title: Astrocyte_SCI1M_rep3

source_name: Astrocyte

growth_protocol: Epicenter spinal cord tissue was harvested at respective time points and dissociated using a mixed digestion solution of 0.01% papain (LS003126, Worthington Biochemical,), 0.025% trypsin-EDTA (25200056, Gibco), 0.01% DNase I (LS002138, Worthington Biochemical) and 0.01% L-Cysteine (2430-100GM, Calbiochem) for 15 min at 37 ℃ with gentle shaking (70 rpm). The cells were separated from undigested pellet by triturating with wide-tipped, fire-polished glass Pasteur pipette for 8 times. After repeating 2 times of digestion and separation, cell suspension was filtered by 40 μm cell strainer and DMEM with 4% high BSA by centrifugation. The single-cell suspension was resuspended in the buffer containing Myelin Removal Beads II (130-096-733, Miltenyi Biotec) followed the manufacturer’s protocol to remove the myelin. TdTomato postive cells were collected for RNA library construction using fluorescence-activated cell sorting (FACS) with BD FACS Aria II flow cytometer (BD Biosciences).

treatment_protocol: The mice were conducted with moderate contusive injury with Infinite Horizons impactor (Precision Systems and Instrumentation) at T9 level of the exposed spinal cord (60 kdyn) and mentained for 7 days, 1 month or 3 months

tag: age

value: 1 mpi (month post-injury)

value: Astrocyte

value: Thoracic (T9) moderate contusion injury for 1 month


title: Astrocyte_SCI1M_rep2

status: Public on Feb 08 2021

type: SRA

city: Houston

first: Haichao

last: Wei

state: TX

address: 1825 Pressler St., SRB 637.C

country: USA

institute: UTHealth

library_source: transcriptomic

data_processing:
The quality of all sequenced samples was analyzed using FastQC.
Reads were mapped to the Mm10. Mapping and transcript assembly were performed with TopHat v2.1.0 and Cufflinks v2.2.1 respectively using default parameters.
The gene read counts of samples were normalized and compared to control samples using DESeq2
Genome_build: Mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample

molecule: total RNA

organism: Mus musculus

extract_protocol:
Total RNA isolation using TRIzol according to detailed manufacturer’s instructions.
Libraries were constructed with the NEBNext Ultra Directional RNA library Prep Kit for Illumina (E7420, New England Biolabs) by following the manufacturer’s instructions.

tag: genotype

tag: cell type

tag: treatment


title: US-1630692

city: London

first: Christopher

last: Chiu

address: Hammersmith Campus, Du Cane Road

department: Infectious Disease

country: United Kingdom

institute: Imperial College London

data_processing:
Adaptors were removal by SeqPrep.
RNAseq reads were mapped to human B38 genome with Omicsoft OSA aligner.
Read counts mapped to the human ensemble genes (Release 75) were calculated with RSEM.
RNAseq that did not pass QC were exclude from downstream analysis. The gene count data were normalized and differential gene expression was calculated by DESeq2 (R package, version 1.18.1)
Genome_build: human B38
Supplementary_files_format_and_content: file contains gene counts for all genes in the samples submitted

organism: Homo sapiens

source_name: Nasal Scrape

extract_protocol:
RNAseq cDNA library was prepared with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat Sample Prep Kit (Illumina, #RS-122-2203). Starting with 100 ng of total RNA, cytoplasmic ribosomal RNA was removed by hybridization to a biotinylated probe selective for ribosomal RNA species, followed by streptavidin bead binding and sample purification.  The resulting cytoplasmic rRNA-depleted sample was chemically fragmented and converted into single-stranded cDNA using reverse transcriptase and random hexamer primers, with the addition of Actinomycin D to suppress DNA-dependent synthesis of the second strand.  Double-stranded cDNA was created by removing the RNA template and synthesizing the second strand in the presence of dUTP in place of dTTP.  A single A base was added to the 3’ end to facilitate ligation of sequencing adapters, which contain a single T base overhang.  Adapter-ligated cDNA was amplified by polymerase chain reaction to increase the amount of sequence-ready library.  During this amplification the polymerase stalls when it encounters a U base, rendering the second strand a poor template.  Accordingly, amplified material used the first strand as a template, thereby preserving the strand information.  Final cDNA libraries were analyzed for size distribution using the Agilent Tapestation 2200 (D1000 kit, Agilent # 5067-5582 and 5067-5583), quantitated by qPCR (KAPA Library Quant Kit, KAPA Biosystems # KK4824), then normalized to 2 nM in preparation for sequencing. Prepared libraries were sequenced with 2 × 50 bp paired-end reads on the Illumina HiSeq 2500 sequencer with a minimum of 3 GB of raw RNA sequencing data (Illumina, San Diego, USA).
TruSeq Stranded Total RNA Ribo-Zero library preparation

tag: donor id

tag: batch

value: new

tag: timepoint

tag: outcome

value: Uninfected

tag: symptom

tag: tissue

value: Nasal Scrape


title: smallRNAseq_KO rep3

city: Barcelona

first: Eva Maria

last: Novoa

address: Dr. Aiguader 88

country: Spain

institute: Center for Genomic Regulation

data_processing:
trimming: bbduk (BBMap version 36.14)
mapping: segemehl 0.2.0
tRNA re-mapping: GATK 3.5
mismatch analysis: mpileup2stats
Genome_build: m38 genome. Mature tRNA reference from gtRNAdb
Supplementary_files_format_and_content: tab delimited file with frequency of mismatches, insertions and deletions obtained with mpileup2stats

growth_protocol: Total RNA was extracted from total mouse brain

extract_protocol:
total RNA was extracted, ribo-depleted and size-selected (30-150bp), and this material was used as starting point for the libraries.
Illumina Total RNASeq

treatment_protocol: TRMT1L KO was compared to WT

value: brain

value: TRMT1L KO


title: US-1635431


title: Astrocyte_SCI3M_rep1

value: 3 mpi (month post-injury)

value: Thoracic (T9) moderate contusion injury for 3 months


title: Astrocyte_SCI1M_rep1


title: US-1630644

value: Infected

value: cold


title: TAT-E2_RNA-seq

city: shanghai

first: qiongqiong

last: hou

address: huanke road 199

country: China

institute: shanghaitech university

data_processing:
based on HiSeq Xten (illunima) sequencing platform and Paired-End was used
Raw data were filtered by FASTX-Toolkit to generate clean reads and were mapped to human GRCh38 using Hisat
Stringtie software was used to count Fragments PerKilobase Million (FPKM)
edgeR software was used to statistical quantification
Gene expression was presented with GO&KEGG annotation
Genome_build: human GRCh38

source_name: cerebral organoid

extract_protocol:
Samples were washed in 1×Hank’s balanced salt solution (HBSS) and Total RNA samples were extracted with Trizol
Basaed on HiSeq Xten (illunima) platform and Base Calling was transformed to Sequenced Reads. Paired-end (PE150) was used.

tag: developmental stage

value: neuroepithellum

tag: brain region

value: derived from cortex

value: cerebral organoid


title: US-1596636

value: pilot


title: longRNAseq_KO rep1

data_processing:
trimming: cutadapt v.1.9.1
mapping: STAR v2.7.0f
mismatch analysis: mpileup2stats
Genome_build: vM21 annotation
Supplementary_files_format_and_content: tab delimited file with frequency of mismatches, insertions and deletions obtained with mpileup2stats

source_name: brain

extract_protocol:
total RNA was extracted and size-selected (>200 bp), and this material was used as starting point for the libraries.
TruSeq Total RNA Illumina sequencing

tag: genotype/variation


title: smallRNAseq_KO rep2


title: US-1635398


title: US-1596618


title: US-1596606


title: smallRNAseq_WT rep3

value: WT


title: US-1596576


title: smallRNAseq_WT rep1


title: 24 somite

city: Bunkyo

first: Ryuichi

last: Yamada

state: Tokyo

address: Yayoi 1-1-1

department: Veterinary Anatomy

country: Japan

institute: The Univerisity of Tokyo

description:
scRNA-seq
processed data file: barcodes.tsv
processed data file: genes.tsv
processed data file: matrix.mtx

data_processing:
The Cell Ranger Single-Cell Software Suite (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) was used to perform sample demultiplexing, barcode processing, and single-cell 3' gene counting. The cDNA insert was aligned to the mm10/GRCm38 reference genome.
BAM files produced by the 10x Genomics/Cell Ranger pipeline.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: There are three files generated using the Cell Ranger Single-Cell Software. matrix.mtx: This file contains the gene-barcode matrix. barcodes.tsv: This file contains the barcodes represented in the mtx file. genes.tsv: This file contains all annotated genes.

source_name: 24 somite stage ocular area

extract_protocol:
A single embryo was dissected under a stereomicroscope, and a pair of optic areas was dissected manually using a fine needle (Austerlitz Insect Pins with a diameter of 0.1 mm). The dissected tissues were incubated with 0.05% Trypsin-EDTA for 3 min at 37°C. Then, 10% fetal calf serum/minimal essential medium was added to stop the proteinase reaction. The cells were dissociated by gentle pipetting and suspended in 0.04% bovine serum albumin/phosphate-buffered saline (PBS). The number of cells was counted using the Countess II FL automated cell counter (Invitrogen, Carlsbad, CA, USA).
2,000 cells/sample were then prepared as scRNA-seq library using Chromium Single Cell 3’ Reagent Kits v3 (10x Genomics, Pleasanton, CA, USA).

tag: strain

value: Wild type

value: Ocular area

value: 24 somite


title: US-1635405

value: new


title: US-1635462


title: 20 somite

source_name: 20 somite stage ocular area

value: 20 somite


title: smallRNAseq_WT rep2


title: 16 somite

source_name: 16 somite stage ocular area

value: 16 somite


title: 26 somite

source_name: 26 somite stage ocular area

value: 26 somite


title: US-1630680

value: Uninfected

value: Nasal Scrape


title: US-1630610


title: US-1630673


title: US-1630652


title: Con_264

city: Shanghai

first: haohao

last: zhang

state: Shanghai

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

data_processing:
Illumina HiSeq™2500 platform was used for basecalling
Sequenced reads were trimmed for adaptor sequence, and filtered low-complexity or low-quality sequences out. Clean data were mapped to mm10 whole genome using bowtie2 (v 2.2.5) with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks software. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: A tab-delimited text file including RPKM values was generated for each sample

source_name: medullary thymic epithelial cells

extract_protocol:
mTECs of Jmjd3fl/fl and Jmjd3fl/fl-Foxn1-cre mice were sorted by flow cytometry. Total RNA was isolated with a RNeasy Mini Kit (QIAGEN, 74104). cDNA was reverse transcribed and amplified using REPLI-g WTA Single Cell Kit (QIAGEN, 150063) following the manufacturer’s instructions.
Transcriptome libraries were prepared for sequencing using standard Illumina protocols

value: primary medullary thymic epithelial cells

value: 4 weeks

value: control


title: cKO_265


title: cKO_263


title: US-1635435


title: Con_253


title: Treat2

city: Camperdown

first: Michael

middle: Khalilur

last: Murray

state: NSW

address: 92 Parramatta Road

department: Pharmacology

country: Australia

institute: The University of Sydney

data_processing:
Illumina’s TruSeq stranded Total RNA sample preparation protocol for processing samples
The primary bioinformatics analysis involved demultiplexing and quality control.
Image analysis was performed in real time by the HiSeq Control Software v2.2.68 and Real Time Analysis v1.18.66.3.
The Illumina bcl2fastq 2.17.1.14 pipeline was used to generate the sequence data.
The data were processed through RNA-Seq expression analysis workflow, which included alignment against the Homo sapiens genome (Build version HG19) and the Tophat aligner v2.0.14 to map these reads, transcriptome assembly with the Stringtie tool v1.0.4, quantification and normalisation.
Genome_build: Differential expression analysis was performed by edgeR and pathway enrichment was performed using the Reactome database as a reference.

growth_protocol: Human MDA-MB-231 breast cancer cells were plated at a density of 1.5×105 cells/well in 6 well plates for 24 h.

