title: USA: Affected individual USA fibroblasts

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

data_processing:
Raw data (bcl-files) were demultiplex and the adapter sequences ("AGATCGGAAGAGCACACGTCTGAACTCCAGTCA","AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT") removed with bcl2fastq2 (v2.20.0.422; Illumina).
Fastq-files were filtered with Trimmomatic (v.0.36; Bolger et al 2014), excluding non-paired, short (<35bp) and low quality (phread score <20) reads.
Filtered reads were mapped to the reference genome (GRCh38) with STAR (v. 2.5.3; Dobin et al., 2013).
The read counts for genes were extracted with Rsubreads (v.1.32.4; Liao et al., 2013) excluding duplicates, multimapping reads, chimeric fragments, and reads with mapping quality below 10.
Differential gene expression was analysed with DESeq2 (v.1.22.2; Love et al., 2014), comparing disease status (Control vs Patient). Genes with low reads depth (<50 reads in total) were excluded.
Genome_build: GRCh38
Supplementary_files_format_and_content: txt (count data and DESeq2 expression results)

source_name: Affected individual USA fibroblasts

growth_protocol: Standard fibroblast culture conditions in DMEM, FBS, Penisillin-streptomycin, Uridine, L-glutamate, grown for 4 days on 10 cm petri dishes

extract_protocol:
Nucleospin RNA isolation kit (#740955.50, Macherey-Nagel)
NEBNext Ultra Directional RNA Library Prep Kit (v.8.0 3/16; Illumina) was used for library preparation. RNA quality and integrity was analyzed with Agilent TapeStation 4200. Libraries were sequences at Biomedicum Functional Genomics Unit (FuGU) using Illumina NextSeq 500 system.

treatment_protocol: No treatment

value: Fibroblast

tag: disease status

value: Patient

tag: mutation

tag: country

value: United States of America

tag: Sex

value: female

tag: phenotype

value: affected

tag: age


title: NL-M: Healthy carrier fibroblasts (mother of NL)

status: Public on Apr 07 2020

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

value: Control

value: Netherlands

value: not affected


title: GACCGC_KO

city: Munich

first: Enric

last: Redondo Monte

state: Bavaria

address: Max-Lebsche-Platz 30

department: Internal Medicine 3

country: Germany

institute: Ludwig-Maximilians University Munich

data_processing:
Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017)
cDNA reads were aligned to the Human Genome (hg38) with STAR 2.6.0a
Quantification was done with ENSEMBL gene models (GRCh38.84)
Genome_build: Human: hg38, Ensembl 84
Supplementary_files_format_and_content: sample (columns) and gene (rows) -wise UMI expression table

extract_protocol:
Cells were Counted, pelletized and dissolved in the lysis buffer.
Libraries were constructed using a bulk adjusted SCRB-seq protocol.

tag: genotype

value: KO

tag: cell line


title: CTGCGG_KO


title: Day_5_Control_2_R1

city: Irvine

first: Ali

last: Mortazavi

state: CA

address: 2300E Biological Sciences 3

country: USA

institute: UC Irvine

description: poly-A+ RNA

data_processing:
Raw data converted to fastq using bcl2fastq v2.18.0.12 from Illumina.
Reads were demultiplexed using ddSeekR (Romagnoli, et al., BMC Genomics, 2019).
Nuclei with at least 500 UMIs detected were mapped using STAR (version 2.5.1b) [38] and quantitated using RSEM (version 1.2.31) [39] with the rsem-calculate-expression with options --star and --estimate-rspd. We kept nuclei with ≥150 genes detected and <20% mitochondrial reads. Genes detected in at least 5 nuclei were kept for downstream analysis.
The data was loaded into Seurat (version 3.1.0) and normalized using the SCTransform function (Butler, et al., Nat. Biotechnol., 2018; Hafemeister & Satija, bioRxiv, 2019).
Genome_build: hg38
Supplementary_files_format_and_content: Abundance files for nuclei with ≥150 genes detected;Supplemental table includes Seurat normalized counts for nuclei used in analysis

molecule: polyA RNA

source_name: Primary myoblasts

extract_protocol:
Myotubes from day 3 or day 5 of differentiation were isolated from mononucleated cells (MNCs) by washing a 35 mm dish once with trypsin, then adding trypsin for about 5 min until myotubes lifted off the plate and MNCs were still attached. Cells were washed once in 1X PBS + 0.1% BSA, and the nuclei were prepared according to Illumina (Document # 1070-2016-014-C) with the following modifications. We used 0.2 U/ul RNasin Plus RNase Inhibitor (Promega) for the cell lysis buffer and nuclei storage buffer, and nuclei were filtered through a 40 um filter (Falcon) after isolation. Nuclear isolation and quality were assessed by staining with ethidium homodimer.
Nuclei were loaded onto the ddSeq Single Cell Isolator (BioRad) for droplet generation, and libraries were prepared using the SureCell WTA 3’ Library Prep Kit (Illumina). Libraries were sequenced on the Illumina NextSeq500 platform using PE 68 bp for read 1 and 75 bp for read 2 with a custom primer with around 370 million reads for four samples.

tag: individual

tag: day of differentiation

value: Day 5

tag: fshd status

tag: cell or nucleus

value: nucleus


title: PostTx: Late-treatment

city: Bethesda

first: Rachel

last: Rosenstein

state: MD

address: 10 Center Drive, 12N240

institute: NIH

description: site was previously affected and now resolved

data_processing:
Alignment and quantification of count data was performed using MAGIC v2017.05.10 as previously described (LaPaglia et al., 2018).
Expression levels were estimated by calculating significant fragments per kilobase per million aligned reads (sFPKM) (Supplemental spreadsheet 1), a metric of expression calculated to correct for library and/or protocol biases (Zhang et al., 2015).
Genome_build: TARGET.human.2016_03_20 (modification of hg19 https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13/ to improve alignment by including viruses, bacteria, decoys, available for download at MAGIC ftp)
Supplementary_files_format_and_content: Excel files: 1) sFPKM 2)raw counts

source_name: skin

extract_protocol:
Skin biopsies were flash frozen on dry ice and stored at -80°C. Qiazol (QIAGEN N.V., Venlo, Netherlands) solution was added to frozen samples, and RNA extraction was performed using a Fastprep 24 bead-beating homogenizer (MPBio, Santa Ana, CA; Lysing Matrix D) and the RNeasy Minikit (QIAGEN).
Stranded paired-end libraries were generated from 1µg total RNA using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina, Inc.) and sequenced on an Illumina HiSeq4000 (2 x 76bp read length). Adapters were IDT for Illumina - TruSeq RNA UD Indexes to eliminate index misassignment. Amplification was performed using 10 cycles which was optimized for the input amount and to minimize over-amplification. Libraries were pooled in equimolar amounts for sequencing. Sequencing was performed in two batches according to when the skin biopsies were collected. In the first batch, a more affected and a less affected site were biopsied and 2 technical replicates of each were sequenced at an average of 45 million reads per technical replicate. For the second batch, a late-treatment biopsy was collected and sequenced together with a third replicate of the original two biopsy samples at an average read depth of 235 million reads.

tag: tissue

value: skin

tag: pigmentation

value: normally pigmented

tag: symptoms

value: asymptomatic

tag: treatment

value: timepoint:15 weeks on acitretin and 9 weeks on tapered dose of mycophenolate mofetil

tag: body site

value: lower back


title: LB2: More affected - technical replicate 2

value: hyperpigmented

value: severe itch

value: pre-treatment


title: LB2: More affected - technical replicate 1


title: FIN2: Affected individual FIN2 fibroblasts

source_name: Affected individual FIN2 fibroblasts

value: Fibroblast

tag: disease status

value: Patient

tag: mutation

value: c.3814G>A p.Val1272Met, c.443delC p.Pro148Leufs*48

value: Finland

value: male


title: LB2-2: More affected - replicate during late-treatment run


title: CGTGGG_KO


title: CX1: Less affected - technical replicate 1

value: mild itch

value: flank


title: CGGTGG_Control

value: Control


title: C2: Control 2 fibroblasts

source_name: Control 2 fibroblasts

tag: country

tag: Sex

value: not affected


title: FIN1: Affected individual FIN1 fibroblasts

source_name: Affected individual FIN1 fibroblasts

value: female

tag: phenotype

value: affected

tag: age


title: CX1: Less affected - technical replicate 2

value: skin

value: normally pigmented


title: Day_3_FSHD2_2_R2

description: poly-A+ RNA

value: Day 3

value: FSHD

value: nucleus


title: CCGGAC_KO

tag: genotype

value: KO


title: WT-HD-1

type: RNA

city: Beijing

first: Huan

last: Gong

address: No.1 Dahua Road, Dong Dan,

country: China

institute: Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology

hyb_protocol: The samples were hybridized on the miRCURY™ LNA Array (v.11.0) with kit  (Cat #208021, Exiqon) as instruction.

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner. GenePix pro V6.0 is used to read the raw intensity of the image.

data_processing: The intensity of green signal is calculated after background subtraction and replicated spots on the same slide have been averaged by getting a median intensity. We use Median Normalization Method to obtain "Normalized Data", Normalized Data=(Foreground-Background)/median, the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction.

organism: Mus musculus

source_name: liver, ad libitum, high-fat diet (HD)

label_protocol: The samples are labeled using the miRCURYTM Array Power Labeling kit (Cat #208032-A, Exiqon) as instruction

extract_protocol: Total RNA was isolated from 20-30 mg tissue using TRIzol reagent (Invitrogen Life Technologies, USA) and RNasey Mini Kit (Qiagen, Germany) following the manufacturer's instructions. Yield and purity of RNA was determined by NanoDrop ND-1000 spectrophotometer (Nanodrop technologies, USA).

value: liver

tag: start age

value: 2 months

tag: treatment time

value: 3 months

value: Male


title: AUS: Affected individual AUS fibroblasts

source_name: Affected individual AUS fibroblasts

tag: cell type

value: Fibroblast

value: Patient

value: Australia

value: different


title: CCCTGG_KO

tag: cell line


title: CCCCGT_KO


title: TAAGAT_KO


title: dRNA-seq HSV-1 Mock control R2

city: Würzburg

first: Florian

last: Erhard

address: Versbacher Str. 7

department: Institut für Virologie und Immunbiologie

institute: Julius-Maximilians-Universität Würzburg

description: dRNA.tsv

data_processing:
3' sequencing adapter sequence were removed from the 50 nt long reads by computing a prefix-suffix sequence alignment (cRNA-seq only)
Barcode sequences (first 9 nt = 3 random bases followed by 4 bases of experiment specific barcodes followed by 2 random bases) were removed from all reads and stored for later use. (cRNA-seq only)
Bowtie 1.0 was used to align all reads to the human genome, Ensembl transcripts (v75), ribosomal rRNA, the HSV1 genome (JN555585, terminal repeats masked), the HSV1 transcripts as well as novel junctions identified in the 4sU data by ContextMap. Only reads aligning to at most 3 distinct genome positions with at most 2 mismatches were kept for further analyses.
Peaks were called by identifying significant enrichment in a sliding-window approach.
Genome_build: JN555585
Supplementary_files_format_and_content: FPKM

source_name: human foreskin fibroblasts (HFF)

growth_protocol: Primary human foreskin fibroblasts were cultured in DMEM supplements with 10% FBS and P/S. Cells at passage 15 were infected with HSV-1 strain 17 at an MOI of 10

extract_protocol:
Cells were lyzed using Trizol and total cellular RNA was isolated.
Sequencing libraries were prepared using the cRNA-seq and dRNA-seq inhouse protocols.

treatment_protocol: Cells were infected for 15 min using an MOI of 10. 15min after infection (time point 0h), cell culture media was replaced with fresh media. Cells were harvested prior to or at 8h p.i. cRNA-seq and dRNA-seq libraries were prepared.

