title: gastrocnemius muscle-10% fat+fiber-C57BL/6J-F (ORSAM9015)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM9015


title: MR49F_siDECR2_6

status: Public on Dec 31 2023

type: SRA

city: Adelaide

first: Chui Yan

last: Mah

address: North Terrace

country: Australia

institute: University of Adelaide

library_source: transcriptomic

data_processing:
The quality and number of reads for each sample were assessed with FastQC v0.11.3 and trimmed with Trimmomatic v0.36
Reads passing all quality control steps were aligned to the hg38 assembly of the human genome using STAR v2.7.9a. Gene count matrix was generated with FeatureCounts version subread-2.0.3. Count matrix were imported into R v4.1.2 for further analysis and visualisation.
Data were normalized across libraries by the trimmed mean of M-values (TMM) normalization method in EdgeR v3.36. Differential gene expression analysis was performed using the glmLRT function in EdgeR.
Assembly: GRCh38
Supplementary files format and content: FeatureCounts per gene counts (.txt)

molecule: total RNA

organism: Homo sapiens

growth_protocol: V16D and MR49F cells were grown in baseline conditions (media supplemented with 10% FBS and/or enzalutamide)

extract_protocol:
Total RNA was extracted using Trizol and the RNeasy Micro Kit (Qiagen), according to the manufacturer's instructions.
Stranded polyA libraries were generated using the Nugen Universal Plus mRNA-seq protocol (M01442 v2) and converted to MGI compatible libraries using the MGIEasy Universal Library Conversion Kit. RNA-seq; MGI DNBSEQ G400 (paired-end, 2 x 98bp)

treatment_protocol: V16D and MR49F cells were transfected with siRNAs for 72h

tag: cell line

tag: cell type

value: prostate cancer cell line

tag: genotype

value: DECR2 knockdown


title: MR49F_siDECR2_5


title: gastrocnemius muscle-44% fat+fiber-C57BL/6J-M (ORSAM9019)

city: Bar Harbor

first: Gary

last: Churchill

state: Maine

address: 600 Main St

country: USA

institute: The Jackson Laboratory

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM9019

data_processing:
raw counts quantified by EMASE and processed by /RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script and gathering_GBRS_total_counts_batch2.R.
counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation).
Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/Processing_normalization.R and Processing_normalization_batch2.R scripts.
gene annotation file ENSEMBL version 84
Assembly: GRCm38
Supplementary files format and content: counts_matrix.csv
Supplementary files format and content: mrna_annots.csv
Supplementary files format and content: vst_matrix.csv

molecule: polyA RNA

organism: Mus musculus

source_name: gastrocnemius muscle

extract_protocol:
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step. RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico or RNA ScreenTape assay (Agilent Technologies).
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction.  Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions. ibraries were sequenced on an Illumina NovaSeq 6000 using the S4 Reagent Kit. Libraries were sequenced 100 bp paired-end to a targeted read depth of 30 million read pairs.

treatment_protocol: Three inbred mouse strains, NZO/HlLTJ, CAST/EiJ, and C57BL/6J, were placed on control or high fat, high sugar diet starting at six weeks of age. Tissue was collected at fifteen weeks of age.

tag: tissue

value: gastrocnemius muscle

tag: diet

value: 44% fat + fiber

tag: strain

tag: Sex

value: Male

value: WT

tag: treatment


title: gastrocnemius muscle-44% fat+fiber-C57BL/6J-F (ORSAM9016)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM9016

value: Female


title: Day41PC_DonorC

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: The University of York

data_processing:
The fastq files were assessed for initial quality using FastQC, trimmed for adapter sequences using TrimGalore  and aligned to GRCh38.p12 (Gencode release 28) with STAR aligner using twopassMode.
Transcript abundance was estimated using RSEM and imported into R using txImport and then processed using DESeq2, generating VST transformed data.
Assembly: GRCh38.p12 (Gencode release 28)
Supplementary files format and content: tab-delimited text files with DESeq2 VST log2 values for each Sample

source_name: Peripheral blood

extract_protocol: RNA was extracted with TRIzol (Invitrogen) then subjected to DNAseI treatment (DNAfree, Ambion).

value: Peripheral blood

value: CD138+ Plasma cells sorted on CD138 and 7-AAD, generated in the upper compartment of a transwell system after 28 days of IL-6, IFN-α and supplemented media, with M2-10B4 in the lower compartment.


title: gastrocnemius muscle-44% fat+fiber-NZO/HlLtJ-M (ORSAM8202)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8202

value: NZO/HlLtJ


title: MR49F_siDECR2_2


title: Day41PC_DonorB


title: DHMC08

city: Lebanon

first: Min Kyung

last: Lee

state: NH

address: 1 Medical Center Dr

institute: Dartmouth College

data_processing:
Quality control for raw single-end RNA-seq data was checked using FastQC v0.11.8
Reads were trimmed of polyA sequences and low-quality bases using Cutadapt v2.4
Reads were aligned to the human pre-mRNA genome GRCh38 with STAR v2.7.7a
Counts per gene were estimated using the htseq-count function in the HTseq software v0.11.2
Assembly: GRCh38
Supplementary files format and content: Count files in .csv file

molecule: nuclear RNA

source_name: brain tumor

extract_protocol:
RNA was isolated following the RNeasy Plus kit
ibraries for bulk RNA-seq were prepared following the Takara Pico v3 low-input protocol

value: brain tumor

tag: tumor type

value: Schwannoma

value: M

tag: age at_diagnosis

value: untreated


title: DHMC11

value: Glioblastoma


title: MR49F_siDECR2_4


title: MR49F_siDECR2_3


title: DHMC14

value: Embryonal


title: Human Embryonic Kidney cells 293

city: Fukuoka

first: Ikumi

last: Imamura

address: 2-3-1 Matsukadai Higashi-ku

department: Life sience

country: Japan

institute: Kyushu sangyo university

data_processing:
The libraries was subjected to sequencing using the DNBSEQ-G400 (MGISEQ-2000RS, MGI Tech) instrument.
The obtained reads were aligned using splitBarcode (https://github.com/MGI-tech-bioinformatics/splitBarcode).
The read data were downsized to 20 M read pairs using seqkit v0.13.0.
The adopter sequences were cleaned with cutadapt ver.2.10, the read data were mapped with HISAT v2.2.1.
The value of FPKMs (reads per kilobase of transcript per million reads mapped) of each gene was estimated with Cuffdiff v2.2.1.
The ratios of the FPKM values for each cell line to those for HEK293 cells were calculated, and then, the ratios of each genes were log2-transformed.
Assembly: hg19
Supplementary files format and content: FPKMs
Supplementary files format and content: The ratios of the FPKM values for each cell line to those for HEK293 cells were calculated, and then, the ratios of each genes were log2-transformed.

growth_protocol: HEK293 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted using RNeasy mini kit (QIAGEN).
The DNA libraries for sequencing were constructed with Truseq Stranded mRNA Library Prep (Illumina,  San Diego, CA) and MGIEasy Universal Library Conversion Kit (MGI Tech, Shenzhen, PRC).

treatment_protocol: genome editing to introduce the vector into cells, 1.0 × 10^6 cells were pre-seeded and cultured at 37°C for 24 hr, and after the vector (1.2 μg) was introduced into the cells using a Lipofectamine 3000 Transfection kit (Thermo Fisher Scientific), the cells were cultured for 3 days.

value: Human Embryonic Kidney cells

value: control


title: DHMC07

value: Glioneuronal/Neuronal


title: DHMC06

value: Ependymoma

value: F


title: MR49F_siDECR2_1

value: prostate cancer cell line

value: DECR2 knockdown


title: MR49F_siControl_6

value: WT


title: 147 Whole Genome Bisulfite Sequencing 30X

city: Seattle

first: Brian

last: Hanratty

state: WA

address: 1100 Fairview Avenue

department: Division of Human Biology

institute: Fred Hutchinson Cancer Cancer

library_source: genomic

data_processing:
Reads were trimmed with Trim Galore 0.6.6
Trimmed reads were aligned to UCSC hg19 and methylation at each base called with Bismark 0.23.0
Methylation call files were subsetted to bedGraph format and then converted to bigWig with UCSC bedGraphToBigWig
Assembly: UCSC hg19

molecule: genomic DNA

source_name: Patient derived xenograft

growth_protocol: subcutaneous patient derived xenograft as detailed in PMID: 28156002

extract_protocol:
As detailed in PMID: 34312180, followed by bisulfite conversion
TruSeq

value: Patient derived xenograft

value: Bisulfite conversion


title: Day20PC_DonorC

value: Peripheral blood

value: CD138+ Plasma cells sorted on CD138 and 7-AAD, generated in the upper compartment of a transwell system after 7 days of IL-6, IFN-α and supplemented media, with M2-10B4 in the lower compartment.


title: gastrocnemius muscle-10% fat+fiber-NZO/HlLtJ-F (ORSAM8200)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8200

value: gastrocnemius muscle

value: 10% fat + fiber

value: NZO/HlLtJ

value: Female


title: DHMC05

value: brain tumor

value: M

value: untreated


title: Day41PC_DonorA

value: CD138+ Plasma cells sorted on CD138 and 7-AAD, generated in the upper compartment of a transwell system after 28 days of IL-6, IFN-α and supplemented media, with M2-10B4 in the lower compartment.


