title: cut and run sample1 minus4


title: cut and run sample1 minus0

status: Public on Dec 10 2019

type: SRA

city: Worcester

first: Alan

middle: G

last: Derr

state: Massachusetts

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

country: USA

institute: University of Massachusetts Medical School

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Quality trimming: trimmomatic v0.32: paired-end reads removed where average quality scores in window size=10 are <15, bases trimmed where leading and trailing quality scores <15
Length filtering: bedtools v2.25.0: Reads longer than 25 bases after trimming are used for analysis
Alignment to hg19 genome: bowtie2 v2.2.3: option: --un-conc to filter out non-concordant reads
Duplicate removal: MarkDuplicates v0.32: from Picard package
Peak calling: MACS2:
Convert aligned reads to tdf files: IGVTools v2.3.31: for visualization in IGV
Genome_build: hg19

molecule: genomic DNA

organism: Homo sapiens

source_name: blood

extract_protocol: Cleavage Under Targets and Release Using Nuclease (CUT&RUN)

tag: cell type

value: PBMCs

tag: tissue

value: blood

tag: population

value: CD36-, CD56dim


title: cut and run sample1 minus3


title: CD94+CD56hi2

description:
ATAC-Seq analysis of CD94+CD56hi2 cells
plusplus2

data_processing:
Low-quality base trimming: trimmomatic v0.32
Alignment to hg19 genome: bowtie2 v2.2.3
Duplicate removal: MarkDuplicates v0.32: from Picard package
End trimming and 10-base extension: bedtools v2.25.0: for Tn5 transposase localization
Peak calling: MACS2
Convert aligned reads to tdf files: IGVTools v2.3.31: for visualization in IGV
Genome_build: hg19
Supplementary_files_format_and_content: tdf: for visualization in IGV

extract_protocol: CD94-CD56dim, CD94+CD56dim and CD94+CD56hi NK cells were sorted then subject to ATAC-Seq


title: cut and run sample1 minus1


title: CD94+CD56hi1

description:
ATAC-Seq analysis of CD94+CD56hi1 cells
plusplus1


title: CD94+CD56dim1

description:
ATAC-Seq analysis of CD94+CD56dim1 cells
plus1


title: CD94-CD56dim1

description:
ATAC-Seq analysis of CD94-CD56dim1 cells
minus1


title: cut and run sample2 minus0


title: cut and run sample1 plusplus3

value: CD36+, CD56hi


title: NKpopulationRNAseq_2

description:
20180721_nk_re_run
Second sequencing run for NK population analysis.
Cytoplasmic mRNA

library_source: transcriptomic

data_processing:
Encode CEL-Seq sample barcode and UMI into R2 read name; Custom Python script; CEL-Seq primers carry a sample barcode and unique molecule identifier (UMI), which is used for removing PCR duplicates.
Align to hg19 genome; tophat v2.0.14; The transcript annotation file contains all RefSeq transcripts with IDs starting with 'NM_', and includes annotation for T cell constant region genes TRAC, TRBC2, TRDC, TRGC1, and TRGC2.
Align to transcripts, PCR duplicate removal, and quantification; ESAT v1.0; ESAT is run in single-cell mode to remove PCR duplicates and separate the samples by sample barcode.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_counts.txt: Tab-delimited text files; ESAT output (raw transcript counts); Final raw gene expression counts from ESAT with PCR duplicates removed.

molecule: total RNA

source_name: PBMCs

extract_protocol:
CEL-Seq2
CEL-Seq2

value: Natural killer (NK) cells

tag: nk population

value: mixed sample (non-demultiplexed)

tag: donor


title: cut and run sample1 plusplus2


title: cut and run sample1 plusplus1


title: NKpopulationRNAseq_1

description:
20180713NKpopulationRNAseq
First sequencing run for NK population analysis.
Cytoplasmic mRNA


title: NKpopulationRNAseq_3

description:
20180722nkpopulation3rdrun
Third sequencing run for NK population analysis.
Cytoplasmic mRNA


title: Bulk RNA-seq dataset: mock-infected HBEpC cells batch #2 replicate #1

city: New York

first: Chang

last: Wang

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

data_processing:
For the single-cell RNA-seq datasets generated in the time course infection assay, the Cell Ranger (v2.1.0) single cell software suite was applied to convert the BCL files and perform the alignment and gene counting with the processed UMIs for each cell. Then the UMI counts for all the viral reads including the gapped reads with the CIGAR string containing a large gap (i.e., “MNM”) were merged into the expression matrix.
For the bulk RNA-seq datasets, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.5.3a) was used for the alignment. featureCounts in the subread package (v.1.5.1) was used for gene counting.
For the viral genome sequencing dataset, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.5.3a) was used for the alignment.
For the single-cell RNA-seq datasets generated from PR8-infected A549 and MDCK cells at different MOIs, the Cell Ranger (v2.1.0) single cell software suite was applied to convert the BCL files and perform the alignment.
Genome_build: hg19 and influenza A/Puerto Rico/8/34/Mount Sinai (H1N1)
Supplementary_files_format_and_content: For the single-cell RNA-seq datasets generated in the time course infection assay, each tab-delimited text file contains the raw gene expression matrix for individual cells harvested at a given time point. For the bulk RNA-seq datasets, each tab-delimited text file contains the raw gene counts for a given sample.

molecule: polyA RNA

source_name: primary human bronchial epithelial cells

growth_protocol: HBEpC cells (PromoCell) were maintained and infected in PromoCell airway epithelial cell growth media with SupplementMix.

extract_protocol:
Cells were trypisinized, extensively washed, and re-suspended in PBS containing 0.04% BSA. The total RNA was extracted using RNeasy Mini Kit (Qiagen) with on-column DNA digestion using RNase-free DNase (Qiagen), followed by poly(A) mRNA enrichment.
The enriched poly(A) mRNAs were subject to bulk RNA-seq library preparatin with NEBNext Ultra II RNA library prep kit for Illumina following the manufacturer’s protocol.

treatment_protocol: Mock-infection

tag: cell types

value: HBEpC

tag: infection time points

value: No infection

tag: virus strain


title: Bulk RNA-seq dataset: mock-infected HBEpC cells batch #2 replicate #2


title: cut and run sample1 plus4

value: CD36+, CD56dim


title: Bulk RNA-seq dataset: mock-infected HBEpC cells batch #1 replicate #2


title: Bulk RNA-seq dataset: mock-infected A549 cells replicate #2

source_name: adenocarcinomic human alveolar basal epithelial cells

growth_protocol: A549 cells (ATCC) were maintained in Kaighn’s modified Ham’s F-12 medium (F-12K) supplemented with 10% fetal bovine serum (FBS) prior to infection. A549 cells were infected in A549 infection media (F-12K supplemented with 2% bovine serum albumin (BSA) and 1% antibiotic-antimycotic).


title: cut and run sample1 minus2


title: Bulk RNA-seq dataset: mock-infected A549 cells replicate #1


title: LSC6_AA5

city: Los Angeles

first: Brigitte

last: Gomperts

state: CA

address: 650 Charles E. Young Drive; 9-240 Factor Building

institute: UCLA

data_processing:
Lung slice cultures from IPF patients treated with AA5 or DMSO were analyzed using the following method. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program. The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. TMM (trimmed mean of M-values) was used to normalize the gene expression. The gene expression estimates were then log2-transformed and genes with no reads across all samples were removed from further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: log2-transformed TMM (trimmed mean of M-values)

source_name: Lung Slice Cultures (LSCs)

growth_protocol: LSCs:  LSC's sections were incubated in a 24 well plate in DMEM/F12 medium supplemented with 10% FBS, 1x Glutamax, 10nM Non-essential amino acids.  Media was renewed every 24 hours.

extract_protocol: LSCs: Tissues were snap-frozen after treatment and stored at -80oC until RNA isolation. Lung slices were homogenized using a handheld homogenizer and passing the homogenate through a Qiashredder (Qiagen). Total RNA from the LSC and cells from the disease model were extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. The RNA concentrations were measured on a NanoDrop ND-1000 spectrophotometer.

treatment_protocol: LSCs: Samples were collected for RNA isolation embedding at 48 and 72 hrs.

tag: type

value: LSC (AA5 treatment)

tag: individual

value: Patient 6

tag: Stage

tag: treatment


title: CD94+CD56dim2

description:
ATAC-Seq analysis of CD94+CD56dim2 cells
plus2


title: LSC5_AA5

value: Patient 5


title: LSC5_DMSO

value: DMSO


title: CD94-CD56dim2

description:
ATAC-Seq analysis of CD94-CD56dim2 cells
minus2


title: LSC6_DMSO


title: LSC4_AA5

value: Patient 4


title: LSC3_AA5

value: Patient 3


title: LSC4_DMSO


title: LSC2_AA5

value: Patient 2


title: P4_S2_ AA5r

data_processing:
The iSDC cultures raw sequence reads were demultiplexed using custom scripts and converted to Sanger fastq format.   After trimming adaptor sequences, the sequence reads were then aligned to the Homo Sapiens genome and gene model from NCBI 37.2 release using Tophat version 2.0.9. The gene expression values as Fragments Per Kilobase of transcripts per Miilion mapped reads (FPKM) were measured and normalized using the cuffnorm program from Cufflinks version 2.2.1 and used in the subsequent analysis. Technical replicates were combined and aligned together in all cases except for the AA5-treated model. The gene expression estimates were then log2-transformed and genes with no reads across all samples were removed from further analysis.
Genome_build: NCBI 37.2 release
Supplementary_files_format_and_content: Text (tab delimited) files report log2-transformed FPKMs

source_name: Aggregate cultures of iSDCs

growth_protocol: iFA model: iSDCs were cultured on 13kPA  polyacrylamide gels functionalized with benzoquinone and coated with 0.1% gelatin.  Cells were cultured in DMEM/F12 medium supplemented with 10% FBS, 1x Glutamax, 10nM Non-essential amino acids.  Media was renewed every three days.

extract_protocol:
iFA model: In-vitro cultures of PF and cells in the iFA model were washed once with PBS and total RNA from the samples were extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
Libraries for RNA-Seq were prepared with the Nugen human FFPE Kit (LSC). The workflow consisted of cDNA generation, end repair to generate blunt ends, adaptor ligation, adaptor cleavage and PCR amplification. Different adaptors were used for multiplexing samples sequenced in the same lane. The libraries of aggregate iSDC cultures treated with AA5 or DMSO were sequenced with 75-bp single-end reads on the Illumina Nextseq500 system.  The libraries of aggregate iSDC cultures at day 4 and day 13 were run with 50-bp paired-end reads on the Illumina system (model HiSeq 2000).

treatment_protocol: iFA model: For AA5 inhibition eperiments, 10uM AA5 or 1% DMSO was added at D0.  Media was replenished every three days and the samples were collected for RNA extraction on Day 8.  For AA5 reversal experiments, 10UM AA5 at DMSO was added to Day13 iFA cultures, and RNA was collected after 24 hours.

value: iFA model (AA5 treatment)

value: AA5 reversing


title: Bulk RNA-seq dataset: mock-infected HBEpC cells batch #1 replicate #1


title: LSC1_AA5

value: Patient 1


title: LSC1_DMSO


title: cut and run sample2 minus2

value: PBMCs

value: blood

value: CD36-, CD56dim


title: P3_S2_ AA5r


title: P3_S1_AA5r


title: P4_S1_ AA5i

value: AA5 inhibiting


title: P4_S2_ AA5i


title: P3_S2_ AA5i


title: P4_S1_ AA5r


title: P4_S2_DMSO


title: P3_S1_AA5i


title: P3_S2_DMSO


title: P4_S1_DMSO


title: P3_S1_DMSO


title: LSC3_DMSO


title: LSC2_DMSO


title: 801-2

city: Boston

first: Chunyang

last: Bao

state: MA

address: 415 Brookline Avenue

institute: Dana-Farber Cancer Institute

description: from mouse organoid

data_processing:
Data was processed using Illumina Bcl2fastq
Sequencing reads were aligned to mm9 reference genome using STAR (v2.5)
Raw gene counts were generated from STAR output
Genome_build: mm9
Supplementary_files_format_and_content: comma seperated value (CSV) files for all samples. STAR_Gene_Counts.csv reports raw counts.