value: primary fibroblasts

tag: time post infection

value: Mock

tag: replicate

value: Replicate 2

tag: enrichment

value: 5' RNA ends (selective)


title: C1: Control 1 fibroblasts

source_name: Control 1 fibroblasts

value: Control

value: Finland

value: female

value: not affected


title: WT-CR-1

source_name: liver, normal-fat diet and 30~35% caloric restriction as in AL (CR)

tag: tissue


title: NL: Affected individual NL fibroblasts

source_name: Affected individual NL fibroblasts

value: Netherlands

value: serious


title: WT-AL-1

source_name: liver, ad libitum, normal-fat diet(AL)

value: liver

value: 2 months


title: ATTCTA_KO

value: KO


title: CCAACC_KO


title: dRNA-seq HSV-1 Mock XRN1 R2

description: dRNA.tsv

tag: treatment


title: lin-32_RNAi_Sample2

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2FastQ v1.8.4
The reads were mapped to the C.elegans reference genome (WBcel235) with the Ensembl gene annotation (release 82) with TopHat2 v2.1.0 (parameters: -g 1 --no-coverage-search –no-convert-bam).
Reads mapped to an Ensembl gene were counted using featureCounts v1.4.6-p4 (parameter: -s 0)
Genome_build: WBcel235.82
Supplementary_files_format_and_content: xls file containing reads counts per gene of all samples

organism: Caenorhabditis elegans

source_name: Whole nematodes

extract_protocol:
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol-chloroform extraction method.
Preparation of libraries was done using Illumina’s TruSeq RNA v2 kit following the manufacturer’s instruction.

tag: strain

value: lin-32 RNAi


title: lin-32_RNAi_Sample3


title: dRNA-seq HSV-1 Mock XRN1 R1

description: dRNA.tsv

value: Replicate 1


title: CCCACG_KO


title: ATGAAT_Control


title: ATCAAA_KO


title: lin-32_RNAi_Sample1


title: WT-EX-1

source_name: liver, ad libitum, normal-fat diet with exercise(EX)

value: 3 months

value: Male


title: CX1-2: Less affected - replicate during late-treatment run

value: skin

tag: pigmentation

value: normally pigmented

tag: symptoms

value: mild itch

value: pre-treatment

tag: body site

value: flank


title: dRNA-seq HSV-1 Mocki control R1

description: dRNA.tsv

value: primary fibroblasts

value: Mock

value: 5' RNA ends (selective)


title: ATTACT_KO


title: hlh-2_RNAi_Sample2

value: hlh-2 RNAi


title: hlh-2_RNAi_Sample3


title: hlh-2_RNAi_Sample1


title: ATATAG_Control

value: Control


title: L4440_Sample2

value: empty plasmid L4440


title: AAGATT_Control


title: L4440_Sample1


title: AAATTG_KO


title: AAAGTT_Control


title: Normal5

city: Madison

first: Kazuya

last: Oikawa

state: WI

address: 1300 University Ave

institute: University of Wisconsin-Madison

data_processing:
Generated raw reads (FASTQ format) were quality-control checked by FastQC after filtering to remove adaptor sequences, low-quality reads (quality score <20) and those that did not meet filter length ( length <28)  by Skewer (ver 0.1.127), a fast and sensitive adapter trimmer for llumina paired-end sequences. Mapping of trimmed reads to the Felis catus reference genome sequence (ICGSC Felis_catus_8.0/ felCat8) was performed using STAR ver 2.4.2a. Gene transcript abundances were estimated by RSEM ver 1.2.22.
Genome_build: ICGSC Felis_catus_8.0/felCat8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Felis catus

source_name: Optic nerve head

extract_protocol:
Total RNA was extracted from the dissected ONH tissue using RNeasy Fibrous Tissue Mini Kit (Qiagen, Germantown, MD) following the manufacturer’s instructions
RNA libraries were prepared for sequencing following Illumina TruSeq® Stranded mRNA Sample Preparation Guide Rev.E

value: WT


title: Normal6


title: Normal2


title: Normal3


title: Normal1


title: AATACA_KO

value: KO


title: Hi-C_HSPC_BMT_DKO_rep2

city: Kyoto

first: Yotaro

last: Ochi

address: Yoshida-Konoe-cho

department: Department of Pathology and Tumor Biology

country: Japan

institute: Kyoto Univiersity

library_source: genomic

data_processing:
The sequencing reads were processed using Juicer.
For comparative analysis, the valid interactions after filtering were randomly resampled and arranged in the number of the lowest sample.
Loops were called at 5kb and 10kb resolutions using HICCUPS.
Genome_build: mm10

molecule: genomic DNA

source_name: bone marrow cells

extract_protocol:
Hi-C experiments were performed using HSPCs obtained from WT-, SKO-, RKO-, or DKO-transplanted mice.
Briefly, two million c-Kit+ HSPCs of WT/SKO/RKO/DKO-transplanted mice were crosslinked with 1% formaldehyde for 10 min at room temperature.  Cells were permeabilized and chromatin was digested with MboI restriction enzyme, and the ends of restriction fragments were labeled with biotinylated nucleotides and ligated.  After crosslink reversal, DNA was purified and sheared with Covaris M220 (Covaris).  Then point ligation junctions were pulled down with streptavidin beads.  Then libraries were constructed with Nextera Mate Pair Sample Preparation Kit (Illumina) according to the manufacturer’s protocol, and subject to sequencing using NovaSeq (Illumina).

value: bone marrow

value: HSPC

value: DKO


title: Hi-C_HSPC_BMT_DKO_rep1


title: Subject G2_BRE_Post

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

description: Subject G2, Post Bed rest + exercise

hyb_protocol: Following fragmentation, cRNA were hybridized for on Affymetrix HTA 2.0 arrays.

scan_protocol: Not provided

data_processing: The probe-set level intensities of the arrays were normalized using the Robust Multi-array Analysis method (RMA) implemented within the Aroma R library

label: biotin

source_name: Human skeletal muscle, Vastus lateralis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

extract_protocol: Biopsies were obtained from the vastus lateralis muscle using the Bergström needle technique. The biopsies were immediately stored in liquid nitrogen until processing. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: Vastus lateralis

tag: gender

value: Male

tag: subject

tag: group

value: Bed rest + exercise

tag: time

value: Post


title: FCG10

tag: genotype

value: LTBP2 homozygous mutant


title: Subject J2_BRE_Post

description: Subject J2, Post Bed rest + exercise


title: Subject H2_BRE_Post

description: Subject H2, Post Bed rest + exercise


title: AAAACT_KO


title: Subject I2_BRE_Pre

description: Subject I2, Pre Bed rest + exercise

value: Pre


title: Subject E2_BR_Post

description: Subject E2, Post Bed rest only

value: Bed rest only


title: Subject D2_BR_Post

description: Subject D2, Post Bed rest only


title: Hi-C_HSPC_BMT_RKO_rep2

value: RKO


title: Subject K2_BRE_Post

description: Subject K2, Post Bed rest + exercise


title: Subject F2_BR_Post

description: Subject F2, Post Bed rest only


title: Hi-C_HSPC_BMT_RKO_rep1


title: Subject I2_BRE_Post

description: Subject I2, Post Bed rest + exercise


title: Subject B2_BR_Post

description: Subject B2, Post Bed rest only


title: Subject H2_BRE_Pre

description: Subject H2, Pre Bed rest + exercise


title: Normal4


title: Subject K2_BRE_Pre

description: Subject K2, Pre Bed rest + exercise


title: Subject A2_BR_Post

description: Subject A2, Post Bed rest only


title: Subject G2_BRE_Pre

description: Subject G2, Pre Bed rest + exercise


title: Subject F2_BR_Pre

description: Subject F2, Pre Bed rest only


title: Hi-C_HSPC_BMT_SKO_rep2

value: SKO


title: FCG8


title: FCG7


title: Hi-C_HSPC_BMT_WT_rep2


title: Subject J2_BRE_Pre

description: Subject J2, Pre Bed rest + exercise


title: Hi-C_HSPC_BMT_WT_rep1


title: FCG9


title: FCG6


title: FCG5


title: FCG4


title: Hi-C_HSPC_BMT_SKO_rep1


title: FCG3


title: FCG2


title: FCG1


title: deletion CBS(5) [C5FT3]

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

data_processing:
short read quality assesment using fastqc
read trimming with trimmomatic ver. 0.38
Splice-aware short read alignment with STAR (ver 2.5.0a)
exonic read counting using featureCounts package (ver 1.5.0-p1)
Genome_build: Drosophila melanogaster BGP6
Supplementary_files_format_and_content: processed files are tab-separated files with Flybase gene ID (1 column) and non-normalized read number in gene (2 column)

organism: Drosophila melanogaster

source_name: deletion CBS(5)_thorax

growth_protocol: Flies (separately males and females) were maintained at 23°C on standard yeast, sugar, and agar medium in 40 ml vials at a density of 20 flies per vial throughout the experiment. All flies were synchronized by age: enclosing individuals were collected daily, transferred to new vials with medium, and then aged appropriately

extract_protocol:
RNA was isolated from 5 days male and female flies: control line-58492, CBS lines-CBS5 and CBS8, CSE1, MST15, with double deletion CBS5 /CSE1, and CBS8 /CSE1 using RNAzol RT according to the manufacturer's protocol. RNA quality was assessed using an Agilent 2100 Bioanalyzer instrument (Agilent Technologies, USA) using the Agilent RNA 6000 nano Kit (Agilent Technologies). The concentration of RNA samples was evaluated on a Qubit 2.0 Thermo fluorimeter (Fisher Scientific)
Libraries were prepared from 1000 ng of total RNA using the NEBNext® Ultra ™ II Directional RNA Library Prep Kit for Illumina (NEB, UK) according to the manufacturer's protocol.

treatment_protocol: No treatment were performent in this experiment

tag: genotype/variation

tag: Sex

value: Female

tag: age

value: 5-day old

value: thorax


title: deletion CBS(5) [C5FT2]


title: deletion CBS(5) [C5MT3]


title: deletion CBS(5) [C5MT1]


title: deletion CBS(5) [C5FT1]


title: Control [58MT3]


title: deletion CBS(5) [C5MT2]


title: Subject D2_BR_Pre

description: Subject D2, Pre Bed rest only


title: Control [58MT2]


title: Subject E2_BR_Pre

description: Subject E2, Pre Bed rest only


title: Subject B2_BR_Pre

description: Subject B2, Pre Bed rest only


title: Subject J1_BR_Post

description: Subject J1, Post Bed rest only


title: Subject I1_BR_Post

description: Subject I1, Post Bed rest only


title: Control [58FT3]


title: Subject H1_BR_Post

description: Subject H1, Post Bed rest only


title: Subject C2_BR_Pre

description: Subject C2, Pre Bed rest only


title: Subject J1_BR_Pre

description: Subject J1, Pre Bed rest only


title: Control [58FT1]


title: Control [58FT2]


title: SPMS Orig_013

city: Ann Arbor

first: qin

last: wang

state: MI

address: 109 Zina Pitcher Place

department: neurology

institute: university of michigan

description: SPMS

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on [Human Gene 2.1 ST Array], and were washed and stained using the Affymetrix GeneTitan system (software version 4.3.0.1592).

scan_protocol: Peg Arrays were scanned using the Affymetrix GeneTitan system (software version 4.3.0.1592).

data_processing: log2 expression values were generated using the RMA technique and linear models were fit using the oligo and limma packages of bioconductor in R version 3.3.0.

source_name: peripheral Blood

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 (200 ng) ng total RNA.

extract_protocol: PAXgene Blood RNA Isolation. Whole blood of subjects was collected into PAXgene Blood RNA Tubes (Qiagen, Hilden, Germany) to perform RNA isolation. The blood was initially mixed into the PAXgene tube buffer to lyse the cells, and stored at -80oC prior to RNA isolation and batch analysis. To isolate blood RNA, the PAXgene tubes with cell lysate were thawed and centrifuged to pellet nucleic acids. The pellet was washed and resuspended, and the RNA was purified according to manufacturer’s suggested protocol. RNA concentration was determined by nanodrop.

