Cord blood ID_226


title: Cord blood ID_225


title: 30mxNMJ_rep4

description:
average insert size: 96
standard deviation: 61.3176
direction: random
nmj_counts.txt
nmj_tpms.txt

value: Tibialis anterior muscle


title: Cord blood ID_228


title: NT_6_TET2i_Bisulfite_Padlock_seq


title: Cord blood ID_224


title: 30mxNMJ_rep3

description:
average insert size: 109
standard deviation: 71.3195
direction: random
nmj_counts.txt
nmj_tpms.txt

value: post natal month 30


title: NT_5_TET2i_Bisulfite_Padlock_seq


title: HNC-60

tag: subsite

tag: Sex

tag: age (years)

tag: smoker

tag: alcohol

tag: hpv infection

tag: t status

tag: n status

tag: dss months


title: HNC-58

tag: pathological grading

tag: therapy

tag: r status

tag: pfs event

tag: pfs months

tag: dss event

tag: tumor cell content


title: HNC-62


title: Cord blood ID_222

tag: tissue

tag: birthweight


title: NT_4R_TET2i_Bisulfite_Padlock_seq

tag: cell line

tag: sirna

tag: transfection hours

tag: replicate


title: HNC-57

tag: subsite

value: oropharynx

tag: Sex

tag: age (years)

tag: smoker

tag: alcohol

tag: hpv infection


title: 30mxNMJ_rep2

description:
average insert size: 107
standard deviation: 63.2286
direction: random
nmj_counts.txt
nmj_tpms.txt

tag: strain

tag: age

tag: genotype


title: 30mxNMJ_rep1

description:
average insert size: 79
standard deviation: 56.9105
direction: random
nmj_counts.txt
nmj_tpms.txt


title: NT_4_TET2i_Bisulfite_Padlock_seq


title: HNC-56

value: hypopharynx

value: male

tag: t status

tag: n status

tag: pathological grading

tag: therapy

tag: r status

tag: pfs event

tag: pfs months

tag: dss event

tag: dss months


title: HNC-59

tag: subsite

tag: Sex

value: yes

value: no

tag: tumor cell content


title: NT_3_TET2i_Bisulfite_Padlock_seq

tag: cell line

tag: sirna

tag: transfection hours

tag: replicate


title: NT_7_TET2i_Bisulfite_Padlock_seq


title: 10mNMJ_rep8

description:
average insert size: 52
standard deviation: 33.7084
direction: random
nmj_counts.txt
nmj_tpms.txt

tag: strain

tag: tissue

tag: age

value: post natal month 10

tag: genotype


title: HNC-55

tag: age (years)

tag: smoker

tag: alcohol

tag: hpv infection

tag: t status

tag: n status

tag: pathological grading

tag: therapy


title: Cord blood ID_220

value: cord blood

tag: birthweight


title: 10mNMJ_rep7

description:
average insert size: 109
standard deviation: 60.809
direction: random
nmj_counts.txt
nmj_tpms.txt


title: NT_2_TET2i_Bisulfite_Padlock_seq

tag: cell line


title: Cord blood ID_223


title: 10mNMJ_rep6

description:
average insert size: 120
standard deviation: 70.912
direction: random
nmj_counts.txt
nmj_tpms.txt


title: HNC-53

tag: subsite

value: nasal cavity

tag: Sex

tag: r status

tag: pfs event

tag: pfs months

tag: dss event

tag: dss months

tag: tumor cell content


title: Cord blood ID_219

tag: tissue


title: NT_1_TET2i_Bisulfite_Padlock_seq

tag: sirna

tag: transfection hours

tag: replicate


title: Cord blood ID_22


title: HNC-50

tag: age (years)

tag: smoker

tag: alcohol

tag: hpv infection

tag: t status

tag: n status

value: SRT


title: 10mNMJ_rep5

description:
average insert size: 112
standard deviation: 60.1648
direction: random
nmj_counts.txt
nmj_tpms.txt

tag: strain

tag: age

tag: genotype


title: Cord blood ID_221

tag: birthweight


title: 10mNMJ_rep4

description:
average insert size: 126
standard deviation: 61.9106
direction: random
nmj_counts.txt
nmj_tpms.txt


title: Cord blood ID_218


title: Cord blood ID_217


title: Cord blood ID_216


title: HNC-54

tag: subsite

tag: Sex

tag: pathological grading

tag: therapy

value: S

tag: r status

tag: pfs event

tag: pfs months

tag: dss event


title: 10mNMJ_rep3

description:
average insert size: 120
standard deviation: 72.9344
direction: random
nmj_counts.txt
nmj_tpms.txt

tag: tissue


title: 10mNMJ_rep2

description:
average insert size: 131
standard deviation: 75.6945
direction: random
nmj_counts.txt
nmj_tpms.txt


title: Cord blood ID_214


title: 10mNMJ_rep1

description:
average insert size: 115
standard deviation: 71.0581
direction: random
nmj_counts.txt
nmj_tpms.txt


title: HNC-52

value: oral cavity

tag: age (years)

