title: SAT_Post_Training_rep13

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from subcutaneous adipose tissue biopsies post training before exercise derived from subject 71

hyb_protocol: According to the Thermo Fisher Scientific expression protocol (HWS kit)

scan_protocol: According to the Thermo Fisher Scientific expression protocol (GeneChip Scanner 3000 7G)

data_processing: Transcriptome Analysis Console (TAC; version 4.0.0.25; Thermo Fisher Scientific) was used for quality control and to obtain annotated normalized SST-RMA gene-level data

source_name: Subcutaneous adipose tissue biopsies post training before exercise derived from subject 71

label_protocol: WT PLUS Reagent Kit (Thermo Fisher Scientific).

growth_protocol: no

extract_protocol: RNA extraction was performed using the miRneasy kit (Qiagen)

treatment_protocol: As described in the paper. Briefly, the participants performed an 8-week supervised aerobic endurance exercise intervention program as described below. Individual training intensity was set at 80% of VO2peak determined before the intervention as described in (Hoffmann, Schneeweiss et al. 2020) and kept constant throughout the training program. Insulin sensitivity was assessed after an overnight fast by 75g-OGTTs before and 5 days after the last exercise bout (blood sampling at timepoints 0, 30, 60, 90, and 120 minutes after glucose intake); blood samples for clinical routine parameters were obtained before the glucose load and routine analysis and anthropometry performed as described in (Hoffmann, Schneeweiss et al. 2020). Subcutaneous adipose tissue biopsies were per- formed under sterile conditions after local anesthesia (2% Scandicaine, Astra Zeneca, Wedel, Germany) going back and forth lateral of the navel with a Menghini-needle (Hepafix, B. Braun, Melsungen, Germany). Skeletal muscle biopsies were obtained from the lateral part of vastus lateralis muscle. After local anesthesia, skin, fat tissue, fascia, and the muscle epimysium were cut under sterile condi- tions using a scalpel, and a piece of muscle was removed using a Bergström needle (Pelomi Medical, Albertslund, Denmark) with suction (Hoffmann, Schneeweiss et al. 2020). All biopsies were performed at 11:00 am (plus/minus 30 minutes) before and after the 8-week intervention as well as 60 minutes after the first and last acute exercise bout of the 8-week intervention.

value: Subcutaneous adipose tissue


title: SAT_Post_Training_rep12

status: Public on Feb 01 2023

type: RNA

country: Germany

description: Gene expression data from subcutaneous adipose tissue biopsies post training before exercise derived from subject 68

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Subcutaneous adipose tissue biopsies post training before exercise derived from subject 68

tag: tissue


title: 01-0006-Baseline

type: SRA

city: Lebanon

first: Timothy

last: Sullivan

state: Grafton

address: 1 Medical Center Dr.

department: Biomedical Data Science

country: USA

institute: Dartmouth College

library_source: transcriptomic

data_processing:
First, we applied the cutadapt (version 1.15) to remove the adapter sequence (in our case it is “AGATCGGAAGAGC”) for the FASTQ files. Then, STAR (version 2.5.3a) was applied to align the reads to the hg19 human genome(17). Next, gene abundance was quantified using RSEM (version 3.3.9)(18). Lastly, normalized RPKM was calculated using TMM function (edgeR package)(19).
Supplementary files format and content: RNA-seq_20180810_normalizedRPKM_GeneSymbol_labelled_fixed.csv contains normalized RPKM values for all samples in the study.

source_name: Skin

extract_protocol:
Samples were stored in RNAlater and subsequently homogenized using a Qiagen Tissuelyser II.  RNA was purified using Qiagen’s RNeasy Fibrous Tissue minikit. Quality and concentration of RNA was assessed on a TapeStation 4400 (Agilent)
100ng of total RNA was used for library preparation using the TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA). Libraries were prepared manually or automated on an epMotion 5075t (Eppendorf, Hauppauge, NY). Libraries were assessed for size and concentration using the TapeStation 4400. Sequencing libraries were quantified on a Qubit fluorometer 3.0 (Thermo Fisher Scientific, Waltham, MA) prior to normalization for equimolar pooling.
Single-index paired-end sequencing was performed on Illumina’s NextSeq 500 to achieve >40 million reads per sample.

value: Skin

tag: treatment

value: Placebo

tag: timepoint

value: Baseline

tag: patient

tag: escape

value: N

tag: intrinsic subtype


title: LZ-WT3 (S9.6 CUT&Tag)

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

country: China

institute: Life Sciences  Institute

library_source: genomic

data_processing:
Library strategy: CUT&Tag
R-loop CUT&Tag raw data was trimmed to filter low-quality bases using TrimGalore.
Trimmed reads were aligned to mm9 genome reference (UCSC) using Bowtie2 aligner
For unique alignments, duplicate reads were marked by “MarkDuplicates” function of Picard software.
The coverage of R-loop CUT&Tag data was calculated and normalized by RPKM using deepTools.
Uniquely mapped reads were used to carry out peak calling using MACS2.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files to perform visualization

molecule: genomic DNA

organism: Mus musculus

source_name: S9.6 CUT&Tag

growth_protocol: All mice were kept in an SPF facility operated in a 12-hour light/dark cycle.

extract_protocol:
After removal of the tunica albuginea, the testes were incubated in 5mL of DPBS containing 120 U/mL of collagenase type I at 32 °C with gentle agitation for 8~10 min until seminiferous tubules were dispersed, The dispersed seminiferous tubules were further digested with 5 ml 0.25% trypsin, plus 0.1 ml 5mg/ml DNase I at 32°C for 8 min. The digestion was terminated by adding 0.5 mL FBS to inactivate trypsin. The cell suspension was filtered through a 70 μm cell strainer and then centrifuged at 500 g for 5 min at 4 °C. The cells’ pellet was resuspended at a concentration of 106 cells/ml in DMEM with Hoechst 33342 (5 μg/106 cells) and 5 μl DNase I, followed by cell suspension was rotated for 30min at 32 °C with gentle rotation. Centrifuged at 500 g for 5 min at 4 °C to remove supernatant. Immediately before sorting, the cells were stained with propidium iodide (1 μg/106 cells) at 25 °C and filtered with a 40 μm cell strainer.
5 × 10^4 spermatogonia were sorted and washed once in 0.5 ml wash buffer [20 mM Hepes (pH 7.5), 150 mM NaCl, 0.5 mM spermidine, and 1× protease inhibitors], and were incubated with 10 μl pre-washed concanavalin A–coated magnetic beads in a 1.5 ml microtube at 25 °C for 10 min. Cells were resuspended in 80 μl ice-cold antibody incubation buffer [20 mM Hepes (pH 7.5), 150 mM NaCl, 0.5 mM spermidine, 1× protease inhibitors, 0.025% digitonin, 0.01% NP-40, and 2 mM EDTA] with S9.6 antibody (MABE1095, Millipore) at 1:100 dilution, and then rotated end-over-end at 4 °C overnight. Subsequently, cells were resuspended in 100 μl dig-wash buffer [20 mM Hepes (pH 7.5), 150 mM NaCl, 0.5 mM spermidine, 1 × protease inhibitors, and 0.025% digitonin] with rabbit anti-mouse IgG (Ab6709, Thermo Fisher) at 1:100 dilution and rotated end-over-end at 25 °C for 1 h. After washing, home-made pA-Tn5 adapter complexes in dig-300 buffer [20 mM Hepes (pH 7.5), 300 mM NaCl, 0.5 mM spermidine, 1 × protease inhibitors, and 0.01% digitonin] were added to samples at a final concentration of 1:100 and then rotated end-over-end at 25 °C for 1 h. After washing, cells were resuspended in 300 μl tagmentation buffer [dig-300 buffer with 10 mM MgCl2] and incubates at 37 °C for 1 h. To stop tagmentation and solubilize DNA fragments, 10 μl 0.5M EDTA, 3 μl 10% SDS and 2.5 μl 20 mg/mL Proteinase K were added to each sample and incubated at 50 °C for 1 h. After extraction with phenol-chloroform and ethanol precipitation, libraries were amplified by PCR. The barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform to generate 150 bp paired-end reads.

treatment_protocol: Mice were kept under steady state, or subjected to different stress conditions such as aging, rosiglitazone diet feeding, sub-lethal irradiation, or mid-diaphyseal femur fracture.

tag: strain

value: Testis

tag: cell type

value: Leptotene/zygotene

tag: genotype

value: Wild-type


title: SAT_Post_Training_rep9

description: Gene expression data from subcutaneous adipose tissue biopsies post training before exercise derived from subject 61

source_name: Subcutaneous adipose tissue biopsies post training before exercise derived from subject 61


title: SAT_Post_Training_rep14

description: Gene expression data from subcutaneous adipose tissue biopsies post training before exercise derived from subject 73

source_name: Subcutaneous adipose tissue biopsies post training before exercise derived from subject 73


title: 01-0003-Month-6

value: Abatacept

value: Inflammatory


title: SAT_Post_Training_rep11

description: Gene expression data from subcutaneous adipose tissue biopsies post training before exercise derived from subject 67

source_name: Subcutaneous adipose tissue biopsies post training before exercise derived from subject 67


title: LZ-WT2 (S9.6 CUT&Tag)


title: SAT_Post_Training_rep7

description: Gene expression data from subcutaneous adipose tissue biopsies post training before exercise derived from subject 59

source_name: Subcutaneous adipose tissue biopsies post training before exercise derived from subject 59


title: PD-WT2 (S9.6 CUT&Tag)

value: Pachytene/diplotene


title: LZ-WT1 (S9.6 CUT&Tag)


title: 01-0003-Baseline


title: Pat3_1_O_CAF_rep3

city: Brno

first: Vaclav

last: Hejret

address: Kamenice 5

country: Czech Republic

institute: Masaryk University

description:
tumor organoids
co-culture

data_processing:
bcl2fastq v. 2.20.0.422 software used for basecalling
The adapters and quality trimming of raw fastq reads was performed using Trimmomatic v. 0.36
Trimmed RNA-Seq reads were mapped against the human genome (hg38) and Ensembl GRCh38 v.91 annotation using STAR v. 2.7.3a with default parameters default parameters except -outFilterMismatchNoverLmax 0.1 and -twopassMode Basic
Gene counts were produced using RSEM tool v1.3.1
The differential gene expression analysis was performed using Bioconductor package DESeq2 v1.20.0. Genes were considered as differentially expressed based on a cut-off of adjusted p-value<0.05 and log2(fold-change) ≥1 or ≤-1
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include expected counts values for each sample
Supplementary files format and content: Matrix table with expected gene counts for every gene and every sample gathered by RSEM tool

source_name: tumor

growth_protocol: tumor organoids and fibroblasts were established from primary tumor or healthy colon tissues. Organoids were grown in matrigel covered by established organoid medium. Fibroblasts were extracted and grown flasks supplemented with EGM-M2 medium.

extract_protocol:
total RNA was extracted with a QIAGEN RNAeasy kit
Library preparation was executed with NEBNext Ultra II RNA Library Prep Kit

treatment_protocol: organoids and fibroblasts were grown either in a co-culture or separately in mono-culture

value: epithelial

value: colon


title: Pat2_1_O_CAF_rep2

description:
tumor organoids
co-culture


title: Pat1_1_O_CAF_rep1

description:
tumor organoids
co-culture


title: SPG-WT3 (S9.6 CUT&Tag)

value: Spermatogonia


title: SPG-WT2 (S9.6 CUT&Tag)


title: Pat3_1_NF_rep3

description:
normal fibroblast
mono-culture

source_name: healthy mucosa

value: fibroblast


title: Post, pembro2, PBMC, bulkTCRseq

city: Boston

first: Deepak

middle: A

last: Rao

state: MA

address: 60 Fenwood Road

department: Division of Rheumatology, Inflammation, and Immunity

institute: Brigham and Women's Hospital

data_processing:
Initial data processing was completed by Adaptive using their Analyzer pipeline. Clone counts, sequences, and VDJ genes were exported from the web-based portal.
Assembly: GRCh38
Supplementary files format and content: tsv files contain output from Adaptive's immunoSEQ assays.
Library strategy: TCRseq

source_name: PBMC

extract_protocol:
PBMC and FFPE-stored tissue samples were sent to Adaptive Biotechnologies, where DNA was extracted.
Multiplex PCR-based (immunoSEQ) assays were completed to isolate and amplify TCR information.

