title: AT/RT CHLA06 TAK-228 A


title: BT20_siHSF1_A

status: Public on Mar 15 2022

type: SRA

city: Chicago

first: Marc

last: Mendillo

state: IL

address: 303 E Superior St

department: Biochemistry and Molecular Genetics

country: USA

institute: Feinberg School of Medicine, Northwestern University

library_source: transcriptomic

data_processing:
RNA-seq: Sequence quality was assessed with FastQC v0.11.2, Fastq files were trimmed using bbduk from BBTools v35.92 according to Lexogen QuantSeq manufacturer parameters, mapped to hg38 using STAR v2.6.0 and gene annotations from Ensembl 78. HTSeq was used to count uniquely mapped reads.
ChIP-seq: Reads were aligned to hg38 using Bowtie v0.12.9. Peaks were called relative to knockout samples using MACS v1.4.2 and annotated from Ensembl 78
Genome_build: hg38
Supplementary_files_format_and_content: htseq counts tables provide counts of uniquely mapped RNAseq reads. Bed files were generated by MACS for peaks

molecule: total RNA

organism: Homo sapiens

source_name: cancer cell line

growth_protocol: Cells were grown at 37°C and 5% CO2

extract_protocol:
Lexogen 3' QuantSeq FWD for Illumina
RNA was extracted using the Qiagen RNeasy kit using the Qiashredder for homogenization of cells grown in vitro and a rotor-stator homogenizer for xenograft tumors

treatment_protocol:
N/A
See sample section for treatment

tag: cell line

tag: vector

tag: sirna/sgrna

tag: antibody


title: E80_HiC_replicate_6

city: Chengdu

first: Jing

last: Li

state: China

address: No. 211 Huimin Road, Wenjiang District

department: College of Animal Science and Technology

country: China

institute: Sichuan Agricultural University

description:
E80_6
all.samples.abindex.txt
E80.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt

library_source: genomic

data_processing:
Reads were mapped to the pig genome (Sscrofa 11.1) by BWA (v 0.7.15).
Juicer were used HiC data processing to filter duplication, low-quality alignment read pairs (MAPQ < 30) as well as intra-fragment read pairs.
High-quality reads  normalized with Knight-Ruiz [KR] algorithm and quantile  algorithm to structure contact matrixes at 20 or 100 kb resolution.
Compartments A/B were identified with A-B index as described by M Jordan Rowley. et al. Mol Cell. 2017 (PMID: 28826674).
Locations of topologically associated domains (TADs) were computed by combining  directionality index (Dixon et al. Nature. 2012 [PMID: 22495300]) and insulation index (Emily Crane et al. Nature. 2017)
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: 20 and 100 kb matrixes, hic file
A-B index, txt file
locations of TAD for each sample, merged replicates, and consensus TAD,txt file
D-score, txt file

molecule: genomic DNA

organism: Sus scrofa

source_name: Liver

extract_protocol:
Livers tissue was homogenized with liquid nitrogen then fixed with 4% formaldehyde solution and incubated at room temperature for 30 min. Glycine were added to a final concentration of 0.2 M to quench the fixing reaction, and incubated at room temperature for 5 min then centrifuge for 10 min at 1,000 g and 4˚C. Discarded supernatants and cells were lysed with 1M Tris-HCl, 1M NaCl, 10% CA-630 and protease inhibitors on ice for 15 min. Cell nucleus were washed twice and were permeabilized at 65˚C for 10 min with 1% SDS to a final concentration of 0.1%. To quench the SDS, added 10% TritonX-100 (0.1% final concentration) and incubated at 37˚C for 15 min. Then 200 U DpnII (a 4-cutter restriction enzyme) was added and digested chromatin at 37˚C for 90 min, 65˚C for 20 min and 25˚C for 5 min. The restriction fragment overhangs were filled and labelled by biotinylated nucleotides, then ligated in a small volume.
After crosslink reversal, ligated DNA was purified and sheared to a length of 300–500 bp, at which point ligation junctions were pulled down with magnetic beads and prepared for BGISEQ-500 sequencing.

treatment_protocol: Six two-years-old female pigs were fed with a high fat diet (15.12 MJ·kg-1 metabolizable energy, 11.26% crude protein, 6.8% fat and 5% lysine) for 22 weeks, compared with the pigs of  two-years-old fed with well-characterized normal diet for 22 weeks.

tag: breed

value: Bama pig

tag: tissue

value: Liver

tag: condition

value: Developmental stage

tag: age

value: embryonic day 80

tag: Sex

value: female

tag: chip antibody

tag: restriction enzyme

value: DpnII


title: BT20_siHSF1siHSF2_A

value: siHSF1 + siHSF2


title: E80_HiC_replicate_3

description:
E80_3
all.samples.abindex.txt
E80.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt


title: 0d_HiC_replicate_1

description:
0d_1
all.samples.abindex.txt
0d.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt

value: the birth day


title: 355E_M1

city: Greenwood

first: Vijay

last: Shankar

state: South Carolina

address: 115 Milford Pines Drive

institute: Clemson University

data_processing:
Demultiplexing: Barcoded sequence reads were demultiplexed using the Illumina pipeline v1.9.
Preprocessing: Adapter sequences were trimmed using cutadapt v1.6. Trimmed sequences were then aligned to multiple target sequence databases, using BWA v0.7.10 (MEM algorithm with parameters ‘-v 2 –t 4’): (1) all trimmed sequences were aligned against a ribosomal RNA database to filter out residual rRNA that escaped depletion during library preparation; (2) remaining sequences were then aligned against a custom database of potential microbiome component species (see below) using BWA; (3) sequences that did not align to either the rRNA or microbiome databases were aligned to all D. melanogaster sequences in RepBase.
Alignment: The remaining sequences that did not align to any of the databases above were then aligned to the D. melanogaster genome (BDGP5) and known transcriptome (FlyBase v5.57) using STAR v2.4.0e
Quantification and Normalization: Read counts for known and novel gene models were quantified using HTSeq-count with the ‘intersection-nonempty’ assignment method. Tabulated read counts for each endogenous gene present in both Baseline and ethanol-treated lines were combined and normalized across all samples using EdgeR.
Genome_build: FlyBase v5.57
Supplementary_files_format_and_content: Matrix table in tab-delimited text file contains raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: Whole fly

extract_protocol:
Briefly, total RNA was extracted with Trizol using the RNeasy Mini Kit (Qiagen, Inc.) and ribosomal RNA was depleted from 5 ug of total RNA using the Ribo-Zero™ Gold Kit (Illumina, Inc.).
Depleted mRNA was fragmented and converted to first strand cDNA. During the synthesis of second strand cDNA, dUTP instead of dTTP was incorporated to label the second strand cDNA.  Samples were processed in batches of 48 and 16 libraries were pooled randomly into 25 pools. Pooled library samples were quantified again to calculate final molarity and then denatured and diluted to 14pM following Illumina guidance. Pooled library samples were clustered on an Illumina cBot; each pool was sequenced on one lane of an Illumina HiSeq 2500 using 125 bp single-read v4 chemistry.

value: Male

tag: line

tag: exposure

value: 10% EtOH in growth media


title: E80_HiC_replicate_1

description:
E80_1
all.samples.abindex.txt
E80.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt


title: AT/RT CHLA06 TAK-228 B

city: Baltimore

first: Jeffrey

last: Rubens

state: MD

address: 1800 Orleans St

department: Oncology

institute: Johns Hopkins University

data_processing:
NOT PROVIDED; REQUESTED
Assembly: mm9
Supplementary files format and content: matrix table with raw gene counts for every gene and every sample

source_name: AT/RT cell model

growth_protocol: BT37 was grown in RPMI media while CHLA02, CHLA06, and CHLA266 were grown in EF media

extract_protocol:
Total RNA was extracted from cell pellets using Qiagen (Germantown, MD) RNeasy mini kit and column DNase treatment.
RNAseq libraries were prepared using Illumina (San Diego, CA) TruSeq stranded mRNA sample preparation kit following manufacturer’s recommended procedure with minor modifications. Briefly, mRNA was purified from 15ng of total RNA using oligo dT RNA purification magnetic beads. The purified mRNA was then fragmented at 94°C for 8 minutes, primed with random primers, and converted to double strand cDNA. The resulting cDNA was end repaired, dA tailed, and ligated to TruSeq adapter (with unique dual index barcodes). Libraries were then PCR amplified using 15 cycles. The final libraries were quality checked, quantitated, and pooled in equal molar for sequencing on NovaSeq SP 100cycle flowcells for 2X50bp sequencing.

treatment_protocol: Samples were treated with 0.1% DMSO or TAK-228 20nM x 4 hours

value: ATRT-MYC

tag: treatment

value: TAK-228 20nM x 4 hours


title: E80_HiC_replicate_2

description:
E80_2
all.samples.abindex.txt
E80.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt


title: SKBR3_siHSF2_B


title: 355E_F2

value: Female


title: SKBR3_siNT_B

value: siNT


title: 355E_F1


title: SKBR3_siHSF1_B


title: AT/RT CHLA06 TAK-228 C


title: E80_HiC_replicate_4

description:
E80_4
all.samples.abindex.txt
E80.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt


title: AT/RT CHLA06 Control C

value: 0.1% DMSO


title: E38_HiC_replicate_6

description:
E38_6
all.samples.abindex.txt
E38.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt

value: embryonic day 38


title: SKBR3_siHSF2_A


title: AT/RT CHLA06 Control B


title: AT/RT CHLA06 Control A


title: E38_HiC_replicate_5

description:
E38_5
all.samples.abindex.txt
E38.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt


title: MCF7_siNT_B


title: AT/RT CHLA02 TAK-228 C

value: ATRT-SHH


title: 340E_M2


title: 340E_M1


title: MCF7_siNT_A


title: AT/RT CHLA02 TAK-228 B


title: MCF7_siHSF2_B


title: 340E_F2


title: MCF7_siHSF2_A


title: 335E_M2


title: SKBR3_siHSF1_A


title: AT/RT CHLA02 Control B


title: MCF7_siHSF1_A


title: AT/RT CHLA02 Control C


title: 335E_M1


title: E38_HiC_replicate_3

description:
E38_3
all.samples.abindex.txt
E38.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt

value: Bama pig


title: MCF7_siHSF1_B


title: AT/RT BT37 TAK-228 C

value: ATRT-TYR molecular subgroup


title: HCC38_siNT_B


title: E38_HiC_replicate_4

description:
E38_4
all.samples.abindex.txt
E38.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt

value: Liver

value: Developmental stage


title: AT/RT CHLA02 TAK-228 A


title: 340E_F1


title: Retinoid-containing lung cells_WI001

city: New York

first: William

middle: S

last: Blaner

state: NY

address: 630 West 168th Street

department: Medicine

institute: Columbia University

data_processing:
Initial data processing, including demultiplexing reads and converting raw base call files into the fastq format, was performed using Cell Ranger version 5.0.1 (10X Genomics).
Expression counts for each gene in all samples were collapsed and normalized to unique molecular identifier (UMI) counts using Cell Ranger 5.0.1 (10X Genomics). The result is a large digital expression matrix with cell barcodes as rows and gene identities as columns.  Filtered feature matrix outputs from Cell Ranger were used for all downstream analyses.
Assembly: mm10-2020-A
Supplementary files format and content: Each element of the feature-barcode matrix is the number of UMIs associated with a feature (row) and a barcode (column)

organism: Mus musculus

source_name: lung retinoid-containing cells

extract_protocol:
Mouse lung digests for single-cell flow cytometry were prepared from wild type C57BL/6 mice using a method involving digestion with pronase and collagenase. Flow cytometry was employed to sort live, individual retinoid-containing cells based on their emission at 455 nm (UV-positive cells).  Singlet discrimination was sequentially performed using plots for forward scatter (FSC-A versus FSC-H) and side scatter (SSC-W versus SSC-H). Dead cells were excluded by scatter characteristics and staining with propidium iodide.  All FACS isolations were performed on a FACSAria cell sorter (Becton Dickinson).
Single cell libraries were prepared using the Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions followed by their sequencing on a NovaSeq 6000 (Illumina) in a 2 x 100 bp configuration