tag: smoker

tag: alcohol

tag: dss months

tag: tumor cell content


title: PD6_G8_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD336

extract_protocol:
Neuronal nuclei from prefrontal cortex were isolated using an antibody (NeuN) and flow cytometry approach. Human prefrontal cortex brain tissue was homogenized and then filtered through Miracloth before being passed through a 1.4 M sucrose cushion by centrifugation at 4000 × g for 30 min 4°C. Nuclei pellets were resuspended and blocking mix (100 μl of 1X PBS with 0.5% BSA and 10% normal goat serum) was added to each sample. Anti-NeuN antibody with Alex Fluor 488 (1:500; Abcam; ab190195) was added and samples were incubated 45 min at 4°C with gentle mixing, followed by staining with 7-AAD. Nuclei positive for 7-AAD and either NeuN+ (neuronal) or NeuN‒ (non-neuronal) were sorted by flow cytometry. Genomic DNA from NeuN+ nuclei was extracted by standard phenol-chloroform extraction.
Libraries were prepared using a targeted bisulfite sequencing approach known as bisulfite padlock probes sequencing. Padlock probes were designed to TET2 gene and surrounding area (±300 kb) and synthesized using a programmable microfluidic platform (Custom Array, Inc.). Genomic DNA was bisulfite converted and purified using the EZ DNA Methylation-Lightning Kit (Zymo Research). The bisulfite-converted DNA (200 ng) was then hybridized to the padlock probes (1.5 ng). PfuTurbo Cx (Agilent Technologies) was used to extend across the target regions and circularization was completed using Ampligase (Epicentre). Non-circularized DNA was digested using an exonuclease cocktail and the remaining circularized DNA was amplified using a common linker sequence in the padlock probe. Libraries were PCR amplified, pooled in equimolar amounts, purified by QIAquick Gel Extraction kit (Qiagen) and quantified by qPCR (Kapa Biosystems) on a ViiA 7 Real-time PCR system (Applied Biosystems). Next-generation sequencing of the libraries was performed on an Illumina HiSeq 2500 machine on HiOutput mode.

value: M

tag: age

tag: pmi

tag: braak stage

tag: tissue/cell type

value: Brain prefrontal cortex neurons(NeuN+)

tag: brain bank

value: Parkinson’s UK Brain Bank

tag: replicate

value: Biological Sample


title: PD6_D4_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD268

tag: Sex


title: PD6_E1_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD286


title: Cord blood ID_213

tag: birthweight


title: 10mxNMJ_rep8

description:
average insert size: 99
standard deviation: 61.9695
direction: random
nmj_counts.txt
nmj_tpms.txt

tag: strain

value: Tibialis anterior muscle

tag: genotype

value: wild type


title: Cord blood ID_212


title: PD6_G9_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD226


title: 10mxNMJ_rep7

description:
average insert size: 100
standard deviation: 61.1948
direction: random
nmj_counts.txt
nmj_tpms.txt


title: HNC-49

tag: subsite

tag: hpv infection

tag: t status

tag: n status

tag: pathological grading

tag: therapy

value: SRCT

tag: r status

tag: pfs event

tag: pfs months

tag: dss event


title: HNC-47

value: larynx

value: female

tag: age (years)

tag: smoker

tag: alcohol

tag: dss months

tag: tumor cell content


title: HNC-48

tag: Sex

value: male


title: Cord blood ID_211

tag: tissue

tag: birthweight


title: HNC-44

tag: subsite

value: oropharynx

value: yes

tag: hpv infection


title: HNC-46

value: no

tag: t status

tag: n status


title: HNC-43

tag: pathological grading

tag: therapy


title: 10mxNMJ_rep6

description:
average insert size: 89
standard deviation: 57.555
direction: random
nmj_counts.txt
nmj_tpms.txt

tag: strain

tag: age

value: post natal month 10

tag: genotype


title: Cord blood ID_210

value: cord blood


title: Cord blood ID_241


title: HNC-45

tag: age (years)

value: S

tag: r status

tag: pfs event

tag: pfs months

tag: dss event


title: PD5_B11_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD184

tag: Sex

tag: pmi

tag: braak stage

tag: tissue/cell type

tag: brain bank

tag: replicate


title: Cord blood ID_240

tag: tissue

tag: birthweight


title: PD6_A1_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD201


title: HNC-42

tag: subsite

tag: smoker

tag: alcohol

tag: hpv infection

tag: t status

tag: n status

tag: pathological grading

tag: therapy

tag: dss months

tag: tumor cell content


title: HNC-40

value: oral cavity

tag: Sex

tag: age (years)

value: SRT

tag: r status

tag: pfs event

tag: pfs months

tag: dss event


title: Cord blood ID_21

tag: tissue

tag: birthweight


title: PD5_B5_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD348

value: M

tag: age

tag: pmi

tag: braak stage

tag: tissue/cell type

value: Brain prefrontal cortex neurons(NeuN+)

tag: brain bank

tag: replicate


title: PD5_E2_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD338

value: Parkinson’s UK Brain Bank

value: Biological Sample


title: Cord blood ID_209


title: PD5_A5_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD387


title: 10mxNMJ_rep5

description:
average insert size: 85
standard deviation: 52.1781
direction: random
nmj_counts.txt
nmj_tpms.txt

tag: strain

value: Tibialis anterior muscle

tag: genotype

value: wild type


title: 10mxNMJ_rep3

description:
average insert size: 91
standard deviation: 65.4214
direction: random
nmj_counts.txt
nmj_tpms.txt


title: Cord blood ID_208


title: HNC-39

tag: subsite

tag: smoker

tag: alcohol

tag: hpv infection

tag: t status

tag: n status

tag: pathological grading

tag: therapy

tag: dss months

tag: tumor cell content


title: PD4_F5_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD171

tag: Sex

tag: age

tag: pmi


title: PD5_D6_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD194

tag: braak stage

tag: tissue/cell type

tag: brain bank


title: 10mxNMJ_rep2

description:
average insert size: 96
standard deviation: 58.8352
direction: random
nmj_counts.txt
nmj_tpms.txt

tag: strain

tag: tissue

tag: genotype


title: Cord blood ID_207

tag: birthweight


title: HNC-38

tag: subsite

tag: age (years)

tag: smoker

tag: alcohol

tag: hpv infection

value: SRCT

tag: r status

tag: pfs event

tag: pfs months

tag: dss event


title: 10mxNMJ_rep1

description:
average insert size: 79
standard deviation: 51.514
direction: random
nmj_counts.txt
nmj_tpms.txt

tag: age


title: PD4_B12_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD216

tag: Sex

tag: pmi

tag: braak stage

tag: replicate


title: Cord blood ID_206

tag: tissue


title: 10mxNMJ_rep4

description:
average insert size: 108
standard deviation: 61.8784
direction: random
nmj_counts.txt
nmj_tpms.txt

