title: antiTNF_Responder_6 (DAS28 criteria)

description:
antiTNF_Responder_6
Immediately after arthroscopy biopsy, samples were kept in RNALater preservation agent and stored at -80ÂºC until extraction.
SAMPLE9

label_protocol: Standard Illumina hybridization protocol

value: male


title: pSNL rep2

status: Public on Jun 30 2020

type: SRA

city: Shenzhen

first: SHAO

middle: MIN

last: YANG

state: guangdong

address: Nanshan

department: Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center

country: China

institute: Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine

library_source: transcriptomic

data_processing:
CASAVA version 1.4 software used for basecalling.
The "dirty" raw reads as reads which contain the sequence of adaptor, high content of unknown bases and low quality reads were  removed, then mapped to Rattus_norvegicus whole genome using bowtie2 with parameters for PE reads: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 16 -k 200
Reads Per Kilobase of exon per Megabase of library size (RPKM) method was used in calculated expression level.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

molecule: total RNA

organism: Rattus norvegicus

source_name: dorsal root ganglia

extract_protocol:
DRG were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. BGIseq500 RNA library kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: dorsal root ganglia

tag: treatment

value: post pSNL day 7


title: antiTNF_Responder_5 (DAS28 criteria)

type: RNA

city: Barcelona

first: Antonio

last: Julià

state: Barcelona

address: c/ Baldiri Reixac nº15

department: Rheumatology Research Group

country: Spain

institute: Vall d'Hebron Hospital Research Institute

description:
antiTNF_Responder_5
Immediately after arthroscopy biopsy, samples were kept in RNALater preservation agent and stored at -80ÂºC until extraction.
SAMPLE6

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were log2 transformed and quantile normalized using R Bioconductor. Only microarray probes matching curated gene sequences from NCBI RefSeq database (release 51) were selected. A final number of 21,189 curated probes representing the expression of 18,524 different human genes were finally selected for analysis.

label: biotin

organism: Homo sapiens

extract_protocol: RNA was extracted using Quiagen Mini Kit Protocol in accordance with the described protocol. Dnase I treatment was used to remove genomic DNA traces.

tag: disease

value: Rheumatoid Arthritis fulfilling ACR/EULAR 2010 diagnostic criteria

tag: age

tag: anti-tnf response wk20

value: European League Against Rheumatoid Arthritis (EULAR) responder

tag: Sex

value: female


title: antiTNF_NONResponder_1 (DAS28 criteria)

description:
antiTNF_NONResponder_1
Immediately after arthroscopy biopsy, samples were kept in RNALater preservation agent and stored at -80ÂºC until extraction.
SAMPLE4

scan_protocol: Standard Illumina hybridization protocol

value: European League Against Rheumatoid Arthritis (EULAR) none responder


title: antiTNF_Responder_4 (DAS28 criteria)

description:
antiTNF_Responder_4
Immediately after arthroscopy biopsy, samples were kept in RNALater preservation agent and stored at -80ÂºC until extraction.
SAMPLE5


title: antiTNF_Responder_3 (DAS28 criteria)

description:
antiTNF_Responder_3
Immediately after arthroscopy biopsy, samples were kept in RNALater preservation agent and stored at -80ÂºC until extraction.
SAMPLE3


title: Fibroblast culture derived from primary lymph node FST97_

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

country: Germany

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

hyb_protocol: Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
Unsupported Human Gene 1.0 ST Array CDF Files
HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)

source_name: derived from primary lymph node

label_protocol: Samples were labelled with Encore biotin module (NUGEN) washed and stained using the HWS Kit (Affymetrix).

growth_protocol: Fib: IMDM, 20% FCS; bFGF 10ng/ml, 4-6 passages; L-428: RPMI; 10% FCS

extract_protocol: RNA was extracted with the RNeasy Micro Kit from Qiagen. 40ng of the total RNA was amplified using the Ovation Pico WTA System V2 from NUGEN.

treatment_protocol: Luteolin working concentration: 30 µM

tag: sample type


title: Fraction_21P

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

description:
Pellet of gradient
Fraction_21P

data_processing:
Adaptor clipping:cutadapt
Read mapping:READemption  align and segemehl
coverage calculationREADemption coverage
Genome_build: NC_000913.3
Supplementary_files_format_and_content: wiggle

organism: Escherichia coli

source_name: Clarified whole cell lysate

growth_protocol: Escherichia coli MG1655 was streaked on LB plates and grown overnight at 37°C. Overnight cultures of single colonies were grown in 2 ml LB at 37°C with shaking at 220 rpm. The next day, 1:100 dilutions in fresh LB of the overnight cultures were used to start the cultures for the experiments and grown to an OD600 nm of 2.0 (early stationary phase) at 37°C with shaking at 220 rpm.

extract_protocol:
Clarified lysates were centrifuged on a glycerol gradient, which was subsequently fractionated and the RNA extracted by P/C/I extraction. Input control was isolated using TRIzol reagent.
RNA was fragmented, and the 3' TruSeq adapter ligated to the 3' end. Following cDNA synthesis, the 5' TruSeq adapter was ligated to the 3' end and the resulting cDNA amplified by PCR.

tag: strain

tag: growth phase

value: Early stationary (OD 2.0)

tag: genotype

value: wild type


title: Fibroblast culture derived from primary lymph node KB36_


title: antiTNF_Responder_8 (DAS28 criteria)

description:
antiTNF_Responder_8
Immediately after arthroscopy biopsy, samples were kept in RNALater preservation agent and stored at -80ÂºC until extraction.
SAMPLE11


title: Fibroblast culture derived from primary lymph node KB34_


title: sham rep3

value: post sham day 7


title: Fibroblast culture derived from primary lymph node KB35_


title: antiTNF_NONResponder_3 (DAS28 criteria)

description:
antiTNF_NONResponder_3
Immediately after arthroscopy biopsy, samples were kept in RNALater preservation agent and stored at -80ÂºC until extraction.
SAMPLE8


title: sham rep1


title: Fraction_18


title: antiTNF_Responder_2 (DAS28 criteria)

description:
antiTNF_Responder_2
Immediately after arthroscopy biopsy, samples were kept in RNALater preservation agent and stored at -80ÂºC until extraction.
SAMPLE2


title: Fraction_17


title: antiTNF_Responder_1 (DAS28 criteria)

description:
antiTNF_Responder_1
Immediately after arthroscopy biopsy, samples were kept in RNALater preservation agent and stored at -80ÂºC until extraction.
SAMPLE1


title: pSNL rep1


title: shTet1-rep2 RNA-seq

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

country: USA

institute: Beckman Research Institute of City of Hope

description:
polyA RNA
rep2
processed data file: KnockDown_vs_Control.all.gene.result.xls

data_processing:
Sequence reads were aligned to the genome by using standard Illumina sequence analysis pipeline.
Genome_build: GRCm38
Supplementary_files_format_and_content: KnockDown_vs_Control.all.gene.result.xls: Excel file containing the expression and p value.

organism: Mus musculus

source_name: MLL-ENL-ERtm

extract_protocol:
RNA was extracted by using Qiazol reagent (Qiagen). NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used for polyA RNA purification.
Library was prepared by NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA).

tag: cell line

value: MLL-ENL-ERtm

tag: tumor

value: acute monocytic leukemia

tag: shRNA


title: shNS-rep3 RNA-seq

description:
polyA RNA
rep1
processed data file: KnockDown_vs_Control.all.gene.result.xls

value: shNS (non-specific control)


title: shTet1-rep3 RNA-seq


title: Fraction_10


title: Fraction_14


title: Fraction_11


title: shNS-rep2 RNA-seq


title: Fraction_08


title: Fraction_15


title: Fraction_16


title: Fraction_09


title: sham rep2


title: shNS-rep1 RNA-seq


title: shTet1-rep1 RNA-seq


title: Fraction_07


title: Fraction_04


title: Fraction_05


title: Fraction_12


title: Fraction_13


title: Fraction_02


title: Fraction_06


title: Fraction_01


title: Fraction_00L

description:
Input control
Fraction_00L


title: Non-injected control-1

city: Fukuoka

first: Kei

last: Miyamoto

address: 744 Moto-oka, Nishi-ku

department: Faculty of Agriculture

country: Japan

institute: Kyushu University

description:
A pool of 5 embryos at the 2-cell stage were subjected to cDNA synthesis
sample name in processed data file:
3_S3

data_processing:
Fastq files from Illumina sequencing were filtered for low quality reads by sliding window trimming (window size 10, <QV20), and low quality bases were trimmed from the ends of the reads (<QV20) using Trimmomatic. Reads less than 20 bases and unpaired reads were removed. Furthermore, adaptor, polyA, polyT and polyG sequences were removed using trim_galore and cutadapt.
The sequencing reads were then mapped to the mouse genome (mm10) using STAR. Reads on annotated genes were counted using featureCounts. FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

molecule: polyA RNA

source_name: Mouse 2-cell stage embryos

growth_protocol: After in vitro fertilization, embryos were cultured in potassium simplex optimized medium (KSOM) at 37°C under 5% CO2 until 2-cell stage (32 hours post insemination: 32 hpi).

extract_protocol:
After the removal of zona pellucida, embryos were washed with PBS containing 0.1% BSA, and then transferred to a 0.2 ml tube containing 9.5 μl of reaction buffer to make a final volume of 10.5 μl. After cell lysis in the buffer, 1 μl of the solution was removed and, instead, 1 μl of the diluted ERCC RNA Spike-In Mix was added (1:40,000 dilution; Thermo Fisher Scientific, 4456740). The lysed RNA solution with the spike-in RNA were subjected to reverse transcription.
The produced cDNA was amplified by PCR with 13 cycles. The amplified cDNA was purified using AMPure XP beads (BECKMAN COULTER, A63882). The purified cDNA was measured on the Bioanalyzer (Agilent) using High Sensitivity DNA Kit (5067-4626) and the normalized volume of DNA was subjected to library preparation using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024) by following the vendor’s instruction. The obtained library was quality-checked by Bioanalyzer and quantified using Qubit (Thermo Scientific). Paired end sequencing (50 bp + 25 bp) was carried out using the Illumina NextSeq system.

treatment_protocol: After insemination, fertilized embryos were collected at 2 hpi for mRNA injection. mRNAs were injected using a piezo manipulator (Prime Tech, Tsukuba, Japan).

tag: mice strain

value: ICR

tag: mrna injected

value: embryos

tag: developmental stage

value: 2-cell stage


title: R62D-2

description:
A pool of 5 embryos at the 2-cell stage were subjected to cDNA synthesis
sample name in processed data file:
5_S5

value: actinWT-HA-NLS


title: Fraction_03


title: Control 52

city: SANTIAGO DE COMPOSTELA

first: Laura

middle: Muinelo

last: Romay

state: A Coruña

address: Rua Magdalena 11, 3J

department: Liquid Biopsy Analysis Unit

institute: IDIS

description: Healthy donnor

hyb_protocol: Labeled cDNA was mixed with the Agilent hybridization master mix, incubated at 95ºC for 3 minutes. Afterwards, samples were dispensed onto 4x44K microarrays. For detailed methods see Agilent G4112-90000 protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:016528_D_F_20070525) to obtain Processed Signal intensities. The following features and/or genes which did not conform to the established quality criteria were filtered: i) non-uniform pixel distributed outliers and population replicate outliers according to the default Agilent feature extraction criteria; ii) features whose ratio between processed signal and its error was below 2; iii) spots not differentiated from background signal (as estimated for each spot). Normalization was done with the quantile method implemented in the Limma Bioconductor package.

source_name: Peripheral Blood

label_protocol: 1.65 µg of cDNA was ULS-Cy3 labeled following manufacturer instructions. Samples were incubated at 85ºC for 30 minutes. After removing non-reacted ULS, labeling degrees were evaluated as recommended. For detailed methods see Agilent G4112-90000 protocol.

extract_protocol: Circulating Tumor Cells (CTC) were immunoisolated from 7.5ml of peripheral blood from six metastatic colorectal patients. Blood was also obtained from three healthy donors. After immunoisolation, RNA was purified with the Qiamp Viral Mini kit (Qiagen) and globally amplified with a whole transcriptome amplification system (WTA2, Sigma-Aldrich). Final cDNA was purified by using the Qiaquick system (Qiagen).