organism: Mus musculus

growth_protocol: Both p53wt/p53mut organoids were grown in coditioned medium (Miyoshi, et al. Nat Protoc. 2013 Dec; 8(12): 2471–2482).

extract_protocol:
RNeasy mini kit (Promega, Inc.) was used for RNA collection.
Libraries were prepared using Roche Kapa mRNA Hyper sample preparation kits from 100ng of purified total RNA according to the manufacturer's protocol

tag: strain

tag: genotype/variation

value: p53 KO

tag: replicate

tag: dysplastic

value: Y

tag: ko in vivo or ex vivo

value: In vivo

value: gastric organoids


title: 801-3

description: from mouse organoid


title: 794-1

description: from mouse organoid


title: 794-3

description: from mouse organoid


title: 794-2

description: from mouse organoid


title: Slc17a6-TRAP (JX883) prefrontal cortex IP Rep2 [1298]

first: Laura

last: Kus

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

description:
Ribosomal-bound RNA
1298_Slc17a6_TRAP_JX883_prefrontal cortex_Rep2_S2

data_processing:
FASTX Toolkit 0.0.13 was used to assess the quality of reads and trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.0.0e_r291 using default settings.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of counts

source_name: Prefrontal cortex

growth_protocol: Not applicable

extract_protocol:
The prefrontal cortex was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

treatment_protocol: No treatment

tag: sample size

value: 3 mice per sample

tag: animal line

value: Slc17a6-TRAP JX883

tag: application

value: RNA-seq

tag: sample type

value: Immunopurified (IP)

value: Prefrontal cortex


title: Slc17a6-TRAP (JX883) deep cerebellar nuclei IP Rep3 [1302]

description:
Ribosomal-bound RNA
1302_Slc17a6_TRAP_JX883_deep_cerebellar_nuclei_Rep3_S6

source_name: Deep nuclei of the cerebellar

extract_protocol:
The deep cerebellar nuclei were homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

tag: tissue

value: cerebellum (Deep nuclei)


title: Slc17a6-TRAP (JX883) deep cerebellar nuclei IP Rep2 [1301]

description:
Ribosomal-bound RNA
1301_Slc17a6_TRAP_JX883_deep_cerebellar_nuclei_Rep2_S5


title: Slc17a6-TRAP (JX883) deep cerebellar nuclei IP Rep4 [1476]

description:
Ribosomal-bound RNA
1476_Slc17a6_TRAP_JX883_deep_cerebellar_nuclei_Rep4_S4


title: Slc17a6-TRAP (JX883) prefrontal cortex IP Rep1 [1297]

description:
Ribosomal-bound RNA
1297_Slc17a6_TRAP_JX883_prefrontal cortex_Rep1_S1


title: Slc17a6-TRAP (JX883) deep cerebellar nuclei IP Rep1 [1300]

description:
Ribosomal-bound RNA
1300_Slc17a6_TRAP_JX883_deep_cerebellar_nuclei_Rep1_S4


title: Slc17a6-TRAP (JX883) prefrontal cortex IP Rep3 [1299]

description:
Ribosomal-bound RNA
1299_Slc17a6_TRAP_JX883_prefrontal cortex_Rep3_S3


title: 801-1

description: from mouse organoid


title: 752-1

description: from mouse organoid

value: WT


title: 752-3

description: from mouse organoid


title: 565-3

description: from mouse organoid


title: 565-1

description: from mouse organoid


title: 650-2

description: from mouse organoid

value: N


title: 565-2

description: from mouse organoid


title: 650-1

description: from mouse organoid


title: 752-2

description: from mouse organoid


title: 1270-2

description: from mouse organoid

value: Ex vivo


title: 300-1

description: from mouse organoid


title: 1269-2

description: from mouse organoid


title: 1269-1

description: from mouse organoid


title: 1270-1

description: from mouse organoid


title: S077.FFPE.Pi.0523T1

city: Chapel Hill

first: Xianlu

middle: Laura

last: Peng

state: NC

address: 450 West Dr.

institute: The University of North Carolina at Chapel Hill

data_processing:
BCL files were converted to FASTQ files using bcl2fastq2 Conversion Software 2.20.0.
Individual lane files were combined into one FASTQ for each sample
FASTQ of PDX samples were split into human and mouse reads using bbmap v37.90
The total expected read counts per gene were quantified by Salmon 0.9.1
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

source_name: PrimaryPDAC

extract_protocol:
RNA and DNA was harvested from FFPE samples using the Roche High Pure RNA Paraffin Kit (CAT#3270289001) following manufacturer's instructions. RNA and DNA was harvested from FF and FNA samples using the Qiagen AllPrep DNA/RNA Mini Kit (CAT#80204) following manufacturer's instructions.
Libraries were constructed from FFPE and FNA samples using the Illumina TruSeq RNA Exome Library Prep Kit (CAT#20020189,#20020490,#20020492,#20020493,#20020183) following manufacturer's instructions. Libraries were constructed from FF samples using the Illumina TruSeq Stranded mRNA Kit (CAT#20020595,#20019792) following manufacturer's instructions.

value: FF

tag: lib prep kit

value: TruSeq

tag: extraction protocol

value: Qiagen AllPrep DNA/RNA Mini Kit


title: P30 Stria Vascularis nuclei capture 1

city: Bethesda

first: Michael

last: Hoa

state: MD

address: 35 Convent Dr, Rm 1F-226

institute: National Institutes on Deafness and Other Communication Disorders, NIH

description: Single nuclei RNA-seq

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the CellRanger v2.0.0 pipeline using default settings.
Secondary analysis was performed using the Seurat2 package
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger v2.0.0 gene counts matrices.

source_name: Stria Vascularis

extract_protocol:
single cell RNA-Seq: Single cell suspension from stria vascularis: Inner ears from ~12 P30 mice were removed and stria vascularis from the cochleae were collected into 200ul DMEM F-12 media. The tissue was lysed in 0.5mg/ml trypsin at 37c for 7 minutes. The media was carefully removed and replaced with 5% FBS to stop the lysis. The tissue was triturated and filtered through a 20um filter. The filtered cells were let to sit on ice for 35 minutes. 150ul of the supernatant was removed and cell pellet was suspended in the remaining 50ul. Cells were counted on a Luna automated cell counter and a cell density of 1x106 cells/ml was used to load onto the 10X genomics chip.
single nucleus RNA-Seq: Single nucleus suspension from stria vascularis: Published single nucleus suspension protocol from 10x genomics was used to isolate the nuclei. Briefly, stria vascularis from ~10 P30 animals were isolated and collected in 3ml DMEM F-12 media. Following collection, the media was replaced with 3ml chilled lysis buffer (10mM Tris-HCl, 10mM Nacl, 3mM MgCl2,0.005% Nonidet P40 in Nuclease free water) and the tissue were lysed at 4c for 25 minutes. The lysis buffer was then replaced with 1.5ml DMEM F-12 media. The tissues were triturated and filtered through a 20um filter. The filtrate was centrifuged at 500rcf for 5 minutes at 4c. The supernatant was removed, and the cell pellet was resuspended in 1ml nuclei wash and resuspension buffer (1xPBS with 1% BSA and 0.2U/ul RNase Inhibitor). The cells were filtered through a 10um filter and centrifuged at 500rcf for 5 minutes at 4c. The supernatant was removed, and pellet resuspended in 50ul of nuclei wash and resuspension buffer. Nuclei were counted in a Luna cell counter and a nuclear density of 1x106 cells/ml was used to load onto the 10X genomics chip.
Library preparation was performed according to the manufacturer’s instructions for the 10x Genomics Chromium platform (10x Genomics). The libraries were sequenced on four lanes on a NextSeq500 sequencer (Illumina).

value: Stria Vascularis

tag: developmental stage

value: CBA/J mice (strain 000656)


title: P30 Stria Vascularis whole cells capture 3

description: Single cell RNA-seq


title: MTB3

city: Durban

first: Adrie

last: Steyn

address: 519 Umbilo Road

department: Medicine

country: South Africa

institute: Africa Health Research Institute

data_processing:
Basecalls performed using Illumina's bcl2fastq version 2.18.0.12
Sequenced reads were aligned to mm10 using STAR version 2.5.3a with parameters --outReadsUnmapped Fastqx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Counts were calculated from STAR alignment file using HTSeq-count verison 0.9.1 with parameters -r pos -t exon -I gene_id -a 10 -s no -f bam
Differential expression was performed using DESeq2 version 1.16.1 in R version 3.4.1
Genome_build: Gencode GRCm38 p4 Release M11
Supplementary_files_format_and_content: tab delimited file that contains the raw counts of each gene for each sample

source_name: Lung CD8+ T cells_virulent Mtb_week 12

growth_protocol: Mice were fed and watered ad libitum and housed 5 animals per cage throughout the length of the experiment Animals were cared for in accordance with South African National standards.

extract_protocol:
Lungs from mice (infected or uninfected controls) were digested and processed into single cell suspensions. CD8+ T cells were purified from these suspensions using magnetic beads. RNA extraction on these purified populations was performed immediately after. RNA was stored at -80 degrees until it was sent for sequencing. RNA extractions were performed on 5 mice per group, and three samples per group with the highest quality RNA were selected for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Eight-week old C57BL/6J mice (bred in-house) were aerosol-infected with ~100 CFU of virulent M. tuberculosis, strain H37Rv (ATCC 27294), or M. bovis BCG strain Pasteur (1173P2) using a Glas-Col Aerosol Exposure System.

tag: infected with

tag: time point (post infection)

value: Week 12

value: Lung

tag: cell type

value: Lung CD8+ T cells


title: U1

source_name: Lung CD8+ T cells_uninfected control_week 12

value: none (uninfected control)


title: U4


title: U2


title: MTB2

value: virulent M. tuberculosis, strain H37Rv (ATCC 27294)


title: BCG2

source_name: Lung CD8+ T cells_vaccine strain BCG_week 12

value: M. bovis BCG strain Pasteur (1173P2)


title: U3_3

source_name: Lung CD8+ T cells_uninfected control_day 21

value: Day 21


title: BCG4


title: BCG5


title: 300-2

description: from mouse organoid

value: gastric organoids


title: U5_5


title: T2_7

source_name: Lung CD8+ T cells_virulent Mtb_day 21


title: T4_9


title: T1_6


title: B4_14

source_name: Lung CD8+ T cells_vaccine strain BCG_day 21


title: B5_15


title: Lymphoma, Bptf.WT.Late (PTB159)

city: Paris

first: Laia

last: Richart

address: 13 Rue Pierre et Marie Curie

department: Developmental Biology

country: France

institute: Institut Curie

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software.
Conversion of Illumina BCL files to bam format was performed with the Illumina2bam tool (Wellcome Trust Sanger Institute - NPG).
Sequencing quality was checked with FastQC (version 0.11.5, Babraham Bioinformatics) and reads were aligned to the mouse genome (GRCm38) using TopHat (version 2.1.1).
Gene expression levels were quantified with cufflinks (version 2.2.1) and normalized for library size with cuffnorm. Cuffdiff was used to find differential gene expression among conditions.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Library-sized normalized gene counts and log2 Fold change values of the multiple comparisons with their corresponding adjusted p-values.

source_name: Lymphoma

extract_protocol:
Lymphoma samples were removed and flash frozen. Total RNA from lymphoma samples was isolated using guanidine thiocyanate, followed by acid phenol–chloroform extraction.
PolyA+ RNA was extracted and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing and ligation to adapters according to Illumina’s ‘TruSeq RNA Sample Preparation Guide’. The adaptor-ligated library was completed by limited-cycle PCR with Illumina PE primers (10 cycles, or 8 cycles for samples using the v.2 protocol). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v.5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v.5 reagents, according to the manufacturer’s protocols.