value: PBMC

value: Post-pembro 2

tag: single-cell or bulk

value: bulk

tag: molecule type

value: T cell receptor beta chain RNA


title: Pat1_1_O_NF_rep1

description:
tumor organoids
co-culture


title: SPG-WT1 (S9.6 CUT&Tag)


title: SAT_Post_Training_rep5

description: Gene expression data from subcutaneous adipose tissue biopsies post training before exercise derived from subject 57

source_name: Subcutaneous adipose tissue biopsies post training before exercise derived from subject 57

value: Subcutaneous adipose tissue


title: Pat2_1_NF_rep2

description:
normal fibroblast
mono-culture


title: SAT_Post_Training_rep4

description: Gene expression data from subcutaneous adipose tissue biopsies post training before exercise derived from subject 53

source_name: Subcutaneous adipose tissue biopsies post training before exercise derived from subject 53


title: scRNA-seq Mouse Breast Cancer

city: Stanford

first: Michael

last: Januszyk

state: CA

address: 257 Campus Dr

department: Surgery

institute: Stanford University

description: Mouse Breast Cancer

data_processing:
Base calls were converted to reads with the software Cell Ranger (10X Genomics; version 3.1)'s implementation mkfastq. These were then aligned against either the  mm10 v3.0.0 (mouse) or GRCh38-3.0.0 (human) genome using Cell Ranger’s count function (an implementation of STAR v2.7.0) with SC3Pv3 chemistry and 5,000 expected cells per sample.
Cell barcodes representative of quality cells were delineated from barcodes of apoptotic cells or background RNA based on a threshold of having at least 1000 transcripts profiled and less than 10% of their transcriptome of mitochondrial origin.
UMIs from each cell barcode were retained for all downstream analysis. Raw UMI counts were normalized with a scale factor of 10,000 UMIs per cell and subsequently natural log transformed with a pseudocount of 1 using the R package Seurat (version 3.1.1).
Since samples were hashtagged and pooled, the cell barcodes for each mouse or human sample are kept in a separate assay embedded within the standard three 10X output files, which is the recommended storage format for HTO-indexed 10X data. Each samples contained tissue from a single mouse or human tumor sample and was not FACS sorted.     Values for each barcode for each cell can be found in the matrix.mtx file.  Please see the associated Seurat vignette for additional details: https://satijalab.org/seurat/v3.1/hashing_vignette.html
Hashtag oligos (HTOs) for samples were demultiplexed using Seurat’s implementation HTODemux. Briefly, k-medoid clustering is performed on the normalized HTO values, after which a ‘negative’ HTO distribution is calculated. For each HTO,  the cluster with the lowest average value is treated as the negative group and a negative binomial distribution is fit to this cluster. Using the 0.99 quantile of this distribution as a threshold, each cell is classified as positive or negative for each HTO. Cells are then assigned to the HTO for which they have the strongest positive signal. This is accomplished using Seurat's workflow as described in this Vignette: https://satijalab.org/seurat/v3.1/hashing_vignette.html
Genome_build:  mm10 v3.0.0 (mouse) or GRCh38-3.0.0 (human)
Supplementary_files_format_and_content: Filtered 10X matrix counts

source_name: endogenous tumor

extract_protocol:
Tumor Tissue Processing  Tumor tissue specimens from mouse or human specimens was minced on ice. The tissue was then digested for 3x 30 minutes in a 37C water bath agitator in 0.5 mg/mL collagenase (collagenase type IV, ThermoFisher) digest buffer in Medium 199 (HyClone, GE Healthcare) consisting of 5% fetal bovine serum (Gibco FBS, ThermoFisher), DNase I (Worthington), Poloxamer 188 (Cat. P5556-100ML, Sigma), HEPES, and CaCl2. The digest was quenched with quench media (DMEM (Gibco DMEM, ThermoFisher) with 15% FBS), then centrifuged at 300 x G for 5 minutes at 4C, resuspended in quench media, and filtered through 100, 70, and 40m cell strainers (Falcon cell strainer, ThermoFisher). Red blood cell lysis was performed using Hybri-Max (Sigma) per the manufacturers protocol. Cells were counted and re-suspended for further processing.
Single Cell Barcoding, Library Preparation, and Sequencing.   Cell suspensions from individual human and mouse samples were labeled with TotalSeq Series B hashtag oligonucleotide-labeled antibodies (BioLegend). Single-cell RNA-seq (scRNA-seq) was then performed at the Stanford Functional Genomics Facility (SFGF) for droplet-based microfluidics using the 10x Chromium Single Cell platform (Single Cell 3’ v3, 10x Genomics, USA). Droplets of the cellular suspensions, reverse transcription master mix, and partitioning oil were mixed, loaded onto a single cell chip, and processed on the Chromium Controller. Reverse transcription was performed, and cDNA was amplified using a BioRad C1000 Touch thermocycler, with cDNA size selected using SpriSelect beads (Beckman Coulter, USA). An Agilent Bioanalyzer High Sensitivity DNA chip was used to analyze cDNA for qualitative control purposes; cDNA was then fragmented using the proprietary fragmentation enzyme blend for 5min at 32°C, followed by end repair and A-tailing at 65°C for 30 min. DNA was double-sided size selected using SpriSelect beats. Sequencing adaptors were ligated to the cDNA at 20°C for 15min. cDNA was amplified using a sample-specific index oligo as primer, followed by another round of double-sided size selection using SpriSelect beads. Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. Libraries were sequenced on a HiSeq 4000 Illumina platform targeting 50,000 reads per cell.

value: Black 6

value: Mouse Breast Cancer

value: Unsorted


title: Pat1_1_NF_rep1

description:
normal fibroblast
mono-culture


title: 01-0003-Month-3

value: Skin

value: N


title: Post, pembro1, PBMC, bulkTCRseq

value: Post-pembro 1


title: Pre, pembro, PBMC, bulkTCRseq

value: Pre-pembro


title: Pat3_1_NF_O_rep3

description:
normal fibroblast
co-culture


title: SAT_Post_Training_rep10

description: Gene expression data from subcutaneous adipose tissue biopsies post training before exercise derived from subject 63

source_name: Subcutaneous adipose tissue biopsies post training before exercise derived from subject 63


title: f8_E024118 [Case_4]

city: Tartu

first: Raivo

last: Uibo

address: Ravila 18

country: Estonia

institute: University of Tartu

data_processing:
Base calling was done using bcl2fastq
Read alignment was done using Star (v. 2.5.2b)
Genewise read counts were calculated using Subread (v. 1.5.1)
Genome_build: human genome hg38
Supplementary_files_format_and_content: Processed data file is tab delimited text file containing the genewise read counts for each sample

source_name: CD19+ B cells

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll density centrifugation and cryopreserved. B cells were isolated from PBMC using superparamagnetic polystyrene beads (Dynabeads™ CD19 Pan B, number  11143D, Thermo Fisher Scientific) coated with a monoclonal antibody specific for the CD19 antigen and beads were then removed using DETACHaBEAD® CD19 kit (number 12506D, Thermo Fisher Scientific). Purified B cells were resuspended in RLT Plus buffer (Qiagen). The total RNA was isolated via AllPrep DNA/RNA/miRNA Universal Kit (Qiagen). Purified RNA was stored at -80°C. The quality of the RNA samples was ensured using Agilent Bioanalyzer 2100 and RNA integrity number for all the samples was >9. Qubit® Fluorometric Quantitation (Life Technologies) was used to measure RNA concentration.
SMART-Seq v4 Ultra Low Input RNA Kit

value: purified peripheral blood CD19+ B cells

tag: subject

tag: disease status

value: Coeliac progressor

tag: Sex

value: M

tag: country

value: Finland


title: d9_E026908 [Case_5]


title: SAT_Post_Training_rep3

description: Gene expression data from subcutaneous adipose tissue biopsies post training before exercise derived from subject 52

source_name: Subcutaneous adipose tissue biopsies post training before exercise derived from subject 52


title: Kidney, FFPE, bulkTCRseq

source_name: Kidney

value: Kidney

value: n/a (FFPE)


title: c7_E014086 [Control_3]

value: Control


title: Pat2_1_NF_O_rep2

description:
normal fibroblast
co-culture

value: fibroblast

value: colon


title: SAT_Post_Training_rep6

description: Gene expression data from subcutaneous adipose tissue biopsies post training before exercise derived from subject 58

source_name: Subcutaneous adipose tissue biopsies post training before exercise derived from subject 58

value: Subcutaneous adipose tissue


title: SAT_Post_Training_Acute_rep15

description: Gene expression data from subcutaneous adipose tissue biopsies post training after exercise derived from subject 73

source_name: Subcutaneous adipose tissue biopsies post training after exercise derived from subject 73


title: SAT_Post_Training_rep1

description: Gene expression data from subcutaneous adipose tissue biopsies post training before exercise derived from subject 50

source_name: Subcutaneous adipose tissue biopsies post training before exercise derived from subject 50


title: Pat1_1_NF_O_rep1

description:
normal fibroblast
co-culture


title: SAT_Post_Training_rep2

description: Gene expression data from subcutaneous adipose tissue biopsies post training before exercise derived from subject 51

source_name: Subcutaneous adipose tissue biopsies post training before exercise derived from subject 51


title: SAT_Post_Training_Acute_rep13

description: Gene expression data from subcutaneous adipose tissue biopsies post training after exercise derived from subject 66

source_name: Subcutaneous adipose tissue biopsies post training after exercise derived from subject 66


title: SAT_Post_Training_Acute_rep14

description: Gene expression data from subcutaneous adipose tissue biopsies post training after exercise derived from subject 68

source_name: Subcutaneous adipose tissue biopsies post training after exercise derived from subject 68


title: g1_E002410 [Case_1]


title: g8_T011454 [Case_6]

value: Estonia


title: Spatial transcriptomics FFPE [D2]

city: London

first: Paul

last: Sharpe

address: Guy's Hospital

department: Centre for Craniofacial and Regenerative Biology

country: United Kingdom

institute: King's College London

description: 10x Genomics

data_processing:
Illumina bcl2fastq was used to convert raw bcl files to fastq format. Fastq files were processed using 10x Genomics Spaceranger (version1.0) software
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Spaceranger outputs - raw feature barcode matrix in mtx format, gene list in tab delimited format, spot, barcodes in tab delimited format, spatial transcriptomics slide H&E image in jpeg format, spot position to image pixel coordinates.

source_name: Oral mucosa

extract_protocol: Adult oral mucosa samples were freshly frozen in OCT blocks or embedded in paraffin blocks and sectioned into an oligo-covered array with subsequent H&E, imaging, sample permeabilisation, RNA removal RT and amplification as per protocol for 10x Visium Spatial Protocol (CG000239 Rev C).