value: Peripheral blood

tag: cell type

value: non-specific immunoisolated cellse:Peripheral blood


title: patien 13 progresion

description: Prostate cancer patient sample

tag: tissue

value: circulating tumor cells


title: Control 51

description: Healthy donnor


title: patient 24 progresion

description: Prostate cancer patient sample


title: patient 21 basal

description: Prostate cancer patient sample


title: patient 24 basal

description: Prostate cancer patient sample


title: ATAC-Seq_HiraKO_2

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

library_source: genomic

data_processing:
The mouse reference genome (GRCm38) and corresponding gene annotation were obtained from Illumina iGenome.
Reads for ATAC-Seq were first processed using Trim Galore 0.4.5, then aligned to mouse reference genome using bowtie 2-2.2.9.
Peak calling for ATAC-Seq was performed by using MACS 2.1.1 with default settings. To identify differential ATAC-Seq peaks between two conditions, we first called peaks by using MACS 2.1.1 after merging all related data, then counted the number of reads located within +/- 125 bp of peak summit with the multicov function of BEDTools. Finally, differential peak calling were performed by using DESeq2 (Love et al., 2014) with threshold: foldChange>2 and FDR<0.05.
Reads for RNA-Seq were aligned to the reference genome using STAR 2.5.3a with parameters: --outSAMstrandField intronMotif --outFilterType BySJout outFilterIntronMotifs RemoveNoncanonical.
To identify differentially expressed genes, we first obtained the read counts for each gene with htseq-count (Anders et al., 2015), then identified differential genes as foldChange>2 and FDR<0.05 using DESeq2  (Love et al., 2014). To visualize the expression profile of representative genes, we first quantified gene expression using RSEM 1.3.0 with parameters: --bowtie2 --calc-ci --ci-memory 1024. The calculated TPM (transcript per million) values were normalized using trimmed mean of M-values normalization (TMM) method. The normalized TPM values were used for visualization.
Genome_build: GRCm38
Supplementary_files_format_and_content: narrowPeak files for the peak calling results generated by using MACS2 for ATAC-Seq data .
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each gene as generated by using RSEM for RNA-Seq data.

molecule: genomic DNA

source_name: Hematopoietic stem and progenitor cells

extract_protocol:
Genomic DNA was extracted using standard methods.
ATAC-seq was performed as described (Buenrostro et al., 2015). In brief, transposed DNA fragments were amplified by PCR for 11 cycles after the transposition reaction and purification. The library quality was check by gel electrophoresis. Libraries were sequenced using paired-end sequencing on an Illumina Next seq500.

value: Bone marrow

value: Hematopoietic stem and progenitor cells

value: Hira conditional KO


title: Non-injected control-2

description:
A pool of 5 embryos at the 2-cell stage were subjected to cDNA synthesis
sample name in processed data file:
6_S6


title: patient 21 progresion

description: Prostate cancer patient sample


title: patient 13 basal

description: Prostate cancer patient sample


title: Wt-1

description:
A pool of 5 embryos at the 2-cell stage were subjected to cDNA synthesis
sample name in processed data file:
1_S1

value: Non-injected


title: Control 42

description: Healthy donnor


title: patient 17 basal

description: Prostate cancer patient sample


title: Control 40

description: Healthy donnor


title: patient 9 basal

description: Prostate cancer patient sample


title: patient 17 progresion

description: Prostate cancer patient sample


title: patient 11 basal

description: Prostate cancer patient sample


title: Control 53

description: Healthy donnor


title: patient 8 progresion

description: Prostate cancer patient sample


title: ATAC-Seq_WT_2

value: WT


title: Control 54

description: Healthy donnor


title: ATAC-Seq_HiraKO_1


title: 51-MB-A

city: London

first: Christopher

middle: Raja Socrates

last: Banerji

address: New Hunts House

department: Randall Division of Cell and Molecular Biophysics

country: United Kingdom

institute: King's College London

description:
FSHD9-MB
Primary_Myoblasts_Myotubes_gene_counts.txt

data_processing:
Raw reads were trimmed using trim-galore, utilising cutadapt14 (v0.4.0) to remove the Illumina Sequencing Adapter (AGATCGGAAGAGC) at the 3' end. Additionally, 12 bases were also trimmed from the 5' end, in both myoblast and LCL samples and 5 bases from the 3' end in the LCL samples, since they showed a biased distribution. Reads were mapped to the human transcriptome using the human genome sequence GRCh38 and v82 gene annotations downloaded from Ensembl. Mapping was performed using tophat 15 (v2.1.0) and bowtie 16 (v1.1.0), enabling the fr-firststrand option of tophat to restrict mapping to the sense strand of the transcript. Reads were assigned to genes using the featureCounts program 17 (v1.5.0), counting fragments and ignoring multi-mapping reads, and restricted to the sense strand. The resulting matrix of read counts was analysed using R. Data describing the myoblast and LCLs were processed in separate batches and therefore analysedas separate datasets. Both datasets were normalised using the DESeq2 package (71)in R.
Genome_build: GRCh38
Supplementary_files_format_and_content: Read count files

source_name: Human primary myoblasts

growth_protocol:
LCLs were obtained from NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research (CIMR) repository, NJ 08103, USA. Lymphoblastoid FSHD cell lines GSM16283, GSM16414, GSM16278 and respective matched control lines GSM16281, GSM16320,GSM16412 were from two directly related families from Southern Utah, USA. LCLs were cultured in suspension in RPMI-1640 medium, supplemented with L-glutamine, sodium bicarbonate (Sigma), 10% foetal bovine serum(FBS) (Sigma) and gentamycin (Gibco). Cell pellets were collected from three independent flasks for each cell line
Cell pellets corresponding to FSHD primary myoblast cell lines FSHD3 (FSHD1, 7RU, female), FSHD6 (FSHD1, 8RU, female) and FSHD9 (FSHD1, 7RU, male) alongside age and sex matched controls, in proliferation and after three days of differentiation into multinucleated myotubes, in singlet, were kind gifts from Dr Dalila Laoudj-Chenivesse (University of Montpellier, Montpellier, France).

extract_protocol:
RNA was isolated using miRNeasy kit (Qiagen) including a DNAse digestion step. RNA was analysed by LabChip Bioanalyzer, Qubit fluorometric quantification and Nanodrop quantification of concentration and stability
RNA-seq libraries were prepared using the sureselect stranded RNAseq protocol (Illumina), which allows polyA selection but was modified to work with ribodepletion (Agilent). Libraries were sequenced on an Illumina HiSeq2500

value: myoblast

tag: disease status

tag: gender

value: M

tag: matched control


title: R62D-1

description:
A pool of 5 embryos at the 2-cell stage were subjected to cDNA synthesis
sample name in processed data file:
2_S2


title: Wt-2

description:
A pool of 5 embryos at the 2-cell stage were subjected to cDNA synthesis
sample name in processed data file:
4_S4


title: ATAC-Seq_WT_1


title: patient 11 progresiton

description: Prostate cancer patient sample


title: 47-MB-A

description:
CTRL9-MB
Primary_Myoblasts_Myotubes_gene_counts.txt

value: Control

value: F


title: Patien 8 basal

description: Prostate cancer patient sample


title: 47-MT-A

description:
CTRL9-MT
Primary_Myoblasts_Myotubes_gene_counts.txt

source_name: Human primary myotubes

value: myotube


title: Patient 5 basal

description: Prostate cancer patient sample


title: 45-MT-A

description:
CTRL3-MT
Primary_Myoblasts_Myotubes_gene_counts.txt


title: 42-MT-A

description:
CTRL6-MT
Primary_Myoblasts_Myotubes_gene_counts.txt


title: 51-MT-A

description:
FSHD9-MT
Primary_Myoblasts_Myotubes_gene_counts.txt


title: 45-MB-A

description:
CTRL3-MB
Primary_Myoblasts_Myotubes_gene_counts.txt


title: patient 9 progresion

description: Prostate cancer patient sample


title: heart organoid ventricle section rep2

city: Tokyo

first: Akito

last: Sutani

address: 1-5-45, Yushima, Bunkyo-ku

institute: Tokyo Medical and Dental University

data_processing:
Illumina NovaSeq6000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes counts and FPKM values for each Sample

source_name: heart organoids

extract_protocol:
Embryonic heart and heart organoids were dissected to atrial and ventricle section respectively, flash frozen in liquid nitrogen, and RNA was harvested using Quiagen All prep micro kit. Illumina TruSeq RNA Sample Prep Kit was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart organoids

tag: compartment

value: ventricle

tag: Stage


title: heart organoid ventricle section rep1


title: heart organoid atrial section rep3

value: atrial


title: heart organoid atrial section rep2


title: 38-MT-A

description:
FSHD3-MT
Primary_Myoblasts_Myotubes_gene_counts.txt


title: Patient 2 basal

description: Prostate cancer patient sample


title: 41-MB-A

description:
FSHD6-MB
Primary_Myoblasts_Myotubes_gene_counts.txt


title: Patien 5 progresion

description: Prostate cancer patient sample


title: Patient 2 progresion

description: Prostate cancer patient sample


title: 38-MB-A

description:
FSHD3-MB
Primary_Myoblasts_Myotubes_gene_counts.txt


title: embryonic heart ventricle section rep3

source_name: embryonic heart

value: embryonic heart


title: embryonic heart ventricle section rep2


title: embryonic heart ventricle section rep1


title: 414C

description:
GSM16414 – repeat 3
Lympoblast_gene_counts.txt

source_name: Human immortalised Lymphoblastoid Cell line

value: LCL


title: heart organoid ventricle section rep3


title: embryonic heart atrial section rep3


title: 414B

description:
GSM16414 – repeat 2
Lympoblast_gene_counts.txt


title: 42-MB-A

description:
CTRL6-MB
Primary_Myoblasts_Myotubes_gene_counts.txt


title: 41-MT-A

description:
FSHD6-MT
Primary_Myoblasts_Myotubes_gene_counts.txt


title: heart organoid atrial section rep1


title: 414A

description:
GSM16414 – repeat 1
Lympoblast_gene_counts.txt


title: 412C

description:
GSM16412 – repeat 3
Lympoblast_gene_counts.txt


title: M1_RNA-seq

city: Qingdao

first: Jun-Jie

last: Wang

state: Shandong

address: Changcheng 700

department: Qingdao Agricultural University

institute: College of Life Sciences

description:
100 paired-end sequence reads
OocyteExpressionProfile.txt

data_processing:
The quantity control is performed to remove low-quality and adapter data with trimmomatic software (version 0.38).
The clean data are aligned to sheep reference genome with STAR (v2.7.1a).
The transcript assembly was performed to stringtie software (v2.0)
The expression levels of mRNA and lncRNA were calculated by featureCounts (v1.6.4)
DESeq2 package is used  to normalize expression levels of mRNAs and lncRNAs under R environment.
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: The single cell expression matrix is stored as tab-delimited text files after normalization.

organism: Ovis aries

source_name: MⅡ stage oocyte

extract_protocol:
The follicular oocytes of 2~8 mm were extracted from the washed ovaries, after settlement for a short time, the supernatant was removed, and cell pellet was resuspended with washing buffer for subsequent selection. Under stereoscopic microscope, the oocytes were divided into two classes, one is denuded oocyte (GV stage), other oocytes surrounded by granulosa cells (cumulus oocyte complexes, COCs)  were treated with hyaluronidase to remove cumulus cells, and cultured in vitro with maturation medium in a humidified incubator at 38.5 ℃ with 5% CO2 for 23-25 hours. The MⅡ stage oocytes were harvested with first polar body extrusion. The sequence samples were prepared with 30-35 oocytes as one biological repeat.
With high quality of RNA, an amount of 3 µg RNA each sample was used as input to prepare sequence. After removement of ribosomal RNA, the sequence libraries were generated with NEB Next® Ultra™ Directional RNA Library Prep Kit (NEB, USA) according to manufacturer’s recommendations, the quality of which was assessed with Agilent Bioanalyzer 2100 system. After samples clustering with TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions, sequence was conducted on Illumina Hiseq 2000 platform with 100 bp paired-end strategy.

value: Xinjiang Sheep

value: oocyte

value: MⅡ stage


title: 412B

description:
GSM16412 – repeat 2
Lympoblast_gene_counts.txt


title: DOs2_RNA-seq

source_name: GV stage oocyte

value: GV stage


title: 412A

description:
GSM16412 – repeat 1
Lympoblast_gene_counts.txt


title: normal brain tissue 2

city: Nanjing

first: Yali

last: Zhou

address: 22 Hankou Road

institute: Nanjing University

description: LncRNA and mRNA expression profiles from normal brain tissue

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45°C on GeneChip Human Transcriptome Array 2.0 in Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned by using Affymetrix® GeneChip Command Console (AGCC) which installed in GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

source_name: normal brain tissue

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA by using Ambion® WT Expression Kit.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: All tissues were collected right after resection in the operating room and quickly frozen in liquid nitrogen for 2-3 hours and stored at -80 °C.