title: DHMC09

value: Glioneuronal/Neuronal


title: gastrocnemius muscle-10% fat+fiber-NZO/HlLtJ-F (ORSAM8199)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8199


title: DHMC04

value: Ependymoma

value: F


title: gastrocnemius muscle-10% fat+fiber-CAST/EiJ-M (ORSAM8198)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8198

value: CAST/EiJ

value: Male


title: Day20PC_DonorA


title: gastrocnemius muscle-44% fat+fiber-NZO/HlLtJ-M (ORSAM8201)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8201

value: 44% fat + fiber

value: WT


title: DHMC03

value: Astrocytoma


title: MR49F_siControl_5

value: prostate cancer cell line


title: Day13PC_DonorC

value: Peripheral blood

value: CD138+ Plasma cells sorted on CD138 and 7-AAD, generated in the upper compartment of a transwell system after 7 days of IL-6, IL-21, IFN-α and supplemented media, with M2-10B4 in the lower


title: MR49F_siControl_3


title: gastrocnemius muscle-44% fat+fiber-CAST/EiJ-M (ORSAM8197)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8197

value: gastrocnemius muscle


title: MR49F_siControl_4


title: gastrocnemius muscle-44% fat+fiber-CAST/EiJ-M (ORSAM8196)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8196


title: gastrocnemius muscle-10% fat+fiber-CAST/EiJ-F (ORSAM8195)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8195

value: 10% fat + fiber

value: Female


title: DHMC02

value: brain tumor

value: M


title: MR49F_siControl_1


title: Day13PC_DonorB


title: Day13PC_DonorA


title: MR49F_siControl_2


title: DHMC01

value: untreated


title: gastrocnemius muscle-44% fat+fiber-CAST/EiJ-F (ORSAM8194)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8194


title: Day20PC_DonorB

value: CD138+ Plasma cells sorted on CD138 and 7-AAD, generated in the upper compartment of a transwell system after 7 days of IL-6, IFN-α and supplemented media, with M2-10B4 in the lower compartment.


title: DIPG-XIII_ATACseq

city: Dallas

first: Lei

last: Guo

state: TX

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

data_processing:
Adaptors were trimmed using Trim Galore (v0.6.4). The trimmed reads were then aligned to human genome (hg38) using Bottie2 (v2.4.2). The SAM files were sorted and converted into BAM files using Samtools (v0.1.19). Peaks were called using Homer (v4.4) with the "findPeaks" command and parameter settings of "-style dnase -fdr 0.001".
Assembly: hg38
Supplementary files format and content: peaks

source_name: parental cell line

growth_protocol: Cell lines were cultured at 37°C, in 5% CO2, in TSM media with growth factors as described previously (Grasso CS et al, Nat Med. 2015 Jul;21(7):827. PMID: 26151328).

extract_protocol: following the protocol from Corces MR et al, Nat Methods. 2017 Oct;14(10):959-962.

treatment_protocol: Cells were treated with DMSO control and 5 uM, 3.0 uM, and 3.5 uM, rough IC50 values of ONC201 for 72 hours, respectively.

value: DIPG cell line

value: brain tumor cell line

value: Diffuse intrinsic pontine glioma (DIPG)


title: Day6PB_DonorC

value: Plasmablasts generated after 3 days of IL-2, IL-21 in supplemented media.


title: DIPG-VII_ATACseq


title: DIPG-IV_ATACseq


title: Day6PB_DonorA


title: gastrocnemius muscle-44% fat+fiber-C57BL/6J-M (ORSAM8191)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8191

value: 44% fat + fiber

value: Male


title: Day3PB_DonorC

value: Activated Total B cells following 3 days of F(ab')2, IL-2, IL-21 and CD40L (feeder layer).


title: gastrocnemius muscle-10% fat+fiber-C57BL/6J-F (ORSAM8190)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8190

value: WT


title: V16D_siDECR2_4

value: prostate cancer cell line

value: DECR2 knockdown


title: gastrocnemius muscle-10% fat+fiber-C57BL/6J-M (ORSAM8192)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8192

value: gastrocnemius muscle


title: gastrocnemius muscle-10% fat+fiber-C57BL/6J-F (ORSAM8189)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8189

value: 10% fat + fiber


title: V16D_siDECR2_3


title: Day3PB_DonorB

value: Peripheral blood


title: MUT_L_rep1

city: Saint Louis

first: Sebla

middle: Bulent

last: Kutluay

state: MO

address: 660 S. Euclid Avenue, Campus Box 8230

institute: Washington University School of Medicine

data_processing:
CLIP-seq reads were trimmed off of the adapters and collapsed using BBDuk
Resulting reads were mapped to the viral and human genomes using Bowtie
PARalyzer and custom scripts were used to generate annotated clusters (i.e. binding sites).
Assembly: hg19
Supplementary files format and content: tab-delimited files showing annotation of clusters (i.e. binding sites).
Library strategy: CLIP-seq

source_name: HEK293T cells

growth_protocol: Cells transfected with myc-tagged hnRNPA1 plasmids were utilized for CLIP-seq.

extract_protocol:
UV crosslinked cells were lysed in detergent containing buffers and  hnRNPA1-RNA complexes were immunoprecipitated from these lysates.RNA complexes were isolated from monomeric hnRNPA1 (denoted_L) or dimeric (denoted _U) complexes.
Libraries were constructed based on previously published methodologies as explained before (Kutluay et al,m 2014, Cell). 3' barcoded adapters include, barcode underlined, "NNTGACTGTGGAATTCTCGGGTGCCAAGG" and 5' common adapter "GTTCAGAGTTCTACAGTCCGACGATC".

treatment_protocol: Prior to isolation, cells were treated with 4-thiouridine to enhance UV crosslinking.

value: HEK293T cells

value: Human embryonic kidney cell line

tag: antibody

value: rabbit polyclonal anti-myc

value: MUT

tag: group

value: monomeric hnRNPA1 complexes


title: V16D_siDECR2_2


title: V16D_siDECR2_1


title: Day3PB_DonorA


title: SK-OV-3 cells, doxorubicin 300 nM treatment, 24 hours, rep1

city: Shanghai

first: Baoyuan

last: Zhang

state: Please Select

address: No.197,Rui Jin Er Road,Shanghai 200025 China

country: China

institute: Ruijin hospital

data_processing:
Tophat, cufflinks, and cuffdiff
Sequence reads were trimmed for adaptor sequence/low-quality sequence and mapped to hg38 using Tophat
Read count extraction and normalization were performed using cufflinks and cuffdiff package
Assembly: hg38
Supplementary files format and content: Excel files include FPKM values for each Sample

source_name: ovarian

extract_protocol:
Transcriptome profiling was performed to determine the mechanism of the observed clinical antitumor effects. In brief, the SK-OV-3 cells were treated with DMSO, 300 nM doxorubicin, 3 μM IN10018, and a combination of IN10018 and doxorubicin for 24 hours. The total mRNA was extracted for the RNA sequencing.
RNA was harvested using RNA iso plus reagent (Takara). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra Directional RNA Library Prep kit for Illumina (New England Biolabs) following manufacturer's protocols.

value: ovarian

value: cancer cells

value: diploid

value: doxorubicin 300 nM


title: gastrocnemius muscle-44% fat+fiber-C57BL/6J-F (ORSAM8188)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8188

value: 44% fat + fiber

value: Female


title: WT_U_rep2

value: WT

value: dimeric hnRNPA1 complexes


title: Day6PB_DonorB

value: Plasmablasts generated after 3 days of IL-2, IL-21 in supplemented media.


title: V16D_siDECR2_6

value: prostate cancer cell line

value: DECR2 knockdown


title: V16D_siDECR2_5


title: WT_U_rep1


title: V16D_siControl_6


title: MUT_L_rep2


title: Day0BC_DonorC

value: Peripheral blood

value: MACS purified (negative selection) Total B cells from healthy donors.


title: WT_L_rep2

value: HEK293T cells

value: Human embryonic kidney cell line


title: gastrocnemius muscle-44% fat+fiber-C57BL/6J-F (ORSAM8187)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8187

value: gastrocnemius muscle


title: V16D_siControl_5


title: Day0BC_DonorB


title: gastrocnemius muscle-44% fat+fiber-CAST/EiJ-F (ORSAM8193)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8193

value: CAST/EiJ


title: V16D_siControl_4


title: Day0BC_DonorA


title: gastrocnemius muscle-44% fat+fiber-NZO/HlLtJ-M (ORSAM7780)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7780

value: NZO/HlLtJ

value: Male


title: gastrocnemius muscle-10% fat+fiber-NZO/HlLtJ-M (ORSAM7778)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7778

value: 10% fat + fiber


title: gastrocnemius muscle-44% fat+fiber-NZO/HlLtJ-M (ORSAM7779)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7779


title: V16D_siControl_3


title: V16D_siControl_2


title: AE-IPF_5

city: Shenyang,

first: Jia

middle: Ran

last: Wang

state: Liaoning

address: No. 79 Chongshan East Road, Huanggu District,

institute: Liaoning University of Traditional Chinese Medicine

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: miRBase 22.0
Supplementary files format and content: excel,expression profiles

source_name: whole blood

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: whole blood

tag: disease state

value: Acute exacerbation of idiopathic pulmonary fibrosis

value: male

tag: age


title: AE-IPF_4

value: female


title: pDC_DON13, R848, 336sup

city: Verona

first: Marzia

last: Rossato

state: Italy

address: Strada Le Grazie,15

department: Department of Biotechnology

country: Italy

institute: University of Verona

data_processing:
Reads were clipped from adapter sequences using Scythe software and low-quality ends (Q score < 20 on a 10-nt window) were trimmed using Sickle.
RNA-seq reads were aligned with HISAT2  to the GRCh38 human reference genome.
Gene counting was performed using GenomicAligments function summarizeOverlaps.
Gene expression analysis was  executed with the DESeq2 package.
Assembly: GRCh38
Supplementary files format and content: Tab delimited text file including RPKM counts for all samples

source_name: Plasmacytoid dendritic cells

extract_protocol: Total RNA isolated by using AllPrep DNA/RNA/miRNA kit following manufacturer’s instructions.