treatment_protocol: Blood was collected at before giving siponomod as baseline and 12 month post treatment

value: unknown

value: Baseline


title: SPMS-repeat Orig_014

description: SPMS-repeat


title: Subject I1_BR_Pre

description: Subject I1, Pre Bed rest only


title: Subject A2_BR_Pre

description: Subject A2, Pre Bed rest only


title: Subject G1_BR_Post

description: Subject G1, Post Bed rest only


title: Control [58MT1]


title: SPMS-repeat Orig_016

description: SPMS-repeat


title: SPMS-repeat Orig_015

description: SPMS-repeat

value: female


title: SPMS 048

description: SPMS

value: Treated


title: Subject H1_BR_Pre

description: Subject H1, Pre Bed rest only


title: Subject G1_BR_Pre

description: Subject G1, Pre Bed rest only


title: deletion MST [MST_3]

source_name: deletion MST_whole fly

value: MST

value: whole fly


title: deletion MST [MST_2]


title: SPMS 047

description: SPMS


title: Subject F1_BR_Post

description: Subject F1, Post Bed rest only

value: Vastus lateralis

value: Male


title: Subject F1_BR_Pre

description: Subject F1, Pre Bed rest only


title: SPMS 046

description: SPMS

value: Placebo


title: deletion MST [MST_1]


title: SPMS 045

description: SPMS


title: Subject E1_BR_Post

description: Subject E1, Post Bed rest only

value: Post


title: Subject E1_BR_Pre

description: Subject E1, Pre Bed rest only

value: Pre


title: SPMS 044

description: SPMS


title: deletion MST [MMST_3]


title: deletion MST [MMST_1]


title: deletion MST [MMST_2]


title: SPMS 043

description: SPMS


title: Subject D1_BRE_Post

description: Subject D1, Post Bed rest + exercise

value: Bed rest + exercise


title: deletion CSE(8) [MCSE_3]

source_name: deletion CSE(8)_whole fly


title: deletion CSE(8) [MCSE_1]


title: deletion CSE(8) [MCSE_2]


title: deletion CBS(8) [MCBS8_3]

source_name: deletion CBS(8)_whole fly


title: SPMS 042

description: SPMS


title: Subject B1_BRE_Post

description: Subject B1, Post Bed rest + exercise


title: deletion CBS(8) [MCBS8_1]


title: Subject D1_BRE_Pre

description: Subject D1, Pre Bed rest + exercise


title: WT11: p53-/-;MDMXWT/WT MEF cell line 11

city: Tampa

first: Jiandong

last: Chen

state: FL

address: 12902 Magnolia Drive

department: Molecular Oncology Department

institute: Moffitt Cancer Center

data_processing:
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 Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. Since a strand-specific library preparation was performed, the reads were strand-specifically counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Genome_build: GRCm38
Supplementary_files_format_and_content: Unique hit counts for each sample: sample.counts.txt

source_name: Mouse embryo fibroblast

growth_protocol: DMEM+10% FBS

extract_protocol:
Total RNA samples were prepared using RNeasy min kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols for mRNA sequencing via polyA selection.

value: p53-null, MDMX wild type double homozygous

tag: passage

value: Passage 4

value: Mouse embryo fibroblast


title: WT9: p53-/-;MDMXWT/WT MEF cell line 9


title: WT3: p53-/-;MDMXWT/WT MEF cell line 3


title: Subject C1_BRE_Post

description: Subject C1, Post Bed rest + exercise


title: Subject A1_BRE_Pre

description: Subject A1, Pre Bed rest + exercise


title: SPMS 039

description: SPMS


title: SPMS 038

description: SPMS


title: SPMS 037

description: SPMS


title: SPMS 040

description: SPMS


title: SPMS 041

description: SPMS


title: SPMS 036

description: SPMS

value: Female


title: SG3: p53-/-;MDMXSG/SG MEF cell line 3

value: p53-null, MDMX-SG double homozygous


title: SPMS 035

description: SPMS

value: unknown


title: SPMS 034

description: SPMS


title: SG2: p53-/-;MDMXSG/SG MEF cell line 2


title: Subject B1_BRE_Pre

description: Subject B1, Pre Bed rest + exercise


title: Subject C1_BRE_Pre

description: Subject C1, Pre Bed rest + exercise


title: Subject A1_BRE_Post

description: Subject A1, Post Bed rest + exercise


title: deletion CBS(5) [MCBS5_2]

source_name: deletion CBS(5)_whole fly

value: 5-day old


title: deletion CBS(8) [MCBS8_2]


title: SG1: p53-/-;MDMXSG/SG MEF cell line 1


title: deletion CBS(5) [MCBS5_1]


title: SPMS 033

description: SPMS

value: male


title: deletion CBS(5) [MCBS5_3]


title: double deletion CBS/CSE(2) - backcross on yw [MBE2_Df_3]

source_name: double deletion CBS/CSE(2) - backcross on yw_whole fly

value: CBS/CSE(2) - backcross on yw


title: double deletion CBS/CSE(2) - backcross on yw [MBE2_Df_2]


title: Sample_21_VavPBcl2_SHMT2_repl6_input

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
RNA-seq: Illumina Casava1.8 software used for basecalling.
RNA-seq: RNA-seq reads were aligned to mm10 using STAR with default parameters
RNA-seq: TPM were obtained using Rsubread and RefSeq gene annotation
ChIP-seq: ChIP-seq reads were aligned to mm10 using BWA
ChIP-seq: Peaks were called using MACS2 with either broad (H3K4me1) or narrow (H3K4me3) parameters
Genome_build: mm10

source_name: B220+ cells

extract_protocol:
VavPBcl2 hematopoietic stem cells (HSCs) collected from fetal liver (E13.5) were infected with either empty vector or MSCV-SHMT2 vector and injected into two times irradiated wild type mice. The lymphomagesis was followed by blood count and blood smear analysis. The B cells (B220+) were isolated from spleen.
RNA-seq: RNA of B cells collected from VavPBcl2;vector or VavPBcl2;SHMT2 tumors were extracted using TRIZOL standard protocol.
ChIP-seq: 3×106 mouse B220+ cells collected from VavPBcl2;vector and VavPBcl2;SHMT2 tumors were fixed with 1% formaldehyde for 10 min at room temperature and lysed. Fragmentation of fixed chromatin was performed by sonication of isolated nuclei (Covaris E220, Covaris) to achieve the enrichment of short chromatin fragments (100 - 500 bp). One μg of antibody (H3K4me1, ab8895, abcam; H3K4me3, ab8580, abcam) was added to the chromatin lysate and incubated overnight at 4 °C. Enriched DNA was isolated by Dynabeads protein A (Thermo Fisher Scientific) and subsequent reverse cross-linking and purification.
RNA-seq: RNA-seq libraries were prepared using the Illumina TruSeq stranded mRNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies)
ChIP-seq: ChIPseq libraries were prepared from 1-5 ng ChIP DNA following the instructions of Illumina TruSeq ChIP Library Preparation Kit (IP-202-1012).

value: Tranfected with MSCV-SHMT2

tag: antibody

value: input


title: double deletion CBS/CSE(2) - backcross on yw [MBE2_Df_1]

value: whole fly


title: Sample_20_VavPBcl2_SHMT2_repl5_input


title: Sample_17_VavPBcl2_control_repl5_input

value: Transfected with emtpy vector


title: 4C_GFP_CAG_270_DOX_rep2

city: Lausanne

first: Gustavo

middle: Agustín

last: Ruiz Buendía

state: Vaud

address: University of Lausanne

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

description: GFP(CAG)270 cells treated with DOX GFP 4C viewpoint replicate 2

data_processing:
Demultiplexing, trimming, and mapping were performed using the BBCF HTSstation (David et al., 2014). Reads were trimmed to keep the first 40 bp. The 4C fragments surrounding the viewpoints (±2.5 kb) were excluded from the rest of the analysis. The demultiplexed reads were mapped to the GRCh38 human reference genome using bowtie2 (v 2.2) (Langmead & Salzberg, 2012).
Fragment read counts were obtained using FourCSeq (v 1.18.0) (Klein et al., 2015). Fragment counts were normalized (reads per million) and smoothed with a running mean (window size = 5 fragments).
Significant chromatin interactions were identified with two 4C-seq data analysis packages: FourCSeq (v 1.18.0) (Klein et al., 2015) and 4C-ker (v 0.0.0.9000) (Raviram et al., 2016).
For the FourCSeq analysis, we defined significant interactions as fragments with a z-score equal to or greater than 1.96 and a false-discovery rate of 0.1, using the following parameters: minCount=20 and fitFun="distFitMonotone" in getZScores function; zScoreThresh=1.96, fdrThresh = 0.1 in addPeaks function.
For the 4C-ker analysis, we used k=5 in the nearBaitAnalysis function, and plotted the high-interacting regions.
Differential interactions were identified with the differentialAnalysis function of 4C-ker, which is based on the DESeq2 (Love et al., 2014) framework, using default parameters (including a p-value threshold of 0.5). The UN-B cell line was used as the reference condition for all comparisons except for Fig. 1 and Fig. S2 where the reference condition was the UN-A cell line.
For plotting the data, the smoothed and normalized fragment counts were averaged among replicates of the same 4C library samples and visualized with gFeatBrowser (http://www.gfeatbrowser.com).
Genome_build: hg38
Supplementary_files_format_and_content: Smoothed and normalized 4C fragment count data (bedGraph) of the cis chromosome, one per viewpoint and per replicate.

growth_protocol: All LCLs were obtained from the Coriell Institute for Medical Research Cell Repository. They were grown at 37ºC and 5% CO2 in RPMI 1640 medium supplemented with 15% FBS, 2 mM L-glutamine, and 1% penicillin-streptomycin. Cells were counted and passaged every 3-4 days depending on cell density. The GFP(CAG)270 and GFP(CAG)15 cell lines were maintained at 37°C and 5% CO2 in DMEM with Glutamax, 1% penicillin-streptomycin, 15 μg mL−1 blasticidine, and 150 μg/mL hygromycin. Transcription of the GFP mini-gene was activated by culturing GFP(CAG)n cells with doxycycline at a final concentration of 2 µg/mL for five days.

extract_protocol:
Samples of 10 million cells were crosslinked in 2% formaldehyde for 10 minutes at room temperature and quenched with glycine to a final concentration 0.13 M. Cross-linked samples were rinsed once with PBS and were either used immediately or flash-frozen in liquid nitrogen and stored at -80ºC for later use. Cells were lysed for 15 minutes on ice in lysis buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, 1x protease inhibitors). The first digestion was performed with 200 U DpnII (NEB) and incubating for 4 hours at 37ºC, then 200 U DpnII and overnight incubation at 37ºC, and finally 200 U DpnII and incubating 4 hours at 37ºC. DpnII digestion efficiency was assessed by agarose gel electrophoresis and DpnII was subsequently heat inactivated. The first ligation was performed at 16ºC overnight with 50 U T4 DNA ligase (Thermo Scientific) in 7 mL. Ligated samples were de-crosslinked with 30 µL Proteinase K (10 mg/mL) at 65ºC overnight followed by RNAse A treatment and phenol-chloroform purification. The second digestion was performed with 50 U of BfaI (NEB) at 37ºC overnight followed by BfaI heat inactivation. The second ligation was performed at 16ºC overnight with 100 U T4 DNA ligase in 14 mL. The resulting 4C template samples were precipitated and purified with the QIAquick PCR purification kit.
4C libraries were generated by amplifying 1 µg total of purified 4C template using the Expand Long Template PCR System (Roche) with 4C viewpoint primers with Illumina sequencing adapters that permitted multiplexing (in 50 µL PCRs), pooling reactions and purifying the PCR products with AMPure XP beads to exclude products less than 130 bp. Single-end sequencing of pooled 4C libraries was performed on Illumina HiSeq 2500.