value: brain


title: normal brain tissue 3


title: M3_RNA-seq


title: paired non-tumor tissue 2

description: LncRNA and mRNA expression profiles from paired non-tumor tissue

source_name: paired non-tumor tissue


title: paired non-tumor tissue 3


title: normal brain tissue 1


title: 320C

description:
GSM16320 – repeat 3
Lympoblast_gene_counts.txt


title: paired non-tumor tissue 1


title: glioblastoma multiforme tissue 3

description: LncRNA and mRNA expression profiles from glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue


title: embryonic heart atrial section rep1


title: 320B

description:
GSM16320 – repeat 2
Lympoblast_gene_counts.txt


title: 320A

description:
GSM16320 – repeat 1
Lympoblast_gene_counts.txt


title: TM5

city: Seoul

first: Ji Yeon

last: Kim

state: Nowon

address: 232 Gongneung-ro

department: Food science & technology

country: South Korea

institute: Seoul National Universiti of Science & Technology

description: Five-week-old mice were given freely diet and TM(Deep sea water sample) for three weeks. One week before sacrifice, colitis was caused by drinking  TM(Deep sea water sample) containing 5% of DSS.

data_processing:
bcl2fastq2 (Version 2.20) software used for basecalling.
Using bowtie to align RNA-seq data to reference genome(Mouse mm10) and get histogram for insert size
Using Tophat v2.0.13 to mapping the read to reference(mm10) and generate bam files.
Fragments Per Kilobase of transcript per Million(FPKM) was calculated from mapped reads using cufflinks v2.2.0.
Genome_build: mm10
Supplementary_files_format_and_content: "expression.csv.gz" contains FPKM values for genes, "mouse.mm10feature_table.txt.gz" contains metadata for genes, "mapping_stats.csv.gz" contains the number and percentages of reads mapped for each samples

source_name: Colon

extract_protocol:
Colons were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Clontech TruSeq Stranded Total RNA H/M/R Prep kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BALB/c

value: colon

tag: age

value: 5 week old

value: wild type


title: TM8

tag: strain


title: TM6


title: E283-14

city: Saskatoon

first: Sheng

address: 107 Wiggins Road

department: Biochemistry, Microbiology and Immunology

country: Canada

institute: University of Saskatchewan

data_processing:
Trimming using Trimmomatics-0.32
Read mapping using STAR-2.4.0j
Alignment using StringTie-1.0.3
Raw counts using htseq-count-0.6.0
Differentially expression analysis using DESeq2 1.12.4
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited .csv files include annotation and normalized counts for each sample

organism: Arabidopsis thaliana

source_name: Leaves

growth_protocol: Arabidopsis thaliana Col-0 WT and ubc22 plants were grown at 22 ℃ with a 16-h photoperiod of ~100 μmol m-2min-1.

extract_protocol:
Total RNA was isolated from leaves at 3-week stage using TRIzol reagent (Invitrogen)
Fifteen cDNA libraries were constructed using the TruSeq RNA Sample Preparation Kit v2 (Illumina) using RNAs from Type I, Type II, Type III, Type IV ubc22 mutant and also WT plants, with three biological replicates for each type.

value: Leaves

value: 21-day old plants

tag: phenotype

value: Type IV


title: TM3

tag: genotype


title: DOs3_RNA-seq


title: TM7


title: E283-15


title: Untreated urethra at 72 hrs post VD-2

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then Human samples were mapped to NCBI reference GRCh38 and Rat samples to NCBI reference Rnor_6.0 whole genome using Hisat2 v2.0.5
Read summarization was performed by the program featureCounts v1.5.0-p2 as part of the SubRead package using the NCBI Homo sapiens Annotation release 106.
Counts Per Million (CPM) values were generated through the edgeR Library v3.16.5 in R
Genome_build: GRCh38 and Rnor_6.0
Supplementary_files_format_and_content: rawCounts.csv: counts as generated by featureCounts, rows are gene features, columns are samples
Supplementary_files_format_and_content: normalizedCounts.csv:remove counts that were all zeroes (across the full set); Perform TMM normalization ; export log2(n+0.25) CPM

source_name: rat Urethral tissue

growth_protocol: in vivo

extract_protocol:
Urethral tissues were cryo-sectioned and counter stained with DAPI. We collected urethral tissue from untreated controls with a Leica LMD6 laser microdissection microscope.. In hMSC treated tissues, sections containing PKH positive cells (hMSC treatment group only) were identified and PKH stained cells were captured. We next captured urethral tissue adjacent to captured hMSC positive area and devoid of stained hMSC as a separate sample.
RNA libraries were prepared for sequencing using the Illumina TruSeq Stranded Total RNA - Globin kit.

treatment_protocol: Saline injection

value: rat Urethral tissue

tag: growth

value: in vivo

tag: treatment

value: Saline injection


title: DOs1_RNA-seq


title: Untreated urethra at 72 hrs post VD-1


title: E283-13


title: Untreated urethra at 72 hrs post VD-3


title: HMLS8

description: Five-week-old mice were given freely diet and HMLS(Deep sea water sample) for three weeks. One week before sacrifice, colitis was caused by drinking  HMLS(Deep sea water sample) containing 5% of DSS.


title: Untreated urethra at 36 hrs post VD-3


title: glioblastoma multiforme tissue 2


title: E283-12

value: Type III


title: HMLS7


title: Untreated urethra at 36 hrs post VD-2


title: 283A

description:
GSM16283 – repeat 1
Lympoblast_gene_counts.txt

value: LCL

value: F


title: HMLS6


title: 283C

description:
GSM16283 – repeat 3
Lympoblast_gene_counts.txt


title: 281C

description:
GSM16281 – repeat 3
Lympoblast_gene_counts.txt

value: Control


title: Untreated urethra at 36 hrs post VD-1


title: HMLS3


title: E283-10


title: glioblastoma multiforme tissue 1


title: Untreated urethra at 24 hrs post VD-3


title: DSS7

description: Five-week-old mice were given freely diet and distilled water for three weeks. One week before sacrifice, colitis was caused by drinking distilled water containing 5% of DSS.


title: E283-9

value: Type II


title: Untreated urethra at 24 hrs post VD-2


title: 281B

description:
GSM16281 – repeat 2
Lympoblast_gene_counts.txt


title: E283-8


title: 281A

description:
GSM16281 – repeat 1
Lympoblast_gene_counts.txt


title: DSS6


title: 283B

description:
GSM16283 – repeat 2
Lympoblast_gene_counts.txt


title: 278C

description:
GSM16278 – repeat 3
Lympoblast_gene_counts.txt

value: M


title: DSS5


title: Untreated urethra at 24 hrs post VD-1


title: E283-7


title: DSS2


title: E283-6

value: Type I


title: 278B

description:
GSM16278 – repeat 2
Lympoblast_gene_counts.txt


title: Untreated urethra at 12 hrs post VD-2


title: Untreated urethra at 12 hrs post VD-3


title: E283-11


title: 278A

description:
GSM16278 – repeat 1
Lympoblast_gene_counts.txt


title: DSS1

value: BALB/c


title: E283-5


title: CON8

description: Five-week-old mice were given freely diet and distilled water for three weeks.

value: colon


title: MSC treated urethra at 72 hrs post VD-3

treatment_protocol: 1x106 PKH-labelled hMSCs through the anterior wall of the vagina and into the periurethral space


title: Untreated urethra at 12 hrs post VD-1


title: E283-4


title: MSC captured from urethra at 72 hrs post VD-2

source_name: human Mesenchymal Stem Cell

growth_protocol: Human hMSCs were isolated from bone marrow aspirated from the iliac crest of a informed and consenting 49 year old, healthy female human donor, under a protocol approved by the Institutional Review Board (IRB) at University Hospitals of Cleveland (IRB 09-90-195, approved 3 December 2012). Human MSCs were cultured in low-glucose DMEM + 10% MSC qualified FBS until passage four then labeled with PKH red fluorescent dye.

treatment_protocol: No treatment

value: human Mesenchymal Stem Cell


title: MSC captured from urethra at 72 hrs post VD-3


title: MSC treated urethra at 72 hrs post VD-2


title: CON6

value: 5 week old

value: wild type


title: MSC captured from urethra at 36 hrs post VD-3


title: E283-3

value: Leaves

value: 21-day old plants

value: WT


title: CON5


title: E283-2


title: MSC captured from urethra at 72 hrs post VD-1


title: CON7


title: MSC treated urethra at 72 hrs post VD-1

value: rat Urethral tissue


title: CON4


title: MSC captured from urethra at 36 hrs post VD-2


title: E283-1


title: MSC captured from urethra at 36 hrs post VD-1


title: MSC treated urethra at 36 hrs post VD-3


title: MSC treated urethra at 36 hrs post VD-2


title: M2_RNA-seq

description:
100 paired-end sequence reads
OocyteExpressionProfile.txt

value: Xinjiang Sheep

value: oocyte

value: MⅡ stage


title: MSC treated urethra at 36 hrs post VD-1


title: CON2


title: MSC captured from urethra at 24 hrs post VD-3


title: A thaliana, HD, rep2, TAP-

city: Norwich

first: Tamas

last: Dalmay

address: Earlham Road

department: School of Biological Sciences

institute: University of East Anglia

data_processing:
the original fastq files were converted to fasta format and reads without Ns were kept for further analysis
the 3' adapters and HD signatures, for the HD samples, were trimmed and the files were converted from redundant to non-redundant format [Beckers et al 2017]
the reads were mapped to the reference genome, allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al 2008]
the reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
the abundances of the reads were normalized using the RPM method [Mortazavi et al 2008]
the differential expression was called on offset fold change, offset = 20
Genome_build: TAIR 10
Supplementary_files_format_and_content: csv, raw abundances

source_name: leaf

growth_protocol: the plants were grown in Panasonic Plant Growth Chambers set at 25 and 18°C ( day and night, respectively) with 16 hours of light

extract_protocol:
Leaf tissue was used for RNA extraction before small RNA library construction
Illumina compatible method using standard Illumina adapters

treatment_protocol: The TAP- libraries were created with the TAP step omitted; the TAP+ libraries were created with the TAP step. TAP removes the cap structure and other possible features from the 5’ end of RNA molecules by hydrolysing a phosphodiester bond and leaves RNA molecules with only one phosphate group in the 5'-end

value: TAP-

tag: adapters

value: HD


title: A thaliana, HD, rep1, TAP-


title: A thaliana, IL, rep2

value: TAP+

value: standard


title: embryonic heart atrial section rep2

value: embryonic heart

value: atrial


title: MSC treated urethra at 24 hrs post VD-3


title: CON1

value: BALB/c

value: colon


title: MSC captured from urethra at 24 hrs post VD-1

value: human Mesenchymal Stem Cell


title: MSC captured from urethra at 24 hrs post VD-2


title: A thaliana, IL, rep1


title: MSC treated urethra at 24 hrs post VD-2


title: MSC captured from urethra at 12 hrs post VD-3


title: MSC treated urethra at 24 hrs post VD-1


title: MSC treated urethra at 12 hrs post VD-3


title: A thaliana, HD, rep1


title: MSC captured from urethra at 12 hrs post VD-2


title: MSC treated urethra at 12 hrs post VD-2


title: MSC captured from urethra at 12 hrs post VD-1


title: Ara_nahg3

description: sRNA-seq

data_processing:
The original fastq files were converted to fasta format and reads without Ns were kept for further analysis.
The 3' adapter and HD signatures [Sorefan et al. 2012] were trimmed and the files were converted from redundant to non-redundant format.
The reads were mapped to the reference genome, allowing 0 mis-matches and 0 gaps using PatMaN [Pruffer et al. 2008].
The reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRBase, release 21.
The abundances of the reads were normalized using the RPM method [Mortazavi et al. 2008].
The differential expression was called on offset fold change on confidence intervals built on replicates, offset = 20.
Genome_build: TAIR10
Supplementary_files_format_and_content: *.csv: Comma-separated text files include sequences and expression levels.

source_name: leaves, nahG overexpressed

growth_protocol: The plants were grown in soil (12 plants/plastic box) at 22°C, 8 h photoperiod, 120 umol/m2/s light intensity, 75% relative humidity for 4 weeks in a growth chamber.

extract_protocol:
RNA was extracted from the youngest leaves of 4-week-old plants using a Viogene RNA extraction kit.
We used a modified version of the ScriptMiner kit, using HD adapters [Sorefan et al. 2012] and TruSeq index primers.