value: Plasmacytoid dendritic cells

value: R848 for 2 hr


title: pDC_DON13, R848, 146sup


title: pDC_DON13, R848, RPMI


title: V16D_siControl_1

value: prostate cancer cell line

value: WT


title: gastrocnemius muscle-10% fat+fiber-NZO/HlLtJ-M (ORSAM7777)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7777


title: gastrocnemius muscle-44% fat+fiber-NZO/HlLtJ-F (ORSAM7776)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7776

value: 44% fat + fiber

value: Female


title: AE-IPF_3


title: gastrocnemius muscle-44% fat+fiber-NZO/HlLtJ-F (ORSAM7775)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7775


title: pDC_DON13, CTRL, 336sup

value: untreated


title: Malignant Pleural Mesothelioma cell line 57

type: genomic

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

country: France

institute: Centre de Recherche des Cordeliers

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_57

hyb_protocol: Standard Illumina protocol.

scan_protocol: Standard Illumina protocol.

data_processing:
Standard Illumina protocol using BeadStudio software. All samples have a call rate higher than 0.95 except MPM_49 with a call rate of 0.75.
Genotype: AA,AB,BB

label: C-Bio and A-DNP

source_name: Malignant Pleural Mesothelioma

label_protocol: Standard Illumina protocol.

growth_protocol: Malignant Pleural Mesothelioma cell lines growth protocol is described in Quetel et al, Molecular oncology, 2020, doi:10.1002/1878-0261.12651.

extract_protocol: Genomic DNA was extracted using a standard isopropanol precipitation procedure.

tag: gender

tag: histology

value: Epithelioid


title: AE-IPF_2


title: gastrocnemius muscle-10% fat+fiber-NZO/HlLtJ-F (ORSAM7774)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7774

value: gastrocnemius muscle


title: WT_L_rep1

value: HEK293T cells

value: Human embryonic kidney cell line

value: rabbit polyclonal anti-myc

value: monomeric hnRNPA1 complexes


title: AE-IPF_1

value: whole blood


title: S-IPF_4

value: Stable IPF


title: S-IPF_3

value: male


title: pDC_DON13, CTRL, RPMI


title: S-IPF_5


title: Malignant Pleural Mesothelioma cell line 37

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_37

value: Male


title: Malignant Pleural Mesothelioma cell line 28

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_28

value: Sarcomatoid


title: gastrocnemius muscle-44% fat+fiber-CAST/EiJ-M (ORSAM7772)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7772

value: CAST/EiJ


title: pDC_DON12, CTRL, 336sup

value: Plasmacytoid dendritic cells


title: Malignant Pleural Mesothelioma cell line 30

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_30


title: gastrocnemius muscle-44% fat+fiber-CAST/EiJ-F (ORSAM7770)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7770

value: WT


title: Malignant Pleural Mesothelioma cell line 27

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_27

value: Biphasic


title: pDC_DON12, CTRL, 146sup


title: S-IPF_2

value: female


title: gastrocnemius muscle-10% fat+fiber-CAST/EiJ-F (ORSAM7769)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7769

value: 10% fat + fiber

value: Female


title: S-IPF_1


title: GM1-Neuron2mo-WT

city: Madison

first: Xinyu

last: Zhao

state: Wisconsin

address: 1500 HIghland Ave, Wiasman Center North Tower T513

institute: University of Wisconsin Madison

description: RNA isolated by CLIP

data_processing:
The demultiplexed FASTQ files were first quality filtered using fastq_quality_filter of FASTX Toolkit (v0.0.14) with parameters “-q25 -p80”. Adapter sequences were then removed from reads using cutadapt (v1.7.1) with parameters “-n 3 -e 0.1 -O 5 -q 6 -m 20 -a AGATCGGAAGAGCACACG”. PCR duplicates were removed using fastx_collapser of FASTX Toolkit. Finally 5’ adapter sequences were trimmed from reads using fastx_trimmer of FASTX Toolkit with parameters “-f 13 -l 94”.
Processed reads were mapped to the genome indices (generated by STAR from sequence file, GRCh38.primary_assembly.genome.fa, and annotation file, gencode.v27.chr_patch_hapl_scaff.basic.annotation.gtf, from GENCODE Release 27) using STAR (v2.5.3a) with parameters “STAR --runMode alignReads --runThreadN 8 --genomeLoad LoadAndKeep --genomeDir $genome --readFilesIn $file --outSAMunmapped None --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterMismatchNmax 2 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 -alignSJDBoverhangMin 1 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype SAM --quantMode GeneCounts --outFileNamePrefix $file_ --outSAMattributes All --outFilterType BySJout --outSAMattrRGline ID:foo --alignEndsType EndToEnd”.
Aligned bam files were analyzed using CLIPper (Van Nostrand et al. 2016). CLIPper pipeline was adapted from the ENCODE eCLIP-seq processing pipeline v2.0. The peaks with fold change > 2 and p values <0.05 were used to define CLIPper lists of FMR1 target genes
Assembly: Gencode GRCh38 primary assembly
Supplementary files format and content: bed files of CLIPper peaks

extract_protocol:
Neurons were crosslinked with 254-nm UV-C followed by cell lysis and partial digestion of RNAs. FMRP-bound RNAs were isolated by immunoprecipitation, dephosphorylated, and ligated to a dye-labeled 3′ adapter.
RNA samples were then resolved using SDS-PAGE and transferred to nitrocellulose membranes. FMRP-bound RNAs were visualized and size selected by cutting the membranes. Size-selected RNAs were purified by Proteinase K digestion and ethanol precipitation. The purified RNAs were converted to cDNAs followed by circularization of the cDNAs. cDNA libraries were constructed from the cDNAs by PCR amplification.

value: neuron

tag: clip antibody

value: FLAG


title: gastrocnemius muscle-44% fat+fiber-C57BL/6J-M (ORSAM7768)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7768

value: gastrocnemius muscle

value: 44% fat + fiber


title: Malignant Pleural Mesothelioma cell line 12

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_12

value: Epithelioid


title: pDC_DON12, CTRL, RPMI

value: untreated


title: pDC_DON11, R848, 336sup

value: R848 for 2 hr


title: GM1-Neuron2mo-SMI

description: RNA isolated by CLIP

tag: cell line

value: FMRP-FLAG


title: GM1-Neuron2mo-FLAG

description: RNA isolated by CLIP

tag: cell type


title: gastrocnemius muscle-10% fat+fiber-C57BL/6J-F (ORSAM7765)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7765

tag: genotype


title: Malignant Pleural Mesothelioma cell line 10

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_10

value: Male


title: pDC_DON11, R848, 146sup


title: pDC_DON11, R848, RPMI


title: Malignant Pleural Mesothelioma cell line 08

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_08

value: Sarcomatoid


title: Malignant Pleural Mesothelioma cell line 09

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_09


title: ovary-44% fat+fiber-NZO/HlLtJ-F (ORSAM9036)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM9036

source_name: ovary

tag: tissue

value: ovary

value: NZO/HlLtJ


title: pDC_DON11, CTRL, 146sup

value: Plasmacytoid dendritic cells


title: pDC_DON12, R848, RPMI


title: H13-Neuron2mo-SMI

description: RNA isolated by CLIP


title: Malignant Pleural Mesothelioma cell line 06

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_06


title: ovary-44% fat+fiber-NZO/HlLtJ-F (ORSAM9035)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM9035

tag: diet

value: WT


title: gastrocnemius muscle-44% fat+fiber-C57BL/6J-F (ORSAM7766)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7766

tag: strain


title: Malignant Pleural Mesothelioma cell line 67

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_67

value: Biphasic


title: pDC_DON12, R848, 336sup


title: H13-Neuron2mo-FLAG

description: RNA isolated by CLIP


title: pDC_DON11, CTRL, RPMI


title: H1-Neuron2mo-WT

description: RNA isolated by CLIP


title: H13-Neuron2mo-WT

description: RNA isolated by CLIP


title: Malignant Pleural Mesothelioma cell line 66

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_66


title: pDC_DON10, R848, 336sup


title: ovary-44% fat+fiber-CAST/EiJ-F (ORSAM9034)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM9034

value: CAST/EiJ

tag: Sex


title: H1-Neuron2mo-SMI

description: RNA isolated by CLIP


title: ovary-10% fat+fiber-CAST/EiJ-F (ORSAM9033)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM9033

value: 10% fat + fiber

value: Female

tag: treatment


title: pDC_DON10, R848, 146sup


title: Malignant Pleural Mesothelioma cell line 64

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_64


title: H1-Neuron2mo-FLAG

description: RNA isolated by CLIP

value: neuron

value: FLAG


title: ovary-10% fat+fiber-CAST/EiJ-F (ORSAM9032)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM9032


title: pDC_DON10, R848, RPMI


title: Malignant Pleural Mesothelioma cell line 60

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_60


title: ovary-44% fat+fiber-C57BL/6J-F (ORSAM9031)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM9031

value: 44% fat + fiber


title: pDC_DON10, CTRL, 336sup


title: ovary-10% fat+fiber-NZO/HlLtJ-F (ORSAM8211)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8211


title: CRIZO CCC-HEH-2 Cells 2

city: Hang Zhou

first: Zhifei

last: Xu

address: 866 Yuhangtang Road

institute: Zhejiang University

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.
Assembly: mm8
Supplementary files format and content: tab-delimited xls files include RPKM values for each sample.

source_name: CCC-HEH-2 Cells

extract_protocol:
Cell culture supernatant was removed and RNA was harvested using TRIzol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA-seq libraries were prepared using Illumina RNA-Seq Preparation Kit.

