title: embryonic stem cells, ATRA/RNase, rep1 [J1_input_RNase]

data_processing:
Sequenced reads were aligned to the mouse genome (mm10) using bowtie2 (v2.2.5) with default parameters.
Processed data files were created usingdeepTools bamCoverage (v3.5.1, with the flag ---normalizeUsing BPM)
Assembly: mm10
Supplementary files format and content: bigwig created using bamCoverage normalized to BPM

growth_protocol: Mouse J1 embryonic stem cells were cultured on 0.1% gelatin coated plates without feeder. DMEM medium supplemented with Glutmax, Non-essential amino acids, 1x penicillin/streptomycin, and leukemia inhibitory factor (LIF) was used. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 20 minutes. After quenching and cell lysis, chromatin was isolated, subjected to RNase sonicated using a M220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the thruplex dna-seq kit

treatment_protocol: After chromatin isolation, cells were split into 2 - 1 control using Tris-HCL/glycine buffer and 1 for treatment with Rnase A (Thermo Fisher, EN0531) at a final concentration of 50ug/mL). Both sets of samples were incubated at 37 degrees celsius for 10 mins and then moved to ice for 1 minute.

value: mouse embryonic stem cell

tag: chip antibody


title: um_berninger_2019_01_039_p1_G05_1c_S39

status: Public on Jan 16 2023

type: SRA

city: Biberach an der Riss

first: Gregorio

last: Alanis-Lobato

address: Birkendorfer Str 65

department: Global Computational Biology and Digital Sciences

country: Germany

institute: Boehringer Ingelheim Pharma

description:
Control-d03
expression of control virus in adult neural stem cells for 3 days

library_source: transcriptomic

data_processing:
Smart-Seq2 raw data demultiplexing was performed using Illumina’s bcl2fastq conversion software v.2.19.1 and overall sequence quality was assessed with FastQC v0.11.5. .
STAR v.2.5.2b with default parameters (except –outFilterMismatchNoverLmax 0.04) was used to align reads to the mouse reference genome GRCm38 (mm10), which was supplemented with ERCC RNA Spike-In Mix (ThermoFischer) control sequences and the GTF gene annotation from Ensembl release 88.
Read summarization at the gene level was performed using Subread featureCounts v.1.6.2 with default parameters.
Genome_build: GRCm38 with ERCC control sequences
Supplementary_files_format_and_content: Raw count matrix with genes in rows and cells in columns

molecule: polyA RNA

organism: Mus musculus

source_name: adult neural stem cell

growth_protocol: Mice were administrated with lentivirus which encode EGFP or Yap1 5SA. DG was dissected from hippocampus and the tissue was enzymatically dissociated in Neural Tissue Dissociation Kit (Miltenyi Biotec, Germany). Dissociation was stopped by adding 10 ml HBSS (Ca+, Mg+) (Invitrogen). Cells were filtered by 70 µm cell strainer, then centrifuged at 300 g for 10 min.  Single cell suspension was resuspended with PBS which contains 5% FBS.

extract_protocol:
All the EGFP positive cells were collected into lysis buffer of 96-wells plates directly by Aria II SORP cell sorter at single cell sorting mode.
Libraries were prepared using the Illumina Nextera XT DNA sample preparation kit. The protocol is based on the Tagmentation protocol from Fluidigm, which uses ¼ of the reagents per tagmentation reaction with a starting amount of 100-125pg of cDNA. Through this tagmentation step, the cDNA is fragmented and partial Nextera adaptors are added to each end of the cDNA fragments. A PCR follows, which adds the rest of the Nextera adaptors and the i5 and i7 dual indexes. Libraries were amplified in 12 PCR cycles. Three microliters of each library were pooled into a single tube and the pool was subsequently bead purified using Agencout AMPure XP beads, with a ratio of 0.9:1 Beads:DNA.   The purified pool was profiled in a High Sensitivity DNA chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies).   Four pools (coming from four 96-well plates) are again pooled together in equimolar ratio and sequenced in a single NextSeq 500 Highoutput Flowcell, single read for 1x 75 cycles for read 1 plus 2x 8 cycles for each index read.
scRNA-Seq

tag: cell type

value: adult neural stem cell

tag: treatment

value: control virus

tag: days post-treatment


title: um_berninger_2019_01_040_p1_H05_1c_S40


title: BT0510, Osmotic stress - control, biological replicate 3

city: Hershey

first: James

middle: R

last: Broach

state: PA

address: 700 HMC Crescent Rd

department: Biochemistry and Molecular Biology

country: USA

institute: Pennsylvania State University College of Medicine

data_processing:
Reads were aligned to the S288C reference genome with hisat2 using the --no-mixed --no-discordant parametrs
FPKM values for each sample and its associated control sample are provided in the gene_exp.diff file with column q1 providing the sample FPKM value and column q2 the control FPKM value
For the analysis presented in Figure 1, each value represents the log2 ratio of the FPKM value for that sample relative to the average of the values for all nine samples for that gene across all nine samples in that particular experiment
Assembly: Saccharomyces cerevisiae S288C R64-1-1

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown at 30 °C with aeration in liquid Synthetic Complete medium (SC) (yeast nitrogen base without amino acids, drop-out mix, 2% Glucose) to exponential growth phase (OD600nm = 1.0) before being exposed to sequential stresses.

extract_protocol:
Total RNA from three biological replicates for each treatment was extracted using the Qiagen RNeasy Mini kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions.
Poly-A tailed RNA was captured, and reverse transcribed to complementary DNA (cDNA), which was used for library preparation by the Stranded Total RNA Prep (Illumina, USA) following the manufacturer’s protocol.

treatment_protocol: For osmotic stress, cells were incubated in liquid SC containing 1 M sorbitol for 30 minutes at 28ºC. Cells were subjected to oxidative stress by incubating them in SC containing 0.6mM hydrogen peroxide for 30 min. Glucose withdrawal was performed by transferring cells in SC + 2% glucose to SC + 0.05% glucose for 30 minutes. After each stress, cells were collected, washed with deionized water and reinoculated in SC supplemented with 8% (v/v) ethanol for 30 minutes at 28ºC at 160 rpm.

tag: cell line

value: WT

value: Osmotic stress control (pre-treatment)


title: embryonic stem cells, ATRA, rep1 [J1_input_control]

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

library_source: genomic

molecule: genomic DNA


title: um_berninger_2019_01_038_p1_F05_0c_S38

description:
Control-d03
sample for QC diagnostics

source_name: empty well

value: empty well


title: BT0510, Osmotic stress  - alcohol stress, biological replicate 2

value: Osmotic stress followed by ethanol stress


title: um_berninger_2019_01_042_p1_B06_1c_S42

description:
Yap-d03
expression of Yap1 in adult neural stem cells for 3 days

value: Yap1 overexpression


title: um_berninger_2019_01_038_p5_F05_0c_S38

description:
Control-d03
sample for QC diagnostics


title: BT0510, Oxidative stress  - control, biological replicate 1

value: Oxidative stress control (pretreatment)


title: BT0510, Osmotic stress  - osmotic stress, biological replicate 2

value: Osmotic stress


title: embryonic stem cells, ATRA/RNase, rep2 [J1_FL-DNMT3A_RNase_2]

value: Flag M2 (Sigma, F3165)


title: embryonic stem cells, ATRA/RNase, rep1 [J1_FL-DNMT3A_RNase_1]


title: um_berninger_2019_01_041_p5_A06_1c_S41


title: BT0510, Osmotic stress - control, biological replicate 2


title: um_berninger_2019_01_036_p5_D05_1c_S36


title: um_berninger_2019_01_037_p5_E05_10c_S37

description:
Control-d03
sample for QC diagnostics

source_name: 10 adult neural stem cells


title: embryonic stem cells, ATRA, rep2 [J1_FL-DNMT3A_control_2]


title: um_berninger_2019_01_036_p1_D05_1c_S36


title: um_berninger_2019_01_037_p1_E05_10c_S37

description:
Control-d03
sample for QC diagnostics


title: um_berninger_2019_01_035_p1_C05_1c_S35


title: um_berninger_2019_01_035_p5_C05_1c_S35


title: BT0510, Osmotic stress  - alcohol stress, biological replicate 1


title: um_berninger_2019_01_034_p1_B05_1c_S34


title: embryonic stem cells, ATRA, rep1 [J1_FL-DNMT3A_control_1]


title: um_berninger_2019_01_034_p5_B05_1c_S34


title: mASPS FLAG JQ1

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

country: Japan

institute: Japanese Foundation for Cancer Research

description: FLAG (Sigma, F7425, lot 085M4774V)

data_processing:
Base calls were performed using Bowtie 2.
ChIP-seq reads were aligned to the mm9 or hg19 genome assembly using samtools 1.2.
Peak call was performed using MACS1.4.
Assembly: mm9 (mouse) and hg19 (human)
Supplementary files format and content: For every 300 bp window, the mapped tag count for ChIP, Cc and that for Input, Ci were used for calculation. Ec and Ei indicates the estimate count for 300 bp window for ChIP and Input. Signal ratio of ‘target TF’ was calculated as, Cc/Ec + 1 ÷ Max (1, Ci/Ei + 1).

growth_protocol: Mouse and human ASPS cells were grown in IMDM supplemented with 10% fetal bovine serum (FBS) and RPMI-1640 supplemented with 10% FBS, respectively.

extract_protocol:
Lysates were clarified from sonicated nuclei and immunoprecipitated with each antibodies
Libraries were prepared according to Illumina's instructions accompanying the ThruPLEX DNA-seq 6S (12) Kit (R400523). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Mouse and human ASPS cells were treated with 100 nM JQ1 for 48 hours. Small interfering RNA-mediated gene silencing of human ASPS cells was performed.

value: murine alveolar soft part sarcoma

value: mASPS cells treated with JQ1


title: BT0510, Osmotic stress  - osmotic stress, biological replicate 1


title: um_berninger_2019_01_033_p5_A05_1c_S33


title: BT0510, Osmotic stress  - control, biological replicate 1


title: um_berninger_2019_01_032_p5_H04_1c_S32


title: um_berninger_2019_01_033_p1_A05_1c_S33


title: um_berninger_2019_01_032_p1_H04_1c_S32


title: mASPS FLAG DMSO

description: FLAG (Sigma, F7425, lot 085M4774V)

value: mASPS cells treated with DMSO control


title: HPr1-AR cells, VDR D3 2

city: WEST HOLLYWOOD

first: Moray

last: Campbell

state: CA

address: 8687 Melrose Avenue, Office B227.5G

institute: Cedars-Sinai Medical Center

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FASTQC and Trimmomatic
Trimmed sequence reads were mapped to hg38 using RSubread
Cistromes were analyzed with Rsubread/csaw along with TF motif analyses (MotifDb) all in R
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Homo sapiens

growth_protocol: All cells were maintained at 37oC and 5.0% CO2 (Sanyo); HPr1AR, RC43N, RC43T,  cells were maintained in keratinocyte serum free media (supplemented with 25mg of Bovine pituitary extract, 10ug EGF and 10% FBS); LNCaP cells were maintained in RPMI 1640 containing 10% FBS. All media contained 100 U/mL Penicillin-Streptomycin. 1α,25(OH)2D3 was kept as 10mM EtOH stocks. Cell lines were authenticated by STR profiling and confirmed mycoplasma free.

extract_protocol:
Briefly, approximately 20x106 cells were crosslinked with 1% formaldehyde solution, quenched with glycine (0.125 M) and harvested in cold PBS. Sonication of crosslinked chromatin was performed using a Bioruptor® UCD-200TM Sonicator (Diagenode) with optimized cycles for each cell type. Immunoprecipitation of sonicated material was performed with antibodies against VDR (D2K6W) – Cell Signaling) or IgG (Rabbit IgG sc2729 – Santa Cruz) for 16 hours, and antibody/bead complexes isolated with Magna ChIPTM Protein A+G magnetic beads (Millipore). Complexes were washed, reverse crosslinked, and treated sequentially with RNase and proteinase K prior to DNA isolation.
Sequencing libraries prepared from immunopreciptiated DNA

treatment_protocol: Cells were grown to 70% confluence and treated with 1α,25(OH)2D3 (100nM, 6hr) or EtOH in biological triplicate samples and analyzed by ChIP-Seq.