treatment_protocol: Reduced level of compounds was achieved through genetic mutations (vtc2-1 and pad2-1) or a transgene (nahG). pad2-1 deficient in glutathione because of the mutation in the gene encoding the first enzyme (gamma-glutamylcysteine synthetase) of glutathione synthesis. It contains 20-25% of the glutathione detected in wild type. vtc2-1 deficient in ascorbate because of the mutation in the gene encoding GDP L-galactose phosphorylase which is involved  in ascorbate synthesis. It contains 25-30% of the ascorbate detected in wild type. nahG overexpresses the gene encoding salicylate hydroxylase involved in the degradation of salicylate to catechol. It contains 30-40% of salicylate present in wild type plants

tag: genotype/variation

value: nahG transgene

value: 4 weeks

value: leaves

tag: replicate


title: Ara_nahg1

description: sRNA-seq


title: Ara_nahg2

description: sRNA-seq


title: MSC treated urethra at 12 hrs post VD-1


title: CON3

value: 5 week old

value: wild type


title: BCG_D19_GMP_BM_D90

city: Bonn

first: Branko

last: Cirovic

address: Carl-Troll Str 31

institute: LIMES

data_processing:
raw data was converted and multiplexed using bcl2fastq2 (v2.20).
reads were aligned to human reference transcriptome hg38 from UCSC and transcript abundance quantified using kallisto (v0.440) with default parameters.
abundance measurements were imported into R using tximport (v1.8.0).
for further filtering transcripts were removed not matching HGNC gene symbols, read sum lower than 10 across all samples or corresponding antisense, LINC or pseudogenes.
filtered data was imported into the DESeq2 package (v1.20.0) in R to generated a normalized expression table.
Genome_build: hg38
Supplementary_files_format_and_content: vst-transformed expression table from DESeq2 containing all samples.

source_name: bone marrow

extract_protocol:
total RNA was isolated from FACS-sorted populations using Qiazol (QIAGEN GmbH, Germany) and the miRNeasy Micro Kit (QIAGEN GmbH, Germany).
libraries were constructed from 1ng total RNA following the QIAseq FX Single Cell RNA Library Kit protocol (QIAGEN GmbH, Germany).

value: GMP

tag: timepoint

tag: condition

value: BCG

tag: donor

value: Homozygous TT


title: UK3_T

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

country: Switzerland

institute: UNIL

data_processing:
Read adapter was trimmed using cutadapt (https://cutadapt.readthedocs.io/en/stable/index.html v. 2.5, option ‘--match-read-wildcards’). Reads were retained if their length was between 26 and 35 (Ribosome profiling samples) or between 21 and 101 (Total RNA samples)
Reads were filtered for rRNA and tRNA contamination mapping them to human tRNA and human rRNA databases using bowtie2  (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml v. 2.3.5, options: -p 2 -L 15 -k 20)
Remaining reads were mapped to human cDNA database using bowtie2 (v 2.3.5, options: -p 2 -L 15 -k 20 --no-unal)
Expression analysis was carried out using Salmon (https://salmon.readthedocs.io/en/latest/index.html v 0.13.0) using trimmed, filtered reads
For ribosome profiling, reads counts was performed using an in-house script (https://github.com/talponer/filterBam/blob/master/bed2counts)
Genome_build: GRCh38.p10, ENSEMBL 89
Supplementary_files_format_and_content: transcript counts, TXT

source_name: UPF1 KD 03 – total RNA seq

extract_protocol:
ribosome-protected fragments were isolated after snap-freezing of HeLa cells and Rnase I digestion using gel filtration columns. Gel purified fragments between 26 nt and 34 nt were isolated, rRNAs were removed using the RiboZero kit (Illumina). RNA-seq libraries were prepared from cells lysed similar as the ribosome profiling samples. totalRNAs was isolated from cleared lysates by addition of TriReagent as for the ribosome-protected fragments.
Sequencing libraries from ribosome footprints were generated as previously described (Aeschimann et al., 2015).  Total RNA was used for library generation with the TruSeq Stranded mRNA Library Prep Kit (Illumina).
Libraries were sequenced on an Illumina HiSeq2500 generating 100 nt single-end reads.

treatment_protocol: siRNA transfection with Lullaby (Ozscience) for 72 hours, two siRNA transfections (20 nM)

tag: cell line

value: HeLa cells

tag: sirna

value: UPF1 knockdowns


title: Ara_vtc3

description: sRNA-seq

source_name: leaves, ascorbate deficient

value: vtc2-1 mutation

tag: tissue


title: UK2_T

source_name: UPF1 KD 02 – total RNA seq


title: Ara_vtc2

description: sRNA-seq


title: UK1_T

source_name: UPF1 KD 01 – total RNA seq


title: BCG_D19_GMP_BM_D0

tag: cell type


title: BCG_D9_GMP_BM_D90

value: Heterozygous CT


title: BCG_D9_GMP_BM_D0


title: A thaliana, HD, rep2

value: TAP+

value: HD


title: Wild-type rep2

first: Jung-Woong

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

institute: Chung-Ang University

data_processing:
Illumina Casava software used for basecalling.
Sequenced read were trimmed for adaptor sequence, and masked for low-quality sequence using systempipeR.
Alignment to GRCh38.97 whole genome with Rsubread 1.34.6 and read feature counting with DESeq2.
Normalized by voom function from limma and edgeR.
FPKM were calculated using a fpkm function from DESeq2 and differential gene expression by edgeR.
Genome_build: GRCh38.97
Supplementary_files_format_and_content: txt files include raw counts, normalized counts(FPKM)

growth_protocol: We established stable KO cell line for Smug1 gene. Smug1-KO HepG2 cells were cultured with DMEM with 10% FBS.

extract_protocol:
Total RNA was extracted using Trizol reagent and mRNA was extracted by mRNA pull-down using poly-A tagged bead.
RNA libraries were prepared for sequencing using standard Truseq RNA Illumina protocols.

treatment_protocol: The cells were not treated with chemicals in both control and KO groups.


title: Smug1-KO rep1

value: Smug1 knock-out


title: Ara_pad1

description: sRNA-seq

source_name: leaves, glutathione deficient

value: pad2-1 mutation


title: BCG_D6_GMP_BM_D0


title: Smug1-KO rep2


title: Ara_pad3

description: sRNA-seq


title: BCG_D6_GMP_BM_D90


title: Wild-type rep1


title: Ctrl_D18_GMP_BM_D90

value: Ctrl

value: Homozygous CC


title: Ara_col3

description: sRNA-seq

source_name: leaves, wild type

value: 4 weeks


title: RNA Control Donor 6 Rep3

city: Sydney

first: Charles

last: Bailey

state: NSW

address: Missenden Rd, Building 93

country: Australia

institute: Centenary Institute

description:
rep3
CA69MANXX_3_160729_FR07887230

data_processing:
The RNA-seq data passed the quality control conducted using FastQC and MulitQC
Sequencing reads were mapped to the human reference genome GRChg38 using STAR aligner
Differentially gene expression analysis was performed using the Bioconductor package DESeq2; genes with low read counts (<5) were removed from the analysis
Differential alternative splicing was anlayzed using rMATS, IRFinder, and DEXSeq
Gene expression levels specified as TPM were determined using Salmon 0.14.1
Fusion detection was performed using STAR-Fusion
Genome_build: hg38
Supplementary_files_format_and_content: countmatrix.txt contains count data for all genes in each sample

source_name: PBMCs

extract_protocol:
total RNA using TRIzol
TruSeq Stranded RNA sample prep kit (Illumina)

tag: disease

value: Healthy Control

tag: Stage

value: adult


title: Ctrl_D18_GMP_BM_D0


title: Ara_col2

description: sRNA-seq

value: wild type

tag: age

value: leaves


title: BCG_D16_GMP_BM_D90

value: GMP

value: BCG


title: Ara_pad2

description: sRNA-seq


title: RNA Control Donor 6 Rep2

description:
rep2
CA69BANXX_2_160729_FR07887230


title: Ara_col1

description: sRNA-seq


title: RNA Control Donor 6 Rep1

description:
rep1
CA69BANXX_1_160729_FR07887230


title: Plate_JM8

city: New York

first: Vilas

last: Menon

state: NY

department: Neurology

institute: Columbia University Medical Center

description:
compiled_data.csv
compiled_data_erccs.csv

data_processing:
Adaptor sequences (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were removed from Read 2 using Trimmomatic 0.36
Trimmed reads (from Read 2) were mapped using STAR 2.5.3a to the Ensembl mouse genome GRCm38.p5, release 90. Unaligned reads were subsequently aligned to standard ERCC (spike-in) reference sequences.
Cell barcodes (first 8 nucleotides) and Unique Molecular Identifiers (subsequent 10 nucleotides) were extracted from Read 1, and appended as additional fields to the aligned Read 2 bam file using Dropseqtools
Distinct exonic UMIs were counted for each gene in each cell, allowing for 1 mismatch, using standard Dropseqtools parameters. The final cell-by-gene counts were tallied into a full counts table
Genome_build: GRCm38.p5, release 90
Supplementary_files_format_and_content: STAR 2.5.3a quantification output, expressed as counts of Unique Molecular Identifiers for every gene in every cell

source_name: Labelled neurons from PVH

growth_protocol: We used male offspring mice of the Agrp-IRES-Cre (Jackson Labs Stock 012899, Agrptm1(cre)Lowl/J) line crossed with Ai9 (Jackson Labs Stock 007909, B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J) mice (> 7 weeks) to isolate tdTomato positive neurons.

extract_protocol:
For each sample, individual labelled cells were isolated by manual cell picking on a fluorescence dissecting scope, after incubating slices in ACSF with neuronal activity blockers (TTX, APV, DNQX) and pronase for 50 minutes. Each isolated cell was transferred to a 0.2mL PCR 8-tube strip containing 3 microliters of lysis buffer (0.2% Triton X-100) in Nuclease-free water with RNase inhibitor. Each 8-tube strip was flash frozen on dry ice and kept at -80C until library prep and sequencing.
Each single cell underwent the RT process, and cDNA was then pooled before amplification, using the SMART-SCRB technique (using SMARTer-based amplification with cell barcodess). Amplified cDNA was fragmented to ~250bp, ligated to Illumina sequencing adaptors with Encore Rapid kit, and sequenced on an Illumina HiSeq 2500 with 4-fold multiplexing (paired end, 25bp for Read 1 and 125bp for Read 2)

tag: fluorescent reporter

value: tdTomato


title: RNA Control Donor 5 Rep3

description:
rep3
CA69MANXX_3_160729_FR07887223


title: Plate_JM7


title: BCG_D16_GMP_BM_D0


title: BCG_D21_GMP_BM_D0


title: BCG_D15_GMP_BM_D90


title: RNA Control Donor 5 Rep2

description:
rep2
CA69BANXX_2_160729_FR07887223


title: Plate_JM6


title: RNA Control Donor 5 Rep1

description:
rep1
CA69BANXX_1_160729_FR07887223


title: Plate_JM5


title: Plate_AL6


title: RNA Control Donor 4 Rep3

description:
rep3
CA69MANXX_2_160729_FR07887216


title: BCG_D15_GMP_BM_D0


title: RNA Control Donor 4 Rep2

description:
rep2
C9JCFANXX_4_160729_FR07887216


title: Plate_Q8


title: Ctrl_D13_GMP_BM_D0


title: Plate_Q7


title: Ctrl_D13_GMP_BM_D90


title: Plate_AL5


title: BCG_D14_GMP_BM_D90


title: Plate_Q6


title: RNA Control Donor 4 Rep1

description:
rep1
C9JCFANXX_3_160729_FR07887216


title: RNA Control Donor 3 Rep2

description:
rep2
C9JCFANXX_4_160729_FR07887209


title: RNA Control Donor 2 Rep3

description:
rep3
CA69MANXX_1_160729_FR07887202


title: RNA Control Donor 3 Rep1

description:
rep1
C9JCFANXX_3_160729_FR07887209


title: BCG_D21_GMP_BM_D90


title: RNA Control Donor 2 Rep2

description:
rep2
C9JCFANXX_2_160729_FR07887202


title: BCG_D14_GMP_BM_D0


title: BCG_D10_GMP_BM_D90

value: Homozygous TT


title: Plate_Q5


title: BCG_D10_GMP_BM_D0


title: RAD51 B6 #2

city: Oxford

first: Anjali

middle: Gupta

last: Hinch

address: Roosevelt Drive

department: WCHG

institute: Oxford University

data_processing:
Alignment with a modified BWA mapper (Khil et al., 2012)
Peaks were called using an in-house algorithm R code available at https://github.com/anjali-hinch/hybrid-rescue
Alleles were called using an in-house algorithm (described in Hinch et al)
[Third-party reanalysis] H3K4me3 and SPO11 measurements
Filtering of false-positive hotspots and overlap with PRDM9-independent H3K4me3 were performed using in-house algorithm (Hinch et al)
Genome_build: mm10
Supplementary_files_format_and_content: text file with column descriptions in commented header; each line corresponds to one hotspot

source_name: whole adult testis

growth_protocol: Data were generated from in vivo tissue samples from adult male mice - no culturing was performed.