tag: strain

value: Lung

value: 3 months

tag: genotype

value: wild type


title: HCC38_siNT_A


title: AT/RT BT37 TAK-228 B


title: HCC38_siHSF2_B


title: 324E_M1


title: E38_HiC_replicate_2

description:
E38_2
all.samples.abindex.txt
E38.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt

value: female

value: DpnII


title: E38_HiC_replicate_1

description:
E38_1
all.samples.abindex.txt
E38.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt


title: AT/RT BT37 TAK-228 A


title: 324E_M2

value: Male

value: 10% EtOH in growth media


title: Sample_MUC17744

city: Neuherberg

first: Wolfgang

last: Wurst

address: Ingolstaedter Landstrasse 1

department: Institute of Developmental Genetics

country: Germany

institute: Helmholtz Zentrum München

description: mice are injected with GFP containing AAV at the age of 12-16 weeks

data_processing:
Cell Ranger 3.1.0 against a modified version of the mouse transcriptome GRCm38 (Ensembl Release 99) that included both GFP and Cre sequences.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts for control (MUC17744) and reprogrammed (MUC17745) mice

source_name: control

growth_protocol: mouse striatum. Animal housing and handling protocols were approved by the committee for the Care and Use of Laboratory animals of the Government of Upper Bavaria (Germany) and were carried out in accordance with the European Communities' Council Directive 2010/63/EU. During the work, all efforts were made to minimize animal suffering. All mouse lines were kept in a controlled pathogen free (SPF) hygiene standard environment on a 12 h light/dark cycle. The mice had access to ad libitum standard feed and water always. All tests were approved for the ethical treatment of animals by the Government of Upper Bavaria.

extract_protocol:
Chromium Single Cell 3´Library & Gel Bead Kit v2 (PN-120237, 10xGenomics) to generate single cell gel beads in emulsion (GEMs).
cDNA synthesis was done according to 10x Genomics guidelines.
Libraries were pooled and sequenced on a NovaSeq6000 (Illumina) according to the Chromium Single Cell v.2 specifications and with an average read depth of 50,000 aligned reads per cell.

treatment_protocol: Cells were dissected from mouse striatum (n=2). Incubation with dissociating enzyme was performed for 90 min.

value: Brain striatal tissue

tag: time

value: 13 weeks post injection

value: Rosa26-dCas9-activator mouse (dCAM)


title: HCC38_siHSF2_A

tag: cell line


title: AT/RT BT37 Control B

value: 0.1% DMSO


title: 335E_F2

value: Female


title: Retinoid-containing lung cells_WI02


title: 324E_F2


title: HCC38_siHSF1_B

tag: vector


title: AAV9-S2

city: Helsinki

first: Markus

last: Räsänen

address: Haartmaninkatu 8

country: Finland

institute: Wihuri Research Insitute

data_processing:
The Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3’ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
Reads were aligned to mouse reference genome mm10
We used the Seurat R package (v2.3.4) for QC, filtering and analysis of the aggregated data (Butler et al. Nature Biotechnology 2018)
Cells were filtered based on the number of genes and the percentage of mitochondrial genes.
For further analysis the Pagoda2 package (version 0.0.0.9003) and Velocyto package and the velocyto.R package (version 0.6) have been used. Pseudotime analysis was done by using the monocle package (v2.8.0) with the default parameters.
Genome_build: mm10

molecule: polyA RNA

source_name: Cardiac endothelial cells

extract_protocol:
Mouse hearts were isolated for single-cell preparation as described previously. Hearts were harvested and coronary arteries were perfused briefly with buffer A (113 mM NaCl, 4.7 mM KCl, 0.6 mM KH2PO4, 0.6 mM Na2HPO4, 1.2 mM MgSO4, 12 mM NaHCO3, 10 mM KHCO3, 10 mM HEPES and 30 mM Taurine) to remove blood in a retrograde manner by cannulating the aorta before Collagenase type II (Worthington) was added to dissociate the ventricular cells. The dissociated cells were then allowed to sediment at 37°C for 10 minutes to allow cardiomyocytes to settle down as a pellet leaving behind a non-myocyte rich supernatant. The non-myocyte enriched supernatant was treated with rat anti-mouse CD16/CD32 (eBioscience, clone 2.4G2) at 4°C for 20 minutes before being incubated with fluorophore-conjugated antibodies at 4°C for 30 minutes. The following antibodies were used: anti-CD45-FITC (Biolegend, clone 30-F11), anti-PDGFR-PECy7 (eBioscience, clone APA5) and anti-CD105-PE (eBioscience, clone MJ7/18). Cell suspensions were triturated through a 40 µm Nylon cell strainer (Falcon) and then subjected to flow cytometry-based sorting using a Biorad S3e cell sorter.
Subsequent cDNA purification, amplification (12 cycles) and library construction (sample index PCR 14 cycles) was performed as instructed
Sample libraries were sequenced on the Illumina NovaSeq 6000 system using S1 flow cell (Illumina)

treatment_protocol: For sample 3, we used an AAV-VEGF-B vector to transduce the VEGF-B expression in the heart. Sample 4 was injected with an empty AAV.

tag: strain background

value: 3-4 months

tag: genotype/variation

value: Control (S2) AAV transduced animal

value: Cardiac endothelial cells


title: AAV9-Vegfb

value: AAV9-Vegfb transduced animal


title: 320E_M2


title: Sample_MUC17745

source_name: dCAM x GFAP-Cre


title: 324E_F1


title: LY6S-iso1 expressing YDFR cells 3

city: Tel-Aviv

first: Daniel

middle: H

last: Wreschner

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

description: Sample DW12

data_processing:
Reads were trimmed using cutadapt
After trimming, the reads were mapped to the human genome (hg38) using STAR  v2.4.2a (using options alignEndsType EndToEnd and outFilterMismatchNoverLmax set to 0.04)
Counting proceeded over genes annotated in Ensembl release 92, using htseq-count (version 0.6.1p1)
Normalization and differential expression was performed using DESeq2 (Version 1.10.1)
Genome_build: hg38
Supplementary_files_format_and_content: Processed file include raw counts and DESeq2 normalized counts.

source_name: M12 human melanoma cell line

growth_protocol: Human melanoma cells were routinely generated by re-plating d 7 adherent melanoma cell cultures (typically 1 × 106 cells into a T25 flask)  in RPMI cell culture medium supplemented with 10% fetal calf serum  ng/ml

extract_protocol:
RNA was extracted from cells using the Qiagen RNA extraction kit.
Libraries were prepared using the INCPM-mRNA-seq. Briefly, the polyA fraction (mRNA) was purified from 500 ng of total input RNA followed by fragmentation and the generation of double-stranded cDNA. After Agencourt Ampure XP beads cleanup (Beckman Coulter), end repair, A base addition, adapter ligation and PCR amplification steps were performed. Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent). Sequencing was done on a Nextseq 75 cycles high output kit, allocating 20M reads per sample (Illumina; single read sequencing).

treatment_protocol: M12 or YDFR human melanoma cells were stably transfected either with control pQCXIP vector or with pQCXIP vector coding for LY6-iso1 protein. Stable transfectants were selected by adding puromycin to the cell culture medium

tag: cell type

value: human melanoma cells

tag: passage

tag: transfection

value: pQCXIP vector coding for LY6-iso1


title: AT/RT BT37 Control A

value: ATRT-TYR molecular subgroup


title: LY6S-iso1 expressing YDFR cells 2

description: Sample DW11


title: aMHC-Vegfb p7 WT

description: aMHC-Vegfb p7 WT

tag: age

value: postnatal day 7

value: control wildtype (WT) animal

tag: tissue


title: MCF7_HSF2_siNT_C

tag: sirna/sgrna

value: siNT

tag: antibody


title: LY6S-iso1 expressing YDFR cells 1

description: Sample DW10


title: ATRT BT37 Control C


title: 320E_M1

tag: Sex

value: Male

tag: line


title: control YDFR cells with pQCXIP vector 2

description: Sample DW8

source_name: YDFR human melanoma cell line

value: pQCXIP vector


title: control YDFR cells with pQCXIP vector 3

description: Sample DW9


title: MCF7_HSF2_siNT_A


title: 318E_M2

tag: exposure

value: 10% EtOH in growth media


title: HCT116 cells - input DNA

city: Shanghai

first: Zhehui

last: Zhu

state: Shanghai

address: Kongjiang Road 1665, Shanghai

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
ChIP-seq reads were aligned to the hg38 reference genome using Bowtie2 (2.4.1).
Sam files were converted to Bam format using Samtools and used for peak calling.
MACS2 (2.2.7.1) was used to call peaks with the sonicated input as a control and an initial threshold q-value of 0.05 as cutoff.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using Deeptools (3.5.0).

source_name: HCT116 CELL LINE

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: colon cancer cell line

tag: chip antibody


title: 318E_F2


title: HCT116 cells - HHEX

value: HHEX (abcam，ab34222)


title: 320E_F2


title: HCC38_siHSF1_A


title: 318E_F1


title: LY6S-iso1 expressing M12 cells 2

description: Sample DW5


title: AT/RT CHLA02 Control A

value: ATRT-SHH

tag: treatment

value: 0.1% DMSO


title: 318E_M1


title: 315E_M2


title: MCF7_HSF2_siHSF1_A


title: Monocyte_BD_3

city: Beijing

first: Wenjie

last: Zheng

address: No1 ShuaiFuYuan，Dong Cheng District ，Beijing, Beijing, CN

institute: Peking Union Medical College Hospital

data_processing:
The Cellranger software suite (https://support.10xgenomics.com/single-cell-gene- expression/software/pipelines/latest/what-is-cell-ranger) from 10X was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens/Info/Index) and perform UMI counting
Assembly: hg38
Supplementary files format and content: Tar files of filtered feature-barcode matrix (output of CellRanger)  and csv file of sample information

source_name: human CD14+monocyte

extract_protocol:
The cell suspension was loaded into Chromium microfluidic chips with 3’ chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2 reagent kit (10X Genomics) according to the manufacturer’s instructions
RNA libraries were prepared using standard 10X genomics protocols were sequenced on Illumina NovaSeq 6000.

treatment_protocol: PBMCs were isolated from blood by density gradient centrifugation and then resuspended in PBS. Monocytes were positively isolated by CD14 MicroBeads (Miltenyi Biotec) according to the manufacturer's instructions.

tag: disease status

value: Behcet's disease (BD)

value: male

value: human CD14+monocyte


title: control YDFR cells with pQCXIP vector 1

description: Sample DW7


title: MCF7_HSF2_siNT_B

tag: cell line


title: MCF7_HSF2_siHSF1_B

tag: vector


title: M008 day 28 biopsy

type: RNA

city: Silver Spring

first: Aarti

last: Gautam

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

description: US11213905_251486834823_1_3 - M008 day 28 biopsy

hyb_protocol: cRNA was hybridized to a mouse genome microarray (Agilent Technologies) following manufacturer's instructions.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C. Images were quantified using Agilent Feature Extraction Software.

data_processing: Agilent Feature Extraction Software (v11.0.1.1) was used for background subtraction and LOWESS normalization, and analyzed using custom R scripts to obtain lists of probe sets differentially expressed.

source_name: Skin biopsy

label_protocol: Total RNA (25-200ng) was used as starting material, which was amplified using the Quick Amp Two-Color Kit (Agilent Technologies). The labelled cDNA was purified using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and eluted, labeled cRNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA).

growth_protocol: Not applicable.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Thermo Fisher, Waltham, MA) and RNA was isolated following the manufacturer’s protocol.