tag: agent

value: Crizotinib-treated

tag: time point

value: 12 hours after treatment


title: Malignant Pleural Mesothelioma cell line 53

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_53

value: Epithelioid


title: CRIZO CCC-HEH-2 Cells 1


title: Malignant Pleural Mesothelioma cell line 49

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_49


title: ovary-10% fat+fiber-NZO/HlLtJ-F (ORSAM8210)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8210


title: pDC_DON10, CTRL, RPMI

value: untreated


title: Malignant Pleural Mesothelioma cell line 14

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_14

value: Male


title: CRIZO CCC-HEH-2 Cells 3


title: Control CCC-HEH-2 Cells 3

value: Control


title: Malignant Pleural Mesothelioma cell line 45

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_45


title: Control CCC-HEH-2 Cells 2


title: liver-10% fat+fiber-NZO/HlLtJ-F (ORSAM7694)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7694

source_name: liver

value: liver


title: Input-LPS-plus-OTX015-2

city: Changsha

first: Nian

state: Hunan

address: No.110 Xiangya Road

institute: Central south university

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base has a quality score>30, using Trimmomatic v0.33, discarding reads left with <20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To creat ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformation in the bigwig file format.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. gappedPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, gappedpeak

growth_protocol: THP1 monocytes were maintained in RPMI 1640  supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes, After quenching the cell lysis, chromatin was sonicated using E220 focused-ultrasonicator.
ChIP-seq libraries were prepared using the KAPA HTP library,preparation kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA  was used as starting material for input and IP samples. Libraries was amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450 bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA kit.

treatment_protocol: lipopolysaccharide (100ng/ml) for 1h

tag: antibody

value: input

value: Human monocytes


title: pDC_DON10, CTRL, 146sup

value: Plasmacytoid dendritic cells


title: Malignant Pleural Mesothelioma cell line 40

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_40


title: Malignant Pleural Mesothelioma cell line 59

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_59


title: Malignant Pleural Mesothelioma cell line 50

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_50

value: Biphasic


title: pDC_DON13, CTRL, 146sup


title: Input-LPS-plus-OTX015-1

value: WT


title: gastrocnemius muscle-10% fat+fiber-CAST/EiJ-M (ORSAM7771)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7771

value: gastrocnemius muscle

value: 10% fat + fiber

value: CAST/EiJ


title: gastrocnemius muscle-10% fat+fiber-NZO/HlLtJ-F (ORSAM7773)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7773

value: NZO/HlLtJ

value: Female


title: ovary-44% fat+fiber-CAST/EiJ-F (ORSAM8208)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8208

value: ovary

value: 44% fat + fiber


title: ovary-10% fat+fiber-CAST/EiJ-F (ORSAM8209)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8209


title: ovary-44% fat+fiber-CAST/EiJ-F (ORSAM8207)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8207


title: Malignant Pleural Mesothelioma cell line 43

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_43

value: Epithelioid


title: gastrocnemius muscle-10% fat+fiber-C57BL/6J-M (ORSAM7767)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7767


title: Control CCC-HEH-2 Cells 1

value: 12 hours after treatment


title: pDC_DON12, R848, 146sup

value: R848 for 2 hr


title: Input-LPS--2

value: lipopolysaccharide


title: Malignant Pleural Mesothelioma cell line 41

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_41

value: Male


title: Malignant Pleural Mesothelioma cell line 35

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_35


title: ovary-10% fat+fiber-C57BL/6J-F (ORSAM8206)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8206


title: Input-LPS-1

value: input


title: MDA-MB-453_DHT, Rep6

city: ADELAIDE UNIVERSITY

first: Geraldine

last: Laven-Law

state: South Australia

address: Adelaide Health & Med Sci Bldg, Corner George St & North Terrace

institute: The University of Adelaide

data_processing:
Reads were trimmed using AdapterRemoval and subsequently aligneD to GRCh38 (Ensembl release 101) using STAR.
Gene feature counting was performed with featureCounts. Replicate counts for a given condition and replicate were then merged as a flow cell and lane variability was dwarded by genuine sample variability. Genes considered undetectable (< 10 counts per million) were removed, leaving an average of 13.6 and 13.3 million reads for MDA-MB-453 and MFM-223 cells, respectively. GC content and gene length bias was corrected using Conditional Quantile Normalisation. The MFM-223 dataset featured one orphaned Vehicle replicate, missing its matching DHT treatment counterpart. This replicate was removed from differential enrichment analysis.
Differential expression was performed using the Quasi-likelihood generalized linear model. Genes were considered differentially enriched using the criteria of a false discovery rate (FDR)-adjusted p-value of < 0.05. Differentially expressed genes were further analysed in R. The complete RMarkdown script is available at Github.com/DRMCRL/apocrine_signature_mdamb453
Assembly: GrCh38 (Ensembl Release 101)
Supplementary files format and content: CQN-normalised counts and differentially expressed genes

source_name: Breast cancer cell line

growth_protocol: MDA-MB-453 cells were grown in standard conditions (DMEM High Glucose + 10% FBS) for 72 h

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Kit according to manufacturer's instructions
Libraries were generated from 1 µg RNA using the TruSeq Total RNA HT Library Prep Kit
Total RNA-seq, Illumina HiSeq 2500 single-end 40 bp reads

treatment_protocol: MDA-MB-453 cells were treated for 6 h with either a vehicle (0.001% ethanol) or 10 nM DHT. Six independent replicates each representing consecutive passages of cells were generated per condition.

value: DHT

tag: replicate

value: Rep 6


title: MDA-MB-453_DHT, Rep5

value: Rep 5


title: Input-Con-2

value: Human monocytes

value: WT

value: PBS


title: Malignant Pleural Mesothelioma cell line 34

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_34


title: Input-Con-1


title: Malignant Pleural Mesothelioma cell line 33

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_33


title: ovary-10% fat+fiber-C57BL/6J-F (ORSAM8205)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8205

value: 10% fat + fiber


title: ovary-44% fat+fiber-C57BL/6J-F (ORSAM8204)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8204


title: MDA-MB-453_DHT, Rep3

value: Rep 3


title: Malignant Pleural Mesothelioma cell line 31

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_31

value: Female


title: Malignant Pleural Mesothelioma cell line 32

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_32


title: ChIP-LPS--2


title: ovary-44% fat+fiber-C57BL/6J-F (ORSAM8203)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8203

value: ovary


title: MDA-MB-453_DHT, Rep2

value: Rep 2


title: ovary-44% fat+fiber-NZO/HlLtJ-F (ORSAM7612)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7612

value: 44% fat + fiber

value: NZO/HlLtJ


title: ovary-44% fat+fiber-NZO/HlLtJ-F (ORSAM7611)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7611


title: ChIP-LPS-plus-OTX015-2


title: Malignant Pleural Mesothelioma cell line 29

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_29

value: Epithelioid


title: MDA-MB-453_DHT, Rep1

value: Rep 1


title: Malignant Pleural Mesothelioma cell line 25

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_25

value: Male


title: ovary-10% fat+fiber-NZO/HlLtJ-F (ORSAM7610)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7610


title: ChIP-LPS-plus-OTX015-1


title: MDA-MB-453_Vehicle, Rep6

value: Vehicle


title: ChIP-LPS-1

value: lipopolysaccharide


title: MDA-MB-453_Vehicle, Rep4

value: Rep 4


title: ovary-44% fat+fiber-CAST/EiJ-F (ORSAM7608)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7608

value: CAST/EiJ


title: ChIP-Con-1

value: Human monocytes


title: MDA-MB-453_Vehicle, Rep3


title: MDA-MB-453_Vehicle, Rep5

value: Rep 5


title: ChIP-IgG-LPS-plus-OTX015

value: WT


title: ovary-10% fat+fiber-NZO/HlLtJ-F (ORSAM7609)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7609

value: 10% fat + fiber


title: ovary-10% fat+fiber-CAST/EiJ-F (ORSAM7607)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7607


title: Malignant Pleural Mesothelioma cell line 22

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_22


title: Malignant Pleural Mesothelioma cell line 24

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_24

value: Biphasic


title: ChIP-IgG-Con

value: PBS


title: ovary-10% fat+fiber-C57BL/6J-F (ORSAM7605)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7605

value: ovary

value: Female


title: MDA-MB-453_DHT, Rep4

value: DHT


title: MDA-MB-453_Vehicle, Rep1


title: Malignant Pleural Mesothelioma cell line 23

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_23

value: Sarcomatoid Desmoplastic


title: Malignant Pleural Mesothelioma cell line 21

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_21

value: Epithelioid


title: ovary-44% fat+fiber-C57BL/6J-F (ORSAM7606)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7606

value: 44% fat + fiber


title: Malignant Pleural Mesothelioma cell line 18

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_18

value: Male


title: DHMC35

value: brain tumor

tag: tumor type

value: Astrocytoma

value: M

tag: age at_diagnosis

value: untreated


title: liver-10% fat+fiber-CAST/EiJ-F (ORSAM7689)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7689

value: liver

value: CAST/EiJ


title: Malignant Pleural Mesothelioma cell line 19

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_19

tag: gender

tag: age


title: ChIP-Con-2

value: Human monocytes

value: WT


title: MDA-MB-453_Vehicle, Rep2

value: Vehicle

value: Rep 2


title: 661_963121-35

first: Naresh

last: Doni Jayavelu

address: 1201 9th AVE

department: Systems Immunology/Bioinformatics

institute: Benaroya Research Institute at Virginia Mason

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2) was used to remove any remaining adapter sequence.
Reads were aligned by STAR v2.4.2a to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2), and HTSeq-count (v0.4.1).
Assembly: GRCh38
Supplementary files format and content: raw_counts_ITN_GRASS_PBMC_samples.csv is a csv file. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library.