tag: genotype

value: Bptf+/+; Em-Myc

tag: tumor onset

value: 58 weeks


title: Lymphoma, Bptf.WT.Late (PTB237)

value: 38 weeks


title: Lymphoma, Bptf.HET.Late (PTB100)

value: Bptf+/{delta}; Em-Myc

value: 66 weeks


title: Lymphoma, Bptf.WT.Early (PTB385)

value: 10 weeks


title: Lymphoma, Bptf.WT.Late (PTB99)

value: 76 weeks


title: Lymphoma, Bptf.WT.Early (PTB264)

value: 13 weeks


title: Lymphoma, Bptf.WT.Late (PTB267)

value: 36 weeks


title: Lymphoma, Bptf.HET.Early (PTB327)

value: 12 weeks


title: MTB4

tag: strain

value: Week 12

value: Lung


title: Lymphoma, Bptf.WT.Early (PTB374)


title: U4_4

value: none (uninfected control)

value: Lung CD8+ T cells


title: Lymphoma, Bptf.HET.Late (PTB125)

value: 30 weeks


title: Lymphoma, Bptf.HET.Late (PTB286)


title: Lymphoma, Bptf.HET.Early (PTB343)

value: 8 weeks


title: Lymphoma, Bptf.HET.Early (PTB257)


title: B2_12

value: M. bovis BCG strain Pasteur (1173P2)

value: Day 21


title: Lymphoma, Bptf.WT.Late (PTB303)

value: Bptf+/+; Em-Myc

value: 28 weeks


title: Lymphoma, Bptf.WT.Early (PTB299)

value: 17 weeks


title: Lymphoma, Bptf.WT.Early (PTB265)


title: Lymphoma, Bptf.WT.Early (PTB312)

value: 9 weeks


title: Pten;Trp53-null tumor BIF135

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

country: Spain

institute: CNIO

description: Pten;Trp53-null tumor

data_processing:
Image analysis and per-cycle basecalling was performed with Illumina Real Time Analysis software (RTA1.13). Conversion to FASTQ read format and sequence alignment with the ELAND algorithm (v2e) was performed with CASAVA-1.8 (Illumina).
Normalized counts correspond to TPM (transcripts per million)
Differential expression analysis was performed using DEseq2
Genome_build: mm10

source_name: MM

extract_protocol:
Total RNA was isolated from frozen from Pik3ca*;Trp53-null (BHV ) and Pten;Trp53-null (BIF) mice  mouse malignant mesothelioma tumors (n=6 each)  using GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich). DNA was eliminated using the DNA-free kit (Ambion-Life Technologies).
2 µg of total RNA samples was used as provided by the user. RNA Integrity Numbers were in the range 7.5 to 8.9 (average 8.5) when assayed on an Agilent 2100 Bioanalyzer. PolyA+ RNA fraction was extracted and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq RNA Sample Preparation Guide" (Part # 15008136 Rev. A). Adapter-ligated library was completed by limited-cycle PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

value: mixed background


title: Pik3ca+/H1047R;Trp53-null tumor BHV105

description: Pik3ca+/H1047R;Trp53-null tumor


title: Pten;Trp53-null tumor BIF139

description: Pten;Trp53-null tumor


title: Pik3ca+/H1047R;Trp53-null tumor BHV138

description: Pik3ca+/H1047R;Trp53-null tumor


title: Pik3ca+/H1047R;Trp53-null tumor BHV125

description: Pik3ca+/H1047R;Trp53-null tumor


title: Pik3ca+/H1047R;Trp53-null tumor BHV108

description: Pik3ca+/H1047R;Trp53-null tumor


title: Pten;Trp53-null tumor BIF99

description: Pten;Trp53-null tumor


title: Pten;Trp53-null tumor BIF134

description: Pten;Trp53-null tumor


title: Pik3ca+/H1047R;Trp53-null tumor BHV122

description: Pik3ca+/H1047R;Trp53-null tumor


title: NU7441#3

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: mm10
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: MC3T3 cells

growth_protocol: MC3T3-E1 cells were grown in αMEM (Gibco) supplemented with 10% FBS (Gibco) to confluency.

extract_protocol:
mRNeasy Mini Kit (Qiagen)
mRNA version 2 library prep kit (Illumina)

treatment_protocol: Cells were treated with NU7441 (1 μM) (Selleckchem) or DMSO (Sigma) for 16h.

tag: cell line

tag: tissue source

value: pre-osteoblasts (mouse calvaria)

tag: background strain


title: Pten;Trp53-null tumor BIF104

description: Pten;Trp53-null tumor


title: Pten;Trp53-null tumor BIF83

description: Pten;Trp53-null tumor


title: NU7441#2


title: NU7441#1


title: DMSO#3


title: DMSO#2


title: Lymphoma, Bptf.HET.Late (PTB252)

value: Bptf+/{delta}; Em-Myc

value: 44 weeks


title: DMSO#1


title: Lymphoma, Bptf.HET.Early (PTB349)


title: WT HFCF 3-months 2 [ThreeMHF1]

city: kansas city

first: Yuxia

last: Zhang

state: KS

address: 3901 Rainbow Blvd, Hemenway 4001

department: Pharmacology, Toxicology, and Therapeutics

institute: University of Kansas Medical Center

description:
3HF2
12126X14

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to mm10 whole genome using CLCBio Genomics Workbench 11 with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2ratios, adjusted p values, raw counts and FPKM values for each Sample

source_name: WT HFCF 3-month_liver

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Zymogen Research Direct-zol RNA Miniprep Plus (Cat#R2072) was used. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded RNA Kit wit Ribo-Zero Gold

tag: age

value: 6 months

tag: diet

value: HFCF diet for 3 months

value: Liver


title: WT HFCF 3-months 1 [ThreeMHF0]

description:
3HF1
12126X4


title: WT HFCF 3-months 3 [ThreeMHF2]

description:
3HF3
12126X24


title: Pik3ca+/H1047R;Trp53-null tumor BHV121

description: Pik3ca+/H1047R;Trp53-null tumor


title: WT Chow 3-months 3 [ThreeMC2]

description:
3CHOW3
12126X23

source_name: WT Chow 3-month_liver

value: normal chow diet for 3 months


title: WT HFCF 1-month 3 [OneMHF2]

description:
1HF3
12126X22

source_name: WT HFCF 1-month_liver

value: 3 months

value: HFCF diet for 1 month


title: WT Chow 3-months 1 [ThreeMC0]

description:
3CHOW1
12126X3


title: WT HFCF 1-month 2 [OneMHF1]

description:
1HF2
12126X12


title: WT Chow 1-month 2 [OneMC1]

description:
1CHOW2
12126X11

source_name: WT Chow 1-month_liver

value: normal chow diet for 1 month


title: WT Chow 1-month 1 [OneMC0]

description:
1CHOW1
12126X1


title: WT Chow 1-month 3 [OneMC2]

description:
1CHOW3
12126X21


title: brown adipocyte

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: brown adipocyte single cell RNA-seq

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline (version 2.0) to generate FASTQ files and aligned to mm10 genome to gene expression count
The subsequent data analysis was performed using “Seurat” package and R scripts
Data were scaled and log2 transformed within Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: CSV file

source_name: Inter-scapular brown adipose tissue

extract_protocol:
Brown adipocytes from 10-week-old C57BL/6J male mice were freshly isolated and resuspended in PBS containing 0.04% BSA at a concentration of 700~1200 cells/µl.
Cell number and viability were measured using a TC20 Automated Cell Counter (BioRad). Single-cell RNA libraries were prepared according to the Chromium™ Single Cell 3' Reagent Kits v2 User Guide (10x Genomics). Approximately 10,000 cells were loaded on a Chromium single cell Controller instrument (10x Genomics) to generate single cell gel beads in emulsion (GEMs). The barcoded sequencing libraries were constructed using the Chromium Single-Cell 3′ Library Kit (10x Genomics) for enzymatic fragmentation, end-repair, A-tailing, adaptor ligation, ligation cleanup, sample index PCR, and PCR cleanup.

value: brown adipose tissue

value: 10 weeks old

value: wild type


title: E14.5 WT FL-derived LSK CD48- HSC cells cross-linked with ESAM mAb

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: fetal liver-derived E14.5 WT LSK CD48- cells incubated with a ESAMmAb

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: mm10

extract_protocol:
RNA was extracted using TRIzol (Invitrogen) according to the manufacturer's instructions.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: LSK CD48- cells of E14 FLs, on which high amount of ESAM is uniformly expressed, were incubated with or without a rat mAb against mouse ESAM. Then, the cells were incubated with goat anti-rat IgG Abs-conjugated microbeads for 4 hrs and were subsequently applied to RNA-sequencing analyses.

value: hematopoietic stem cells


title: ESAM-WT

description: E14.5 LSK CD48- ESAM-WT fetal liver HSC cells

source_name: E14.5 LSK CD48- ESAM-WT FL-derived HSC cells

extract_protocol:
RNA was extracted using TRIzol (Invitrogen) according to the manufacturer's instructions.
cDNA was generated using a Clontech SMART-Seq v4 Ultra Low Input RNA Kit (Takara Clontech, Mountain View, CA, USA). Each cDNA sample was sheared (200 - 500 bp) using the Covaris S220 (Covaris, Woburn, MA, USA) and prepared using KAPA Library Preparation Kits (Kapa Biosystems, Wilmington, MA) for 75 bp single-end reads, according to the manufacturer’s instructions.

treatment_protocol: LSK CD48- cells were sorted from ESAM KO or WT fetal liver in 3 ml of Methocult GF M3434 (StemCell Technologies), distributed them into three 35-mm dishes, and incubated them in 5% CO2 at 37℃.


title: ESAM-null

description: E14.5 LSK CD48- ESAM-null fetal liver HSC cells

source_name: E14.5 LSK CD48- ESAM-null FL-derived HSC cells


title: WT Chow 3-months 2 [ThreeMC1]

description:
3CHOW2
12126X13


title: WT HFCF 1-month 1 [OneMHF0]

description:
1HF1
12126X2


title: E14.5 WT FL-derived LSK CD48- HSC cells untreated with ESAM mAb

description: fetal liver-derived E14.5 WT LSK CD48- cells incubated without a ESAMmAb


title: Control-3: 0 (control) for 2 weeks, biological rep3

type: RNA

city: Osaka

first: Takako

last: Fukuda

address: 1-98, Kasugadenaka 3-chome, Konohana-ku

institute: Sumitomo Chimical Co., Ltd

description: Gene expression data from liver of mouse fed diets containing 0 (control) ppm chemical for 2 weeks

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained with GeneChip Hybridization, Wash and Stain Kit (Affymetrix).

scan_protocol: GeneChips were scanned with a GeneChip Scanner 3000 (Affymetrix) and the image files were obtained.