tag: cell type

value: HEK293 T-Rex Flp-In

tag: disease

value: Not Applicable


title: 4C_GFP_CAG_270_DOX_rep3

description: GFP(CAG)270 cells treated with DOX GFP 4C viewpoint replicate 3


title: double deletion CBS/CSE(2) [MBE2_2]

source_name: double deletion CBS/CSE(2)_whole fly

value: Male

tag: tissue


title: double deletion CBS/CSE(2) [MBE2_1]


title: SPMS 030

description: SPMS

tag: treatment

value: Placebo


title: SPMS 028

description: SPMS

value: Baseline


title: SPMS 031

description: SPMS

value: Treated


title: SPMS 029

description: SPMS


title: SPMS 032

description: SPMS


title: 4C_GFP_CAG_270_DOX_rep1

description: GFP(CAG)270 cells treated with DOX GFP 4C viewpoint replicate 1


title: Sample_19_VavPBcl2_SHMT2_repl4_input


title: double deletion CBS/CSE(1) [MBE1_3]

source_name: double deletion CBS/CSE(1)_whole fly


title: SPMS 027

description: SPMS


title: SPMS 025

description: SPMS


title: Sample_14_VavPBcl2_SHMT2_H3K4me3_repl5


title: 4C_GFP_CAG_270_DMSO_rep3

description: GFP(CAG)270 cells treated with DMSO GFP 4C viewpoint replicate 3


title: 4C_GFP_CAG_270_DMSO_rep2

description: GFP(CAG)270 cells treated with DMSO GFP 4C viewpoint replicate 2


title: double deletion CBS/CSE(1) [MBE1_2]


title: Sample_15_VavPBcl2_SHMT2_H3K4me3_repl6


title: Sample_18_VavPBcl2_control_repl6_input


title: double deletion CBS/CSE(2) [MBE2_3]


title: Sample_13_VavPBcl2_SHMT2_H3K4me3_repl4


title: Sample_16_VavPBcl2_control_repl4_input


title: double deletion CBS/CSE(1) [MBE1_1]


title: 4C_GFP_CAG_270_DMSO_rep1

description: GFP(CAG)270 cells treated with DMSO GFP 4C viewpoint replicate 1


title: Sample_12_VavPBcl2_control_repl6_H3K4me3


title: SPMS 026

description: SPMS


title: Control [M58492_3]

source_name: Control_whole fly


title: SPMS 021

description: SPMS


title: 4C_GFP_CAG_15_DOX_rep3

description: GFP(CAG)15 cells treated with DOX GFP 4C viewpoint replicate 3


title: Sample_10_VavPBcl2_SHMT2_rep5_H3K4me1


title: Sample_11_VavPBcl2_control_repl4_H3K4me3


title: 4C_GFP_CAG_15_DOX_rep2

description: GFP(CAG)15 cells treated with DOX GFP 4C viewpoint replicate 2


title: SPMS 022

description: SPMS


title: Control [M58492_2]


title: Control [M58492_1]


title: SPMS 023

description: SPMS


title: SPMS 020

description: SPMS


title: Sample_9_VavPBcl2_SHMT2_repl4_H3K4me1


title: 4C_GFP_CAG_15_DOX_rep1

description: GFP(CAG)15 cells treated with DOX GFP 4C viewpoint replicate 1


title: 4C_GFP_CAG_15_DMSO_rep2

description: GFP(CAG)15 cells treated with DMSO GFP 4C viewpoint replicate 2


title: Sample_8_VavPBcl2_control_repl5_H3K4me1


title: SPMS 018

description: SPMS


title: 4C_GFP_CAG_15_DMSO_rep3

description: GFP(CAG)15 cells treated with DMSO GFP 4C viewpoint replicate 3


title: deletion CSE(8) [CSE_3]


title: SPMS 017

description: SPMS


title: deletion CSE(8) [CSE_2]


title: SPMS 019

description: SPMS


title: Sample_7_VavPBcl2_control_repl4_H3K4me1


title: Sample_6_VavPBcl2_SHMT2_repl3_RNAseq


title: 4C_GFP_CAG_15_DMSO_rep1

description: GFP(CAG)15 cells treated with DMSO GFP 4C viewpoint replicate 1


title: deletion CBS(8) [CBS8_3]


title: Sample_5_VavPBcl2_SHMT2_repl2_RNAseq


title: deletion CBS(8) [CBS8_2]


title: Sample_4_VavPBcl2_SHMT2_repl1_RNAseq


title: SPMS 014_2

description: SPMS


title: deletion CBS(8) [CBS8_1]


title: deletion CBS(5) [CBS5_3]


title: KO rep8: RNA-seq Dnmt3a KO Tumor cells rep8

city: Barcelona

first: Lorenzo

last: Rinaldi

state: Spain

address: Carrer Reixac Baldiri 10

department: Oncology

country: Spain

institute: IRB

data_processing:
RNA-seq datasets were pre-processed by removing both low quality bases from the 3¢- ends of the reads and adapter sequences using Trimmomatic (version 0.33) (Bolger et al. 2014). The trimmed reads were aligned to the mouse genome (UCSC mm10) using TopHat (version 2.0.13) (Trapnell et al. 2009), with default parameters and –g 5. Gene and transcript expression levels were quantified with HTSeq (version 0.6.1p1) (Anders et al. 2015). From the raw counts, counts per million (cpm) and fragments per kilobase of transcript per million mapped reads (fpkm) values were calculated. Differential expression analysis was performed using DESeq2 (Love et al. 2014) using a q-value cutoff of 0.05 and a fold-change cutoff of 1.5 to identify differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: Fpkm values and differential expression values calculated with DESeq2

source_name: RNA-seq of FACS Sorted Dnmt3a KO Skin Tumor Cells

extract_protocol:
To isolate pre-cancerous epidermal cells following short DMBA/TPA treatment, back skins were dissected and processed to single-cell suspensions as previously described (Jensen et al. 2010).  To purify tumor cells, DMBA/TPA-induced SCCs were mechanically dissociated using a McIlwain Tissue Chopper (The Mickle Laboratory Engineering Co. LTD). Minced tumor tissue was digested under agitation in serum-free EMEM medium without calcium containing 2.5 mg/ml Collagenase I (Sigma Aldrich) and 0.75 mg/ml trypsin (Life Technologies) for 90 min at 37°C. Cells were pelleted, resuspended in 1–2 ml of 0.25% pre-warmed trypsin/EDTA (Life Technologies) containing 100 µg/ml DNase (Sigma Aldrich) per tumor, and incubated at 37°C for 2 min. Trypsin was inactivated by adding EMEM without calcium containing 10% chelated FBS. Cells were washed twice in PBS and filtered sequentially through 100 µm and 40 µm cell strainers.
The libraries of total RNA from wild-type and Dnmt3a cKO tumors was prepared using the TruSeq®Stranded Total Sample Preparation kit (Illumina Inc.) according to the manufacturer’s protocol. Each library was sequenced using TruSeq SBS Kit v3-HS, in paired end-mode with the read length 2 ´ 76 bp. A minimal of 137 million paired-end reads were generated for each sample run in one sequencing lane on HiSeq2000 (Illumina, Inc) following the manufacturer’s protocol. Images analysis, base calling, and quality scoring of the run were processed using the manufacturer’s software Real-Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA.

treatment_protocol: the back skin of 8 week-old mice—at which time hair follicles are in their resting phase (telogen)—was shaved and treated with the mutagen 7,12-dimethylbenz[a]anthracene (DMBA; 200 µl of 0.25 mg/ml solution in acetone) and the pro-inflammatory and pro-proliferation agent 12-O-tetradecanoyl phorbol-13-acetate (TPA; 200 µl of 0.02 mg/ml solution in acetone) once weekly for 6 weeks. Specifically, DMBA was given on Monday and TPA always on the Friday of the same week. For short DMBA experiments, animals were sacrificed and back skins were processed three days after the sixth TPA application.

value: Skin Tumor Cells

tag: age animal

tag: genetic background

value: CU Black Six

value: Dnmt3a flox/flox Krt14CRE(Dnmt3a KRT14 KO)


title: Sample_3_VavPBcl2_control_repl3_RNAseq


title: SPMS 015

description: SPMS

value: Female


title: SPMS 012

description: SPMS


title: KO rep7: RNA-seq Dnmt3a KO Tumor cells rep7


title: SPMS 013

description: SPMS


title: deletion CSE(8) [CSE_1]

value: 5-day old


title: Sample_2_VavPBcl2_control_repl2_RNAseq


title: Sample_1_VavPBcl2_control_repl1_RNAseq


title: deletion CBS(5) [CBS5_2]


title: SPMS 011

description: SPMS


title: KO rep5: RNA-seq Dnmt3a KO Tumor cells rep5


title: deletion CBS(5) [CBS5_1]


title: KO rep2: RNA-seq Dnmt3a KO Tumor cells rep2


title: CIE+IL17 Ab-1

city: La Jolla

first: Tatiana

last: Kisseleva

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Base-calling was performed using Illumina Real Time Analysis RTA 1.18.64 with default parameters
Sequenced reads were mapped to the Mouse Genomes Project GRCm38_68.fa reference genome using STAR v2.5.1a with default parameters
Read quantification was performed with RSEM v1.3.0 and Ensembl annotation Mus_musculus.GRCm38.68.gtf
Genome_build: GRCm38.68
Supplementary_files_format_and_content: processed data is in supplementary file, which is a comma-separated text file containing a matrix of read counts for each gene accession number and sample

source_name: Hippocampus

extract_protocol:
Illumina Truseq Stranded mRNA kit (20020595)
Strand specific mRNA-sequencing libraries (polyA+) were generated using Illumina's TruSeq stranded mRNA library prep kits

value: ab

tag: addiction

value: CIE


title: CIE+IgG-3

value: iso


title: CIE+IL17 Ab-3


title: KO rep3: RNA-seq Dnmt3a KO Tumor cells rep3

tag: gender


title: double deletion CBS/CSE(2) [BE2_2]


title: CIE+IL17 Ab-2


title: double deletion CBS/CSE(1) [BE1_3]


title: KO rep1: RNA-seq Dnmt3a KO Tumor cells rep1


title: double deletion CBS/CSE(1) [BE1_2]


title: CIE+IgG-1


title: WT rep4: RNA-seq WT Tumor cells rep4

source_name: RNA-seq of FACS Sorted WT Skin Tumor Cells

value: Dnmt3a flox/flox (wild type)


title: WT rep3: RNA-seq WT Tumor cells rep3


title: KO rep6: RNA-seq Dnmt3a KO Tumor cells rep6


title: KO rep4: RNA-seq Dnmt3a KO Tumor cells rep4


title: Air+IgG-3

value: air


title: Control [58492_3]

value: whole fly


title: Air+IgG-2


title: double deletion CBS/CSE(2) [BE2_1]


title: Air+IgG-1


title: double deletion CBS/CSE(2) [BE2_3]


title: WT rep1: RNA-seq WT Tumor cells rep1


title: Control [58492_1]


title: WT rep2: RNA-seq WT Tumor cells rep2


title: 123_KO_BULGE: RNA-seq Dnmt3a KO DMBA Backskin bulge treated rep3

source_name: FACS Sorted of Dnmt3a KO Bulge (Hair Follicle Stem Cells) after six weeks of DMBA/TPA treatment

value: Bulge (Hair Follicle Stem Cells)

value: 14 weeks


title: CIE+IgG-2


title: RNA_LSK_BMT_RKO_rep3

data_processing:
RNA-seq experiments were performed in three or more biological replicates.  The sequencing reads were aligned to the mouse reference genome (mm9) using STAR7 (v2.5.3).
Reads on each gene were counted with featureCounts (v1.5.3) from Subread package, and edgeR package in R was used to identify the differentially expressed genes with FDR threshold of 0.05 and to generate the multidimensional scaling (MDS) plot.
The analysis was performed in genes expressed at >1 count per million (CPM) in two or more samples, and generalized linear models were used to compare gene expression data.
Genome_build: mm9
Supplementary_files_format_and_content: Reads on each gene were counted with featureCounts (v1.5.3) from Subread package, and edgeR package in R was used.

source_name: bone marrow cells

extract_protocol:
RNA-seq experiments were performed using LSK or CMP cells obtained from WT-, SKO-, RKO-, or DKO-transplanted mice.
RNA was extracted using RNeasy Mini Kit (QIAGEN) or NucleoSpin RNA XS (Macherey-Nagel).  Libraries for RNA-seq were prepared using the NEBNext Ultra RNA Library Prep kit for Illumina (New England BioLabs) and were subjected to sequencing using HiSeq 2500 instrument (Illumina) with a standard 125-bp paired-end protocol.

tag: strain

value: bone marrow

value: LSK

value: RKO


title: RNA_LSK_BMT_RKO_rep2


title: Small RNA sequencing in cwf10-1rrp6D cells

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

description: cwf10-1rrp6D smRNAseq

data_processing:
Alignment was done using Novoalign (Novocraft).
Aligned reads were processed to retain 21-24 nucleotide reads and generate SGR files using a python script.
Mapped reads were normalized to total reads mapped.
Genome_build: asm294v2.28
Supplementary_files_format_and_content: SGR (The first column denotes the chromosome, second column denotes the position on the chromosome counted from the 5' end on the + strand, and the 3rd column denotes the count (normalized to million mapped reads).)