value: Oral mucosa

tag: subject status

value: disease


title: Lymph, node, FFPE, bulkTCRseq

source_name: Lymph Node

value: Lymph Node

value: bulk

value: T cell receptor beta chain RNA


title: Spatial transcriptomics FFPE [C2]

description: 10x Genomics


title: Pat2_1_ENAS_rep2

description:
tumor organoids
mono-culture

source_name: tumor

value: epithelial


title: Pat3_1_ENAS_rep3

description:
tumor organoids
mono-culture


title: Pat1_1_ENAS_rep1

description:
tumor organoids
mono-culture


title: Spatial transcriptomics FFPE [B2]

description: 10x Genomics


title: e3_E024118 [Case_4]

value: purified peripheral blood CD19+ B cells


title: Pat3_1_control_rep3

description:
tumor organoids
mono-culture


title: f7_E026343 [Control_5]


title: Spatial transcriptomics FFPE [A2]

description: 10x Genomics

value: Health


title: Pat2_1_control_rep2

description:
tumor organoids
mono-culture


title: f9_E006118 [Control_2]

value: F


title: SAT_Post_Training_Acute_rep11

description: Gene expression data from subcutaneous adipose tissue biopsies post training after exercise derived from subject 64

source_name: Subcutaneous adipose tissue biopsies post training after exercise derived from subject 64


title: Pat1_1_control_rep1

description:
tumor organoids
mono-culture


title: f4_E002410 [Case_1]

value: Coeliac progressor

value: M

value: Finland


title: SAT_Post_Training_Acute_rep9

description: Gene expression data from subcutaneous adipose tissue biopsies post training after exercise derived from subject 60

source_name: Subcutaneous adipose tissue biopsies post training after exercise derived from subject 60


title: SAT_Post_Training_Acute_rep12

description: Gene expression data from subcutaneous adipose tissue biopsies post training after exercise derived from subject 65

source_name: Subcutaneous adipose tissue biopsies post training after exercise derived from subject 65


title: Spatial transcriptomics cryo technical replicate 1 [C1]

description: 10x Genomics


title: SAT_Post_Training_Acute_rep8

description: Gene expression data from subcutaneous adipose tissue biopsies post training after exercise derived from subject 59

source_name: Subcutaneous adipose tissue biopsies post training after exercise derived from subject 59


title: Spatial transcriptomics cryo technical replicate 2 [B1]

description: 10x Genomics


title: SAT_Post_Training_rep8

description: Gene expression data from subcutaneous adipose tissue biopsies post training before exercise derived from subject 60

source_name: Subcutaneous adipose tissue biopsies post training before exercise derived from subject 60


title: Pat3_1_CAF_rep3

description:
cancer associated fibroblasts
mono-culture


title: SAT_Post_Training_Acute_rep7

description: Gene expression data from subcutaneous adipose tissue biopsies post training after exercise derived from subject 58

source_name: Subcutaneous adipose tissue biopsies post training after exercise derived from subject 58


title: f1_T011454 [Case_6]

source_name: CD19+ B cells


title: Pat2_1_CAF_rep2


title: e5_E026343 [Control_5]

value: Control


title: Spatial transcriptomics cryo technical replicate 2 [D1]

description: 10x Genomics


title: Spatial transcriptomics cryo technical replicate 1 [A1]

description: 10x Genomics


title: d4_E024118 [Case_4]


title: DCH12_DOX-pulse_IFNg_biol rep 3 [RNA-seq]

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

data_processing:
we used Trimmomatic to trim the 3’ adapter sequence and aligned the trimmed reads to GRCh38 (p13) using Rsubread.
We counted mapped reads that overlapped with exons of gene features using the summarizeOverlaps function of Bioconductor's GenomicAlignments package with the IntersectionStrict mode. The gene features were annotated by Gencode v35.
We applied DESeq2 for gene expression normalization, log transformation, and differential analysis on different comparisons between treatment conditions.
Assembly: GRCh38.p13
Supplementary files format and content: Bioconductor's RangedSummarizedExperiement instance (.rda) of gene counts based on CDS regions and feature info (gencode v35) , and a table of non-normalized gene counts (.csv)

growth_protocol: MB135iDUX4 myoblasts were grown in Ham’s F-10 (Gibco) supplemented with 10% FBS (HyClone), 1% penicillin/streptomycin (Thermo Fisher Scientific), 10ng/mL rhFGF (Promega), 1uM dexamethasone (Sigma), and 3ug/mL puromycin (Sigma)

extract_protocol:
RNA was harvested using NucleoSpin RNA kit (Machery-Nagel) following manufacturer's protocols.
RNA-seq libraries were prepared using the Illumina TruSeq RNA Sample Prep v2 Kit following manufacturer's protocols.

treatment_protocol: MB135iDUX4 myoblasts were pulsed with or without 1ug/mL doxycycline for 4 hours, incubated for 48 hours, supplemented with or without 50ng/mL IFNg for 16 hours, and harvested at a terminal time point of 68 hours.

tag: cell line

value: myoblasts

value: WT

value: DOX+IFNg


title: e2_E006118 [Control_2]


title: SAT_Post_Training_Acute_rep10

description: Gene expression data from subcutaneous adipose tissue biopsies post training after exercise derived from subject 63

source_name: Subcutaneous adipose tissue biopsies post training after exercise derived from subject 63

tag: tissue

value: Subcutaneous adipose tissue


title: Pat1_1_CAF_rep1

value: fibroblast

value: colon


title: SAT_Post_Training_Acute_rep6

description: Gene expression data from subcutaneous adipose tissue biopsies post training after exercise derived from subject 57

source_name: Subcutaneous adipose tissue biopsies post training after exercise derived from subject 57


title: SAT_Post_Training_Acute_rep5

description: Gene expression data from subcutaneous adipose tissue biopsies post training after exercise derived from subject 54

source_name: Subcutaneous adipose tissue biopsies post training after exercise derived from subject 54


title: Pat3_1_CAF_O_rep3

description:
cancer associated fibroblasts
co-culture


title: d5_E002410 [Case_1]


title: DCH11_DOX-pulse_IFNg_biol rep 2 [RNA-seq]

tag: treatment


title: SAT_Post_Training_Acute_rep3

description: Gene expression data from subcutaneous adipose tissue biopsies post training after exercise derived from subject 52

source_name: Subcutaneous adipose tissue biopsies post training after exercise derived from subject 52


title: DCH10_DOX-pulse_IFNg_biol rep 1 [RNA-seq]


title: Pat2_1_CAF_O_rep2


title: DCH9_DOX-pulse_biol rep 3 [RNA-seq]

value: DOX


title: g4_T010562 [Control_6]

value: Estonia


title: Pat1_1_CAF_O_rep1


title: DCH8_DOX-pulse_biol rep 2 [RNA-seq]


title: e9_E015784 [Case_3]


title: d8_E026343 [Control_5]


title: SAT_Post_Training_Acute_rep2

description: Gene expression data from subcutaneous adipose tissue biopsies post training after exercise derived from subject 51

source_name: Subcutaneous adipose tissue biopsies post training after exercise derived from subject 51


title: DCH7_DOX-pulse_biol rep 1 [RNA-seq]


title: Skin, FFPE, bulkTCRseq

source_name: Skin

value: Skin

tag: timepoint

value: n/a (FFPE)

value: bulk

value: T cell receptor beta chain RNA


title: PC-3-TetOn-PARG-H6 exp "N" DOX Rep3

city: Grand Forks

first: Yaroslava

last: Karpova

state: ND

address: 501 Columbia Road

department: Biomedical Sciences

institute: University of North Dakota

description: experiment "N"

data_processing:
Illumina FQ sequencing files were imported into CLC Genomics Workbench version 12.0.
The reads were trimmed to remove adapters then the trimmed reads were mapped to the Mouse genome using CLC’s default parameters (mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8, auto-detect paired distanc-es, maximum number of hits per read = 10).
Differential expression for RNA-seq analyses was performed in CLC Genomics Workbench 12.0 on the gene-level expression tracks using whole transcriptome RNA-seq with TMM normalization.
Differential expression due to treatment (hPARG+ or control) was tested with the comparison against the control group.
Genome_build: HG38 human genome
Supplementary_files_format_and_content: csv, Maximum group expression value and expression changes

source_name: PC-3 cell line

growth_protocol: PC-3_pLVX_TetOne-Puro cells were cultured in RPMI-1640 (Bio-Whittaker, Walkersville, MD) supplemented with 10% FBS (Hyclone, Logan, UT), pen/strap (1x), non-essential amino acids (0.1mM)

extract_protocol:
RNeasy kit (Qiagen), mRNA was enriched via Poly(A) selection.
For experiment "N" Novogene libraries were prepared with NEB’s Ultra II RNA library kit (both strands), for experiment "B" QB3 libraries were prepared with Roche KAPA HyperPrep library kits (strand specific-reverse).

treatment_protocol: PC-3 cells were transduced with lentivirus construct encoding PARG cDNA with cleavable mClover3 under TetOne Doxycycline inducible promoter, signle clones were generated. Cells were plated to single well of 6 well plate, grown at 37°C in 5% CO2 for 72 hours without or with 500ng/ml doxycycline and RNA isolated. 3 wells for untreated control group, 3 wells for treated inducible experimental group.

tag: parg

value: PARG overexpression

tag: type

value: prostate cancer

value: 500ng/ml doxycycline


title: b8_E006118 [Control_2]

value: purified peripheral blood CD19+ B cells

value: F

value: Finland


title: DCH6_IFNg_biol rep 3 [RNA-seq]

value: myoblasts

value: WT

value: IFNg


title: c9_E002410 [Control_1]

value: Control

value: M


title: PC-3-TetOn-PARG-H6 exp "N" DOX Rep1

description: experiment "N"


title: PC-3-TetOn-PARG-H6 exp "N" noDOX Rep3

description: experiment "N"

value: control


title: DCH5_IFNg_biol rep 2 [RNA-seq]


title: SAT_Post_Training_Acute_rep4

description: Gene expression data from subcutaneous adipose tissue biopsies post training after exercise derived from subject 53

source_name: Subcutaneous adipose tissue biopsies post training after exercise derived from subject 53

value: Subcutaneous adipose tissue


title: e6_T010562 [Control_6]

value: Estonia


title: DCH4_IFNg_biol rep 1 [RNA-seq]


title: SAT_Baseline_rep13

description: Gene expression data from subcutaneous adipose tissue biopsies untrained before exercise derived from subject 73

source_name: Subcutaneous adipose tissue biopsies untrained before exercise derived from subject 73


title: PC-3-TetOn-PARG-H6 exp "N" noDOX Rep2

description: experiment "N"


title: SAT_Baseline_rep11

description: Gene expression data from subcutaneous adipose tissue biopsies untrained before exercise derived from subject 68

source_name: Subcutaneous adipose tissue biopsies untrained before exercise derived from subject 68


title: PC-3-TetOn-PARG-H6 exp "N" DOX Rep2

description: experiment "N"


title: f3_E024277 [Control_4]


title: PC-3-TetOn-PARG-H6 exp "N" noDOX Rep1

description: experiment "N"


title: DCH3_untreated_biol rep 3 [RNA-seq]

value: untreated


title: PC-3-TetOn-PARG-I4 exp "N" DOX Rep3

description: experiment "N"


title: SAT_Baseline_rep9

description: Gene expression data from subcutaneous adipose tissue biopsies untrained before exercise derived from subject 65

source_name: Subcutaneous adipose tissue biopsies untrained before exercise derived from subject 65


title: DCH2_untreated_biol rep 2 [RNA-seq]


title: SAT_Post_Training_Acute_rep1

description: Gene expression data from subcutaneous adipose tissue biopsies post training after exercise derived from subject 50

source_name: Subcutaneous adipose tissue biopsies post training after exercise derived from subject 50


title: SAT_Baseline_rep12

description: Gene expression data from subcutaneous adipose tissue biopsies untrained before exercise derived from subject 71

source_name: Subcutaneous adipose tissue biopsies untrained before exercise derived from subject 71


title: PC-3-TetOn-PARG-I4 exp "N" DOX Rep2

description: experiment "N"


title: SAT_Baseline_rep7

description: Gene expression data from subcutaneous adipose tissue biopsies untrained before exercise derived from subject 60

source_name: Subcutaneous adipose tissue biopsies untrained before exercise derived from subject 60


title: DCH1_untreated_biol rep 1 [RNA-seq]


title: DCH12_DOX-pulse_IFNg_biol rep 3 [Ribo-seq]

data_processing:
library strategy: Ribo-seq
Clip the 3’ adapter sequence and trim the first and last four bases from the adapter-clipped reads (cutadapt).
Remove rRNA and other small RNA such as tRNA and snoRNA. In this step, we customized the rRNA reference genome from the RNA central database (https://rnacentral.org/) and then used Bowtie2 to align the trimmed reads against it; the unmapped reads are the desirable RPFs. Due to the caveats of maintaining congruent paired-reads after removing rRNA containmanation from forword and reverse reads by Bowtie2, we decided to just use forward reads (R1) for following RPF alignment.
Align the RPFs (R1) to the GRCh38 (p.13) genome built by STAR.
Assess the quality of the mapped RPFs using Bioconductor’s ribosomeProfilingQC package. Here, we calculated the size distribution of the RPFs. It confirmed that most RPFs are congruent with the actual size of ribosomes (26 - 29 nt). We plotted the meta-gene coverage of p-sites densities. It revealed the enrichment of the ribosome footprints at the start codon and, most importantly, shows the trinucleotide footprint periodicity confirming that most p-sites are in-frame with the start codon.
Profile ribosome footprints. Using ribosomeProfilingQC and the Gencode (v35) annotation, we computed the p-sites counts of RPFs of the dominant length (26 - 29 nt) for five different genomic features including the 5’ UTRs, translation start sites (TSS; 13 nucleotides extended up/downstream from the start codon), CDS and 3’ UTRs
Assembly: GRCh38.p13
Supplementary files format and content: Bioconductor's RangesSummarizedExperiment instance (*.rda) of gene counts in CDS region (gencode v35) and a table of non-normalized gene counts (*.csv)

extract_protocol:
RNA was harvested using the Direct-zol RNA Miniprep Kit (Zymo Research) following manufacturer's protocols.
RNA-seq libraries were prepared using the NEXTflex Small RNA-Seq Kit v3 (PerkinElmer) following manufacturer's protocols.