treatment_protocol: Mice were exposed to 1, 3, 6, or 20Gy of whole-body x-ray ionizing radiation. Mice exposed to 20Gy were euthanized under the humane endpoint of an IACUC approved study protocol at d7 while mice that received 1, 3, 6Gy survived the full 28 days time course.

tag: strain

tag: gender

value: Skin biopsy

value: Whole-body x-ray ionizing radiation

tag: dosage

tag: time point

value: Day 28

tag: mouse id

source_name: Agilent's Universal Mouse Reference RNA

treatment_protocol: Not applicable.

tag: sample type

value: Reference


title: M002 day 21 biopsy

description: US11213905_251486834832_1_3 - M002 day 21 biopsy

tag: tissue

value: Day 21


title: M008 day 21 biopsy

description: US11213905_251486834823_1_2 - M008 day 21 biopsy


title: MCF7_HSF1_siNT_C

tag: sirna/sgrna


title: MCF7_HSF2_siHSF1_C

tag: antibody


title: aMHC-Vegfb p7 TG

description: aMHC-Vegfb p7 TG

tag: strain background

tag: age

value: postnatal day 7

tag: genotype/variation

value: cardiomyocyte-specific overexpression of VEGFB (transgenic (TG) animal)

value: Cardiac endothelial cells


title: MCF7_HSF1_siHSF2_C


title: 320E_F1

tag: Sex

value: Female

tag: line

tag: exposure


title: 315E_F1

value: 10% EtOH in growth media


title: LY6S-iso1 expressing M12 cells 3

description: Sample DW6

tag: cell type

value: human melanoma cells

tag: passage

tag: transfection

value: pQCXIP vector coding for LY6-iso1


title: M007 day 21 biopsy

description: US11213905_251486834823_1_4 - M007 day 21 biopsy

tag: strain

tag: gender

value: Male

tag: treatment


title: MCF7_HSF1_siHSF2_B

tag: cell line

tag: vector


title: 315E_M1


title: MCF7_HSF1_siHSF2_A


title: LY6S-iso1 expressing M12 cells 1

description: Sample DW4


title: control M12 cells with pQCXIP vector 3

description: Sample DW3

value: pQCXIP vector


title: 313E_M2


title: control M12 cells with pQCXIP vector 1

description: Sample DW1


title: 315E_F2


title: MCF7_HSF1_siNT_A

value: siNT


title: M018 day 21 biopsy

description: US11213905_251486834823_1_1 - M018 day 21 biopsy

tag: tissue

tag: dosage

tag: time point

tag: mouse id

tag: sample type


title: control M12 cells with pQCXIP vector 2

description: Sample DW2


title: E2 (10nM)

city: Cambridge

first: Zhaojie

last: Zhang

state: MA

address: 300 Tech Sq

institute: H3 Biomedicine

description: 10_02EE_00AOH3Bio_H3B_s10_ERalpha_hs_i89

data_processing:
Reads were aligned to the human genome (hg19) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome.
The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Genome_build: hg19
Supplementary_files_format_and_content: bw files

source_name: breast cancer cell line

growth_protocol: MCF7 cells were washed 3x with PBS and cultured for 72 hours in phenol red-free DMEM media supplemented with 10% charcoal-stripped serum.

extract_protocol:
Fixation was stopped with 2.5M glycine and cells were washed 2X in PBS/0.5% Igepal CA-630.  Cell pellets were snap frozen and chromatin isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer.
Genomic DNA regions of interest were isolated using antibodies against ERa (Santa Cruz polyclonal sc-543). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65ºC, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Illumina sequencing libraries were prepared from the ChIP and input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.

treatment_protocol: Indicated compounds were added to cells for 45 minutes followed by a 15-minute formaldehyde fixation (1% formaldehyde, 100 mM NaCl, 0.1 mM EDTA pH8.0, 5 mM Hepes pH 7.9).

value: breast cancer cell line

tag: chip antibody

value: ERa (Santa Cruz polyclonal sc-543)


title: M003 day 28 biopsy

description: US11213905_251486834450_1_4 - M003 day 28 biopsy

value: Skin biopsy


title: MCF7_HSF1_siNT_B

tag: sirna/sgrna

tag: antibody


title: M013 day 21 biopsy

description: US11213905_251486834558_1_1 - M013 day 21 biopsy

value: Whole-body x-ray ionizing radiation


title: M009 day 21 biopsy

description: US11213905_251486834558_1_3 - M009 day 21 biopsy


title: M019 day 21 biopsy

description: US11213905_251486834559_1_3 - M019 day 21 biopsy


title: M008 day 4 biopsy

description: US11213905_251486834450_1_1 - M008 day 4 biopsy

value: Day 4


title: MCF7_GFP_siNT_B

value: GFP-Flag


title: MCF7_GFP_siNT_C


title: M003 day 21 biopsy

description: US11213905_251486834558_1_2 - M003 day 21 biopsy

value: Day 21

value: Reference


title: Fulvestrant (100nM)

value: Fulvestrant    (100nM)


title: 313E_M1

tag: Sex

tag: line

tag: exposure


title: M003 day 7 biopsy

description: US11213905_251486834450_1_3 - M003 day 7 biopsy

value: Day 7


title: M018 day 7 biopsy

description: US11213905_251486834449_1_3 - M018 day 7 biopsy


title: 313E_F2

value: Female


title: MCF7_GFP_siHSF2_B


title: H3B-9709 (1uM)

tag: cell type


title: MCF7_GFP_siNT_A


title: 306E_M2

value: 10% EtOH in growth media


title: 313E_F1


title: M013 day 28 biopsy

description: US11213905_251486834415_1_3 - M013 day 28 biopsy

tag: strain

value: Day 28


title: MCF7_GFP_siHSF2_C


title: 28E_M2


title: M015 day 28 biopsy

description: US11213905_251486834415_1_4 - M015 day 28 biopsy

tag: gender


title: H3B-9709 #3 [GS044412]

data_processing:
TPM values and counts for genes were obtained using Kallisto.
Genome_build: hg19
Supplementary_files_format_and_content: gene expressions in counts and tpm

growth_protocol: Cell cultures were in log phase growth for the duration of the experiment.

extract_protocol:
Cell lysates were collected 6 days following treatment initiation in TRIzol and immediately frozen with liquid nitrogen prior to analysis.
Stranded RNASEQ library prep

treatment_protocol: MCF7 parental cells were treated with various compounds at 100 nM. Media and compounds were refreshed after 3 days, and cell lysates were collected 6 days following treatment initiation.

tag: treatment


title: 306E_F2


title: MCF7_GFP_siHSF2_A

tag: cell line


title: 306E_M1


title: MCF7_GFP_siHSF1siHSF2_C

tag: vector

value: siHSF1 + siHSF2


title: H3B-6545 (1uM)


title: M014 day 28 biopsy

description: US11213905_251486834415_1_2 - M014 day 28 biopsy

value: Male

tag: tissue


title: DMSO

value: DMSO


title: 306E_F1


title: H3B-9709 #2 [GS044411]


title: 28E_F2


title: M009 day 28 biopsy

description: US11213905_251486834415_1_1 - M009 day 28 biopsy

tag: dosage


title: 28E_M1


title: M018 day 4 biopsy

description: US11213905_251486834449_1_2 - M018 day 4 biopsy

tag: time point


title: H3B-9709 #1 [GS044410]


title: Tamoxifen (1uM)

value: Tamoxifen    (1uM)


title: 335E_F1


title: MCF7_GFP_siHSF1_C


title: H3B-6545 #2 [GS044408]

value: breast cancer cell line


title: 287E_M1


title: MCF7_GFP_siHSF1siHSF2_A


title: H3B-6545 #1 [GS044407]


title: PC3M_WT_D_R1

source_name: cancer cell line xenograft tumor

extract_protocol:
NEBNext Ultra II RNA Library Prep Kit for Illumina
RNA was extracted using the Qiagen RNeasy kit using the Qiashredder for homogenization of cells grown in vitro and a rotor-stator homogenizer for xenograft tumors

value: PC3M Clonal Xenograft Tumor


title: 287E_M2


title: Fulvestrant #3 [GS044403]

value: Fulvestrant


title: MCF7_GFP_siHSF1_B


title: MCF7_GFP_siHSF1siHSF2_B


title: Fulvestrant #2 [GS044402]


title: PC3M_WT_C_R1


title: M006 day 28 biopsy

description: US11213905_251486834414_1_3 - M006 day 28 biopsy

value: Skin biopsy

value: Whole-body x-ray ionizing radiation

tag: mouse id


title: M007 day 28 biopsy

description: US11213905_251486834414_1_4 - M007 day 28 biopsy

tag: sample type


title: MCF7_GFP_siHSF1_A

value: GFP-Flag


title: Fulvestrant #1 [GS044401]


title: 28E_F1


title: M002 day 28 biopsy

description: US11213905_251486834414_1_2 - M002 day 28 biopsy


title: PC3M_WT_B_R1


title: M007 day 7 biopsy

description: US11213905_251486834413_1_1 - M007 day 7 biopsy


title: 287E_F2


title: M007 day 4 biopsy

description: US11213905_251486834412_1_3 - M007 day 4 biopsy

value: Day 4


title: 280E_F2


title: H3B-6545 #3 [GS044409]


title: 287E_F1


title: PC3M_sgHSF2_I_R1


title: PC3M_sgHSF2_H_R1


title: 280E_M2


title: Tamoxifen #3 [GS044400]

value: Tamoxifen


title: M009 day 4 biopsy

description: US11213905_251486834412_1_4 - M009 day 4 biopsy

value: Reference


title: 239E_M2


title: M009 day 0 biopsy

description: US11213905_251486834412_1_2 - M009 day 0 biopsy

value: Day 0 (hour 2)


title: M002 day 0 biopsy

description: US11213905_251486834412_1_1 - M002 day 0 biopsy


title: 280E_M1


title: PC3M_sgHSF2_G_R1


title: M020 day 28 biopsy

description: US11213905_251486834407_1_3 - M020 day 28 biopsy


title: DMSO #2 [GS044396]


title: 280E_F1

value: Female


title: DMSO #1 [GS044395]


title: Tamoxifen #1 [GS044398]


title: DMSO #3 [GS044397]


title: PC3M_WT_A_R1


title: 239E_F2

value: 10% EtOH in growth media


title: 239E_M1


title: M019 day 28 biopsy

description: US11213905_251486834407_1_2 - M019 day 28 biopsy

value: Day 28


title: 239E_F1


title: PC3M_sgHSF2_E_R1


title: 229E_M2


title: PC3M_sgHSF2_F_R1


title: 229E_M1


title: M016 day 28 biopsy

description: US11213905_251486834406_1_4 - M016 day 28 biopsy


title: Tamoxifen #2 [GS044399]


title: PC3M_sgHSF2_D_R1


title: M015 day 21 biopsy

description: US11213905_251486834406_1_2 - M015 day 21 biopsy

value: Day 21


title: PC3M_sgHSF2_A_R1


title: PC3M_sgHSF2_C_R1


title: 228E_M2

value: Male


title: M018 day 28 biopsy

description: US11213905_251486834407_1_1 - M018 day 28 biopsy


title: 229E_F2


title: 228E_M1


title: M006 day 21 biopsy

description: US11213905_251486834390_1_3 - M006 day 21 biopsy


title: M012 day 21 biopsy

description: US11213905_251486834390_1_4 - M012 day 21 biopsy


title: 229E_F1


title: M014 day 7 biopsy

description: US11213905_251486834390_1_1 - M014 day 7 biopsy

value: Day 7


title: M016 day 21 biopsy

description: US11213905_251486834406_1_3 - M016 day 21 biopsy


title: PC3M_sgHSF1_D_R1


title: PC3M_sgHSF1_B_R1


title: M014 day 21 biopsy

description: US11213905_251486834406_1_1 - M014 day 21 biopsy


title: 217E_M2


title: PC3M_sgHSF1_A_R1


title: 228E_F2


title: MB231_sgHSF2_C_R1

description: MDAMB231_Xenografts_htseq.all.counts.txt

value: MDAMB231 Xenograft Tumor


title: 217E_F2


title: MB231_sgHSF2_D_R1


title: MB231_sgHSF2_B_R1


title: 217E_F1


title: MB231_sgHSF2_A_R1


title: PC3M_sgHSF1_C_R1


title: MB231_sgHSF1_D_R1


title: M013 day 7 biopsy

description: US11213905_251486834389_1_4 - M013 day 7 biopsy


title: 228E_F1


title: 217E_M1


title: 208E_M2


title: M006 day 7 biopsy

description: US11213905_251486834389_1_2 - M006 day 7 biopsy


title: M020 day 4 biopsy

description: US11213905_251486834388_1_4 - M020 day 4 biopsy


title: M002 day 7 biopsy

description: US11213905_251486834389_1_1 - M002 day 7 biopsy


title: M020 day 7 biopsy

description: US11213905_251486834390_1_2 - M020 day 7 biopsy


title: M012 day 7 biopsy

description: US11213905_251486834389_1_3 - M012 day 7 biopsy


title: DU12

source_name: U87 glioblastoma cells expressing human LY6S-iso1 protein

growth_protocol: U87 cells were grown with DMEM cell growth medium supplemented with 10% fetal calf serum.