extract_protocol:
Testes samples were stripped of the tunica and processed as described in Khil et al, Genome Research, 2012). Single-stranded DNA sequencing and double-strand break detection were performed using a modified ssDNA ChIPseq protocol. Full experimental procedures are reported in accompanying manuscript (Hinch et al).
Libraries were prepared according to Illumina's instructions

tag: strain

value: testis

tag: prdm9 genotype


title: Ctrl_D3_GMP_BM_D0


title: RAD51 B6 #1


title: RNA Control Donor 1 Rep2

description:
rep2
C9JCFANXX_2_160729_FR07887195


title: Ctrl_D3_GMP_BM_D90


title: BCG_D17_GMP_BM_D90

value: Heterozygous CT


title: RNA Control Donor 2 Rep1

description:
rep1
C9JCFANXX_1_160729_FR07887202


title: RPA B6


title: RPA B6CASTF1 PRDM9hc

value: HUM/CAST


title: RNA Control Donor 1 Rep3

description:
rep3
CA69MANXX_1_160729_FR07887195


title: BCG_D17_GMP_BM_D0


title: RNA Diagnosis Patient 27 Rep3

description:
rep3
CA69MANXX_3_160729_FR07887237

value: Chronic Myeloid Leukemia

value: chronic phase


title: RNA Control Donor 1 Rep1

description:
rep1
C9JCFANXX_1_160729_FR07887195


title: RAD51 B6CASTF1 PRDM9hc


title: RNA Diagnosis Patient 27 Rep1

description:
rep1
CA69BANXX_1_160729_FR07887237


title: F4: FosB knockout

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing reads from mice were mapped to mm9 using TopHat (Trapnell, C. et al.)
Counts of reads mapping to genes were obtained using HTSseq-counts (Anders, S. et al.) software against Gencode vM1 (mm9) annotation
Differential expression was done using the DESeq2 (Love, M. I. et al.) package
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file

source_name: Brain (pooled from n=3 mice)

extract_protocol:
Three weeks following injection of retrograde HSV-Cre into NAc, Cre-dependent L10-GFP-expressing mice (Rosa26eGFP/L10a ) were sacrificed and brains were immediately dissected into 1 mm coronal sections. Transduced tissue from ventral hippocampi (vHPC) of both wildtype and FosBfl/fl mice was collected using 14 gauge biopsy punches guided by a fluorescent dissecting microscope (Leica) and stored at -80 C until processing (n = 3/group, 3-4 mice pooled per n).  Polyribosome-associated RNA was affinity purified as  described: Briefly, tissue was homogenized in ice-cold tissue-lysis buffer (20 mM HEPES [pH 7.4], 150 mM KCl, 10 mM MgCl2, 0.5 mM dithiothreitol, 100 µg/ml cycloheximide, protease inhibitors, and recombinant RNase inhibitors) using a motor-driven Teflon glass homogenizer. Homogenates were centrifuged for 10 min at 2000 g (4° C), supernatant was supplemented with 1% NP-40 (AG Scientific, #P1505) and 30 mM DHPC (Avanti Polar Lipids, #850306P), and centrifuged again for 10 min at 20000 g (4°C). Supernatant was collected and incubated with Streptavidin MyOne T1 Dynabeads (Invitrogen, #65601) that were coated with anti-GFP antibodies (Memorial Sloan-Kettering Monoclonal Antibody Facility; clone names: Htz-GFP-19F7 and Htz-GFP-19C8, 50 ug per antibody per sample) using recombinant biotinylated Protein L (Thermo Fisher Scientific, # 29997) for 16-18 h on a rotator (4° C) in low salt buffer (20 mM HEPES [pH 7.4], 350 mM KCl, 1% NP-40, 0.5 mM dithiothreitol, 100 µg/ml cycloheximide). Beads were isolated and washed with high salt buffer (20 mM HEPES [pH 7.4], 350 mM KCl, 1% NP-40, 0.5 mM dithiothreitol, 100 µg/ml cycloheximide) and RNA was purified using the RNeasy Micro Kit (Qiagen, #74004). In order to increase yield, each RNA sample was initially passed through the Qiagen MinElute™ column 3 times. Following purification, RNA was quantified using a Qubit fluorometer (Invitrogen) and RNA quality was analyzed using a 4200 Agilent Tapestation (Agilent Technologies). cDNA libraries from 5 ng total RNA were prepared using the SMARTer® Stranded Total RNA-Seq Kit (Takara Bio USA, #635005), according to manufacturer’s instructions. cDNA libraries were pooled following Qubit measurement and TapeStation analysis, with a final concentration ~7 nM. Sequencing was performed at the Icahn School of Medicine at Mount Sinai Genomics Core Facility (https://icahn.mssm.edu/research/genomics/core-facility).
cDNA libraries from 5 ng total RNA were prepared using the SMARTer® Stranded Total RNA-Seq Kit (Takara Bio USA, #635005), according to manufacturer’s instructions.

value: Hippocampus neurons

tag: genotype

value: FosB knockout


title: F4input: FosB knockout


title: BCG_D1_GMP_BM_D90


title: F3input: FosB knockout


title: RNA Diagnosis Patient 21 Rep3

description:
rep3
CA69MANXX_3_160729_FR07887231


title: BCG_D1_GMP_BM_D0


title: RNA Diagnosis Patient 27 Rep2

description:
rep2
CA69BANXX_2_160729_FR07887237


title: RNA Diagnosis Patient 21 Rep2

description:
rep2
CA69BANXX_2_160729_FR07887231


title: BCG_D12_GMP_BM_D90


title: F2input: FosB knockout


title: BCG_D12_GMP_BM_D0


title: F3: FosB knockout


title: BCG_D8_GMP_BM_D90

value: Homozygous CC


title: F2: FosB knockout


title: BCG_D8_GMP_BM_D0


title: RNA Diagnosis Patient 17 Rep3

description:
rep3
CA69MANXX_3_160729_FR07887224


title: C3input: wildtype

value: wildtype


title: RNA Diagnosis Patient 17 Rep2

description:
rep2
CA69BANXX_2_160729_FR07887224


title: BCG_D2_GMP_BM_D90


title: BCG_D2_GMP_BM_D0


title: Ctrl_D7_GMP_BM_D0

value: Ctrl


title: C2: wildtype


title: C3: wildtype


title: Ctrl_D7_GMP_BM_D90


title: RNA Diagnosis Patient 17 Rep1

description:
rep1
CA69BANXX_1_160729_FR07887224

value: adult


title: C2input: wildtype


title: RNA Diagnosis Patient 15 Rep2

description:
rep2
C9JCFANXX_4_160729_FR07887221


title: C1input: wildtype


title: C1: wildtype


title: Ctrl_D11_GMP_BM_D90


title: RNA Diagnosis Patient 15 Rep1

description:
rep1
C9JCFANXX_3_160729_FR07887221


title: RNA Diagnosis Patient 13 Rep1

description:
rep1
C9JCFANXX_3_160729_FR07887219


title: RNA Diagnosis Patient 13 Rep3

description:
rep3
CA69MANXX_2_160729_FR07887219


title: BCG_D5_GMP_BM_D0


title: RNA Diagnosis Patient 13 Rep2

description:
rep2
C9JCFANXX_4_160729_FR07887219


title: BCG_D5_GMP_BM_D90


title: BCG_D20_GMP_BM_D90


title: RNA Remission Patient 11 Rep3

description:
rep3
CA69MANXX_3_160729_FR07887218

value: remission


title: Ctrl_D11_GMP_BM_D0


title: RNA Diagnosis Patient 21 Rep1

description:
rep1
CA69BANXX_1_160729_FR07887231


title: RNA Remission Patient 11 Rep2

description:
rep2
CA69BANXX_2_160729_FR07887218


title: S21Tm3

data_processing:
raw data was converted and multiplexed using bcl2fastq2 (v2.20).
reads were aligned to human hg19 index with bowtie1 (v1.1.1).
duplicates were filtered by applying the Picard (v1.134) tool.
removal of adapter offset and creation of bam files was done with samtools.
open chromatin peaks were called using MACS2  (v2.1.0.20140616).
blacklisted regions (ENCFF001TDO_hg19_blacklist.bed.gz) were excluded.
peaks were annotated using HOMER (applying annotatePeaks.pl). Downstream analysis was performed within the DESeq2 (v1.20.0) package environment.
Genome_build: hg19
Supplementary_files_format_and_content: filtered data was imported into the DESeq2 package (v1.20.0) in R to generated a normalized expression table. CSV file includes normalised peak count table.

source_name: MACS-enriched CD14+ monocytes

extract_protocol:
Samples for ATAC-seq analysis were prepared from CD14+-MACS-enriched monocytes from fresh PBMCs (Pan Monocyte Isolation Kit, Miltenyi Biotec). 50,000 cells were washed in cold PBS and resuspended in cold lysis buffer (10 mM NaCL, 3 mM MgCl2, 0.1 % IGEPAL, 10mM Tris-HCl pH7.4).
After centrifugation, pellets were incubated in primer-loaded transposase Tn5 in reaction buffer (10 mM TAPS-NaOH (pH 8.5) at 25°C, 5 mM MgCl2, 10% DMF) for 30 min at 37ºC. Samples were subsequently immediately purified using the MinElute kit (Qiagen GmbH) according to the manufacturer’s guidelines, eluted in 10 µl H2O and stored at -20 ºC until further processing.

value: blood

value: CD14+ monocytes


title: RNA Diagnosis Patient 15 Rep3

description:
rep3
CA69MANXX_2_160729_FR07887221


title: RNA Remission Patient 11 Rep1

description:
rep1
CA69BANXX_1_160729_FR07887218


title: S21Td0


title: RNA Diagnosis Patient 11 Rep3

description:
rep3
CA69MANXX_3_160729_FR07887217


title: S20Tm3


title: R848 challenge Donor 4-1

city: Palo Alto

first: Samuel

last: Yang

address: 1201 Welch Road

department: Emergency Medicine

institute: Stanford University School of Medicine

data_processing:
ATAC-seq peak calling was done using PEPATAC by including all Donor and Replicate fastqs for each challenge and control
Genome_build: hg19
Supplementary_files_format_and_content: Peaks called from Donor and Replicate merged fastqs, includes coverages

source_name: Healthy primary neutrophils challenged with R848 for 1 hour

extract_protocol:
ATAC-seq was performed as previously published and excess primers were removed using AMPpure bead kit.
Libraries generated using KAPA PolyA enrichment mRNA library prep

treatment_protocol: Neutrophils from healthy female voulnteers betewen 31-40 were challenged with 6 pathogen mimicking ligands and whole blood from vounteers were challenged with 2 whole organisms.

value: neutrophils


title: RNA Diagnosis Patient 11 Rep1

description:
rep1
CA69BANXX_1_160729_FR07887217


title: RNA Remission Patient 10 Rep3

description:
rep3
CA69MANXX_3_160729_FR07887227


title: LTA challenge Donor 4-2

source_name: Healthy primary neutrophils challenged with LTA for 1 hour


title: BCG_D20_GMP_BM_D0

value: GMP

value: BCG


title: LPS challenge Donor 4-2

source_name: Healthy primary neutrophils challenged with LPS for 1 hour


title: S17Tm3


title: S19Td0


title: RNA Diagnosis Patient 10 Rep3

description:
rep3
CA69MANXX_3_160729_FR07887226


title: RNA Remission Patient 10 Rep1

description:
rep1
CA69BANXX_1_160729_FR07887227


title: S17Td0


title: S16Tm3


title: RNA Remission Patient 10 Rep2

description:
rep2
CA69BANXX_2_160729_FR07887227


title: HMGB1 challenge Donor 4-2

source_name: Healthy primary neutrophils challenged with HMGB1 for 1 hour


title: R848 challenge Donor 4-2


title: Fig4_Tg_CD44hi_CD69hi_CD103hi_rep2

city: Yachiyo-City

first: Kota

last: Kokubo

state: Chiba

address: Yachiyodai-minami 1-10-12

department: Department of Immunology

institute: Chiba University

description:
without 7w resting phase
processed data file: Fig4_FPKM.csv

data_processing:
For RNA-Seq, read sequences (50 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using Bowtie (version 0.12.8) and TopHat (version 1.3.2).
Fragments per kilobase of exon per million mapped reads (FPKM) for each gene were calculated using Cufflinks (version 2.0.2).
For ATAC-Seq, read sequences (50 bp) were aligned to the mm9 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using Bowtie (version 0.12.8).
Bigwig files for each peaks were created by using samtools (version 1.3) and deeptools (version 3.2.0).
Genome_build: mm10 for RNA-Seq. mm9 for ATAC-Seq.
Supplementary_files_format_and_content: CSV files include FPKM values for each sample of RNA-Seq. And processed data of ATAC-Seq show in bigWig files.