tag: tissue

tag: genotype

value: European American non-malignant prostate

value: VDR


title: um_berninger_2019_01_030_p5_F04_1c_S30


title: um_berninger_2019_01_030_p1_F04_1c_S30


title: um_berninger_2019_01_031_p1_G04_1c_S31


title: HPr1-AR cells, VDR D3 1


title: um_berninger_2019_01_029_p5_E04_1c_S29


title: HPr1-AR cells, IgG control 2

value: IgG

value: Vehicle


title: HPr1-AR cells, IgG control 3


title: Mice DMSO Rep 3

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

description: DMSOplus

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without novel splicing form calls
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts
Genome_build: GRCz11 and GRCm38
Supplementary_files_format_and_content: FPKM

molecule: total RNA

source_name: freshly isolated mice muscle stem cells

growth_protocol: Freshly isolated mice muscle stem cells were sorted into collagen/laminin-coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells, which were cultured in a zESC medium composed of 70% LDF medium (50% Leibowitz’s L-15 (Invitrogen), 35% DMEM (Invitrogen), and 15% Ham’s F-12 (Invitrogen)), with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein (Sigma-Aldrich), 15 mM sodium bicarbonate, 15 mM HEPES (Invitrogen),1% L-glutamine (Invitrogen), 10 nM sodium selenite (Sigma-Aldrich), 1% N2 (Invitrogen), 2% B27 (Invitrogen), 0.1 mg/ml Primocin (Invivogen) and at 28°C without CO2 for 48 hours.

extract_protocol:
Treated freshly isolated mice muscle stem cells  and zebrafish myogenic progenitor cells were washed with DPBS, then total RNA was extracted with the micro RNeasy kit (QIAGEN).
cDNA was prepared using SMART Seq v4 Ultra Low RNA-Seq kit (Takara) and a Nextera kit was used for library construction.

treatment_protocol: Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 (GIBCO), 20% horse serum (Atlanta Biologics), 1% penicillin-streptomycin (Invitrogen), 1% GlutaMAX (Invitrogen), and 5 ng/ml bFGF (Sigma) at 37°C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C, respectively.

value: muscle stem cells

value: DMSO


title: Mice DMSO Rep 2

description: DMSOplus


title: Mice DMSO Rep 1

description: DMSOplus


title: um_berninger_2019_01_028_p1_D04_1c_S28

value: adult neural stem cell


title: um_berninger_2019_01_027_p5_C04_1c_S27


title: um_berninger_2019_01_027_p1_C04_1c_S27


title: LNCaP cells, VDR, D3 2

source_name: LNCaP

value: LNCaP

value: WT

value: European American prostate cancer


title: Mice NFA Rep 2

value: NFA


title: um_berninger_2019_01_026_p5_B04_1c_S26

value: Yap1 overexpression


title: Mice NFA Rep 3


title: um_berninger_2019_01_025_p5_A04_1c_S25


title: um_berninger_2019_01_026_p1_B04_1c_S26


title: LNCaP cells, VDR, D3 1


title: um_berninger_2019_01_025_p1_A04_1c_S25


title: um_berninger_2019_01_031_p5_G04_1c_S31


title: um_berninger_2019_01_024_p5_H03_1c_S24

value: control virus


title: LNCaP cells, VDR, control 2


title: um_berninger_2019_01_029_p1_E04_1c_S29


title: Mice LPA Rep 2

value: LPA


title: um_berninger_2019_01_023_p5_G03_1c_S23


title: um_berninger_2019_01_024_p1_H03_1c_S24


title: LNCaP cells, VDR, control 1


title: HPr1-AR cells, IgG control 1


title: um_berninger_2019_01_022_p5_F03_1c_S22


title: Mice LPA Rep 3


title: um_berninger_2019_01_028_p5_D04_1c_S28


title: um_berninger_2019_01_022_p1_F03_1c_S22


title: um_berninger_2019_01_023_p1_G03_1c_S23


title: LNCaP cells, IgG control 1


title: P4 Shox2-Cre/+; R26 tdTomato/+ mouse SAN scRNA-seq library

city: Dallas

first: Nikhil

middle: V

last: Munshi

address: 6000 Harry Hines Blvd.

department: Internal Medicine-Cardiology

institute: UT Southwestern Medical Center

data_processing:
Binary base call (BCL) files generated were demultiplexed and converted to standard FASTQ files using the mkfastq function from Cell Ranger pipeline (version 3.1.0).
The demultiplexed reads were merged and processed using the Salmon Alevin with default parametersexcept for --forceCells=10000 to generate the expression matrix. The reference and gene annotation were downloaded from GENCODE website (GRCm38.p6/mm10).
Technical artifacts (ambient RNA and random barcode swapping) were eliminated using CellBender with default parameters except for --expected-cells=6000, --total-droplets-included 10000 and --epocs=200.
Genome_build: mm10
Supplementary_files_format_and_content: Raw UMI count matrices representing gene expression values (comma-separated) were generated as described above. Each column represents a single cell, each row represents a single gene.

source_name: scRNA-seq library

growth_protocol: Hearts from neonatal P4 mice were dissected out, Cre+ hearts were selected based on tdTomato fluorescence expression, and SAN region was strictly microdissected guided by fluorescence reporter expression

extract_protocol:
Single cell suspension was washed with 1X PBS (0.04% BSA) before 10x Genomics procedure. The concentration of single cell suspension was adjusted to about 500 to 1000 cells/µL and was loaded on the 10x Genomics’ Chromium™ system (10x Genomics, Pleasanton, CA) with the aim of 6000 to 10000 cells per channel (Chromium™ Single Cell 3' Library & Gel Bead Kit v2, catalog number 120237).
scRNA-Seq libraries were constructed following the manufacturer’s instructions (Zheng et al., 2017).
Library was sequenced using Illumina NextSeq 500/550 sequencing systems (Illumina, San Diego, CA).

treatment_protocol: Microdissected SAN was minced, digested, and single cell suspension was prepared using the Pierce Cardiomyocyte Isolation Kit as stated in Methods section

tag: strain

value: heart/SAN

tag: Stage


title: LNCaP cells, IgG control 2


title: um_berninger_2019_01_021_p5_E03_1c_S21


title: Mice LPA Rep 1


title: um_berninger_2019_01_021_p1_E03_1c_S21


title: um_berninger_2019_01_020_p5_D03_1c_S20


title: um_berninger_2019_01_020_p1_D03_1c_S20


title: Mice NFA Rep 1


title: RC43N cells, VDR, D3 3

value: African American non-malignant prostate


title: um_berninger_2019_01_019_p5_C03_1c_S19


title: RC43N cells, VDR, D3 2


title: RC43N cells, VDR, D3 1


title: um_berninger_2019_01_019_p1_C03_1c_S19


title: um_berninger_2019_01_018_p5_B03_1c_S18


title: RC43N cells, VDR, control 2


title: um_berninger_2019_01_018_p1_B03_1c_S18


title: RC43N cells, VDR, control 1


title: um_berninger_2019_01_017_p1_A03_1c_S17


title: um_berninger_2019_01_015_p5_G02_1c_S15


title: um_berninger_2019_01_017_p5_A03_1c_S17


title: um_berninger_2019_01_016_p5_H02_1c_S16


title: RC43N cells, IgG control 2


title: Dr, D949 muscle

city: Columbus

first: Genevieve

last: Kendall

state: OH

address: 700 Children's Drive, WA5014

institute: Nationwide Children's Hospital / The Ohio State University

description: alternate title: none

data_processing:
Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp
Reads were aligned with STAR 2.7.2b against the zebrafish genome (danRer11) or the mouse genome (mm10)
Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R
Read counts were normalized in R using EdgeR
All code used in processing is available at https://github.com/MVesuviusC/2022_VGLL2_NCOA2_paper
Assembly: danRer11 or mm10
Supplementary files format and content: geneCountsCombinedDr_norm.txt.gz and geneCountsCombinedDr_norm.txt.gz are tables containing normalized gene counts

organism: Danio rerio

source_name: Normal Back Skeletal Muscle

growth_protocol: Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish, Gateway cloning was performed to generate CMV-GFP2A-VGLL2NCOA2 and BetaActin-GFP2A-CICDUX4 injection constructs, each containing the human form of the fusion-oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage, and fish were monitored for tumor formation. For our mouse allograft models, C2C12 cells were grown in DMEM+20% FBS, and were stably transfected with pcDNA3.1-control or pcDNA3.1-VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2-NCOA2 tumor models.

extract_protocol:
For zebrafish, GFP positive (and thus transgene positive) tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Normal Back Skeletal Muscle

value: Wildtype (AB/TL)

tag: age at sac

value: 118 days

tag: transgene

tag: model

value: no transgene


title: Dr, D951 muscle

description: alternate title: none


title: Dr, D952 muscle

description: alternate title: none


title: RC43N cells, IgG control 1

value: IgG

value: Vehicle


title: Dr, D948 muscle

description: alternate title: none


title: Dr, D812-tail

description: alternate title: none

source_name: VGLL2-NCOA2 Tumor

value: VGLL2-NCOA2 Tumor

value: 47 days

value: ptz876 cmv-GFP2A-VGLL2NCOA2 injected

value: mosaic genetic tumor model


title: um_berninger_2019_01_016_p1_H02_1c_S16

value: adult neural stem cell


title: RC43T cells, VDR D3  2

value: WT

value: VDR


title: RC43N cells, IgG control 3


title: Dr, D950 muscle

description: alternate title: none


title: Dr, D874

description: alternate title: none

value: 145 days


title: Dr, D815

description: alternate title: none


title: um_berninger_2019_01_012_p5_D02_1c_S12

value: Yap1 overexpression


title: um_berninger_2019_01_012_p1_D02_1c_S12


title: um_berninger_2019_01_015_p1_G02_1c_S15


title: um_berninger_2019_01_014_p5_F02_1c_S14


title: um_berninger_2019_01_011_p5_C02_1c_S11


title: um_berninger_2019_01_014_p1_F02_1c_S14


title: Dr, D809

description: alternate title: none

value: 44 days


title: um_berninger_2019_01_013_p5_E02_1c_S13


title: um_berninger_2019_01_013_p1_E02_1c_S13


title: RC43T cells, VDR D3  1

value: African American prostate cancer


title: Dr, D814

description: alternate title: none


title: Dr, D812-head

description: alternate title: none


title: Dr, D811

description: alternate title: none


title: Zebrafish DMSO Rep 2

source_name: zebrafish myogenic progenitor cells

value: myogenic progenitor cells

value: DMSO


title: um_berninger_2019_01_009_p5_A02_1c_S9


title: um_berninger_2019_01_011_p1_C02_1c_S11


title: RC43T cells, IgG control 2


title: Zebrafish NFA Rep 3

value: NFA


title: um_berninger_2019_01_010_p5_B02_1c_S10


title: RC43T cells, VDR control 2


title: RC43T cells, VDR control 1


title: um_berninger_2019_01_010_p1_B02_1c_S10


title: um_berninger_2019_01_007_p5_G01_1c_S7

value: control virus


title: Zebrafish DMSO Rep 3


title: um_berninger_2019_01_008_p5_H01_1c_S8


title: RC43T cells, IgG control 3

value: IgG


title: Zebrafish DMSO Rep 1


title: um_berninger_2019_01_007_p1_G01_1c_S7


title: um_berninger_2019_01_008_p1_H01_1c_S8


title: um_berninger_2019_01_004_p5_D01_1c_S4


title: um_berninger_2019_01_005_p1_E01_1c_S5


title: um_berninger_2019_01_006_p1_F01_1c_S6


title: RC43T cells, IgG control 1

value: Vehicle


title: um_berninger_2019_01_005_p5_E01_1c_S5


title: um_berninger_2019_01_004_p1_D01_1c_S4


title: Zebrafish LPA Rep 2

value: LPA


title: um_berninger_2019_01_009_p1_A02_1c_S9


title: N2-NC-1_L1_1003666

city: Beijing

first: Hailian

last: Zhao

state: Beijing

address: 15 Datun Road

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

description:
replicates were merged for processing
N2-NC_merge.bigwig

data_processing:
Illumina bcl2fastq-1.8.4 conversion software used for basecalling.
After sequencing of LACE-seq libraries, the adapter sequences at the 3' end were removed using Cutadapt v1.15 with the parameter: -a ATCTCGTATGCCGTCTTCTGCTT
After filtering, the LACE-seq reads were aligned to C. elegans pre-rRNA by bowtie with default parameters.
The unmapped reads to C. elegans pre-rRNA were then aligned to the C. elegans reference genome.
Assembly: wormbase_WS266
Supplementary files format and content: LACE-seq reads coverage in bigwig format

organism: Caenorhabditis elegans

source_name: hermaphrodite

growth_protocol: Culture in NGM medium at 20 °C.