extract_protocol:
CTU-treated cells were collected, and total RNA was extracted using Bioline Isolate II RNA Mini Kit (Alexandria, NSW, Australia) following the manufacturer’s instructions.
RNA libraries were prepared using Illumina Truseq Stranded Total RNA kit (San Diego, USA).

treatment_protocol: After 24 h of seeding cells were starved for another 24 h in serum-free medium.Cells were then treated with CTU 10 μM or DMSO (control) for 6 h.

tag: celll line

tag: tissue source

value: Breast Tumor

value: CTU 10 μM for 6 h


title: Treat1


title: smallRNAseq_KO rep1

value: brain

value: TRMT1L KO


title: cKO_262


title: Con_261


title: Cont3

value: DMSO (control) for 6 h


title: US-1635397

value: Infected

value: cold


title: 12 somite

source_name: 12 somite stage ocular area

value: Wild type

value: Ocular area

value: 12 somite


title: Cont2


title: US-1630631

value: new


title: Treat3


title: Cont1


title: longRNAseq_MUT_rep2

data_processing:
trimming: cutadapt
mapping: STAR
Genome_build: hg38 genome
Supplementary_files_format_and_content: tab delimited file, read counts per gene (STAR output)

source_name: Lymphoblastoid cell line

growth_protocol: Total RNA was extracted from patient-derived lymphoblastoid cell lines

extract_protocol:
total RNA was extracted, ribodepleted, and this material was used as starting point for the libraries.
Illumina Total RNASeq

treatment_protocol: TRMT1 frameshift deletion in heterozygosis vs TRMT1 frameshift in homozygosis

value: lymphoblastoid cell line

value: homozygous frame-shift mutation in TRMT1 gene


title: longRNAseq_WT rep2

value: heterozygous frame-shift mutation in TRMT1 gene


title: longRNAseq_MUT_rep1


title: Input

library_source: genomic

data_processing:
Basecalls were performed using  Illumina HiSeq™2500
ChIP-seq reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence and aligned to the mm10 genome assembly using Bowtie2 (v 2.2.5).
Peaks were called using MACS2 software.
Genome_build: mm10
Supplementary_files_format_and_content: tdf files were generated using Homer software. Scores represent the degree of enrichment.

molecule: genomic DNA

extract_protocol:
ChIP assays were performed with EZ-ChIP™ Chromatin Immunoprecipitation Kit (Millipore, #17-371). 5 × 105 sorted mTECs of wild-type mice and 2μg antibodies were used for each immunoprecipitation. ChIPed DNA was amplified by SeqPlexTM Enhanced DNA Amplification Kit (Sigma Aldrich, SEQXE) according to manufacturer’s protocol and sequenced
Libraries were prepared according to Illumina's instructions. 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 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, library fragments were band isolated from an agarose gel. Libraries were sequenced on the Illumina HiSeq™2500 following the manufacturer's protocols.

value: primary medullary thymic epithelial cells

tag: chip antibody


title: H3K27Me3

tag: age

value: 4 weeks

value: H3K27Me3 (Millipore, 07-449)


title: H3K4Me3

value: H3K4Me3 (Millipore, 17-614)


title: Donor71_unstim

city: Toronto

first: Daniel

last: De Carvalho

state: Ontario

address: 101 College St

department: Princess Margaret Cancer Centre

country: Canada

institute: UHN

data_processing:
Single end data were aligned to hg19 using Bowtie2 with default settings.
Duplicates were identified and removed with samtools.
MACS2 was then used to generate a catalogue of ATAC seq peaks, with no-model, shift of -100 and extend parameters of 200 to account for integration of the transposase into the middle of fragments.
Peaks were called at an FDR of 0.25, but only peaks with an FDR of 0.05 were incorporated into downstream analysis.
Common and unique nucleosome-free regions were identified using the GenomicRanges package in R.
Genome_build: hg19

source_name: Primary CD8+ T-cells

growth_protocol: Human CD8+ T-cells were isolated using a negative selection kit (Miltenyi Biotec USA, catalogue No. 130-096-495) from peripheral blood mononuclear cells (PMBC) collected from healthy blood donors. Blood from healthy donors was collected in the clinic after obtaining appropriate informed consent under an UHN-REB (No. 11-0343-CE) approved protocol.     Purified CD8+ T-cells were seeded in specialized non-adherent round-bottom 96-well plates at a concentration of 10,000 cells per well, in a final media volume of 200μL. The media used for CD8+ T-cells cultures was RPMI 1640 conditioned with 2mM HEPES, 0.1% Pen Strep, 0.1% L-glutamine, 10% Human Serum, and 10IU/mL human recombinant IL-2.    Treatments included: unstimulated (no beads added); stimulated; stimulated plus 300nM Decitabine, respectively. In order to stimulate CD8+ T-cells, α-CD3/CD28 beads (ThermoFisher Scientific, catalogue No. 11131D) were added to the wells at a 1 bead: 2 cells ratio and left in the wells until harvesting date. For the stimulation of CD8+ T cells with Decitabine (Sigma; catalogue No. A3656), fresh media with Decitabine was replaced every 48 hours (i.e. Day 0, day 2 and day 4) to maintain respective treatment concentrations.

extract_protocol: Genomic material for transposase-accessible chromatin sequencing (ATAC-seq) was extracted as processed as previously reported (Buenrostro et al., 2013).

treatment_protocol: Treatments included: unstimulated (no beads added); stimulated; stimulated plus 100nM or 300nM Decitabine, respectively. In order to stimulate CD8+ T-cells, α-CD3/CD28 beads (ThermoFisher Scientific, catalogue No. 11131D) were added to the wells at a 1 bead: 2 cells ratio and left in the wells until harvesting date. For the stimulation of CD8+ T cells with Decitabine (Sigma; catalogue No. A3656), fresh media with Decitabine was replaced every 48 hours (i.e. Day 0, day 2 and day 4) to maintain respective treatment concentrations.

value: PBMC-derived primary CD8+ T-cells

value: Untreated


title: Donor70_stim_DAC300

value: α-CD3/CD28, Decitabine (300 nm)


title: Donor71_stim


title: Donor70_stim


title: Donor70_unstim


title: Donor61_stim_DAC300


title: Donor61_stim


title: 1334_Tung.3

city: Philadelphia

first: Jeffrey

middle: R

last: Peterson

state: PA

address: 333 Cottman Avenue

department: Cancer Biology

institute: Fox Chase Cancer Center

description:
tung oil-treated tumor.3
Tung_3

data_processing:
Raw sequence reads were aligned to the mouse genome (mm10) using the Tophat algorithm
 Cufflinks  was implemneted to assemble transcripts and estimate their abundance.
Cuffdiff was used to statistically assess expression changes in quantified genes in different conditions
Genome_build: HG38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all Sample

source_name: orthotopic xenograft, mammary fat pad

growth_protocol: MDA-MB-231 cells were grown on 10 cm culture plates to approximately 40% confluence.Orthotopic xenografts were generated by implanting 2.5 million MDA-MB-231 cells in 100 µL phosphate-buffered saline (PBS) mixed with 100 µL growth factor-reduced Matrigel (Corning) bilaterally into the fourth inguinal fat pad of four- to six-week-old female NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice. After 14 days, when tumors were roughly 50-75 mm3, animals were randomized into treatment groups.

extract_protocol:
Three biological replicate tung-oil or control MDA-MB-231 xenograft tumor samples were homogenized in ice-cold PBS using a dounce homogenizer and total RNA was isolated using the RNeasy kit (Qiagen).
The stranded mRNA-seq library was generated from 1000 ng of total RNA from each sample using Truseq stranded mRNA library kit (Illumina) according to the product instructions. In short, mRNAs were enriched twice via poly-T-based RNA purification beads, and subjected to fragmentation at 94 C for 8 minutes via the divalent cation method. The first strand cDNA was synthesized by SuperscriptII (ThermoFisher Scientific) and random primers at 42 C for 15 mins, followed by second strand synthesis at 16 C for 1 hour. During second strand synthesis, the dUTP was used to replace dTTP, thereby the second strand was quenched during amplification. A single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments at 37 C for 30 minutes. Adapters with illuminaP5, P7 sequences as well as indices were ligated to the cDNA fragment at 30 C for 10 minutes. After Ampure bead (BD) purification (Beckman Coulter), a 15-cycle PCR reaction was used to enrich the fragments. PCR was set at 98 C for 10 s, 60 C for 30 s and extended at 72 C for 30 s. Libraries were again purified using AmPure beads, checked for quality check with a Bioanalyzer (Agilent Technologies) and quantified with Qubit (Invitrogen). Sample libraries were subsequently pooled and loaded to the HiSeq2500 and sequenced using a Hiseq rapid SRcluster kit and HiSeq rapid SBS kit (Illumina). Single 50bp were generated for the bioinformatic analysis.

treatment_protocol: MDA-MB-231 cells were incubated for 5 hours with ML162 (125 nM) or ESA (100  µM) and 2 replicates for the control incubated with the vehicle for ESA (methanol).Orthotopic MDA-MB-231 xenografts in NSG mice were treated orally with either 100 uL of safflower oil (control) or tung oil 5 days a week for 24 days

tag: cell line

tag: cell line origin

value: triple-negative breast cancer

tag: agent

value: tung oil


title: 1331_Tung.1

description:
tung oil-treated tumor.1
Tung_1


title: 1327_Ctrl.3

description:
control tumor (safflower oil, high-oleic).3
Control_3

value: safflower oil, high-oleic


title: 1332_Tung.2

description:
tung oil-treated tumor.2
Tung_2


title: Donor61_unstim

tag: treatment


title: 1324_Ctrl.1

description:
control tumor (safflower oil, high-oleic).1
Control_1


title: 1326_Ctrl.2

description:
control tumor (safflower oil, high-oleic).2
Control_2


title: MB231ESA.3

description:
aESA-treated.3
ESA_3

source_name: human breast cancer cell line

value: alpha-eleostearic acid


title: iMS2 [AY8]

city: Sydney

first: Dominik

last: Beck

address: Level 10, UTS Building 11 (CB11 81-113, Broadway, Ultimo)

department: School of Biomedical Engineering

institute: University of Technology Sydney

description: RNA-seq iMS #2

data_processing:
Paired-end RNA-seq reads aligned to the human genome (hg19) using the software package STAR with standard parameters.
Expression profiles in samples were generated using featureCounts.
Differential expression analysis was performed on normalized read counts using the DeSeq2 package.
Genome_build: hg19
Supplementary_files_format_and_content: Summary of raw counts and deSeq2 normalised values per gene per sample (.txt)

source_name: Generated by in vitro reprogramming of mature adipocytes

growth_protocol: All cells were cultured in standard tissue culture conditions in complete Alpha MEM medium supplemented with autologous serum

extract_protocol:
Total RNA was extracted using Qiagen miRNEasy kit, following manufacturer's instructions
mRNA was extracted using the miRNeasy Mini kit (QIAGEN, 217004) according to manufacturer’s instructions.

treatment_protocol: Primary adipocytes were reprogrammed in vitro in the presence of AZA (2 days only) and rhPDGF-AB (25 days) to generate iMS cells

tag: cell type/population

value: Reprogrammed cell population


title: AdMSC2 [AY6]

description: RNA-seq AdMSC #2

source_name: Abdominal subcuaneous fat tissue

value: Control


title: Primary2 [AY5]

description: RNA-seq Primary #2

value: Starting cell population


title: MB231ESA.2

description:
aESA-treated.2
ESA_2


title: Donor71_stim_DAC300


title: iMS1 [AY4]

description: RNA-seq iMS #1


title: MB231ESA.1

description:
aESA-treated.1
ESA_1


title: longRNAseq_WT rep1

value: lymphoblastoid cell line

tag: genotype


title: MB231ML162.3

description:
ML162-treated.3
ML162_3

value: ML162, GPX4 inhibitor


title: AdMSC1 [AY2]

description: RNA-seq AdMSC #1


title: MB231ML162.2

description:
ML162-treated.2
ML162_2


title: Primary1 [AY1]

description: RNA-seq Primary #1


title: M_73

city: Auburn

first: Wellison

middle: J. S.