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

label: biotin

label_protocol: Biotin-labeled cRNA were prepared from 5 ug of total RNA using GeneChip IVT Labeling Kit (Affymetrix) following the manufacturer's protocol.

growth_protocol: Crlj:CD1(ICR) female mice aged 9 weeks were purchased, quarantined for 1 weeks and maintained at 22 - 26°C and a relative humidity range of 40 - 70% with frequent ventilation. A powdered diet and water were provided ad libitum.

extract_protocol: The livers were stored in RNAlater RNA Stabilization Reagent (Qiagen, Hilden, Germany) at –20°C. Total RNA samples were extracted from liver using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: Animals were fed diets containing 0 (control), 5000 ppm permethrin, and 5000 ppm clofibrate for periods of 2 weeks.

tag: gender

value: female

value: liver


title: Clofibrate-1: 5000 ppm clofibrate for 2 weeks, biological rep1

description: Gene expression data from liver of rats fed diets containing 5000 ppm clofibrate for 2 weeks

source_name: liver of mouse fed diets containing 5000 ppm clofibrate for 2 weeks


title: Permethrin-3: 5000 ppm permethrin for 2 weeks, biological rep3

description: Gene expression data from liver of rats fed diets containing 5000 ppm permethrin for 2 weeks

source_name: liver of mouse fed diets containing 5000 ppm permethrin for 2 weeks


title: Nos2-/- macrophages_LPS-IFNy stimulated_8h_biological rep2

city: Frederick

first: Erika

middle: M

last: Palmieri

address: 1050 Boyles Street BG 560 RM 31-45

institute: National Cancer Institute, NIH

description: Gene expression data from Bone Marrow Derived Macrophages from Nos2 Knock Out mice, after 8h of proinflammatory stimulation.

hyb_protocol: Three replicates of each group were prepared, labeled, and hybridized to Affymetrix mouse 430 2.0 GeneChip

scan_protocol: Samples were scanned on Affymetrix GeneChip scanner 3000

data_processing: Data were collected using Affymetrix AGCC software. Analysis was performed with Partek Genomics Suite software using RMA normalization algorithm.

source_name: macrophages stimulated with LPS/IFNy for 8hours

label_protocol: RNA (100 ng) was reverse transcribed and labeled with biotin using Affymetrix 3’ IVTexpress Labeling kit following manufacturer’s protocol.

growth_protocol: Total cells from the bone marrow were plated at 7.0 x 10^5 / mL for 5-7 days in complete Dulbecco’s modified eagles media (DMEM) (Gibco #11965) supplemented with 2mM Glutamine, 10% FBS, 100U/mL Penicillin/Streptomicin and 20ng/ml mouse M-CSF allowing for proper BMDM differentiation and growth.

extract_protocol: Total RNA was isolated using the Hig-Pure Rna isolation kit (Roche, 11828665001), as per manufacturer's instructions (with the addition that 2-mercaptoethanol (1%v/v) was added to the lysis buffer. RNA quality was checked on Agilent Bioanalyzer.  All samples used for microarray analysis have high quality score (RIN >8).

treatment_protocol: After growing BMDM for 6 days in culture, cells were placed in complete culture media and treated with vehicle (PBS) or the combination of LPS (100ng/mL) and 50ng/mL of IFNγ for 8h for proinflammatory activation.

value: bone marrow derived macrophages

tag: treatment


title: H1299_NT2_2 [s_21]

city: Jacksonville

first: E. Aubrey

last: Thompson

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

data_processing:
RNA-seq reads were aligned to the GRCh38 genome assembly using TopHat v2.1 and bowtie v1.1.2 with the following options: --keep-fasta-order, --keep-tmp, --no-coverage-search, --bowtie1, --library-type fr-unstranded, --max-multihits 20, --solexa1.3-quals, --fusion-search, --fusion-ignore-chromosomes chrM, --fusion-min-dist 50000
Gene counts are generated by FeatureCounts using the gene definitions files from Ensembl v78. Option "-O" within FeatureCounts is used to account for the expression derived from regions shared by multiple genomic features.
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated.
Genome_build: GRCh38
Supplementary_files_format_and_content: abundance measurements

extract_protocol:
Total RNA was extracted using theRNAqueous phenol-free total RNA isolation protocols (Ambion, Life Technologies, Grand Island, NY). Extracted RNA was subjected to DNase treatment to eliminate DNA contamination according to provider’s instructions using TURBO DNA-freeTM (Ambion, Life Technologies, CA). Quality of RNA samples was determined using an Agilent Bioanalyzer and only samples with RINs >9.0 were used for genomic sequencing analysis. Sequencing was carried out at Mayo Clinic Advanced Genomic Technology Center at Rochester, MN.
RNA libraries were prepared using 120 ng of total RNA according to the manufacturer’s instructions for the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA).  The concentration and size distribution of the completed libraries was determined using an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA) and Qubit fluorometry (Invitrogen, Carlsbad, CA).   Libraries were sequenced at 50-80 million read pairs per sample following Illumina’s standard protocol using the Illumina cBot and Paired end cluster kit version 3. The flow cells were sequenced as 101 X 2 paired end reads on an Illumina HiSeq 2000 using TruSeq SBS sequencing kit version 3 and HCS 2.2.58 data collection software. Base-calling is performed using Illumina’s RTA version 1.18.64.

value: non-small cell lung cancer cell line

tag: culture type

value: spheroid cultured tumor cells

tag: genotype/variation

value: NT


title: Clofibrate-3: 5000 ppm clofibrate for 2 weeks, biological rep3

tag: tissue


title: H1299_SOX2_KD_1 [s_20]

value: SOX2 KD


title: H1299_NT2_3 [s_23]


title: Control-1: 0 (control) for 2 weeks, biological rep1

source_name: liver of mouse fed diets containing 0 (control) ppm chemical for 2 weeks


title: H1299_SOX2_KD_2 [s_22]


title: Permethrin-1: 5000 ppm permethrin for 2 weeks, biological rep1


title: Permethrin-2: 5000 ppm permethrin for 2 weeks, biological rep2


title: H1299_NT2_1 [s_19]


title: Nos2-/- macrophages_LPS-IFNy stimulated_8h_biological rep3

value: after 8h of proinflammatory stimulation.


title: H1299_PRKCI_KD_3 [s_12]

value: PRKCI KD


title: H1299_SOX2_KD_3 [s_24]


title: Nos2-/- macrophages_LPS-IFNy stimulated_8h_biological rep1


title: Control-2: 0 (control) for 2 weeks, biological rep2


title: Nos2-/- macrophages_untreated_biological rep1

description: Gene expression data from Bone Marrow Derived Macrophages from Nos2 Knock Out mice, before proinflammatory stimulation.

source_name: macrophages unstimulatd

value: before proinflammatory stimulation.


title: Clofibrate-2: 5000 ppm clofibrate for 2 weeks, biological rep2


title: Wild type macrophages_untreated_biological rep3

description: Gene expression data from Bone Marrow Derived Macrophages from WT mice, before proinflammatory stimulation.

value: Wild Type


title: Wild type macrophages_untreated_biological rep1


title: Nos2-/- macrophages_untreated_biological rep3


title: Nos2-/- macrophages_untreated_biological rep2


title: Wild type macrophages_LPS-IFNy stimulated_8h_biological rep3

description: Gene expression data from Bone Marrow Derived Macrophages from WT mice, after 8h of proinflammatory stimulation.


title: H1299_NT1_3 [s_11]


title: Wild type macrophages_LPS-IFNy stimulated_8h_biological rep1


title: H1299_NT1_2 [s_9]


title: Wild type macrophages_untreated_biological rep2


title: Wild type macrophages_LPS-IFNy stimulated_8h_biological rep2


title: GE0089197

city: Oslo

first: Xavier

last: Tekpli

address: Ullernchauséen 70

department: Cancer Genetics

country: Norway

institute: Oslo University Hospital Radiumhospitalet

data_processing:
Raw sequencing read data were demultiplexed and filtered using Bowtie2 against ribosomal, phiX174, and UCSC RepeatMasker sequences. The remaining reads were aligned using TopHat2 v2.0.13  to the GRCh38. Cufflinks v2.2.1 was used to calculate expression levels in the form of fragments per kilobase of exon per million mapped reads (FPKM). Isoform-level gene expression data were collapsed to unique gene symbols (sum of FPKM values of each matching transcript).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for all samples

source_name: Breast

extract_protocol:
RNA was isolated using the QIAgene kit Allprep DNA/RNA/miRNA universal on the QIAcube machine and method
Illuminas TruSeq Stranded mRNA Library Prep Kit for NeoPrep

treatment_protocol: Breast tumors were snap-frozen  after surgery

value: Breast

tag: disease state

value: Tumor

tag: er status

value: Pos

value: Normal

tag: ror score

tag: immune cluster

value: ClusterB


title: GE0089198

value: Neg

value: ClusterC


title: GE0089204

value: LumB


title: GE0089207


title: GE0089201

value: ClusterA


title: H1299_PRKCI_KD_1 [s_8]

tag: cell type

value: non-small cell lung cancer cell line


title: H1299_NT1_1 [s_7]

value: spheroid cultured tumor cells


title: GE0089123

value: LumA


title: GE0089194

value: Basal


title: GE0089121


title: GE0089184


title: GE0089185


title: GE0089175


title: GE0089179


title: GE0089177


title: GE0089180


title: GE0083768


title: GE0083728


title: GE0089203


title: GE0089196


title: GE0089178


title: GE0089195


title: GE0083680


title: GE0083720


title: GE0083576


title: GE0083600


title: GE0083664


title: GE0083672


title: GE0083704


title: GE0083568


title: GE0083552


title: GE0083544


title: GE0083640


title: GE0083512


title: GE0083632


title: GE0083608


title: GE0083400


title: GE0083464


title: GE0083448


title: GE0083384


title: GE0083392


title: GE0083408


title: GE0083424


title: GE0083416


title: GE0089186


title: GE0083368


title: GE0081441


title: GE0081445


title: GE0081444


title: GE0083696


title: GE0081440


title: GE0081439


title: GE0081433


title: GE0081438


title: GE0081436


title: GE0081432


title: GE0081435


title: GE0081434


title: GE0081430


title: GE0081431


title: GE0081426


title: GE0081429


title: GE0081427


title: GE0081424


title: GE0081423


title: GE0084009


title: GE0084013


title: GE0084010


title: GE0084014


title: GE0089188


title: GE0084015


title: GE0081422


title: GE0084016


title: GE0084008


title: GE0082990


title: GE0084007


title: 3523

city: New Orleans

first: Jay

middle: K

last: Kolls

state: LA

address: 333 S. Liberty St, JBJ 375

department: Center for Translational Research in Infection and Inflammation

institute: Tulane University School of Medicine

data_processing:
10x Cellranger V.2.1.0 was used to generate Fastq files, perform alignment, filtering, barcode counting, UMI counting, and aggregation.
Seurat V.2.3.1 for scRNA QC and further analysis
R1 and I1 are technical reads. R1 has the barcode in bp 1-16, and the UMI 17-26. Files with I1 are the separate index reads. R2 is the biological read.
Genome_build: mm10
Supplementary_files_format_and_content: H5 file filtered-gene-barcode-matrix can be deconvoluted to tsv and mtx files

source_name: Liver

extract_protocol:
RNA was extracted from liver single cell suspension using the 10X Genomics Chromium™ Single Cell A Chip Kit V2
Library construction was performed according to 10X v2 kit protocol.

treatment_protocol: Naïve or 25mg/kg intravenous Concanavalin A injected 90 minutes prior to sample collection

tag: time point

tag: agent

value: concanavalin


title: GE0083925


title: GE0083926


title: GE0082982


title: 3520

tag: strain


title: GE0082974


title: GE0082966


title: GE0082958


title: GE0082950


title: GE0082934


title: GE0082942


title: 968

value: Naïve


title: 3521


title: 962


title: 965


title: 964


title: GE0082918


title: GE0082926


title: GE0082910


title: Pfalciparum_3D7_hour60

city: Durham

first: Steven

last: Haase

state: North Carolina

institute: Duke University

data_processing:
Reads were aligned using STAR_2.4.1d with parameters --runMode alignReads --outFilterType BySJout --alignIntronMin 10 --alignIntronMax 3000 --outFilterIntronMotifs RemoveNoncanonical
Aligned, sorted SAM files were created with cuffquant v2.2.1 with parameter --library-type=fr-firststrand
Samples from each strain were normalized by Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using cuffnorm v2.2.1 with parameter --library-type=fr-firststrand
Genome_build: The Sanger Institute's P. falciparum 3D7 v3.0 genome
Supplementary_files_format_and_content: Tab-delimited text files for each strain with FPKM values for all genes per timepoints, which are given in hours

organism: Plasmodium falciparum

source_name: in vitro culture

growth_protocol: Parasites were synchronized by alanine treatment and temperature cycling as decribed in Haynes and Moch 2002 (PMID:12125145). For the course of the experiment, strains were grown at 37C in RPMI 1640 with 10% human serum and 4% hematocrit. Flasks were gassed with 5% CO2, 5% O2, 90% N2. Cultures were sampled every 3 hours, and sampling began between late schizont and early ring stages.