tag: strain

tag: genotype


title: Cord blood ID_203

tag: birthweight


title: PD4_B6_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD398

tag: tissue/cell type

tag: brain bank


title: PD4_A6_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD295


title: HNC-37

tag: subsite

value: larynx

tag: age (years)

tag: smoker

tag: alcohol

tag: t status

tag: n status

tag: pathological grading

tag: therapy

tag: dss months

tag: tumor cell content


title: Cord blood ID_202


title: HNC-36

tag: Sex

value: male

tag: hpv infection

tag: r status

tag: pfs event

tag: pfs months

tag: dss event


title: HNC-35

value: oropharynx


title: Cord blood ID_201

tag: tissue

tag: birthweight


title: PD3_G10_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD017

tag: age

tag: pmi

tag: braak stage

tag: tissue/cell type

tag: brain bank

tag: replicate


title: PD3_D7_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD081


title: Cord blood ID_20


title: PD4_D11_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD239


title: Cord blood ID_200


title: PD3_B3_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD084


title: Cord blood ID_2


title: Cord blood ID_199


title: HNC-34

tag: subsite

value: female

tag: age (years)

tag: smoker

tag: alcohol

tag: t status

tag: n status

tag: pathological grading

tag: therapy


title: HNC-33

tag: Sex

value: yes

value: no

tag: hpv infection

tag: r status

tag: pfs event

tag: pfs months

tag: dss event

tag: dss months

tag: tumor cell content


title: HNC-29


title: Cord blood ID_198

tag: tissue

value: cord blood

tag: birthweight


title: PD3_A11_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD028

tag: age

tag: pmi

tag: braak stage

tag: tissue/cell type

tag: brain bank

tag: replicate


title: HNC-31

tag: subsite

tag: age (years)

tag: smoker

tag: alcohol

tag: t status

tag: n status

tag: pathological grading

tag: therapy


title: CTRL_P2A4_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:90

tag: Sex

value: Michigan


title: Cord blood ID_197

tag: tissue


title: CTRL_P2A3_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:16


title: Cord blood ID_196

tag: birthweight


title: CTRL_H10_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:5657

tag: age

value: Maryland


title: PD3_C7_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD032

tag: pmi


title: Cord blood ID_195


title: HNC-28

tag: hpv infection

value: S

tag: r status

tag: pfs event

tag: pfs months

tag: dss event

tag: dss months

tag: tumor cell content


title: Cord blood ID_194


title: Cord blood ID_193


title: CTRL_H9_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:5089

value: M

tag: braak stage

tag: tissue/cell type

tag: brain bank

tag: replicate


title: CTRL_H6_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:Hct15HBC

value: Brain prefrontal cortex neurons(NeuN+)

value: Miami


title: HNC-27

tag: subsite

tag: age (years)

tag: smoker

tag: alcohol

tag: t status

tag: n status

tag: pathological grading

tag: therapy


title: HNC-24

value: oral cavity

tag: Sex

tag: hpv infection

tag: r status

tag: pfs event


title: HNC-26

value: nasal cavity

tag: pfs months

tag: dss event

tag: dss months

tag: tumor cell content


title: CTRL_F11_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD030

tag: age

tag: pmi

tag: braak stage

tag: tissue/cell type

tag: brain bank

value: Parkinson’s UK Brain Bank

tag: replicate

value: Biological Sample


title: HNC-23

tag: subsite

value: larynx

tag: age (years)

tag: smoker

tag: alcohol

tag: t status

tag: n status

value: SRT


title: HNC-21

tag: Sex

value: male

tag: hpv infection

tag: pathological grading

tag: therapy

value: SRCT

tag: r status

tag: pfs event


title: HPC-7 input

city: Singapore

first: Jia

last: Li

address: 8 College Road

country: Singapore

institute: Duke-NUS

data_processing:
The paired-end ChIP-seq reads are mapped by bowtie2 to the mouse reference genome GRCm38 (mm10)
PCR duplicates are filtered out from the resulting BAM files using samtools rmdup.
Alignments with mapping quality below 20 are also filtered out.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files are converted by bedGraphToBigWig from bedGraph generated by bedtools. The ChIP-seq signal will be shrunk to fit the size of its control if the control is smaller in size.
The paired-end RNA-seq reads are mapped by STAR to the mouse reference genome GRCm38 (mm10).
Alignments with mapping quality below 20 are filtered out.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files are converted by bedGraphToBigWig from bedGraph generated by bedtools. Normalization between the samples was based on the proportionality of the numbers of the mapped reads.

source_name: HPC-7 input

growth_protocol: LSK or c-Kit+ cells were sorted from fetal liver of Rosa26 Cre-ERT2; Tip60f/f and Tip60f/f embryos (E13.5-15.5) by FACS Aria (BD Biosciences), cultured in Stemline II (Sigma-Aldrich) supplemented with 5% FBS, murine recombinant SCF 100ng/uL, IL-3 6 ng/uL, IL-6 10ng/uL, IL-11 20 ng/uL (Peprotech). HPC-7 cells were grown in SCF.

extract_protocol:
RNA was isolated using RNeasy mini columns (Qiagen). As for ChIP, briefly, cells were fixed with 1% formaldehyde and then neutralized with glycine at a final concentration of 0.125M. Fixed chromatin were fragmented using a Bioruptor sonicator (Diagenode) to an average size around 300-500 base pairs. Sonicated chromatin was incubated with antibody overnight at 4°C. The antibodies used are Tip60 50, H2A.Z (abcam, ab4174), acH2A.Z (abcam, ab18262), H3K27ac (abcam, ab4729), and H3K27me3 (CST, 9733BC). Protein A and Protein G Dynabeads (Life Technologies) were added to the mixture and incubated for 2 hours at 4°C. Antibody:chromatin complexes were collected with a magnet and washed two times with a solution of 50 mM HEPES-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40 and 0.7% Na-Deoyxcholate. After a TE wash, samples are eluted, RNase and proteinase K treated and purified using a QIAGEN PCR purification kit. A mimunim of 10 ng of DNA was used for library construction using ThruPLEX kits (Rubicon Genomics).
RNA-seq libraries were prepared using Illumina ScriptSeq™ v2 RNA-Seq  Library Preparation Kit, according to the manufacturer’s instructions (Illumina, San Diego, California, USA). Libraries were validated with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA), diluted and applied to an Illumina flow cell using the Illumina Cluster Station. ChIP-seq libraries were prepared using ThruPLEX® DNA-seq Kit (Rubicon), and multiplexed.