source_name: CD44hi CD69hi CD103hi T cells in Foxp3-DTR Tg lung treated with Aspergillus antigen

growth_protocol: mice were intranasally treated with Aspergillus antigen 7weeks and rested as indicated in the 'description' field

extract_protocol:
Total cellular RNA was extracted with TRIzol reagent (Invitrogen). And total cellular DNA was extracted in accordance with Omni-ATAC protocol(Nature Methods volume 14, pages 959–962 (2017)).
For RNA-Seq, TruSeq Stranded mRNA Library Preparation Kit (Illumina) was used according to the manufacturer's protocol. For ATAC-Seq, library construction was done in accordance with Omni-ATAC protocol(Nature Methods volume 14, pages 959–962 (2017)).

tag: strain background

value: BALB/c

value: Foxp3-DTR Tg

tag: treatment

value: Aspergillus antigen

value: CD44hi CD69hi CD103hi T cells


title: RNA Diagnosis Patient 11 Rep2

description:
rep2
CA69BANXX_2_160729_FR07887217

value: Chronic Myeloid Leukemia

value: chronic phase


title: S16Td0


title: FLAG challenge Donor 4-2

source_name: Healthy primary neutrophils challenged with FLAG for 1 hour


title: HMGB1 challenge Donor 4-1


title: S14Tm3


title: S20Td0


title: RNA Diagnosis Patient 10 Rep2

description:
rep2
CA69BANXX_2_160729_FR07887226


title: Fig4_WT_CD44hi_CD69hi_CD103hi_rep2

source_name: CD44hi CD69hi CD103hi T cells in Wild type lung treated with Aspergillus antigen

tag: genotype/variation

value: Wild type


title: S19Tm3

tag: timepoint


title: Fig4_Tg_CD44hi_CD69hi_CD103low_rep2

source_name: CD44hi CD69hi CD103low T cells in Foxp3-DTR Tg lung treated with Aspergillus antigen

value: CD44hi CD69hi CD103low T cells


title: LTA challenge Donor 4-1


title: RNA Diagnosis Patient 10 Rep1

description:
rep1
CA69BANXX_1_160729_FR07887226


title: RNA Remission Patient 9 Rep3

description:
rep3
CA69MANXX_3_160729_FR07887215


title: FLAG challenge Donor 4-1


title: Fig4_Tg_CD44low_rep2

source_name: CD44low T cells in Foxp3-DTR Tg lung treated with Aspergillus antigen

value: CD44low T cells


title: Fig4_WT_CD44hi_CD69hi_CD103low_rep2

source_name: CD44hi CD69hi CD103low T cells in Wild type lung treated with Aspergillus antigen


title: LPS challenge Donor 4-1


title: S14Td0


title: RNA Remission Patient 9 Rep2

description:
rep2
CA69BANXX_2_160729_FR07887215


title: Fig4_Tg_CD44hi_CD69hi_CD103hi_rep1


title: S12Td0


title: S12Tm3


title: Control Donor 4-2

source_name: Healthy untreated neutrophils


title: Control Donor 4-1


title: RNA Remission Patient 9 Rep1

description:
rep1
CA69BANXX_1_160729_FR07887215


title: Fig4_WT_CD44hi_CD69hi_CD103hi_rep1


title: RNA Diagnosis Patient 9 Rep2

description:
rep2
CA69BANXX_2_160729_FR07887214


title: BGP challenge Donor 4-2

source_name: Healthy primary neutrophils challenged with BGP for 1 hour


title: BGP challenge Donor  4-1

source_name: Healthy primary neutrophils challenged with  BGP for 1 hour


title: Fig4_WT_CD44hi_CD69hi_CD103low_rep1


title: S10Tm3


title: R848 challenge Donor 3-2


title: Fig4_Tg_CD44hi_CD69hi_CD103low_rep1


title: RNA Remission Patient 8 Rep3

description:
rep3
CA69MANXX_2_160729_FR07887213

source_name: PBMCs


title: RNA Diagnosis Patient 9 Rep1

description:
rep1
CA69BANXX_1_160729_FR07887214


title: Fig4_Tg_CD44low_rep1


title: RNA Remission Patient 8 Rep2

description:
rep2
C9JCFANXX_4_160729_FR07887213


title: S9Td0


title: R848 challenge Donor 3-1


title: RNA Remission Patient 8 Rep1

description:
rep1
C9JCFANXX_3_160729_FR07887213


title: Fig4_WT_CD44low_rep2

source_name: CD44low T cells in Wild type lung treated with Aspergillus antigen


title: Fig4_WT_CD44low_rep1


title: RNA Diagnosis Patient 9 Rep3

description:
rep3
CA69MANXX_3_160729_FR07887214


title: Fig2_CD44hi_CD69hi_CD103hi_rep2

description:
without 7w resting phase
processed data file: Fig2_FPKM.csv

source_name: CD44hi CD69hi CD103hi T cells in lung treated with Aspergillus antigen


title: LTA challenge Donor 3-1


title: S8Td0

source_name: MACS-enriched CD14+ monocytes


title: RNA Diagnosis Patient 8 Rep3

description:
rep3
CA69MANXX_2_160729_FR07887212


title: S10Td0


title: RNA Diagnosis Patient 8 Rep2

description:
rep2
C9JCFANXX_4_160729_FR07887212


title: S9Tm3


title: Fig2_CD44hi_CD69low_rep2

source_name: CD44hi CD69low T cells in lung treated with Aspergillus antigen

value: CD44hi CD69low T cells


title: Fig2_CD44low_rep2

source_name: CD44low T cells in lung treated with Aspergillus antigen


title: RNA Diagnosis Patient 8 Rep1

description:
rep1
C9JCFANXX_3_160729_FR07887212

value: adult


title: HMGB1 challenge Donor 3-2


title: S2Tm3


title: LPS challenge Donor 3-1

source_name: Healthy primary neutrophils challenged with LPS for 1 hour


title: LTA challenge Donor 3-2

source_name: Healthy primary neutrophils challenged with LTA for 1 hour


title: S5Td0


title: RNA Remission Patient 7 Rep3

description:
rep3
CA69MANXX_2_160729_FR07887211

value: remission


title: HMGB1 challenge Donor 3-1

source_name: Healthy primary neutrophils challenged with HMGB1 for 1 hour


title: S8Tm3

value: blood


title: Fig2_CD44hi_CD69hi_CD103hi_rep1


title: S2Td0

value: CD14+ monocytes


title: RNA Remission Patient 7 Rep2

description:
rep2
C9JCFANXX_4_160729_FR07887211


title: FLAG challenge Donor 3-2

source_name: Healthy primary neutrophils challenged with FLAG for 1 hour

value: neutrophils


title: RNA Remission Patient 7 Rep1

description:
rep1
C9JCFANXX_3_160729_FR07887211


title: Fig2_CD44hi_CD69hi_CD103low_rep1

source_name: CD44hi CD69hi CD103low T cells in lung treated with Aspergillus antigen


title: Fig2_CD44hi_CD69hi_CD103low_rep2


title: FLAG challenge Donor 3-1


title: S1Tm3


title: LPS challenge Donor 3-2


title: S1Td0


title: S5Tm3


title: RNA Diagnosis Patient 7 Rep3

description:
rep3
CA69MANXX_2_160729_FR07887210


title: Fig2_CD44low_rep1


title: BCG_D19_HSPC_BM_D90

data_processing:
raw data was converted and multiplexed using bcl2fastq2 (v2.20).
reads were aligned to human reference transcriptome hg38 from UCSC and transcript abundance quantified using kallisto (v0.440) with default parameters.
abundance measurements were imported into R using tximport (v1.8.0).
for further filtering transcripts were removed not matching HGNC gene symbols, read sum lower than 10 across all samples or corresponding antisense, LINC or pseudogenes.
filtered data was imported into the DESeq2 package (v1.20.0) in R to generated a normalized expression table.
Genome_build: hg38
Supplementary_files_format_and_content: normalised expression table from DESeq2 containing all samples.

source_name: bone marrow

value: bone marrow

value: HSPC

tag: condition


title: BCG_D19_HSPC_BM_D0

value: BCG

tag: donor


title: Control Donor 3-1


title: RNA Diagnosis Patient 7 Rep1

description:
rep1
C9JCFANXX_3_160729_FR07887210


title: SLU Subject J Day 14

city: Rockville

first: Johannes

last: Goll

state: MD

address: 401 N Washington St

department: Bioinformatics Service Group

institute: The Emmes Company

data_processing:
Reads were mapped against the human reference using the STAR splice-aware read aligner (Version 2.5.2a). Gene expression quantification was carried out using the featureCounts function as implemented in the  Subread software (Version 1.5.0-p2). Options for featureCounts were set to count reads that were successfully mapped to a gene. For strand-specific RNA-sequencing data generated by Emory University,  the strand mapping option of feature counts was set to count the antisense strand (-s 2). For Saint  Louis University which did not use a strand-specific protocol, the option was set to count both sense  and antisense strands (-s 0). Reads that overlapped with multiple genes or had multiple mapping locations on the reference genome were excluded.
Genome_build: GRCh38 [ENSEMBL (Version 84, March 2016)]: The genomic reference was built by merging all  human chromosomes except X and Y chromosomes (to avoid gender-specific effects).
Supplementary_files_format_and_content: Feature counts matrix: columns=samples [EMO denotes samples sequenced at Emory University, and SLU indicates samples sequenced at Saint Louis University]; rows=features [genes].

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
Total RNA was extracted using the miRNeasy Mini kit (Qiagen, CA).
250 ng of total RNA was used for library preparation. For Emory Univerity samples, Libraries were prepared using the  Illumina TruSeq mRNA stranded kit as per manufacturer’s instructions. For Saint Louis University samples, Libraries were prepared using the Illumina TruSeq v2 RNA library kit as per manufacturer’s instruction.