extract_protocol:
Samples were spun down, media aspirated, and pellet snap frozen and stored at -80C. Total RNA was extracted using a phenol-chloroform protocol as described in Leman et al 2014 (PMID: 24906319), except citrate-buffered phenol was substituted for acid phenol. The ratios of reagent to sample as found in the cited protocol were retained, with the exception of the initial thawing in TES buffer, which was changed to a 2:1 ratio of TES to sample.
Libraries were prepared using Stranded Total RNA Kapa kits with rRNA Ribo-Zero Globin depletion


title: Pfalciparum_3D7_hour51


title: Pfalciparum_3D7_hour57


title: Pfalciparum_3D7_hour54


title: GE0082902


title: GE0081589


title: Pfalciparum_3D7_hour45


title: Pfalciparum_3D7_hour48


title: Pfalciparum_3D7_hour42


title: GE0081588


title: GE0081587


title: GE0081586


title: Pfalciparum_3D7_hour36


title: GE0081584


title: GE0081585


title: Pfalciparum_3D7_hour33


title: H1299_PRKCI_KD_2 [s_10]

tag: cell line

value: PRKCI KD


title: 3522


title: Pfalciparum_3D7_hour27


title: PC9-TAZ4SA

first: Ann Marie

last: Pendergast

address: 308 Research Drive LSRC

department: Pharmacology and Cancer Biology

data_processing:
Libraries were sequences on an Illumina HiSeq 2000 sequencing system using 50-bp single-ended reads by the Duke University Genome Sequencing facility.
RNA-seq data was processed using the TrimGalore toolkit, and reads that were 20 nt or longer after trimming were used for further analysis.
Reads were mapped to the GRCh37 version of the human genome and transcriptome using the STAR RNA-seq alignment tool.
Reads were used for subsequent analysis if they mapped to a single genomic location.
Gene counts were compiled using the HTSeq tool. Only genes that had at least 10 reads in any given library were used in subsequent analysis. Normalization and differential expression were carried out using the DESeq2 package in the R statistical programming environment.
Genome_build: GRCh37
Supplementary_files_format_and_content: diff expression files including log2fold change values for each sample

source_name: non-small cell lung adenocarcinoma

growth_protocol: Cells were cultured in RPMI 1640 medium containing 10% FBS + 10 mM HEPES, 1 mM Sodium Pyruvate and 0.2% glucose

extract_protocol:
RNA was harvested using the Qiagen RNeasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols by the Duke University Sequencing and Genomic Technologies core facility.

treatment_protocol: PC9 parental cells were lentivirally-transduced with control pLVX-Tet-On Advanced and/or pLVX-TP-3F-TAZ4SA plasmids. Expression of TAZ4SA was induced by treating sub-confluent monolayers of cells with 50 ng/mL doxycycline for 24 hrs prior to RNA harvest.

value: adenocarcinoma

value: expressing active mutant TAZ4SA


title: PC9 Control

value: control


title: Pfalciparum_3D7_hour30


title: Pfalciparum_3D7_hour21


title: P3_D13

city: Los Angeles

first: Brigitte

last: Gomperts

address: 650 Charles E. Young Drive; 9-240 Factor Building

institute: UCLA

description: iFA_model_stepwise_progression_Vijayaraj.txt

data_processing:
The iSDC cultures raw sequence reads were demultiplexed using custom scripts and converted to Sanger fastq format.   After trimming adaptor sequences, the sequence reads were then aligned to the Homo Sapiens genome and gene model from NCBI 37.2 release using Tophat version 2.0.9. The gene expression values as Fragments Per Kilobase of transcripts per Miilion mapped reads (FPKM) were measured and normalized using the cuffnorm program from Cufflinks version 2.2.1 and used in the subsequent analysis. Technical replicates were combined and aligned together in all cases except for the AA5-treated model. The gene expression estimates were then log2-transformed and genes with no reads across all samples were removed from further analysis.
Genome_build: NCBI 37.2 release
Supplementary_files_format_and_content: Text (tab delimited) files report log2-transformed FPKMs

source_name: Aggregate cultures of iSDCs

extract_protocol:
iFA model: In-vitro cultures of PF and cells in the iFA model were washed once with PBS and total RNA from the samples were extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
Libraries for RNA-Seq were prepared with the Nugen human FFPE Kit (LSC). The workflow consisted of cDNA generation, end repair to generate blunt ends, adaptor ligation, adaptor cleavage and PCR amplification. Different adaptors were used for multiplexing samples sequenced in the same lane. The libraries of aggregate iSDC cultures treated with AA5 or DMSO were sequenced with 75-bp single-end reads on the Illumina Nextseq500 system.  The libraries of aggregate iSDC cultures at day 4 and day 13 were run with 50-bp paired-end reads on the Illumina system (model HiSeq 2000).

tag: type

value: iFA model (stepwise progression)

tag: individual

value: Patient 3

tag: Stage

value: Day 13


title: P7_D13

value: Patient 7


title: P7_D4

value: Day 4


title: Pfalciparum_3D7_hour15


title: P3_D4


title: P4_D4

value: Patient 4


title: Pfalciparum_3D7_hour18


title: Pfalciparum_3D7_hour9


title: Pfalciparum_3D7_hour39


title: Pfalciparum_3D7_hour3


title: Pfalciparum_3D7_hour6


title: Pfalciparum_3D7_hour0


title: Pfalciparum_3D7_hour24


title: P4_D13


title: WT_E1h_Veh_ER

first: Yukitomo

last: Arao

address: 111 TW Alexandr Dr.

institute: NIEHS

data_processing:
Raw sequencing reads were trimmed to 36bp then filtered to retain only those with average base quality score > 20.
Reads were mapped against the mm9 reference assembly via Bowtie2 (v2.1.0) with parameters "--end-to-end --sensitive", then filtered via samtools to require a minimum mapping score of 30.
Duplicate reads within a given library were removed via Picard MarkDuplicates.jar.
For samples with two libraries, mapped deduplicated hits were aggregated via Picard MergeSamFiles.jar.
Peaks were called via HOMER (v4.10.3) findPeaks with parameters "-style factor -fdr 0.00001 -F 12" using GSM894057 as the corresponding input.  Peaks were then re-defined as 200bp regions centered on the called peak midpoint.
To generate depth tracks the mapped non-duplicate reads were extended to the estimated average fragment size of 150bp, converted to bedGraph via BEDtools (v2.24.0) genomeCoverageBed, normalized to 20M reads, then converted to bigWig format by UCSC utility bedGraphToBigWig.
Genome_build: mm9
Supplementary_files_format_and_content: Peaks in BED format; normalized depth tracks in bigWig format.

source_name: mouse uterus

growth_protocol: Animals were maintained on a NIH-31 regular diet.

extract_protocol:
Frozen mouse tissue was submersed in PBS + 1% formaldehyde, cut into small pieces and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final). The tissue pieces were then treated with a TissueTearer and finally spun down and washed 2x in PBS. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.

treatment_protocol: OVX 12-wk-old AF2ERKI or WT littermate female mice (six animals per group) were injected intraperitoneally with 2 mg/kg fulvestrant/ICI182780 (ICI) or 2 mg/kg tamoxifen (Tam) dissolved in DMSO respectively. 50 µl DMSO was injected as vehicle (Veh). After 1h injection, animals were euthanized with carbon dioxide, then uterus was collected. Collected tissues were stored at -70 ˚C until processed.

value: uterus

tag: chip antibody

value: ER[alpha] Santa Cruz SC-542

value: wild type

value: 50 ul DMSO


title: Af2KI_E1h_Veh_ER

value: ERalpha AF-2 mutant

tag: treatment


title: Pfalciparum_3D7_hour12


title: Af2KI_E1h_ICI_ER

value: 2 mg/kg fulvestrant/ICI182780 (ICI)


title: Salmonella RiboZero 2

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

description: Sample 3

data_processing:
Mapping and read counting with reademption 0.4.3 using the RefSeq Salmonella Typhimurium SL1344 sequence and annotation
Genome_build: RefSeq Salmonella Typhimurium SL1344 (NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1)
Supplementary_files_format_and_content: [gene_wise_quantifications.csv]  Raw read table

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Salmonella RiboZero 2

growth_protocol: Salmonella cells were grown in liquid Lennox broth (LB) medium at 37°C with shaking at 220 rpm to an OD600 of 2.0

extract_protocol:
Cultures grown to an OD600 of 2 were mixed with 0.2 volumes of STOP solution (95% ethanol, 5% phenol) and RNA was extracted using the TRIzol reagent (Invitrogen) according to the manufacturer's protocol
Before library preparation, rRNA depletion was performed for samples 1-3 using either the RiboZero Kit bacteria according to the manufacturer's protocol (Illumina; samples 2 and 3) or the riboPOOL protocol described in Kim et al. 2019 (Efficient depletion of ribosomal RNA for RNA sequencing in planarians; sample 1). For the riboPOOL protocol, 1 µg of total RNA and 1 µl 100 µM Salmonella-specific riboPOOLs (siTOOLS) were used and the amount of Streptavidin beads was reduced to 80 µl per sample.
Sequencing libraries were prepared by IMGM Laboratories, Martinsried, Germany

tag: condition

value: RiboZero depleted RNA


title: Salmonella RiboPools

description: Sample 1

source_name: Salmonella RiboPools

value: RiboPools depleted RNA


title: XY5_SJL

first: Yuichiro

last: Itoh

state: California

address: 635 Charles E. Young Drive South

department: Neurology

description: RNA from auto antigen specific CD4+ T cells

data_processing:
Data quality check was done on Illumina SAV
De-multiplexing was performed with Illumina Bcl2fastq2 v 2.17 program
R package “QuasR” was used for the read alignment to mouse genome (mm10) followed by the counting at gene level
Genome_build: mm10
Supplementary_files_format_and_content: "mm10.gene_SJLFCG_ensGene.xlsx" has raw count values for each sample

source_name: Lymph node

growth_protocol: Animals were maintained under standard conditions in a 12 h dark/12 h light cycle with access to food and water ad libitum.

extract_protocol:
surgery protocol: Young mice (age 4-6 weeks) were gonadectomized (females: ovariectomy, males: castration). Prior to surgery and 24 hours after, the mice received 1.2 mg/mL Carprofen (Zoetis). The mice were given Amoxicillin (50 mg/mL, Virbac) as antibiodic in the water source for 7 days following surgery.
culture protocol: Auxillary, brahcial, and inguinal draning lymph nodes were collected and processed into single cell suspensions. Cells were sorted for CD4+ T cells by magnetic negative selection using EasySep Mouse CD4+ T cell isolation kit (STEMCELL). The cells were cultured in the presence of anti-CD3/CD28 DynaBeads for 36 hours.
RNA was isolated from CD4+ T cells using the Direct-zol™ RNA MiniPrep Plus kit (Zymo Research).
Double-stranded cDNA and the sequencing library were made using the Kapa RNA Kit Full kit.

value: SJL

value: Lymph node

value: CD4+ T cell

tag: Sex

value: Female

tag: genotype

value: XY


title: XY3_SJL

tag: tissue


title: Af2KI_E1h_Tam_ER

tag: genotype/variation

value: 2 mg/kg tamoxifen


title: WT_E1h_Tam_ER


title: Macrophages from aCXCR2 2

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: Six-hundred ng of labelled specimens were hybridized on Agilent SurePrint G3 Mouse 8x60K Gene Expression arrays.

scan_protocol: After 17 hours the slide was washed and scanned using the Agilent Scanner version C (G2505C, Agilent Technologies).

data_processing: Raw data were processed using the Bioconductor package Limma (Linear models for microarray analysis). Background correction was performed with the normexp method with an offset of 50, and quantile was used for the between-array normalization. The  empirical

source_name: CD45+CD11b+F480+ cells isolated from the whole prostate of a Pten KO; Trp53 KO mouse

label_protocol: Briefly, 100 ng of totRNA were amplified, labelled with Cy3-CTP and purified with columns.