treatment_protocol: U87 cells were stably transfected either with controlpQCXIP vector or with pQCXIP vector coding for LY6-iso1 protein. Stable transfectants were selected by adding puromycin to the cell growth medium.

tag: transfection


title: 208E_M1


title: M016 day 4 biopsy

description: US11213905_251486834388_1_3 - M016 day 4 biopsy


title: DU11

value: pQCXIP vector coding for LY6-iso1 protein


title: M015 day 4 biopsy

description: US11213905_251486834388_1_2 - M015 day 4 biopsy


title: MB231_sgHSF1_C_R1

tag: sirna/sgrna


title: MB231_sgHSF1_B_R1

tag: antibody


title: 208E_F2

tag: Sex


title: 208E_F1

tag: line


title: MB231_sgD_C_R1

value: sgNon-Targeting


title: DU9

source_name: U87 glioblastoma cells

value: controlpQCXIP vector


title: MB231_sgHSF1_A_R1


title: M014 day 4 biopsy

description: US11213905_251486834388_1_1 - M014 day 4 biopsy

value: Skin biopsy


title: MB231_sgD_D_R1


title: DU10


title: 195E_M2

tag: exposure


title: M012 day 4 biopsy

description: US11213905_251486834387_1_3 - M012 day 4 biopsy

value: Whole-body x-ray ionizing radiation


title: DU7


title: M002 day 4 biopsy

description: US11213905_251486834387_1_2 - M002 day 4 biopsy


title: 195E_M1


title: 195E_F2


title: M020 day 0 biopsy

description: US11213905_251486834387_1_1 - M020 day 0 biopsy


title: M013 day 4 biopsy

description: US11213905_251486834387_1_4 - M013 day 4 biopsy


title: 195E_F1


title: Colon flush, Res4

city: Aldiwaneyah

first: Esraah

middle: Sattar Mahmood

last: Alharris

state: Alqadiseyah

address: 2465 Altahadee postal office

department: Pathology and Forensic Medicine

country: Iraq

institute: university of Alqadiseyah

data_processing:
sequenced data were collected from the Illumina Miseq system in FASTQ files along with map file in excel format
Data then were uploaded to the online 16S analysis platform Nephele (https://nephele.niaid.nih.gov), supported by the Office of Cyber Infrastructure and Computational Biology (OCICB), National Institute of Allergy and Infectious Diseases (NIAID), NIH
The default setting of Nephele was excluding any samples with the median OUT less than 0.2 OUT fractions of the highest sample in the same run in order to increase the quality of the reads, and then the generated FASTA files were blasted into Greengenes_99 database at 70% cutoff similarity
The 16S metagenomics was analyzed through 16S Paired-end QIIME method,
Supplementary_files_format_and_content: the groups of related DNA sequences were assigned to operational taxonomic units (OTUs), and Nephele-generated output pipeline files were analyzed to determine targeted tissue-microbial compositions.

source_name: Colon flush

growth_protocol: Female BALB/c mice, aged 6-8 weeks were housed for 7 days in specific pathogen-free conditions.The mice were maintained under a 12 h light/dark cycle at an ambient temperature of 24 ± 1°C, and received ad libitum access to normal chow diet and water

extract_protocol:
colon:  Gut contents were collected by conducting a colon flush, Bacterial genomic DNA was isolated,
lung:  Quick-DNA Fungal/Bacterial Midiprep Kit was used in the isolation of bacterial genomic DNAs from lungs. Briefly, 500 mg of lung tissue was added to ZR Bashing/Bead lysis filtration tube with 6 ml of genomic lysis buffer containing β-mercaptoethanol (0.5% v/v). The tubes were placed in a 50ml–tube holder for 1 minute, followed by centrifugation at 3,000 g for 5 minutes. Following centrifugation, the samples were filtered through Zymo-Spin V-E columns in a vacuum manifold with a vacuum pressure of 600 mmHg. After filtering, the columns were transferred to collection tubes for centrifugation at 10,000 g for 1 minute. The columns were washed with 400 µl of genomic DNA-wash buffer and then DNA samples were eluted from the columns with 150 µl DNA Elution Buffer under centrifugation at 10,000 g for 1 minute.
DNA samples were stored at -80ºC and used in the library preparation for 16S ribosomal RNA sequencing using 16S Metagenomic Sequencing Library Preparation Kit
ribosomal RNA sequencing

treatment_protocol: After one week of housing, each mouse received an intraperitoneal (i.p.) injection of 100 µl sterile phosphate-buffered saline (PBS) solution containing 250µg chicken egg ovalbumin (OVA) and 4mg/ml aluminum hydroxide on day 0. On day 7, the sensitized mice were challenged with 50 μg OVA suspended in 50 μl of sterile PBS intranasally under short anesthesia.On days 1-14, mice in the treatment group (res) were administered daily with oral gavage of 200µl carboxymethyl cellulose (CMC) solution containing RES (100mg/kg) while the vehicle group (veh) received 200µl CMC solution alone.

value: Colon flush

tag: mouse strain

value: Balb/c mice

value: Resveratrol


title: DU8


title: MDAMB231_sgHSF2_C

source_name: cancer cell line


title: Colon flush, Res3


title: MDAMB231_sgHSF2_A


title: MDAMB231_sgHSF2_B


title: 181E_M2

source_name: Whole fly


title: Colon flush, Res2


title: MDAMB231_sgHSF1_C


title: M016 day 0 biopsy

description: US11213905_251486834386_1_3 - M016 day 0 biopsy

tag: strain

value: Reference


title: M019 day 0 biopsy

description: US11213905_251486834386_1_4 - M019 day 0 biopsy

tag: gender

value: Day 0 (hour 2)


title: Colon flush, Res1

tag: treatment


title: M014 day 0 biopsy

description: US11213905_251486834386_1_1 - M014 day 0 biopsy


title: 181E_F2

value: Female


title: Colon flush, Veh4

value: Vehicle


title: MDAMB231_sgHSF1_B

tag: cell line


title: MDAMB231_sgHSF1_A

tag: vector


title: 181E_M1

value: 10% EtOH in growth media


title: M015 day 0 biopsy

description: US11213905_251486834386_1_2 - M015 day 0 biopsy

tag: tissue


title: M013 day 0 biopsy

description: US11213905_251486834374_1_4 - M013 day 0 biopsy

tag: dosage


title: 181E_F1


title: Colon flush, Veh3


title: 177E_M1


title: Colon flush, Veh2


title: M007 day 0 biopsy

description: US11213905_251486834374_1_2 - M007 day 0 biopsy

tag: time point


title: 177E_M2


title: Colon flush, Veh1


title: MDAMB231_CTL_B


title: MDAMB231_CTL_A


title: M012 day 0 biopsy

description: US11213905_251486834374_1_3 - M012 day 0 biopsy

tag: mouse id


title: 177E_F2


title: M006 day 0 biopsy

description: US11213905_251486834374_1_1 - M006 day 0 biopsy

tag: sample type


title: MDAMB231_sgHSF1sgHSF2_C

value: sgHSF1.1 + sgHSF2.1


title: 177E_F1


title: M024 day 4 biopsy

description: SG12054172_251486834589_1_4- M024 day 4

value: Male

value: Day 4


title: 176E_M2


title: MDAMB231_CTL_C


title: MDAMB231_sgHSF1sgHSF2_B


title: M023 day 4 biopsy

description: SG12054172_251486834589_1_3 - M023 day 4


title: Colon flush, Naive5

value: Naive


title: MDAMB231_sgHSF1sgHSF2_A


title: 176E_M1


title: MDAMB231_siNT_C

extract_protocol:
Lexogen 3' QuantSeq Pool for Illumina
RNA was extracted using the Qiagen RNeasy kit using the Qiashredder for homogenization of cells grown in vitro and a rotor-stator homogenizer for xenograft tumors

value: siNT


title: Colon flush, Naive2


title: M022 day 4 biopsy

description: SG12054172_251486834589_1_2- M022 day 4


title: Colon flush, Naive3


title: 176E_F2


title: Colon flush, Naive4


title: M021 day 4 biopsy

description: SG12054172_251486834589_1_1- M021 day 4


title: 158E_M2


title: PC3M_sgHSF2_B_R1

value: PC3M Clonal Xenograft Tumor


title: 158E_M1


title: Lung, Res2

source_name: Lung

value: Lung


title: Colon flush, Naive1


title: M021 day 0 biopsy

description: SG12054172_251486834588_1_1- M021 day 0

value: Skin biopsy


title: 176E_F1


title: Lung, Res3


title: M022 day 0 biopsy

description: SG12054172_251486834588_1_2- M022 day 0

value: Whole-body x-ray ionizing radiation


title: MDAMB231_siHSF2_B


title: M024 day 0 biopsy

description: SG12054172_251486834588_1_4- M024 day 0


title: MDAMB231_siNT_A


title: 158E_F1


title: M023 day 0 biopsy

description: SG12054172_251486834588_1_3- M023 day 0


title: M017 day 4 biopsy

description: SG12054172_251486834585_1_2- M017 day 4


title: MDAMB231_siNT_B


title: M024 day 7 biopsy

description: SG12054172_251486834577_1_2 - M024 day 7 biopsy

value: Day 7


title: MDAMB231_siHSF1siHSF2_C

value: siHSF1 + siHSF2


title: MDAMB231_siHSF2_C


title: Lung, Veh1

value: Balb/c mice


title: 153E_M1


title: M017 day 0 biopsy

description: SG12054172_251486834585_1_1- M017 day 0

value: Reference


title: Lung, Naive3


title: 158E_F2


title: M022 day 7 biopsy

description: SG12054172_251486834576_1_4 - M022 day 7 biopsy


title: Lung, Naive2


title: 153E_F1


title: M005 day 7 biopsy

description: SG12054172_251486834576_1_2 - M005 day 7 biopsy


title: Lung, Res1

value: Resveratrol


title: Lung, Naive1


title: 142E_M2


title: E coli cell - microaerobic_rep7

city: Taipei

first: Gan-Guang

last: Liou

state: Taiwan

address: Institute of Molecular Biology, Academia Sinica., 128 Sec. 2, Academia Rd, Nankang,

country: Taiwan

data_processing: The output fastq files were processed and analyzed using CLC Genomics Workbench 10.0.1 (CLC bio, Cambridge, MA; now: Qiagen Digital Insights, Redwood City, CA), based on its built-in default parameter setting workflows, including sequence read trimming and filtering, quality control and read mapping to a reference genome of E. coli (NC_000913), gene identification and reads per gene quantifying.