treatment_protocol:
MB135iDUX4 myoblasts were pulsed with or without 1ug/mL doxycycline for 4 hours, incubated for 48 hours, supplemented with or without 50ng/mL IFNg for 16 hours, and harvested at a terminal time point of 68 hours.
Ribo-seq was performed as described previously (Calviello et al., 2016).

value: DOX+IFNg


title: SAT_Baseline_rep10

description: Gene expression data from subcutaneous adipose tissue biopsies untrained before exercise derived from subject 66

source_name: Subcutaneous adipose tissue biopsies untrained before exercise derived from subject 66


title: PC-3-TetOn-PARG-I4 exp "N" noDOX Rep3

description: experiment "N"


title: DCH11_DOX-pulse_IFNg_biol rep 2 [Ribo-seq]


title: SAT_Baseline_rep8

description: Gene expression data from subcutaneous adipose tissue biopsies untrained before exercise derived from subject 64

source_name: Subcutaneous adipose tissue biopsies untrained before exercise derived from subject 64


title: DCH10_DOX-pulse_IFNg_biol rep 1 [Ribo-seq]


title: PC-3-TetOn-PARG-I4 exp "N" noDOX Rep2

description: experiment "N"


title: SAT_Baseline_rep6

description: Gene expression data from subcutaneous adipose tissue biopsies untrained before exercise derived from subject 59

source_name: Subcutaneous adipose tissue biopsies untrained before exercise derived from subject 59


title: SAT_Baseline_rep4

description: Gene expression data from subcutaneous adipose tissue biopsies untrained before exercise derived from subject 57

source_name: Subcutaneous adipose tissue biopsies untrained before exercise derived from subject 57


title: SAT_Baseline_rep5

description: Gene expression data from subcutaneous adipose tissue biopsies untrained before exercise derived from subject 58

source_name: Subcutaneous adipose tissue biopsies untrained before exercise derived from subject 58


title: e4_E024277 [Control_4]

source_name: CD19+ B cells


title: b1_E002410 [Case_1]

value: Coeliac progressor


title: d1_E015784 [Case_3]


title: c3_T010562 [Control_6]


title: DCH9_DOX-pulse_biol rep 3 [Ribo-seq]

value: DOX


title: PC-3-TetOn-PARG-I4 exp "N" noDOX Rep1

description: experiment "N"

value: prostate cancer


title: SAT_Baseline_rep3

description: Gene expression data from subcutaneous adipose tissue biopsies untrained before exercise derived from subject 54

source_name: Subcutaneous adipose tissue biopsies untrained before exercise derived from subject 54


title: DCH8_DOX-pulse_biol rep 2 [Ribo-seq]


title: PC-3-TetOn-PARG-I4 exp "N" DOX Rep1

description: experiment "N"

value: PARG overexpression

value: 500ng/ml doxycycline


title: DCH7_DOX-pulse_biol rep 1 [Ribo-seq]


title: CD45-CD31- cells - ORL activated Lymph Node

city: Paris

first: Floriane

last: Noël

address: 1 avenue Claude Vellefaux

country: France

institute: INSERM

data_processing:
FASTQ files were processed using the CellRanger pipeline (10X Genomics; V3), and reads were aligned to the human genome hg38.
Genome_build: GRCh38
Supplementary_files_format_and_content: output files from CellRanger (filtered gene matrices :barcodes, features and matrix) for each scRNA-seq sample.

extract_protocol:
Fresh lymph nodes and tonsils were cut into small pieces and treated with an enzymatic cocktail containing collagenase D (1 mg/mL; Sigma Aldrich), DNase I (0.1 mM; Roche) and Dispase I (2 U/mL; Roche) in serum-free RPMI for 40 minutes at 37°C. The resulting cell suspension was passed through a 100 µm-mesh filter and the cells were washed in phosphate-buffered saline (PBS) containing 6 mM EDTA. Red blood cells were removed by magnetic isolation in EasySepTM RBC Depletion Reagent (Stem Cell Technology) according to the manufacturer’s instructions. The remaining cells were then washed in 10% fetal calf serum (FCS) and 2 mM EDTA in PBS. Immune cells were removed by magnetic isolation with a human CD45 microbeads kit (Miltenyi) use according to the manufacturer’s instructions. The resulting CD45- cell-enriched suspension was washed with PBS and stained directly. The CD45- cell-enriched suspension was stained by incubation with a Live/Dead fixable yellow fluorescence kit (Invitrogen, 1:200) in PBS for 20 minutes at room temperature before surface staining. Cells were then incubated for 40 minutes at 4°C in PBS containing 1% FCS and 2 mM EDTA plus the following antibodies: APC-Cy7 anti-CD45 (BD Biosciences), FITC anti-CD31 (BD Biosciences), biotinylated anti-FDC (Thermo Fisher Scientific) and PE anti-PDPN (Thermo Fisher Scientific). The biotinylated antibody was detected with streptavidin conjugated BV421 (Biolegend). Viable FRCs and epithelial cells were sorted by flow cytometry (ARIA III, BD) on the basis of their CD45-CD31- phenotype. This CD45-CD31- cell fraction was enriched in FDCs and non-FDC-FRCs by sorting PDPN+CNA.42+ cells and PDPN+CNA.42- cells, respectively. PDPN-CNA.42+ and PDPN-CNA.42- cells were also sorted to obtain tonsillar epithelial cells and to identify other CD31-PDPN-FRCs subsets.
Sorted CD45-CD31- cells were analyzed with the 10X chromium system (10X Genomics). Single-cell libraries were generated according to the manufacturer’s instructions (chromium 10X Next GEM Single-cell 3’ Kit (V.3.3)). Next-generation sequencing was performed on an Illumina NovaSeq 6000. ScRNAseq data processing and FASTQ file analysis were performed at the NGS platform of the Curie Institute, Paris (Tonsil 1) and the sequencing platform of the Paris Brain Institute (Tonsil 2-4, LNs) with the Cell Ranger pipeline (10X Genomics, version 3).

value: lymph node


title: SAT_Baseline_rep2

description: Gene expression data from subcutaneous adipose tissue biopsies untrained before exercise derived from subject 53

source_name: Subcutaneous adipose tissue biopsies untrained before exercise derived from subject 53


title: d7_E003953 [Case_2]

value: purified peripheral blood CD19+ B cells

value: F

value: Finland


title: f5_E003953 [Case_2]


title: e1_E015784 [Case_3]


title: f2_E001292 [Control_1]


title: CD45-CD31- cells - resting Lymph Node


title: SAT_Baseline_rep1

description: Gene expression data from subcutaneous adipose tissue biopsies untrained before exercise derived from subject 52

source_name: Subcutaneous adipose tissue biopsies untrained before exercise derived from subject 52


title: SAT_Baseline_Acute_rep12

description: Gene expression data from subcutaneous adipose tissue biopsies untrained after exercise derived from subject 73

source_name: Subcutaneous adipose tissue biopsies untrained after exercise derived from subject 73


title: DCH5_IFNg_biol rep 2 [Ribo-seq]

value: myoblasts

value: WT

value: IFNg


title: f6_E026908 [Case_5]

value: M


title: d3_E024277 [Control_4]

value: Control


title: CD45-CD31- cells - Tonsil 4

value: tonsil


title: SAT_Baseline_Acute_rep11

description: Gene expression data from subcutaneous adipose tissue biopsies untrained after exercise derived from subject 68

source_name: Subcutaneous adipose tissue biopsies untrained after exercise derived from subject 68

value: Subcutaneous adipose tissue


title: CD45-CD31- cells - Tonsil 3


title: CD45-CD31- cells - Tonsil 2


title: DCH4_IFNg_biol rep 1 [Ribo-seq]


title: c5_E003953 [Case_2]


title: DCH3_untreated_biol rep 3 [Ribo-seq]

value: untreated


title: CD45-CD31- cells - Tonsil 1

source_name: Tonsil


title: DCH2_untreated_biol rep 2 [Ribo-seq]


title: c4_E001292 [Case_1]

value: Coeliac progressor


title: SAT_Baseline_Acute_rep8

description: Gene expression data from subcutaneous adipose tissue biopsies untrained after exercise derived from subject 61

source_name: Subcutaneous adipose tissue biopsies untrained after exercise derived from subject 61


title: INDY_4

city: Cologne

first: Björn

last: Schumacher

address: Joseph-Stelzmann-Str. 26

institute: CECAD Research Center

description:
Poly A+ selection
142042

data_processing:
Reads were quantified with Salmon-1.1 with a decoy-aware transcriptome (gencode.v37 transcripts and the GRCh38.primary_assembly genome).
The raw transcript abundance files were imported and summarized to the gene-level with tximport(1.14.2). Differential gene analysis was done with edgeR(3.28.1)
Genome_build: GRCh38.primary_assembly genome
Supplementary_files_format_and_content: One comma-delimited .csv file with the raw gene-level read counts for all samples.

molecule: polyA RNA

source_name: U2OS cells

growth_protocol: U2OS were cultured in DMEM, high glucose GlutaMAX Supplement, Pyruvate with 10% fetal bovine serum  and 1% Penicillin-Streptomycin. Cells were kept at 37 °C in a 5% CO2 incubator.

extract_protocol:
Cells were disrupted with RLT buffer from the RNeasy Mini Kit (QIAGEN, 74106), and homogenized with QIAshredder spin columns (QIAGEN, 79656). The RNeasy Mini Kit procedure was performed following the manufacturer's specifications.
Illumina TruSeq mRNA stranded

treatment_protocol: 48 hours before extraction, confluent cells were transferred to FBS-free media. 24 hours before extraction, cells received 10 µM Harmine Hydrochloride, 25 µM INDY, or the respectives amounts of water or DMSO (control of Harmine and control of INDY respectively).

value: INDY


title: SAT_Baseline_Acute_rep9

description: Gene expression data from subcutaneous adipose tissue biopsies untrained after exercise derived from subject 64

source_name: Subcutaneous adipose tissue biopsies untrained after exercise derived from subject 64


title: DCH1_untreated_biol rep 1 [Ribo-seq]


title: SAT_Baseline_Acute_rep7

description: Gene expression data from subcutaneous adipose tissue biopsies untrained after exercise derived from subject 59

source_name: Subcutaneous adipose tissue biopsies untrained after exercise derived from subject 59


title: e7_E026908 [Case_5]


title: INDY_3

description:
Poly A+ selection
142040


title: SAT_Baseline_Acute_rep10

description: Gene expression data from subcutaneous adipose tissue biopsies untrained after exercise derived from subject 67

source_name: Subcutaneous adipose tissue biopsies untrained after exercise derived from subject 67


title: INDY_2

description:
Poly A+ selection
142038


title: MCF7 cells, control, biol rep2

first: Pavel

last: Bouchal

department: Biochemistry

institute: Masaryk University, Faculty of Science

data_processing:
The raw reads were filtered to remove the adaptors and low-quality bases using Trimmomatic (v0.36) with Truseq2 s well as any reads that were shorter than 65 bases.
Filtered reads were aligned to the human genome (Homo_sapiens.GRCh38.dna.primary_assembly) using STAR (v2.5.2b) in end-to-end mode to scan splice junctions.
Counts in exon genomic features were calculated subread (v1.5.2).
Differential expression analysis was performed in R 3.5.3 under the Deseq2 package version 1.22.2.
BiomaRt package version 2.38.0. was used for annotation the results from differential expression analysis.
Assembly: genome: Ensembl GRCh38, annotation: Ensembl v94
Supplementary files format and content: tab-delimited text file DESeq2.tsv containing results from differential gene expression by DESeq2; raw_counts.xlsx, normalized_counts.xlsx - excel files containing information of raw and normalized counts for each gene, respectively

source_name: breast cancer cell line MCF7

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle Medium (DMEM; high glucose) with 10% fetal bovine serum (Sigma-Aldrich, USA) and blasticidin (10 μg/ ml; InvivoGen, USA) at 37°C in 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated according to TRI reagent protocol (Sigma-Aldrich, T9424) and its concentration was determined using Qubit RNA BR assay kit (Q10210, Invitrogen). 240 ng of total RNA at 20ng/µl was used in RNA-Seq analysis.
The TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina) was used to convert total RNA into a library of template molecules. Library was validated using Bioanalyzer (DNA 1000 Kit, Agilent) and quantified according to manufacturer instructions by qPCR (KAPA Library Quantification Kit Illumina platforms, Kapa Biosystems) using Quant studio (QuantStudio 5, Thermo Fisher Scientific).