extract_protocol:
Many L4 stage hermaphrodites were collected.
Anti-GFP enriches AMG-1 binding RNA for library.
LACE-seq

treatment_protocol: Simultaneous culture to L4 stage  after bleach.

value: hermaphrodite

tag: antibody

value: Mouse monoclonal anti-GFP; RRID:AB_390913

tag: developmental stage

value: L4 stage


title: N2-NC-3_L1_1003668


title: N2-NC-2_L1_1003667


title: Zebrafish NFA Rep 1


title: RC43T cells, IgG control 4


title: RC43T cells, D3 treat 3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FASTQC and Trimmomatic
Trimmed sequence reads were mapped to hg38 using RSubread
Differential chromatin accessability was analyzed with Rsubread/csaw along with TF motif analyses (MotifDb) all in R
Supplementary files format and content: hg38
Supplementary files format and content: Significant regions are presented with genomic coordinates and signficance

extract_protocol: Mixing, cleanup and library preparation, quantification and sequencing was performed using NovaSeq6000 S1 PE150bp Sequencing as per protocol51 (28846090). (ATAC-Seq data were separated into nucleosome free (NF), mono-, di- and tri-nucleosome compartments (ATACSeqQC)

treatment_protocol: Cells were grown to 70% confluence and treated with 1α,25(OH)2D3 (100nM, 4hr) or EtOH in biological triplicate samples and analyzed by ATAC-Seq.

value: LNCaP

value: European American

tag: disease state

value: prostate cancer


title: Zebrafish NFA Rep 2


title: GFP-CO4-2_L1_1003862

description:
replicates were merged for processing
GFP-CO4_merge.bigwig


title: RC43T cells, D3 treat 2

value: WT


title: um_berninger_2019_01_003_p1_C01_1c_S3

value: adult neural stem cell


title: RC43T cells, D3 treat 1


title: GFP-CO4-1_L1_1003861


title: Zebrafish LPA Rep 3


title: um_berninger_2019_01_002_p5_B01_1c_S2


title: RC43T cells, veh treat 1


title: RC43T cells, veh treat 2

value: non-malignant prostate


title: GFP-CO4-3_L1_1003510


title: FM5

description: replicates were merged for processing

data_processing:
Illumina bcl2fastq-1.8.4 conversion software used for basecalling.
After removing adaptor sequences, clean reads were aligned to the C. elegans pre-rRNA.
After filtering, unmapped reads were aligned to the C. elegans reference genome using the HISAT2 software (v.2.1.0).
Assembly: wormbase_WS266
Supplementary files format and content: RNA-seq reads coverage in bigwig format

source_name: hermaphrodite germline

growth_protocol: Hermaphrodite nematodes were grown on NGM medium at 20 °C.

extract_protocol:
Many L4 stage him-5 and amg-1;him-5 hermaphrodites were collected, the hermaphroditic germline were dissected out, quickly frozen on dry ice, and RNA was collected using Trizol reagent.
The extracted RNA was used to build the library.

treatment_protocol: Simultaneously cultured to L4 stage after bleaching.

value: hermaphrodite germline

tag: phenotype

value: fertility

value: Simultaneous culture after bleach


title: um_berninger_2019_01_002_p1_B01_1c_S2


title: human CD34 stem and progenitor cells, Cas9, rep2 [hHSC_Cas9_2]

description:
hHSC.txt
Processed tables include the average IR score for each phenotype and group. The intron retention (IR) score was then computed as the ratio of the RPKM-normalized “intronic” read density over the RPKM-normalized “spanning” read density.

data_processing:
Hisat2-aligned reads were filtered for proper-paired reads (-f 2 flag in samtools).
Intron annotations were parsed from RefSeq gene annotation files and were filtered to exclude features that overlap genomic loci on the same strand. Reads mapping to introns were counted using the Python module Pysam (https://github.com/pysam-developers/pysam). For each intron feature, we defined the following two read classes: (1) “intronic” reads mapping at least 6 bases contiguously within the intron and (2) “spanning” reads with ends mapping to the flanking exons. The intron retention (IR) score was then computed as the ratio of the RPKM-normalized “intronic” read density over the RPKM-normalized “spanning” read density. Introns with <10 spanning reads were excluded from all analyses. For analysis of introns with robust changes in expression, a spanning read threshold of 50 was implemented, and only introns with >2-fold changes in the IR score were kept. Statistical analyses were performed using R. Empirical cumulative distributions of IR scores were compared, and p-values estimated using a two-sided Kolmogorov-Smirnov test.
Assembly: mm10, hg38
Supplementary files format and content: tab-delimited text files include Intron rentention ratios for each Sample

extract_protocol:
Total RNA was isolated from mouse HSCs and human HSPCs using PicoPure RNA isolation kit (KIT0204). RNA from mESC and hESC was isolated using the Qiagen mini kit
mRNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: CD34 stem and progenitor cells

tag: time

tag: ir group


title: RC43N cells, veh treat 2

tag: cell type


title: Zebrafish LPA Rep 1

value: myogenic progenitor cells

tag: treatment


title: RC43T cells, veh treat 3


title: RC43N cells, veh treat 1

value: African American


title: human CD34 stem and progenitor cells, sgDNMT3A, rep2 [hHSC_sgDNMT3A_2]

value: DNMT3A Knockout


title: RC43N cells, D3 treat 3


title: human CD34 stem and progenitor cells, sgDNMT3A, rep1 [hHSC_sgDNMT3A_1]


title: RC43N cells, veh treat 3

value: Vehicle


title: um_berninger_2019_01_003_p5_C01_1c_S3

value: control virus

tag: days post-treatment


title: um_berninger_2019_01_001_p5_A01_1c_S1


title: FM4

description: replicates were merged for processing


title: CO4-4

description: replicates were merged for processing

value: infertility


title: human CD34 stem and progenitor cells, Cas9, rep1 [hHSC_Cas9_1]

tag: cell line


title: FM3

description: replicates were merged for processing

value: L4 stage


title: LNCaP cells, veh treat 3

tag: tissue


title: um_berninger_2019_01_001_p1_A01_1c_S1


title: embryonic stem cells, ATRA, rep2 [hESC_dTAG-13_ATRA_2]

description:
hESC.txt
Processed tables include the average IR score for each phenotype and group. The intron retention (IR) score was then computed as the ratio of the RPKM-normalized “intronic” read density over the RPKM-normalized “spanning” read density.

value: Embryonic Stem Cells

tag: genotype

value: DNMT3A degradation

value: ATRA

value: 12 hours


title: embryonic stem cells, ATRA, rep1 [hESC_dTAG-13_ATRA_1]


title: CO4-6

description: replicates were merged for processing


title: CO4-5

description: replicates were merged for processing


title: embryonic stem cells, ATRA, rep2 [hESC_DNMT3AWT_ATRA_2]

value: WT


title: LNCaP cells, veh treat 2

value: non-malignant prostate


title: um_berninger_2019_01_006_p5_F01_1c_S6

value: adult neural stem cell


title: LNCaP cells, veh treat 1


title: RC43N cells, D3 treat 1


title: embryonic stem cells, ATRA, rep1 [hESC_DNMT3AWT_ATRA_1]


title: ATAC-seq of L1MC1 KO GM12878 cells, clone 1

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

data_processing:
AIAP ( Liu et. Al 2021)
Assembly: hg19
Supplementary files format and content: bigWig of ATAC read counts

extract_protocol:
Zymo DNA Clean & Concentrator
ATAC-seq (as described in Dong, 2020)

value: L1MC1 KO


title: ATAC-seq of GM12878 WT cells


title: Ts65Dn42N6b

type: RNA

city: Bethesda

first: Faycal

last: Guedj

state: Maryland

address: 35A Convent DR

department: NHGRI

institute: National Institute of Health

description:
Embryonic day 18.5 (E18.5) forebrain
Forebrain gene expression data from day 18.5 embryo

hyb_protocol: Arrays were washed and stained using the GeneTitan Hybridization, wash and stain kit with streptavidin-phycoerythrin protocol according to the manufacturer's instructions (Cat. No. 901622, Affymetrix, Santa Clara, CA).

scan_protocol: Arrays were scanned on the GeneTitan automated microarrays system (Affymetrix, Santa Clara, CA).

data_processing: Quality control and normalization were performed in R software using the 'oligo' library and the 'pd.clariom.s.mouse.ht' platform. Normalization was done using the Robust Multichip Average (RMA) algorithm. Normalization output consisted of data for 29129 probesets. The 'control' probesets (labeled with AFFX, ERCC, MG-1, RPTR) were removed, leaving the 22206 'main' genome probesets for further analysis.

label: biotin

source_name: Embryo N6 from dam TS42

label_protocol: Samples were labeled with Biotin Allonamide Triphosphate using the Mouse Clariom S Assay HT and the GeneTitan automated microarrays system (Cat. No. 902972, Thermo Fisher Scientific, Waltham, MA).

growth_protocol: All experiments were approved by the NHGRI Institutional Animal Care and Use Committee (IACUC) (Protocol G-17-1). Mice were housed in standard cages with food and water ad libitum in a controlled environment (temperature: 20°C; humidity: 60%; light and dark cycles of 12 hours with lights on at 7:00 AM). The Ts65Dn and Ts66Yah mouse strains used in these studies were maintained on a B6 X C3H mixed genetic background.  We obtained three Ts66Yah founder female mice from the Herault Lab (Strasbourg, France) on a B6C3B genetic background (with the C3B line as a C3H/HeH congenic line for the BALB/c allele at the Pde6b locus). The founder Ts66Yah females were mated with B6EiC3Sn.BLiAF1/J males (F1 hybrid; Jackson Laboratories stock number 003647).  The sperm of four different Ts66Yah males were then used via in vitro fertilization to expand the colony. Ts(1716)65Dn/DnJ (Ts65Dn; stock number 005252) mice were obtained from the Jackson Laboratory (Bar Harbor, ME). Since Ts65Dn male mice are infertile, Ts65Dn female mice were mated with B6EiC3Sn.BLiAF1/J (F1 hybrid; stock number 003647) males. Thus, the extra chromosome could only be transmitted through the female parent. For embryonic studies, the presence of a vaginal plug was defined as embryonic day 0.5 (E0.5) and 10-15% weight gain at embryonic day 10 was used to confirm pregnancy. Pregnant females were anesthetized with 2.5% isoflurane in a 3/7 02/N2O mixture and euthanized by decapitation at embryonic day E18.5. Embryos were extracted and decapitated in ice-cold phosphate-buffered-saline (PBS1X). Embryonic brains were rapidly removed and brain hemispheres dissected on a cold platform and snap frozen in liquid nitrogen before storage at -80°C.

extract_protocol: Total RNA was isolated from the developing E18.5 forebrain using the NuceloMag® RNA/DNA extraction kit following the manufacturer’s instructions (Cat. No. 744350.4, Macherey-Nagel, Bethlehem, PA). RNA concentrations were measured as absorbance at 260 nm on the Nanodrop instrument (Thermo Fisher Scientific, Waltham, MA). RNA quality was analyzed with the Bioanalyzer (Agilent Biotechnologies, Santa Clara, CA) using the RNA 6000 Nano kit according to the manufacturer’s instructions. Only samples displaying an A260/A280 ratio of 2.0-2.1 and a RIN (RNA Integrity Number) > 9 were used for hybridization to the arrays.

treatment_protocol: No treatment protocol was used in this study

value: forebrain

tag: Sex

value: F


title: RNA-seq of L1MC1 KO GM12878 cells, clone 47

data_processing:
STAR Alignment
Assembly: hg19
Supplementary files format and content: zipped bedgraph of RNA-seq read counts

extract_protocol:
Zymo RNA Clean & Concentrator-5
NUGEN RNA-seq kit


title: ATAC-seq of L1MC1 KO GM12878 cells, clone 47


title: RC43N cells, D3 treat 2


title: LNCaP cells, D3 treat 3


title: LNCaP cells, D3 treat 2


title: RNA-seq of L1MC1 KO GM12878 cells, clone 1


title: Ts65Dn42N5b

source_name: Embryo N5 from dam TS42


title: RNA-seq of GM12878 WT cells


title: HiC^2 of L1MC1 KO GM12878 cells (chr7:157.1-159.1MB) clone 47

data_processing:
Juicer (Rapo et. Al 2014)
Assembly: hg19
Supplementary files format and content: hic interactions

extract_protocol:
Zymo DNA Clean & Concentrator
HiC^2 (Rao et. Al 2014)


title: LNCaP cells, D3 treat 1

value: prostate cancer


title: HPr1ARcells, veh treat 2

value: African American


title: Ts65Dn42N1b

source_name: Embryo N1 from dam TS42

value: M


title: Ts65Dn42N2b

source_name: Embryo N2 from dam TS42


title: Ts65Dn42N7b

source_name: Embryo N7 from dam TS42


title: HPr1ARcells, veh treat 1

value: Vehicle


title: mASPS25_2

hyb_protocol: Following fragmentation, 7.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Human Genome HG-U133 PM Array. GeneChips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneAtlas Imaging Station.