treatment_protocol: The cells were treated with 4-Hydroxytamoxifen (4-OHT) (Sigma-Aldrich) 400 nM for 72 hours.

tag: cell type

value: murine hematopoietic stem and prgenitor cell


title: Cord blood ID_192

tag: tissue

tag: birthweight


title: HNC-22

value: oropharynx

value: yes

value: no

tag: pfs months

tag: dss event

tag: dss months

tag: tumor cell content


title: Cord blood ID_191

value: cord blood


title: CTRL_E10_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:AN05209

tag: age

tag: pmi

tag: braak stage

tag: tissue/cell type

tag: brain bank

value: Harvard

tag: replicate


title: CTRL_E9_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:PD549

tag: Sex

value: M


title: Cord blood ID_19


title: HNC-20

tag: subsite

tag: age (years)

tag: smoker

tag: alcohol

tag: hpv infection

tag: t status

tag: n status

tag: pathological grading

tag: therapy


title: Cord blood ID_190

tag: tissue

tag: birthweight


title: HPC-7 Tip60

source_name: HPC-7 Tip60

tag: cell type


title: CTRL_C6_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:4320

tag: age

tag: pmi

tag: braak stage

value: Brain prefrontal cortex neurons(NeuN+)

value: Sepulveda


title: HNC-19

tag: r status

tag: pfs event

tag: pfs months

tag: dss event

tag: dss months

tag: tumor cell content


title: HNC-18

tag: subsite

tag: Sex

tag: age (years)

tag: smoker

tag: alcohol

tag: hpv infection


title: Tip60 KO HSPC acH2A.Z

source_name: Tip60f/f Rosa26ERCreT2 embryo


title: HNC-17

tag: t status

tag: n status

tag: pathological grading

tag: therapy

value: S


title: Mother_TOF02_d15_4.8

description: Sequenced with Illumina HiSeq 2500 (2x51bp)

tag: cell type

value: cardiomyocytes

tag: differentiation stage


title: Cord blood ID_189

tag: tissue

tag: birthweight


title: Tip60 KO HSPC H2A.Z


title: Cord blood ID_188


title: Mother_TOF02_d15_4.6


title: HNC-16

tag: r status

tag: pfs event

tag: pfs months

tag: dss event


title: HNC-15

tag: subsite

tag: Sex

tag: dss months

tag: tumor cell content


title: Mother_TOF02_d15_4.3


title: HNC-14

value: nasal cavity

tag: age (years)

tag: smoker

tag: alcohol

tag: hpv infection


title: HNC-13

tag: t status

tag: n status

tag: pathological grading

tag: therapy


title: Tip60 WT HSPC Tip60

extract_protocol:
RNA was isolated using RNeasy mini columns (Qiagen). As for ChIP, briefly, cells were fixed with 1% formaldehyde and then neutralized with glycine at a final concentration of 0.125M. Fixed chromatin were fragmented using a Bioruptor sonicator (Diagenode) to an average size around 300-500 base pairs. Sonicated chromatin was incubated with antibody overnight at 4°C. The antibodies used are Tip60 50, H2A.Z (abcam, ab4174), acH2A.Z (abcam, ab18262), H3K27ac (abcam, ab4729), and H3K27me3 (CST, 9733BC). Protein A and Protein G Dynabeads (Life Technologies) were added to the mixture and incubated for 2 hours at 4°C. Antibody:chromatin complexes were collected with a magnet and washed two times with a solution of 50 mM HEPES-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40 and 0.7% Na-Deoyxcholate. After a TE wash, samples are eluted, RNase and proteinase K treated and purified using a QIAGEN PCR purification kit. A mimunim of 2 ng of DNA was used for library construction using ThruPLEX kits (Rubicon Genomics).
RNA-seq libraries were prepared using Illumina ScriptSeq™ v2 RNA-Seq  Library Preparation Kit, according to the manufacturer’s instructions (Illumina, San Diego, California, USA). Libraries were validated with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA), diluted and applied to an Illumina flow cell using the Illumina Cluster Station. ChIP-seq libraries were prepared using ThruPLEX® DNA-seq Kit (Rubicon), and multiplexed.

tag: cell type


title: Tip60 WT HSPC acH2A.Z


title: Cord blood ID_187

tag: tissue

tag: birthweight


title: Cord blood ID_186


title: Tip60 WT HSPC H2A.Z


title: Mother_TOF02_d0_4.8

source_name: iPSC d0

value: induced pluripotent stem cells

tag: differentiation stage

tag: passages


title: Tip60 KO LSK #3


title: HNC-12

tag: subsite

value: hypopharynx

tag: r status

tag: pfs event

tag: pfs months

tag: dss event


title: Cord blood ID_184


title: Mother_TOF02_d0_4.6


title: Cord blood ID_185


title: Tip60 KO LSK #2


title: HNC-11

tag: Sex

tag: age (years)

tag: smoker

tag: dss months

tag: tumor cell content


title: Mother_TOF02_d0_4.3


title: Tip60 KO LSK #1


title: Cord blood ID_183


title: TOF02_d0_5.9


title: Cord blood ID_181


title: Tip60 WT LSK #3


title: HNC-10

tag: alcohol

tag: hpv infection

tag: t status

tag: n status

tag: pathological grading


title: HNC-7

tag: therapy


title: TOF02_d0_5.6

tag: cell type

tag: differentiation stage

tag: passages


title: HNC-9

tag: subsite

tag: r status

tag: pfs event


title: HNC-6

tag: Sex

tag: pfs months

tag: dss event


title: TOF02_d0_5.2


title: Cord blood ID_180

tag: tissue

tag: birthweight


title: Tip60 WT LSK #2


title: HNC-4

tag: age (years)