growth_protocol: Macrophages were isolated from the prostatic tissue of Pten KO; Trp53 KO mice and immediately processed

extract_protocol: Total RNA was quantified by NanoDrop ND-1000 Spectro-photometer (NanoDrop Technologies, Wilming-ton, DE) and RNA quality was assessed using Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Mice were treated with intraperitoneal injections of 100ml of the vehicle or 100ml aCXCR2 (AZD5069) from Astrazeneca, at a final concentration of 100mg/kg daily for a period of 3 weeks

value: CD45+CD11b+F480+ cells

value: a Pten KO; Trp53 KO

value: Prostate


title: Macrophages from aCXCR2 1


title: Macrophages from Untreated 1

value: untreated


title: Salmonella Total RNA

description: Sample 4

source_name: Salmonella Total RNA

value: Undepleted control


title: shTHOC5

city: Hannover

first: Doan Duy Hai

last: Tran

state: Niedersachsen

address: Carl-Neubergsstr. 1

department: Institut of physiological Chemistry

institute: Hannover Medical School

data_processing:
bcl2fastq v2.17.1.14 used for basecalling.
Sequenced reads were trimmed for adaptor sequence using Trim Galore!, then mapped to GRCh38 whole genome using bowtie2 (Galaxy Version 2.3.4.1) with parameters -D 20 -R 3 -N 0 -L 20 -i S,1,0.50.
The gene expression values (Fragments Per Kilobase Million (FPKM)) were calculated by Cuffdiff (Galaxy Version 2.2.1.5) using human NONCODEv5 transcript reference.
Genome_build: GRCh38
Supplementary_files_format_and_content: tabular file includes FPKM values for shRNA control sample and shTHOC5 sample

growth_protocol: HepG2 cells were grown in DMEM supplemented with 10% FCS.

extract_protocol:
Total RNAs were isolated using High Pure RNA isolation kit (Roche) in accordance with the manufacturer's recommendations.
RNA-seq libraries were generated using NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: HepG2 cells were infected with lenti virus carry shRNA control and shTHOC5. 3 days after infection, total RNAs were isolated.

tag: shRNA

value: HepG2 was derived from a liver hepatocellular carcinoma of a 15 year old Caucasian male.

value: liver

tag: disease

value: Hepatocellular carcinoma


title: Macrophages from aCXCR2 3

tag: cell type


title: Macrophages from Untreated 3


title: BeWo_IGF_TNF100n_rep2

city: Mitaka

first: Kei

last: Tanaka

state: Tokyo

institute: Kyorin University

hyb_protocol: The fragmented cRNA (600 ng) was hybridized to the SurePrint G3 Human GE microarray 8x60K Ver. 3.0 (Agilent). After hybridization, the array slides were washed using Gene Expression Wash Buffer 1 and 2 (Agilent Technologies),

scan_protocol: After washing, slides were scanned with the Agilent microarray scanner G2505B.

data_processing: Feature extraction software (version 10.7.3.1) was used to calculate signal intensities from the scanned images.

source_name: BeWo, IGF-I, TNF-alpha 100ng/ml, replicate2

label_protocol: Total RNA samples (100 ng) were amplified and labelled with Cy3 using the Low Input QuickAmp Labeling Kit (Agilent).

growth_protocol: BeWo cells were incubated with Ham F-12 medium supplemented with 10% fetal calf serum at 5% CO2 and 95% air at 37°C.

extract_protocol: Toral RNA was extracted from BeWo cells using Quiagen AllPrep DNA/RNA Mini Kit according to standard instructions.

treatment_protocol: Bewo cells were incubated with TNF-α (100pg/ml, 100ng/ml) and IGF-I (100ng/ml) for 48  hrs.

value: choriocarcinoma cell line

value: BeWo


title: BeWo_IGF_TNF100n_rep1

source_name: BeWo, IGF-I, TNF-alpha 100ng/ml, replicate1


title: XY4_SJL


title: PC3_sgHIC1_4

city: Shanghai

first: Tianqi

address: No.270 Dong'an Road

department: Cancer institute

country: China

institute: Fudan University Shanghai Cancer Center

description: Gene expression

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) was used followed by the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Agilent Feature Extraction (FE) software.

source_name: cell line

label_protocol: Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-2305) was used to label cRNA according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104) purification. Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: The human PCa cell line PC3 were obtained from American Type Culture Collection (ATCC) and cultured according to standard protocols.The cells were all cultured in a 37℃ water-saturated 5% CO2 atmosphere.

extract_protocol: Total RNA was isolated from the tissues using TRI Reagent (Cat.no.T9424; Sigma) according to the manufacturer’s protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The Cas9 expression constructs Lenticas9-blast and the sgRNA expression plasmid Lentiguid-puro was used to generate stable HIC1 knockout PC3 cell line. These plasmids were generated and preserved by our group.The sgRNA sequence of HIC1: CCGCCGCGAAATGGGTCGGAAGG.The knockdown efficiency was evaluated by western blotting.

tag: transfection


title: shRNA control

value: shRNA control


title: BeWo_IGF_TNF100p_rep2

source_name: BeWo, IGF-I, TNF-alpha 100pg/ml, replicate2


title: BeWo_IGF_TNF100p_rep1

source_name: BeWo, IGF-I,TNF-alpha 100pg/ml, replicate1


title: PC3_ctrl

description: Gene expression

value: Ctrl


title: BeWo_IGF_rep1

source_name: BeWo, IGF-I, replicate1


title: BeWo_IGF_rep2

source_name: BeWo, IGF-I, replicate2


title: Salmonella RiboZero 1

description: Sample 2

source_name: Salmonella RiboZero 1

value: RiboZero depleted RNA


title: XY2_SJL

value: SJL

value: Lymph node

value: CD4+ T cell


title: Macrophages from Untreated 2


title: BeWo_TNF100n_rep2

source_name: BeWo, TNF-alpha 100ng/ml, replicate2


title: XXSry5_SJL

value: Male

value: XXSry


title: XY1_SJL

value: Female

value: XY


title: XXSry4_SJL


title: XXSry3_SJL


title: XXSry2_SJL


title: XX5_SJL

value: XX


title: XX4_SJL


title: XXSry1_SJL


title: BeWo_TNF100n_rep1

source_name: BeWo, TNF-alpha 100ng/ml, replicate1


title: XX3_SJL


title: WT_crassa_Rapid-2

city: Eugene

first: Jeffrey

middle: N

last: McKnight

state: OR

address: 1229 University of Oregon, 1318 Franklin Blvd, Rm 273 Onyx Bridge

department: Institute of Molecular Biology

institute: University of Oregon

description: Nucleosomal DNA

data_processing:
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) with Bowtie2
Dyads were calculated by taking the midpoint of paired-end reads from fragments between 100 and 200 bp
Data were normalized such that average value at a genomic position was 1.0
Genome_build: S. cerevisiae genome build sacCer3 (R64)
Genome_build: S. pombe genome build ASM294v2
Genome_build: N. crassa genome build NC12, but with the large inversion on LGVI corrected (see Series-level supplementary files neurospora_crassa_or74a_12_genome_FIXED.fasta and neurospora_crassa_or74a_12_transcripts_FIXED.gtf)
Supplementary_files_format_and_content: tab-delimited chromosome/position/normalized dyad counts; coverage file (chr, position, count)

organism: Neurospora crassa

source_name: germinated conidia from WT N crassa

growth_protocol: exponentially-growing yeast were grown in YPD until OD600 was between 0.6 and 1.0. Yeast patches were grown overnight on YPD or selective agar. S. pombe was grown to OD600=0.8 in YES(5) media. N. crassa conidia (2.5*10^7 cells) were grown in Vogel's solution plus 1.5% sucrose for 3.5 hours until >70% of conidia were germinated.

extract_protocol:
cells were crosslinked with 1% formaldehyde for 15 min (10min for N. crassa), spheroplasted,  digested with micrococcal nuclease and quenched. For "standard" protocol, crosslinks reversed overnight at 65 degrees with proteinase K treatment, phenol-chloroform extracted, RNase-treated, mononucleosome band gel-extracted and CIP-treated. For Rapid protocol, RNase was added for 30 minutes, then crosslinks were reversed at 65 degrees with proteinase K treatment for 45 minutes. DNA was recovered by MinElute column (eluted into 1x cutsmart buffer) and incubated with Quick CIP for 10 minutes.
CIP-treated nucleosome-sized DNA footprints were converted to libraries with NuGEN Ovation Ultralow kit

tag: strain background

value: WT


title: XX2_SJL

tag: strain


title: XX1_SJL


title: XYSry4_SJL

value: XYSry


title: XYSry5_SJL


title: WT_crassa_Rapid-1

description: Nucleosomal DNA


title: BeWo_control_rep2

source_name: BeWo, control, replicate2

tag: cell line


title: XYSry2_SJL


title: isw2_cerevisiae_Rapid_Patch-2

description: Nucleosomal DNA

organism: Saccharomyces cerevisiae

source_name: patched W303 yeast ISW2::KANMX


title: XYSry1_SJL


title: isw2_cerevisiae_Rapid_Patch-1

description: Nucleosomal DNA

source_name: patched W303 yeast ISW2::URA3


title: N2_P0_sRNA-seq

city: Paris

first: Germano

last: Cecere

address: Institut Pasteur, 28 Rue Du Docteur Roux, Batiment Monod, 4eme Etage

department: Development and stem cell biology

institute: Institut Pasteur

description: total sRNA

data_processing:
The 3' adaptor (TGGAATTCTCGGGTGCCAAGG) was trimmed from the raw reads using cutadapt (version 1.15)
The trimmed reads were sorted by sequence using fastq-sort (from fastq-tools version 0.8) with option -s and deduplicated using a custom haskell program, keeping the highest quality among duplicates, at any given position
The 5' and 3' 4 nt UMIs were removed from the deduplicated reads using cutadapt (version 1.15) with options -u 4 and -u -4
After removing UMIs, the reads from 18 to 24 nt were selected using bioawk version 20110810
The size-selected reads were mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.1) with options -L 6 -i S,1,0.8 -N 0
The reads that failed to map were inspected using grep -E -B 1 -A 2 "^G[ACGTN]{20,25}T+$" to detect possible reads starting with G with 20 to 25 nt followed by a poly-U tail that might have prevented the mapping, and this tail was removed from such reads using a custom haskell program before re-mapping them.
Mapped and remapped reads were used to estimate the abundance of small RNAs derived from structural RNAs using featureCounts (version 1.5.2) with options -O -s 1 --fracOverlap 1 and annotations corresponding to tRNA, snRNA, snoRNA, rRNA or RNA (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)
The abundance of non-structural RNAs was estimated by subtracting the above counts from the number of mapped and remapped reads.
Initially mapped reads were classified using a custom python program according to their length, composition and on the annotations on which they mapped. Reads that didn't match miRNA and piRNA annotations were considered as potential endo-siRNAs.
The potential endo-siRNAs of size 21 to 23 nt that started with G were classified as “si_22G” if they mapped antisense to annotation belonging to the following categories: DNA transposons, RNA transposons, satellites, simple repeats (as annotated in http://hgdownload.cse.ucsc.edu/goldenPath/ce11/database/rmsk.txt.gz) or pseudogene or protein-coding genes (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)
The “si_22G” reads were re-mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.1) with options -L 6 -i S,1,0.8 -N 0
The resulting alignment was used to generate the normalized bigwig file using millions of non-structural RNAs as normalizer. This was done with a custom bash script using bedtools (version 2.27.1), bedops (version 2.4.26) and bedGraphToBigWig (version 4)
Genome_build: C. elegans ce11 (WBcel235)
Supplementary_files_format_and_content: bigwig files allowing to display the normalized abundance of “si_22G” RNAs along the genome

organism: Caenorhabditis elegans

source_name: nematodes

growth_protocol: Strains were maintained at 20°C, using standard methods (Brenner, 1974). Bristol N2 was the wild-type strain used.