value: Peripheral Blood Mononuclear Cells

tag: day

tag: subject

value: Subject J

tag: sequencing core

value: Saint Louis University


title: SLU Subject J Day 07

tag: cell type


title: BGP challenge Donor 3-2


title: SLU Subject J Day 02


title: BCG_D9_HSPC_BM_D90

tag: tissue


title: RNA Remission Patient 6 Rep3

description:
rep3
CA69MANXX_2_160729_FR07887208

tag: disease

value: Chronic Myeloid Leukemia

tag: Stage


title: BGP challenge Donor  3-1


title: Fig2_CD44hi_CD69low_rep1

value: BALB/c

value: Aspergillus antigen


title: RNA Remission Patient 6 Rep2

description:
rep2
C9JCFANXX_4_160729_FR07887208

tag: age


title: BCG_D6_HSPC_BM_D90


title: SLU Subject J Day 01


title: BCG_D6_HSPC_BM_D0


title: RNA Remission Patient 6 Rep1

description:
rep1
C9JCFANXX_3_160729_FR07887208


title: SLU Subject J Day 00


title: Control Donor 3-2


title: SLU Subject I Day 14

value: Subject I


title: Ctrl_D18_HSPC_BM_D90

value: Ctrl


title: RNA Diagnosis Patient 6 Rep3

description:
rep3
CA69MANXX_2_160729_FR07887207

value: chronic phase


title: Whole Blood Donor 2-2

source_name: Untreated whole blood from healthy donor

value: whole blood


title: SLU Subject I Day 07


title: RNA Diagnosis Patient 7 Rep2

description:
rep2
C9JCFANXX_4_160729_FR07887210

value: adult


title: RNA Diagnosis Patient 6 Rep2

description:
rep2
C9JCFANXX_4_160729_FR07887207


title: BCG_D16_HSPC_BM_D90


title: SLU Subject I Day 02


title: RNA Diagnosis Patient 6 Rep1

description:
rep1
C9JCFANXX_3_160729_FR07887207


title: BCG_D16_HSPC_BM_D0


title: SLU Subject I Day 01


title: R848 challenge Donor 2-1

source_name: Healthy primary neutrophils challenged with R848 for 1 hour


title: SA challenge 10^3 Donor 2-2

source_name: Whole blood challenged with 10^3 cells of Staphylococcus aureus


title: RNA Remission Patient 5 Rep2

description:
rep2
C9JCFANXX_4_160729_FR07887206

value: remission


title: SLU Subject I Day 00


title: R848 challenge Donor 2-2


title: LTA challenge Donor 2-2


title: SA challenge 10^3 Donor 2-1


title: SLU Subject H Day 14

value: Subject H


title: BCG_D21_HSPC_BM_D90


title: LTA challenge Donor 2-1

value: neutrophils


title: Ctrl_D18_HSPC_BM_D0

value: bone marrow


title: RNA Diagnosis Patient 5 Rep3

description:
rep3
CA69MANXX_1_160729_FR07887205


title: BCG_D21_HSPC_BM_D0

value: HSPC


title: SLU Subject H Day 07


title: BCG_D15_HSPC_BM_D90

value: BCG


title: RNA Diagnosis Patient 5 Rep2

description:
rep2
C9JCFANXX_2_160729_FR07887205


title: SLU Subject H Day 02

value: Peripheral Blood Mononuclear Cells


title: Whole Blood Donor 2-1


title: LPS challenge Donor 2-2


title: LPS challenge Donor 2-1


title: RNA Diagnosis Patient 5 Rep1

description:
rep1
C9JCFANXX_1_160729_FR07887205


title: Ctrl_D13_HSPC_BM_D90


title: BCG_D15_HSPC_BM_D0


title: SLU Subject H Day 01


title: Ctrl_D13_HSPC_BM_D0


title: SLU Subject H Day 00


title: RNA Remission Patient 5 Rep3

description:
rep3
CA69MANXX_2_160729_FR07887206


title: RNA Remission Patient 4 Rep3

description:
rep3
CA69MANXX_1_160729_FR07887204


title: RNA Remission Patient 5 Rep1

description:
rep1
C9JCFANXX_3_160729_FR07887206


title: HMGB1 challenge Donor 2-1


title: SLU Subject G Day 14

value: Subject G


title: FLAG challenge Donor 2-2


title: RNA Remission Patient 4 Rep2

description:
rep2
C9JCFANXX_2_160729_FR07887204


title: HMGB1 challenge Donor 2-2


title: BCG_D14_HSPC_BM_D0


title: BCG_D14_HSPC_BM_D90


title: SLU Subject G Day 07

value: Saint Louis University


title: FLAG challenge Donor 2-1


title: RNA Remission Patient 4 Rep1

description:
rep1
C9JCFANXX_1_160729_FR07887204

value: Chronic Myeloid Leukemia


title: RNA Diagnosis Patient 4 Rep3

description:
rep3
CA69MANXX_1_160729_FR07887203


title: RNA Diagnosis Patient 4 Rep2

description:
rep2
C9JCFANXX_2_160729_FR07887203


title: Control Donor 2-2

source_name: Healthy untreated neutrophils


title: Control Donor 2-1


title: BCG_D10_HSPC_BM_D90


title: SLU Subject G Day 01


title: SLU Subject G Day 00


title: SLU Subject G Day 02


title: Ctrl_D3_HSPC_BM_D0


title: Ctrl_D3_HSPC_BM_D90


title: BCG_D10_HSPC_BM_D0


title: RNA Diagnosis Patient 4 Rep1

description:
rep1
C9JCFANXX_1_160729_FR07887203

source_name: PBMCs


title: RNA Remission Patient 3 Rep3

description:
rep3
CA69MANXX_1_160729_FR07887201


title: SLU Subject F Day 14

value: Subject F


title: BGP challenge Donor 2-2

source_name: Healthy primary neutrophils challenged with BGP for 1 hour


title: BGP challenge Donor  2-1

source_name: Healthy primary neutrophils challenged with  BGP for 1 hour


title: BCG_D17_HSPC_BM_D90


title: RNA Remission Patient 3 Rep2

description:
rep2
C9JCFANXX_2_160729_FR07887201


title: noEC 4h challenge Donor 1-2

source_name: Untreated whole blood, 4 hour


title: SLU Subject F Day 07


title: RNA Remission Patient 3 Rep1

description:
rep1
C9JCFANXX_1_160729_FR07887201


title: BCG_D1_HSPC_BM_D90


title: BCG_D17_HSPC_BM_D0


title: noEC 4h challenge Donor 1-1


title: SLU Subject F Day 01


title: BCG_D1_HSPC_BM_D0


title: RNA Diagnosis Patient 3 Rep3

description:
rep3
CA69MANXX_1_160729_FR07887200


title: noEC 1h challenge Donor 1-2

source_name: Untreated whole blood, 1 hour


title: RNA Diagnosis Patient 3 Rep2

description:
rep2
C9JCFANXX_2_160729_FR07887200


title: SLU Subject E Day 07

value: Subject E


title: SLU Subject F Day 00


title: BCG_D12_HSPC_BM_D0


title: noEC 1h challenge Donor 1-1


title: BCG_D8_HSPC_BM_D90


title: RNA Diagnosis Patient 3 Rep1

description:
rep1
C9JCFANXX_1_160729_FR07887200


title: EC 1h challenge Donor 1-2

source_name: Escherichia coli challenged whole blood, 1 hour


title: EC 4h challenge Donor 1-2

source_name: Escherichia coli challenged whole blood, 4 hour


title: SLU Subject E Day 02


title: BCG_D8_HSPC_BM_D0


title: EC 4h challenge Donor 1-1


title: RNA Remission Patient 2 Rep3

description:
rep3
CA69MANXX_1_160729_FR07887199


title: BCG_D12_HSPC_BM_D90


title: RNA Remission Patient 2 Rep2

description:
rep2
C9JCFANXX_2_160729_FR07887199


title: RNA Remission Patient 2 Rep1

description:
rep1
C9JCFANXX_1_160729_FR07887199


title: SLU Subject E Day 01


title: EC 1h challenge Donor 1-1


title: SLU Subject F Day 02


title: BCG_D2_HSPC_BM_D90


title: RNA Diagnosis Patient 2 Rep3

description:
rep3
CA69MANXX_1_160729_FR07887198


title: SLU Subject E Day 00


title: BCG_D2_HSPC_BM_D0


title: SLU Subject E Day 14


title: RNA Diagnosis Patient 2 Rep2

description:
rep2
C9JCFANXX_2_160729_FR07887198


title: SA challenge 10^5 Donor 1-2

source_name: Whole blood challenged with 10^5 cells of Staphylococcus aureus


title: SLU Subject D Day 14

value: Subject D


title: SA challenge 10^5 Donor 1-1


title: RNA Diagnosis Patient 2 Rep1

description:
rep1
C9JCFANXX_1_160729_FR07887198


title: SLU Subject D Day 07


title: SA challenge 10^3 Donor 1-2


title: Ctrl_D7_HSPC_BM_D0

value: Ctrl


title: SA challenge 10^3 Donor 1-1


title: RNA Remission Patient 1 Rep2

description:
rep2
C9JCFANXX_2_160729_FR07887197


title: Ctrl_D7_HSPC_BM_D90


title: SLU Subject D Day 01


title: SA challenge 10^1 Donor 1-2

source_name: Whole blood challenged with 10^1 cells of Staphylococcus aureus


title: BCG_D5_HSPC_BM_D0


title: SLU Subject D Day 02


title: RNA Diagnosis Patient 1 Rep3

description:
rep3
CA69MANXX_1_160729_FR07887196

value: chronic phase


title: RNA Remission Patient 1 Rep1

description:
rep1
C9JCFANXX_1_160729_FR07887197


title: SA challenge 10^1 Donor 1-1

value: whole blood


title: BCG_D5_HSPC_BM_D90


title: Ctrl_D11_HSPC_BM_D90


title: SLU Subject D Day 00


title: Whole Blood Donor 1-2


title: SLU Subject C Day 14

value: Subject C


title: RNA Diagnosis Patient 1 Rep2

description:
rep2
C9JCFANXX_2_160729_FR07887196

value: adult


title: Ctrl_D11_HSPC_BM_D0


title: RNA Diagnosis Patient 1 Rep1

description:
rep1
C9JCFANXX_1_160729_FR07887196


title: SLU Subject C Day 07


title: Whole Blood Donor 1-1


title: BCG_D20_HSPC_BM_D90


title: SLU Subject C Day 02


title: BCG_D20_HSPC_BM_D0


title: SLU Subject C Day 01


title: AK3_T

description:
total RNA seq
AK3_T

source_name: ABCE1 KD 03 - total RNA seq

tag: cell line

value: HeLa cells

value: siRNA-mediated ABCE1 KD

tag: strategy

value: RNA-Seq


title: R848 challenge Donor  1-1

source_name: Healthy primary neutrophils challenged with  R848 for 1 hour

value: neutrophils


title: AK2_T

description:
total RNA seq
AK2_T

source_name: ABCE1 KD 02 - total RNA seq

tag: genotype


title: SLU Subject C Day 00

source_name: Peripheral Blood Mononuclear Cells


title: SW620_FOXA2

city: Beijing

first: Yang

middle: Eric

last: Li

state: Beijing

address: Room 2-110, Biotechnology Building, School of Life Sciences, Tsinghua University

department: School of Life Sciences

institute: Tsinghua University

data_processing:
Fastq files from ChIP-seq experiments were mapped to the human genomes (hg19) by using STAR41 with parameters --outFilterMismatchNoverLmax 0.05.
For the ChIP-seq of histone modification, enriched loci were identified by using the findPeaks command from HOMER (http://homer.salk.edu/homer/) with the option –style histone, 4-fold enrichment over the input sample, 4-fold enrichment over local background, at FDR = 0.001, and normalization to 10 million mapped reads per experiment.
Genomic binding peaks for transcription factor FOXA2 were identified with option -style factor, 2-fold enrichment over the input sample, 2-fold enrichment over local background, at the false discovery rate of 0.001.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files and peaks were generated using HOMER.

source_name: SW620 cell line

growth_protocol: SW480 and SW620 cell lines were obtained from China Infrastruture of Cell Line Resources and cultured as described37. Briefly, SW480 and SW620 cells were cultured in DMEM (Gibco Cat. No. C11995500BT) supplemented with 10% fetal bovine serum (Gemini Cat. No. 900-108) and 1% penicillin/streptomycin (Gibco Cat. No. 15140-122). Cells were cultured at 37°C with 5% CO2. Cells used to inject mice were stably transfected with luciferase.

extract_protocol:
ChIP-sequencing libraries were prepared by using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB Cat. No. E7370), according to the manufacturer’s instructions.
The sequencing was performed by Hiseq1500 (Illumina).

tag: chip antibody

value: FOXA2 (Proteintech Cat. No. 22474-1-AP)

tag: tumor stage

value: Dukes' type C, colorectal adenocarcinoma


title: SLU Subject B Day 07

value: Peripheral Blood Mononuclear Cells

value: Subject B


title: SLU Subject B Day 14

value: Saint Louis University


title: SW620_H3K36me3

value: H3K36me3 (Abcam Cat. No. ab9050)

tag: treatment


title: LTA challenge Donor 1-2

source_name: Healthy primary neutrophils challenged with LTA for 1 hour


title: LTA challenge Donor  1-1

source_name: Healthy primary neutrophils challenged with  LTA for 1 hour


title: AK1_T

description:
total RNA seq
AK1_T

source_name: ABCE1 KD 01 - total RNA seq


title: SW620_H3K27ac

value: H3K27ac (Abcam Cat.  No. ab4729)


title: SK3_T

description:
total RNA seq
SK3_T

source_name: CTRL KD 03 - total RNA seq

value: control


title: LPS challenge Donor 1-2

source_name: Healthy primary neutrophils challenged with LPS for 1 hour


title: SK2_T

description:
total RNA seq
SK2_T

source_name: CTRL KD 02 - total RNA seq


title: SW620_H3K4me3

value: H3K4me3 (Millipore Cat. No. 07-473)


title: LPS challenge Donor  1-1

source_name: Healthy primary neutrophils challenged with  LPS for 1 hour


title: SLU Subject B Day 02


title: SLU Subject B Day 01


title: HMGB1 challenge Donor 1-2

source_name: Healthy primary neutrophils challenged with HMGB1 for 1 hour


title: AK3_M (L7)

description:
ribosome-protected fragments
AK3_M

source_name: ABCE1 KD 03 - riboseq

value: Ribo-Seq


title: SW620_H3K4me2

value: H3K4me2 (Millipore Cat. No. 07-030)


title: R848 challenge Donor 1-2

source_name: Healthy primary neutrophils challenged with R848 for 1 hour


title: AK2_M (L7)

description:
ribosome-protected fragments
AK2_M

source_name: ABCE1 KD 02 - riboseq


title: SK1_T

description:
total RNA seq
SK1_T

source_name: CTRL KD 01 - total RNA seq


title: SLU Subject B Day 00


title: HMGB1 challenge Donor  1-1

source_name: Healthy primary neutrophils challenged with  HMGB1 for 1 hour


title: SW620_Input

value: Input


title: SW480_FOXA2

source_name: SW480 cell line

value: Dukes' type B, colorectal adenocarcinoma


title: FLAG challenge Donor 1-2

source_name: Healthy primary neutrophils challenged with FLAG for 1 hour


title: SLU Subject A Day 14

source_name: Peripheral Blood Mononuclear Cells

value: Subject A


title: SW480_H3K27ac


title: AK1_M (L7)