tag: smoker

tag: alcohol

tag: dss months

tag: tumor cell content


title: Tip60 WT LSK #1


title: Sister_TOF01_d0_3.7


title: Cord blood ID_179


title: Sister_TOF01_d0_3.4


title: MEFD5plu_4

city: Abu Dhabi

first: Mohamed

last: Al-Sayegh

address: Saadiyaat Island - 1st floor ERB, Room 136, P.O. Box 129188

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Mus musculus GRCm38 (mm10) genome using tophat2 v2.1.0 with the parameters “–no-novel-junctions” and “–G” when specifying the genome file
Raw counts of mapped reads of each genes were derived using HTseq count
DESeq2 was used for differential expression analysis.
Mus musculus GRCm38 (mm10) genome version
Genome_build: tab-delimited text files include raw counts for each Sample

source_name: connective tissue - MEFs

growth_protocol: DMEM + 10 %FBS

extract_protocol:
Total RNA was extracted using TriZol LS and Rneasy Mini Kit (Qiagen) according to manufacturer protocol.
Total RNA was used for library construction at the Center for Genomics and Systems Biology, New York University Abu Dhabi, using TruSeq RNA Library Prep Kit v2 (Illumina).

treatment_protocol: DMEM + 10 %FBS supplemented with 0.5 mM 3-isobutyl-1-methylxanthine, 10 μg/mL insulin, 1 μM dexamethasone, and 10 μM rosiglitazone

tag: strain

value: BALB/c

tag: age

value: 10.5 day old embryos

tag: genotype

value: wild-type

value: MEFs

tag: time

value: day 5 treated


title: 9M_TSCmKO_RAPA_rep5

description:
average insert size: NA
standard deviation: NA
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz

data_processing:
RNA-seq reads were subjected to 3’ adapter and poly(A) tail trimming using Cutadapt v1.9.1 from Martin et al., EMBnet.journal, 2011. The following 3’ adapter sequence was utilized for generating RNA-Seq libraries and subsequently trimmed: mate1 5’-TGGAATTCTCGGGTGCCAAG-3’.
Reads shorter than 20 nucleotides were discarded.
The kallisto v0.43.1 software from Bray et al., Nature Biotechnology, 2016 was used for building transcriptome index and aligning filtered reads. The default options of kallisto were utilized for building transcriptome index. For aligning filtered reads we used options “--single”, “-l”, “-s”, “--fr-stranded” and “--pseudobam”.
Mapped reads were assigned to transcripts in a weighted manner: if a read was uniquely mapped to a transcript, then the transcript’s read count was incremented by 1; if a read was mapped to n different transcripts, each transcript’s read count was incremented by 1/n.
The expression of each transcript was estimated in transcripts per million (TPM) units by dividing its read count by the transcript length and normalizing to the library size. The expression of a gene was obtained by summing up the normalized expression of the transcripts associated with it. For every gene, read counts of transcripts associated with this gene were also summed up and further used for the differential expression analysis.
Genome_build: As the reference mouse transcriptome, we considered sequences of protein coding transcripts with the support level 1-3 based on genome assembly GRCm38 (release 92) and transcript annotations from Ensembl database (see Hubbard et al., Nucleic Acids Research, 2002).
Supplementary_files_format_and_content: tab-delimited text files include raw counts and TPM values at the gene level for each sample

source_name: Extensor digitorum longus muscle

growth_protocol: Mice were maintained on standard laboratory chow.

extract_protocol:
RNA was extracted from whole EDL muscle lysates using the Dynabeads mRNA DIRECT Kit (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were injected I.P. with either vehicle or rapamycin (4 mg.kg-1) for 3 days prior to extraction.

value: Extensor digitorum longus muscle

value: post natal month 9

value: TSCmKO

tag: treatment

value: rapamycin


title: MEFD5plu_3

tag: cell type


title: MEFD5plu_1


title: Father_TOF01_d0_2.4

tag: differentiation stage

tag: passages


title: 9M_TSCmKO_RAPA_rep4

description:
average insert size: 262
standard deviation: 45.16
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: Cord blood ID_176

extract_protocol: DNA was extracted from buffy coats according to standard protocol

value: cord blood


title: HNC-3

tag: subsite

value: oropharynx

tag: Sex

value: male

value: yes

tag: hpv infection

tag: t status

tag: n status

tag: pathological grading

tag: therapy

value: SRCT

tag: r status

tag: pfs event

tag: pfs months


title: MEFD5min_4

tag: strain

tag: age

value: day 5 untreated


title: Cord blood ID_175

tag: tissue

tag: birthweight


title: CTRL_P2A2_PD_TET2_Bisulfite_Padlock_Seq

description: Brain bank Sample code:5824

value: M

tag: pmi

tag: braak stage

tag: tissue/cell type

value: Brain prefrontal cortex neurons(NeuN+)

tag: brain bank

value: Maryland

tag: replicate

value: Biological Sample


title: HNC-1

tag: subsite

tag: Sex

tag: age (years)

tag: smoker

value: no

tag: alcohol

tag: hpv infection

tag: dss event

tag: dss months

tag: tumor cell content


title: HNC-2

value: female

tag: t status

tag: n status

tag: pathological grading

tag: therapy

value: SRT

tag: r status

tag: pfs event

tag: pfs months


title: Cord blood ID_177

tag: tissue

tag: birthweight


title: Cord blood ID_174


title: Cord blood ID_18


title: MEFD5min_1

tag: strain

value: BALB/c

tag: age

value: 10.5 day old embryos

tag: genotype

value: wild-type

tag: cell type

value: MEFs

tag: time


title: MEFD3plu_4

value: day 3 treated


title: 9M_TSCmKO_RAPA_rep1

description:
average insert size: 273
standard deviation: 45.04
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz

value: Extensor digitorum longus muscle

value: post natal month 9

value: TSCmKO

tag: treatment

value: rapamycin


title: Cord blood ID_171

value: cord blood


title: 9M_TSCmKO_RAPA_rep2

description:
average insert size: 262
standard deviation: 46.56
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: 9M_TSCmKO_rep4

description:
average insert size: 266
standard deviation: 44.78
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz

value: vehicle


title: TOF01_d0_1.3

value: induced pluripotent stem cells

tag: differentiation stage

tag: passages


title: Father_TOF01_d0_2.1


title: MEFD3plu_1


title: Sister_TOF01_d0_3.9


title: MEFD5min_3

value: day 5 untreated


title: TOF01_d0_1.2


title: Cord blood ID_170


title: MEFD3min_4

value: day 3 untreated


title: LIPA+/+ 2

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University

description: Sample 5

data_processing:
Base calling was done by RTA v1.13.48.0
Sequence reads were aligned to hg19 genome using STAR with default options.
Alignment was filtered using the following specifications: 1) reads from the same pair were mapped to the same chromosome with expected orientations and mapping distance between the read pair was < 500,000 bp, 2) read was uniquely mapped
Fragments Per Kilobase of exon per Million reads mapped (FPKM) was estimated by Cufflinks 2.1.1. Differential expression was tested by Cuffdiff with options "-u --max-bundle-frags 50000000 --library-type fr-firststrand". Annotation from RefSeq coding genes, GENCODE v19 lincRNAs and the stringent set of lincRNAs from Cabili et al. 2011 was used.
Genome_build: hg19
Supplementary_files_format_and_content: control_LIPA_KO_FPKM.tsv contains FPKM values of coding genes from LIPA+/+ and LIPA-/- samples

source_name: Macrophage

growth_protocol: iPSC lines were maintained in hESC media consisting of Dulbecco modified Eagle medium/F12 (50:50; Life Technologies, Grand Island, NY) supplemented with 20% knockout serum replacement, 100 μM nonessential amino acids, 50 U/ml penicillin, 50 μg/ml streptomycin (Life Technologies), 10−4 M β-mercaptoethanol (Sigma-Aldrich, St. Louis, MO), and 10 ng/ml human basic fibroblast growth factor (bFGF) on irradiated mouse embryonic feeder cells (MEF, GlobalStem, Rockville, MD). Knock-out of LIPA in iPSC was achieved by CRISPR/Cas9 gene editing. The parental iPSC line derived from a healthy subject was transiently transfected with plasmids encoding a Cas9-GFP fusion protein and the guide RNA targeting exon 7 of the LIPA gene. LIPA+/+ (unedited) and LIPA-/- iPSC were differentiated to macrophages according to established protocols and maintained in 20% FBS/RPMI with 100 ng/ml human M-CSF (PMID: 25904599).

extract_protocol:
RNA samples were extracted using miRNeasy mini Kit (Qiagen, Valencia, CA). Extracted RNA samples underwent quality control (QC) assessment using the Agilent Bioanalyzer (Agilent, Santa Clara, CA)
With a minimum of 100 ng input RNA, we generated first-strand cDNA using random hexamer-primed reverse transcription, followed by second-strand cDNA synthesis using RNase H and DNA polymerase, and ligation of sequencing adapters using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA). Fragments of ~350 bp were selected by gel electrophoresis. To minimize lane and batch effects in RNA-Seq experiments, barcoded libraries were mixed and pooled in equimolar (2 nmol/L) amounts and diluted to 4 pmol/L for cluster formation on a single flow cell lane, followed by 101 bp paired-end sequencing on Illumina’s HiSeq 2500.

value: iPSC derived macrophage (IPSDM)

value: LIPA+/+


title: 9M_TSCmKO_rep2

description:
average insert size: 273
standard deviation: 49.05
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: 9M_TSCmKO_RAPA_rep3

description:
average insert size: 302
standard deviation: 47.34
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: Cord blood ID_17

data_processing:
An in-house software written for the R statistical computing environment was used to preprocess the data as follows: removal of probes based on signal intensities and control probes, background subtraction and dye bias correction (for probes using the Infinium II design). Additionally, data were trimmed removing the outliers as defined by observations exceeding three interquartile ranges below the first quartile or above the fourth quartile. Sample failing quality control and with potential sex mismatch were removed.
normalized Average Beta in supplementary file


title: Father_TOF01_d0_2.2


title: MEFD3min_3


title: TOF01_d0_1.5


title: 9M_TSCmKO_rep5

description:
average insert size: 225
standard deviation: 26.96
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: Cord blood ID_172


title: Cord blood ID_173


title: 9M_TSCmKO_rep1

description:
average insert size: 308
standard deviation: 48.95
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: Cord blood ID_169


title: LIPA+/+ 1-2

description: Sample 4


title: MEFD3min_1


title: MEFD3plu_3


title: LIPA-/- 2

description: Sample 6

value: LIPA-/-


title: Cord blood ID_168


title: 9M_CTRL_RAPA_rep5

description:
average insert size: 270
standard deviation: 43.84
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: LIPA+/+ 1-1

description: Sample 3


title: MEFD0_4

value: BALB/c

value: day 0


title: LIPA-/- 1-2

description: Sample 2


title: 9M_TSCmKO_rep3

description:
average insert size: 282
standard deviation: 48.95
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: Cord blood ID_166


title: MEFD0_3

value: 10.5 day old embryos

value: wild-type


title: LIPA-/- 1-1

description: Sample 1


title: Cord blood ID_167


title: 9M_CTRL_RAPA_rep3

description:
average insert size: 258
standard deviation: 44.27
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: 9M_CTRL_RAPA_rep4

description:
average insert size: 305
standard deviation: 48.76
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: Cord blood ID_165