organism: Escherichia coli

source_name: E coli cells

growth_protocol: E. coli K-12 strain MG1655 was grown overnight at 37°C for 16 hours in M9 medium supplemented with 0.4% glucose and trace elements (462.56 µM H3BO3, 34.71 µM MnCl2, 10.80 µM FeCl3, 7.72 µM ZnSO4, 3.16 µM CuSO4, 2.30 µM (NH4)6Mo7O24, 1.68 µM Co(NO3)2). The 16-hour fresh overnight culture was diluted into 750 ml fresh M9 medium (to OD460 0.04 to 0.05) in 1 L fermentation vessel chamber (Winpact Parallel Fermentation System FS-05-220). For aerobic culture condition, air is continuously pumped at 0.4 LPM (liters per min). For microaerobic culture conditions, we usually supply N2 at 0.4 LPM to the chamber containing fresh M9 medium until the dissolved oxygen (DO) reaches 0, keep N2 pumping for 30 min, then dilute overnight culture, and turn off N2. The chamber containing culture was completely sealed and the culture was grown under microaerobic conditions. All cultures were grown at 200 rpm, 37oC and maintained at pH 7.0 by automatic titration with sterile 1 M KOH. Cultures were harvested at OD460 = 0.5 to 0.6.

extract_protocol:
Bacterial pellet was resuspended in 4 ml KJ medium (50 mM glucose, 25 mM Tris-HCl, pH 8.0, 10 mM EDTA, pH 8.0, 100 mM NaCl), lysed by adding boiling 4 ml buffer (0.2 M NaCl, 20 mM Tris-HCl, pH 7.5, 40 mM EDTA, 0.5 % SDS), boiled in a boiling water bath for 45 seconds, then added equal volume of acidic phenol (i.e., acidic phenol 8 ml, pH = 4.5), slowly inverted about 20 times and mixed gently. Extract RNA from the above cell lysates by centrifugation at 4,000 g for 1 hour at 4°C, the supernatant was collected, and the total RNA was precipitated in 1 volume of isopropanol and 1/10 volume of 3 M sodium acetate (pH 7.8) at -20°C and the sample was kept at -20°C until use.
The purified RNA was first analyzed by Bioanalyzer (Agilent 2100), with ratio of rRNA [23S / 16S] greater than 1.4 was considered high/good quality and was further used for RNA-seq analysis. The rRNA removal was performed in accordance with the manufacturer's Ribo-Zero™ Magnetic Kit (Gram-Negative Zero rRNA removal Magnetic kit (bacteria) instructions, followed by the Illumine total RNA stranded kit for the RNA fragmentation and cDNA library construction. And 150 bp-600 bp Blue pippin 2% gel was cut out for size selection and then purified via Qiagene minElute PCR kit. Samples O-1 to O-4 and N-1 to N-4 were sequenced for 150 cycles on the MiSeq system using the Illumina MiSeq Reagent kit. The Illumina NextSeq 500 Mid Output kit was used to sequence samples O-5 and N-5 to N-10 for 150 cycles on the NextSeq 500 System.

tag: growth condition

value: microaerobic


title: Lung, Veh3

value: Vehicle


title: MDAMB231_siHSF2_A

tag: sirna/sgrna


title: M011 day 0 biopsy

description: SG12054172_251486834571_1_3- M011 day 0

value: Day 0 (hour 2)


title: MDAMB231_siHSF1_A

tag: antibody


title: M023 day 7 biopsy

description: SG12054172_251486834577_1_1 - M023 day 7 biopsy


title: 153E_F2

tag: Sex

value: Female

value: 10% EtOH in growth media


title: MDAMB231_siHSF1_B


title: Bursa RCT-035 Degenerative

city: St. Louis

first: Muhammad Farooq

last: Rai

state: MO

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Genome_build: Ensembl GRCh38.101
Supplementary_files_format_and_content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Bursa

extract_protocol:
Samples received in the laboratory were stored at 4oC for 12-24 h for complete immersion of RNAlater solution to protect RNA integrity and to avoid RNA degradation. Samples were the held at -80oC until extraction of total RNA. Total RNA was isolated using RNAeasy Mini Kit (Thermo Fisher Scientific, Carlsbad, CA) according to manufacturer’s protocol. Briefly, tissues were allowed to thaw, then dissected into 23 mm3 cubes using two scalpels under the tissue culture hood. RNAlater was replaced with 1 mL TRIzol reagent (Life Technologies, Carlsbad, CA) and tissues were individually homogenized at 30,000 rpm for 2 min in 1.5 mL Eppendorf tubes with the use of an electric homogenizer. After 10 min of incubation of lysate at room temperature, 200 µL of chloroform was added followed by 30 sec of vigorous vortexing. Samples were then incubated at room temperature for 10 min, followed by centrifugation at 13,000 rpm for 10 min at 4oC. Next, aqueous upper phase containing total RNA was transferred to a fresh 1.5 mL Eppendorf tube and  an equal volume of RNase-free isopropanol (2-propanol) was dispensed prior to brief but extensive shaking. The contents were incubated at room temperature for 10 min, after which centrifuged at 13,000 rpm for 15 min at 4oC to obtain a pellet. Next, supernatant was removed and the pellet was washed once with RNase-free 70% ethyl alcohol (1 mL volume) by centrifugation (13,000 rpm for 5 min). Then, the supernatant was removed, and residual ethyl alcohol was allowed to air dry for a few minutes. Lastly,  the pellet was eluted in 30 L RNase-free water. The qulity of total RNA was assessed using RNA integrity number (RIN) system with the use of an Agilent 2100 BioAnalyzer (Agilent technologies, Santa Clara, CA) and the concentration of each samples was measured with a NanoDrop ND-1000 instrument (NanoDrop Technologies). All samples were stored at 80°C until use for RNA-seq or real-time qPCR.
Qiagen FastSelect

value: Male

value: Bursa

tag: age

tag: bmi

tag: condition

value: Degenerative


title: MDAMB231_siHSF1siHSF2_A


title: MDAMB231_siHSF1siHSF2_B


title: E coli cell - microaerobic_rep6

institute: Institute of Molecular Biology, Academia Sinica.

tag: strain


title: M010 day 4 biopsy

description: SG12054172_251486834571_1_2- M010 day 4

tag: gender

value: Day 4


title: Bursa RCT-034 Traumatic

value: Traumatic


title: 153E_M2

tag: line

tag: exposure


title: 142E_M1


title: 142E_F2


title: M005 day 4 biopsy

description: SG12054172_251486834570_1_4- M005 day 4

value: Skin biopsy

tag: treatment


title: M005 day 0 biopsy

description: SG12054172_251486834570_1_3- M005 day 0

tag: tissue

value: Whole-body x-ray ionizing radiation


title: Bursa RCT-036 Degenerative


title: MDAMB231_siHSF1_C

tag: cell line

tag: vector


title: 142E_F1


title: Bursa RCT-032 Traumatic


title: M011 day 4 biopsy

description: SG12054172_251486834571_1_4- M011 day 4

tag: dosage

tag: time point

tag: mouse id


title: E coli cell - aerobic_rep2

tag: growth condition

value: aerobic


title: E coli cell - microaerobic_rep5


title: Lung, Veh2

value: Lung

tag: mouse strain


title: 129E_M2

tag: Sex


title: E coli cell - aerobic_rep5


title: 105E_M2


title: M004 day 4 biopsy

description: SG12054172_251486834570_1_2- M004 day 4

tag: sample type


title: Bursa RCT-033 Degenerative

tag: age

tag: bmi


title: E coli cell - microaerobic_rep1

tag: strain


title: 129E_M1


title: E coli cell - aerobic_rep4


title: Bursa RCT-029 Traumatic

tag: condition


title: 105E_M1

tag: line


title: 129E_F2

tag: exposure


title: E coli cell - microaerobic_rep10


title: Bursa RCT-028 Traumatic


title: M001 day 0 biopsy

description: SG12054172_251486834569_1_3- M001 day 0

tag: gender

tag: treatment


title: E coli cell - microaerobic_rep9


title: Bursa RCT-027 Degenerative

tag: tissue


title: M001 day 7 biopsy

description: SG12054172_251486834576_1_1 - M001 day 7 biopsy

value: Day 7


title: 105E_F2


title: E coli cell - aerobic_rep1


title: Bursa RCT-031 Traumatic


title: E coli cell - microaerobic_rep8


title: Bursa RCT-026 Traumatic


title: 129E_F1


title: USP10 WT rep2

first: hongchang

last: li

address: Changping District, Beijing

institute: State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing)

description: Gene expression of wildtyped neonates after birth at 6 hours

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent GEx Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent Mouse 4x44K Gene Expression Microarrays v2 for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Gene Expression Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to Hi 100% and Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: USP10 WT replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Quick Amp Labeling Kit(Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Cryopulverization of tissues using the Biopulverizer(biospec), homogenization of tissues using the Mini-Bead-Beater-16(biospec), RNA was prepared using the TRIzol® Reagent (Invitrogen life technologies) following the manufacturer's recommendations. The protocol includes RNA Clean-up, RNA quantification and quality control. RNA was purified using RNasey Mini Kit(Qiagen p/n 74104), quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly kidney tissues from the indicated genotyped neonates were collected and used to analysise gene expression profiling.

value: Kidney

value: male

tag: genotype

value: USP10 WT


title: M010 day 0 biopsy

description: SG12054172_251486834571_1_1- M010 day 0

tag: dosage

value: Reference


title: Bursa RCT-025 Degenerative


title: Lipopolysaccharide treated 3

city: Dallas

first: Tamia

middle: Alisha

last: Harris-Tryon

state: TX

address: 5323 Harry Hines Blvd., UT Southwester Medical Center- Department of Dermatology

institute: UT Southwestern Medical Center

description: LPS 6

data_processing:
Sequence reads were mapped against the hg19 genome using TopHat.
For each gene, read counts were computed using HTSeq-count and analyzed for differential expression using DESeq2.
Genome_build: hg19 genome
Supplementary_files_format_and_content: text files includes compiled FPKM values for each Sample

source_name: Sebocytes

growth_protocol: SZ95 sebocytes were maintained in Sebomed Basal Medium (Fischer Scientific NC9711618) supplemented with 10% fetal bovine serum (GeminiBio 100-106), 5 ng/ml human epidermal growth factor (ThermoFisher PHG0313) and 1% Antibiotic-Antimycotic (Gibco 15240062).

extract_protocol:
RNA was extracted from SZ95 sebocyte cells using the RNAeasy Plus universal kit (Qiagen 73404).
RNA quality was assessed using Agilent 2100 Bioanalyzer. Truseq RNA sample preparation kit v2 (Illumina) was used for the preparation of sequencing libraries.
Sequencing was performed on an Illumina HiSeq 2500 for signal end 50 bp length reads.

treatment_protocol: SZ95 human sebocytes were stimulated with 1μg/ml LPS (Sigma L4524). 16 hours post-stimulation cells were harvested and analyzed as described below.

tag: cell line

value: Lipopolysaccharide treated


title: USP10 WT rep3

source_name: USP10 WT replicate 3


title: Bursa RCT-030 Traumatic

value: Female


title: Lipopolysaccharide treated 1

description: LPS 4


title: Bursa RCT-024 Degenerative


title: Lipopolysaccharide treated 2

description: LPS 5


title: E coli cell - microaerobic_rep2

value: microaerobic


title: M004 day 0 biopsy

description: SG12054172_251486834570_1_1- M004 day 0

value: Male

tag: time point

value: Day 0 (hour 2)

tag: mouse id


title: 105E_F1

extract_protocol:
Briefly, total RNA was extracted with Trizol using the RNeasy Mini Kit (Qiagen, Inc.) and ribosomal RNA was depleted from 5 ug of total RNA using the Ribo-Zero™ Gold Kit (Illumina, Inc.).
Depleted mRNA was fragmented and converted to first strand cDNA. During the synthesis of second strand cDNA, dUTP instead of dTTP was incorporated to label the second strand cDNA.  Samples were processed in batches of 48 and 16 libraries were pooled randomly into 25 pools. Pooled library samples were quantified again to calculate final molarity and then denatured and diluted to 14pM following Illumina guidance. Pooled library samples were clustered on an Illumina cBot; each pool was sequenced on one lane of an Illumina HiSeq 2500 using 125 bp single-read v4 chemistry.