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

source_name: mouse sarcoma cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was purified using RNA Easy kit (QIAGEN) according to the manufacturer's protocol

treatment_protocol: No treatment was achieved.

value: expressing ASPSCR1-TFE3

value: ASPS cell line


title: mASPS25_null_3

value: without ASPSCR1-TFE3


title: Ts65Dn42N3b

source_name: Embryo N3 from dam TS42


title: Ts65Dn42N4b

source_name: Embryo N4 from dam TS42


title: mASPS25_null_2


title: mASPS25_3


title: Ts65Dn18N6b

source_name: Embryo N6 from dam TS18


title: Ts65Dn18N7b

source_name: Embryo N7 from dam TS18


title: Ts65Dn18N4b

source_name: Embryo N4 from dam TS18


title: HiC^2 of L1MC1 KO GM12878 cells (chr7:157.1-159.1MB) clone 1


title: mASPS25_null_1


title: mASPS25_1


title: ASPS1_siTFE3_1

data_processing:
Row reads were trimmed to remove adaptor sequences by Skewer (v0.2.2).
UMIs were extracted by umi_tools ‘extract’ and UMI adaptor sequences were also removed by cutadapt (v1.15).
The processed reads were mapped to hg38 genome by STAR (v.2.7.8a), and then de-duplicated by umi_tools ‘dedup’.
The mapped reads were counted by featureCounts (v.2.0.10).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include log2tpm values for each sample

growth_protocol: Human ASPS cells were grown in  RPMI-1640 supplemented with 10% FBS.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Small interfering RNA-mediated gene silencing of human ASPS cells was performed.

value: human alveolar soft part sarcoma

value: hASPS cells treated with siTFE3


title: HPr1ARcells, D3 treat 1


title: HPr1ARcells, veh treat 3


title: mASPS_null_JQ1_3

description: Gene expression data from mouse sarcoma cell

source_name: ASPS cell line without ASPSCR1-TFE3

treatment_protocol: Mouse ASPS cells were treated with 100 nM JQ1 for 48 hours. Small interfering RNA-mediated gene silencing of human ASPS cells was performed.

value: Alveolar soft part sarcoma


title: Ts65Dn18N5b

source_name: Embryo N5 from dam TS18


title: HPr1ARcells, D3 treat 2


title: HPr1-AR cells, treat 2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FASTQC and Trimmomatic
Trimmed sequence reads were mapped to hg38 using RSubread
Read count extraction and normalization were performed featureCounts and an edgeR workflow in R
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA was isolated via TRIzol® reagent
Sequencing libraries prepared with the TruSeq Stranded Total RNA kit (Illumina Inc), from 1ug total RNA

treatment_protocol: Cells were grown to 70% confluence and treated with 1α,25(OH)2D3 (100nM, 8hr) or EtOH in biological triplicate samples and analyzed by RNA-Seq.

value: European American prostate cancer


title: hASPS BRD4 JQ1

description: Brd4 (Bethyl Laboratories, A301-985A100, lot 7)

source_name: ASPS-KY

value: ASPS-KY

value: hASPS cells treated with JQ1


title: mASPS_null_JQ1_2


title: ASPS1_siTFE3_2


title: Ts65Dn18N3b

source_name: Embryo N3 from dam TS18


title: Ts65Dn137N8b

source_name: Embryo N8 from dam TS137


title: mASPS_null_JQ1_1


title: Ts65Dn137N6b

source_name: Embryo N6 from dam TS137


title: Ts65Dn18N2b

source_name: Embryo N2 from dam TS18


title: hASPS BRD4 DMSO

value: hASPS cells treated with DMSO control


title: mASPS_null_DMSO_3

value: DMSO


title: ASPS1_siNC_2

value: hASPS cells treated with negative control siRNA


title: HPr1-AR cells, veh control 3

value: WT


title: ASPS1_siNC_1


title: HPr1-AR cells, veh control 2


title: HPr1-AR cells, treat 1


title: Ts65Dn18N1b

source_name: Embryo N1 from dam TS18

value: forebrain

value: F


title: mASPS17_JQ1_1

source_name: ASPS cell line expressing ASPSCR1-TFE3


title: hASPS ASPSCR1 DMSO

description: ASPSCR1 (Sigma-Aldrich, HPA026749, lot R12203)


title: mASPS17_JQ1_3


title: HPr1-AR cells, treat 3


title: Ts65Dn137N3b

source_name: Embryo N3 from dam TS137

value: M


title: mASPS17_JQ1_2


title: mASPS_null_DMSO_2


title: hASPS ASPSCR1 JQ1


title: Ts65Dn137N4b

source_name: Embryo N4 from dam TS137


title: LNCaP cells, treat 2

source_name: LNCaP

value: LNCaP

value: European American non-malignant prostate


title: Ts65Dn137N5b

source_name: Embryo N5 from dam TS137


title: Ts65Dn137N1b

source_name: Embryo N1 from dam TS137


title: HPr1-AR cells, veh control 1

value: Vehicle


title: mASPS17_DMSO_1


title: mASPS_null_4


title: mASPS17_DMSO_3


title: four copies of 1q (4X) [600319c1q001]

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description: MM with four copies of 1q (4X)

data_processing:
Adapters were trimmed using skewer embedded in docker4seq package (https://pubmed.ncbi.nlm.nih.gov/29069297/)
Reads were mapped with STAR embedded in docker4seq package
Counts were generated using RSEM embedded in docker4seq package
Genome_build: HG38
Supplementary_files_format_and_content: tab deliminted, counts

source_name: Multiple Myeloma (MM)

extract_protocol:
Total RNA was extracted usingRNeasy mini kit (Qiagen) and following manufacturer’s instructions
TruSeq RNA Exome Illumina kit was used following the procedure suggested by  manufacturer

tag: disease

value: Multiple Myeloma (MM)

tag: group

value: four copies of 1q (4X)


title: LNCaP cells, treat 1


title: MSC_HiChIP_rep

city: Charlestown

first: Rui

last: Dong

address: 149 13th Street

institute: Massachusetts General Hospital

description: raw data not provided due to patient privacy concerns.

data_processing:
Illumina Casava v.2.19 software used for basecalling.
Paired-end HiC reads were aligned against the hg19 genome using HiC-Pro.
The hichipper tool (v 0.7.7) (Lareau et al., 2018) was used for loop calling within H3K27ac ChIP-seq peak (q-value < 0.00001) regions, by applying the following parameters: --max-distance 100000000 --read-length 100
Assembly: hg19
Supplementary files format and content: HiC all valid interaction read pairs (allValidPairs). Columns are: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size
Supplementary files format and content: HiChIP loop contacts (.bedpe). Intrachromosomal looping between anchor loci.

source_name: Primary Mesenchymal stem cells

growth_protocol: The Ewing sarcoma cell lines A673 and SKNMC (ATCC) were grown in RPMI medium containing 10% FCS at 37°C with 5% CO2.  Primary pediatric mesenchymal stem cells were cultured in Iscove’s modified Dulbecco’s medium containing 10% fetal calf serum (FCS) and 10 ng/ml platelet-derived growth factor. shRNA mediated knock-down was used to remove EWS-FLI1 protien  from ewing cells.

extract_protocol:
Genomic DNA/ChIP DNA was isolated from x-linked nuclei after Mbo1 restriction digestion, end filling with biotin-14ATP and following ligation, according to in-situ HiC protocol. H3K27ac antibody was used to pull-down ChIP following HiC and proceed to library construction.
Followed Next Gen DNA Library Kit & Next Gen Indexing Kit from Active Motif

treatment_protocol: Untreated

value: mesenchymal stem cells

value: untreated


title: A673_shFLI1_HiChIP_rep

source_name: Ewing sarcoma cells

value: Ewing sarcoma cells


title: A673_shGFP_HiChIP_rep


title: LNCaP cells, veh control 2


title: mASPS17_DMSO_2

value: Alveolar soft part sarcoma


title: Ts65Dn125N4b

source_name: Embryo N4 from dam TS125


title: four copies of 1q (4X) [600288c1q001]

description: MM with four copies of 1q (4X)


title: four copies of 1q (4X) [600293c1q001]

description: MM with four copies of 1q (4X)


title: mASPS_null_2

source_name: ASPS cell line without ASPSCR1-TFE3


title: Ts65Dn125N8b

source_name: Embryo N8 from dam TS125


title: LNCaP cells, veh control 1


title: four copies of 1q (4X) [600471c1q001]

description: MM with four copies of 1q (4X)


title: mASPS_null_1


title: Ts65Dn125N3b

source_name: Embryo N3 from dam TS125


title: Ts65Dn125N7b

source_name: Embryo N7 from dam TS125


title: LNCaP cells, treat 3


title: Ts65Dn125N5b

source_name: Embryo N5 from dam TS125


title: LNCaP cells, veh control 3


title: mASPS17_2


title: RC43N cells, treat 3

value: African American prostate cancer


title: mASPS17_3


title: four copies of 1q (4X) [600417c1q001]

description: MM with four copies of 1q (4X)


title: Ts65Dn125N1b

source_name: Embryo N1 from dam TS125


title: RC43N cells, treat 1


title: Ts65Dn113N7b

source_name: Embryo N7 from dam TS113


title: Ts65Dn125N2b

source_name: Embryo N2 from dam TS125


title: four copies of 1q (4X) [600448c1q001]

description: MM with four copies of 1q (4X)


title: three copies of 1q (3X) [60031c1q010]

description: MM with three copies of 1q (3X)

value: three copies of 1q (3X)


title: RC43N cells, veh control 2


title: RC43N cells, treat 2


title: four copies of 1q (4X) [600332c1q001]

description: MM with four copies of 1q (4X)


title: RC43N cells, veh control 1


title: RC43N cells, veh control 3


title: RC43T cells, treat 3

value: African American non-malignant prostate


title: three copies of 1q (3X) [600394c1q010]

description: MM with three copies of 1q (3X)


title: HiC^2 of GM12878 WT cells (chr7:157.1-159.1MB)


title: Ts65Dn113N5b

source_name: Embryo N5 from dam TS113


title: RC43T cells, treat 2


title: three copies of 1q (3X) [600450c1q010]

description: MM with three copies of 1q (3X)


title: three copies of 1q (3X) [600388c1q010]

description: MM with three copies of 1q (3X)


title: RC43T cells, treat 1


title: Ts65Dn113N3b

source_name: Embryo N3 from dam TS113


title: Ts65Dn113N4b

source_name: Embryo N4 from dam TS113


title: three copies of 1q (3X) [600382c1q010]