title: MEFD0_1

value: MEFs


title: 9M_CTRL_RAPA_rep2

description:
average insert size: 274
standard deviation: 44.04
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz

value: Extensor digitorum longus muscle


title: TKO_serum_3

city: Edinburgh

first: Heidi

middle: Katharina

last: Mjoseng

address: Crewe Road South

institute: HGU, IGMM, The university of Edinburgh

data_processing:
A sailfsh (version 0.9.2) index was built using kmer length 25 against the Ensembl  mm10 transcript database
RNA transcript abundance was calculated using  Sailfish version 0.9.2, libType": "ISR","numBootstraps": "30".
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Ensembl Transcript ID, Length, EffectiveLength, TPM, NumReads

source_name: Mouse ES cells

growth_protocol: Serum culture conditions: Dulbecco's Modified Eagle's medium (DMEM) high-glucose supplemented with 15% FCS, 1x Non-essential amino acids, 1mM Sodium Pyruvate, 50mg/ml Penicillin/Streptomycin, 0.1% beta-mercaptoethanol and 500U/ml ESGRO LIF (Millipore).

extract_protocol:
Snap frozen pellets of mESCs were stored in -80 ̊C prior to extraction of RNA. Qiashredder columns (Qiagen) were used to homogenise the samples according to manufacturers protocol. Total RNA was extracted using an RNeasy kit (Qiagen), following the manufacturer’s protocol. RNA was then treated with Turbo Dnase (Ambion, ThermoFisher) according to manufacturers protocol. Total RNA samples were quantified using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific Inc, #Q32866) and the Qubit RNA HS assay kit (#Q33855). RNA integrity (RIN) was assessed using an Agilent 2100 Bioanlyser System (Agilent Technologies Inc, # GS2938B) and Agilent RNA 6000 Nano kit (#5067-1511), samples used had a RIN score of ≥9.9.
Libraries were prepared from 500ng of each total-RNA sample using the TruSeq Stranded  mRNA Library Kit (Illumina Inc, #20020594) according to the provided protocol. PolyA selection method was used. Libraries were quantified by fluorometry using the Qubit dsDNA HS assay and assessed for  quality and fragment size using the Agilent Bioanalyser with the DNA HS Kit (#5067-4626).
Sequencing was performed using the NextSeq 500/550 High-Output v2 (150 cycle) Kit (#FC-404-2002). This was done on the NextSeq 550 platform (Illumina Inc, #SY-415-1002). 24 libraries were  combined in two equimolar pools of 12 based on the library quantification results and each  pool was run across a single High-Output Flow Cell.

treatment_protocol: 2i culture conditions: N2B27 medium (DMEM F-12:  GIBCO,  Neurobasal: GIBCO, N2: GIBCO, B27: GIBCO,  50ug/ml Penicillin/streptomycin, 3.3% BSA (GIBCO), 0.15 mM monothioglycerol and MEK inhibitor PD0325901 [1uM] and Gsk3 beta inhibitor CHIR99021 (3uM) with 1000U/ml ESGRO LIF (Millipore).

tag: culture condition

value: Serum+LIF

tag: biologial replicate

tag: cell line

value: TKO


title: TKO_serum_2


title: Cord blood ID_164


title: granulosa cells, T2

city: East Lansing

first: Aritro

last: Sen

state: Michigan

address: 766 Service Rd., ISTB

department: Animal Science

institute: Michigan State University

data_processing:
After investigating the quality of the raw data (the quality was judged based on Illumina’s Q score, which represents the error rate at
each base, built on a log10 score), sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor
quality using Trimmomatic v.0.36. The trimmed reads were mapped to the reference mouse genome available on ENSEMBL (Mus musculus GRCm38) using the STAR aligner v.2.5.2b.
The STAR aligner uses a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: DEGs of Control vs Treatment with raw values in csv file

source_name: Ovary

extract_protocol:
Total RNA was extracted from fresh frozen whole ovary samples using Qiagen RNeasy Plus Universal mini kit. The samples were sequenced using a 2x150bp Paired End (PE) configuration. The total number of reads/sample were 45-50 million. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq files and de-multiplexed using Illumina'’s bcl2fastq 2.17 software. configuration. The total number of reads/sample were 45-50 million. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq wereas converted into fastq files and de-multiplexed using Illumina'’s bcl2fastq 2.17 software.
RNA sequencing libraries were prepared using 500 ng RNA, and the NEB Next Ultra RNA Library Prep Kit for Illumina using the manufacturer’s instructions (NEB, Ipswich, MA, USA)

treatment_protocol: Granulosa cells were treated with  DHT (dihydrotestosterone, 25nM) for 24h

value: Ovary

value: Granulosa cells

value: 8-9 weeks

value: wild type

value: DHT (dihydrotestosterone, 25nM)


title: granulosa cells, T3


title: TKO_serum_1


title: 9M_CTRL_rep5

description:
average insert size: 273
standard deviation: 40.69
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz

value: post natal month 9

value: vehicle


title: Cord blood ID_163

first: Michelle

last: Plusquin

value: cord blood


title: granulosa cells, T1


title: 9M_CTRL_rep4

description:
average insert size: 223
standard deviation: 30.56
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: Cord blood ID_162


title: TKO_2i_3


title: granulosa cells, C3

value: control


title: 9M_CTRL_rep3

description:
average insert size: 289
standard deviation: 56.52
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: Cord blood ID_161


title: TKO_2i_2


title: Cord blood ID_16


title: Cord blood ID_160


title: 9M_CTRL_rep1

description:
average insert size: 280
standard deviation: 52.28
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: granulosa cells, C2