last: Diniz

state: Alabama

address: CASIC Building 559 Devall Drive Auburn University, 205

department: Animal Sciences

institute: Auburn University

data_processing:
Illumina Casava software
Sequenced reads were trimmed for adaptor sequence, filtered for low-quality sequence, and quality checked using the FastQC v. 0.11.8. The mapping to the bovine genome reference ARS-UCD 1.2 was performed by STAR aligner v. 2.7.3a using the -quantMode Gene.Counts flag to obtain the raw counts per gene.
Genome_build: Bos taurus ARS-UCD 1.2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Bos taurus

source_name: muscle

growth_protocol: Heifers were acclimated to individual bunk feeding (American Calan, Northwood, NH) for 2 wk before the beginning of the trial. All heifers were exposed to the 5-d CO-Synch + CIDR estrus synchronization protocol and bred via AI to a common sire at 12 h after observed estrus. Immediately post-breeding, heifers were randomly assigned to one of two treatment groups.  The diet was delivered via total mixed ration and consisted of grass hay, corn silage, alfalfa haylage, as well as a grain and mineral mix. Dried distillers grains with solubles (53.4% NDF, 31.3% CP) were supplemented in addition to the TMR and fed to achieve the target nutrient content of the CON and RES diets (Crouse et al., 2019).

extract_protocol:
RNA was extracted with the RNeasy Plus Universal Mini Kit (Qiagen, Hilden, Germany) and quantified using a NanoDrop for 260/280 (Min = 1.93, Max = 2.10) and 260/230 (Min = 1.53, Max = 2.23) ratios as well as Quant-iT RiboGreen Assay Kit for RNA concentration (Min = 280.3 ng/µL, Max = 2680 ng/µL; Invitrogen, Carlsbas, CA). RNA integrity was measured with the Agilent TapeStation/BioAnalyzer (Agilent Technologies, Santa Clara, CA) for RNA quality (Min = 5.7, Max = 9.5).
RNA-seq library creations were strand specific. RNA sequencing analysis was conducted on the Illumina HiSeq 2500 platform and multiplexed with 21 samples per lane (42 samples total: 14 liver, 14 muscle, and 14 cerebrum) using 50-bp paired-end reads at a depth of 2 × 10.4M reads/sample in both forward and reverse directions.

treatment_protocol: Control heifers (CON, n = 7) received 100% of (NRC, 2000) requirements for 0.45 kg/d gain to reach 80% of mature body weight at first calving. Restricted heifers (RES, n = 7) were placed on a 40% global nutrient restriction, which was accomplished by reducing total diet delivery to 60% of the control delivery (Crouse et al., 2019).

value: left hind limb

value: fetus 50 days old

tag: gender

value: M

tag: group

value: C


title: MB231_Neg.2

description:
control (vehicle-treated, methanol).2
Neg_2

value: vehicle, methanol


title: MB231ML162.1

description:
ML162-treated.1
ML162_1


title: MB231_Neg.1

description:
control (vehicle-treated, methanol).1
Neg_1


title: M_70

tag: tissue

value: F

value: R


title: human integrin β3-rescued, integrin β3 kockout PyMT-BO1 cells treated with DTX, rep 3 [B3KO-HB3-DTX.3]

city: St. Louis

first: Katherine

middle: N.

last: Weilbaecher

state: MO

address: 660 S. Euclid Ave., Box 8069

institute: Washington University School of Medicine

description: run_2504_s_*_withindex_sequence.txt_ATGACAG

data_processing:
Sequencing reads were checked for quality using FastQC
Alignment to the mouse reference genome (mm10) was performed using the splice-aware alignment tool HISAT2, guided by the transcript annotation downloaded from the UCSC genome browser.
Subsequently, featureCounts was used to quantify the raw count of reads mapped to the transcripts.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

growth_protocol: pMx, Δβ3, and hβ3 lines were cultured in biological triplicate on tissue culture-treated 6-well plates in DMEM (10% FBS, 1% pen-strep)

extract_protocol:
Cells were lysed and RNA extracted using the Rneasy Plus Mini Kit according to manufacturer's directions.
Library preparation was performed with 1ug of total RNA. Ribosomal RNA was removed by a hybridization method using Ribo-ZERO kits (Illumina-EpiCentre). mRNA was then fragmented and reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 13 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq3000 using single end reads extending 50 bases.

treatment_protocol: Cells were treated for 24hr with either DMSO or 10nM docetaxel, then harvested.

tag: strain background

tag: cell type

value: PyMT-BO1 murine breast cancer (luminal B-like) cells

value: integrin {beta}3 knockout

tag: retroviral rescue

value: functional human integrin β3 (hβ3)

value: 10nM docetaxel 24hr


title: Donor 57 - Day 5 Stimulated + 300 AZA (RNA-seq)

state: ON

institute: Princess Margaret Cancer Centre

data_processing:
FastQ files were aligned to hg19 by calling Bowtie2 withing the bismark software (version 0.10.1), with the number of mismatches allowed set to 1, to yield SAM files.
SAM files were converted to BAM files using Samtools; unaligned reads were retained.
Sorted SAM files were read in with the read.bismark() command in the methylKit software, and subsequently processed by the filterByCoverage() command with parameters lo.count=10, lo.perc=NULL, hi.count=NULL & hi.perc=99.9.
The resulting R objects were read into text files using the getData() functionality, and then converted to BED files using a custom awk script that calculates the actual Beta Values for each CpG.
Genome_build: hg19
Supplementary_files_format_and_content: BED files containing Beta values
Paired-end FastQ files were pseudoaligned to GENCODE hg19 lncRNAs and protein-coding genes and quantified using Kallisto.
The resulting abundance estimates were converted to gene-wise estimated counts using custom R functions.
Genome_build: hg19
Supplementary_files_format_and_content: TEXT files containing gene-wise estimated counts

source_name: Peripheral blood

growth_protocol: Purified CD8+ T cells were seeded in specialized non-adherent round-bottom 96-well plates at a concentration of 10,000 cells per well, in a final media volume of 200uL. The media used for CD8+ T cell cultures was RPMI 1640 conditioned with 2mM HEPES, 0.1% Pen Strep, 0.1% L-glutamine, 10% Human Serum, and 10IU/mL human recombinant IL-2.

extract_protocol:
mRNA for RNA-seq was extracted using the RNeasy Plus Mini Kit (Qiagen, cat # 74104). mRNA was isolated from cells harvested from unstimulated T cells collected at day 0, and T cells stimulated in the presence or absence of 300nM 5-AZA-CdR at day 5 post stimulation.
Libraries were prepared using the TruSeq Stranded mRNA kit (Illumina).

treatment_protocol: unstimulated (no beads added); stimulated; and stimulated plus 300nM 5-AZA-CdR. In order to stimulate CD8+ T cells, anti-CD3/CD28 beads (ThermoFisher Scientific, Cat#11131D) were added to the wells at a 1 bead: 2 cells ratio and left in the wells until the last time point of data collection (day 12). For the stimulation of CD8+ T cells with 5-AZA-CdR (Sigma-Aldrich, Cat#A3656), two concentrations were used during the CD8+ T cell expansion protocol: 100nM and 300nM.

value: CD8+ T cells

tag: stimulated

value: anti-CD3 and anti-CD28 ex vivo in the presence of 300nM of 5-AZA-CdR


title: Donor 57 - Day 0 Unstimulated (RNA-seq)

value: unstimulated


title: M_69

tag: developmental stage


title: human integrin β3-rescued, integrin β3 kockout PyMT-BO1 cells treated with DTX, rep 2 [B3KO-HB3-DTX.2]

description: run_2504_s_*_withindex_sequence.txt_TACAGAC


title: M_68


title: human integrin β3-rescued, integrin β3 kockout PyMT-BO1 cells treated with DTX, rep 1 [B3KO-HB3-DTX.1]

description: run_2504_s_*_withindex_sequence.txt_TCCCAGC


title: Donor 25 - Day 5 Stimulated + 300 AZA (RNA-seq)


title: Donor 25 - Day 0 Unstimulated (RNA-seq)


title: human integrin β3-rescued, integrin β3 kockout PyMT-BO1 cells treated with DMSO, rep 2 [B3KO-HB3-DMSO.2]

description: run_2504_s_*_withindex_sequence.txt_CTCCCGA

value: DMSO 24hr


title: signaling mutant-rescued ,integrin β3 kockout PyMT-BO1 cells treated with DTX, rep 3 [B3KO-DB3-DTX.3]

description: run_2504_s_*_withindex_sequence.txt_CCTAATC

value: signaling deficient mutant integrin β3 construct (Δβ3)


title: Donor 28 - Day 5 Stimulated + 300 AZA (RNA-seq)


title: M_6


title: Donor 28 - Day 5 Stimulated (RNA-seq)

value: anti-CD3 and anti-CD28 ex vivo


title: human integrin β3-rescued, integrin β3 kockout PyMT-BO1 cells treated with DMSO, rep 1 [B3KO-HB3-DMSO.1]

description: run_2504_s_*_withindex_sequence.txt_CCGGACC


title: signaling mutant-rescued, integrin β3 kockout PyMT-BO1 cells treated with DTX, rep 1 [B3KO-DB3-DTX.1]

description: run_2504_s_*_withindex_sequence.txt_GCCGTTT


title: Donor 57 - Day 5 Stimulated (RNA-seq)


title: signaling mutant-rescued, integrin β3 kockout PyMT-BO1 cells treated with DTX, rep 2 [B3KO-DB3-DTX.2]

description: run_2504_s_*_withindex_sequence.txt_TGATTAC


title: M_55

value: left hind limb


title: Donor 28 - Day 0 Unstimulated (RNA-seq)


title: M_54

value: fetus 50 days old


title: signaling mutant-rescued, integrin β3 kockout PyMT-BO1 cells treated with DMSO, rep 3 [B3KO-DB3-DMSO.3]

description: run_2504_s_*_withindex_sequence.txt_GTACGGC


title: signaling mutant-rescued, integrin β3 kockout PyMT-BO1 cells treated with DMSO, rep 2 [B3KO-DB3-DMSO.2]

description: run_2504_s_*_withindex_sequence.txt_TACATGG


title: signaling mutant-rescued, integrin β3 kockout PyMT-BO1 cells treated with DMSO, rep 1 [B3KO-DB3-DMSO.1]

description: run_2504_s_*_withindex_sequence.txt_CGGTGGC


title: Donor 25 - Day 5 Stimulated (RNA-seq)


title: M_52

value: M


title: human integrin β3-rescued, integrin β3 kockout PyMT-BO1 cells treated with DMSO, rep 3 [B3KO-HB3-DMSO.3]

description: run_2504_s_*_withindex_sequence.txt_GCAACGC


title: empty vector-rescued, integrin β3 kockout PyMT-BO1 cells treated with DTX, rep 3 [B3KO-DTX.3]

description: run_2504_s_*_withindex_sequence.txt_TGTTTGT

value: empty vector (pMx)


title: Donor 57 - Day 5 Stimulated + 300 AZA (RRBS)

extract_protocol:
Genomic DNA was extracted using Thermofisher PureLink® Genomic DNA Mini Kit and eluted in EB buffer.
Libraries were prepared following the reduced representation bisulfite sequencing protocol outlined in Gu et. al. Indexing adaptors used were from the TruSeq chip library preparation kit - Set A (IP-202-1012), and bisulfite conversion was carried out using the Zymo EZ DNA Methylation Kit (Illumina protocol).