source_name: PBMC

extract_protocol:
RNA was extracted from TRIzol following the manufacturer’s protocol (Invitrogen)
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.

value: PBMC

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions

tag: median cv_coverage

tag: participant id

tag: visit number

value: SCIT

tag: sts timepoint

value: PostChallenge


title: 659_970803-35

tag: tissue

tag: Sex

value: Female


title: 660_963121-31

tag: treatment

value: PreChallenge


title: PC3DR-RU486_DOC1

city: Mainz

first: Maximilian

middle: Peter

last: Brandt

state: Rheinland Palatine

address: Langenbeckstrasse 1

department: Urology and Pediatric Urology

country: Germany

institute: University Medical Center Mainz

data_processing:
NextSeq 500 according to manual instructions, software: Nextseq System Suite v2.2.0
Sequence reads (fastq files) were trimmed for adaptor sequence removal and quality controlled using Trimmomatic (0.36) and reads were trimmed at a length of 148 bases. Sequencing quality was checked using FastQC (v0.11.8). Reads were mapped using STAR splice-aware aligner (v2.6.0c) on human genome version hg38 (UCSC) with RefGene annotation and index with 200 bases splice junction overhang. HTSeq was used to quantify gene raw counts. Analysis of differentially expressed genes and normalization (regularized log expression) was performed using the R package DESeq2.
Supplementary files format and content: hg19
Supplementary files format and content: Processed data sheet_Brandt.xlsx

source_name: PCa cell lines

growth_protocol: All cell lines were cultured with RPMI 1640 medium supplemented with 10% fetal calf serum

extract_protocol: RNA was isolated from cell lines with the EXTRACTME TOTAL RNA KIT

treatment_protocol: Treatment was performed with and without docetaxel 12.5 nM for DMSO (vehicle), RU-486 3 µM and 10 µM

tag: cell line

tag: cell type

value: PCa cell line from bone metastasis


title: metanephros-44% fat+fiber-NZO/HlLtJ-F (ORSAM8982)

first: Gary

address: 600 Main St

institute: The Jackson Laboratory

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8982

data_processing:
raw counts quantified by EMASE and processed by /RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script and gathering_GBRS_total_counts_batch2.R.
counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation).
Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/Processing_normalization.R and Processing_normalization_batch2.R scripts.
gene annotation file ENSEMBL version 84
Assembly: GRCm38
Supplementary files format and content: counts_matrix.csv
Supplementary files format and content: mrna_annots.csv
Supplementary files format and content: vst_matrix.csv

source_name: metanephros

extract_protocol:
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step. RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico or RNA ScreenTape assay (Agilent Technologies).
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction.  Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions. ibraries were sequenced on an Illumina NovaSeq 6000 using the S4 Reagent Kit. Libraries were sequenced 100 bp paired-end to a targeted read depth of 30 million read pairs.

value: metanephros

tag: diet

value: 44% fat + fiber

tag: strain

value: NZO/HlLtJ

tag: genotype


title: PC3DR-RU486_DOC2


title: metanephros-10% fat+fiber-NZO/HlLtJ-M (ORSAM8983)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8983

value: 10% fat + fiber

value: Male


title: 658_966741-31


title: Malignant Pleural Mesothelioma cell line 16

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_16

tag: gender

tag: histology

value: Epithelioid


title: Malignant Pleural Mesothelioma cell line 17

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_17

tag: age


title: PC3DR-RU4863


title: metanephros-10% fat+fiber-NZO/HlLtJ-M (ORSAM8984)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8984


title: Malignant Pleural Mesothelioma cell line 15

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_15


title: PC3DR-RU486_DOC3


title: metanephros-44% fat+fiber-NZO/HlLtJ-F (ORSAM8981)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8981


title: 656_959053-35

tag: fastq total_reads

tag: percent aligned


title: PC3DR-RU4861


title: PC3DR-RU4862


title: metanephros-10% fat+fiber-CAST/EiJ-M (ORSAM8979)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8979

value: CAST/EiJ


title: PC3DR-DOC3

value: DOC


title: 657_970803-31

tag: aligned counts_in_millions

tag: median cv_coverage


title: metanephros-44% fat+fiber-CAST/EiJ-F (ORSAM8978)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8978

value: WT


title: metanephros-10% fat+fiber-CAST/EiJ-F (ORSAM8977)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8977


title: Malignant Pleural Mesothelioma cell line 05

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_05


title: PC3DR-DOC2


title: Malignant Pleural Mesothelioma cell line 11

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_11


title: metanephros-44% fat+fiber-CAST/EiJ-M (ORSAM8980)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8980


title: Malignant Pleural Mesothelioma cell line 07

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_07


title: 654_959053-31

tag: participant id

tag: visit number


title: 653_958688-35

tag: tissue

tag: sts timepoint


title: 655_966741-35

tag: Sex

tag: treatment


title: PC3DR-DMSO2

tag: cell line

tag: cell type

value: DMSO


title: metanephros-44% fat+fiber-C57BL/6J-M (ORSAM8975)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8975

tag: diet

tag: strain


title: metanephros-44% fat+fiber-C57BL/6J-M (ORSAM8974)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8974

tag: genotype


title: PC3DR-DMSO1


title: Malignant Pleural Mesothelioma cell line 02

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_02

tag: gender

tag: histology


title: Malignant Pleural Mesothelioma cell line 01

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_01

tag: age


title: DU145DR-RU486-DOC3

value: PCa cell line from central nervous system metastasis


title: 651_966743-35

value: PBMC

tag: fastq total_reads

tag: percent aligned


title: metanephros-10% fat+fiber-C57BL/6J-M (ORSAM8972)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8972


title: 649_963084-31

tag: aligned counts_in_millions

tag: median cv_coverage

value: SCIT


title: metanephros-10% fat+fiber-CAST/EiJ-F (ORSAM8976)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8976


title: 646_958688-31

tag: participant id

tag: visit number


title: Breaker + 7day stage of slnor WT rep3

city: Shenzhen

first: yujing

last: lin

address: No. 1088 Xueyuan Avenue, Nanshan District, Shenzhen City, Guangdong Province

institute: Southern University of Science and Technology

data_processing:
Prior to assembly, the low quality reads (1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
The cleaned reads were mapped to the reference genome SL4.0 (ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG4.0_release) using HISAT package (Kim et al., 2015).
UMI-tools ( Smith et al., 2017) was used for removing sequence-dependent bias and amplification noise.
The mapped reads of each sample were assembled using StringTie (Pertea et al., 2015).
All transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts.
StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform   expression level for mRNAs by calculating FPKM.
The differentially expressed mRNAs and genes were selected with log2   (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – edgeR (M.D.Robinson et al., 2010).
Genome_build: SL4.0
Supplementary_files_format_and_content: counts files

organism: Solanum lycopersicum

source_name: Breaker + 7day stage of slnor WT

growth_protocol: Wild type tomato (Solanum lycopersicum) Ailsa Craig (AC), NAC-NOR CRISPR mutant (slnor)  plants (AC background) were grown in a condition-controlled greenhouse (16 h:8 h, 25 ℃:20 ℃, light:dark cycle).

extract_protocol:
Total RNA isolation was performed according to a previous published protocol (Gao et al., 2020).
Total RNA samples were sent to LC-Bio Technologies (Hangzhou) CO., LTD. (Hangzhou, China) for library construction and sequencing.

tag: Stage

value: B7 (Breaker + 7day stage)

tag: tissue

value: Fruits


title: DU145DR-RU486-DOC1

tag: treatment


title: DU145DR-RU4863

tag: cell line


title: Breaker + 7day stage of slnor mutant rep2

source_name: Breaker + 7day stage of slnor mutant

value: slnor


title: Breaker + 7day stage of slnor WT rep2


title: DU145DR-RU4862

tag: cell type


title: Breaker + 7day stage of slnor mutant rep1


title: Malignant Pleural Mesothelioma cell line 04

description:
Genomic DNA extracted from Malignant Pleural Mesothelioma cell line was genotyped using  HumanOmniExpress-24 v1.0 BeadChip (Illumina).
MPM_04

value: Biphasic


title: PC3DR-DOC1

value: PCa cell line from bone metastasis


title: 650_963084-35

tag: Sex

tag: sts timepoint

value: PostChallenge


title: metanephros-10% fat+fiber-C57BL/6J-M (ORSAM8973)

city: Bar Harbor

last: Churchill

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8973

value: metanephros

tag: diet

tag: strain

tag: genotype


title: 644_957465-35

tag: age


title: metanephros-44% fat+fiber-NZO/HlLtJ-M (ORSAM8138)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8138

value: 44% fat + fiber

value: NZO/HlLtJ


title: metanephros-44% fat+fiber-NZO/HlLtJ-M (ORSAM8137)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8137

value: Male


title: DU145DR-RU486-DOC2


title: 648_970849-35

tag: fastq total_reads


title: PC3DR-DMSO3


title: Breaker stage of slnor WT rep2

source_name: Breaker stage of slnor WT

value: B (Breaker stage)


title: Breaker + 7day stage of slnor WT rep1


title: 645_957465-31

tag: percent aligned

value: PreChallenge


title: 652_966743-31

tag: aligned counts_in_millions


title: Breaker + 7day stage of slnor mutant rep3


title: metanephros-44% fat+fiber-C57BL/6J-F (ORSAM8971)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8971

value: Female

value: WT


title: DU145DR-RU4861

value: PCa cell line from central nervous system metastasis


title: DU145DR-DOC3

value: DOC


title: metanephros-10% fat+fiber-C57BL/6J-F (ORSAM8970)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8970