organism: Schizosaccharomyces pombe

source_name: log. growing cells

growth_protocol: Standard conditions were used for logarithmically growing cultures in rich media (YEA). Cultures were grown at 26C overnight and then shifted to 33C for 5hrs.

extract_protocol:
Small RNAs between 15 and 30 nucleotides were extracted from 17% Urea-PAGE gels and eluted using Corning Costar Spin-X columns (Sigma Aldrich) followed by ethanol precipitation.
NEBnext Small RNA Library for Illumina (NEB-E7330) was used according to the manufacturer's protocol
Libraries were analyzed using an Agilent 4200 TapeStation system (Agilent) and sequenced on the Illumina MiSeq platform.

treatment_protocol: Temperature sensitive mutation of Pir2 and Cwf10 and deletion of Rrp6.

tag: growth stage

value: log. growing cells

value: cwf10-1 mutant and Rrp6 Deletion


title: double deletion CBS/CSE(1) [BE1_1]


title: Small RNA sequencing in cells carrying pho1 intron mutation and rrp6D

description: pho1-intron-mutant-rrp6D smRNAseq

value: Cryptic intron mutations at pho1 and Rrp6 Deletion


title: 122_KO_BULGE: RNA-seq Dnmt3a KO DMBA Backskin bulge  treated rep2

value: CU Black Six

value: Dnmt3a flox/flox Krt14CRE(Dnmt3a KRT14 KO)


title: 105_KO_BULGE: RNA-seq Dnmt3a KO DMBA Backskin bulge treated rep1

value: Female


title: Small RNA sequencing in pir2-1rrp6D cells

description: pir2-1rrp6D smRNAseq

value: pir2-1 mutant and Rrp6 Deletion


title: RNA_LSK_BMT_WT_rep6

value: WT


title: RNA_LSK_BMT_RKO_rep1


title: 118_WT_BULGE: RNA-seq WT DMBA Backskin Bulge treated rep3

source_name: FACS Sorted of WT Bulge (Hair Follicle Stem Cells) after six weeks of DMBA/TPA treatment


title: RNA_LSK_BMT_WT_rep5


title: Small RNA sequencing in rrp6D cells

description: rrp6D smRNAseq

value: Rrp6 Deletion


title: RNA_LSK_BMT_WT_rep4


title: Small RNA sequencing in WT cells

description: WT smRNAseq

value: wild type cells


title: Small RNA sequencing in pir2-1 cells

description: pir2-1 smRNAseq

value: pir2-1 mutant


title: 117_WT_BULGE: RNA-seq WT DMBA Backskin Bulge  treated rep2

value: Dnmt3a flox/flox (wild type)


title: 123_KO_IFE: RNA-seq Dnmt3a KO DMBA Backskin IFE treated rep4

source_name: FACS Sorted of Dnmt3a KO IFE (Interfollicular Epidermal Stem Cells) after six weeks of DMBA/TPA treatment


title: 104_WT_BULGE: RNA-seq WT DMBA Backskin Bulge treated rep1

value: Bulge (Hair Follicle Stem Cells)


title: RNAseq of pir2-1 cells

data_processing:
Alignment was done using Tophat.
FPKM values were calculated using cufflinks
Genome_build: asm294v2.28
Supplementary_files_format_and_content: Tab delimited text files, from cufflinks

extract_protocol:
RNA was extracted using hot phenol method.
NEB Ultra Directional RNA Library Prep kit (NEB, E7420S) was used according to manufacturer's recommendation.
Libraries were analyzed using an Agilent 4200 TapeStation system (Agilent) and sequenced on the Illumina MiSEQ system.

treatment_protocol: Temperature sensitive mutation of Pir2.


title: 122_KO_IFE: RNA-seq Dnmt3a KO DMBA Backskin IFE treated rep3

value: IFE (Interfollicular Epidermal Stem Cells)

value: 14 weeks


title: RNA_LSK_BMT_DKO_rep3

value: bone marrow

value: LSK

value: DKO


title: RNAseq of WT cells

description: WT-RNAseq

value: log. growing cells


title: 106_KO_IFE: RNA-seq Dnmt3a KO DMBA BackskinIFE  treated rep2


title: RNA_LSK_BMT_DKO_rep2


title: RNA_LSK_BMT_DKO_rep1


title: 118_WT_IFE: RNA-seq WT DMBA Backskin IFE treated rep4

source_name: FACS Sorted of WT IFE (Interfollicular Epidermal Stem Cells) after six weeks of DMBA/TPA treatment


title: RNA_LSK_BMT_SKO_rep2

value: SKO


title: RNA_LSK_BMT_SKO_rep3


title: RNA_LSK_BMT_SKO_rep1


title: 117_WT_IFE: RNA-seq WT DMBA Backskin IFE treated rep3

value: CU Black Six


title: 107_WT_IFE: RNA-seq WT DMBA BackskinIFE  treated rep2


title: 104_WT_IFE: RNA-seq WT DMBA Backskin IFE treated rep1


title: RNA_LSK_BMT_WT_rep2


title: 3-2: control2

city: suzhou

first: shouli

address: renai road 199, suzhou industrial park

department: pathology

institute: soochow university school of medicine

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9

source_name: renal tubular epithelial cells

extract_protocol:
RNA was harvested using Trizol reagent.
miRNA libraries were prepared for sequencing using standard Illumina protocols

value: renal tubular epithelial cells

value: stimulated with TGF-β1 for 48h

tag: co-cultured


title: 3-3: control3


title: RNA_LSK_BMT_WT_rep1

tag: genotype


title: RNA_CMP_nonBMT_SKO_rep3

value: CMP


title: 2-3: treat3

value: with mesenchymal stem cells


title: 3-1: control1


title: RNA_CMP_nonBMT_SKO_rep1


title: RNA_CMP_nonBMT_SKO_rep2


title: RNA_CMP_nonBMT_WT_rep3

value: WT


title: 2-1: treat1


title: RNA_CMP_nonBMT_WT_rep1


title: 105_KO_IFE: RNA-seq Dnmt3a KO DMBA Backskin IFE treated rep1

value: Female

value: Dnmt3a flox/flox Krt14CRE(Dnmt3a KRT14 KO)


title: m8: obob_rep2

city: Milano

first: Pietro

last: Delfino

address: Via Olgettina 58

country: Italy

institute: San Raffaele Scientific Institute

data_processing:
Quality of raw reads was checked with FASTQC (Leggett et al., 2013). Transcripts were quantified with the alignment-free method implemented in Salmon 0.11.3 (Patro et al., 2017). Mouse genome and transcriptome from Genecode Release M18 (GRCm38.p6) were used. Quantified transcripts were imported to the statistical software R with the tximport package (Soneson 2015) and aggregated to the gene level using the option tx2gene. The matrix of gene counts was then converted to a DESeq data set with the function DESeqDataSetFromTximport function implemented in DEseq2 package version 1.22.2 (Love et al., 2014) and normalized using the rlog function.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: A single file containing rLog normalized counts from each sample with gene symbols in row.

extract_protocol:
Total RNA was isolated from pancreata tissue samples using the Trizol reagent (Invitrogen), following the manufacturer’s instructions.
RNA was quantified using the NanoDrop (Thermo ScientificTM NanoDrop 2000) and purity of samples was checked on 1% agarose gels for evaluating the 28S and 18S ribosomal RNA bands (28S/18S ratio). All samples with a ratio (28S/18S) of above 1.8 and an OD 260/280 ratio greater than 1.9 were sent to BGI Company in China for sequencing. RNA integrity number (RIN) was also measured on an Agilent Bio Analyzer 2100 system. Only RNA samples with a RIN > 7 were used for cDNA library construction. All cDNA libraries were sequenced using paired-end strategy (read length 150 bp) on an Illumina HiSeq 2000 platform.

value: C57BL/6J; ob/ob

value: male

value: pancreas


title: m6: HFD_rep3

value: C57BL/6 WT


title: m5: HFD_rep2


title: RNA_LSK_nonBMT_SKO_rep1

value: bone marrow


title: RNA_LSK_nonBMT_WT_rep3

value: LSK


title: RNA_LSK_nonBMT_SKO_rep3


title: RNA_LSK_BMT_WT_rep3


title: m4: HFD_rep1


title: RNA_LSK_nonBMT_SKO_rep2


title: RNA_LSK_nonBMT_WT_rep2


title: m1: LFD_rep1


title: m2: LFD_rep2


title: 2-2: treat2


title: ChIP_HSPC_Ser5-P_PolII_input_DKO_rep2

data_processing:
The sequencing reads were aligned to the mouse reference genome (mm9) using bowtie (v1.2.2) following trimming of adapters and read tails to a total length of 50 base pairs using cutadapt.
Duplicates and reads on blacklisted regions (ENCODE) were removed by Picard and bedtools, respectively.
Peaks were called using MACS (v2.1.1) for each replicate individually with a p value threshold of 1 x 10–3.
Genome_build: mm9
Supplementary_files_format_and_content: Peaks were called using MACS (v2.1.1) for each replicate individually with a p value threshold of 1 x 10–3.

extract_protocol:
ChIP-seq experiments were performed using c-Kit+ HSPCs.
Cells were fixed in PBS with 1% formaldehyde (Thermo Fisher Scientific) for 10 min at room temperature with gentle mixing.  The reaction was stopped by adding glycine solution (10x) (Cell Signaling Technology) and incubating for 5 minutes at room temperature, and the cells were washed in cold PBS twice.  The cells were then processed with SimpleChIP Plus Sonication Chromatin IP Kit (Cell Signaling Technology) and Covaris E220 (Covaris) according to the manufacturer’s protocol.  The antibodies used for ChIP are as follows: STAG1 (Protein Tech, 14015-1-AP), STAG2 (Novus, NBP1-30472), SMC1 (Abcam, ab9262), CTCF (Cell Signaling Technology, D31H2), RUNX1 (Abcam, 23980), Pol2 (Abcam, ab5408), H3K27ac (Cell Signaling Technology, D5E4), H3K27me3 (Cell Signaling Technology, C36B11), H3K4me1 (Cell Signaling Technology, D1A9), or H3K4me3 (Cell Signaling Technology, C42D8).  ChIP-seq libraries were constructed using ThruPLEX DNA-seq kit (Takara) according to the manufacturer’s protocol, and then subjected to sequencing using HiSeq 2500 (Illumina).

value: HSPC

value: DKO


title: RNA_LSK_nonBMT_WT_rep1


title: ChIP_HSPC_Ser5-P_PolII_input_DKO_rep1


title: RNA_CMP_nonBMT_WT_rep2


title: ChIP_HSPC_Ser5-P_PolII_input_RKO_rep2

value: RKO


title: ChIP_HSPC_Ser5-P_PolII_input_RKO_rep1


title: ChIP_HSPC_Ser5-P_PolII_input_SKO_rep2

value: SKO


title: ChIP_HSPC_Ser5-P_PolII_input_SKO_rep1


title: m7: obob_rep1


title: ChIP_HSPC_Ser5-P_PolII_DKO_rep2


title: ChIP_HSPC_Ser5-P_PolII_DKO_rep1


title: Healthy Donor 3 - 7d - Tregs

first: Stefan

middle: A

last: Muljo

address: 10 CENTER DR RM 11N306

institute: NIH/NIAID

data_processing:
Reads from RNA-seq were mapped to the human genome (GRCh37, hg19) using the splice-aware aligner TopHat with option – mate-inner-dist 160 – coverage-search – microexon-search – max-multi hits [23].
Aligned reads were then visualized on a local mirror of the UCSC Genome Browser [24]. Quantification of gene expression was performed by counting aligned reads on each gene, for each condition in Tregs and Tconvs for same HD.
DEGseq was then applied to identify differentially expressed genes between Tregs and Tconvs with p value ⩽ 1e−5 [25].
Genome_build: GRCh37, hg19
Supplementary_files_format_and_content: Tab-delimited text tables present DEGseq output results-- transcript ID, raw counts, log2FCs, p-values, q-values, RefSeq IDs, Gene Names, chromosomal coordinates, etc. Excel spreadsheet contains Supplementary Tables 1 and 3 directly from the Supplementary Material of the paper-- DEGseq DE gene lists and intersections across donors and timepoints, based on log2FC > 0.5 or < -0.5.