description: MM with three copies of 1q (3X)


title: mASPS17_1

source_name: ASPS cell line expressing ASPSCR1-TFE3


title: HPr1ARcells, D3 treat 3

value: African American

value: prostate cancer


title: Ts65Dn113N6b

source_name: Embryo N6 from dam TS113

value: forebrain


title: three copies of 1q (3X) [600371c1q010]

description: MM with three copies of 1q (3X)

source_name: Multiple Myeloma (MM)


title: Ts65Dn113N1b

source_name: Embryo N1 from dam TS113


title: Ts65Dn113N2b

source_name: Embryo N2 from dam TS113

value: F


title: Ts65Dn11N8b

source_name: Embryo N8 from dam TS11


title: RC43T cells, veh control 2

value: WT


title: three copies of 1q (3X) [600358c1q010]

description: MM with three copies of 1q (3X)


title: RC43T cells, veh control 3


title: RC43T cells, veh control 1


title: Ts65Dn11N7b

source_name: Embryo N7 from dam TS11


title: three copies of 1q (3X) [600350c1q010]

description: MM with three copies of 1q (3X)


title: Ts65Dn11N6b

source_name: Embryo N6 from dam TS11

value: M


title: two copies of 1q (2X) [600481c1q100]

description: MM with two copies of 1q (2X)

value: two copies of 1q (2X)


title: mASPS_null_DMSO_1

source_name: ASPS cell line without ASPSCR1-TFE3

value: DMSO


title: Ts65Dn11N5b

source_name: Embryo N5 from dam TS11


title: Ts65Dn11N4b

source_name: Embryo N4 from dam TS11


title: Ts65Dn11N3b

source_name: Embryo N3 from dam TS11


title: DEG-35 1

city: new york

first: Michael

last: Kharas

state: New York

address: 417 68th street

department: Molecular Pharmacology Program

institute: Mamorial Sloan Kettering Cancer Center

data_processing:
RNA-seq data was processed using analysis pipelines by basepairtech. com.
Reads were aligned reads STAR (illumina) and counted using FeatureCounts.
Differential gene expression analysis was done using DESeq2 - Bioconductor
Assembly: hg19
Supplementary files format and content: csv file is the differential anaysis results that includes log2FoldChange, pvalue, padj values for each genes

growth_protocol: MOLM-13 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS), glutamine and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were treated with DMSO or 50nM DEG-35 for 24hr.

value: AML Cells


title: DEG-35 3


title: Ts65Dn11N1b

source_name: Embryo N1 from dam TS11


title: two copies of 1q (2X) [600483c1q100]

description: MM with two copies of 1q (2X)

value: Multiple Myeloma (MM)


title: DMSO 3


title: WT19-N10-Brain

source_name: Embryo N10 from dam WT19

value: Female


title: two copies of 1q (2X) [600473c1q100]

description: MM with two copies of 1q (2X)


title: DEG-35 2


title: peripheral CD4 T cells 86

type: genomic

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Minfi R package standard protocol. Normalization using ssNoob preprocessing method.

label: Cy5 and Cy3

source_name: peripheral CD4 T cells

label_protocol: Standard Illumina protocol.

growth_protocol: CD4 T cells purified by negative selection from peripheral blood mononuclear cells from HIV uninfected and infected individuals

extract_protocol: DNA extracted with Qiagen kit

tag: hiv infection group

value: Healthy control

tag: gender

tag: age

value: peripheral CD4 T cells


title: DMSO 2


title: two copies of 1q (2X) [600465c1q100]

description: MM with two copies of 1q (2X)


title: peripheral CD4 T cells 85

value: Male


title: peripheral CD4 T cells 79


title: M048R DP IFNg_24h

city: Amsterdam

first: Joleen

last: Traets

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
To remove the sequenced reads of mouse origin from the low passage patient-derived xenografted cell lines, sequenced reads were aligned in parallel using tophat (v2.0.12) to mouse GRCm38 and human GRCh38.
Subsequent alignments to reference were compared according to the edit distance by XenofilteR to keep only sequences more likely human.
For all the samples, the range of filtered reads is between 0.41 to 2.34%.
Of the filtered human reads, per gene reads were counted using itreecount and annotated using Ensembl gtf GRCh38.82.
Assembly: Mouse GRCm38 and human GRCh38
Supplementary files format and content: Raw counts and fastq files

source_name: Patient derived xenograft (PDX) established low passage cell lines

extract_protocol:
Total RNA was extracted using TRIzol reagent (15596-018, Ambion life technologies)  according to the manufactures protocol. Briefly, 0.2x volumes of chloroform (Chloroform stab./Amylene, Biosolve) was added to the Trizol homogenate and the tube(s) (Falcon, 15mL) were shaken vigorously. The tube(s)  were incubated for 2-3 minutes at room temperature and centrifuged  (4500 RCF) (Hettich, rotanta 46 RS) for 1 hour at 4 °C. Approximately 70% of the upper aqueous phase  was transferred to a clean 15 mL tube and 0.5x volume of isopropanol  (33539, Sigma-Aldrich, ) was added. The tube(s) were incubated overnight  at -20 °C and centrifuged (4500 RCF)  for 30 minutes at 4 ° C. The supernatant was removed and the pellet was washed twice with 80% ethanol  (32221-2.5L, Sigma-Aldrich). The total RNA pellet was air-dried for 8 minutes and dissolved  in an appropriate volume of nuclease free water (AM9937, Ambion life technologies) and quantified using  Nanodrop UV-VIS Spectrophotometer.  The total RNA was further purified using  the  RNeasy Mini kit (74106, Qiagen), including an on-column DNase digestion (79254, Qiagen),  according to the manufacture’s instructions. Quality and quantity of the total RNA was assessed by the 2100 Bioanalyzer using a Nano chip (Agilent, Santa Clara, CA).  Total RNA samples having RIN>8 were subjected to library generation. Strand-specific  libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina Inc., San Diego, RS-122-2101/2) according to the manufacturer's instructions (Illumina, Part # 15031047 Rev. E). Briefly, polyadenylated RNA from  intact total RNA was purified using oligo-dT beads. Following purification, the RNA was fragmented, random primed and reverse transcribed using SuperScript II Reverse Transcriptase (Invitrogen, part # 18064-014) with the addition of Actinomycin D. Second strand synthesis was performed using Polymerase I and RNaseH with replacement of dTTP for dUTP. The generated cDNA fragments were 3' end adenylated and ligated to Illumina Paired-end sequencing adapters and subsequently amplified by 12 cycles of PCR. The libraries were analyzed on a 2100 Bioanalyzer using a 7500 chip (Agilent, Santa Clara, CA), diluted and pooled equimolar into multiplex sequencing pools. The  libraries were sequenced with 65 base single reads on a HiSeq2500 using V4 chemistry (Illumina Inc., San Diego).
TruSeq Stranded mRNA sample preparation kit

value: Patient tumor material


title: peripheral CD4 T cells 82


title: two copies of 1q (2X) [600327c1q100]

description: MM with two copies of 1q (2X)


title: peripheral CD4 T cells 83


title: M048R DP Untreated

value: Untreated


title: DMSO 1


title: two copies of 1q (2X) [60022c1q100]

description: MM with two copies of 1q (2X)


title: WT19-N6-Brain

source_name: Embryo N6 from dam WT19

tag: developmental stage


title: peripheral CD4 T cells 84


title: WT19-N9-Brain

source_name: Embryo N9 from dam WT19


title: M048R TS IFNg_24h


title: four copies of 1q (4X) [600381c1q001]

description: MM with four copies of 1q (4X)

value: four copies of 1q (4X)


title: two copies of 1q (2X) [600355c1q100]

description: MM with two copies of 1q (2X)


title: WT19-N5-Brain

source_name: Embryo N5 from dam WT19


title: peripheral CD4 T cells 72


title: peripheral CD4 T cells 81


title: M048R TS Untreated


title: peripheral CD4 T cells 77


title: peripheral CD4 T cells 80


title: WT19-N3-Brain

source_name: Embryo N3 from dam WT19


title: peripheral CD4 T cells 73


title: Dupilumab-induced-psoriasis skin 7

city: Paris

first: Chloé

last: Grolleau

address: 1 avenue Claude Vellefaux

department: Hopital saint Louis

country: France

institute: INSERM U1342, eq 16

hyb_protocol: Each sample was hybridized onto GeneChip® Human Transcriptome Array 2.0 (ThermoFisher Scientific), washed, and stained with the Affymetrix® Fluidics Station 450

scan_protocol: Scanning was performed with the Affymetrix® GeneChip Scanner 3000 7G (ThermoFisher Scientific)

data_processing: The data were analyzed using the Affymetrix Transcriptome Analysis Console (TAC) software v.4 (ThermoFisher Scientific)

label: Biotin

source_name: lesional cutaneous biopsy

label_protocol: Ten nanogram of Total RNA was amplified, labeled, and fragmented using GeneChip WT Pico Reagent Kit (ThermoFisher Scientific)

extract_protocol: Total RNA was automatically extracted from tissue samples using the Maxwell RSC RNA FFPE kit according to the manufacturer’s protocol

value: skin

value: Dupilumab-induced psoriasis


title: two copies of 1q (2X) [600477c1q100]

description: MM with two copies of 1q (2X)

source_name: Multiple Myeloma (MM)


title: peripheral CD4 T cells 76


title: peripheral CD4 T cells 74


title: WT19-N2-Brain

source_name: Embryo N2 from dam WT19

value: forebrain


title: M029R DP IFNg_24h


title: peripheral CD4 T cells 71


title: M029R DP Untreated


title: peripheral CD4 T cells 69


title: Dupilumab-induced-psoriasis skin 6


title: M029R TS IFNg_24h


title: peripheral CD4 T cells 70


title: M029R TS Untreated


title: peripheral CD4 T cells 75


title: Dupilumab-induced-psoriasis skin 5


title: peripheral CD4 T cells 68


title: WT19-N7-Brain

source_name: Embryo N7 from dam WT19


title: Healthy control skin 4

source_name: Biopsy of cutaneous plastic surgery waste


title: WT18-N10-Brain

source_name: Embryo N10 from dam WT18


title: WT18-N12-Brain

source_name: Embryo N12 from dam WT18


title: Healthy control skin 3

description: Gene expression data from skin biopsy of healthy control


title: Healthy control skin 1


title: M029 DP Untreated


title: M029 DP IFNg_24h


title: Healthy control skin 2


title: peripheral CD4 T cells 67


title: WT18-N11-Brain

source_name: Embryo N11 from dam WT18


title: WT19-N8-Brain

source_name: Embryo N8 from dam WT19


title: WT18-N9-Brain

source_name: Embryo N9 from dam WT18


title: M029 TS IFNg_24h


title: M029 TS Untreated


title: peripheral CD4 T cells 78


title: M027 DP IFNg_24h


title: WT18-N5-Brain

source_name: Embryo N5 from dam WT18


title: mASPS_null_3

source_name: ASPS cell line without ASPSCR1-TFE3

value: Alveolar soft part sarcoma


title: M002 DP IFNg_24h

source_name: Patient derived xenograft (PDX) established low passage cell lines


title: WT18-N8-Brain

source_name: Embryo N8 from dam WT18


title: M027 DP Untreated


title: Atopic dermatitis skin 2

description: Gene expression data from skin biopsy of atopic dermatitis

value: Atopic Dermatitis


title: M027 TS IFNg_24h


title: WT19-N1-Brain

source_name: Embryo N1 from dam WT19


title: WT18-N4-Brain

source_name: Embryo N4 from dam WT18


title: Atopic dermatitis skin 4


title: WT18-N3-Brain

source_name: Embryo N3 from dam WT18


title: M027 TS Untreated


title: Atopic dermatitis skin 3

source_name: lesional cutaneous biopsy


title: peripheral CD4 T cells 63

source_name: peripheral CD4 T cells

value: ART


title: WT18-N2-Brain

source_name: Embryo N2 from dam WT18


title: Psoriasis skin 3

description: Gene expression data from skin biopsy of psoriasis lesion

value: Psoriasis


title: Psoriasis skin 2


title: Atopic dermatitis skin 1


title: M002 DP Untreated


title: peripheral CD4 T cells 65


title: WT18-N1-Brain

source_name: Embryo N1 from dam WT18


title: M026R DP IFNg_24h


title: WT15-N8-Brain

source_name: Embryo N8 from dam WT15


title: Psoriasis skin 1


title: M026R DP Untreated


title: peripheral CD4 T cells 64


title: peripheral CD4 T cells 60

value: EC


title: M026R TS IFNg_24h


title: Dupilumab-induced-psoriasis skin 3

description: Gene expression data from skin biopsy of psoriasis lesions induced under dupilumab treatment initiated for atopic dermatitis