value: 10% fat + fiber


title: 642_966724-31

value: PBMC

tag: median cv_coverage

value: SCIT


title: 639_963039-35

tag: participant id


title: Breaker stage of slnor mutant rep3

source_name: Breaker stage of slnor mutant

value: slnor

value: Fruits


title: metanephros-10% fat+fiber-NZO/HlLtJ-F (ORSAM8136)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8136


title: metanephros-44% fat+fiber-CAST/EiJ-M (ORSAM8133)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8133

value: CAST/EiJ


title: metanephros-10% fat+fiber-CAST/EiJ-M (ORSAM8134)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8134


title: 641_970786-35

tag: visit number

value: PostChallenge


title: Breaker stage of slnor WT rep3

tag: Stage


title: metanephros-10% fat+fiber-NZO/HlLtJ-F (ORSAM8135)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8135

tag: tissue

value: metanephros


title: DU145DR-DOC2

tag: treatment


title: Breaker stage of slnor mutant rep1


title: Breaker stage of slnor WT rep1


title: DU145DR-DOC1

tag: cell line


title: DU145DR-DMSO1

tag: cell type

value: DMSO


title: DU145DR-DMSO3


title: 638_963039-31

tag: Sex


title: Breaker stage of slnor mutant rep2


title: DU145DR-DMSO2


title: metanephros-44% fat+fiber-CAST/EiJ-F (ORSAM8130)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8130

value: 44% fat + fiber


title: 635_966732-31

value: Male

value: SLIT

tag: sts timepoint


title: WT_season2_4

data_processing:
To remove low-quality sequence and adapters via Trimmomatic (Bolger, Lohse, & Usadel, 2014) was used
The paired-end reads were mapped to the SL4.0 genome of Solanum lycopersicum by BSMAP with -r parameter to remove PCR duplications
To extract methylation ratio with methyratio.py script from BASMAP
DMRs and DMCs were identified using the R packages, methylKit (Akalin et al., 2012)
Genome_build: SL4.0
Supplementary_files_format_and_content: Bigwig files that represent the number of reads that contain methylated sites

source_name: Fruits

growth_protocol: Wild type tomato (Solanum lycopersicum) Ailsa Craig (AC), NAC-NOR CRISPR mutant (slnor), and SlDML2 CRIPSR mutant (sldml2) plants (AC background) were grown in a condition-controlled greenhouse (16 h:8 h, 25 ℃:20 ℃, light:dark cycle).

extract_protocol:
WGBS was performed according to a previous published protocol (Zhang et al., 2016).
DNA samples were sent to LC-Bio Technologies (Hangzhou) CO., LTD. (Hangzhou, China) for library construction and sequencing or sent to the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) for library construction and Illumina sequencing.

value: fruit

tag: cultivar

value: Ailsa Craig (AC)

tag: season

tag: replicate


title: RhS, epidermis, biol rep 4

city: Amsterdam

first: Jonas

last: Jäger

address: De Boelelaan 1108

country: Netherlands

institute: Amsterdam UMC

description:
epidermis of skin model without adipose layer
Sample_15

data_processing:
STAR aligner (Spliced Transcripts Alignment to a Reference) was used to align the reads
RSEQC Quality control package was used for aggregated quality control
DESeq2 v 1.34.0 was used for differential expression analysis
MULTIQC tool was used for aggregated quality control
Assembly: GRCh38.94
Supplementary files format and content: processed-counts includes .tsv files with a summary count table
Supplementary files format and content: sample_annotations is .xlsx file indicating sample annotations

source_name: RhS

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini Kit according to the manufacturers instructions
RNA libraries for RNA-seq were prepared by Lexogen using the Lexogen QuantSeq FWD Library Prep Kit

value: RhS


title: RhS, dermis, biol rep 4

description:
dermis of skin model without adipose layer
Sample_16


title: 637_959052-35

tag: age


title: metanephros-44% fat+fiber-CAST/EiJ-M (ORSAM8132)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8132

tag: diet

tag: strain

tag: genotype

value: WT


title: metanephros-10% fat+fiber-CAST/EiJ-F (ORSAM8131)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8131

value: Female


title: RhS, dermis, biol rep 3

description:
dermis of skin model without adipose layer
Sample_14


title: 631_963066-35

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions

tag: median cv_coverage


title: 633_970828-35

tag: tissue

tag: participant id

tag: visit number


title: sldml2_season2_1


title: sldml2_season2_2


title: 632_963066-31

tag: treatment

value: PreChallenge


title: metanephros-10% fat+fiber-C57BL/6J-M (ORSAM8128)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8128

value: 10% fat + fiber

tag: Sex


title: metanephros-44% fat+fiber-C57BL/6J-M (ORSAM8127)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8127


title: WT_season2_2


title: adipose-RhS, epidermis, biol rep 4

description:
epidermis of skin model with adipose layer
Sample_13

source_name: adipose-RhS

value: adipose-RhS


title: RhS, dermis, biol rep 2

description:
dermis of skin model without adipose layer
Sample_12


title: WT_season2_1


title: 634_970828-31

value: PBMC

tag: sts timepoint


title: 630_959052-31


title: 629_958503-31

value: Placebo


title: WT_season2_3

tag: cultivar


title: RhS, epidermis, biol rep 3

description:
epidermis of skin model without adipose layer
Sample_11


title: metanephros-44% fat+fiber-CAST/EiJ-F (ORSAM8129)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8129

value: CAST/EiJ


title: slnor_season2_2

value: slnor

tag: season


title: 628_966688-31


title: metanephros-10% fat+fiber-C57BL/6J-F (ORSAM8125)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8125

value: metanephros


title: metanephros-44% fat+fiber-C57BL/6J-F (ORSAM8124)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8124


title: 627_966688-35

value: PostChallenge


title: 202163550181_R02C01:BDB1P03058

city: Lebanon

first: Ji-Qing

last: Chen

state: New Hampshire

address: 1 Medical Center Drive, Williamson level 6

department: Epidemiology

institute: Dartmouth College

description:
IlluminaHumanMethylationEPIC
White blood cell

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina protocol

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

data_processing:
R studio
minfi Processed Average Beta

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

value: Blood

tag: gender

value: male

tag: muscle-invasive

value: no


title: metanephros-44% fat+fiber-NZO/HlLtJ-M (ORSAM7716)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7716

tag: diet

value: 44% fat + fiber

value: NZO/HlLtJ

value: Male


title: 202172220075_R04C01:BDB1P01044

tag: age


title: metanephros-44% fat+fiber-C57BL/6J-F (ORSAM8123)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8123

tag: strain

tag: genotype

value: WT


title: adipose-RhS, epidermis, biol rep 3

description:
epidermis of skin model with adipose layer
Sample_9


title: adipose-RhS, dermis, biol rep 4

description:
dermis and adipose layer of skin model with adipose layer
Sample_8


title: 626_970866-35

value: Female

tag: fastq total_reads

tag: percent aligned


title: 623_963076-35

tag: aligned counts_in_millions

tag: median cv_coverage


title: RhS, epidermis, biol rep 2

description:
epidermis of skin model without adipose layer
Sample_7

tag: tissue

value: RhS


title: metanephros-10% fat+fiber-C57BL/6J-F (ORSAM8126)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8126

value: 10% fat + fiber


title: 202163530080_R06C01:BDB1P02094


title: metanephros-44% fat+fiber-NZO/HlLtJ-M (ORSAM7715)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7715


title: adipose-RhS, dermis, biol rep 3

description:
dermis and adipose layer of skin model with adipose layer
Sample_6

value: adipose-RhS


title: 624_963076-31

value: PBMC

tag: participant id

tag: visit number

value: PreChallenge


title: metanephros-10% fat+fiber-NZO/HlLtJ-M (ORSAM7714)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7714

tag: Sex

tag: treatment


title: 202172220150_R06C01:BDB1P04022


title: 622_958503-35

value: Placebo

tag: sts timepoint


title: metanephros-10% fat+fiber-NZO/HlLtJ-M (ORSAM7713)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7713


title: 621_963105-31


title: 202163530099_R07C01:BDB1P03023


title: metanephros-44% fat+fiber-NZO/HlLtJ-F (ORSAM7712)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7712


title: adipose-RhS, dermis, biol rep 2

description:
dermis and adipose layer of skin model with adipose layer
Sample_4


title: 620_966711-31


title: RhS, dermis, biol rep 1

description:
dermis of skin model without adipose layer
Sample_10


title: slnor_season2_1

value: fruit

tag: cultivar

value: Ailsa Craig (AC)

value: slnor

tag: season

tag: replicate


title: RhS, epidermis, biol rep 1

description:
epidermis of skin model without adipose layer
Sample_3


title: metanephros-44% fat+fiber-NZO/HlLtJ-F (ORSAM7711)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7711

value: metanephros

tag: diet


title: 202172220109_R07C01:BDB1P02031

value: Blood

tag: gender

value: male

tag: age

tag: muscle-invasive


title: adipose-RhS, dermis, biol rep 1

description:
dermis and adipose layer of skin model with adipose layer
Sample_2


title: metanephros-10% fat+fiber-NZO/HlLtJ-F (ORSAM7710)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7710

tag: strain

tag: genotype


title: 202172220149_R07C01:BDB1P04015

description:
IlluminaHumanMethylationEPIC
White blood cell

value: no


title: adipose-RhS, epidermis, biol rep 1

description:
epidermis of skin model with adipose layer
Sample_1


title: 615_963105-35

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions

value: PostChallenge


title: 202163530089_R02C01:BDB1P03010

tag: tissue


title: metanephros-10% fat+fiber-CAST/EiJ-M (ORSAM7707)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7707

value: CAST/EiJ

value: Male


title: metanephros-10% fat+fiber-NZO/HlLtJ-F (ORSAM7709)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7709

value: NZO/HlLtJ

value: Female

value: WT


title: 202172220148_R08C01:BDB1P04008


title: metanephros-44% fat+fiber-CAST/EiJ-M (ORSAM7708)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7708

value: 44% fat + fiber


title: APC/KRAS/TP53 mutant colonoid RNA-seq sample  #3 [JV7]

city: Ithaca

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

department: Biomedical Science

institute: Cornell University

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017). APC Exon 8 indel,  KRAS G12V mutation, and TP53-/- mutation induced using CRISPR.
RNA_DESeq_normCounts.csv
AKP_DoxR1

data_processing:
Sequencing was aligned and quantiitated using miRquant2.0 (small RNAseq), aligned and quantified using STAR/Salmon (RNA-seq), or proseq2.0 (leChRO).
smRNA- and RNA-seq data was normalized using DESeq2. leChRO-seq data was rlog transformed followed by limma batch correction.
Assembly: leChRO-seq (hg38), RNA-seq (hg38), smRNA-seq (hg19)
Supplementary files format and content: DESeq2 normalized counts, Rlog normalized + limma batch corrected counts

source_name: APC/KRAS/TP53 mutant colonoid RNA-seq

extract_protocol:
Libraries were prepared according to the Qiagen HMR kit protocol
RNA was isolated using the the Norgen Total RNA Purification Kit according to the manufacturer's protocol.