source_name: 7d - Tregs

growth_protocol: FACS-sorted Tregs (CD4+CD127loCD25hi) and Tconvs (CD4+CD127hiCD25lo) were expanded in RPMI (Lonza) supplemented with 10% heat inactivated FBS (Lonza) in the presence of recombinant human IL-2 (rIL-2, 100 U/ml, Roche).

extract_protocol:
Total RNA was isolated using mirVana (Applied Biosystems) isolation kit.
RNA-seq libraries were prepared from 4 μg of total RNA using the TruSeq RNA sample preparation kit following manufacturer’s protocol (Illumina). Briefly, oligo-dT purified mRNA was fragmented and subjected to first and second strand cDNA synthesis. cDNA fragments were blunt-ended, ligated to Illumina adaptors, and PCR amplified to enrich for the fragments ligated to adaptors. The resulting cDNA libraries were verified and quantified on Agilent Bioanalyzer and RNA-seq was conducted using the GAIIx Genome Analyzer (Illumina).

treatment_protocol: Plates were coated with anti-CD3 (clone OKT3, 10 μg/ml, eBioscience) and anti-CD28 (clone 28.2, 2 μg/ml, eBioscience) for 6 h, 24 h. For 7d Treg sample, Cells were expanded for longer time periods under similar conditions with changes in medium every third day.

tag: subject status/donor

value: Healthy Donor 3

value: Male

value: unknown

value: peripheral blood

value: Tregs (CD4+ CD25hi CD127-)

tag: time point

value: after further in vitro activation at longer timepoints (7d)


title: Healthy Donor 3 - 6hr - Tregs

source_name: 6hr - Tregs

tag: Sex

tag: age

value: after further in vitro activation at longer timepoints (6hr)


title: Healthy Donor 3 - 24hr - Tregs

source_name: 24hr - Tregs

value: after further in vitro activation at longer timepoints (24hr)


title: ChIP_HSPC_Ser5-P_PolII_SKO_rep2


title: ChIP_HSPC_Ser5-P_PolII_RKO_rep1


title: Healthy Donor 3 - 24hr - Tconvs

source_name: 24hr - Tconvs

value: Tconvs (CD4+ CD25lo CD127+)


title: m3: LFD_rep3

value: male

value: pancreas


title: Healthy Donor 3 - 6hr - Tconvs

source_name: 6hr - Tconvs


title: Healthy Donor 3 - 0hr - Tconvs

source_name: 0hr - Tconvs

value: upon fresh explantation (0hr)


title: ChIP_HSPC_Ser5-P_PolII_WT_rep2

value: bone marrow

value: WT


title: Healthy Donor 2 - 0hr - Tregs

source_name: 0hr - Tregs

value: Healthy Donor 2

value: Female

value: 54 years old


title: ChIP_HSPC_Input_WT_rep2

value: HSPC


title: ChIP_HSPC_Input_WT_rep1


title: ChIP_HSPC_Ser5-P_PolII_WT_rep1


title: ChIP_HSPC_Ser5-P_PolII_input_WT_rep2


title: Healthy Donor 2 - 0hr - Tconvs


title: Healthy Donor 1 - 0hr - Tregs

value: Healthy Donor 1

value: Male

value: 50 years old


title: ChIP_HSPC_Ser5-P_PolII_input_WT_rep1


title: ChIP_HSPC_Runx1_WT_rep1


title: ChIP_HSPC_Runx1_WT_rep2


title: Healthy Donor 1 - 0hr - Tconvs

value: peripheral blood


title: ChIP_HSPC_Ser5-P_PolII_RKO_rep2

value: RKO


title: ChIP_HSPC_Ctcf_WT_rep1


title: ChIP_HSPC_Smc1_WT_rep1


title: ChIP_HSPC_Stag2_WT_rep1


title: Healthy Donor 3 - 0hr - Tregs

value: Healthy Donor 3

value: unknown

value: Tregs (CD4+ CD25hi CD127-)


title: ChIP_HSPC_Stag1_WT_rep2


title: ChIP_HSPC_Ser5-P_PolII_SKO_rep1

value: SKO


title: ChIP_HSPC_Stag1_WT_rep1


title: ChIP_HSPC_H3K27me3_WT_rep1


title: ChIP_HSPC_H3K4me3_WT_rep2


title: ChIP_HSPC_H3K27me3_WT_rep2


title: ChIP_HSPC_H3K4me3_WT_rep1


title: Control [58492_2]

source_name: Control_whole fly

tag: genotype/variation

value: 5-day old

value: whole fly


title: ChIP_HSPC_Stag2_WT_rep2

value: bone marrow

tag: cell type


title: ChIP_HSPC_H3K4me1_WT_rep1

value: WT


title: ChIP_HSPC_Smc1_WT_rep2


title: ChIP_HSPC_H3K27ac_WT_rep2


title: ChIP_HSPC_Ctcf_WT_rep2


title: ChIP_HSPC_H3K27ac_WT_rep1


title: ChIP_HSPC_H3K4me1_WT_rep2


title: ATAC_CMP_BMT_RKO_rep1

data_processing:
Reads were aligned to the mouse mm9 reference genome using bowtie2 (v2.3.3) with -X 2000 --no-mixed --very-sensitive parameters following adapter trimming using cutadapt (v1.14).
Duplicates were removed by Picard (v2.6.0), and reads on mitochondria genome or blacklisted regions (ENCODE) were removed by bedtools (v2.27.1).
Peaks were called with MACS (v2.1.1) with –nomodel –broad parameters with a q value threshold of 1 x 10–5 for individual replicate as well as merged data of all replicates.
Genome_build: mm9
Supplementary_files_format_and_content: Peaks were called with MACS (v2.1.1) with –nomodel –broad parameters with a q value threshold of 1 x 10–5 for individual replicate as well as merged data of all replicates.

extract_protocol:
ATAC-seq experiments were performed using LSK or CMP cells obtained from WT-, SKO-, RKO-, or DKO-transplanted mice.
Briefly, freshly isolated 10,000 cells were pelleted and fifty microliters of transposase mixture (25 ul of 2 x TD buffer, 2.5 ul of TDE1, 0.5 ul of 1% digitonin, and 22 ul of nuclease-free water) (FC-121-1030, Illumina; G9441) was added to the cells.  After transposition reactions at 37°C for 30 min, transposed DNA was purified using QIAGEN MinElute Reaction Cleanup kit.  Transposed fragments were PCR-amplified, and the resulting library was sequenced on Hiseq 2500.

value: CMP


title: ATAC_CMP_BMT_RKO_rep2


title: ATAC_CMP_BMT_WT_rep4


title: GEM-UP-4755_S19

first: Akanksha

last: Verma

state: New York

address: 1300, York Avenue

department: Department of Physiology and Biophysics

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq: Sequence reads were aligned to hg38 STAR with default parameters
RNAseq: FPKM were obtained using CuffLinks
Genome_build: hg38
Supplementary_files_format_and_content: RNAseq: tab-delimited FPKM values for each  gencode V22 gene.

source_name: kidney allograft recipient

growth_protocol: Urinary cells

extract_protocol:
Total RNA isolated using RNeasy kit (QIAGEN)
TruSeq sample preparation kit v2 (ILLUMINA)

value: Urinary Cells

tag: diagnosis

value: Antibody Mediated Rejection


title: Esophageal squamous carcinoma 1805_04Sty

type: genomic

city: Johannesburg

first: Jacqueline

last: Brown

state: Gauteng

address: 7 York Rd Parktown

department: Molecular Medicine and Haematology

country: South Africa

institute: National Health Laboratory Services

description:
1805_04Sty
Hybridized to 250K Sty SNP array.

hyb_protocol: As per manufacturer (Affymetrix) in GeneChip 640 ovens.

scan_protocol: The arrays were washed using Affymetrix GeneChip 450 Fluidics Stations, and scanned using the GeneChip Scanner 3000 7G.

data_processing: CEL files were generated using the Affymetrix algorithm and were then imported into Partek Genomics Suite for DNA copy number analysis. The copy number data were segmented using the circular binary algorithm in GenePattern (Broad Institute) To assess the significance of gains and losses, the segmentation file was analysed using GISTIC 2.0 (Genomic Identification of Significant Targets in Cancer).

label: Biotin

source_name: esophageal squamous carcinoma 1805_04

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: DNA was extracted using a phenol/chloroform protocol from 80% tumour cells that were macrodissected from the tissue blocks. The reference samples were also extracted in the same way. DNA quality was assessed using the Nanodrop, standard gel electrophoresis and a multiplex PCR.

tag: disease state

value: esophageal squamous carcinoma

tag: tissue

value: esophageal squamous epithelium

value: male

tag: sample identifier


title: ATAC_CMP_BMT_WT_rep3


title: Esophageal squamous carcinoma 1708_04Sty

description:
1708_04Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma 1708_04


title: Normal tissue URCONT47Sty

description:
URCONT47Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT47

value: normal

value: epididymis


title: Esophageal squamous carcinoma 2136_04Sty

description:
2136_04Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma 2136_04

value: female


title: Esophageal squamous carcinoma 2134_04Sty

description:
2134_04Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma 2134_04


title: GEM-UP-3954_S7


title: GEM-UP-2491_S14


title: Normal tissue URCONT42Sty

description:
URCONT42Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT42

value: skin


title: Normal tissue URCONT38Sty

description:
URCONT38Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT38

value: lymph node


title: GEM-UP-220_S1


title: ATAC_CMP_BMT_DKO_rep1

source_name: bone marrow cells

value: DKO


title: Normal tissue URCONT44Sty

description:
URCONT44Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT44

value: appendix


title: Normal tissue URCONT34Sty

description:
URCONT34Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT34

value: sigmoid


title: Normal tissue URCONT43Sty

description:
URCONT43Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT43

value: larynx


title: Normal tissue URCONT39Sty

description:
URCONT39Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT39

value: kidney


title: ATAC_CMP_BMT_SKO_rep2

value: bone marrow

value: SKO


title: GEM-UP-1424_S13

value: Urinary Cells


title: Normal tissue URCONT35Sty

description:
URCONT35Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT35


title: Normal tissue URCONT46Sty

description:
URCONT46Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT46

value: omentum


title: ATAC_CMP_BMT_WT_rep2

value: CMP

value: WT


title: U13

value: Antibody Mediated Rejection


title: U15


title: Normal tissue URCONT41Sty

description:
URCONT41Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT41

value: normal

value: esophagus

value: male


title: ATAC_CMP_BMT_SKO_rep1


title: Normal tissue URCONT33Sty

description:
URCONT33Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT33


title: U12

source_name: kidney allograft recipient


title: Normal tissue URCONT37Sty

description:
URCONT37Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT37

value: small bowel


title: Normal tissue URCONT28Sty

description:
URCONT28Styb
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT28

value: Fallopian tube

value: female


title: Normal tissue URCONT29Sty

description:
URCONT29Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT29

value: appendix


title: Normal tissue URCONT32Sty

description:
URCONT32Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT32


title: GEM-UP-6575_S48

value: No Rejection


title: Normal tissue URCONT48Sty

description:
URCONT48Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT48

value: liver


title: ATAC_LSK_BMT_RKO_rep2

value: LSK

value: RKO


title: GEM-UP-6358_S9


title: ATAC_CMP_BMT_WT_rep1

value: bone marrow


title: ATAC_LSK_BMT_RKO_rep1


title: GEM-UP-3494_S14

value: Urinary Cells


title: GEM-UP-4233b_S24


title: Normal tissue URCONT26Sty

description:
URCONT26Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT26

value: ovary and tube


title: Normal tissue URCONT22Sty

description:
URCONT22Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT22

value: kidney


title: ATAC_LSK_BMT_WT_rep4

source_name: bone marrow cells

value: WT


title: ATAC_LSK_BMT_WT_rep3


title: GEM-UP-5407_S35


title: GEM-UP-5660b_S17


title: ATAC_LSK_BMT_DKO_rep1

value: DKO


title: GEM-UP-1192b_S3


title: ATAC_LSK_BMT_SKO_rep2

value: SKO


title: Normal tissue URCONT27Sty

description:
URCONT27b
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT27

value: normal


title: ATAC_LSK_BMT_DKO_rep2


title: Normal tissue URCONT16Sty

description:
URCONT16Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT16


title: Normal tissue URCONT19Sty

description:
URCONT19Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT19

value: endometrium


title: GEM-UP-7347_S30


title: ATAC_LSK_BMT_SKO_rep1


title: GEM-UP-6956b_S19


title: Normal tissue URCONT14Sty

description:
URCONT14Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT14


title: ATAC_LSK_BMT_WT_rep2


title: GEM-UP-7030_S28


title: GEM-UP-1983_S32


title: Normal tissue URCONT13Sty

description:
URCONT13Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT13


title: GR siRNA + DEX [RNA-seq]

city: New Haven

first: Julie

last: Goodwin

address: 333 Cedar St

institute: Yale University

data_processing:
Reads were trimmed for quality.  The reads were aligned to the mm10 genome using TopHat2.  The aligned files were processed using cuffdiff with reference annotation for mm10 to generate transcript abundace estimates, and differential gene expression.
The output from cuffdiff was processed using R and cummeRbund and plotted.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM matrix

source_name: mouse lung endothelial cells

growth_protocol: Cells were cultured in EBM-2 and 10% serum.