title: WT15-N6-Brain

source_name: Embryo N6 from dam WT15


title: WT15-N7-Brain

source_name: Embryo N7 from dam WT15


title: peripheral CD4 T cells 61


title: WT15-N3-Brain

source_name: Embryo N3 from dam WT15


title: peripheral CD4 T cells 59


title: M026R TS Untreated


title: M026 DP IFNg_24h


title: WT18-N6-Brain

source_name: Embryo N6 from dam WT18


title: Dupilumab-induced-psoriasis skin 1


title: Dupilumab-induced-psoriasis skin 2


title: Psoriasis skin 4


title: WT15-N5-Brain

source_name: Embryo N5 from dam WT15


title: peripheral CD4 T cells 58


title: Dupilumab-induced-psoriasis skin 4


title: peripheral CD4 T cells 57


title: WT15-N2-Brain

source_name: Embryo N2 from dam WT15


title: M026 DP Untreated


title: M026 TS IFNg_24h


title: M026 TS Untreated


title: peripheral CD4 T cells 55


title: WT13-N8-Brain

source_name: Embryo N8 from dam WT13


title: M002 TS IFNg_24h

source_name: Patient derived xenograft (PDX) established low passage cell lines


title: peripheral CD4 T cells 53


title: M019R DP IFNg_24h


title: M019R DP Untreated


title: peripheral CD4 T cells 56


title: WT13-N4-Brain

source_name: Embryo N4 from dam WT13


title: WT13-N7-Brain

source_name: Embryo N7 from dam WT13


title: peripheral CD4 T cells 66


title: peripheral CD4 T cells 54


title: P30 wildtype harvested following 5h of sleep deprivation, replicate 4 [WTSD5_P90_PFC_4]

city: Spokane

first: Lucia

last: Peixoto

state: WA

address: PO Box 1495

department: College of Medicine

institute: Washington State University, Spokane

description: Reanalyzed from GSE113754

data_processing:
Raw sequencing reads in FASTQ files  were processed with Salmon v1.8 using the ‘mapping mode’. To prepare the index, Gencode (release M28) reference genome (‘GRCm39.primary_assembly.genome.fa.gz’) and reference transcriptome (‘gencode.vM28.transcripts.fa.gz)’ were downloaded, along with GTF coordinates (‘gencode.vM28.annotation.gtf.gz’). To improve the accuracy of quantification estimates from Salmon, an index was built that incorporated a set of genome targets as decoys. Using the concatenated list of transcriptome targets along with genome targets, the `salmon index` function was used to build the index with the flags: `--gencode`, `--threads 4`, and  `-k 31`.
`salmon quant` was used to perform quantification with the flags `--threads 6` and `--numBootstraps 30`. To create the final SummarizedExperiment object at the gene level, the summarizeToGene()` function from the tximeta (v1.14) R/Bioconductor package was used.
Assembly: GRCm39
Supplementary files format and content: text file, summarized experiment with gene counts (Tximeta) for gene level analysis

source_name: Pre Frontal Cortex

growth_protocol: Timed breeding pairs were established to obtain wild type (WT) at specific postnatal ages. Mice were house in standard cages on a 12:12 h light:dark cycle with food and water ad libitum. P16 mice were housed with the littermates and parents until the experiment. P24 mice were weaned and single housed at P18. P30 and P90 animals were weaned at P21 and single housed for a week before SD.

extract_protocol:
RNA was extracted from thawed tissue using the Qiagen RNAeasy Microarray Tissue kit with RWT buffer. The tissue was lysed and homogenized using a TissueLyzer. Briefly, 1ml of Qiazol was added to the pre-sterilized 2ml round bottom tubes with one 5mm steel bead inside,before adding the frozen tissue. The tissue was liyed for 2x 2min at 30Hz. Samples were spun down and the clear lysate was transfere to a clean tube. RNA was isolated through phase separation. For this, 200 µl of water saturated chloroform with isoamylalcohol (ChCl3:IAA 24:1) was added followed by vigorous shaking, incubated at rorom temparature of 3 min and then centrifuged at 12,000 g for 15 min at 4C. The aqueous phase was transfered to a new tube and 600ul of 100% EtOH was added. The ethanol-lysate mix was then loaded on a RNAeasy mini spin column and centrifuged at max speed for 30sec at room temparature. The loaded colums were washed using 500 µl of RWT (Qiagen), centrifuged again for 30s at max speed at room temparature. The flowthrough was discarded. The membrane was washed twice with 500 µl of RPE buffer (Qiagen) followed by a 30s (first wash) or 2min (second wash) spin at max speed at room temparature. RNA was eluted from the membrane with 30ul of RNase free water. The RNase free water was loaded directly onto the semi dry membran, centrifuged for one min at max speed at RT. This step was reapeated once by re-loading the eluat and centrigation again for 1min at room temparature. 1ul of the RNA eluat was used to measure concentrations in the Nanodrop. The extraced RNA sampel was aliquoted in 2x15ul aliquots and stored at -80C until further processing.
The integrity of total RNA was assessed using Fragment Analyzer (Advanced Analytical Technologies, Ankeny, IA) with the High Sensitivity RNA Analysis Kit.  RNA Quality Numbers (RQNs) from 1 to 10 were assigned to each sample to indicate its integrity or quality.  RNA samples with RQNs ranging from 7 to 10 were used for RNA library preparation with the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA).  Briefly, mRNA was isolated from 2.5 µg of total RNA using poly-T oligo attached to magnetic beads and then subjected to fragmentation, followed by cDNA synthesis, dA-tailing, adaptor ligation and PCR enrichment.  The sizes of RNA libraries were assessed by Fragment Analyzer with the High Sensitivity NGS Fragment Analysis Kit.  The concentrations of RNA libraries were measured by StepOnePlus Real-Time PCR System (ThermoFisher Scientific, San Jose, CA) with the KAPA Library Quantification Kit (Kapabiosystems, Wilmington, MA).  The libraries were diluted to 2 nM with RSB (10 mM Tris-HCl, pH8.5) and denatured with 0.1 N NaOH.  Eighteen pM libraries were clustered in a high-output flow cell using HiSeq Cluster Kit v4 on a cBot (Illumina).  After cluster generation, the flow cell was loaded onto HiSeq 2500 for sequencing using HiSeq SBS kit v4 (Illumina).  DNA was sequenced from both ends (paired-end) with a read length of 100 bp.

treatment_protocol: Begining at light onset, sleep deprived mice were kept awake for 3 or 5 hours via gentle handling. P16 animals for SD or homecage control were separated from the dam and housed in groups of 2 or 3 in a prewarmed cage. Prefrontal cortex tissue was collected at the conclusion of sleep deprivation (SD) and immediately flash frozen in liquid nitrogen. Control animals that were left in their home cage to sleep were dissected at the same time of day (HC).

value: Pre Frontal Cortex

value: Brain Tissue Homogenate

value: wild type

value: Sleepdeprivation


title: M019R TS IFNg_24h


title: peripheral CD4 T cells 48

value: peripheral CD4 T cells


title: WT13-N3-Brain

source_name: Embryo N3 from dam WT13

value: Female


title: P30 wildtype harvested following 5h of sleep deprivation, replicate 3 [WTSD5_P90_PFC_3]

description: Reanalyzed from GSE113754


title: peripheral CD4 T cells 49

value: Male


title: WT15-N1-Brain

source_name: Embryo N1 from dam WT15


title: P30 wildtype harvested following 5h of sleep deprivation, replicate 2 [WTSD5_P90_PFC_2]

description: Reanalyzed from GSE113754


title: M016 DP IFNg_24h

value: Patient tumor material


title: WT13-N5-Brain

source_name: Embryo N5 from dam WT13


title: WT13-N2-Brain

source_name: Embryo N2 from dam WT13


title: peripheral CD4 T cells 51

source_name: peripheral CD4 T cells


title: M019R TS Untreated

value: Untreated


title: P30 wildtype harvested following 5h of sleep deprivation, replicate 1 [WTSD5_P90_PFC_1]

description: Reanalyzed from GSE113754


title: M016 DP Untreated


title: WT12-N10-Brain

source_name: Embryo N10 from dam WT12


title: P90 wildtype homecage control harvested at ZT hour 5, replicate 5 [WTHC5_P90_PFC_5]

description: Reanalyzed from GSE113754

value: control


title: M016 TS IFNg_24h


title: peripheral CD4 T cells 46


title: P90 wildtype homecage control harvested at ZT hour 5, replicate 4 [WTHC5_P90_PFC_4]

description: Reanalyzed from GSE113754


title: M016 TS Untreated


title: P90 wildtype homecage control harvested at ZT hour 5, replicate 3 [WTHC5_P90_PFC_3]

description: Reanalyzed from GSE113754


title: peripheral CD4 T cells 50


title: WT13-N6-Brain

source_name: Embryo N6 from dam WT13


title: WT12-N7-Brain

source_name: Embryo N7 from dam WT12


title: peripheral CD4 T cells 52


title: peripheral CD4 T cells 47


title: P90 wildtype homecage control harvested at ZT hour 5, replicate 2 [WTHC5_P90_PFC_2]

description: Reanalyzed from GSE113754


title: WT12-N9-Brain

source_name: Embryo N9 from dam WT12


title: M011-5R DP Untreated


title: M011-5R DP IFNg_24h


title: peripheral CD4 T cells 42


title: WT13-N1-Brain

source_name: Embryo N1 from dam WT13


title: WT12-N8-Brain

source_name: Embryo N8 from dam WT12


title: WT12-N6-Brain

source_name: Embryo N6 from dam WT12


title: peripheral CD4 T cells 41


title: peripheral CD4 T cells 43


title: M091 DP Untreated


title: WT12-N5-Brain

source_name: Embryo N5 from dam WT12


title: M091 TS IFNg_24h

source_name: Patient derived xenograft (PDX) established low passage cell lines


title: M091 DP IFNg_24h


title: M091 TS Untreated


title: peripheral CD4 T cells 38


title: M082 DP IFNg_24h


title: M082 DP Untreated


title: WT11-N4-Brain

source_name: Embryo N4 from dam WT11


title: peripheral CD4 T cells 39


title: M082 TS IFNg_24h


title: WT12-N3-Brain

source_name: Embryo N3 from dam WT12


title: WT12-N2-Brain

source_name: Embryo N2 from dam WT12


title: P30 wildtype harvested following 5h of sleep deprivation, replicate 5 [WTSD5_P90_PFC_5]

description: Reanalyzed from GSE113754

source_name: Pre Frontal Cortex


title: WT12-N4-Brain

source_name: Embryo N4 from dam WT12


title: M082 TS Untreated


title: WT11-N1-Brain

source_name: Embryo N1 from dam WT11


title: peripheral CD4 T cells 40


title: WT11-N2-Brain

source_name: Embryo N2 from dam WT11


title: peripheral CD4 T cells 44

source_name: peripheral CD4 T cells

value: Viremic


title: M011-5R TS IFNg_24h


title: peripheral CD4 T cells 35


title: RHE_multiplexed_2011 BC

city: Southampton

first: Francesca

last: Ciccarelli

address: Southampton General Hospital

country: United Kingdom

institute: University of Southampton

description: Hashtag barcode sequencing file (BC) to assign cells to each of the three bacterial conditions. Cells are labelled with one of three multiplexing barcodes which should be used to annotate the cells in the corresponding GEX sequencing file. Both BC and GEX files are in paired-end format.