extract_protocol:
Synchronous populations of worms were grown at 20°C on NGM plates seeded with OP50 E. coli concentrated food at a density of maximum 40,000 animals per 15 cm Petri dish and harvested at Young Adult stage at 48 hours post hatching. The harvested animals were washed three times with M9 buffer and 40 µl of worm pellet was frozen in dry ice with TRI Reagent (MRC, Inc.). After five repetitions of freeze and thaw, total RNA was isolated according to the TRI Reagent protocol. Ten micrograms of RNA were treated with 2 U of Turbo DNase (Ambion) at 37°C for 30 minutes followed by phenol-extraction and isopropanol precipitation. Agilent 2200 TapeStation System was used to evaluate the RIN indexes of all the RNA preps, and only samples with RIN > 8 was used for downstream applications. 10 µg of total DNase treated RNAs with RIN > 8 was size seleceted from 15% UREA PAGE gel and used to generate small RNA libraries.
The library preparation was performed as essentially described by Jayaprakash et al., 2011, except that a 5’ polyphosphatase (lucigen RP8092H) treatment was performed to be able to clone tri-phosphate small RNAs, and that the PAGE gel extraction after each ligation was substitute with purification by 1.8 volumes of Agencourt RNAClean XP Beads (Beckman Coulter, NC0068576) and 3 volumes of isopropanol. The multiplexed amplified libraries were further purified using PippinPrep DNA size selection with 3% gel cassettes and the following parameters for the selection: BP start (115) and the BP end (165). The purified libraries were quantified using Qubit Fluorometer High Sensitivity dsDNA assay kit (ThermoFisher, Q32851) and sequenced either on NextSeq-500 Illumina platform using the NextSeq 500/550 High Output v2 kit 75 cycles (FC-404-2005) or Illumina MiniSeq platform using MiniSeq High Output Reagent Kit 75-cycles (FC-420-1001).

treatment_protocol: RNAi treatment was performed using worms grown on 15 cm Petri dishes seeded with concentrated RNAi food. The Arhinger RNAi library was used to pick the selected bacteria clones.

value: whole worm

tag: developmental stage

value: young adult, 48 hours post hatching


title: WT_cross_line3_F6_sRNA-seq

description: total sRNA


title: WT_cerevisiae_Rapid_Patch-2

description: Nucleosomal DNA

source_name: patched W303 yeast

value: W303 WT


title: XYSry5_B6

description: RNA from healthy CD4+ T cells simulated with anti-CD3/CD28

data_processing:
Data quality check was done on Illumina SAV
De-multiplexing was performed with Illumina Bcl2fastq2 v 2.17 program
R package “QuasR” was used for the read alignment to mouse genome (mm10) followed by the counting at gene level
Genome_build: mm10
Supplementary_files_format_and_content: "mm10.gene_B6CD4M_ensGene.xlsx" has raw count values for each sample

source_name: Lymph node

extract_protocol:
surgery protocol: Young mice (age 4-6 weeks) were gonadectomized (females: ovariectomy, males: castration). Prior to surgery and 24 hours after, the mice received 1.2 mg/mL Carprofen (Zoetis). The mice were given Amoxicillin (50 mg/mL, Virbac) as antibiotic in the water source for 7 days following surgery.
immunization protocol: At 8 weeks of age, the mice were immunized with MOG 35-55 peptide (Mimotopes) emulsified in Complete Freund's adjuvant supplemented with mycobacterium tubercusosis H37Ra (Difco Laboratories) for 10 days.
culture protocol: Auxillary, brahcial, and inguinal draining lymph nodes were collected and processed into single cell suspensions. Cells were sorted for CD4+ T cells by magnetic negative selection using EasySep Mouse CD4+ T cell isolation kit (STEMCELL). The cells were cultured in the presence of anti-CD3/CD28 DynaBeads for 36 hours.
RNA was isolated from CD4+ T cells using the Direct-zol™ RNA MiniPrep Plus kit (Zymo Research).
Double-stranded cDNA and the sequencing library were made using the Kapa RNA Kit Full kit.


title: BeWo_TNF100p_rep1

source_name: BeWo, TNF-alpha 100pg/ml, replicate1

value: choriocarcinoma cell line

value: BeWo


title: BeWo_control_rep1

source_name: BeWo, control, replicate1


title: WT_cross_line1_F6_sRNA-seq

description: total sRNA


title: piwi_CRISPR_line2_F12_mut16_RNAi_sRNA-seq

description: total sRNA

value: CRISPR-cas9 piwi mutant line 2

value: RNAi treatment mut-16


title: XYSry4_B6


title: WT_cerevisiae_Rapid_Patch-1

description: Nucleosomal DNA


title: XYSry2_B6


title: XYSry1_B6


title: XXSry5_B6


title: XYSry3_SJL

value: SJL


title: XXSry4_B6

value: Lymph node


title: XXSry3_B6

value: CD4+ T cell


title: WT_cerevisiae_Rapid

description: Nucleosomal DNA

source_name: exponentially-growing W303 yeast cells


title: BeWo_TNF100p_rep2

source_name: BeWo, TNF-alpha 100pg/ml, replicate2


title: XXSry2_B6

value: Male


title: WT_cross_line2_F6_sRNA-seq

description: total sRNA


title: XXSry1_B6

value: XXSry


title: XYSry3_B6


title: isw2_cerevisiae_standard-2

description: Nucleosomal DNA

source_name: exponentially-growing W303 yeast cells ISW2::URA3


title: WT_CRISPR_WAGO-1-FLAG_IP_sRNA-seq

description: immunoprecipitated sRNA

extract_protocol:
Synchronous population of 40,000 worms were harvested at 48 hours post hatching and suspended in the extraction buffer (50 mM Tris, 300 mM NaCl, 1 mM EDTA, 0.1% NP40, protease inhibitor cocktails (Fermentas)) followed by 30 strokes using a metal dounce on ice. Crude protein extracts were spun at 12,000 rpm at 4°C for 10 minutes. Protein concentration was quantified by the Bradford assay, and 1 mg of protein extract was incubated with 15 μl of packed Anti-FLAG M2 Magnetic Agarose Beads (Sigma M8823) for 1 hour at 4°C. After four washes with RIP washing buffer (50 mM Tris, 500 mM NaCl, 1 mM EDTA, 0.1% NP40, protease inhibitor cocktails (Fermentas)), the beads were resuspended in 750 µL of TRI Reagent (MRC, Inc.) to extract the immunoprecipitated RNAs. 750 µL of TRI Reagent (MRC, Inc.) was also added to 10% of protein extract before the immunoprecipitation (Input). RNA extracted from IPs and Inputs were size seleceted from 15% UREA PAGE gel.
The library preparation was performed as essentially described by Jayaprakash et al., 2011, except that a 5’ polyphosphatase (lucigen RP8092H) treatment was performed to be able to clone tri-phosphate small RNAs, and that the PAGE gel extraction after each ligation was substitute with purification by 1.8 volumes of Agencourt RNAClean XP Beads (Beckman Coulter, NC0068576) and 3 volumes of isopropanol. The multiplexed amplified libraries were further purified using PippinPrep DNA size selection with 3% gel cassettes and the following parameters for the selection: BP start (115) and the BP end (165). The purified libraries were quantified using Qubit Fluorometer High Sensitivity dsDNA assay kit (ThermoFisher, Q32851) and sequenced either on NextSeq-500 Illumina platform using the NextSeq 500/550 High Output v2 kit 75 cycles (FC-404-2005) or Illumina MiniSeq platform using MiniSeq High Output Reagent Kit 75-cycles (FC-420-1001).

value: CRISPR-cas9 wild type line 1


title: WT_CRISPR_WAGO-1-FLAG_input_sRNA-seq

description: total sRNA


title: piwi_CRISPR_WAGO-1-FLAG_input_sRNA-seq

description: total sRNA

value: CRISPR-cas9 piwi mutant line 1


title: XYSry_5

data_processing:
Data quality check was done on Illumina SAV
De-multiplexing was performed with Illumina Bcl2fastq2 v 2.17 program
R package “QuasR” was used for the read alignment to mouse genome (mm10) followed by the counting at gene level
Genome_build: mm10
Supplementary_files_format_and_content: "maleFCGcd4_rowcounts.xlsx" has raw count values for each sample

extract_protocol:
Auxillary, brahcial, and inguinal draning lymph nodes were collected and processed into single cell suspensions. The cells were cultured at a concentration of 1x10^6 in complete RPMI medium with MOG 35-55 (25 ug/mL) and IL-12 (20 ng/mL) for 36 hours.
After culture, cells were sorted for CD4+ T cells by magnetic negative selection using EasySep Mouse CD4+ T cell isolation kit (STEMCELL). RNA was isolated from CD4+ T cells using the Direct-zol™ RNA MiniPrep Plus kit (Zymo Research).
Double-stranded cDNA and the sequencing library were made using the Kapa RNA Kit Full kit.

treatment_protocol:
Young mice (age 4-6 weeks) were gonadectomized (females: ovariectomy, males: castration). Prior to surgery and 24 hours after, the mice received 1.2 mg/mL Carprofen (Zoetis). The mice were given Amoxicillin (50 mg/mL, Virbac) as antibiodic in the water source for 7 days following surgery.
At 8 weeks of age, the mice were immunized with MOG 35-55 peptide (Mimotopes) emulsified in Complete Freund's adjuvant supplemented with mycobacterium tubercusosis H37Ra (Difco Laboratories) for 10 days.

value: XY-Sry


title: isw2_cerevisiae_standard-1

description: Nucleosomal DNA

source_name: exponentially-growing W303 yeast cells ISW2::KANMX


title: XXSry_5A


title: XYSry_1


title: WT_cerevisiae_standard-2

description: Nucleosomal DNA


title: piwi_CRISPR_WAGO-1-FLAG_IP_sRNA-seq

description: immunoprecipitated sRNA


title: WT_cerevisiae_standard-1

description: Nucleosomal DNA


title: XXSry_4A


title: XXSry_3A


title: XXSry_1A


title: Gr_4D_MP_6

city: South San Francisco

first: Peichuan

last: Zhang

address: 1070 Veterans Blvd

institute: Calico Life Sciences

description:
cells treated with Gr-4D-MP (10uM)
sample name:
cjopb8gwi001e3h5y9roqawfx

data_processing:
Illumina bcl2fastq v2.20.0 was used for basecalling.
Salmon v0.9.1 was used to pseudo-align reads to GRCh38, producing transcripts-per-million (TPM) estimates.
Isoform-level TPM estimates were aggregated to get genes-per-million (GPM) estimates.
Gene counts were de-noised by clamping low count values to the 5th percentile value, then log2-transformed, to produce normalized gene counts.
Differential expression analysis was performed using Sleuth v0.29.0, producing gene-level effect sizes and Q-values.
Genome_build: GRCh38
Supplementary_files_format_and_content: comma-separated text files including genes-per-million values for each sample

source_name: cells treated with Gr-4D-MP (10uM)

growth_protocol: WI-38 cells of mid-age (PDL ~32) were cultured in OptiMEM (Invitrogen) supplemented with 10% FBS in a 37C incubator (5% CO2, 21% O2) to ~70%.

extract_protocol:
Cells were rinsed briefly with PBS and frozen with liquid nitrogen and stored at -80C before processed for the isolation of total RNA.  Total RNA was isolated and purified using the RNeasy kit (Qiagen), with on-column DNase digest.
Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries from 375 ng of total RNA.

treatment_protocol: Cells were then subjected to treatment with 0.1% DMSO (control), or 10uM Gr-4D (Gr-4D-CB, from ChemBridge; or Gr-4D-MP, from MolPort), or no treatment for 24 hours.