value: 10% EtOH in growth media


title: Vehicle treated 3

description: VEH 3

value: Vehicle treated


title: Bursa RCT-023 Degenerative

value: Bursa

value: Degenerative


title: PANC-1 cell line shHDAC5 #3

city: Wuhan

first: Haixin

last: Yu

state: Hubei Province

address: 1277, Jiefang Avenue

institute: Wuhan union hospital

data_processing:
Basecalls performed using Hisat2 v2.0.5
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 25).
Paired-end reads were aligned to the hg19.featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg19
Supplementary_files_format_and_content: text file include gene name, position,log2(Fold_change),p-value,q-value for each Sample
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read-counts and FPKM values for each Sample.

extract_protocol:
RNA was harvested using Trizol reagent(Life Technologies). Illumina NEB Ultra directional RNA library Prep Kit was used with 1 ug of total RNA for the construction sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First   Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). 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.


title: E coli cell - microaerobic_rep3

tag: growth condition


title: E coli cell - microaerobic_rep4


title: PANC-1 cell line shHDAC5 #1


title: PANC-1 cell line shControl #3

value: shControl


title: Bursa RCT-021 Degenerative

tag: Sex


title: E coli cell - aerobic_rep3

value: aerobic


title: USP10 WT rep1

source_name: USP10 WT replicate 1


title: Bursa RCT-022 Degenerative


title: M001 day 4 biopsy

description: SG12054172_251486834569_1_4- M001 day 4

value: Skin biopsy

value: Whole-body x-ray ionizing radiation

value: Day 4

tag: sample type


title: ST-S-S3

city: Yangzhou

first: Yijun

last: Wang

state: Jiangsu

address: Wenhui

institute: Yangzhou University

data_processing:
Clean reads were aligned to the maize reference genome (AGPv3) with Tophat2.
Aligned reads of single sample were assembled to generate transcripts with Cufflinks.
FPKM (expected fragments per kilobase of transcript per million fragments sequenced) values were evaluated by the Cuffdiff utility embedded in the Cufflinks package.
Genome_build: AGPv3
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample. A fasta file with the novel transcript sequences is available on the series record.

organism: Zea mays

source_name: Young shoot

growth_protocol: Maize plants were grown in normal conditions.

extract_protocol:
Total RNA was extracted with the RNeasy Plant Mini Kit.
RNA libraries were prepared according to standard Illumina protocols.

treatment_protocol: At three leaf stage, seedlings were treated with water or 100 mM salinity solution.

tag: cultivar

value: ST

value: salinity

value: Young shoot

tag: developmental stage

value: three-leaf stage


title: ST-S-S1


title: ST-S-S2


title: USP10 KO rep3

description: Gene expression of neonates after birth at 6 hours with Usp10 gene knockout

source_name: USP10 KO replicate 3

value: Kidney

value: male

value: USP10 KO


title: PANC-1 cell line shHDAC5 #2


title: Vehicle treated 2

description: VEH 2


title: USP10 KO rep2

source_name: USP10 KO replicate 2


title: PANC-1 cell line shControl #2


title: ST-W-S3

value: water


title: Vehicle treated 1

description: VEH 1


title: Mix_culture

city: Bethesda

first: Ryo

last: Sato

address: 10 Center Dr

department: NHLBI

institute: National Institutes of Health

data_processing:
The mRNA libraries were  sequenced with a HiSeq2500 instrument (Illumina).
The reads were mapped to the hg19 reference human genome with the use of TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 1.0.
Gene expression was quantified with Cuffdiff version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: A549 3D culture

extract_protocol:
Solid- and Acinar-types of tumor cells were extracted from A549 xenograft mouse tumors by the laser microdissection technique. For the 3D coculture samples, GFP-labeled A549 cells were sorted from the 3D tumor colonies formed in the presence or absence of CAFs.
The mRNA libraries were prepared according to the TruSeq RNA Sample Prep Kit protocol

tag: protocol

value: 3D culture


title: H3K27me3 control (biological replicate 2)

city: Boston

first: Gracia

last: Bonilla

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
ChIP-seq reads were aligned to the hg19 genome using BWA version 0.7.15, technical replicates were pooled together.
bigWig files were generated using the deepTools bamCoverage command, normalized using CPM, and with bin size of 50, and smooth length of 100.
Normalized bigWig files were used to calculate intensities at promoters from the Ensembl gene annotation (GRCh37 release 75) using the deepTools multiBigwigSummary command, with a BED file obtained by extending the TSS by +/- 3000 bp.
Genome_build: hg19
Supplementary_files_format_and_content: Table with normalized ChIP-seq intensities for every promoter and every sample

source_name: Peripheral Blood-derived Macrophages

growth_protocol: Peripheral blood mononuclear cells were isolated from  buffy coats of healthy donors and differentiated into macrophages with 100ng/mL M-CSF for 7 days

extract_protocol:
100,000 cells were used for each MintChIP v3
Library was constructed as part of MINTChIP v3 protocol. Sequencing was done on a HiSeq2500 flow cell.

treatment_protocol: On Day 7, Cells were treated with siControl and siSP140 for 48 hours in the presence of IFN-g (100ng/mL)

tag: strain

value: Healthy donor

value: Blood

value: Human Macrophages

value: Unstimulated


title: Single_culture


title: Bursa RCT-016 Degenerative

value: Female

value: Bursa

tag: age

tag: bmi

tag: condition

value: Degenerative


title: Bursa RCT-018 Degenerative

value: Male


title: ST-W-S2

value: ST

tag: treatment


title: Bursa RCT-019 Degenerative

tag: tissue


title: ST-W-S1


title: PANC-1 cell line shControl #1

value: shControl


title: ST-S-R2

source_name: Root

value: salinity

value: Root


title: Bursa RCT-015 Degenerative


title: Bursa RCT-020 Traumatic

value: Traumatic


title: ST-S-R3

value: three-leaf stage


title: Acinar

source_name: A549 tumor

tag: tumor type

value: cinar-type


title: Bursa RCT-014 Traumatic


title: Bursa RCT-013 Degenerative


title: USP10 KO rep1

source_name: USP10 KO replicate 1

value: Kidney

tag: gender

value: male

tag: genotype

value: USP10 KO


title: Solid

value: solid-type

tag: cell line


title: Bursa RCT-009 Traumatic


title: T3

city: Springfield

first: Laszlo

middle: G

last: Kovacs

state: Missouri

address: 901 S  National Avenue

department: Biology

institute: Missouri State University

data_processing:
Raw corresponding datasets from lanes 1 and 2 of the sequencer were concatenated tail-to-head (cat) using Galaxy v0.1.0 (https://usegalaxy.org/)
Concatenated sequences were imported as paired reads and filtered by length (between 15 and 1,000 nt) and quality (limit 0.05) using default settings implemented by CLC Genomics Workbench 20.0.4 (Qiagen).
Filtered sequences were mapped to Arabidopsis TAIR10 reference genome sequence (downloaded from ENSEMBL) using gene and mRNA annotations on the default settings in the forward direction (CLC Genomics Workbench 20.0.4).
Mapped reads were normalized as RPKMs, and differential transcript abundance analysis was performed between treatment and control with replicates using the "EDGE" test on default settings (CLC Genomics Workbench 20.0.4).
The resulting EDGE test results were subjected to both FDR and Bonferroni corrections (CLC Genomics Workbench 20.0.4).
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: Format: CSV; Content: AgNO3 vs Control fold-change values, p-value, tagwise dispersions fold-change, weighted difference, Bonferroni-corrected p-value, FDR-corrected p-value, Read counts, RPKM, exon-exon reads, intron reads, and chromosomal coordinates of genes.

organism: Arabidopsis thaliana

source_name: whole plant

growth_protocol: Plants were seeded and grown in 1/2 MS, 2.5% MOPS and 0.8% agar media. After 3 days of stratification at 4°C , plants were transferred to a Conviron Adaptis A1000-AR Growth Chamber for 14 days at 21°C and a 10h light/14h dark cycle.

extract_protocol:
Thirty seedlings (entire organisms) from each replicate were harvested and flash frozen using liquid nitrogen, then pulvarized using a mortar and a pestle. RNA extraction was performed using the standard Trizol method. RNA was purified using RNeasy RNA-Extraction Kit (Qiagen) following the manufacturer's protocols. 1 µg of RNA was used to construct libraries using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina).
RNA libraries were constructed with TruSeq Stranded mRNA Sample Preparation Kit (Illumina) following the protocol provided by Illumina.
RNA-seq libraries were purified, amplified and paired-end sequenced (100-nt length) on two flow cells of Illumina NovaSeq-6000 Sequencer using  S1 100PE v1.5 chemistry at the Genome Sequencing Facility of the University of Kansas Medical Center.

treatment_protocol: Treated seedlings were grown for 14 days on 1/2 MS agar-solidified medium containing silver nitrate at concentration of 4 µg/mL.  Control seedlings were grown for 14 days on 1/2 MS agar-solidified medium in the absence of silver nitrate. Plants were seeded directly on the treatment or control media.

tag: ecotype

value: Columbia

value: whole plant

value: silver nitrate at 4 ug/mL

value: 14 days


title: T5


title: Bursa RCT-008 Degenerative

value: Female

value: Bursa

value: Degenerative


title: T4


title: C5

value: water (control)


title: H3K27me3 control (biological replicate 1)

value: Healthy donor

value: Blood

value: Human Macrophages

value: Unstimulated


title: ST-W-R3

value: ST

value: water

value: Root

value: three-leaf stage


title: Bursa RCT-006 Traumatic

value: Traumatic


title: C4

value: Columbia


title: ST-W-R2


title: SS-S-S3

value: SS

value: salinity

value: Young shoot


title: ST-S-R1


title: C3

value: whole plant

value: 14 days


title: Bursa RCT-004 Traumatic

value: Male

value: Bursa


title: SS-S-S1


title: Bursa RCT-001 Degenerative

value: Degenerative


title: Bursa RCT-002 Degenerative

value: Female


title: 3P: Adjacent tissue circRNAs

city: Guangzhou

first: Yongxin

address: 58 Zhongshan  9 2nd Road

institute: the First Affiliated Hospital, Sun Yat-sen University

data_processing:
Quality control  Raw data(raw reads) of fastq format were firstly processed through in-house perl   scripts. In this step, clean data(clean reads) were obtained by removing reads   containing adapter, reads on containing ploy-N and low quality reads from raw data.   At the same time, Q20, Q30 and GC content of the clean data were calculated. All the   down stream analyses were based on the clean data with high quality.
Mapping to the reference genome  Reference genome and gene model annotation files were downloaded from genome   website directly. Index of the reference genome was built using bowtie2 v2.2.8 and   paired-end clean reads were aligned to the reference genome using HISAT2(Langmead,   B.et al) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set   as default.
Transcriptome assembly  The mapped reads of each sample were assembled by StringTie (v1.3.1) (Mihaela   Pertea.et al. 2016) in a reference-based approach. StringTie uses a novel network flow   algorithm as well as an optional de novo assembly step to assemble and quantitate full_x0002_length transcripts representing multiple splice variants for each gene locus.
Quantification of gene expression level  Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in   each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the   FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of   exon per million fragments mapped, calculated based on the length of the fragments   and reads count mapped to this fragment.
circRNA identification  The circRNA were detected and identified using find_circ (Sebastian Memczak   et al., 2013) and CIRI2 (Gao et al., 2017). Circos software was used to construct   the circos figure.
Genome_build: human NCBI genome
Supplementary_files_format_and_content: tab-delimited xls. files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Gastric adjacent tissue

extract_protocol:
RNA-seq of ribosomal RNA-depleted total RNA were performed to screen differential expressed mRNAs, long chain non-coding RNAs  between paired gastric cancer tissues and adjacent normal tissues.For the linear RNA was digested with 3 U of RNase R per µg of RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Gastric adjacent tissue

tag: tumor stage


title: 3C: Gastric cancer circRNAs

source_name: Gastric cancer

value: Gastric cancer


title: Bursa RCT-011 Traumatic

tag: Sex


title: 2C: Gastric cancer circRNAs


title: 1P: Adjacent tissue circRNAs


title: SS-S-S2


title: SS-W-S1


title: 1C: Gastric cancer circRNAs


title: SS-S-R2


title: 3P: Adjacent tissue mRNAs and long chain noncoding RNAs


title: Tendon RCT-035 Degenerative

source_name: Tendon

extract_protocol: Qiagen FastSelect

value: Tendon


title: Tendon RCT-033 Degenerative


title: Tendon RCT-032 Traumatic


title: SS-S-R3


title: 3C: Gastric cancer mRNAs and long chain noncoding RNAs


title: Tendon RCT-031 Traumatic


title: Tendon RCT-034 Traumatic


title: 2P: Adjacent tissue circRNAs


title: SS-W-S2

value: water


title: SS-W-R3

value: Root


title: SS-S-R1

value: three-leaf stage


title: ST-W-R1

value: ST


title: SS-W-S3


title: Tendon RCT-036 Degenerative


title: SS-W-R2


title: Bursa RCT-003 Traumatic

source_name: Bursa

value: Traumatic


title: R2SKO_rep4 [5_F5_R2SKO]