extract_protocol: Total RNA was isolated using the RNeasy kit (Qiagen).

treatment_protocol: Cells were treated with control or GR siRNA ofr 48 hours with and without dexamethasone 100 nM for 18 hours.

value: mouse lung endothelial cells

tag: treatment

value: GR siRNA + DEX


title: Normal tissue URCONT11Sty

description:
URCONT11Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT11

value: uterus

value: female


title: GEM-UP-4947b_S20

value: No Rejection


title: Normal tissue URCONT6Sty

description:
URCONT6Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT6

value: Fallopian tube


title: GR siRNA [RNA-seq]

value: GR siRNA


title: Normal tissue URCONT8Sty

description:
URCONT8Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT8

value: oral biopsy


title: GEM-UP-3003_S9

source_name: kidney allograft recipient


title: ATAC_LSK_BMT_WT_rep1

value: bone marrow

value: LSK


title: control siRNA [RNA-seq]

value: control siRNA


title: Normal tissue URCONT5Sty

description:
URCONT5
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT5

value: ovary


title: Normal tissue URCONT4Sty

description:
URCONT4
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT4


title: GEM-UP-2829b_S17

value: Urinary Cells


title: Normal tissue URCONT3Sty

description:
URCONT3Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT3


title: GEM-UP-2783_S6


title: ATAC_CMP_BMT_DKO_rep2

value: CMP

value: DKO


title: DDB_G0272386- 8h

city: London

first: Jonathan

last: Chubb

address: Gower Street

department: MRC Laboratory for Molecular Cell Biology

country: United Kingdom

institute: University College London

data_processing:
Paired end reads were mapped to the Dictyostelium genome (version obtained from Gareth Bloomfield, masking the duplication on chromosome 2) using Tophat v2.0.9; library type parameter fr-firststrand, -p 4, -g 0
reads for each gene were counted with HtSeqCount v0.5.4p3. -m union -s reverse -a 0
Genome_build: dicty_2.7
Supplementary_files_format_and_content: tab-delimited text file with read counts for all samples

organism: Dictyostelium discoideum

source_name: dedifferentiating cells

growth_protocol: Before development, cells were grown in HL5 (Formedium, UK).

extract_protocol:
Cells were pelleted and flash frozen. Total RNA was extracted by SDS-based lysis, followed by phenol extraction and ethanol preciptiation to remove protein.
100 ng total RNA was used to prepare mRNA libraries using NEBNext mRNA isolation kit and NEBNext Ultra II Directional RNA Library preparation kit. mRNA fragmentation used manufacturer recommended conditions for a 300bp insert size. Library amplification used 13 cycles of PCR. 75bp paired-end reads were generated using an Illumina NextSeq 500.

treatment_protocol: Cells were developed for 14 h on Whatman #50 filter paper in a humified chamber. Developed cells were disaggregated in KK2 + 20 mM EDTA then dedifferentiated in HL5 growth medium as a shaken suspension

tag: timepoint


title: DDB_G0272386- 24h


title: GEM-UP-2386_S5


title: DDB_G0272386- 6h


title: GEM-UP-1958_S16


title: GEM-UP-2366b_S8


title: DDB_G0272386- 2h


title: control siRNA + DEX [RNA-seq]

value: control siRNA + DEX


title: Esophageal squamous carcinomaUROC171Sty

description:
UROC171Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC171

value: esophageal squamous carcinoma

value: esophageal squamous epithelium

tag: gender

value: male


title: GEM-UP-1921b_S4


title: Esophageal squamous carcinoma UROC172Sty

description:
UROC172Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC172


title: Esophageal squamous carcinoma UROC167Sty

description:
UROC167Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC167


title: Esophageal squamous carcinoma UROC158Sty

description:
UROC158Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC158


title: GEM-UP-4902b_S10


title: DDB_G0272386- 0h

tag: strain


title: DDB_G0272386- 4h


title: DDB_G0269374- 24h


title: Esophageal squamous carcinoma UROC156Sty

description:
UROC156Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC156


title: GEM-UP-1792_S3


title: GEM-UP-1701_S4


title: DDB_G0269374- 6h


title: GEM-UP-1905_S12


title: U20


title: Normal tissue URCONT25Sty

description:
URCONT25Sty
Hybridized to 250K Sty SNP array.

source_name: normal tissue URCONT25

value: normal

value: appendix


title: DDB_G0269374- 4h


title: Esophageal squamous carcinoma UROC151Sty

description:
UROC151Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC151


title: DDB_G0269374- 8h


title: DDB_G0269374- 2h


title: U19

value: No Rejection


title: U18


title: Esophageal squamous carcinoma UROC133Sty

description:
UROC133Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC133

value: unknown


title: DDB_G0281091- 24h


title: GEM-UP-5032_S20

value: T- cell mediated rejection


title: Esophageal squamous carcinoma UROC144Sty

description:
UROC144Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC144

value: female


title: Esophageal squamous carcinoma UROC142Sty

description:
UROC142Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC142


title: U17


title: Esophageal squamous carcinoma UROC132Sty

description:
UROC132Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC132


title: DDB_G0281091- 8h


title: Esophageal squamous carcinoma UROC131Sty

description:
UROC131Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC131


title: GEM-UP-3981_S8

source_name: kidney allograft recipient


title: Esophageal squamous carcinoma UROC128Sty

description:
UROC128Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC128


title: GEM-UP-2934_S16


title: DDB_G0269374- 0h


title: Esophageal squamous carcinoma UROC125Sty

description:
UROC125Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC125


title: DDB_G0281091- 4h


title: DDB_G0281091- 2h


title: Esophageal squamous carcinoma UROC130Sty

description:
UROC130Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC130


title: GEM-UP-1474_S14


title: GEM-UP-334b_S2


title: U10


title: DDB_G0281091- 0h

source_name: dedifferentiating cells


title: U9


title: nfyA- 24h

value: nfyA-


title: Esophageal squamous carcinoma UROC103Sty

description:
UROC103Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC103


title: nfyA- 8h


title: Esophageal squamous carcinoma UROC148Sty

description:
UROC148Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC148


title: nfyA- 6h


title: nfyA- 4h


title: GEM-UP-3132_S33


title: nfyA- 2h


title: U7


title: nfyA- 0h


title: Esophageal squamous carcinoma UROC70Sty

description:
UROC70Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC70


title: Esophageal squamous carcinoma UROC71Sty

description:
UROC71Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC71


title: GEM-UP-3180b_S5


title: GEM-UP-6174_S37


title: GEM-UP-4462b_S42


title: mybD- 24h

value: mybD-


title: GEM-UP-6115_S27


title: Esophageal squamous carcinoma UROC84Sty

description:
UROC84Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC84


title: Esophageal squamous carcinoma UROC86Sty

description:
UROC86Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC86


title: Esophageal squamous carcinoma UROC124Sty

description:
UROC124Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC124


title: Esophageal squamous carcinoma UROC69Sty

description:
UROC69Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC69


title: mybD- 8h


title: GEM-UP-6584_S18


title: GEM-UP-7173b_S29


title: Esophageal squamous carcinoma UROC67Sty

description:
UROC67Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC67


title: Esophageal squamous carcinoma UROC65Sty

description:
UROC65Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC65


title: Esophageal squamous carcinoma UROC63Sty

description:
UROC63Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC63


title: Esophageal squamous carcinoma UROC98Sty

description:
UROC98Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC98


title: mybD- 4h


title: mybD- 6h


title: Esophageal squamous carcinoma UROC62Sty

description:
UROC62Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC62


title: GEM-UP-2314_S23

source_name: kidney allograft recipient


title: GEM-UP-6549_S10


title: GEM-UP-4726_S8


title: Esophageal squamous carcinoma UROC59Sty

description:
UROC59Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC59


title: GEM-UP-6264_S46


title: mybD- 0h


title: bzpS- 8h

value: bzpS-


title: bzpS- 4h


title: GEM-UP-7370_S40


title: Esophageal squamous carcinoma UROC54Sty

description:
UROC54StyB
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC54


title: Esophageal squamous carcinoma UROC55Sty

description:
UROC55StyC
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC55


title: bzpS- 24h

source_name: dedifferentiating cells


title: GEM-UP-7597_S50


title: U6


title: Esophageal squamous carcinoma UROC53Sty

description:
UROC53Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC53


title: Esophageal squamous carcinoma UROC60Sty

description:
UROC60Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC60


title: AX2 24h

value: wild type


title: bzpS- 6h


title: mybD- 2h


title: bzpS- 0h


title: AX2 8h


title: AX2 6h


title: DDB_G0281091- 6h


title: MDA_treatment_1

city: Solna

first: Toon

last: Verheyen

address: Tomtebodavägen 16

department: Medical Biochemistry and Biophysics

data_processing:
Clustering was done by 'cBot' and samples were sequenced on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 2x126 setup using 'HiSeq SBS Kit v4' chemistry. The Bcl to FastQ conversion was performed using bcl2fastq_2.19 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
Sequenced reads were trimmed for adaptor sequence and low quality bases using Trimmomatic (v. 0.35)  for paired-end reads using the following parameters: -phred33 ILLUMINACLIP:'./adapters/NexteraPE.fa':2:30:10 TRAILING:15 SLIDINGWINDOW:4:18 MINLEN:36.
Trimmed RNA-Seq reads were mapped to the GRCg38 genome using the STAR package (v. 2.2.1) using default settings
Count tables were generated for each mapped sample using htseq-count (v. 0.5.4p3). This was performed using default settings except for the following: --stranded= No, and all reads below an alignment quality of 10 were skipped.
Differential expression analysis was tested using the DESeq2 (v. 1.24.0) R package using default settings. For the analysis, both paired and single reads (whose pair was not of sufficient quality) were used.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files containing the count tables per sample generated by the htseq-count package

source_name: Human Breast Adenocarcinoma Cell Line

growth_protocol: For the U3013 cell line, a T25 flask was coated with 10 µg/ml of poly-L-ornithine (Sigma-Aldrich) and allowed to incubate for 3 h at room temperature.After 3 h, the flask was washed with twice with 1XDPBS (Gibco). The plate was then coated with 10 µg/ml laminin (Sigma-Aldrich) and allowed to incubate for 30 min at 37°C, 5% CO2. After incubation, most of the laminin was removed. The U3013 cell line was cultured in coated T25 flasks in GBM media  (For 50 ml: 25 ml Neurobasal media (Thermofisher Scientific), 25 ml DMEM/F-12, GlutaMAX suppl. (ThermoFisher Scientific), 10 ng/ml EGF (R&D Systems), 10 ng/ml bFGF (ThermoFisher Scientific), 1 ml B27 (ThermoFisher Scientific) and  0.5 ml N2 Supplement (ThermoFisher Scientific) supplemented with 1% penicillin/streptomycin. 1x10E6 U3013 cells were then added to the T25 flask. The MDA-MB-231 Cell Line (ATCC) was cultured in Dulbecco’s Modified Eagle Medium (Gibco) supplemented with 10 % fetal bovine serum and 1% penicillin/streptomycin. For the RNA-Seq, 4,000 cells were plated in a 96-well plate format and allowed to attach for 24 hrs, MDA-MB-231 were subjected to serum starvation and U3013 were seeded onto the coated wells, as detailed above.