title: C1HTsmall_s6_1911011085_Col17_S195

city: Barcelona

first: Atefeh

last: Lafzi

address: Baldiri Reixac 4

department: CNAG

institute: Center for Genomic Regulation

description:
cryopreserved HCA reference
C1HTsmall_human_exp_mat.tsv, C1HTsmall_human_metada.tsv, C1HTsmall_mouse_exp_mat.tsv, C1HTsmall_mouse_metada.tsv

data_processing:
zUMIs was used to filtering, mapping and quantification of reads.
Low quality reads were removed (barcodes and UMI sequences with more than 1 base below the Phred quality threshold of 20) .
We also excluded barcodes with less than 100 reads.
For techniques with known barcodes, we provided zUMIs with these barcode sequences, and used the automatic barcode detection function to detect the sequenced cells for other techniques.
cDNA reads were mapped to the human GRCh38, mouse GRCm38, and a human-mouse-dog mixed (for species level doublet detection) reference genomes using STAR
Reads were then assigned to exonic and intronic features using featureCounts and counted using the default parameters of zUMIs for human-only, mouse-only and mixed bam-files, separately.
The output expression matrix of reads mapping to both exonic and intronic regions was selected for the downstream analysis.
Genome_build: human GRCh38, mouse GRCm38
Supplementary_files_format_and_content: tab-deimited text files (.tsv) containing gene expression values as UMI counts for all protocols except SMARTseq2 which contains read counts. For each expression matrix there is a corresponding metadata file.
R1 = BC (1-6), UMI (7-11), R2 = cDNA

organism:
Homo sapiens
Canis lupus familiaris
Mus musculus

source_name: human PBMC, mouse colon, HEK293, NIH3T3, MDCK

growth_protocol: NIH3T3-GFP, MDCK-TurboFP650 and HEK293-RFP were cultured at 37ºC in an atmosphere of 5% (v/v) carbon dioxide in Dulbecco’s Modified Eagle’s Medium, supplemented with 10% (w/v) fetal bovine serum, 100 U penicillin, and 100 µg/L streptomycin (Invitrogen).

extract_protocol:
PBMCs were isolated according to the manufacturer’s instructions for FICOLL extraction (pluriSelect).Minced mouse colon was digested in 1X HBSS and 83 µl of collagenase IV (final concentration 166 U/ml) for 15 min at 37ºC and filtered through a 70 µm nylon mesh.
Sequencing librraries were prepared according to the respective single-cell RNA-seq protocols as detailed in the Methods and referenced in TableS1.
Library selection and sequencing was performed following recommendations of to the respective single-cell RNA-seq protocols as detailed in the Methods.

treatment_protocol: Untreated cells and donors.

tag: protocol

tag: centre

value: Stanford

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: C1HTsmall_s6_1911011085_Col18_S196


title: C1HTsmall_s6_1911011085_Col16_S194


title: C1HTsmall_s6_1911011085_Col15_S193


title: Sample 12: XYSry3

data_processing:
Data quality check was done on Illumina SAV
De-multiplexing was performed with Illumina Bcl2fastq2 v 2.17 program
R package “QuasR” was used for the read alignment to mouse genome (mm10) followed by the counting at gene level
Genome_build: mm10
Supplementary_files_format_and_content: "SJLcd4FCGhealthy_rawcounts.xlsx" has raw count values for each sample

extract_protocol:
RNA was isolated from CD4+ T cells using the Direct-zol™ RNA MiniPrep Plus kit (Zymo Research).
Double-stranded cDNA and the sequencing library were made using the Kapa RNA Kit Full kit.

treatment_protocol:
Young mice (age 4-6 weeks) were gonadectomized (females: ovariectomy, males: castration). Prior to surgery and 24 hours after, the mice received 1.2 mg/mL Carprofen (Zoetis). The mice were given Amoxicillin (50 mg/mL, Virbac) as antibiodic in the water source for 7 days following surgery.
Auxillary, brahcial, and inguinal draning lymph nodes were collected and processed into single cell suspensions. Cells were sorted for CD4+ T cells by magnetic negative selection using EasySep Mouse CD4+ T cell isolation kit (STEMCELL). The cells were cultured in the presence of anti-CD3/CD28 DynaBeads for 36 hours.


title: Sample 11: XYSry2


title: Gr_4D_MP_5

description:
cells treated with Gr-4D-MP (10uM)
sample name:
cjopb8gwi001d3h5ys5y6vsnc


title: Sample 10: XYSry1


title: Gr_4D_MP_4

description:
cells treated with Gr-4D-MP (10uM)
sample name:
cjopb8gwi001c3h5yqovk9uh6


title: XYSry_3


title: C1HTsmall_s6_1911011085_Col14_S192


title: Gr_4D_MP_3

description:
cells treated with Gr-4D-MP (10uM)
sample name:
cjopb8gwi001b3h5yr3r95o3f


title: Sample 7: XXSry1


title: Sample 6: XY3

value: Female

value: XY-


title: Sample 8: XXSry2


title: C1HTsmall_s6_1911011085_Col13_S191


title: Gr_4D_MP_2

description:
cells treated with Gr-4D-MP (10uM)
sample name:
cjopb8gwi001a3h5yox8gsk86


title: Sample 4: XY1


title: Sample 5: XY2


title: XXSry_2A


title: C1HTsmall_s6_1911011085_Col12_S183


title: Sample 3: XX3

value: XX


title: Gr_4D_MP_1

description:
cells without any treatment
sample name:
cjopb8gwi00193h5y0wfem3yv

source_name: cells without any treatment


title: C1HTsmall_s6_1911011085_Col10_S184


title: XY 5

data_processing:
Data quality check was done on Illumina SAV
De-multiplexing was performed with Illumina Bcl2fastq2 v 2.17 program
R package “QuasR” was used for the read alignment to mouse genome (mm10) followed by the counting at gene level
Genome_build: mm10
Supplementary_files_format_and_content: "CD4healthy_rawcounts.xlsx" has raw count values for each sample

extract_protocol:
Auxillary, brahcial, and inguinal draning lymph nodes were collected and processed into single cell suspensions. Cells were sorted for CD4+ T cells by magnetic negative selection using EasySep Mouse CD4+ T cell isolation kit (STEMCELL). The cells were cultured in the presence of anti-CD3/CD28 DynaBeads for 36 hours.
RNA was isolated from CD4+ T cells using the Direct-zol™ RNA MiniPrep Plus kit (Zymo Research).
Double-stranded cDNA and the sequencing library were made using the Kapa RNA Kit Full kit.


title: Sample 1: XX1


title: Sample 2: XX2


title: Sample 9: XXSry3


title: no_DMSO_5

description:
cells without any treatment
sample name:
cjopb8gwi00173h5y2ef1jrb9


title: XY 4


title: C1HTsmall_s6_1911011085_Col09_S200


title: XY 3


title: no_DMSO_4

description:
cells without any treatment
sample name:
cjopb8gwi00163h5yeskrzwtp


title: XY 2


title: C1HTsmall_s6_1911011085_Col08_S185


title: no_DMSO_3

description:
cells without any treatment
sample name:
cjopb8gwi00153h5ysiseqr2s


title: C1HTsmall_s6_1911011085_Col07_S186


title: XX 4


title: piwi_CRISPR_line1_F12_mut16_RNAi_sRNA-seq

description: total sRNA

value: whole worm

value: young adult, 48 hours post hatching


title: no_DMSO_2

description:
cells without any treatment
sample name:
cjopb8gwi00143h5yiqasqngq


title: XX 2


title: XX 1


title: C1HTsmall_s6_1911011085_Col06_S187


title: no_DMSO_1

description:
cells without any treatment
sample name:
cjopb8gwi00133h5yty664ap3


title: C1HTsmall_s6_1911011085_Col11_S199


title: no_DMSO_6

description:
cells without any treatment
sample name:
cjopb8gwi00183h5yj6bli8vf


title: C1HTsmall_s6_1911011085_Col05_S188


title: Gr_4D_CB_6

description:
cells treated with Gr-4D-CB (10uM)
sample name:
cjopb8gwi00123h5yip867uig

source_name: cells treated with Gr-4D-CB (10uM)


title: Gr_4D_CB_5

description:
cells treated with Gr-4D-CB (10uM)
sample name:
cjopb8gwi00113h5y1z1gpkli


title: XY 1


title: C1HTsmall_s6_1911011085_Col03_S182


title: XX 3


title: C1HTsmall_s6_1911011085_Col04_S198


title: C1HTsmall_s6_1911011085_Col02_S197


title: C1HTsmall_s6_1911011085_Col01_S181


title: Gr_4D_CB_4

description:
cells treated with Gr-4D-CB (10uM)
sample name:
cjopb8gwi00103h5ynqce6n87


title: C1HTsmall_s5_1911004005_Col19_S170


title: C1HTsmall_s5_1911004005_Col20_S169


title: PAB_F(+)_rep3

city: Tokyo

first: Toru

last: Akaike

address: 3-25-8 Nishi-Shimbashi, Minato-ku

department: Cell Physiology

institute: The Jikei University

description: Gene expression data from rat right ventricle

hyb_protocol: Following fragmentation, 25μg of cRNA were hybridized for 17 hr at 45C on Affymetrix GeneChip® Rat Gene 1.0 ST-v1 Array. GeneChips were washed and stained.

scan_protocol: GeneChips were scanned using  Affymetrix GeneChip® Scanner.

data_processing: The data were analyzed with Affymetrix® GeneChip® Command Console® Software version 2.0 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Rattus norvegicus

source_name: rat right ventricle, PAB, fibrosis

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

extract_protocol: Sepasol®-RNA I Super G extraction of total RNA was performed according to the manufacturer's instructions.

value: right ventricle

value: SD

tag: gender

value: male

tag: group

value: pulmonary artery banding, fibrosis


title: Gr_4D_CB_3

description:
cells treated with Gr-4D-CB (10uM)
sample name:
cjopb8gwi000z3h5ybbdjfhnm

tag: treatment


title: Gr_4D_CB_1

description:
cells treated with Gr-4D-CB (10uM)
sample name:
cjopb8gwi000x3h5ytlc0xp6a


title: DMSO_6

description:
cells treated with DMSO (0.1%)
sample name:
cjopb8gwi000w3h5yi1r3d46y

source_name: cells treated with DMSO (0.1%)

value: mock


title: PAB_F(+)_rep1


title: Gr_4D_CB_2

description:
cells treated with Gr-4D-CB (10uM)
sample name:
cjopb8gwi000y3h5yndds3o28


title: PAB_F(+)_rep2


title: C1HTsmall_s5_1911004005_Col17_S175

description:
cryopreserved HCA reference
C1HTsmall_human_exp_mat.tsv, C1HTsmall_human_metada.tsv, C1HTsmall_mouse_exp_mat.tsv, C1HTsmall_mouse_metada.tsv


title: PAB_F(-)_rep2

source_name: rat right ventricle, PAB

value: pulmonary artery banding


title: PAB_F(-)_rep1


title: PAB_F(-)_rep3


title: Sham_rep2

source_name: rat right ventricle, sham

value: sham


title: DMSO_5

description:
cells treated with DMSO (0.1%)
sample name:
cjopb8gwi000v3h5yv93bybij


title: C1HTsmall_s5_1911004005_Col18_S176


title: Sham_rep3


title: C1HTsmall_s5_1911004005_Col14_S172


title: DMSO_3

description:
cells treated with DMSO (0.1%)
sample name:
cjopb8gwi000t3h5y8tghajnv


title: DMSO_2

description:
cells treated with DMSO (0.1%)
sample name:
cjopb8gwi000s3h5ywkx20tcm


title: DMSO_4

description:
cells treated with DMSO (0.1%)
sample name:
cjopb8gwi000u3h5ygpm9konu


title: piwi_CRISPR_line1_F12_sRNA-seq

description: total sRNA

source_name: nematodes


title: C1HTsmall_s5_1911004005_Col16_S174


title: C1HTsmall_s5_1911004005_Col13_S171


title: XYSry_4

description: RNA from auto antigen specific CD4+ T cells

value: Lymph node

value: CD4+ T cell

tag: Sex

value: Male


title: C1HTsmall_s5_1911004005_Col15_S173

value: Stanford


title: piwi_CRISPR_line2_F12_sRNA-seq

description: total sRNA

tag: genotype

value: CRISPR-cas9 piwi mutant line 2


title: Sham_rep1

tag: tissue


title: isw2_cerevisiae_Rapid

description: Nucleosomal DNA