value: breast cancer cell line MCF7

value: epithelial cell

value: mock


title: g5_E024118 [Case_4]


title: DCH6_IFNg_biol rep 3 [Ribo-seq]


title: e8_E014086 [Control_3]


title: d6_E014086 [Control_3]


title: MCF7 cells, control, biol rep1


title: b2_E003953 [Case_2]


title: INDY_1

description:
Poly A+ selection
142036


title: SAT_Baseline_Acute_rep3

description: Gene expression data from subcutaneous adipose tissue biopsies untrained after exercise derived from subject 52

source_name: Subcutaneous adipose tissue biopsies untrained after exercise derived from subject 52


title: SAT_Baseline_Acute_rep6

description: Gene expression data from subcutaneous adipose tissue biopsies untrained after exercise derived from subject 58

source_name: Subcutaneous adipose tissue biopsies untrained after exercise derived from subject 58


title: SAT_Baseline_Acute_rep4

description: Gene expression data from subcutaneous adipose tissue biopsies untrained after exercise derived from subject 53

source_name: Subcutaneous adipose tissue biopsies untrained after exercise derived from subject 53


title: Control_INDY4

description:
Poly A+ selection
142034

value: Control INDY


title: MCF7 cells, COMT, biol rep2

value: COMT overexpression


title: a9_E001292 [Control_1]

value: purified peripheral blood CD19+ B cells


title: SAT_Baseline_Acute_rep5

description: Gene expression data from subcutaneous adipose tissue biopsies untrained after exercise derived from subject 54

source_name: Subcutaneous adipose tissue biopsies untrained after exercise derived from subject 54


title: NPC-mid-SCZ-PRS-553-10-GDO

city: New York

first: Kayla

last: Townsley

state: New York

address: 240 E. 89th Street, Apt. #1C

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
mRNA sequencing reads were mapped to the GRCh38 reference genome using the Cellranger Software
To generate count matrices for HTO and GDO libraries, the kallisto indexing and tag extraction (kite) workflow were used
Count matrices were used as input into the R/Seurat package to perform downstream analyses, including QC, normalization, cell clustering, and gRNA and HTO/GDO demultiplexing
Data was transformed into log2CPM using VOOM (Limma), tested for differential expression using EdgeR and Limma, and bayesian bi-clustering using BicMix.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: features as tsv, barcodes as tsv, cDNA or GDO counts as mtx (10x Genomics File format for Seurat)

source_name: human-induced pluripotent stem cell

growth_protocol: hiPSC or hiPSC-derived NPCs were dissociated with Accutase Cell Detachment Solution (Innovative Cell Technologies, # AT-104), counted and transduced with rtTA (Addgene 20342) and NGN2 (Addgene 99378) lentiviruses in StemFlex media containing 10 M Thiazovivin (Millipore, #S1459). They were subsequently seeded at 1x106 cells/well in the prepared 6-well plate. On day 1, medium was switched to non-viral induction medium (DMEM/F12 (Thermofisher, #10565018), 1% N-2 (Thermofisher, #17502048), 2% B-27-RA (Thermofisher, #12587010)) and doxycycline (dox) was added to each well at a final concentration of 1 μg/mL. At day 2, transduced hiPSCs were treated with 500 μg/mL G418 (Thermofisher, #10131035). At day 4, medium was replaced including 1 μg/mL dox and 4 μM cytosine arabinoside (Ara-C) to reduce the proliferation of non-neuronal cells. On day 5, young neurons were dissociated with Accutase Cell Detachment Solution (Innovative Cell Technologies, # AT-104), counted and seeded at a density of 1x106 per well of a Matrigel-coated 12-well plate. Medium was switched to Brainphys neuron medium (Brainphys (STEMCELL, # 05790), 1% N-2, 2% B--27-RA, 1 μg/mL Natural Mouse Laminin (Thermofisher, # 23017015), 10 ng/mL BDNF (R&D, #248), 10 ng/mL GDNF (R&D, #212), 500 μg/mL Dibutyryl cyclic-AMP (Sigma, #D0627), 200 nM L-ascorbic acid (Sigma, # A4403)). For seeding, 10 M Thiazovivin (Millipore, #S1459), 500 μg/mL G418 and 4 μM Ara-C and 1 μg/mLdox were added. At day 6, medium was replaced with Brainphys neuron medium with 4 μM Ara-C and 1 μg/mL dox. Subsequently, 50% of the medium was replaced with fresh neuronal medium (lacking dox and Ara-C) once every other day until the neurons were harvested

extract_protocol:
Glutamatergic NGN2-neurons were generated from hiPSCs in two batches harvested at separate time-points (Day 7 of protocol and Day 21) (batch 1 n=2 mid-PRS control lines 2607 and 690; batch 2 n=2 mid-PRS control lines 553 and 2607). For NGN2-neurons, RNA was harvested with RNeasy plus micro kit (Qiagen).
Standard prep for 10X Genomics Chromium
ECCITE-seq/scRNA-seq/10X Genomics

treatment_protocol: CRISPRa hiPSC NGN2-neurons (mid-PRS control donors 2607 (XY) and 690 (XY)) were transduced with the pooled gRNA at day -1. After maturation, 7-day-old NGN2-neurons were dissociated to single cell suspensions with papain, antibody-hashed59, and bar-coded single cell cDNA generated using 10X Genomics Chromium60. NPC-derived NGN2-neurons (mid-PRS control donors 2607 (XY) and 553 (XY)) were transduced with the mixed-pooled gRNA vectors (Addgene 99374) at day 17. At day 21, media was replaced by 0.5ml/well accutase containing 10 μm Rock inhibitor, THX (catalog no. 420220; Millipore) for 1 hour to dissociate neurons. Neurons were spun down (3 mins X 300g) and resuspended in DMEM/F12 + THX before proceeding to single cell sequencing.

tag: cell-type

value: NPC-derived NGN2 Neurons

tag: developmental timepoint

value: Day 21

tag: scz prs

value: mid (control lines)

tag: karyotypic sex

value: XY

tag: moi

value: high


title: SAT_Baseline_Acute_rep2

description: Gene expression data from subcutaneous adipose tissue biopsies untrained after exercise derived from subject 51

source_name: Subcutaneous adipose tissue biopsies untrained after exercise derived from subject 51


title: MCF7 cells, COMT, biol rep1

tag: cell type

tag: genotype


title: Control_INDY2

description:
Poly A+ selection
142030


title: 4653_42

city: Lewisburg

first: Olivia

last: Boerman

state: PA

address: One Dent Drive

department: Biomedical Engineering

institute: Bucknell University

description: Subject F

data_processing:
Torrent Suite Software v. 5.12.3
Adapters were trimmed and low quality reads filtered by the Torrent Suite Software v. 5.12.3
StrandNGS software v. 3.4
Raw reads were mapped to Hg19 human reference genome using a proprietary algorithm named computationally-optimized Burrows Wheeler Transformed (COBWeb) by the Strand.
Read count extraction and Normalization was performed by StrandNGS using Deseq algorithm.
Assembly: Hg19
Supplementary files format and content: Tab separated value (TSV) text file containing raw counts for each sample.

source_name: venous ulcer

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 10 ng of total RNA was used for the construction of sequencing libraries.
Ampliseq Transcriptome libraries were constructed using the Ampliseq Transcriptome kit (Thermofisher) and manufacturers recommended protocol.

value: venous ulcer

value: Sham


title: 4654_44

description: Subject G


title: Control_INDY3

description:
Poly A+ selection
142032


title: SAT_Baseline_Acute_rep1

description: Gene expression data from subcutaneous adipose tissue biopsies untrained after exercise derived from subject 50

source_name: Subcutaneous adipose tissue biopsies untrained after exercise derived from subject 50

value: Subcutaneous adipose tissue


title: H1299-Input

city: Changsha

first: Yan

last: Hu

address: No.139 Middle Renmin Road

institute: Second Xiangya Hospital of Central South University

description: Input control

data_processing:
Raw fastq files were generated from BCL files using software bcl2fastq
Filtered reads were mapped to human genome GRCh38 using STAR2 with default settings.
Only uniquely mapped reads were kept, then duplicated reads were removed by samtools rmdup command.
Peaks were identified by MACS2 ( version 2.2.7 ) using the q-value cutoff of 0.05.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files were generated using deepTools
Supplementary_files_format_and_content: peak text files were generated using MACS2

source_name: lung cancer cell line

growth_protocol: Lung cancer cell line H1299 was preserved in our laboratory and maintained in RPMI-1640 medium (Gibco, Waltham, MA). H1299 was supplemented with 10% fetal bovine serum (FBS; Gibco), 100 U/mL penicillin, and 100 mg/mL streptomycin and grown at 37 °C and 5% CO2. The cells with confluence of 80% were used for the experiments.

extract_protocol:
The cell lysates of H1299 were incubated with METTL14 antibody. Associated RNA-protein complexes were collected and washed, then subjected to proteinase K digestion and RNA extraction by TRIzol.
Total RNA was isolated from H1299 cells.The quantity and quality of RNA were assessed by the NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific). RNA integrity was determined by RNA integrity number with the 2200 TapeStation analyzer (Agilent Technologies), and samples that had an RNA integrity number above 7.0 were considered acceptable. The isolated RNAs were used for preparing cDNA libraries by NEBNext Ultra RNA Library Prep Kit for Illumina (ENB). Products were purified with Agencourt AMPure XP beads (Beckman) and diluted to 10 pM for cluster generation in situ on a HiSeq 3000 paired‐end flow cell. The clustering of the index‐coded samples was carried out using a HiSeq Rapid PE Cluster Kit V2 (Illumina). After cluster generation, the libraries were sequenced (2 × 150 bp) on the HiSeq 3000 platform.

treatment_protocol: None.

value: lung cancer cell line

value: untreated

tag: rip antibody


title: H1299 MERIP RIP

description: RNA m6A methyalion in H1299 MERIP.

data_processing:
library strategy: MeRIP-seq
Raw fastq files were generated from BCL files using software bcl2fastq
Trim galore was used for trimming the adaptors and filtering the raw reads. Then the filtered reads were mapped to human genome GRCh38 using STAR2 with default settings.
Only uniquely mapped reads were kept, then duplicated reads were removed by samtools rmdup command.
Peaks were identified by MACS2 ( version 2.2.7 ) using the q-value cutoff of 0.05.
Differentially binding regions were identified by DiffBind R package with the following cutoff: FDR <=0.05.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files were generated using deepTools
Supplementary_files_format_and_content: peak text files were generated using MACS2

source_name: METTLE14 knockdown meRIP

extract_protocol:
Total RNA of H1299 cells or the tissues were extracted and rRNA was removed. Then the clean RNA was incubated with m6A antibody for 2 hours at 4 °C. The mixture was then immunoprecipitated by incubation with Protein A beads for 2 hours at 4 °C. Captured RNA was purified and used for the following library construction according to the manufacturer’s instructions.
The quantity and quality of RNA were assessed by the NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific). RNA integrity was determined by RNA integrity number with the 2200 TapeStation analyzer (Agilent Technologies), and samples that had an RNA integrity number above 7.0 were considered acceptable. The isolated RNAs were used for preparing cDNA libraries by NEBNext Ultra RNA Library Prep Kit for Illumina (ENB). Products were purified with Agencourt AMPure XP beads (Beckman) and diluted to 10 pM for cluster generation in situ on a HiSeq 3000 paired‐end flow cell. The clustering of the index‐coded samples was carried out using a HiSeq Rapid PE Cluster Kit V2 (Illumina). After cluster generation, the libraries were sequenced (2 × 150 bp) on the HiSeq 3000 platform.