value: Colon

tag: cell type

value: APC/KRAS/TP53 mutant colonoid


title: APC/KRAS/TP53 mutant colonoid RNA-seq sample  #2 [JV6]

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017). APC Exon 8 indel,  KRAS G12V mutation, and TP53-/- mutation induced using CRISPR.
RNA_DESeq_normCounts.csv
AKP_DoxRC2


title: 612_966664-35

city: Seattle

value: PBMC

tag: Sex

tag: median cv_coverage

tag: participant id

tag: visit number

value: SLIT


title: 202178770015_R03C01:BDB1P03083


title: APC/KRAS/TP53 mutant colonoid RNA-seq sample  #1 [JV5]

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017). APC Exon 8 indel,  KRAS G12V mutation, and TP53-/- mutation induced using CRISPR.
RNA_DESeq_normCounts.csv
AKP_DoxRC1


title: 202172220123_R03C01:BDB1P01075

value: female


title: metanephros-44% fat+fiber-CAST/EiJ-F (ORSAM7706)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7706

tag: treatment


title: 203723060084_R05C01:A00000EGL


title: metanephros-10% fat+fiber-CAST/EiJ-F (ORSAM7705)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7705

value: 10% fat + fiber


title: iGFP dox colonoid RNA-seq sample #4 [JV4]

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017).
RNA_DESeq_normCounts.csv
iGFP_DoxR2

source_name: iGFP dox colonoid RNA-seq

value: iGFP dox colonoid


title: adipose-RhS, epidermis, biol rep 2

description:
epidermis of skin model with adipose layer
Sample_5

value: adipose-RhS


title: 609_963026-35

tag: sts timepoint


title: 202172220109_R05C01:BDB1P02029

value: Blood

value: male


title: 613_957476-31

value: PreChallenge


title: 610_963026-31


title: 608_970776-35

value: PostChallenge


title: 202176290020_R02C01:BDB1P03034

value: no


title: 617_970777-31

value: Placebo


title: 202163550183_R05C01:BDB1P03069

value: yes


title: metanephros-10% fat+fiber-C57BL/6J-M (ORSAM7703)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7703

value: metanephros

tag: diet

value: Male

value: WT


title: iGFP dox colonoid RNA-seq sample #2 [JV2]

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017).
RNA_DESeq_normCounts.csv
iGFP_DoxRC2

value: Colon


title: metanephros-44% fat+fiber-C57BL/6J-M (ORSAM7704)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7704

value: 44% fat + fiber


title: 607_957476-35

value: PBMC

value: SLIT


title: iGFP dox colonoid RNA-seq sample #3 [JV3]

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017).
RNA_DESeq_normCounts.csv
iGFP_DoxR1


title: iGFP dox colonoid RNA-seq sample #1 [JV1]

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017).
RNA_DESeq_normCounts.csv
iGFP_DoxRC1


title: 611_966664-31


title: 202172220158_R04C01:BDB1P04036

description:
IlluminaHumanMethylationEPIC
White blood cell

tag: gender


title: 606_970776-31

tag: age


title: islets of Langerhans-10% fat+fiber-NZO/HlLtJ-M (ORSAM8939)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8939

data_processing:
raw counts quantified by EMASE and processed by /RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script and gathering_GBRS_total_counts_batch2.R.
counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation).
Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/Processing_normalization.R and Processing_normalization_batch2.R scripts.
gene annotation file ENSEMBL version 84
Assembly: GRCm38
Supplementary files format and content: counts_matrix.csv
Supplementary files format and content: mrna_annots.csv
Supplementary files format and content: vst_matrix.csv
Supplementary files format and content: Three Bears Islet Numbers.csv

source_name: islets of Langerhans

extract_protocol:
KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step. RNA was isolated from pancreatic islets using the RNeasy Micro kit (Qiagen), according to manufacturers’ protocols, including the optional DNase digest step. RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico or RNA ScreenTape assay (Agilent Technologies).
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction.  Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions. Libraries were sequenced on an Illumina NovaSeq 6000 using the S4 Reagent Kit.  Pancreatic islet libraries were sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs.

value: islets of Langerhans

value: 10% fat + fiber

value: NZO/HlLtJ


title: 202172220076_R02C01:BDB1P01050

value: Blood

value: female

tag: muscle-invasive


title: metanephros-10% fat+fiber-C57BL/6J-F (ORSAM7701)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7701

tag: strain

value: Female


title: 603_966737-31

value: PreChallenge


title: 605_970832-31


title: APC/KRAS/TP53 mutant colonoid smRNA-seq sample  #2

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017). APC Exon 8 indel,  KRAS G12V mutation, and TP53-/- mutation induced using CRISPR.
smRNAseq_DESeq_normalized_counts.csv
AKP_DoxRC1

source_name: APC/KRAS/TP53 mutant colonoid smRNA-seq

extract_protocol:
Libraries were prepared according to the TriLink CleanTag Small RNA Library Preparation Kit protocol
RNA was isolated using the the Norgen Total RNA Purification Kit according to the manufacturer's protocol.

value: APC/KRAS/TP53 mutant colonoid

tag: molecule subtype

value: small RNA


title: APC/KRAS/TP53 mutant colonoid smRNA-seq sample  #1

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017). APC Exon 8 indel,  KRAS G12V mutation, and TP53-/- mutation induced using CRISPR.
smRNAseq_DESeq_normalized_counts.csv
AKP_DoxR1


title: 203755070032_R05C01:A00000FBG

value: yes


title: islets of Langerhans-10% fat+fiber-NZO/HlLtJ-M (ORSAM8938)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8938

tag: genotype


title: APC/KRAS mutant colonoid smRNA-seq sample  #4

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017). APC Exon 8 indel and KRAS G12V mutation induced using CRISPR.
smRNAseq_DESeq_normalized_counts.csv
AK_DoxRC2

source_name: APC/KRAS mutant colonoid smRNA-seq

value: APC/KRAS mutant colonoid


title: 602_966737-35

value: Male

tag: fastq total_reads

tag: percent aligned

value: Placebo

value: PostChallenge


title: 203734290015_R04C01:A00000EC4

tag: tissue

value: male

value: no


title: islets of Langerhans-44% fat+fiber-NZO/HlLtJ-F (ORSAM8937)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8937

value: 44% fat + fiber

value: WT


title: APC/KRAS mutant colonoid smRNA-seq sample  #3

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017). APC Exon 8 indel and KRAS G12V mutation induced using CRISPR.
smRNAseq_DESeq_normalized_counts.csv
AK_DoxRC1

value: Colon

tag: cell type


title: 601_963097-31

value: PBMC

tag: Sex

tag: aligned counts_in_millions


title: metanephros-44% fat+fiber-C57BL/6J-F (ORSAM7702)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7702

value: metanephros


title: APC/KRAS mutant colonoid smRNA-seq sample  #2

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017). APC Exon 8 indel and KRAS G12V mutation induced using CRISPR.
smRNAseq_DESeq_normalized_counts.csv
AK_DoxR5


title: APC/KRAS mutant colonoid smRNA-seq sample  #1

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017). APC Exon 8 indel and KRAS G12V mutation induced using CRISPR.
smRNAseq_DESeq_normalized_counts.csv
AK_DoxR4


title: islets of Langerhans-44% fat+fiber-NZO/HlLtJ-F (ORSAM8936)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8936

value: islets of Langerhans

value: NZO/HlLtJ


title: 203751380110_R05C01:A00000EFX

value: Blood

value: female


title: 599_958684-31

tag: median cv_coverage

tag: participant id

value: PreChallenge


title: 203734290102_R02C01:A00000FBW


title: 600_958684-35

tag: visit number

tag: treatment


title: islets of Langerhans-44% fat+fiber-CAST/EiJ-M (ORSAM8935)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8935

tag: diet

value: CAST/EiJ


title: islets of Langerhans-10% fat+fiber-CAST/EiJ-M (ORSAM8934)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8934

value: 10% fat + fiber


title: APC mutant colonoid smRNA-seq sample  #3

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017). APC Exon 8 indel induced using CRISPR.
smRNAseq_DESeq_normalized_counts.csv
A_DoxRC2

source_name: APC mutant colonoid smRNA-seq

value: APC mutant colonoid

value: small RNA


title: islets of Langerhans-44% fat+fiber-CAST/EiJ-F (ORSAM8933)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8933