title: Donor 57 - Day 0 Unstimulated (RRBS)


title: empty vector-rescued, integrin β3 kockout PyMT-BO1 cells treated with DTX, rep 2 [B3KO-DTX.2]

description: run_2504_s_*_withindex_sequence.txt_GGTCCTC


title: empty vector-rescued, integrin β3 kockout PyMT-BO1 cells treated with DMSO, rep 3 [B3KO-DMSO.3]

description: run_2504_s_*_withindex_sequence.txt_GTCGATA


title: M_46

value: C


title: empty vector-rescued, integrin β3 kockout PyMT-BO1 cells treated with DTX, rep 1 [B3KO-DTX.1]

description: run_2504_s_*_withindex_sequence.txt_GCTTAGA


title: Donor 57 - Day 5 Stimulated (RRBS)


title: empty vector-rescued, integrin β3 kockout PyMT-BO1 cells treated with DMSO, rep 1 [B3KO-DMSO.1]

description: run_2504_s_*_withindex_sequence.txt_GGGTCAA


title: M_33


title: M_23


title: empty vector-rescued, integrin β3 kockout PyMT-BO1 cells treated with DMSO, rep 2 [B3KO-DMSO.2]

description: run_2504_s_*_withindex_sequence.txt_AGATACT


title: M_2


title: M_25


title: MCF7_DMSO.rep3

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

institute: Kindai University

description: mRNA-seq (polyA+) data from MCF-7 treated DMSO as control, replicate 3

data_processing:
Basecalls performed using Torrent Suite version 5.0.4
The seuqence data was mapped to the genome sequence with STAR ver. 2.4.1d .
Genome_build: hg19
Supplementary_files_format_and_content: Expression values of refseq gene models were calculated with RSEM ver. 1.3.0.

molecule: polyA RNA

growth_protocol: MCF-7 cells were expanded in DMEM containing 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted from MCF-7 cells using the RNeasy mini kit (QIAGEN).
Ion Total RNA-Seq Kit (Life Technology)

treatment_protocol: Incubated with 10 μM ALESIA racemate in DMEM containing 5% fetal bovine serum and 1% penicillin-streptomycin for 6 hours, and then harvested for extraction of RNA

tag: condition

value: cancer cell line

tag: derived tissue

value: mammary gland, breast; derived from metastatic site:pleural effusion


title: Tpr_1

city: Montréal

first: Moutih

last: Rafei

state: Québec

address: 2900 Boul. Édouard-Montpetit

institute: Université de Montréal

description: Test

data_processing:
Sequencing was performed with the Illumina HiSeq 2000 and basecalls analyzed using Illumina RTA 1.17.21.3.
Samples demultiplexed using Illumina Casava 1.8.2 using adapter masking.
Sequenced reads were trimmed for masked adapters and low quality extremities using Trimmomatic 0.35 and then mapped to the reference genome using Tophat version 2.1.0, guided by transcript annotations from RefSeq.
Expression values were computed usingHTseq-count version 0.6.1 and RefSeq annotations.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited file where columns correspond to each sample (first line identifies the columns) and lines identifies genes, count

source_name: MSC-TPr

growth_protocol: Cells grown in AMEM + 10% FBs + PS

extract_protocol:
Trizol extraction and Qiagen Rneasy column purification
KAPA RNA Stranded PolyA

value: Bone marrow-derived MSC

value: Transduced with Tpr


title: MSC_3

description: Control

source_name: MSC

value: control


title: M_1

value: R


title: L_70

source_name: liver

value: liver

value: F


title: L_73


title: MSC_1

description: Control


title: MSC_2

description: Control


title: Tpr_2

description: Test


title: Tpr_3

description: Test


title: L_69


title: Donor 25 - Day 0 Unstimulated (RRBS)

value: CD8+ T cells

value: unstimulated


title: Astrocyte_Zeb2os_KD2

data_processing:
The quality of all sequenced samples was analyzed using FastQC.
Reads were mapped to the Mm10. Mapping and transcript assembly were performed with TopHat v2.1.0 and Cufflinks v2.2.1 respectively using default parameters.
The gene read counts of samples were normalized and compared to control samples using DESeq2
Genome_build: Mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample

source_name: Astrocyte

growth_protocol: Briefly, mouse brains were dissociated into single-cell suspensions with Neural Tissue Dissociation Kit (P) (MACS Miltenyi Biotec; 130-092-628) according to detailed manufacturer’s instructions. After 7 days, microglia, fibroblasts and oligodendrocytes were removed by shaking at 220 rpm overnight, the remaining cells were incubated and seeded in 6-well plate with 70-80% confluency. Either control or Zeb2os knockdown lentiviruses were transduced into seeded cells and selected using puromycin (1ug/ml) after 24hr for 3 days.

extract_protocol:
Total RNA isolation using TRIzol according to detailed manufacturer’s instructions.
Libraries were constructed with the NEBNext Ultra Directional RNA library Prep Kit for Illumina (E7420, New England Biolabs) by following the manufacturer’s instructions.

treatment_protocol: Cells were transduced with Zeb2os knockdown lentivirus and selected using puromycin (1ug/ml) after 24hr for 5 days.

tag: strain

tag: age

value: Primary astrocytes from P4-P7 postnatal brain

value: Zeb2os -/-

value: Astrocyte


title: Donor 28 - Day 5 Stimulated (RRBS)

value: anti-CD3 and anti-CD28 ex vivo


title: Donor 25 - Day 5 Stimulated + 300 AZA (RRBS)

value: anti-CD3 and anti-CD28 ex vivo in the presence of 300nM of 5-AZA-CdR


title: Donor 28 - Day 0 Unstimulated (RRBS)


title: Donor 28 - Day 5 Stimulated + 300 AZA (RRBS)


title: Donor 25 - Day 5 Stimulated (RRBS)


title: Astrocyte_Zeb2os_KD1


title: Astrocyte_Zeb2os_ctr1

treatment_protocol: Cells were transduced with control lentivirus and selected using puromycin (1ug/ml) after 24hr for 5 days.

value: WT


title: Astrocyte_SCI3M_rep3

value: 3 mpi (month post-injury)

value: Thoracic (T9) moderate contusion injury for 3 months


title: Astrocyte_SCI7D_rep3

value: 7 dpi (days post-injury)

value: Thoracic (T9) moderate contusion injury for 7 days


title: Astrocyte_SCI7D_rep2


title: Astrocyte_SCI7D_rep1


title: MCF7_DMSO.rep1

description: mRNA-seq (polyA+) data from MCF-7 treated DMSO as control, replicate 1

value: cancer cell line

value: mammary gland, breast; derived from metastatic site:pleural effusion


title: MCF7_ALESIA.rep1

description: mRNA-seq (polyA+) data from MCF-7 treated ALESIA racemate, replicate 1


title: MCF7_ALESIA.rep3

description: mRNA-seq (polyA+) data from MCF-7 treated ALESIA racemate, replicate 3


title: MCF7_ALESIA.rep2

description: mRNA-seq (polyA+) data from MCF-7 treated ALESIA racemate, replicate 2


title: Astrocyte_SCI_Sham3

treatment_protocol: Sham mice received laminectomy (T9) only for 7 days.

value: Laminectomy for 7 days

value: Thoracic (T9) laminectomy for 7 days


title: Astrocyte_SCI_Sham2


title: Astrocyte_Zeb2os_ctr2


title: Astrocyte_SCI_Sham1


title: SCI3M_rep3

source_name: Spinal cord

growth_protocol: Epicenter spinal cord tissue was harvested from SCI mice at 1 month or 3 months

value: Spinal cord


title: SCI3M_rep2


title: SCI3M_rep1


title: SCI1M_rep3

value: 1 mpi (month post-injury)

value: Thoracic (T9) moderate contusion injury for 1 month


title: SCI1M_rep2


title: MDSC-PIM-KO-2

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

data_processing:
Reads were aligned to mouse reference genome mm10 using Star.
Genome_build: mm10

source_name: bone-marrow-derived MDSCs

growth_protocol: Femurs were collected from C57BL/6 or Pim1-/- mice and flushed with 10% FBS RPMI medium to harvest bone marrow precursors. These cells were cultured at 37°, 5% CO2 in the presence of GM-CSF (40 ng/mL, 200-15, Shenandoah) and IL-6 (40 ng/mL, 200-02, Shenandoah) for 7 days to generate BM-MDSCs.

extract_protocol: Bulk RNA sequencing was performed according to a published Smart-seq2 protocol with minor modification. https://doi.org/10.1038/nprot.2014.006

value: Bone-marrow-derived MDSCs

tag: cell population

value: CD11b+ Gr1+


title: MDSC-PIM-KO-3


title: L_55

value: liver

value: fetus 50 days old

value: F

value: R


title: L_33

value: M


title: L_52


title: L_68

value: C


title: L_54


title: L_6


title: L_46


title: L_25


title: MDSC-PIM-KO-1


title: ICB Responder scRNA-seq

data_processing:
Reads were aligned to mouse reference genome mm10
Genome_build: mm10
Supplementary_files_format_and_content: Matrix files were generated using Cell Ranger (10x Genomics).

source_name: CD45+ cells from tumor

extract_protocol:
10x Genomics
10x Genomics

treatment_protocol: Immune cells were isolated from tumors and stained as previously described. Then, CD45+ (103106, Biolegend) and live (7AAD-, 420404, Biolegend) cells were sorted using a BD FACSMelody cell sorter. ILCs were FACS-sorted from influenza-infected mice on day 5 and day 10 post infection and were loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol. Libraries were loaded onto an Illumina NextSeq with the NextSeq 500/550 High Output Kit v2 (150 cycles)

tag: tumor and treatment

value: MC38 tumor and anti-PD-L1 mAb

value: CD45+ cells from tumor


title: ICB Non-responder scRNA-seq


title: SCI1M_rep1

tag: treatment


title: MEF Rev3l HET + Empty Vector #4

city: Smithville

first: Sara

last: Martin

state: Texas

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Basecalling was done by Illumina HiSeq Control Software (version HD 3.4.0.38).
The reads were mapped to the mouse genome (mm10) by TopHat (version 2.0.10).
The number of fragments in each known gene from GENCODE Release M19 was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genes with less than 10 fragments in all the samples were removed, and then the cpm (count per million fragments) value for each gene was calculated by R/Bioconductor package edgeR (version 3.8.6).
Genome_build: mm10
Supplementary_files_format_and_content: The first column is Ensembl gene id. The other columns are cpm values (estimated by edgeR) for all the samples.

source_name: Mouse embryonic fibroblast (MEF)

extract_protocol:
RNA, from flash frozen cell pellets, was harvested using Qiagen RNeasy kit (#74104) following the manufacturer’s instructions including the on-column DNase I digestion (Qiagen #79254).
Libraries were prepared with Illumina TruSeq Stranded mRNA kit using manufacturer's instructions

treatment_protocol: Untreated

value: Large T antigen immortalized mouse embryonic fibroblast

value: Rev3L(+/delta), mT/mG (+/-)

tag: construct

value: empty vector


title: MEF Rev3l KO + Empty Vector #4

tag: genotype

value: Rev3L(-/delta), mT/mG (+/-)


title: MEF Rev3l KO + TR4-2  #8


title: MEF Rev3l KO + TR4-2 #18


title: MEF Rev3l KO + Empty Vector #15


title: MEF Rev3l HET + Empty Vector #8


title: MEF Rev3l KO + Empty Vector #3


title: MEF Rev3l KO + TR4-2  #21


title: MEF Rev3l HET + Empty Vector #11


title: L_2

tag: gender


title: L_23

tag: group


title: MDSC-PIM-WT-3

value: WT

tag: tissue


title: SCI_input

institute: UTHealth

data_processing:
All reads were mapped to the mm10 reference genome using Bowtie2, and only unique mapped reads were used for subsequent analysis.
STAT3 ChIP-Seq data were analyzed using the transcription factor pipeline from ENCODE. Peaks for STAT3 were called using SPP and filtered to exclude regions blacklisted by ENCODE, and peaks with FDR > 0.05 and fold-enrichment < 5.
Genome_build: Mm10
Supplementary_files_format_and_content: peak files

source_name: Spinal cord dissociated cells

growth_protocol: Epicenter spinal cord tissue was harvested at respective time points and dissociated using a mixed digestion solution of 0.01% papain (LS003126, Worthington Biochemical,), 0.025% trypsin-EDTA (25200056, Gibco), 0.01% DNase I (LS002138, Worthington Biochemical) and 0.01% L-Cysteine (2430-100GM, Calbiochem) for 15 min at 37 ℃ with gentle shaking (70 rpm). The cells were separated from undigested pellet by triturating with wide-tipped, fire-polished glass Pasteur pipette for 8 times. After repeating 2 times of digestion and separation, cell suspension was filtered by 40 μm cell strainer and DMEM with 4% high BSA by centrifugation to obtain the single-cell suspension.