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

data_processing:
Illumina basecalling.
Standard Illumina bioinformatics analysis were used to generate fastq files, followed by quality assessment [MultiQC v1.7 https://multiqc.info/], trimming and demultiplexing.
Rsubread v1.34.6 was used for mapping to the mm10 genome and creating a matrix of RNA-Seq counts.
Next, a DGElist object was created with the edgeR package v3.26.7.
After filtering (min.count = 10, min.total.count = 15) and normalization for composition bias, genewise exact tests were computed for differences in the means between groups.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file with raw count values for each sample

source_name: TGFb-RII/Smad4 KO CD8 T cells

extract_protocol:
CD8 T cells were extracted from lymph nodes and spleen of WT and KO mice
The different steps are the PolyA mRNA capture with oligo dT beads, cDNA double strand synthesis, adaptors ligation, library amplification and sequencing.
RNA sequencing was performed using the NextSeq500 Illumina sequencer in 75 bp paired-end.

treatment_protocol: WT, SKO and R2KO mice were used to obtain RNA-seq data

tag: strain/cell background

value: F5 transgenic CD8 T cells in a RAG2KO background

value: lymph nodes and spleen

tag: cell type

value: TGFb-RII/Smad4 KO CD8 T cells

tag: batch

value: Batch 2

tag: replicate

value: Replicate 4


title: Tendon RCT-030 Traumatic


title: 2C: Gastric cancer mRNAs and long chain noncoding RNAs


title: SS-W-R1

tag: cultivar

value: SS

tag: developmental stage


title: R2SKO_rep3 [4_F5_R2SKO]

value: Replicate 3


title: Tendon RCT-028 Traumatic

tag: age

tag: bmi


title: 1P: Adjacent tissue mRNAs and long chain noncoding RNAs


title: 2y_HiC_replicate_5

city: Chengdu

first: Jing

last: Li

address: No. 211 Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

data_processing:
Reads were mapped to the pig genome (Sscrofa 11.1) by BWA (v 0.7.15).
Juicer were used HiC data processing to filter duplication, low-quality alignment read pairs (MAPQ < 30) as well as intra-fragment read pairs.
High-quality reads  normalized with Knight-Ruiz [KR] algorithm and quantile  algorithm to structure contact matrixes at 20 or 100 kb resolution.
Compartments A/B were identified with A-B index as described by M Jordan Rowley. et al. Mol Cell. 2017 (PMID: 28826674).
Locations of topologically associated domains (TADs) were computed by combining  directionality index (Dixon et al. Nature. 2012 [PMID: 22495300]) and insulation index (Emily Crane et al. Nature. 2017)
Assembly: Sscrofa11.1
Supplementary files format and content: 20 and 100 kb matrixes, hic file
Supplementary files format and content: A-B index, txt file
Supplementary files format and content: locations of TAD for each sample, merged replicates, and consensus TAD,txt file
Supplementary files format and content: D-score, txt file

source_name: Liver

extract_protocol:
Livers tissue was homogenized with liquid nitrogen then fixed with 4% formaldehyde solution and incubated at room temperature for 30 min. Glycine were added to a final concentration of 0.2 M to quench the fixing reaction, and incubated at room temperature for 5 min then centrifuge for 10 min at 1,000 g and 4˚C. Discarded supernatants and cells were lysed with 1M Tris-HCl, 1M NaCl, 10% CA-630 and protease inhibitors on ice for 15 min. Cell nucleus were washed twice and were permeabilized at 65˚C for 10 min with 1% SDS to a final concentration of 0.1%. To quench the SDS, added 10% TritonX-100 (0.1% final concentration) and incubated at 37˚C for 15 min. Then 200 U DpnII (a 4-cutter restriction enzyme) was added and digested chromatin at 37˚C for 15 min, 65˚C for 20 min and 25˚C for 5 min. The restriction fragment overhangs were filled and labelled by biotinylated nucleotides, then ligated in a small volume.
After crosslink reversal, ligated DNA was purified and sheared to a length of 300–500 bp, at which point ligation junctions were pulled down with magnetic beads and prepared for BGISEQ-500 sequencing.

treatment_protocol: Six two-years-old female pigs were fed with a high fat diet (15.12 MJ·kg-1 metabolizable energy, 11.26% crude protein, 6.8% fat and 5% lysine) for 22 weeks, compared with the pigs of  two-years-old fed with well-characterized normal diet for 22 weeks.

tag: breed

value: Bama pig

tag: tissue type

value: Developmental stage

value: female

tag: restriction enzyme

value: DpnII


title: Tendon RCT-027 Degenerative

value: Female

tag: tissue

value: Tendon

tag: condition

value: Degenerative


title: 1C: Gastric cancer mRNAs and long chain noncoding RNAs

value: Gastric cancer

tag: genotype


title: 2y_HiC_replicate_6


title: Tendon RCT-026 Traumatic

value: Male


title: Tendon RCT-025 Degenerative


title: R2KO_rep3 [CD8_WT3_S9]

source_name: TGFb-RII KO CD8 T cells

value: TGFb-RII KO CD8 T cells

value: Batch 1


title: WT_rep4 [1_F5_WTSKO]

source_name: wild type CD8 T cells (pool of 3 WT mice)

value: F5 transgenic CD8 T cells in a RAG2KO background

value: lymph nodes and spleen


title: 2P: Adjacent tissue mRNAs and long chain noncoding RNAs

value: Gastric adjacent tissue


title: R2SKO_rep1 [2_F5_R2SKO]

value: TGFb-RII/Smad4 KO CD8 T cells

value: Batch 2

value: Replicate 1


title: 2y_HiC_replicate_4

value: Bama pig


title: 2y_HiC_replicate_3

value: Developmental stage


title: R2KO_rep2 [CD8_WT2_S8]

value: Replicate 2


title: Tendon RCT-023 Degenerative


title: R2KO_rep1 [CD8_WT1_S7]


title: 2y_HiC_replicate_2

value: female

value: DpnII


title: 2y_HiC_replicate_1


title: HT29 treated with linderapyrone derivative (5 mM)

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: human colorectal cancer (HT29)

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: HT29 was cultured in Dulbecco's modified Eagle's medium (DMEM) with low glucose supplemented with 5% fetal bovine serum, 1% penicillin/streptomycin to reach 70-80% confluence on 10cm dish

extract_protocol: Total RNA was isolated from the cells using miRNeasy mini kit (QIAGEN)

treatment_protocol: The culture medium was replaced with the medium containing various concentrations of the test sample, and the cells were further incubated for 24hr

tag: cell line

tag: treatment

value: linderapyrone derivative (5microM)


title: Tendon RCT-022 Degenerative

tag: Sex

value: Female

value: Tendon

value: Degenerative


title: HT29 treated with linderapyrone derivative (20 mM)

value: linderapyrone derivative (20microM)


title: R2SKO_rep2 [3_F5_R2SKO]

tag: strain/cell background


title: Tendon RCT-021 Degenerative

value: Male


title: SKO_rep3 [CD8_SKO_6_S12]

source_name: Smad4 KO CD8 T cells

value: F5 transgenic CD8 T cells in a RAG2KO background

tag: cell type

value: Smad4 KO CD8 T cells

value: Batch 1

value: Replicate 3


title: SKO_rep2 [CD8_SKO_5_S11]

value: lymph nodes and spleen

tag: batch


title: Tendon RCT-024 Degenerative


title: SKO_rep1 [CD8_SKO_4_S10]

tag: replicate

value: Replicate 1


title: sg4841 3'-seq

first: wei

middle: zi

last: guo

state: Beijing

address: ZhongGuanCun

institute: tsinghua university

data_processing:
The adapters of reads were trimmed and quality control check were carried out using trim-galore (version 0.6.4)
Reads were aligned to mouse genome mm10 and Drosophila genome dm6 from GENCODE using STAR (version 2.7.1a).
Only reads that were properly paired and uniquely mapped were used for next analyses.
BPM normalized bigwig files were created with deepTools (bamCoverage).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deeptools

source_name: pancreatic ductal adenocarcinoma

growth_protocol: Pancreatic cancer cells were cultured at 37℃ in DMEM medium, supplemented with 10% (v/v) fetal bovine serum and 1% (v/v) penicillin-streptomycin.

extract_protocol:
RNA was extracted with TRIzol (Invitrogen, 15596018) according to the manual
500ng RNA of each sample was used to prepare libraries. Total 3’ end-seq libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit REV for Illumina (Lexogen, 016.24). Deep sequencing (HiSeq Xten, Illumina) was conducted by Novogene.
3'-seq

treatment_protocol: 1μg/mL doxycycline was added into medium for 72hr before harvesting cells to induced dCas9-KRAB expression and nascent RNA labeled with biotin-NTPs was carried out as previously described (Mahat et al., 2016)

value: pancreatic ductal adenocarcinoma cells

value: untreated


title: WT_rep3 [CD8_R2KO_9_S15]

source_name: wild type CD8 T cells

value: wild type CD8 T cells


title: WT_rep2 [CD8_R2KO_8_S14]

value: Replicate 2


title: sg9270 3'-seq


title: Tendon RCT-019 Degenerative


title: sgPaf1-1 Paf1KD Ints11 ChIP-seq

data_processing:
The adapters of paired-end reads were trimmed and quality control check were carried out using trim-galore (version 0.6.4)
Trimmed reads were aligned to mouse genome mm10 from GENCODE using bowtie2 (version 2.3.4.3) of which the parameter is “–very-sensitive –X 2000”.
Aligned reads stored in SAM format were manipulated to generate bam files using samtools (version 1.9) with parameter is “samtools view –b –h –F 1028 –f 3”.
BPM normalized bigwig files were created with deepTools (bamCoverage).
Peak detection was done using MACS2. BPM normalized bigwig files were created with deepTools (bamCoverage).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deeptools

source_name: pancreatic ductal adenocarcinoma cells

extract_protocol:
Briefly, cells were crosslinked at room temperature for 10 min with 1% formaldehyde,  washed twice with PBS and sonicated in lysis buffer (50 mM HEPES/KOH pH 7.5, 140  mM NaCl, 0.1% Na-Deoxycholate, 1% Triton X-100, 1 mM EDTA, complete protease  inhibitor cocktail). Samples were immunoprecipitated at 4 ºC overnight and washed six  times with ChIP wash buffer (20 mM Tris, pH 7.9, 500 mM NaCl, 2 mM EDTA, 1% Triton  X-100, 0.1% SDS) and once with TE buffer. Bound DNA was eluted in 1% SDS buffer  and reverse-crosslinked for 6 h at 65 ºC
DNA samples were treated sequentially with   RNase A and Protease K and then purified with ChIP DNA Clean & Concentrator-5  (Zymo Research, D4014).The End-It DNA End-Repair Kit (Lucigen, ER81050) was used to convert purified DNA to 5′-phosphorylated, blunt-end DNA. After treated with Klenow Fragment (3'→5' exo-), barcodes (BIOO Scientific, 514120) were ligated with Quick Ligation kit (NEB, M2200). After size selection, 15 cycles of PCR were used to amplify the library.