value: Female


title: 203752110095_R04C01:A00000EFD

description:
IlluminaHumanMethylationEPIC
White blood cell

tag: gender

value: male


title: 202163530099_R08C01:BDB1P03024

tag: age

value: no


title: 598_963097-35

value: Male

value: Placebo

tag: sts timepoint

value: PostChallenge


title: 203752100070_R06C01:5286DS

tag: muscle-invasive


title: APC mutant colonoid smRNA-seq sample  #2

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017). APC Exon 8 indel induced using CRISPR.
smRNAseq_DESeq_normalized_counts.csv
A_DoxRC1

value: Colon

tag: molecule subtype


title: APC mutant colonoid smRNA-seq sample  #1

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017). APC Exon 8 indel induced using CRISPR.
smRNAseq_DESeq_normalized_counts.csv
A_DoxR1


title: 202172220095_R06C01:BDB1P01062


title: 596_958459-35

value: PBMC

value: SCIT


title: 594_966690-31


title: islets of Langerhans-10% fat+fiber-CAST/EiJ-F (ORSAM8932)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8932

value: islets of Langerhans

tag: strain

tag: genotype

value: WT


title: 202172220173_R01C01:BDB1P02041

value: Blood

value: female


title: iGFP dox colonoid smRNA-seq sample #4

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017).
smRNAseq_DESeq_normalized_counts.csv
iGFP_DoxRC2

source_name: iGFP dox colonoid smRNA-seq

value: iGFP dox colonoid


title: islets of Langerhans-10% fat+fiber-CAST/EiJ-F (ORSAM8931)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8931

value: 10% fat + fiber

value: CAST/EiJ


title: 593_970790-31

source_name: PBMC

tag: fastq total_reads

tag: percent aligned

value: PreChallenge


title: islets of Langerhans-44% fat+fiber-C57BL/6J-M (ORSAM8930)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8930

tag: tissue

value: 44% fat + fiber


title: 203755070012_R08C01:A00000EDA

value: male


title: 592_963063-31

tag: Sex

value: Female


title: iGFP dox colonoid smRNA-seq sample #3

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017).
smRNAseq_DESeq_normalized_counts.csv
iGFP_DoxRC1

tag: cell type

value: small RNA


title: iGFP dox colonoid smRNA-seq sample #2

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017).
smRNAseq_DESeq_normalized_counts.csv
iGFP_DoxR2


title: 203752100058_R08C01:A00000FBP

value: no


title: islets of Langerhans-10% fat+fiber-C57BL/6J-M (ORSAM8928)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8928

value: Male


title: islets of Langerhans-44% fat+fiber-C57BL/6J-M (ORSAM8929)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8929


title: 591_963063-35

tag: aligned counts_in_millions

tag: median cv_coverage

value: PostChallenge


title: iGFP dox colonoid smRNA-seq sample #1

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017).
smRNAseq_DESeq_normalized_counts.csv
iGFP_DoxR1

value: Colon


title: 590_958459-31

value: PBMC

tag: participant id

tag: visit number

value: SCIT


title: 203751380062_R04C01:A00000EBV


title: 202172220041_R02C01:BDB1P01018


title: iGFP noDox colonoid smRNA-seq sample #4

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017).
smRNAseq_DESeq_normalized_counts.csv
iGFP_noDoxRC2

source_name: iGFP noDox colonoid smRNA-seq

value: iGFP noDox colonoid


title: islets of Langerhans-44% fat+fiber-C57BL/6J-F (ORSAM8926)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8926

value: islets of Langerhans

tag: diet

value: WT

tag: treatment


title: iGFP noDox colonoid smRNA-seq sample #3

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017).
smRNAseq_DESeq_normalized_counts.csv
iGFP_noDoxRC1


title: islets of Langerhans-10% fat+fiber-C57BL/6J-F (ORSAM8925)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8925


title: 588_966652-31

tag: age

value: Placebo


title: 586_970860-31

tag: sts timepoint


title: islets of Langerhans-44% fat+fiber-NZO/HlLtJ-M (ORSAM8090)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8090

value: NZO/HlLtJ


title: iGFP noDox colonoid smRNA-seq sample #2

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017).
smRNAseq_DESeq_normalized_counts.csv
iGFP_noDoxR4


title: 202172220032_R08C01:BDB1P01016

description:
IlluminaHumanMethylationEPIC
White blood cell

value: Blood

tag: gender

value: female

tag: muscle-invasive


title: iGFP noDox colonoid smRNA-seq sample #1

description:
Batch 1. Colonoids generated from HUES8 pluripotent stem cells as described in Crespo et al. Nature Medicine (2017).
smRNAseq_DESeq_normalized_counts.csv
iGFP_noDoxR2

tag: molecule subtype


title: 202163530097_R04C01:BDB1P04052


title: islets of Langerhans-44% fat+fiber-NZO/HlLtJ-M (ORSAM8089)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8089

value: 44% fat + fiber

tag: strain

tag: genotype


title: 585_963085-35

tag: fastq total_reads

tag: percent aligned


title: 203752110028_R02C01:A00000EH3

tag: tissue

value: male


title: HT1080_FUS-DDIT3-EGFP_3D_4

city: Göteborg

first: Emma

last: Jonasson

address: Medicinaregatan 1F, floor 5

department: Sahlgrenska Center for Cancer Research

country: Sweden

institute: University of Gothenburg

data_processing:
Alignment was performed using STAR version 2.6 using the ENSEMBL GRCh38 assembly reference genome
Gene expression was quantified using HTseq python framework version 0.9.1
MLS_2645-94_2D_3.1 and MLS_2645-94_2D_3.2 were sequenced from the same sample and were collapsed as technical replicates after read count, before downstream analysis. The collapsed sample is referred to as MLS_2645-94_2D_3_collapsed in the read count file.
Assembly: ENSEMBL GRCh38
Supplementary files format and content: Excel file containing matrix of unnormalized reads mapped to each transcript as a result from HTseq analysis.

source_name: Fibrosarcoma cell line

growth_protocol:
For monolayer culture, RPMI Glutamax cell culture media was supplemented with 5% or 10% fetal bovine serum, 100U/ml penicillin and 100 mg/ml streptomycin. Stable expression of EGFP constructs were maintained by addition of 500µg/ml Geneticin.
For scaffold culture, tumor pieces retrieved from a myxoid liposarcoma patient-derived xenograft model were decellularized using detergent wash. The scaffolds were cut into small pieces and added to 48-well culture plates. 3x105 cells were added onto the scaffold in 0.5ml complete media and cultured for 21 days before harvesting for downstream analysis. Scaffold pieces were transferred to new wells with fresh media if cells were growing outside the scaffold area.

extract_protocol:
Scaffold samples were lysed in RLT lysis buffer and homogenized in a Qiagen TissueLyzer II using stainless steel beads. 2D samples were lysed in RLT lysis buffer or QIAzol lysis buffer. RNA was extracted from all samples using Qiagen RNeasy micro kit or miRNeasy micro kit, including DNase treatment.
The library was generated using the Smart-seq2 protocol (Picelli, Faridani et al. 2014) with some modifications.

tag: cell line

tag: transfected gene

tag: culture method

value: Scaffold culture


title: 203751390067_R04C01:A00000FBE

value: yes


title: 583_958690-35

tag: Sex

tag: aligned counts_in_millions

tag: median cv_coverage

tag: participant id


title: 584_963085-31

tag: age

tag: visit number

tag: treatment

value: PreChallenge


title: islets of Langerhans-10% fat+fiber-NZO/HlLtJ-F (ORSAM8088)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8088

tag: diet

value: 10% fat + fiber

value: Female


title: islets of Langerhans-10% fat+fiber-NZO/HlLtJ-F (ORSAM8087)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8087


title: HT1080_FUS-DDIT3-EGFP_3D_2


title: islets of Langerhans-10% fat+fiber-C57BL/6J-M (ORSAM8927)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8927

value: Male


title: HT1080_FUS-DDIT3-EGFP_3D_3


title: 582_958690-31

value: PBMC

tag: sts timepoint


title: 202172220149_R05C01:BDB1P04013

tag: gender

tag: muscle-invasive

value: no


title: 202172220016_R01C01:BDB1P02001


title: 589_966652-35

tag: fastq total_reads

value: PostChallenge


title: islets of Langerhans-10% fat+fiber-CAST/EiJ-M (ORSAM8086)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8086

value: islets of Langerhans

tag: strain

value: CAST/EiJ

tag: genotype


title: 581_966708-31

tag: tissue

tag: percent aligned

value: SCIT


title: 203751380062_R06C01:5385DS


title: HT1080_FUS-DDIT3-EGFP_3D_1

tag: cell line

tag: transfected gene

tag: culture method


title: HT1080_EGFP_3D_5

value: EGFP


title: islets of Langerhans-44% fat+fiber-CAST/EiJ-M (ORSAM8085)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8085

tag: Sex

value: WT


title: 202172220158_R03C01:BDB1P04035

value: Blood

value: female


title: 203755070021_R07C01:A00000FC6

value: male


title: 580_963080-35

tag: aligned counts_in_millions

tag: median cv_coverage

tag: participant id


title: islets of Langerhans-44% fat+fiber-CAST/EiJ-M (ORSAM8084)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8084

value: 44% fat + fiber

tag: treatment


title: HT1080_EGFP_3D_4

value: Scaffold culture


title: islets of Langerhans-10% fat+fiber-CAST/EiJ-F (ORSAM8083)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8083

tag: diet


title: HT1080_EGFP_3D_3


title: 579_957445-31

tag: age

tag: visit number

tag: sts timepoint

value: PreChallenge


title: 578_957445-35

tag: fastq total_reads


title: HT1080_EGFP_3D_2


title: 577_963080-31