data_processing:
Illumina-generated BCL (base call files) containing raw sequencing data were converted to fastq format by using the bcl2fastq tool.
transcript-to-gene mapping was performed in the Kallisto (v.0.46.1) Bustools (v.0.39.3) workflow to generate gene counts and a cell by gene matrix, which was exported as an h5ad file.
Genome_build: hg19
Supplementary_files_format_and_content: h5ad, a set of associated annotated data matrices including count matrix and associated metadata.

source_name: reconsituted human epidermis (RHE)

extract_protocol:
Single cell suspensions of dissociated pooled models after cell hashtagging were enscapsulated using the DropSeq protocol.
cDNa libraries were generated from template-switching, reverse transcription and preperation using the Illumina Nextera XT DNA library preperation kit.

value: reconsituted human epidermis (RHE)

value: multiplexed by cell hashing

value: TotalSeq-A0251 (GTCAACTCTTTAGCG)

value: TotalSeq-A0252 (TGATGGCCTATTGGG)

value: TotalSeq-A0253 (TTCCGCCTCTCTTTG)


title: peripheral CD4 T cells 34


title: M080 DP Untreated


title: RHE_multiplexed_1811 GEX


title: M080 TS IFNg_24h


title: RHE_multiplexed_0110 GEX


title: RHE_multiplexed_1811 BC


title: P90 wildtype homecage control harvested at ZT hour 5, replicate 1 [WTHC5_P90_PFC_1]

description: Reanalyzed from GSE113754


title: M080 TS Untreated


title: RHE_multiplexed_0110 BC


title: peripheral CD4 T cells 32

value: EC


title: peripheral CD4 T cells 36


title: M067 DP IFNg_24h


title: peripheral CD4 T cells 45

value: ART


title: M067 DP Untreated


title: peripheral CD4 T cells 33


title: peripheral CD4 T cells 30


title: M080 DP IFNg_24h


title: M067 TS IFNg_24h


title: WT11-N3-Brain

source_name: Embryo N3 from dam WT11

value: forebrain


title: STA_21

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

country: Czech Republic

institute: Institute for Clinical and Experimental Medicine

data_processing:
High throughput sequencing of final pool was performed using NovaSeq6000 S4 system (Illumina) with following instrument settings: paired-end, 150 b, 4500-5000 million reads per lane.
Raw data were automatically processed by Basespace cloud interface (Illumina) in default settings.
The basecalling, adapter clipping, and quality filtering were carried out using bcl2fastq v2.20.0.422 Conversion Software (Illumina).
The quality of raw reads was evaluated using FastQC (v0.11.5) and MultiQC (v1.6).
Clipping adaptor sequences was carried out using cutadapt (v1.18). The trimmed reads were aligned to the human cDNA reference (GeCh38) using bowtie2 (v 2.1.0). The counts of reads mapped to the reference were extracted and used for differential gene expression analysis using SAMtools (v1.2).
DESeq2 R library version 1.2 was applied to normalize read counts and to identify differences in gene expression between sample groups
Assembly: human transcriptome reference (GeCh38)
Supplementary files format and content: Matrix table with raw transcript counts for every transcript and every sample

source_name: peripheral blood

extract_protocol:
Total RNA was isolated from peripheral blood (PAXgene blood RNA kit, Qiagen), concentration was measured by Qubit fluorimetr and RNA integrity number was checked using Agilent Bioanalyzer 2100. Isolated RNA (800ng) was rRNA and globin depleted using NEBNext® Globin & rRNA Depletion Kit (New England, BioLabs, Inc).
Transcriptome libraries for differential gene expression were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads according to the manufacturer’s protocol (New England, BioLabs, Inc). In brief, depleted RNA was randomly sheared by heat digestion in the presence of a divalent metal cation (Mg2+). Sheared RNA was reversibly transcribed making 1st strand of cDNA using random hexamers as primers and reverse transcriptase. The second strand was created using dUTPs and after purification with Sample Purification Beads, NEBNext adapters were ligated. After removal of 2nd strand by uracil-DNA-dependent glycosylase, final amplification of adaptor ligated DNA using NEBNext® Multiplex Oligos for Illumina® was done. Library quality was assessed on a Bioanalyzer 2100 using Agilent DNA 1000 assay.

value: peripheral blood

tag: condition

value: STA

tag: age at sampling (years)

tag: creatinine at sampling (umol/l)

tag: clinical diagnosis

value: >= 15 years after transplantation with stable renal function (creatinine in last 5 years <150 umol/l  and no proteinuria)


title: M067 TS Untreated


title: STA_20


title: peripheral CD4 T cells 29

tag: cell type

value: peripheral CD4 T cells


title: M063R DP IFNg_24h

tag: treatment


title: STA_19


title: STA_18


title: peripheral CD4 T cells 28

value: Male


title: M063R DP Untreated

value: Patient tumor material


title: peripheral CD4 T cells 31


title: M063R TS IFNg_24h


title: STA_17


title: peripheral CD4 T cells 26


title: STA_16


title: peripheral CD4 T cells 37


title: M063R TS Untreated

value: Untreated


title: M011-5R TS Untreated


title: STA_15


title: M061R DP IFNg_24h


title: RHE_multiplexed_2011 GEX


title: STA_14


title: peripheral CD4 T cells 23


title: peripheral CD4 T cells 25


title: M061R DP Untreated


title: STA_13


title: STA_12


title: STA_22


title: peripheral CD4 T cells 21


title: M061R TS IFNg_24h


title: M061R TS Untreated


title: STA_11


title: peripheral CD4 T cells 22


title: M002 TS Untreated


title: peripheral CD4 T cells 17


title: peripheral CD4 T cells 24


title: P16 wildtype harvested following 3h of sleep deprivation, replicate 5 [WTSD3_P16_PFC_5]

value: Pre Frontal Cortex

value: Brain Tissue Homogenate

value: wild type

value: Sleepdeprivation


title: STA_10


title: STA_23


title: STA_9


title: Normal rep2

city: Shanghai

first: Lian-Qun

last: Wu

address: 83 Fenyang Road

institute: Fudan University

data_processing:
Basecalls performed using CASAVA version 1.8.
Trimmomatic software was first used for adpter removing, And then low-quality bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads.
In order to generate SAM file, we used BWA[10] software to align the sequencing reads of each sample with reference genome.
CircRNA Identifier (CIRI) software  was used to scan paired chiastic clipping (PCC) signals in SAM files, and circRNA sequences were predicted based on junction reads and GT-AG splicing signals. Meanwhile, the predicted circRNAs were compared with the circRNAs recorded in circBase (http://www.circbase.org/), which provides scripts to identify known and novel circRNAs
Differentially expressed  circRNAs were screened by the DESeq package  in R, with the cut-off criteria of |log2 FC (fold change) | ≥ 1 and p value < 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include back-spliced reads values and RPM

source_name: orbital adipose/connective tissue samples of  control individuals

extract_protocol:
Total RNA was isolated from each orbital adipose/connective tissue sample using mirVana miRNA Isolation Kit (Ambion, Austin, TX) according to the manufacturer’s protocol.
The ribosomal RNA (rRNA) was removed from the extracted total RNA, and strand-specific RNA-seq libraries were built by TruSeq Stranded Total RNA with Ribo-Zero Gold (Illumina, San Diego, CA) according to the manufacturer’s instructions.

value: Orbital adipose/connective tissue

value: control


title: STA_8


title: peripheral CD4 T cells 16

value: Viremic


title: Normal rep3


title: peripheral CD4 T cells 19


title: peripheral CD4 T cells 20

value: EC

value: Female


title: STA_7


title: P16 wildtype harvested following 3h of sleep deprivation, replicate 2 [WTSD3_P16_PFC_2]


title: TAO rep3

source_name: Orbital adipose/connective tissue samples of patients diagnosed as TAO

value: thyroid-associated ophthalmopathy


title: P16 wildtype harvested following 3h of sleep deprivation, replicate 3 [WTSD3_P16_PFC_3]


title: STA_6

value: peripheral blood


title: peripheral CD4 T cells 15


title: P16 wildtype harvested following 3h of sleep deprivation, replicate 1 [WTSD3_P16_PFC_1]


title: TAO rep2


title: peripheral CD4 T cells 11


title: P16 wildtype homecage control harvested at ZT hour 3, replicate 5 [WTHC3_P16_PFC_5]


title: P16 wildtype harvested following 3h of sleep deprivation, replicate 4 [WTSD3_P16_PFC_4]


title: peripheral CD4 T cells 10


title: peripheral CD4 T cells 27


title: peripheral CD4 T cells 13


title: CCD_OxSB2 Ox/SB treated, biological rep 2

city: Barcelona

first: Alexandre

last: CALON

address: Dr. Aiguader, 88

institute: Hospital del Mar Medical Research Institute (IMIM)

description:
Ox/SB treated, biological rep 2
gene expression data from Ox/SB treated cells

hyb_protocol: cDNA was hybridized to Affymetrix PrimeView human gene expression arrays for 16 hours at 45ºC.Washing and staining of microarrays was performed using a GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned in a GeneAtlas Imaging Station (Affymetrix, Santa Clara, CA)

data_processing: Analyses were performed with Transcriptome Analysis Console (TAC) Software (Applied Biosystems) applying RMA summarization.

source_name: CCD-18Co treated with oxaliplatin and SB431542

label_protocol: 25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Human Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Fibroblasts were grown using standard methods at 37ºC and 5% CO2.

extract_protocol: RNA extraction was done in TRIZOL and washed with Qiagen kit following manufacturer's instructions.

treatment_protocol: CCD-18Co cells were treated with oxaliplatin (100 µM) for 6 days. When indicated, cells were treated with 5 µM TGFBR1 receptor inhibitor (SB431542). Gene expression profiles from treated and control cells were measured in duplicate using Affymetrix PrimeView human gene expression arrays.

value: treated


title: peripheral CD4 T cells 12


title: P16 wildtype homecage control harvested at ZT hour 3, replicate 3 [WTHC3_P16_PFC_3]


title: STA_3

value: STA

value: >= 15 years after transplantation with stable renal function (creatinine in last 5 years <150 umol/l  and no proteinuria)


title: Z119_MI2

city: New Orleans

first: Nakhle

last: Saba

state: LA

address: 1415 Tulane Ave, Room 118

department: Internal Medicine/Hematology

institute: Tulane University

data_processing:
Reads were aligned to hg38 using STAR v2.6.1d (--outReadsUnmapped Fastx --outSAMtype BAM   SortedByCoordinate --outSAMunmapped Within --outWigType bedGraph --outWigStrand Unstranded --outWigNorm None --alignIntronMax 100000 --alignMatesGapMax 100000 --alignSJDBoverhangMin 5 --alignSJstitchMismatchNmax 5   -1   5   5 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimOutType Junctions WithinBAM --chimSegmentReadGapMax 3 --chimOutJunctionFormat 1 --twopassMode Basic)
Reads were psuedo-aligned to hg38 transcriptome using kallisto quant v.0.46.0 for abundance measurements
Assembly: hg38
Supplementary files format and content: tab deliminted text file with read counts for genes across all samples

source_name: Acute lymphoblastic leukemia

growth_protocol: cells were cultured in RPMI1640 with 5%FBS and antibiotics (penicillin and streptimycin) at 37C and 5%CO2

extract_protocol: Qiagen RNeasy kit

treatment_protocol: Coculture with MI-2 at a concentration of during 48hrs

value: Acute lymphoblastic leukemia


title: TOM1_MI2


title: STA_2


title: STA_5


title: CCD_OxSB1 Ox/SB treated, biological rep 1

description:
Ox/SB treated, biological rep 1
gene expression data from Ox/SB treated cells


title: P16 wildtype homecage control harvested at ZT hour 3, replicate 2 [WTHC3_P16_PFC_2]


title: peripheral CD4 T cells 8

value: Male

value: peripheral CD4 T cells


title: CCD_Ox2 Ox treated, biological rep 2

description:
Ox treated, biological rep 2
gene expression data from Ox treated cells

source_name: CCD-18Co treated with oxaliplatin


title: SMS-SB_MI2

value: SMS-SB


title: P16 wildtype homecage control harvested at ZT hour 3, replicate 4 [WTHC3_P16_PFC_4]