title: T3

data_processing:
Only uniquely mapped reads were used for subsequent analyses. MACS2 (version 2.1.1) (cite) was then applied to identify signal peaks of H3K27me3 signals, in broad peak calling mode since H3K27me3 distribution along the genome is more diffusive and demonstrate broader peaks.
PCR duplicates were removed in peak calling. Peaks with q-value <= 0.05 were used as the significant signal peaks. Peaks in control samples and treatment samples are center-aligned separately with +/-10kb flanking regions.
Gene promoters overlapping with control-specific H3K27me3 peaks were center-aligned with +/- 1kb flanking regions, and the average peak densities per 50bp bins were plotted.
Hi-C and Capture-C, were used to identify candidate distal enhancers that can interact with promoters of differentially expressed genes. Hi-C datasets include: GSE81503, GSE82144, GSE119171, GSE121753, and GSE63525. Capture-C dataset includes GSE81503.
For the long-range chromatin interactions profiled in these dataset, they were first compared with promoters of differentially expressed genes and a subset of chromatin interactions was then identified, if one of the interacting anchors overlaped with promoters. Only enhancer-gene pairs with correlations < -0.4 were considered as true regulatory pairs and the corresponding enhancers were used for subsequent analysis. For each group of enhancers, the top five enriched sequence motifs were identified using MEME. TomTom (version 5.0.4) was then applied on the top-enriched motifs
Genome_build: mouse genome (mm9) using Bowtie2 (version 2.3.4)
Supplementary_files_format_and_content: Upregulated_gene_body_overlap_peaks.txt  The list of up-regulated genes with their gene body (TSS to TES) overlapping the H3K27me3 peaks (control peaks or treatment peaks)  Downregulated_gene_body_overlap_peaks.txt  The list of down-regulated genes with their gene body (TSS to TES) overlapping the H3K27me3 peaks (control peaks or treatment peaks) Gene_body_overlapping_control_peaks_gene_list.txt  The list of genes with their gene body (TSS to TES) overlapping the 16345 control H3K27me3 peaks  Gene_body_overlapping_treatment_peaks_gene_list.txt  The list of genes with their gene body (TSS to TES) overlapping the 3975 treatment H3K27me3 peaks  Promoter_overlapping_control_peaks.txt  The list of genes with their promoter regions (TSS +/- 1KB) overlapping the 16345 control H3K27me3 peaks  UpRegulated_genes_regulated_by_H3K27me3_enhancers.txt  The list of up-regulated genes that regulated by enhancers. The H3K27me3 signals on these enhancers are negatively-correlated with the gene expression.   DownRegulated_genes_regulated_by_H3K27me3_enhancers.txt  The list of down-regulated genes that regulated by enhancers. The H3K27me3 signals on these enhancers are negatively-correlated with the gene expression.

extract_protocol:
Granulosa cells were collected from 30 mice and plated in six petri dishes (each with at least 1×107 cells). Chromatin was isolated using the ChromaFlash Chromatin Extraction Kit (EpiGentek, Cat. #P-2001) and sheared using the EpiSonic 2000 Sonication System (EpiGentek, Cat. #EQC-2000). DNA fragment size distribution was determined to be 100 to 300 bp by Agilent Bioanalyzer analysis. The concentration of DNA following ChIP was between 3.5-16.3 ng.
Library Preparation was done by DNA end polishing and adaptor ligation, library amplification using indexed primers and library purification. Library was verified on a Bioanalyzer and KAPA qPCR Library Quantification.RNA sequencing libraries were prepared using 500 ng RNA, and the NEB Next Ultra RNA Library Prep Kit for Illumina using the manufacturer’s instructions (NEB, Ipswich, MA, USA)

tag: agent

value: dihydrotestosterone, 25nM

tag: antibody


title: granulosa cells, C1


title: T2


title: Cord blood ID_159


title: 30m_GAS_RM_rep6

description:
direction_1st_mate: antisense, direction_2nd_mate: sense
aging_rm_counts.txt.gz
aging_rm_tpms.txt.gz

data_processing:
RNA-seq reads were subjected to 3’ adapter and poly(A)/poly(T) tail trimming using Cutadapt v1.9.1 from Martin et al., EMBnet.journal, 2011. The following 3’ adapter sequences were utilized for generating RNA-Seq libraries and subsequently trimmed: mate1 5’-AGATCGGAAGAGCACACGTC-3’, mate2 5’-AGATCGGAAGAGCGTCGTGT-3’.
Reads shorter than 30 nucleotides were discarded.
The kallisto v0.43.1 software from Bray et al., Nature Biotechnology, 2016 was used for building transcriptome index and aligning filtered reads. The default options of kallisto were utilized for building transcriptome index. For aligning filtered reads we used options “--rf-stranded” and “--pseudobam”.
Mapped reads were assigned to transcripts in a weighted manner: if a read was uniquely mapped to a transcript, then the transcript’s read count was incremented by 1; if a read was mapped to n different transcripts, each transcript’s read count was incremented by 1/n.
The expression of each transcript was estimated in transcripts per million (TPM) units by dividing its read count by the transcript length and normalizing to the library size. The expression of a gene was obtained by summing up the normalized expression of the transcripts associated with it. For every gene, read counts of transcripts associated with this gene were also summed up and further used for the differential expression analysis.
Genome_build: As the reference mouse transcriptome, we considered sequences of protein coding transcripts with the support level 1-3 based on genome assembly GRCm38 (release 92) and transcript annotations from Ensembl database (see Hubbard et al., Nucleic Acids Research, 2002).
Supplementary_files_format_and_content: tab-delimited text files include raw counts and TPM values at the gene level for each sample.

source_name: Gastrocnemius muscle

extract_protocol:
Snap frozen muscles were pulverized and lysed in RLT buffer (Qiagen). RNA was extracted using an AccuPure Tissue RNA Mini Kit (R20096) with an iColumn 24 (AccuBioMed). TruSeq Stranded mRNA HT Sample Prep Kit was used for the library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were fed encapsulated rapamycin incorporated into a standardised AIN93M diet at 42 ppm (i.e. mg per kg of food), equating to a dose of ~4mg/kg/day starting at 15 months of age.

value: Gastrocnemius muscle

value: post natal month 30

value: rapamycin


title: 30m_GAS_RM_rep5