extract_protocol:
Chromatin immunoprecipitation (IP) was performed using STAT3 antibody (sc-482x, Santa Cruz Biotechnology). IP DNA and input DNA were extracted using phenol:chloroform  as described in our previous study
Libraries were constructed with the DNA SMART ChIP-Seq Kit (634865, Clontech) by following the manufacturer’s instructions

treatment_protocol: The mice were conducted with moderate contusive injury with Infinite Horizons impactor (Precision Systems and Instrumentation) at T9 level of the exposed spinal cord (60 kdyn) and mentained for 7 days.

value: Spinal cord dissociated cells

tag: chip antibody

value: Thoracic (T9) moderate contusion injury for 7 days


title: SCI_STAT3

tag: cell type

value: Rabbit anti-STAT3_(sc-482x)


title: L_1


title: MDSC-PIM-WT-1

value: Bone-marrow-derived MDSCs

value: CD11b+ Gr1+


title: C_73

source_name: cerebrum

value: cerebrum

value: fetus 50 days old


title: Sham_input

value: Thoracic (T9) laminectomy for 7 days


title: MDSC-PIM-WT-2


title: Saline Rep1

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: inguinal primary white adipocytes obtained from male C67Bl6 mice aged 6-8 weeks, treated with Saline for 24 hours

data_processing:
Following removal of primers and barcodes, reads were aligned and quantified using Kallisto (Pachter lab), which employs psuedoalignment for the accurate and rapid determination of compatibility of reads with targets.   We used the mm10 mouse genome with annotations provided by UCSC.  The output is transcripts per million (TPM).
TPM were lognormalized and baselined to the median of all samples. Further, reads were filtered to require TPM>3 in all samples of at least one experimental condition.
Genome_build: mm10
Supplementary_files_format_and_content: Text file with TPM and gene symbol

source_name: primary white adipocytes

growth_protocol: Inguinal white adipose tissue was obtained from 6-8 week old male C57Bl6 mice.  Fat pads were miced and digested for 40 minutes at 37C (1mg/m Collagenase IV; 3U/ml Dispase II; 0.01-mM CaCl2 in PBS). The suspension was filtered, centrifuged, and resuspended in growth medium.  Primary white adipocytes were grown to confluence.

extract_protocol:
RNA was harvested using mirVana reagent, and Illumina TruSeq RNA Sample Prep Kit was used according to standard protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: White adipose tissue were treated with either rAPRIL (500ng/ml), rBAFF (500ng/ml), LPS (100ng/ml), Norepinephrine (1mM), or saline for 24 hours.

value: Saline

tag: trt duration

tag: Sex

value: male


title: Norepinephrine Rep1

description: inguinal primary white adipocytes obtained from male C67Bl6 mice aged 6-8 weeks, treated with Norepinephrine for 24 hours

value: Norepinephrine

tag: trt concentration


title: Norepinephrine Rep2


title: Saline Rep2


title: Sham_STAT3

city: Houston

first: Haichao

last: Wei

address: 1825 Pressler St., SRB 637.C


title: C_69

tag: developmental stage

value: M

value: C


title: RJ423c141C (miRNA-seq)

city: Guelph

first: Roger

last: Moorehead

address: 50 Stone Rd E

department: Biomedical Sciences

institute: University of Guelph

data_processing:
the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads
adapter sequences were trimmed with cutadapt and the adaptor-trimmed-reads (>= 15nt) were left
miRDeep2 software was used to quantify known miRNA and predict the novel miRNAs
The CPM value for miRNA were calculated with R package edgeR and differentially expressed miRNAs were filtered using edgeR
Genome_build: GRCm38/miRBase22

source_name: murine mammary tumor cell line

growth_protocol: cells were grown in DMEM media supplemented with 10% FBS, 1 mM sodium pyruvate, 4 mM glutamine, 1% antibiotic/antimycotic and 300ug/ml puromycin (InvivoGen, San Diego, CA). RNA was extracted from sub-confluent cells

extract_protocol:
RNA extracted using mirVana miRNA Isolation Kit following the manufacturer's protocol
NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) RiboZero Magnetic Gold Kit (Human/Mouse/Rat), NEB multiplex small RNA library Prep set for Illumina

tag: cell line

value: murine mammary tumor cell line

value: stably transfected with vector containing miR-200c and miR-141


title: LPS Rep1

description: inguinal primary white adipocytes obtained from male C67Bl6 mice aged 6-8 weeks, treated with LPS for 24 hours

value: LPS

value: 100 ng/ml

tag: strain


title: APRIL Rep2

description: inguinal primary white adipocytes obtained from male C67Bl6 mice aged 6-8 weeks, treated with APRIL for 24 hours

value: APRIL

value: 500 ng/ml


title: APRIL Rep1


title: BAFF Rep1

description: inguinal primary white adipocytes obtained from male C67Bl6 mice aged 6-8 weeks, treated with BAFF for 24 hours

value: BAFF


title: RJ423c141A (miRNA-seq)


title: BAFF Rep2


title: C_6

value: R


title: C_68

value: F


title: RJ423EV2C (miRNA-seq)

value: stably transfected with empty vector


title: C_55

value: cerebrum

value: fetus 50 days old


title: C_54


title: C_52


title: RJ423EV1C (miRNA-seq)


title: LPS Rep2


title: RJ423ba429C (miRNA-seq)

value: stably transfected with vector containing miR-200b. miR-200a and miR-429


title: C_33


title: RJ423ba429B (miRNA-seq)


title: C_70


title: C_46


title: C_25


title: RJ423ba429A (miRNA-seq)


title: RJ423c141B (miRNA-seq)


title: RJ423EV2B (miRNA-seq)


title: RJ423EV3B (miRNA-seq)


title: C_23


title: C_2


title: RJ423EV1B (miRNA-seq)


title: RJ423EV3C (miRNA-seq)


title: C_1


title: CD34-GYPA- RNA

city: Boston

first: Carlos

last: Villacorta-Martin

state: MA

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

description: polyA RNA

data_processing:
The sample was processed using the standard Cellranger v.3 pipeline
Reads were mapped to GRCh38 and GRCm38
ADT counts were summarized using CITE-Seq-Count v 1.4.2
Downstream analysis and QC done on Seurat v.3
Differential expression using MAST models
ADT count data were centered-log-ratio transformed in Seurat and background cells removed
Trajectory analysis done using Monocle v.3
Genome_build: GRCh38 and GRCm38
Supplementary_files_format_and_content: R Seurat v.3 Object containing single cell mRNA and ADT data. The meta data contains clustering information at different resolutions and molecular signature scores.

source_name: human fetal liver

extract_protocol:
We followed standard Chromium 10x guidelines (10x Genomics user guide document number CG000185, Rev B.) for Chromium Single Cell 3ʹ Reagent Kits v3 with Feature Barcoding technology for Cell Surface Protein
CITE-seq (scRNA-seq + ADT sequencing)

treatment_protocol: CD34+ and CD34- fetal liver cells were thawed and allowed to recover at 37C for an hour prior to staining. Cells were blocked with TruStain FcX and stained with TotalSeq A antibody mix containing 1ug of each TotalSeq A antibody per sample. FACS antibodies were added to each sample. All samples were stained with calcein blue for live/dead exclusion and cell populations were sorted as described in 'overall design' prior to loading onto a 10X genomics chip

value: fetal liver week 21

tag: isolation method

value: CD34-GYPA- live sorted cells


title: CD34-GYPA+ RNA

description: polyA RNA

value: CD34-GYPA+ live sorted cells


title: CD34-GYPA+ ADT

description: cell surface protein via antibody-derived tag


title: CD34-GYPA- ADT


title: GPI-80+ RNA

description: polyA RNA

value: CD34+GPI-80+ live sorted cells


title: GPI-80+ ADT


title: CD34+ bulk ADT

value: CD34+ live sorted cells


title: NCC-HN64-GR

city: Singapore

first: Joo-Leng

last: Low

address: 60 Biopolis Street, #02-01 Genome

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Data was processed by Theragen Etex Bioinstitute using their bioinformatics pipeline
Adapters and low quality reads were trimmed with FASTX Toolkit, and mapped to GRCh37 using TopHat
FPKM and readcount values were obtained using Cufflinks
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel files for each samples with FPKM and Readcount values for gene expression

source_name: HNSCC cells

growth_protocol: cells were grown in RPMI 1640 medium with 10% FBS, and supplemented with PenStrep

extract_protocol:
total RNA was extracted using RNeasy Plus mini RNA extraction kit
TruSeq RNA sample prep kit (Illumina)

treatment_protocol: cells were treated with either 0.1% DMSO or 6.4 uM gefitinib

tag: gefitinib sensitivity

value: resistant

value: 6.4uM gefitinib


title: CD34+ bulk RNA

description: polyA RNA


title: NCC-HN90-GR


title: NCC-HN90

value: sensitive

value: 0.1% DMSO


title: NCC-HN64


title: NCC-HN19-GR


title: NCC-HN19


city: Memphis

first: Patrick

middle: Allen

last: Schreiner

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Children's Research Hospital

description:
total RNA depleted for rRNA
tripleCopy - H3G34K Mutant - Replicate 3
tripleCopy.counts.txt

data_processing:
Read alignment was performed using STAR software
Gene level quantification was performed by featureCounts (subread)
Differentially expressed genes were identified using limma voom. External RNA spike-ins were used to confirm no global expression changes amongst modified histones.
Genome_build: Schizosaccharomyces_pombe.ASM294v2.29
Supplementary_files_format_and_content: raw counts

organism: Schizosaccharomyces pombe

source_name: PY A513

growth_protocol: Cultures were grown overnight in PMG complete media at 25°C to a density of 2.5 x 10-6 cells/ml in a 25mL culture

extract_protocol:
Hot phenol extraction was used to prepare total RNA (Leeds et al. 1991. PubMed PMID: 1748286). cells were pelleted by centrifugation and washed in DEPC H2O. The pellet was resuspended in 750 uL TES Buffer [50mM Tris-HCl pH 7.5, 10mM EDTA, 100mM NaCl, 0.5% SDS made in DEPC H2O] along with an equal volume of 5:1 phenol:chloroform pH 4.7 and incubated at 65°C for one hour with vortexing for 10 seconds every 10 minutes. The samples were then cooled on ice and centrifuged for five minutes at 13,000 RPM. The aqueous phase was transferred to a 2 mL phase lock tube and an additional phenol:chloroform extraction was performed. After centrifugation, the aqueous phase was transferred to a new tube and re-extracted using an equal volume of chloroform. To precipitate the RNA, the aqueous phase was transferred to a 2 mL microcentrifuge tube and three volumes of ice cold ethanol and 1/10th volume 3M NaOAc pH 5.2 were added and the samples were kept at -20°C overnight. The next day, samples were centrifuged at 14,000 RPM and 4°C for 15 minutes to pellet the RNA. The pellet was washed with ice cold 70% ethanol and air dried for 30 minutes. A Turbo DNAse (Ambion) reaction was set up with 100 ug of RNA in a 150 uL reaction containing 5 uL of Turbo DNAse. The reaction was incubated at 37°C for 30 minutes and another 5 uL of Turbo DNAse was added and incubated for an additional 30 minutes prior to the removal of the DNAse using 50 uL of inactivation beads. An RNeasy Mini kit (Sigma) was used to further clean up and concentrate the RNA which was eluted in a final volume of 30 uL of DEPC H2O. 5 ug total RNA was diluted to 10 ul, and 2 ul of a 1:20 dilution of ERCC RNA Spike-in mix (Invitrogen) was added to each sample. RNA-seq was performed by the St. Jude Hartwell Center. Ribosomal RNA was removed from the samples using Ribo-Zero Gold rRNA Removal Kit (Yeast) following manufacturer instructions (Illumina).RNA was quantified using a Quant-iT assay (Life Technology). The quality was checked by 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or LabChip RNA Pico Sensitivity assay (Perkin Elmer) before library generation. Libraries were prepared from 2 ug of RNA.
Libraries were prepared using the TruSeq Strand Total RNA Library Prep Kit, beginning at Elution 2 – Fragment – Prime step immediately preceding cDNA synthesis according to the manufacturer instructions (Illumina) with the following modifications; the 94o C Elution 2 – Fragment – Prime incubation was reduced to five minutes and the PCR was reduced to 11 cycles. Libraries were quantified using the Quant-iT PicoGreen dsDNA assay (Life Technologies) or Kapa Library Quantification kit (Kapa Biosystems).
One hundred cycle paired end sequencing was performed on an Illumina HiSeq 4000 (single copy strains) or on an Illumina Novaseq 6000 (triple copy strains). Three biological replicates were used for each strain analyzed.  The total RNA was sequenced using stranded protocol with 2x100bp setting.