tag: tissue/cell line

value: METTLE14 knockdown


title: 4643_11

description: Subject D


title: Harmine4

description:
Poly A+ selection
142026

value: Harmine Hydrochloride


title: H1299 MERIP input

description: RNA m6A methyalion in H1299 input.

source_name: METTLE14 knockdown input


title: NPC-mid-SCZ-PRS-2607-10-cDNA


title: Control_INDY1

description:
Poly A+ selection
142028


title: Harmine3

description:
Poly A+ selection
142024


title: 4640_7

description: Subject C

value: Ultrasound


title: NPC-mid-SCZ-PRS-2607-GDO

value: low


title: 4639_5

description: Subject B


title: NPC-mid-SCZ-PRS-2607-cDNA


title: Lung cancer tissue7

description: RNA m6A methyalion in lung cancer tissue 7.

source_name: Lung cancer tissue

value: Lung cancer tissue


title: Harmine2

description:
Poly A+ selection
142022

source_name: U2OS cells


title: Harmine1

description:
Poly A+ selection
142020


title: Lung cancer tissue6

description: RNA m6A methyalion in lung cancer tissue 6.


title: H1299-METTL14 RIP

description: METTL14 RIP sequencing

value: METTL14 (Abcam, ab252562)


title: 4636_1

description: Subject A


title: NPC-mid-SCZ-PRS-553-10-cDNA

value: hgih


title: Lung cancer tissue5

description: RNA m6A methyalion in lung cancer tissue 5.


title: 4649_24

description: Subject E


title: NPC-mid-SCZ-PRS-553-cDNA

value: NPC-derived NGN2 Neurons


title: Harmine_Control4

description:
Poly A+ selection
142018

value: Control Harmine


title: Harmine_Control3

description:
Poly A+ selection
142016


title: NPC-mid-SCZ-PRS-553-GDO

value: Day 21

value: mid (control lines)


title: Lung cancer tissue3

description: RNA m6A methyalion in lung cancer tissue 3.


title: hiPSC-mid-SCZ-PRS-2607_690-HTO

value: hiPSC-derived NGN2 Neurons

value: Day 7

value: XY


title: Lung cancer tissue2

description: RNA m6A methyalion in lung cancer tissue 2.


title: hiPSC-mid-SCZ-PRS-2607_690-GDO


title: Harmine_Control1

description:
Poly A+ selection
142012


title: Bsu_lacZ_30um_IPTG

city: Cambridge

first: Gene-Wei

last: Li

address: 77 Massachusetts Ave.

department: Biology

institute: Massachusetts Institute of Technology

data_processing:
RNA sequencing reads were processed by removing poly(A) tails with cutadapt (options -a AAAAAAAAAAAAAAAAAAAA;min_overlap=10)
mapped using Bowtie (options -v 2 -k 1 --best)
Assembly: NC_000964.3
Supplementary files format and content: Processed data files contain number of reads mapped to each primer in excel format

organism: Bacillus subtilis

extract_protocol:
RNA was extracted and gDNA depleted using RNeasy Plus mini kit (Qiagen) following manufacturer’s instructions
Libraries were generated using custom TBaM-seq protocol described herein.

tag: growth condition

value: LB + 30 uM IPTG

tag: variation in tbam-seq protocol


title: Bsu_lacZ_20um_IPTG

value: LB + 20 uM IPTG


title: hiPSC-mid-SCZ-PRS-2607_690-cDNA


title: IVD_d40_rep2

city: Fukuoka city

first: Mayumi

last: Shono

state: Japan

address: 3-1-1, Maidashi, Higashi-ku, Fukuoka city

country: Japan

institute: Kyushu university

data_processing:
Obtained reads were mapped to the Callithrix_jacchus_cj1700_1.1 genome using STAR. Mapped reads were counted and processed to TPM value by RSEM.
For RNA-seq analysis, common genes between Callithrix jacchus and humans were used. The common genes were defined as in the “Common genes listed in the marmoset–human one-to-one annotation table”.
Assembly: Callithrix_jacchus_cj1700_1.1
Supplementary files format and content: Matrix table with TPM values for every sample

organism: Callithrix jacchus

extract_protocol:
Total RNAs were extracted and purified using an RNeasy Micro Kit, and mRNAs were isolated with the NEBNext poly(A) mRNA magnetic isolation module (NEB).
Purified RNAs were subjected to library construction using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB). cDNAs were enriched by 12-cycle PCR.

tag: cell line

value: BT(+) cells of aggregate

tag: pre-treatment state

value: cjPGCLC induced by BLSERI at day6

value: aggregated with mouse gonadal somatic cells

tag: time

value: 40 days

tag: reporters

value: BLIMP1-tdTomato (BT), NANOS3-eGFP (NG)

value: wild type

tag: facs

value: tdTomato(+)


title: Bsu_lacZ_0IPTG_1

value: LB


title: IVD_d70_rep2

tag: treatment

value: 70 days


title: IVD_d70_rep1


title: Bsu_BC12

description:
Test reproducibility between barcodes for technical replicates
wt_replicates.xlsx

value: WT


title: Normal tissue7

description: RNA m6A methyalion in normal tissue 7.

source_name: Lung cancer adjacent normal tissue

value: Lung cancer adjacent normal tissue

value: untreated


title: Normal tissue5

description: RNA m6A methyalion in normal tissue 5.


title: WDP24_YP24_3

city: Houston

first: Charles

middle: Yang

last: Lin

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: RNA-Seq for PBMC treated with YKL-5-124 - 24Hr

data_processing:
The RNA-Seq data was first preprocessed with BBDuk for single end samples
All RNA-seq datasets were aligned with HISAT2 and quantified via Cuffquant 2.2 with the hg19 ERCC annotation
Cuffnorm was utilized to normalize data
Top 3 replicates (based on correlation) were used
Inactive genes (no samples with FPKM > 10) were filtered out prior to additional analysis
Genome_build: hg19 ERCC
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: PBMC Line

growth_protocol: Cells were grown in 12 well plates in 1 mL of RPMI media with 10% FBS

extract_protocol:
Samples (~2.5x10^5 cells) were lysed with trizol and RNA was extracted via the Zymo Directzol RNA extraction kit
RNA-Seq libraries were prepared for sequencing using standard Quantseq 3' library prep protocols

treatment_protocol: Treatment with DMSO or YKL for 6 or 24 Hr

value: PBMC

tag: treatment time


title: Bsu_BC11


title: Bsu_lacZ_100um_IPTG

value: LB + 100 uM IPTG


title: Lung cancer tissue4

description: RNA m6A methyalion in lung cancer tissue 4.

value: Lung cancer tissue


title: IVD_d40_rep1


title: Normal tissue4

description: RNA m6A methyalion in normal tissue 4.


title: Harmine_Control2

description:
Poly A+ selection
142014

value: Control Harmine


title: IVD_d20_rep2

value: 20 days


title: Bsu_BC10


title: Bsu_lacZ_10um_IPTG

value: LB + 10 uM IPTG


title: IVD_d20_rep1

value: BT(+) cells of aggregate

value: cjPGCLC induced by BLSERI at day6


title: WDP22_YP24_1


title: Normal tissue3

description: RNA m6A methyalion in normal tissue 3.


title: Lung cancer tissue1

description: RNA m6A methyalion in lung cancer tissue 1.


title: Bsu_BC9


title: WDP23_YP24_2


title: WDP18_DP24_3

description: RNA-Seq for PBMC treated with DMSO - 24Hr

value: DMSO


title: Normal tissue2

description: RNA m6A methyalion in normal tissue 2.


title: Bsu_lacZ_0IPTG_2


title: Normal tissue6

description: RNA m6A methyalion in normal tissue 6.


title: Bsu_BC8


title: Normal tissue1

description: RNA m6A methyalion in normal tissue 1.


title: BLSERI_BH_d6_rep1

value: cjPGCLC

value: pre-induced cells from cjESC maintained in PESFA

value: BMP4, LIF, SCF, EGF, Rock inhibitor, and IWR1

value: 6 days

value: BLIMP1-tdTomato (BT), NANOS3-eGFP (NG)


title: WDP17_DP24_2


title: Bsu_BC7

value: WT

value: LB


title: WDP16_DP24_1


title: BLSERIBMS_BH_96h_rep2

value: BMP4, LIF, SCF, EGF, Rock inhibitor, IWR1, and BMS493

value: 96 hr

value: wild type

value: tdTomato(+)


title: VCaP-CT 10nM T 48h rep 3

city: Tampere

first: Reetta

last: Nätkin

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology, Prostate Cancer Research Center

country: Finland

institute: Tampere University and Tays Cancer Center

data_processing:
The base calling was performed using Illumina’s standard bcl2fastq2 software and automatic adapter trimming was used.
Alignment using STAR aligner version 2.5.4b and Ensembl reference genome GRCh38
Quantification of genewise read counts using featureCounts version 1.6.2 and Gencode annotations release 28
Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0
Genome_build: hg38
Supplementary_files_format_and_content: Genewise read counts for each sample (featureCounts, .txt) and protein coding gene filtered DESeq2 normalized count matrix (.csv)

source_name: VCaP prostate cancer cells

growth_protocol: VCaP cell line (passage (p.) 15.) representing androgen sensitive prostate cancer cells was a gift from Dr. Tapio Visakorpi, University of Tampere, Finland. VCaP cells were cultured in RPMI 1640 supplemented with 10 % DCC-FBS, 1 % L-glutamine, 1 % A/A and 10 nM testosterone (T) for seven months to establish T-dependent subclone VCaP-T. VCaP-T cells were then cultured in the presence of 0.1 nM T for 10 months to establish a subclone, VCaP-CT, that could grow at low T level. The VCaP-T and VCaP-CT cells used in this study were cultured for 20 months and represent p.84. and p.73., respectively.

extract_protocol:
RNA was extracted using Direct-Zol Miniprep Plus Kit (Zymo Research #R2070) according to manufacturer's instructions.
Library preparation was done according to Illumina TruSeq Stranded mRNA Sample Preparation Guide (part # 15031047).

treatment_protocol: VCaP-T cells were cultured in 10 nM T and VCaP-CT cells were cultured in 0.1 nM T. Additionally, VCaP-T cells were treated with 0.1 nM T for 48h and VCaP-CT cells were treated with 10 nM T for 48h.