extract_protocol:
The cells were lysed according to the SMART-Seq2 protocol
The Smart-Seq2 protocol was used for the library construction with minor changes. After stimulation and lysis, rather then using 2 µl of the cell lysate, 5 µl was used and subsequent steps, ie. reverse transcription and PCR preamplification, were performed in twice the volume, 20 and 50 µl instead of 10 and 25 µl, to prevent any inhibitory effects from occurring. For the tagmentation step, 200 pg of cDNA was used for input. The final libraries for both experiments were prepared utilizing Illumina Paired-end  sequencing using the Nextera XT library prep kit (Illumina).  The library was sequenced on the HiSeq2500 platform with a 2x126 setup using  'HiSeq SBS Kit v4' chemistry

treatment_protocol: For both cell lines, 4,000 cells were plated per well in a 96-well plate. The cells were treated with either IgG or  IgG-clustered Ephrin-A5 (ICE) in a total volume of 50 µl for  30 min at 37℃, 5% CO2. This was performed in duplicates which were pooled together after cell lysis.

tag: cell line

value: IgG-clustered Ephrin-A5


title: AX2 4h


title: AX2 2h


title: Esophageal squamous carcinoma UROC40Sty

description:
UROC40Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC40


title: MDA_treatment_3


title: U3013_treatment_3

source_name: Human Glioma Cell Line


title: MDA_ctrl_3

value: IgG (ctrl)


title: MDA_ctrl_2


title: MDA_ctrl_1


title: AX2 0h


title: U3013_treatment_2


title: MDA_treatment_2


title: GC-JN-8372-2

data_processing:
Analysis of barcode counting, UMI counting and filtering was performed by Cell Ranger v2.2.0 using default parameters
Supplementary_files_format_and_content: counts

extract_protocol:
Cell suspensions from different timepoints were pooled before loading onto the 10X Chromium Single Cell A Chip using the Chromium 3' Library and Gel Bead Kit v2. Samples were split between two chip inlets and treated as technical replicates
The purified GEM-RT product was subjected to 14 cycles of cDNA amplification. 35 microlitres of cDNA was used to prepare the 10X 3' RNA library, with 12/11 cycles used for sample index PCR. Final libraries were run on a NextSeq500 mid-output 150-cycle kit with a 26[8]98 cycle configuration to generate 130 million read pairs in total

treatment_protocol: Cells were developed for 14 h on Whatman #50 filter paper in a humified chamber. Developed cells were disaggregated in KK2 + 20 mM EDTA then dedifferentiated in HL5 growth medium as a shaken suspension. Start times of development and dedifferentiation were staggered to allow simultaneous collection of samples into ice-cold KK2 at 0, 1, 2, 3, 4, 5 and 6 h of dedifferentiation.

tag: biological replicate

tag: technical replicate


title: Esophageal squamous carcinoma UROC48Sty

description:
UROC48Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC48


title: U3013_treatment_1


title: Esophageal squamous carcinoma UROC87Sty

description:
UROC87Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC87


title: Esophageal squamous carcinoma UROC37Sty

description:
UROC37Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC37


title: Esophageal squamous carcinoma UROC47Sty

description:
UROC47Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC47


title: GC-JN-8372-1


title: Esophageal squamous carcinoma UROC46Sty

description:
UROC46Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC46


title: U3013_ctrl_3


title: GC-JC-8097-JC2


title: U3013_ctrl_1


title: U3013_ctrl_2


title: Treatment 11

city: Frederiksberg C

first: Andrew

last: Williams

state: --- Select One ---

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

data_processing:
BGI internal software used to remove adpators and low quality reads.
Mapped to Sus Scrofa (ss11.1) using HISAT
DEG assessed using DeSeq2 and NOIseq
Genome_build: ss11.1
Supplementary_files_format_and_content: text file with count data and FPKM for each sample.

organism: Sus scrofa

source_name: Intestinal tissue

growth_protocol: Piglets were followed from birth to 24-25 days of age and fed milk replacer (DI-9224, Arla Foods, Denmark), or the same product with added wheat.

extract_protocol:
Tissue was collected at euthanasia. Total RNA was extracted using miRNAeasy kits (Qiagen).
Standard BGI protocol.

tag: breed

value: Danish Landrace/Yorkshire

value: distal small intestine


title: Esophageal squamous carcinoma UROC42Sty

description:
UROC42Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC42

value: esophageal squamous carcinoma


title: Esophageal squamous carcinoma UROC33Sty

description:
UROC33sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC33

value: esophageal squamous epithelium


title: Treatment 10


title: forG- 24h rep2

growth_protocol: Cells were grown on Klebsiella bacteria on SM agar and harvested before clearing of the bacterial lawn. Cells were washed free of bacteria before further processing

extract_protocol:
Cells were pelleted and flash frozen. Total RNA was extracted by SDS-based lysis, followed by phenol extraction and ethanol preciptiation to remove protein.
100 ng total RNA was used to prepare mRNA libraries using NEBNext mRNA isolation kit and NEBNext Ultra Directional RNA Library preparation kit. mRNA fragmentation used manufacturer recommended conditions for a 300bp insert size. Library amplification used 13 cycles of PCR. 75bp paired-end reads were generated using an Illumina NextSeq 500.

value: forG-

tag: genotype

tag: replicate


title: forG- 8h rep2


title: Treatment 9

tag: age


title: GC-JC-8097-JC1


title: forG- 6h rep2


title: Lung_A18

city: Houston

first: Valerie

last: LeBleu

state: TX

address: 1881 East Road

institute: MDACC

description:
SAMPLE10
Mouse 10

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Genome Studio 5.0
background subtraction, rank invariant normalization

source_name: mouse lung

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: N/A: adult mouse kidney and lung tissue

extract_protocol: RNA was extracted with Trizol reagent,Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Mice were healthy, or subjected to Unilateral Ureter Obstruction (UUO), or to intratracheal bleomycin injection.

value: BALB/C

tag: developmental stage

value: adult

value: fibrotic lung


title: forG- 4h rep2


title: Treatment 7


title: Treatment 8


title: Treatment 6


title: Esophageal squamous carcinoma UROC31Sty

description:
UROC31Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC31

value: male


title: Treatment 5


title: forG- 0h rep2


title: Lung_H563

description:
SAMPLE6
Mouse 6

value: healthy lung


title: Lung_H557

description:
SAMPLE7
Mouse 7

value: female


title: Lung_A16

description:
SAMPLE9
Mouse 9


title: Esophageal squamous carcinoma UROC30Sty

description:
UROC30Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC30


title: Lung_H565

description:
SAMPLE8
Mouse 8


title: forG- 24h rep1

source_name: dedifferentiating cells


title: Kidney_658D

description:
SAMPLE5
Mouse 5

source_name: mouse kidney

value: fibrotic kidney


title: Esophageal squamous carcinoma UROC29Sty

description:
UROC29Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC29


title: Esophageal squamous carcinoma UROC16Sty

description:
UROC16Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC16


title: Lung_981

description:
SAMPLE11
Mouse 11


title: forG- 2h rep2


title: Treatment 4


title: forG- 8h rep1


title: Treatment 3


title: STIM1 KO+Snail1 OE  rep3

city: Chongqing

first: Huakan

last: Zhao

state: State...

address: Xinqiao Street 183, Shapingba district

department: Clinical Medicine Research Center

institute: Xinqiao Hospital, Third Military Medical University

description: Testl (6)

data_processing:
For the normalization in this study, we useed ACTB as the housekeeping gene. Target gene signals normalized to housekeeping gene; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)].
Fold Change worksheet reports test/control (i.e., STIM1 KO/WT; Snail1+STIM1 dOE/Mock ratios.
Results were analyzed using 2^-ΔΔCt and 2^-ΔΔCt relative quantification methods. mRNAs that displayed threshold cycles (Ct) >35 were excluded from the analysis. ACTB was used as housekeeping gene. Data were analyzed with Statminer software (Integromics, Philadelphia, PA) and normalized against WT-group.

label: SYBR Green II

source_name: SMMC7721 cell line

label_protocol: Reverse transcription was performed from 1μg total RNA using PrimeScript™ RT reagent Kit with gDNA Eraser (TAKARA).3 ng cDNA was added into each 20 μL reaction mix. MRNA expressions of selected genes were assessed by RT-quantitative PCR using TB Green® Premix Ex Taq™ II (TAKARA) on BioRad CFX386 (Bio-Rad, CA) with 40 cycles at 95 °C for 10 seconds, 59 °C for 20 seconds and 72 °C for 30 seconds.

growth_protocol: Cells  were cultured in DMEM supplemented with 10% (v/v) FBS at 37°C in 5% CO2.

extract_protocol: When the cells grow to 60~70% confluent, Total RNA was extracted by using Trizol (TAKARA, Japan).

treatment_protocol: STIM1 knockout(STIM1 KO)-SMMC7721 cells were constructed by CRISPR/Cas9.STIM1 KO+Snail1 OE-SMMC7721 cells were established via lentiviral Infection of Snail1 overexpression (Snail1 OE) in STIM1 KO-SMMC7721 cells.

tag: genotype/variation

value: STIM1 KO+Snail1 OE-SMMC7721 cells were established via lentiviral Infection of Snail1 overexpression in STIM1 KO-SMMC7721 cells


title: forG- 6h rep1


title: Kidney_H563

description:
SAMPLE2
Mouse 2

value: healthy kidney


title: Esophageal squamous carcinoma UROC20Sty

description:
UROC20Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC20


title: Esophageal squamous carcinoma UROC22Sty

description:
UROC22Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC22


title: Kidney_656D

description:
SAMPLE4
Mouse 4


title: Treatment 2


title: forG- 4h rep1


title: forG- 2h rep1


title: Control 10


title: Treatment 1


title: Esophageal squamous carcinoma UROC26Sty

description:
UROC26Sty
Hybridized to 250K Sty SNP array.

source_name: esophageal squamous carcinoma UROC26


title: forG- 0h rep1


title: Control 9


title: Kidney_H565

description:
SAMPLE3
Mouse 3


title: STIM1 KO  rep3

description: Testl (3)

value: STIM1 Knockout-SMMC7721 generated by CRISPR-Cas9


title: AX2 24h rep2

value: wild type


title: Control 8


title: Control 7


title: STIM1 KO  rep2

description: Testl (2)


title: STIM1 KO  rep1

description: Testl (1)


title: WT rep2

description: Control (2)

value: SMMC7721 without any gene editing


title: STIM1 KO+Snail1 OE  rep1

description: Testl (4)


title: AX2 8h rep2


title: AX2 6h rep2


title: Control 6

value: Danish Landrace/Yorkshire


title: Control 5

value: distal small intestine


title: Control 4


title: AX2 2h rep2


title: melanoma_K411_blood_GEX

city: San Francisco

first: Kelly

middle: Maria

last: Mahuron

address: 513 Parnassus Avenue, HSW 1201B

institute: UCSF

description: total RNA

data_processing:
Cell Ranger analysis pipelines (version 3.0.2, 10X Genomics) were used to process the generated sequencing data.
Data was demultiplexed into FASTQ and aligned to the GRCh38 human reference genome and counted.
TCR library reads were assembled into single cell V(D)J sequences and annotations.
Genome_build: GRCh38
Supplementary_files_format_and_content: GEX samples have three files each: tsv file containing filtered cellular barcodes, tsv file containing filtered cellular genes, and mtx file containing filtered cellular matrix. VDJ samples have two files each; csv file containing clonotypes and csv file containing the sequence for each cell barcode.
Supplementary_files_format_and_content: VDJ samples have two files each: csv file containing clonotypes and csv file containing the sequence for each cell barcode.

source_name: human melanoma

growth_protocol: Live cells were sort-purified using an BD FACSAria Fusion (BD Biosciences) from collagenase-digested human melanoma samples or from PBMCs isolated by Ficoll gradient.

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium instrument.
Reverse transcription was performed and libraries were constructed according to the 10X Chromium Single Cell 5' Gene Expression and V(D)J Profiling Solution kit.

value: PBMC

tag: treatment status

value: naive

tag: sort purification strategy

value: Cells were sort-purified as live, singlet, CD45+CD3+CD4-CD8+ and CD45+CD3+CD4+CD8- loaded into a single channel in a 60:40 ratio


title: melanoma_K411_LN_GEX

description: total RNA

tag: tissue

value: melanoma

tag: tumor site

value: Involved regional lymph node

value: Cells were sort-purified as live, singlet, CD45+CD3+CD4-CD8+ and CD45+CD3+CD4+CD8- loaded into a single channel in a 80:20 ratio


title: AX2 0h rep2