treatment_protocol: not applicable

tag: strain genotype


title: Patient10 with LM primary CRC cancer tissue (miRNA)

type: RNA

city: Soochow

first: Qiaoming

last: Zhi

address: No.188 Shizi Road

institute: Soochow university

description: miRNA expression

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering

source_name: Tissue specimen

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

tag: disease state

value: Colorectal cancer (CRC) with liver metatasis

value: female

tag: age

value: colorectal cancer tissue


title: Patient8 with LM primary CRC cancer tissue (miRNA)

description: miRNA expression


title: SLAM_CH22_PARENTAL_THZ1_8H_2

first: Charles

middle: Yang

last: Lin

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
Library strategy: Nascent RNA-seq (SLAM-seq)
RNA-sequencing data was processed using the Genialis platform (www.genialis.com). In brief, reads were first preprocessed by BBDuk to remove adaptors. Preprocessed reads were aligned to HG19 by HISAT2 (Kim et al., 2019), per sample quantification was performed with Cuffquant, and Cuffnorm was used to estimate gene abundance (Trapnell et al., 2010). FPKM values were normalized to ERCC spike-in RNAs as described previously (Loven et al., 2012).
SLAM-seq data were processed as in the original SLAM-seq publication using the SlamDunk pipeline (https://t-neumann.github.io/slamdunk/index.html) with the following parameters ( -5 12 -n 100 -t 32 -m -rl 75).
Genome_build: HG19
Supplementary_files_format_and_content: Total RNA-seq: tab-delimited text files include FPKM values for each sample. SLAM-seq: tab-delimited text file including CPM values for all samples processed with the SlamDunk pipeline and conversion fraction of to identify nascent transcripts (a measure of the fraction of reads that have a converted C->T (indicative of metabolic labeling and therefore nascent transcription).

source_name: CH22 Sacral chordoma cell line

growth_protocol: UM-Chor1 chordoma cells were maintained in IMDM/RPMI (4:1) + 10% fetal bovine serum (FBS). CH22 chordoma cells were maintained in RPMI media + 10% FBS. All cell lines were maintained on tissue-culture treated plates.

extract_protocol:
Total RNA-seq: RNA extraction was performed using the RNA Clean and Concentrator-5 kit (Zymo R1017). ERCC RNA Spike-In Control Mixes (ThermoFisher 4456740) were added to each sample. SLAM-seq: RNA was extracted as described in Herzog et al., 2017. ERCC RNA Spike-In Control Mixes (ThermoFisher 4456740) were added to each sample.
Total RNA-seq: Libraries were constructed using the NEB Ultra II Directional Library Prep Kit for Illumina (NEB E7760L). SLAM-seq: Libraries were constructed using the Quant-seq 3’-end mRNA library preparation kit for Illumina (Lexogen 015)
Total RNA-seq: NEB Ultra II Directional Library Prep Kit for Illumina (NEB E7760L). SLAM-seq: Libraries were constructed using the Quant-seq 3’-end mRNA library preparation kit for Illumina (Lexogen 015).

treatment_protocol: Please see characteristics:treatment for each individual sample. Treatment was performed by addition of compound to growth media for the indiciated time point

value: CH22 Parental

tag: treatment

value: Treated with 60 nM THZ1 for 8 hours


title: SLAM_CH22_PARENTAL_THZ1_8H_1


title: SLAM_CH22_PARENTAL_DMSO_8H_3

value: Treated with DMSO for 8 hours


title: SLAM_CH22_PARENTAL_DMSO_8H_2


title: SLAM_CH22_PARENTAL_DMSO_8H_1


title: SLAM_CH22_PARENTAL_THZ1_8H_3


title: Patient7 with LM primary CRC cancer tissue (miRNA)

description: miRNA expression

tag: gender

value: male


description:
total RNA depleted for rRNA
tripleCopy - H3G34R Mutant - Replicate 2
tripleCopy.counts.txt


title: tripleCopy - H3 WT - Replicate 4

description:
total RNA depleted for rRNA
tripleCopy - H3 WT - Replicate 4
tripleCopy.counts.txt

source_name: PY 42


title: MDA-231ba429D (RNA-seq)

data_processing:
reads are preprocessed by BBDuk which removes adapters, trims reads for quality from the 3'-end, and discards reads that are too short after trimming
preprocessed reads are aligned by STAR aligner
aligned reads are summarized to gene-level counts by the featureCounts tool
Genome_build: GRCh38_ens92_ercc_sirv
Supplementary_files_format_and_content: counts

source_name: human mammary tumor cell line

growth_protocol: cells were grown in DMEM media supplemented with 10% FBS, 1 mM sodium pyruvate, 4 mM glutamine, 1% antibiotic/antimycotic and 60ug/ml puromycin (InvivoGen, San Diego, CA). RNA was extracted from sub-confluent cells

extract_protocol:
RNA extracted using mirVana miRNA Isolation Kit following the manufacturer's protocol
KAPA stranded Illumina kits for the RNA-seq library preparation, which include procedures of RNA fragmentation, random hexamer primed first strand cDNA synthesis, dUTP based second strand cDNA synthesis, end-repairing, A-tailing, adaptor ligation and library PCR amplification. Library prep performed by Arraystar Inc (Rockville, MD)

value: human mammary tumor cell line

tag: genotype

value: stably transfected with vector containing miR-200b, miR-200a and miR-429


title: Patient6 with LM primary CRC cancer tissue (miRNA)

description: miRNA expression

tag: tissue


title: MDA-231ba429C (RNA-seq)


title: MDA-231ba429B (RNA-seq)


title: SLAM_CH22_DTAG_T_THZ1_8H_3

value: Enginered cell ine derived from CH22 parental chordoma cell line


title: LSKs from littermate control mice, biological rep1

city: Beijing

first: Wang

middle: meng

last: meng

address: No. 58 Jinghai Five Road

institute: Beijing Cnkingbio Biotechnology corporation

description: Gene expression data from LSKs of littermate control mice

hyb_protocol: Following fragmentation, 5.5 ug of sscDNA were hybridized for 16 hr at 45C on GeneChip MTA 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: LSKs sorted from the bone marrow

label_protocol: Biotinylated sscDNA were prepared according to the standard Affymetrix protocol from  250ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 4- to 6-week-old miR-21flox/flox:Mx1-Cre+ mice and miR-21flox/flox:Mx1-Cre- mice were intraperitoneally injected with 250 μg of pIpC (Sigma) every other day for a total of 7 doses. Four weeks after pIpC injection, these mice were used in subsequent experiments. miR-21 was deleted only in miR-21flox/flox:Mx1-Cre+ mice (miR-21 conditional knockout mice) but not in miR-21flox/flox:Mx1-Cre- mice (littermate control mice). All mice were bred and maintained at the specific pathogen free (SPF) laboratory animal room and were given access to water and food ad libitum.

extract_protocol: Total RNA from sorted LSKs were extracted using the RNAqueous kit (Ambion) according to the manufacturer's instructions.

treatment_protocol: Bone marrow cells were flushed from the femur and tibia of miR-21 conditional knockout mice and littermate control mice. Red blood cells were lysed using a red cell lysis buffer (Stem Cell Technologies). Then, cells were stained with anti-Lineage, anti-c-Kit and anti-Sca1 antibodies (ebioseience). After that, Lineage- c-Kit+ Sca1+ cells (LSKs) were sorted by on a FACSAriaII sorter (BD Biosciences).

value: Bone marrow

tag: genotype/variation

value: control


title: LSKs from miR-21 conditional knockout mice, biological rep2

description: Gene expression data from LSKs of miR-21 conditional knockout mice

value: miR-21 conditional knockout mice


title: LSKs from miR-21 conditional knockout mice, biological rep3


title: LSKs from littermate control mice, biological rep3


description:
total RNA depleted for rRNA
tripleCopy - H3G34K Mutant - Replicate 2
tripleCopy.counts.txt


title: Patient5 with LM primary CRC cancer tissue (miRNA)

description: miRNA expression


title: LSKs from miR-21 conditional knockout mice, biological rep1


title: Patient9 with LM primary CRC cancer tissue (miRNA)

description: miRNA expression


title: MCF7_DMSO.rep2

description: mRNA-seq (polyA+) data from MCF-7 treated DMSO as control, replicate 2

tag: condition

value: cancer cell line

tag: derived tissue

value: mammary gland, breast; derived from metastatic site:pleural effusion


title: Patient4 with LM primary CRC cancer tissue (miRNA)

description: miRNA expression


title: SLAM_CH22_DTAG_T_THZ1_8H_2


title: SLAM_CH22_DTAG_T_THZ1_8H_1


description:
total RNA depleted for rRNA
tripleCopy - H3G34K Mutant - Replicate 1
tripleCopy.counts.txt


title: tripleCopy - H3 WT - Replicate 3

description:
total RNA depleted for rRNA
tripleCopy - H3 WT - Replicate 3
tripleCopy.counts.txt


title: LSKs from littermate control mice, biological rep2


title: MDA-231c141E (RNA-seq)

tag: cell type

value: stably transfected with vector containing miR-200c and miR-141


title: MDA-231c141F (RNA-seq)


description:
total RNA depleted for rRNA
tripleCopy - H3G34R Mutant - Replicate 1
tripleCopy.counts.txt


title: MDA-231c141D (RNA-seq)


title: SLAM_CH22_DTAG_T_DMSO_8H_1


title: Patient10 without LM primary CRC cancer tissue (miRNA)

description: miRNA expression

value: Colorectal cancer (CRC) without liver metatasis


title: tripleCopy - H3 WT - Replicate 2

description:
total RNA depleted for rRNA
tripleCopy - H3 WT - Replicate 2
tripleCopy.counts.txt


title: SLAM_CH22_DTAG_T_DMSO_8H_2


title: Patient3 with LM primary CRC cancer tissue (miRNA)

description: miRNA expression

value: Colorectal cancer (CRC) with liver metatasis


title: Patient1 with LM primary CRC cancer tissue (miRNA)

description: miRNA expression


title: MDA-231ba429A (RNA-seq)


title: tripleCopy - H3 WT - Replicate 1

description:
total RNA depleted for rRNA
tripleCopy - H3 WT - Replicate 1
tripleCopy.counts.txt


title: SLAM_CH22_DTAG_T_DMSO_8H_3


title: MDA-231EV3 (RNA-seq)

value: stably transfected with empty vector


title: MDA-231EV2 (RNA-seq)


title: SLAM_CH22_DTAG_T_DEGRON_8H_2

value: Treated with 1 µM degron


title: SLAM_CH22_DTAG_T_DEGRON_8H_3


title: Patient9 without LM primary CRC cancer tissue (miRNA)

description: miRNA expression

value: colorectal cancer tissue


title: Patient8 without LM primary CRC cancer tissue (miRNA)

description: miRNA expression


title: Patient7 without LM primary CRC cancer tissue (miRNA)

description: miRNA expression

value: female


title: SLAM_CH22_DTAG_T_DEGRON_8H_1


title: MDA-231EV1 (RNA-seq)


title: Patient6 without LM primary CRC cancer tissue (miRNA)

description: miRNA expression


title: MDA-231EV (RNA-seq)


title: RNA_UMCHOR1_PARENTAL_THZ1_24H_3

data_processing:
RNA-sequencing data was processed using the Genialis platform (www.genialis.com). In brief, reads were first preprocessed by BBDuk to remove adaptors. Preprocessed reads were aligned to HG19 by HISAT2 (Kim et al., 2019), per sample quantification was performed with Cuffquant, and Cuffnorm was used to estimate gene abundance (Trapnell et al., 2010). FPKM values were normalized to ERCC spike-in RNAs as described previously (Loven et al., 2012).
SLAM-seq data were processed as in the original SLAM-seq publication using the SlamDunk pipeline (https://t-neumann.github.io/slamdunk/index.html) with the following parameters ( -5 12 -n 100 -t 32 -m -rl 75).
Genome_build: HG19
Supplementary_files_format_and_content: Total RNA-seq: tab-delimited text files include FPKM values for each sample. SLAM-seq: tab-delimited text file including CPM values for all samples processed with the SlamDunk pipeline and conversion fraction of to identify nascent transcripts (a measure of the fraction of reads that have a converted C->T (indicative of metabolic labeling and therefore nascent transcription).