value: VCaP-CT

value: treated with 10 nM T for 48h


title: Bsu_BC6


title: VCaP-CT 10nM T 48h rep 2


title: Bsu_BC5


title: WDP21_YM24_3

value: PBMC


title: BLSERIBMS_BH_96h_rep1


title: VCaP-CT 10nM T 48h rep 1


title: Bsu_BC4


title: VCaP-CT 0.1nM T rep 3

value: 0.1nM T


title: BLSERIBMS_48h_rep2

value: differentiated cells

value: 48 hr

value: all


title: WDP15_DM24_3

value: DMSO


title: WDP19_YM24_1


title: Bsu_BC3


title: VCaP-CT 0.1nM T rep 2


title: BLSERIBMS_48h_rep1

value: pre-induced cells from cjESC maintained in PESFA


title: VCaP-CT 0.1nM T rep 1


title: WDP14_DM24_2


title: BLSERIBMS_24h_rep2

value: 24 hr


title: BLSERI_BH_d6_rep2

value: cjPGCLC

value: BMP4, LIF, SCF, EGF, Rock inhibitor, and IWR1

value: 6 days

value: BLIMP1-tdTomato (BT), NANOS3-eGFP (NG)


title: WDP20_YM24_2


title: BLSERIBMS_24h_rep1

value: BMP4, LIF, SCF, EGF, Rock inhibitor, IWR1, and BMS493


title: Bsu_BC1

value: WT

value: LB


title: VCaP-T 0.1nM T 48h rep 3

value: VCaP-T

value: treated with 0.1 nM T for 48h


title: Bsu_rho_10cycle

value: {delta}}rho

value: 10 2nd strand synthesis cycles


title: Bsu_WT_10cycle_5


title: BLSERIBMS_12h_rep1

value: differentiated cells

value: 12 hr

value: wild type


title: VCaP-T 0.1nM T 48h rep 1


title: BLSERI_BH_96h_rep2

value: 96 hr

value: tdTomato(+)


title: WDP11_YP6_2

description: RNA-Seq for PBMC treated with YKL-5-124 - 6Hr

value: PBMC


title: Bsu_WT_10cycle_4


title: VCaP-T 10nM T rep 3

value: 10 nM T


title: Bsu_BC2


title: BLSERI_BH_96h_rep1

value: cjPGCLC

value: pre-induced cells from cjESC maintained in PESFA

value: BMP4, LIF, SCF, EGF, Rock inhibitor, and IWR1


title: Bsu_WT_10cycle_3


title: BLSERI_48h_rep2

value: 48 hr

value: BLIMP1-tdTomato (BT), NANOS3-eGFP (NG)

value: all


title: WDP06_DP6_3

description: RNA-Seq for PBMC treated with DMSO - 6Hr

value: DMSO


title: BLSERI_48h_rep1


title: VCaP-T 10nM T rep 1

value: VCaP-T


title: WDP05_DP6_2


title: BLSERI_24h_rep2

value: 24 hr


title: WDP04_DP6_1


title: VCaP-T 10nM T rep 2


title: BLSERIBMS_12h_rep2

value: BMP4, LIF, SCF, EGF, Rock inhibitor, IWR1, and BMS493


title: WDP13_DM24_1


title: VCaP-T 0.1nM T 48h rep 2

value: treated with 0.1 nM T for 48h


title: Bsu_rho_1cycle

value: {delta}}rho

value: LB


title: Bsu_WT_10cycle_2

value: WT

value: 10 2nd strand synthesis cycles


title: Bsu_WT_10cycle_1


title: WDP09_YM6_3

value: PBMC


title: WDP12_YP6_3


title: BLSERI_24h_rep1

value: differentiated cells

value: wild type


title: Bsu_WT_1cycle_5


title: WDP10_YP6_1


title: WDP08_YM6_2


title: BLSERI_12h_rep2

value: pre-induced cells from cjESC maintained in PESFA

value: 12 hr


title: Bsu_WT_1cycle_4


title: WDP07_YM6_1


title: BLSERI_12h_rep1

value: BMP4, LIF, SCF, EGF, Rock inhibitor, and IWR1


title: Bsu_WT_1cycle_3


title: WDP03_DM6_3


title: Bsu_WT_1cycle_2


title: A. thaliana_lecrk-I.9_0hr_rep2

city: Auzeville-Tolosane

first: Hervé

last: CANUT

address: Chemin de Borde Rouge

institute: CNRS-Université Paul Sabatier

description: gene expression of 7d-old seedlings

hyb_protocol: Following fragmentation, cRNA was hybridized on ArrayXS Arabidopsis, a 8x60K Agilent microarray containing 32072 gene-specific tags, corresponding to 30541 gene loci. For the hybridisation, the Agilent Gene Expression Hybridisation Kit (Agilent Technologies) was used following the manufacturer's protocol. For example, 600 ng of cRNA was hybridised on a 8x60K microarray for 17 h at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with the GE Wash Buffer 1 (Agilent) and 1 min with the GE Wash buffer 2 (Agilent) at 37°C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for AgilentG3_GX for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel set to Green and Green PMT set to 100%, Tiff 20bit).

data_processing:
Data of all samples were quantile normalised using the ranked median quantiles as previously described (Bolstad et al., 2003). Briefly, the mean signal of each target was ranked relative to all other targets. The ranked signal value was replaced with the median value of the sample rank. So the highest value in all samples became the mean of the highest, the second highest value became the mean of the second highest values, and so on.
To identify differentially regulated genes on the analysis of microarray data, it is important to avoid values around background levels. Typically, an arbitrary cut-off of 20 or 25 is used. In order to identify differentially regulated genes, we performed a statistical analysis (Student's t-test) of the difference in signal intensities between Col0 and lecrk-I.9-1, fold-change between the signals, and one mean raw value >100. A gene was considered to be significantly differentially regulated if the difference in signal intensities between Col0 and lecrk-I.9-1 was supported by a confidence level >95% (P < 0.05) and the mean background-adjusted fold-change of the signal intensities was >2 (up-regulated genes) or <0.5 (down-regulated genes).

organism: Arabidopsis thaliana

label_protocol: The Low Input QuickAmp Labeling Kit (Agilent Technologies) was used for generation of fluorescent cRNA (complementary RNA) following the manufacturer's protocol. For 1st strand synthesis, oligo-dT primer was used. After 2nd strand synthesis, an in vitro transcription for synthesis of cRNA labelled with cyanine 3-CTP was performed. Dye incorporation and cRNA yield were checked with a NanoDrop 2000 Spectrophotometer.

growth_protocol: Col-0 and lecrk-I.9-1 seedlings were grown from seeds in a half Murashige and Skoog liquid medium for 7 days. Three biological replicates were conducted with one flask yielding a single biological replicate. Thus, the total RNAs that were used for microarray experiments were extracted from six independent plant populations. Upon harvest, plant material was washed with UHQ water. For each flask, ∼1000 root segments between root apical meristem and root-hypocotyl junction were pooled, frozen in liquid nitrogen, and stored at −80°C until use.

extract_protocol: RNA isolation was performed by OakLabs (Germany - http://www.oak-labs.com). The quality of the RNA samples were checked by electrophoresis via the 2100 Bioanalyzer (Agilent Technologies) and photometrical measurement with a Nanodrop 2000 spectrophotometer (Thermo Scientific) for determination of the RNA integrity number (RIN) and detection of DNA contaminantion.

tag: tissue

value: roots


title: A. thaliana WT_0hr_rep3

description: gene expression of 7d-old seedlings

value: Wild type


title: Bsu_WT_1cycle_1


title: WDP02_DM6_2

description: RNA-seq for PBMC treated with DMSO - 6Hr

value: DMSO


title: A. thaliana_lecrk-I.9_0hr_rep3

description: gene expression of 7d-old seedlings


title: Pre_rep1

value: pre-induced cells

value: cjESC maintained in PESFA

value: IM12 and activin A

value: BLIMP1-tdTomato (BT), NANOS3-eGFP (NG)


title: A. thaliana_lecrk-I.9_0hr_rep1

description: gene expression of 7d-old seedlings


title: TG_LSERSOX17_BH_96h_rep2

value: cjESC maintained in DK20FA

value: enforced expression of SOX17, LIF, SCF, EGF, and Rock inhibitor

value: 96 hr

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP26C

value: tdTomato(+)


title: Pre_rep2

value: 24 hr


title: Fish 40

city: Bodø

first: Pål

middle: A.

last: Olsvik

address: Universitetsalléen 11

department: Faculty of Biosciences and Aquaculture

country: Norway

institute: Nord University

data_processing:
The library preparations were sequenced on an Illumina platform and 150 bp paired-end reads were generated.
Clean reads were obtained by removing adapter and poly-N sequences and reads with low quality from the raw data. Paired-end clean reads were mapped to the Atlantic salmon reference genome (https://salmobase.org) using HISAT2 software. The Cufflinks Reference Annotation Based Transcript (RABT) assembly method was used to assemble the set of transcript isoforms of each bam file obtained in the mapping step. HTSeq was used to calculate the number of mapped reads to each gene.
RPKM (reads per kilobase of transcript per million reads mapped) was calculated based on gene length and reads mapped to each gene. Differential expression between controls and exposed fish at day 8 and 14 was performed using DESeq2 R package.
Assembly: Atlanitc salmon genome deposited in Ensembl (2020 version).
Supplementary files format and content: Excel file with each line consisting of Salmo salar sequence name (Gene ID), readcount per sample, and annotation (top blast hits) are provided in the Excel file.

organism: Salmo salar

source_name: Liver

extract_protocol:
Homogenization of liver tissue was conducted with a Precellys 24 homogenizer (Bertin Technologies, Montigny-le-Bretonneux, France). Total RNA was extracted and treated with DNase using the BioRobot EZ1 and RNA Tissue Mini Kit (Qiagen, Hilden, Germany). Characterization of total RNA was done with the Agilent 2100 Bioanalyzer using the 6000 Nano LabChip kit (Agilent Technologies, Palo Alto, CA, USA). The RNA integrity number (RIN), which is a measure of degradation in RNA samples, was 9.5 ± 0.2 (n=40) in liver (mean ± st.dev).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions.

treatment_protocol: No specific treatment except sorting fish according to sampling day and exposure

tag: time point

value: day 14

tag: agent

value: Exposed with lufenuron

tag: body weight (g)

tag: length (cm)

tag: dose

value: 5 mg/kg


title: Fish 39


title: WDP01_DM6_1

tag: cell type

value: PBMC


title: A. thaliana WT_0hr_rep2

description: gene expression of 7d-old seedlings

tag: genotype

value: roots


title: Bsu_lacZ_30um_IPTG_BaM_seq

data_processing:
RNA sequencing reads were processed by removing poly(A) tails with cutadapt (options -a AAAAAAAAAAAAAAAAAAAA;min_overlap=10)
mapped using Bowtie (options -v 2 -k 1 --best)
Assembly: NC_000964.3, NC_000913.3
Supplementary files format and content: wig files generated using custom scripts

source_name: bacteria

extract_protocol:
RNA was extracted and gDNA depleted using RNeasy Plus mini kit (Qiagen) following manufacturer’s instructions
Libraries were generated using custom BaM-seq protocol described herein.

tag: growth condition

value: LB + 30 uM IPTG


title: NoeH3-4_S4

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

institute: University of Oxford

data_processing:
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/cgat-developers)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.1.0 with parameters --score-min L,0.0,-0.2
Genome_build: Hg38
Supplementary_files_format_and_content: comma-delimited text files of read counts for each sample

source_name: HeLa

extract_protocol:
RNA from cells was harvested using Trizol reagent. Libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®
RNA libraries were prepared for sequencing using standard NEB protocols

tag: modification

tag: repeat


title: Bsu_lacZ_100um_IPTG_BaM_seq

value: LB + 100 uM IPTG


title: NoeH3-3_S3


title: TG_LSERSOX17_48h_rep2

tag: cell line

value: differentiated cells

tag: pre-treatment state

value: 48 hr

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP24C

value: all


title: A. thaliana WT_0hr_rep1

description: gene expression of 7d-old seedlings

value: Wild type


title: Fish 38


title: Bsu_lacZ_20um_IPTG_BaM_seq

value: LB + 20 uM IPTG


title: Fish 37


title: NoeH3-2_S2


title: Fish 36


title: TG_LSERSOX17_48h_rep1

value: cjESC maintained in DK20FA

value: enforced expression of SOX17, LIF, SCF, EGF, and Rock inhibitor

tag: time

tag: reporters

value: BLIMP1-tdTomato (BT), NANOS3-eGFP (NG)

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP23C


title: Bsu_lacZ_10um_IPTG_BaM_seq

value: LB + 10 uM IPTG


title: TG_LSERSOX17_24h_rep2

tag: treatment

value: 24 hr

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP22C

tag: facs


title: NoeH3-1_S1


title: TG_LSERSOX17_BH_96h_rep1

value: 96 hr

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP25C

value: tdTomato(+)


title: NPC-mid-SCZ-PRS-2607-10-GDO

tag: cell-type

value: NPC-derived NGN2 Neurons

tag: developmental timepoint

value: Day 21

tag: scz prs

value: mid (control lines)

tag: karyotypic sex

value: XY

tag: moi

value: high


title: Fish 34

tag: time point

value: day 14

tag: agent

value: Exposed with lufenuron

tag: body weight (g)

tag: length (cm)

tag: dose

value: 5 mg/kg


title: eH3WTox-4_S20

tag: modification

tag: repeat


title: Bsu_lacZ_0IPTG_1_BaM_seq

tag: genotype

tag: growth condition

value: LB


title: Fish 33


title: eH3WTox-3_S19


title: TG_LSERSOX17_12h_rep1

tag: cell line

tag: cell type

value: differentiated cells

tag: pre-treatment state

value: cjESC maintained in DK20FA

value: enforced expression of SOX17, LIF, SCF, EGF, and Rock inhibitor

tag: time

value: 12 hr

tag: reporters

value: BLIMP1-tdTomato (BT), NANOS3-eGFP (NG)