treatment_protocol: For PAF1 KD H3K27ac ChIP-seq, 1μg/mL doxycycline was added into medium for 72hr before harvesting cells to induced dCas9-KRAB expression. For HQ461 treatment PAF1 ChIP-seq, 10μM HQ461 was added into medium for 8h before harvesting cells

tag: strain

tag: chip antibody

value: treated with Paf1KD

tag: genotypes

value: Paf1 knockdown


title: sgPaf1-1 3'-seq


title: Tendon RCT-016 Degenerative

value: Female

tag: age

tag: bmi


title: HT29 treated with DMSO

description: Control

value: DMSO


title: sg9270 Paf1KD Ints11 ChIP-seq

value: WT


title: sgPaf1-2 3'-seq


title: Tendon RCT-020 Traumatic

value: Tendon

value: Traumatic


title: Tendon RCT-015 Degenerative

value: Degenerative


title: Input

data_processing:
The 75-nt single-end (SE75) sequence reads generated by Illumina sequencing (using NextSeq 500) were mapped to the mm10 genome using the BWA algorithm with default settings.
Only reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches, and mapped uniquely to the genome were used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) were removed.
To identify the density of fragments (extended tags) along the genome, the genome was divided into 32-nt bins and the number of fragments in each bin was determined. This information (“signal map”; histogram of fragment densities) was stored in bigWig file.
Peak calling algorithm: MACS 2.1.0 Normalization method: Standard
Genome_build: mm10
Supplementary_files_format_and_content: signal bigWIG files

source_name: pooled input

extract_protocol:
CD8 T cells were extracted from lymph nodes and spleen of WT and KO mice
ChIP libraries were prepared (Active Motif) and sequenced (Illumina NextSeq500) using a standard workflow.

treatment_protocol: WT, SKO and R2KO mice were used to obtain ChIPseq data

value: F5 transgenic CD8 T cells in a RAG2KO background

value: pooled input CD8 T cells


title: Tendon RCT-014 Traumatic

value: Male


title: R2KO

value: lymph nodes and spleen

value: TGFb-RII KO CD8 T cells

tag: chip anitbody

value: anti-SMAD4 (EP618Y), Abcam (ab40759)


title: sg4841 Paf1KD Ints11 ChIP-seq

value: pancreatic ductal adenocarcinoma cells

value: untreated


title: Tendon RCT-012 Traumatic


title: Tendon RCT-009 Traumatic


title: SKO

value: Smad4 KO CD8 T cells


title: Tyr-H B16 cells 3

city: Shanghai

first: Xuefeng

address: 320 Yueyang Road

institute: Chinese Academy of Sciences

data_processing:
Clean reads were accuired by the Trimmomatic software using a protocol from Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014 Aug 1;30(15):2114-20. doi: 10.1093/bioinformatics/btu170.
Gene information were accuired by comparing CleanReads with Reference genome (Mus musculus reference, GRCm38.p6) through the hisat2 software using a protocol from Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015 Apr;12(4):357-60. doi: 10.1038/nmeth.3317.
Fragments Per kb Per Million Reads (FPKM) were calculated using a protocol from Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol. 2011;12(3):R22. doi: 10.1186/gb-2011-12-3-r22.
Genome_build: Mus musculus reference (GRCm38.p6)
Supplementary_files_format_and_content: Excel files include FPKM values for Sample 1, Sample 2, Sample 3, Sample 4, Sample 5, Sample 6 (Tyr-H1.FPKM, Tyr-H2.FPKM, Tyr-H3.FPKM, Tyr-L1.FPKM, Tyr-L2.FPKM, Tyr-L3.FPKM).

source_name: skin melanocytes derived tumor

growth_protocol: Tyr-L B16 cells and Tyr-H B16 cells were cultured in DMEM (low glucose) medium with 10 % fatal bovine serum and 1% penicillin & streptomycin in a 5% CO2 humidified atmosphere at 37 °C.

extract_protocol:
Total RNA of Tyr-L cells and Tyr-H cells were extracted with TRIzol reagent (Invitrogen).
The transcriptome library was generated utilizing VAHTS mRNA-seq v2 Li-brary Prep Kit for Illumina (Vazyme Biotech, Nanjing, China) following the manufacturer’s recommendations.

tag: sample type

value: subtype from melanoma cell line

tag: tyr activity

value: High tyrosinase activity


title: Tendon RCT-017 Traumatic

value: Female

tag: tissue

tag: condition


title: Tendon RCT-011 Traumatic


title: Tyr-H B16 cells 1


title: WT_rep1 [CD8_R2KO_7_S13]

value: wild type CD8 T cells

value: Batch 1

value: Replicate 1


title: Tyr-H B16 cells 2


title: Tyr-L B16 cells 1

value: Low tyrosinase activity


title: WT

source_name: wild type


title: Tyr-L B16 cells 2


title: Tendon RCT-003 Traumatic

value: Tendon

value: Traumatic


title: Tendon RCT-008 Degenerative

value: Degenerative


title: Tyr-L B16 cells 3


title: Tendon RCT-004 Traumatic

value: Male


title: CC_11

city: Munich

first: Maria

middle: Elena

last: Torres-Padilla

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

data_processing:
Quality control of the sequencing was analyzed with FastQC
Demultiplexed reads were aligned using STAR (version 2.7.3a) with the default parameters, the gene counts were produced with the same command using the option “--quantMode GeneCounts”. The annotation used was downloaded from iGenomes (UCSC as the source), the ERCC genes and mitochondrial genes (from ENSEMBL) were added to the annotation for quality control metrics.
Using unix commands, a count matrix was created by joining the individual count files produced by STAR
The count matrix was processed with custom R (version 4.0.2) scripts. The scripts were used for the quality control, cleaning of the matrix, and principal component analyses
Genome_build: mm10
Supplementary_files_format_and_content: Txt, named counts and FPKM table ready to load in R with rows as genes, and columns as samples

source_name: Cumulus cell

growth_protocol: MII oocytes were collected and enucleated in CZB medium and were then let to recover in KSOM until they were used for nuclear transfer. The nuclei of donor cumulus cells were injected into the enucleated oocytes using a Piezo-driven micromanipulator. After reconstruction, oocytes were cultured for 1 h in KSOM and activated for 6 h in KSOM containing 10 mM Sr2+ and 5 ug/ml CB supplemented with 2 mM EGTA.

extract_protocol:
Individual cells were manually picked into the lysis solution with macrocapilary pipettes and cDNA was synthesized acording to the Smart-seq2 protocol. Quality of cDNA was checked by the bioanalyzer both after and before the tagmentation.
Libraries were prepared with Smart-seq2 protocol.

treatment_protocol: Embryos were then randomly distributed in medium with or without HU (10uM), which was replaced by fresh medium without HU after 24 h.

value: cumulus cell


title: Tendon RCT-005 Traumatic

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Genome_build: Ensembl GRCh38.101
Supplementary_files_format_and_content: Gene counts with CPM and RPKM in tab-delimitted text format


title: sgPaf1-2 Paf1KD Ints11 ChIP-seq

city: Beijing

value: treated with Paf1KD

value: Paf1 knockdown


title: CC_12


title: LDC000067-CDK9 inhibition Paf1 ChIP

value: pancreatic ductal adenocarcinoma cells

value: WT


title: Tendon RCT-006 Traumatic


title: DMSO-CDK9 inhibition Paf1 ChIP

value: DMSO


title: CC_9


title: sgInts11-3 Ints11 PRO-seq

description: nascent RNA

data_processing:
The adapters of reads were trimmed and quality control check were carried out using trim-galore (version 0.6.4)
Reads were aligned to mouse genome mm10 from GENCODE using Bowtie2.
Only reads that were properly paired and uniquely mapped were used for next analyses.
BPM normalized bigwig files were created with deepTools (bamCoverage).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deeptools

extract_protocol:
Nascent RNA was extracted as previously described (Mahat et al., 2016)
The libraries were prepared using the Multiplex Small RNA Library Prep Set for Illumina (NEB, E7300) according to the manual
PRO-Seq

value: treated with Ints11KD


title: Tendon RCT-002 Degenerative


title: CC_10


title: CC_8


title: Tendon RCT-001 Degenerative


title: sgInts11-1 Ints11 PRO-seq

description: nascent RNA


title: sg4841 Ints11 PRO-seq

description: nascent RNA

value: untreated


title: CC_5


title: CC_7


title: Nuclear HK2 knockdown 2 (RNA-seq)

city: Toronto

first: Aaron

middle: D

last: Schimmer

state: CA-ON

address: 101 College St

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
Reads adapters were removed using Trim Galore v. 0.4.0 and reads were aligned against hg19 using Tophat v. 2.0.11. Read counts per gene were obtained through htseq-count v.0.6.1p2 in the mode “intersection_nonempty”.
After removing genes whose cpm (counts per million reads) were less than 0.5, edgeR R package v.3.8.6 was used to normalize the data using the TMM (trimmed mean of M values) method and to estimate differential expression by applying a generalized linear model between the control vs knockdown cells.A score that ranks genes in nuclear HK2 knockdown samples from the most upregulated to the most downregulated compared to control shRNA samples was calculated using the formula ‘-log10(pvalue) * sign(logFC)‘.
Genome_build: hg38 (RefSeq gene models)
Supplementary_files_format_and_content: Htseq read counts

source_name: OCI AML 8227 Cells

growth_protocol: 8227 cells were cultured in X-VIVO 10 (Lonza 04-380Q) with 20% bovine serum albumin (BSA)–insulin-transferrin (STEMCELL Technologies 09500), human Fms-related tyrosine kinase 3 ligand (Flt3-L; 50 ng/ml) (PeproTech 300-19), IL-6 (10 ng/ml) (PeproTech 200-06), SCF (50 ng/ml) (PeproTech 300-07), thrombopoietin (25 ng/ml) (PeproTech 300-18), IL-3 (10 ng/ml) (PeproTech 200-03), and granulocyte colony-stimulating factor (G-CSF; 10 ng/ml) (Amgen 121181-53-1).

extract_protocol:
RNeasy Plus Mini Kit. Quality of total RNA samples were checked on an Agilent Bioanalyzer 2100 RNA Nano chip following Agilent Technologies’ recommendation. Concentration was measured by Qubit RNA HS Assay ona Qubit fluorometer (ThermoFisher)
RNA library preparation was performed following the NEB NEBNext Ultra Directional Library Preparation protocol

treatment_protocol: Nuclear HK2 knockdown was performed by expressing mitochondrial tethered HK2 (OMMLS-HK2) and knocking down native HK2 using UTR shRNA performed with lentiviral infections.

tag: cell line

value: Engineered leukemic stem cell line OCI AML 8227

value: Blood

tag: genotype

value: Nuclear HK2 knockdown


title: CC_6


title: sg9270 Ints11 PRO-seq

description: nascent RNA

tag: treatment


title: Nuclear HK2 knockdown 1 (RNA-seq)


title: sgPaf1-1 Paf1 PRO-seq

description: nascent RNA

value: treated with Paf1KO


title: sg9270 Paf1 PRO-seq

description: nascent RNA