source_name: UM-Chor1 Clival chordoma cell line

value: UM-Chor1 Parental

value: Treated with 500 nM THZ1 for 24 hours


title: Msm MSMEG_2225::hyg/pMV261 [X5_FPKM]

city: Wu han

first: Xu

last: Hui

address: 1st shizishan

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mycobacterium_smegmatis_MC2_155_uid57701 whole genome using bowtie2 v2-2.0.5
Fragments per kilobase of exon per million fragments mapped(FPKM). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Mycobacterium smegmatis str. MC2 155
Supplementary_files_format_and_content: gene_expression.xls file includes FPKM values for each Sample

organism: Mycolicibacterium smegmatis

source_name: MSMEG_2225 knockout

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNeasy Mini Kit (Cat#74106, Qiagen) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MSMEG_2225 knockout


title: Msm MSMEG_2225::hyg/pMV261 [X4_FPKM]


title: Msm/pMV261 [CK3_FPKM]

source_name: wild type

value: wild type


title: SKN3_RNA

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

institute: McGill University

data_processing:
Sequences were all aligned to the GRCh38 analysis set.
Reads from ChIP-seq and targeted sequencing for knock-out validation were mapped using BWA v0.7.17 with default settings of the BWA-MEM algorithm.
WGBS/RNA-seq reads were adapter and quality (Q10) trimmed using BBDuk from BBTools v38.73 (https://sourceforge.net/projects/bbmap/) (t=10 ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=rl trimq=10 minlen=2)
Trimmed WGBS reads were aligned as well as deduplicated using BISCUIT  v0.3.12 (https://github.com/zhou-lab/biscuit) with default options
Per-base methylation calling was performed with MethylDackel  v0.4.0 (https://github.com/dpryan79/MethylDackel) after excluding biased ends
Trimmed RNA-seq reads were aligned using STAR v2.7.3a based on GENCODE Release 33 annotations with the ENCODE standard options
ENCODE blacklisted regions were excluded from all analyses.
Variants were identified with GATK v4.1.5.0 using HaplotypeCaller.
Genome_build: hg38
Supplementary_files_format_and_content: Salmon quantification files were obtained using Salmon v1.1.0 with default settings of the gentrome-based option
Supplementary_files_format_and_content: ChIP-seq bigWig files were obtained through first binning raw tag counts into 10 kb windows using bedtools76 v2.29.0 with intersectBed (-c) in combination with the makewindows command. Next, library size normalization consisted of dividing binned tag counts by the total number of mapped reads after filtering, while input normalization involved taking the log2 ratio of ChIP signals by those of the input (i.e., without immunoprecipitation) with the addition of pseudocount (1) to avoid division by 0. Additionally, quantitative normalization entailed the multiplication of original signal (either in CPM or as log2 ratio over input) by the genome-wide modification percentage information obtained from mass spectrometry.
Supplementary_files_format_and_content: narrowPeak of H3K27ac peaks were called using MACS v2.2.6 (-g hs -q 0.01)
Supplementary_files_format_and_content: WGBS bigWig files in 1 kb bins were calculated by taking per-base methylation calls and dividing the number of methylated base-calls divided by the total number of calls per window.
Supplementary_files_format_and_content: RNA-seq bigWig files were created through deepTools v3.3.1 with bamCoverage --normalizeUsing CPM
Supplementary_files_format_and_content: RData file containing the H3K27ac consensus peakset count matrix (dba.rda) was produced with DiffBind v2.14.0.
Supplementary_files_format_and_content: RData file containing a subsetted beta value matrix (mCG.450k.rda) was generated by filtering the genome-wide CpG matrix to include only CpG sites also covered by the Illumina 450k array.

source_name: SKN-3 cells

extract_protocol:
Total RNA was extracted from cell pellets of approximatively 1 million cells, washed with PBS, spun down and preserved at -80, using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s instructions including DNAse treatment option.
Library preparation was performed with ribosomal RNA depletion according to the manufacturer’s instructions (NEB) to achieve greater coverage of mRNA and other long non-coding transcripts.

value: Patient-derived head and neck squamous cell carcinoma cell line

value: NSD1 mutant


title: RNA_UMCHOR1_PARENTAL_THZ1_24H_2

state: TX


title: SKN3_Input

source_name: SKN-3 cells & S2 cells (spiked-in)

extract_protocol:
About 10 million cells per cell line were grown and directly crosslinked on the plate with 1% formaldehyde (Sigma) for 10 minutes at room temperature and the reaction was stopped using 125nM Glycine for 5 minutes. Fixed cell preparations were washed with ice-cold PBS, scraped off the plate, pelleted, washed twice again in ice-cold PBS and flash frozen pellets stored at -80°C. Thawed pellets were resuspended in 500ul cell lysis buffer (5 mM PIPES-pH 8.5, 85 mM KCl, 1% (v/v) IGEPAL CA-630, 50 mM NaF, 1 mM PMSF, 1 mM Phenylarsine Oxide, 5 mM Sodium Orthovanadate, EDTA-free Protease Inhibitor tablet) and incubated 30 minutes on ice. Samples were centrifugated and pellets resuspended in 500ul of nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% (w/v) SDS, 50 mM NaF, 1 mM PMSF, 1 mM Phenylarsine Oxide, 5 mM Sodium Orthovanadate and EDTA-free protease inhibitor tablet) and incubated 30 minutes on ice. Sonication of lysed nuclei was performed on a BioRuptor UCD-300 at max intensity for 60 cycles, 10s on 20s off, centrifuged every 15 cycles, chilled by 4°C water cooler. Samples were checked for sonication efficiency using the criteria of 150-500bp by gel electrophoresis of a reversed cross-linked and purified aliquot. After the sonication, the chromatin was diluted to reduce SDS level to 0.1% and concentrated using Nanosep 10k OMEGA (Pall). Before ChIP reaction 2% of sonicated drosophila S2 cell chromatin was spiked-in the samples for quantification of total levels of histone mark after the sequencing.
ChIP reaction for histone modifications was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. Dynabeads Protein A (Invitrogen) were washed, then incubated with specific antibodies, 1.5 million cells of sonicated cell lysate, and protease inhibitors for 10 hr, followed by 20 min wash cycle using the provided wash buffers (DIAGENODE Immunoprecipitation Buffers, iDeal ChIP-seq kit for Histone). Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail at 65°C for 30 min followed by 2ul Proteinase K at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol. Library preparation was carried out using KAPA Hyper Prep library preparation reagents, following the manufacturer’s protocol.

tag: chip antibody


title: Msm/pMV261 [CK1_FPKM]


title: Msm MSMEG_2225::hyg/pMV261 [X6_FPKM]


title: Msm/pMV261 [CK2_FPKM]


title: RNA_UMCHOR1_PARENTAL_THZ1_24H_1


title: MDA-231c141C (RNA-seq)

value: human mammary tumor cell line


title: Patient4 without LM primary CRC cancer tissue (miRNA)

description: miRNA expression


title: RNA_UMCHOR1_PARENTAL_THZ1_12H_3

value: Treated with 500 nM THZ1 for 12 hours


title: Patient5 without LM primary CRC cancer tissue (miRNA)

description: miRNA expression

value: male


title: MCR:SATB2 tumor 3

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

data_processing:
Quality control of RNA-Seq datasets was performed by FastQC18 and Cutadapt19 to remove adaptor sequences and low quality regions. The high-quality reads were aligned to UCSC build danRer7 of zebrafish genome using Tophat20 2.0.11 without novel splicing form calls. Transcript abundance and differential expression were calculated with Cufflinks21 2.2.1. FPKM values were used to normalize and quantify each transcript.
Genome_build: Danio rerio UCSC danRer7
Supplementary_files_format_and_content: tab-delimited text file containg the FPKM value of each gene

organism: Danio rerio

extract_protocol:
Zebrafish melanomas were isolated and mechanically homogenized in RTL buffer (Qiagen) containing β-mercaptoethanol. Tumor lysates were transferred onto a QiaShredder column (Qiagen), and RNA isolation was performed using the RNA Micro Plus kit (Qiagen) according to the manufacturers instruction. Total RNA was depleted of ribosomal RNA with the Ribo-Zero Gold kit (Epicentre).
Ribosome-depleted RNA was used to create multiplexed RNA-seq libraries (NEBNext Ultra), according to manufacturer's protocol

treatment_protocol: Zebrafish Tg(mitfa:BRAFV600E); p53-/-; mitfa-/- one cell stage embryos were injected with a MiniCoopR expression vector to induce melanocyte-specific overexpression of either EGFP (control) or human SATB2, raised to adulthood and monitored for melanoma formation.

value: primary melanoma tumor

value: Tg(mitfa:BRAFV600E); p53-/-; mitfa-/-


title: SKN3_H3K27me3

value: H3K27me3 (Cell Signaling, 9733)


title: Patient3 without LM primary CRC cancer tissue (miRNA)

description: miRNA expression

value: Colorectal cancer (CRC) without liver metatasis


title: MCR:SATB2 tumor 2


title: RNA_UMCHOR1_PARENTAL_THZ1_12H_2


title: SKN3_H3K36me2

value: H3K36me2 (Cell Signaling, 2901)


title: RNA_UMCHOR1_PARENTAL_THZ1_12H_1


title: MCR:SATB2 tumor 1


title: Patient2 without LM primary CRC cancer tissue (miRNA)

description: miRNA expression


title: Patient1 without LM primary CRC cancer tissue (miRNA)

description: miRNA expression


title: RNA_UMCHOR1_PARENTAL_THZ1_08H_3

value: Treated with 500 nM THZ1 for 8 hours


title: SCC4_RNA

source_name: SCC-4 cells


title: SCC4_Input

source_name: SCC-4 cells & S2 cells (spiked-in)


title: RNA_UMCHOR1_PARENTAL_THZ1_08H_2


title: MCR:EGFP tumor 3


title: SCC4_H3K27me3


title: MCR:EGFP tumor 2


title: MCR:EGFP tumor 1


title: MCR:SATB2_H3K27Ac_Input

data_processing:
ChIP-Seq aligned to zebrafish Zv9 with Bowtie with max mismatch 2bp
peaks were called using MACS 2.0 with the following setting: q-value 0.05
Genome_build: danRer7
Supplementary_files_format_and_content: called peaked in bed file

source_name: zebrafish primary melanoma tumor

growth_protocol: Zebrafish Tg(mitfa:BRAFV600E); p53-/-; mitfa-/- one cell stage embryos were injected with a MiniCoopR (MCR) expression vector to induce melanocyte-specific overexpression of either EGFP (control) or human SATB2, raised to adulthood and monitored for melanoma formation.