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP19C

value: all


title: SM4458

city: Odense M

first: Kim

last: Ravnskjaer

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Reads were aligned with STAR (v.2.4.1c) to the mouse genome (mm10, Ens79)
Next-Generation Sequencing HOMER pipeline16 with default settings was used to generated gene-level counts
Quality of raw sequencing was assessed using FastQC and MultiQC
Assembly: mm10, Ens79
Supplementary files format and content: txt files with gene-level counts

organism: Mus

extract_protocol:
Whole-liver RNA was extracted from pulverized snap-frozen livers by phenol/chloroform extraction and column purification using the RNeasy Mini Kit
According to the manufacture's protocol, libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina and paired-end was sequenced on the NovaSeq 6000 platform

treatment_protocol: Male C57BL6/JBomTac mice were housed under standard conditions, with a 12h light/12h dark cycle and ad libitum access to food and drinking water. Advanced-NASH was introduced in mice by Western diet feeding (829100, SDS Research Diet) supplemented with fructose (42 g/L) in drinking water for 52 weeks (WD). Age-matched control mice were fed standard chow diet (altromin #1324) and pure drinking water. Mice were fasted o.n. before sacrifice and weighing.

tag: tissue

value: Whole liver

tag: treatment

value: 52 weeks chow diet


title: TG_LSERSOX17_24h_rep1

value: 24 hr

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP21C

tag: facs


title: Bsu_lacZ_0IPTG_2_BaM_seq


title: Fish 31

tag: time point


title: Fish 32

tag: agent


title: TG_LSERSOX17_12h_rep2

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP20C


title: eH3WT-4_S12


title: eH3WTox-1_S17


title: eH3WTox-2_S18


title: SM4456


title: Fish 30

value: Control

tag: body weight (g)


title: SM4455


title: TG_BLSERSOX17_BH_96h_rep2

value: cjPGCLC

value: enforced expression of SOX17, BMP4, LIF, SCF, EGF, and Rock inhibitor

value: 96 hr

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP18C

value: tdTomato(+)


title: eH3WT-3_S11


title: TG_BLSERSOX17_48h_rep2

value: differentiated cells

value: cjESC maintained in DK20FA

value: 48 hr

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP16C


title: SM4454


title: Fish 29

value: day 14

tag: length (cm)


title: TG_BLSERSOX17_BH_96h_rep1

value: BLIMP1-tdTomato (BT), NANOS3-eGFP (NG)

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP17C


title: Fish 35

value: Exposed with lufenuron

tag: dose

value: 5 mg/kg


title: SM4453

value: Whole liver

value: 52 weeks chow diet


title: TG_BLSERSOX17_48h_rep1

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP15C

value: all


title: Fish 28

value: Control


title: eH3WT-1_S9

tag: modification


title: TG_BLSERSOX17_24h_rep2

value: enforced expression of SOX17, BMP4, LIF, SCF, EGF, and Rock inhibitor

value: 24 hr

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP14C


title: Fish 27


title: SM4457


title: SM4452


title: SM4451


title: TG_BLSERSOX17_24h_rep1

value: differentiated cells

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP13C


title: eH3K9me3-4_S32

tag: repeat


title: Fish 26


title: TG_BLSERSOX17_12h_rep2

value: cjESC maintained in DK20FA

value: 12 hr

tag: genotype

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP12C


title: eH3K9me3-3_S31


title: SM4450


title: eH3K9me3-2_S30


title: Fish 25

value: day 14


title: SM4449

value: 52 weeks western diet


title: TG_BLSERSOX17_12h_rep1

value: BLIMP1-tdTomato (BT), NANOS3-eGFP (NG)

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP11C


title: Fish 24


title: TG_BLSER_96h_rep2

value: BMP4, LIF, SCF, EGF, and Rock inhibitor

value: 96 hr

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP10C


title: SM4448

value: Whole liver


title: Fish 23

value: Control


title: eH3WT-2_S10


title: SM4447


title: eH3K4me3-4_S24


title: TG_BLSER_96h_rep1

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP9C

value: all


title: eH3K4me3-3_S23


title: Fish 22


title: TG_BLSER_48h_rep2

value: 48 hr

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP8C


title: Fish 21


title: eH3K4me3-2_S22


title: TG_BLSER_48h_rep1

value: differentiated cells

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP7C


title: SM4445


title: TG_BLSER_24h_rep2

value: cjESC maintained in DK20FA

value: 24 hr

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP6C


title: Fish 19

value: day 8

value: Exposed with lufenuron

value: 5 mg/kg


title: SM4444

value: 52 weeks western diet


title: eH3K4me3-1_S21


title: Fish 20


title: eH3K9me3-1_S29


title: TG_BLSER_24h_rep1

value: BMP4, LIF, SCF, EGF, and Rock inhibitor

value: BLIMP1-tdTomato (BT), NANOS3-eGFP (NG)

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP5C


title: eH3K27Mox-4_S36


title: eH3K27Mox-3_S35


title: SM4442

value: Whole liver


title: TG_BLSER_12h_rep2

value: 12 hr

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP4C


title: SM4443


title: eH3K27Mox-2_S34


title: Fish 16


title: TG_BLSER_12h_rep1

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP3C

value: all


title: eH3K27Mox-1_S33


title: Fish 18


title: cjESC_PESFA_rep2

value: cjESC

value: wild type


title: eH3K27me3-4_S48


title: Fish 15


title: cjESC_PESFA_rep1


title: Fish 14


title: SM4446


title: YSS-GrpXII-R04

city: Baltimore

first: Michael

middle: T

last: McCoy

state: Maryland

address: Molecular Neuropsychiatry Branch, 251 Bayview Blvd. Suite 200, 251 Bayview Blvd. Suite 200, 251 Bayview Blvd. Suite 200

institute: NIDA

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Rattus norvegicus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts were added to the table
Assembly: Rattus norvegicus Rnor6.0

organism: Rattus norvegicus

source_name: Dorsal striatum

extract_protocol:
RNA was extracted using the protocol from RNeasy Mini Handbook (Qiagen)
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).  RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).  The sequencing libraries were clustered on two flowcell lanes. After clustering, the flowcells were loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration.

treatment_protocol: Rats self-administered (SA) METH for 21 days followed by footshocks for 8 days. The drug-naïve control rats (CT) will be the same as the METH-trained rats except sterile saline is infused after the active lever press. The control animals for footshock also received saline but were yoked to the METH-trained rats that receive contingent shocks. There were separate groups of rats that were yoked (Y) to the corresponding METH shock-resistant (SR) and shock-sensitive (SS) rats. They are termed YSR and YSS, respectively. The animals were euthanized 2 hours the last day of SA, the hippocampal brain region was dissected, snap frozen on dry ice and then stored in the -70C freezer.

tag: strain

value: Sprague Dawley

value: Dorsal striatum

tag: age

value: adult

value: Yoked Shock Sensitive


title: eH3K27me3-3_S47


title: cjESC_DK20FA_rep2

tag: cell line

tag: cell type


title: Fish 13

value: day 8

value: Exposed with lufenuron


title: eH3K27me3-2_S46


title: YSS-GrpXIII-R04


title: cjESC_DK20FA_rep1

tag: pre-treatment state

tag: time

value: rtTA; tetO-BLIMP1; SOX17-GR; DD-TFAP2C


title: Fish 17

value: 5 mg/kg


title: Fish 12


title: eH3K27me3-1_S45


title: YSS-GrpXIII-L04

tag: tissue


title: YSS-GrpXIII-L06

tag: treatment


title: KO CD11c

city: INDIANAPOLIS

first: Cong

last: Yan

state: INDIANA

address: 975 W WALNUT ST IB420

institute: Indiana University School of Medicine

library_source: transcriptomic single cell

data_processing:
CellRanger 3.0.2 was utilized to process the raw sequence data generated. The filtered gene-cell barcode matrices generated by CellRanger were used for further analysis.
Seurat was used for data normalization, data scaling, graph-based clustering, cluster marker genes idenfificationa.
The CCA function from Seurat was used for integrative analysis of the WT and KO samples.
Assembly: hg38
Supplementary files format and content: filtered matrix

source_name: blood

extract_protocol:
Fresh blood was harvested from the wildtype and knockout mice, and treated with RBC lysis buffer. After three times wash with PBS, cells were sorted using anti-CD11c microbeads.
library construction was done by the Center for Medical Genomics at Indiana University School of Medicine following the recommended protocol for the Chromium Single Cell 3’ Reagent Kit.

value: lal-/-


title: YSS-GrpXIII-L02


title: WT CD11c

value: lal+/+


title: Fish 10

value: Control


title: Fish 11


title: eH3K27M-4_S28


title: Fish 9


title: eH3K27M-3_S27


title: eH3K27M-2_S26


title: Fish 8


title: YSR-GrpXII-R06

value: Yoked Shock Resistant


title: YSR-GrpXII-R10


title: eH3K27M-1_S25


title: A14

city: Sengnam

first: Sohyun

last: Hwang

address: 59, Yatap-ro, Bundang-gu

department: Pathology

country: South Korea

institute: Cha University

hyb_protocol: The capture probeSet (2 μL) of the nCounter PanCancer Immune Profiling Panel was added after which the samples were placed in a 65℃ thermocycler (Bio-Rad Laboratories Inc., Hercules, California, USA) for 16 hours. The samples were transferred to the preparation station (NanoString Technologies) with prepared nCounter Master Kit and a cartridge. The preparation station runs for approximately 2.5 to 3 hours.

scan_protocol: The cartridges were transferred to the Digital Analyzer (NanoString Technologies) and were scanned on the Digital Analyzer at 555 fields of view.

data_processing: nSolverTM Analysis Software version 4.0 and NanoString QCPro version 1.14.0 were used to perform a quality check of the NanoString nCounter data. For data normalization for quantifying gene expression values, we used geNorm algorithm in nCounter Advanced Analysis version 2.0.115.

label: Nanostring

source_name: recurred glioblastoma multiforme tissue

label_protocol: The extracted RNAs were run on the NanoString nCounter Analysis System (NanoString Technologies, Inc., WA, USA) according to the manufacturer's instructions. Each RNA (5 μL, 100–300 ng) was mixed with 8 μL of Master Mix (reporter codeSet and hybridization buffer).

extract_protocol: For RNA extraction, 2-10 sections of 5 μm-thick formalin-fixed paraffin-embedded (FFPE) tissue were prepared after selection of one representative block which contained tumor and tumor microenvironment. The FFPE tissues were deparaffinized and homogenized using the Covaris Focused-ultrasonicator (Covaris, Mannheim, Germany). The truXTRAC FFPE total NA Ultra Kit (Covaris, Mannheim, Germany) was used for efficient and sequential extraction of RNA from FFPE tissue samples using Adaptive Focused Acoustics (AFA) according to manufacturer’s instructions.

tag: Sex

value: male

tag: response

value: Responder

tag: survival


title: Fish 7

tag: time point

tag: agent

tag: body weight (g)


title: YSR-GrpXII-R02


title: A11

value: female


title: A12

value: Non-responder


title: A10


title: A08


title: Fish 6

tag: length (cm)

tag: dose


title: YSR-Grp-XIII-R10

tag: genotype

value: wild type


title: A07


title: YSR-GrpXIII-R08

tag: strain

value: Sprague Dawley


title: eH3K18me3-3_S39

tag: modification

tag: repeat


title: SS-GrpXII-R03

value: Dorsal striatum

tag: age

value: METH Shock Sensitive


title: Fish 5