value: Pre Frontal Cortex

value: Brain Tissue Homogenate


title: CCD_Ox1 Ox treated, biological rep 1

description:
Ox treated, biological rep 1
gene expression data from Ox treated cells


title: peripheral CD4 T cells 7


title: P16 wildtype homecage control harvested at ZT hour 3, replicate 1 [WTHC3_P16_PFC_1]

value: wild type


title: peripheral CD4 T cells 5


title: TAO rep1

value: Orbital adipose/connective tissue


title: 697_MI2


title: peripheral CD4 T cells 4


title: OT_71

value: OT

value: stable graft function  for >=1 year after complete immunosuppression withdrawal


title: Mm, DSX, 204

description: alternate title: A377-A378T8

data_processing:
Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp
Reads were aligned with STAR 2.7.2b against the zebrafish genome (danRer11) or the mouse genome (mm10)
Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R
Read counts were normalized in R using EdgeR
All code used in processing is available at https://github.com/MVesuviusC/2022_VGLL2_NCOA2_paper
Assembly: danRer11 or mm10
Supplementary files format and content: geneCountsCombinedDr_norm.txt.gz and geneCountsCombinedDr_norm.txt.gz are tables containing normalized gene counts

source_name: C2C12_pcDNA Control

extract_protocol:
For zebrafish, GFP positive (and thus transgene positive) tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: C2C12_pcDNA Control

tag: strain

value: Swiss Nude

tag: age at sac

value: 74 days

tag: transgene

value: C2C12 + pcDNA3.1 allograft

value: myoblasts

tag: model

value: allograft model


title: peripheral CD4 T cells 14

value: Viremic


title: STA_1

tag: tissue

value: peripheral blood

value: STA

value: >= 15 years after transplantation with stable renal function (creatinine in last 5 years <150 umol/l  and no proteinuria)


title: CCD_Ct2 control, biological rep 2

description:
control, biological rep 2
gene expression data from control cells

source_name: CCD-18Co control

value: non-treated


title: RS4;11_MI2

value: Acute lymphoblastic leukemia

tag: cell line


title: Dr, D689

description: alternate title: A374-A375T22

source_name: CICDUX4 Tumor

value: CICDUX4 Tumor

tag: genotype

value: Wildtype (AB/TL)

value: 72 days

value: ptz725 BetaActin-GFP2A-CICDUX4 injected

value: mosaic genetic tumor model


title: RCH-ACV_MI2

value: RCH-ACV


title: OT_69

value: OT

value: stable graft function  for >=1 year after complete immunosuppression withdrawal


title: Dr, D687

description: alternate title: A374-A375T20


title: Dr, D688

description: alternate title: A374-A375T21


title: Normal rep1

value: Orbital adipose/connective tissue

tag: disease

value: control


title: CCD_Ct1 control, biological rep 1

description:
control, biological rep 1
gene expression data from control cells


title: NALM6_MI2


title: peripheral CD4 T cells 9

tag: hiv infection group

tag: gender

value: Male

value: peripheral CD4 T cells


title: OT_67

value: peripheral blood


title: Dr, D686

description: alternate title: A374-A375T19


title: OT_65


title: KOPN8_MI2


title: Dr, D685

description: alternate title: A374-A375T18

value: 69 days


title: Mm, DSX, 207

description: alternate title: A377-A378T4

source_name: C2C12-VGLL2NCOA2 Tumor

value: C2C12-VGLL2NCOA2 Tumor

value: Swiss Nude

value: 74 days

value: C2C12 + pcDNA3.1-VGLL2NCOA2 allograft

value: myoblasts

value: allograft model


title: OT_66


title: peripheral CD4 T cells 2

value: Viremic

tag: age


title: Dr, D684

description: alternate title: A374-A375T17

value: CICDUX4 Tumor

value: Wildtype (AB/TL)

value: ptz725 BetaActin-GFP2A-CICDUX4 injected

value: mosaic genetic tumor model


title: OT_64

tag: condition

value: OT

value: stable graft function  for >=1 year after complete immunosuppression withdrawal


title: OT_63

tag: age at sampling (years)


title: KASUMI-2_MI2

value: Acute lymphoblastic leukemia


title: peripheral CD4 T cells 1

value: Male

value: peripheral CD4 T cells


title: Mm, DSX, 203

description: alternate title: A377-A378T2


title: Dr, D682

description: alternate title: A374-A375T16

value: 66 days


title: HB11;19_MI2


title: OT_62

value: peripheral blood

tag: creatinine at sampling (umol/l)


title: Mm, DSX, 201

description: alternate title: A377-A378T1

value: C2C12-VGLL2NCOA2 Tumor

value: Swiss Nude


title: Dr, D681

description: alternate title: A374-A375T15

value: 62 days


title: OT_34

tag: clinical diagnosis


title: BV173_MI2


title: Mm, DSX, 205

description: alternate title: A377-A378T3

value: 74 days

value: C2C12 + pcDNA3.1-VGLL2NCOA2 allograft

tag: cell type

value: myoblasts


title: Mm, DSX, 209

description: alternate title: A377-A378T5

value: allograft model


title: peripheral CD4 T cells 18

value: Viremic


title: Z119_untreated

tag: treatment

value: Control


title: peripheral CD4 T cells 6

value: ART


title: TOM1_untreated


title: Mm, DSX, 211

description: alternate title: A377-A378T6

tag: strain


title: Dr, D669

description: alternate title: A374-A375T13

value: CICDUX4 Tumor

value: Wildtype (AB/TL)

tag: age at sac

value: 49 days

value: ptz725 BetaActin-GFP2A-CICDUX4 injected

value: mosaic genetic tumor model


title: peripheral CD4 T cells 3

value: Male

value: peripheral CD4 T cells


title: Dr, D678

description: alternate title: A374-A375T14

value: 58 days

tag: transgene


title: OT_23

value: peripheral blood

value: OT

value: stable graft function  for >=1 year after complete immunosuppression withdrawal


title: Dr, D668

description: alternate title: A374-A375T12

tag: model


title: SMS-SB_untreated

tag: tissue

value: Acute lymphoblastic leukemia

value: SMS-SB


title: OT_21


title: Dr, D655

description: alternate title: A374-A375T11

value: 85 days

tag: cell line


title: 697_untreated


title: OT_18


title: RS4;11_untreated


title: hASPS_siTFE3_4

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

institute: Japanese Foundation for Cancer Research

description: Gene expression data from human sarcoma cell

source_name: human ASPS cell line with ASPSCR1-TFE3 knockdown

value: Alveolar soft part sarcoma


title: hASPS_siTFE3_2


title: hASPS_siTFE3_3


title: OT_17


title: Dr, Muscle2

city: Columbus

first: Genevieve

last: Kendall

address: 700 Children's Drive, WA5014

institute: Nationwide Children's Hospital / The Ohio State University

description: alternate title: A374-A375T23

source_name: Normal Back Skeletal Muscle

value: Normal Back Skeletal Muscle

tag: genotype

value: 258 days

value: no transgene


title: RCH-ACV_untreated

value: RCH-ACV

value: Control


title: OT_05


title: hASPS_siTFE3_1


title: NALM6_untreated


title: KOPN8_untreated


title: HC_14

value: HC

value: healthy people with no transplant and no immunosuppression


title: Dr, D813-Back

description: alternate title: A667T28

source_name: VGLL2-NCOA2 Tumor

value: VGLL2-NCOA2 Tumor

value: Wildtype (AB/TL)

value: 47 days

value: ptz876 cmv-GFP2A-VGLL2NCOA2 injected

value: mosaic genetic tumor model


title: HC_13

value: peripheral blood


title: Dr, D808

description: alternate title: A667T27

value: 44 days


title: hASPS_siNC_4

source_name: human ASPS cell line expressing ASPSCR1-TFE3


title: OT_33

value: OT

value: stable graft function  for >=1 year after complete immunosuppression withdrawal


title: KASUMI-2_untreated

value: Acute lymphoblastic leukemia


title: HC_12


title: Dr, D807

description: alternate title: A667T26

value: 100 days


title: HPB-NULL_untreated

value: HPB-NULL


title: HC_11


title: Dr, D813-Tail

description: alternate title: A667T29


title: Dr, D801

description: alternate title: A667T25

value: 75 days


title: Dr, Muscle3

description: alternate title: A374-A375T24

value: Normal Back Skeletal Muscle

value: 258 days

value: no transgene


title: BV173_untreated

value: Control


title: Dr, D800

description: alternate title: A667T24

value: VGLL2-NCOA2 Tumor


title: HB11;19_untreated


title: HC_9

value: HC

value: healthy people with no transplant and no immunosuppression


title: HC_10


title: hASPS_siNC_3

value: Alveolar soft part sarcoma


title: Dr, D799

description: alternate title: A667T23

value: Wildtype (AB/TL)

value: ptz876 cmv-GFP2A-VGLL2NCOA2 injected

value: mosaic genetic tumor model


title: CCD_T_1 treated, biological rep 1

description:
treated, biological rep 1
gene expression data from treated cells

hyb_protocol: cDNA was hybridized to GeneAtlas Human Genome HG-133+PM strip arrays for 16 hours at 45ºC.Washing and staining of microarrays was performed using a GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

source_name: CCD-18Co treated with recombinant human TGF-β1

treatment_protocol: CCD-18Co cells were treated with recombinant human TGF-β1 (5ng/mL) for 8 hours in DMEM supplemented with 0.2% FBS. Gene expression profiles from treated and control cells were measured in duplicate using Affymetrix HT_HG-U133_Plus_PM human gene expression arrays.

value: treated


title: HC_8

value: peripheral blood


title: Dr, D742

description: alternate title: A667T21

value: tp53M214K mutant

value: 51 days


title: hASPS_siNC_2


title: Dr, D777

description: alternate title: A667T22

value: 50 days


title: Dr, D739

description: alternate title: A667T20

value: 49 days


title: HC_6


title: HC_5


title: CCD_T_2 treated, biological rep 2

description:
treated, biological rep 2
gene expression data from treated cells


title: CCD_Ct_2 control, biological rep 2

value: non-treated


title: CCD_Ct_1 control, biological rep 1


title: HC_4


title: HC_3


title: Neu (PB): Peripheral Blood Neutrophils

city: Yokohama

first: Hidehiro

last: FUKUYAMA

state: Kanagawa

address: 1-7-22, Suehirocho, Tsurumi-ku

department: IMS

institute: RIKEN

data_processing:
Read alignment: TopHat2 v2.0.8 and Bowtie2 v2.1.0 with default settings
expression level: Cufflinks v2.1.1 with default settings
FPKM (Fragments per Kirobase per Million reads) were calculated.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Peripheral blood

extract_protocol:
Neutrophils and DP cells were fractionated from mice by using a cell sorter after LPS intranasal instillation. Sorted cells were lysed in TRIzol LS reagent (Thermo Fisher Scientific) and total RNA was extracted.
DNA library preparation for RNA-Seq analysis using a [an NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB)].

treatment_protocol: LPS intranasal instillation (10 µg of LPS in 10 µL of PBS into bilateral nostrils)

value: 6-15 weeks

value: wild-type

tag: lps treatment

value: 1 day after LPS

value: Peripheral blood


title: HC_7

value: HC


title: Neu (Nose): Nasal Neutrophils

source_name: nose

value: nose


title: HC_2

source_name: peripheral blood

value: healthy people with no transplant and no immunosuppression


title: DP: Nasal Double positive cells

value: 2 days after LPS


title: STA_4

value: STA

value: >= 15 years after transplantation with stable renal function (creatinine in last 5 years <150 umol/l  and no proteinuria)


title: HC_1


title: Mm, DSX, 202

description: alternate title: A377-A378T7

value: C2C12_pcDNA Control

value: Swiss Nude

value: 74 days

value: C2C12 + pcDNA3.1 allograft

value: myoblasts

value: allograft model


title: Dr, D738

description: alternate title: A667T19

value: VGLL2-NCOA2 Tumor

value: tp53M214K mutant

value: 44 days

value: ptz876 cmv-GFP2A-VGLL2NCOA2 injected

value: mosaic genetic tumor model