extract_protocol:
Zebrafish melanomas were excised, finely minced using a scalpel blade and cross linked using 1.1% formaldehyde. The tumor suspension was mechanically homogenized on ice, and passed through a 100 μm filter. Whole cell extracts were sonicated to solubilize the chromatin, and target bound fragments (average size of 300 bp) were isolated with antibodies as indicated.
Purified immunoprecipitated DNA was prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end-repaired and libraries were prepared using the NEBNext Multiplex Oligos Kit (18-cycle PCR enrichment step). Amplified fragments between 150 and 350bp were isolated by agarose gel electrophoresis, and run on an Illumina Hi-Seq2000.

tag: antibody


title: BICR78_RNA

source_name: BICR-78 cells

tag: cell line


title: RNA_UMCHOR1_PARENTAL_THZ1_08H_1

tag: strain


title: SCC4_H3K36me2


title: RNA_UMCHOR1_PARENTAL_THZ1_04H_2

value: Treated with 500 nM THZ1 for 4 hours


title: RNA_UMCHOR1_PARENTAL_THZ1_04H_3


title: MCR:SATB2_H3K27Ac

value: H3K27ac (Abcam:ab4729)


title: MCR:EGFP_H3K27Ac_Input


title: RNA_UMCHOR1_PARENTAL_THZ1_04H_1

value: UM-Chor1 Parental


title: BICR78_Input

source_name: BICR-78 cells & S2 cells (spiked-in)


title: BICR78_H3K27me3


title: RNA_UMCHOR1_PARENTAL_THZ1_00H_3

value: No treatment


title: MCR:EGFP_H3K27Ac


title: BICR78_H3K36me2


title: RNA_UMCHOR1_PARENTAL_THZ1_00H_2


title: Caco-2 cells, grown in a microfluidic device, replicate 4

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.52.1).

source_name: Caco-2 cells, grown in a microfluidic device (seeding density of 75,000 cell per cm2; exposed to a continuous flow of 100 µL/h) until 21 days

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: A Caco-2 cell line (HTB-37), derived from a human colorectal adenocarcinoma, was obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA). The cells were grown (at passage number 29-45) in DMEM supplemented with 10 % FBS, 1 % penicillin-streptomycin, and 1 % MEM non-essential amino acid, further referred to as DMEM+.

extract_protocol: Cells were first washed with PBS. RNA was then isolated using Qiagen RNeasy Mini Kit (Qiagen), quantified using NanoDrop, and quality was checked with the Agilent 2100 bioanalyzer (Agilent Technologies). Samples were only included for further analyses in case of intact bands corresponding to 18S and 28S ribosomal subunits and absence of chromosomal peaks or RNA degradation products.

treatment_protocol: The cells were seeded at a density of ~75,000 cells per cm2 on 12-well Transwell PET inserts (0.4 µm pore size, 1.12 cm2 surface area, Corning Amsterdam, The Netherlands) and cultured in DMEM+ for 21 days. The medium was changed every two to three days. In the microfluidic device, the cells were seeded at a density of 75,000 cell per cm2 and were allowed to attach to the membrane for 24 h, without the fluid flow. The membrane was then inserted in the microfluidic chip and cells were exposed to a continuous flow of 100 µL/h DMEM+ until day 21 of culturing (Fig. 1B). By doing so, the shear stress in the AP compartment was ~0.002 dyne/cm2 at the cell membrane area where the cells were grown. The DMEM+ medium contained sodium bicarbonate (10 mM) to optimize the pH buffering capacity.

value: Caco-2 (HTB-37)

tag: passage number

value: between 29-45

tag: growth

value: grown in a microfluidic device


title: RNA_UMCHOR1_PARENTAL_THZ1_00H_1


title: Caco-2 cells, grown in a microfluidic device, replicate 3


title: FaDu_KO1_Input

source_name: FaDu cells & S2 cells (spiked-in)

value: FaDu

value: Patient-derived head and neck squamous cell carcinoma cell line

value: NSD1 knock-out


title: FaDu_KO1_H3K27me3


title: 2_GM_21MO - IonXpress013

city: Munich

first: Moritz

middle: J

last: Rossner

address: Nussbaumstr. 7

department: Psychiatry

country: Germany

data_processing:
Barcode Splitting
Mapping to Mouse Genome
Raw Counts using Partek Flow Software
Normalisation using DESeq2
Differential Gene Expression (DESeq2)
Supplementary_files_format_and_content: text files with raw counts and normalised counts

extract_protocol:
microglia cells were isolated using CD11b microbeads by Magnetic separation with MS columns (MACS technology)
Libraries were generated for Ion Proton Sequencer

value: 21 Months

value: Grey Matter

tag: region

value: corpus callosum


title: 2_WM_21MO - IonXpress011

value: White Matter


title: Caco-2 cells, grown on Transwell inserts, replicate 2

source_name: Caco-2 cells, grown on a Transwell PET insert (0.4 µm pore size, 1.12 cm2 surface area) for 21 days

value: grown on a Transwell PET insert


title: Caco-2 cells, grown on Transwell inserts, replicate 4

source_name: Caco-2 cells, grown on a Transwell PET insert (0.4 µm pore size, 1.12 cm2 surface area) until 21 days


title: RNA_CH22_PARENTAL_THZ1_24H_2

source_name: CH22 Sacral chordoma cell line

value: CH22 Parental

value: Treated with 60 nM THZ1 for 24 hours


title: Caco-2 cells, grown in a microfluidic device, replicate 2


title: RNA_CH22_PARENTAL_THZ1_24H_3


title: Caco-2 cells, grown on Transwell inserts, replicate 1


title: 1_WM_21MO - IonXpress010


title: FaDu_RNA

source_name: FaDu cells

value: NSD1 wild-type


title: RNA_CH22_PARENTAL_THZ1_24H_1


title: Complete root meristem_rep3

city: Rosario

first: Ramiro

last: Rodriguez

address: Ocampo y Esmeralda

country: Argentina

institute: IBR

hyb_protocol: Following fragmentation, cRNA was hybridized on ATH1 Array. GeneChips were washed and stained according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with GC-RMA using default analysis settings.

organism: Arabidopsis thaliana

source_name: Complete root meristems obtained by microdissection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Arabidopsis thaliana accession Col-0 was used. Plants were grown in long photoperiods (16 h light/8 h dark) in solid medium containing 1× Murashige and Skoog salt mixture, 1% sucrose, and 2.3 mM MES (pH 5.8) in 1% agar. Seeds were placed in the dark at 4°C for 2 days. After stratification, the Petri dishes were placed in a vertical orientation inside growing chambers in continuous light condition.

extract_protocol: Total RNA was extracted using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific)

treatment_protocol: G2/M cells were obtained by FACS from roots expressing the CYCB1;1-GFP repoter, complete meristems were microdissected from root under a binocular microscope.

value: Root meristem

tag: cultivar


title: 2_GM_4MO - IonXpress009

tag: age


title: FaDu_Input


title: Caco-2 cells, grown on Transwell inserts, replicate 3


title: RNA_CH22_PARENTAL_THZ1_8H_3

tag: treatment

value: Treated with 60 nM THZ1 for 8 hours


title: Complete root meristem_rep2


title: FaDu_H3K27me3

value: H3K27me3 (Cell Signaling, 9733)


title: RNA_CH22_PARENTAL_THZ1_8H_2


title: Caco-2 cells, grown in a microfluidic device, replicate 1

value: Caco-2 (HTB-37)


title: FaDu_H3K36me2

value: H3K36me2 (Cell Signaling, 2901)


title: 1_GM_21MO - IonXpress012


title: 2_WM_4MO - IonXpress007


title: G2M cells_rep3

source_name: G2/M cells obtained by FACS from roots expressing CYCB1;1-GFP.

value: G2/M cells from roots


title: G2M cells_rep2


title: 1_WM_4MO - IonXpress006


title: Complete root meristem_rep1


title: G2M cells_rep1


title: Det562_KO4_RNA

source_name: Detroit-562 cells


title: FaDu_KO1_H3K36me2

value: FaDu


title: RNA_CH22_PARENTAL_0H_3

value: No treatment


title: Det562_KO4_Input

source_name: Detroit-562 cells & S2 cells (spiked-in)

value: Patient-derived head and neck squamous cell carcinoma cell line

value: NSD1 knock-out


title: RNA_CH22_PARENTAL_0H_2


title: RNA_CH22_PARENTAL_0H_1


title: 1_GM_4MO - IonXpress008

value: Grey Matter


title: Det562_KO4_H3K36me2


title: RNA_CH22_DTAG_T_THZ1_24H_3

value: Enginered cell ine derived from CH22 parental chordoma cell line


title: RNA_CH22_DTAG_T_THZ1_24H_2


title: Det562_KO2_Input


title: Det562_KO2_RNA


title: Det562_KO4_H3K27me3


title: Det562_KO2_H3K27me3


title: Det562_KO2_H3K36me2


title: RNA_CH22_DTAG_T_THZ1_24H_1


title: t10

city: Austin

first: Amy

last: Brock

address: 107 West Dean Keeton St.

institute: University of Texas at Austin

description: 10 weeks after doxorubicin treatment

data_processing:
The GTF file included with cellranger’s GRCh38 3.0.0 reference was modified to create a “pre-mRNA” GTF file so that pre-mRNAs would be included as counts in the later analysis.
Cellranger’s (v3.0.2) mkref command was then used to create a pre-mRNA reference from the GTF file and a genome FASTA file from the GRCh38 3.0.0 reference.
FASTQ files of the scRNA-seq libraries were then aligned to the new pre-mRNA reference using the cellranger count command, producing gene expression matrices.
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered cell barcodes and gene expression counts produced by cellranger

source_name: MDA-MB-231 cell line

extract_protocol:
Cryopreserved samples from drug-naïve and two samples of doxorubicin-treated cells frozen at 7 and 10 weeks post-treatment were harvested, sorted by FACS to collect the BFP+ population.
Cells were loaded into wells of a Chromium A Chip, and libraries were prepared using the 10XGenomics 3’ Single Cell Gene Expression (v2) protocol. Paired end (PE) sequencing of the libraries was conducted using a NovaSeq 6000 with an S1 chip (100 cycles) according to the manufacturer’s instructions (Illumina).

treatment_protocol: Cells were passaged into the center 60 wells of 96 well plates at a density of about 2000 cells per well. Two days later, cells were treated with a 24 hour pulse-treatment of doxorubicin at concentrations ranging from 0-1000 nM, with 6 replicates of each dose. Dosed media was applied to cells and treatment response was monitored using the Incucyte. After 24 hours, the dosed media was replaced with normal media and monitoring continued. Cells were fed fresh media every 2-3 days for the duration of the monitoring period (up to 5 weeks).

value: epithelial, adenocarinoma

tag: time point

value: 10 weeks

tag: agent

value: doxorubicin


title: RNA_CH22_DTAG_T_THZ1_8H_3


title: healthy donor2-4

city: shanghai

first: boke

last: zhang

address: 600 Yishan Road

institute: Shanghai Jiao Tong University Affiliated Sixth People's hospital

description:
4
Peripheral blood monocytes from healthy donor2 was treated by INT-HA, which was considered as experimental group

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

source_name: INT-HA-treated

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-2000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

tag: donor id

value: healthy donor2

value: peripheral blood monocytes

tag: treated with

value: 50 μg/ml INT-HA for 72 h


title: healthy donor3-8

description:
8
Peripheral blood monocytes from healthy donor3 was treated by INT-HA, which was considered as experimental group

value: healthy donor3


title: healthy donor3-7

description:
7
Peripheral blood monocytes from healthy donor3 was not treated by INT-HA, which was considered as negative control

source_name: INT-HA-untreated

value: none (untreated control)


title: healthy donor2-3

description:
3
Peripheral blood monocytes from healthy donor2 was not treated by INT-HA, which was considered as negative control


title: RNA_CH22_DTAG_T_THZ1_8H_2

value: Treated with 60 nM THZ1 for 8 hours


title: healthy donor1-2

description:
2
Peripheral blood monocytes from healthy donor1 was treated by INT-HA, which was considered as experimental group

value: healthy donor1