description:
ribosome-protected fragments
AK1_M

source_name: ABCE1 KD 01 - riboseq

value: HeLa cells

value: siRNA-mediated ABCE1 KD


title: FLAG challenge Donor 1-1

value: neutrophils


title: SK2_M (L7)

description:
ribosome-protected fragments
SK2_M

source_name: CTRL KD 02 - riboseq


title: Control Donor 1-2

source_name: Healthy untreated neutrophils


title: SK3_M (L7)

description:
ribosome-protected fragments
SK3_M

source_name: CTRL KD 03 - riboseq


title: SLU Subject A Day 02


title: SW480_H3K4me3


title: SW480_H3K36me3


title: Control Donor 1-1


title: SW480_H3K4me2


title: AK3_M (L6)

description:
ribosome-protected fragments
AK3_M


title: BGP challenge Donor 1-2

source_name: Healthy primary neutrophils challenged with BGP for 1 hour


title: SLU Subject A Day 01


title: SLU Subject A Day 07


title: SLU Subject A Day 00


title: SW480_Input


title: AK2_M (L6)

description:
ribosome-protected fragments
AK2_M


title: SK1_M (L7)

description:
ribosome-protected fragments
SK1_M

source_name: CTRL KD 01 - riboseq


title: SW620_shNC_3

description: replicate 3

data_processing:
The fastq files from RNA-seq experiments were mapped to the human genome (hg19) by using STAR41 with parameters --outFilterMismatchNoverLmax 0.05.
To measure expression, we calculated the raw counts for each gene by using the analyzeRepeats command from HOMER (http://homer.salk.edu/homer/) with the option “rna” and the default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count and RPKM values for each Sample

source_name: SW620 cell line

extract_protocol:
RNA-sequencing (RNA-seq) libraries were prepared by using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB Cat. No. E7420), according to the manufacturer’s instructions.
The sequencing was performed by Hiseq1500 (Illumina).

treatment_protocol: A lentiviral U6-based expression vector containing PuroR-T2A-mCherry was used to express shRNAs. The lentiviral vector was digested by BsmbI, followed by annealed shRNA oligos insertion, to clone shRNA expression plasmids. We used two shRNA targeting sites against FOXA2, as follows: FOXA2-shRNA1: 5’ GAACGGCATGAACACGTACAT 3’ (from Sigma-Aldrich Corporation, TRCN0000014915); FOXA2-shRNA2: 5’ GCAAGGGAGAAGAAATCCATA 3’, as previously described38. shControl: 5’ CAACAAGATGAAGAGCACCAA 3’. Lentiviral vector particles were produced by tri-transfection of plasmids harboring the packaging construct, the transfer vector and the envelope-expressing construct into 293T cells using DNAfect reagents (Cwbio Cat. No. CW0806). Viral supernatants were harvested and used for infections or stored at -80°C. Stable FOXA2 knockdown cell lines were generated by using lentiviral U6-based expression vectors. Stable populations were selected with 2 μg/ml puromycin (Sigma-Aldrich Cat. No. P9620). Knockdown was confirmed by RT-qPCR and western blotting.

value: shNC


title: EMORY Subject J Day 07

value: Subject J

value: Emory University


title: SW620_shNC_2

description: replicate 2

value: Dukes' type C, colorectal adenocarcinoma


title: EMORY Subject J Day 02

value: Peripheral Blood Mononuclear Cells


title: SK3_M (L6)

description:
ribosome-protected fragments
SK3_M


title: EMORY Subject J Day 14


title: 41629

city: Los Angeles

first: Sandra

last: Orsulic

address: 10833 Le Conte Ave

department: Obstetrics and Gynecology

institute: David Geffen School of Medicine at UCLA

data_processing:
Sequencing was performed using the Illumina HiSeqX platform
Alignment using STAR (2.4.1) aligner
The raw read counts were estimated using HTSeq-0.6.1
Read count data were normalized using DESeq2
Hierarchical clustering analysis is performed for normalized counts of all the protein coding genes for all the samples
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: xlsx files for Raw.Read.Count and Normalized.Read.Count(using DESeq2 for normalization)

source_name: human omental metastasis

extract_protocol:
Total RNA was isolated using the miRNeasy FFPE kit (cat # 217504) according to the manufacturer's instructions (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols (SMARTer® Stranded Total RNA-Seq Kit v2)

treatment_protocol: FFPE tissue was collected at the time of surgery. FFPE blocks were sectioned onto uncharged glass slides. One 4 µm section was used for H&E  staining and delineating tumor areas by a pathologist. Depending on the tumor size, 1 to 3 unstained 10 µm sections were macrodissected (removal of non-tumor areas based on the H&E template) with a clean razor blade.

value: metastatic ovarian cancer

tag: organ site

value: omentum

tag: age at diagnosis

tag: height (inches)

tag: weight (pounds)

tag: bmi

tag: race

value: CAUCASIAN

tag: ethnicity

value: NON-HISPANIC

tag: debulking

value: Optimal

tag: cancer stage

value: IIIC

tag: tumor grade

tag: assumed progression free survival (months)

tag: assumed overall survival (months)

tag: patient survival

value: Alive


title: SK2_M (L6)

description:
ribosome-protected fragments
SK2_M

tag: cell line

tag: genotype

value: control

tag: strategy

value: Ribo-Seq


title: EMORY Subject J Day 01

tag: cell type

tag: day

tag: subject

tag: sequencing core


title: 41303

tag: tissue

tag: organ site

tag: age at diagnosis

tag: height (inches)

tag: weight (pounds)

value: HISPANIC


title: SW620_shNC_1

description: replicate 1

tag: chip antibody

tag: tumor stage

tag: treatment


title: SW620_shFOXA2_1_3

description: replicate 3


title: EMORY Subject J Day 00


title: 39541

tag: bmi

tag: race

tag: ethnicity

tag: debulking

tag: cancer stage

value: IV

tag: tumor grade

tag: assumed progression free survival (months)

tag: assumed overall survival (months)

value: DWD-Died with Disease


title: BGP challenge Donor 1-1

tag: cell type

value: neutrophils


title: EMORY Subject I Day 14

tag: day

tag: subject

value: Subject I

tag: sequencing core


title: 39301

tag: tissue

tag: organ site

tag: age at diagnosis

tag: height (inches)

tag: brca mutation status

value: WT

tag: brca mutation description

value: WT - No Mut

tag: patient survival


title: SK1_M (L6)

description:
ribosome-protected fragments
SK1_M

tag: cell line

value: HeLa cells

tag: genotype

tag: strategy


title: EMORY Subject I Day 07

value: Peripheral Blood Mononuclear Cells

value: Emory University


title: D7_A283__plus__chondro

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: 283 and chondrocyte co-culture

extract_protocol:
Total RNA was isolated from the samples using the Direct-zolTM RNA kit as instructed by the manufacturer (Zymo Research, Irvine, California).
mRNA version 2 library prep kit (Illumina)

value: Adipo tissue + Cartilage


title: SW620_shFOXA2_1_1

description: replicate 1

tag: chip antibody

tag: tumor stage

value: Dukes' type C, colorectal adenocarcinoma

tag: treatment


title: D7_A258__plus__chondro

source_name: 258 and chondrocyte co-culture


title: D7_A211__plus__chondro

source_name: 211 and chondrocyte co-culture


title: EMORY Subject I Day 02

tag: cell type


title: AK1_M (L6)

description:
ribosome-protected fragments
AK1_M

value: siRNA-mediated ABCE1 KD


title: SW620_RNAseq


title: 38681

value: metastatic ovarian cancer

value: omentum

tag: weight (pounds)

tag: bmi

tag: race

value: CAUCASIAN

tag: ethnicity

tag: debulking

value: Optimal

tag: cancer stage

value: IIIC

tag: tumor grade

tag: assumed progression free survival (months)

tag: assumed overall survival (months)


title: EMORY Subject I Day 01

tag: day

tag: subject

tag: sequencing core


title: 36762

tag: tissue

tag: organ site

tag: age at diagnosis

tag: height (inches)

value: ASIAN

value: NON-HISPANIC

value: Suboptimal

value: IV

value: Unknown

tag: patient survival


title: SW480_RNAseq

tag: chip antibody

tag: tumor stage

value: Dukes' type B, colorectal adenocarcinoma

tag: treatment


title: D7_A283

source_name: AMSC 283

value: Adipose tissue


title: EMORY Subject I Day 00

tag: cell type

value: Peripheral Blood Mononuclear Cells

value: Subject I


title: D7_A211

source_name: AMSC 211


title: D7_A258

source_name: AMSC 258


title: EMORY Subject H Day 14

value: Subject H

value: Emory University


title: SW620_shFOXA2_1_2

description: replicate 2

value: Dukes' type C, colorectal adenocarcinoma


title: EMORY Subject H Day 02


title: EMORY Subject H Day 07


title: 14282

value: metastatic ovarian cancer

tag: race

tag: debulking

value: DWD-Died with Disease


title: 12638

value: omentum

tag: weight (pounds)

tag: bmi

tag: cancer stage

tag: tumor grade

value: Alive


title: EMORY Subject H Day 00

tag: day

tag: subject


title: EMORY Subject H Day 01

tag: sequencing core


title: EMORY Subject G Day 14

value: Subject G


title: 13553

tag: tissue

tag: organ site

value: CAUCASIAN

tag: ethnicity

value: UNKNOWN

value: IIIC

tag: assumed progression free survival (months)

tag: assumed overall survival (months)


title: EMORY Subject G Day 07


title: 14810

tag: age at diagnosis

value: Optimal

tag: patient survival


title: 14676

value: Unknown


title: EMORY Subject G Day 01

tag: cell type


title: 14898

tag: race


title: EMORY Subject G Day 02


title: EMORY Subject G Day 00


title: 35581

tag: height (inches)

value: NON-HISPANIC

tag: brca mutation status

value: Mut

tag: brca mutation description

tag: debulking


title: EMORY Subject F Day 14

value: Peripheral Blood Mononuclear Cells

value: Subject F


title: EMORY Subject F Day 07


title: 14318

value: HISPANIC

tag: cancer stage

tag: tumor grade


title: 14785

value: IV


title: EMORY Subject F Day 02

tag: day

tag: subject

value: Emory University


title: 45180

tag: tissue

value: metastatic ovarian cancer

tag: weight (pounds)

tag: bmi

value: WT

value: WT - No Mut


title: 45695

tag: organ site

value: omentum

tag: ethnicity

tag: assumed progression free survival (months)

value: DWD-Died with Disease


title: D7_chondro

source_name: Chodrocytes

value: Cartilage


title: EMORY Subject F Day 01

tag: sequencing core


title: 44535

tag: age at diagnosis

value: CAUCASIAN

tag: assumed overall survival (months)

tag: patient survival

value: Alive


title: 30824

tag: height (inches)

tag: race

value: Suboptimal

value: IIIC

value: No recurrence to date


title: 34344

value: NON-HISPANIC

tag: debulking

value: Optimal


title: EMORY Subject F Day 00

tag: cell type

value: Peripheral Blood Mononuclear Cells

value: Subject F


title: 14364

tag: cancer stage

tag: tumor grade

value: Unknown


title: 44513


title: 44496

tag: brca mutation status

tag: brca mutation description


title: EMORY Subject E Day 07

tag: day

tag: subject

value: Subject E

value: Emory University


title: 44392

tag: tissue

value: metastatic ovarian cancer

tag: organ site

tag: weight (pounds)

tag: bmi

value: WT


title: 44376

value: omentum

tag: age at diagnosis

tag: ethnicity

tag: assumed progression free survival (months)


title: 14566

value: Mut

tag: assumed overall survival (months)

tag: patient survival

value: DWD-Died with Disease


title: 44233

tag: height (inches)

tag: race

value: CAUCASIAN

tag: debulking


title: EMORY Subject E Day 01

tag: cell type

tag: sequencing core


title: 44215

tag: brca mutation status

tag: brca mutation description

tag: cancer stage

tag: tumor grade

value: Alive


title: EMORY Subject E Day 00

tag: day

tag: subject


title: EMORY Subject D Day 14

value: Subject D


title: EMORY Subject D Day 02


title: 43209

tag: tissue

tag: organ site

tag: weight (pounds)

tag: bmi

value: ASIAN

value: IIIC


title: 44111

tag: age at diagnosis

tag: ethnicity

value: NON-HISPANIC

value: WT - No Mut

tag: assumed progression free survival (months)

tag: assumed overall survival (months)