title: smRNA_Hela_Drosha_KD

description:
Small RNA-seq for control HeLa cells.
small RNA
processed data file: smRNA_Hela_Drosha_KD_miRNA_counts.txt

extract_protocol:
Total RNA was extracted with TRIzol and Direct-zol RNA Kits (Zymo Research).
The small RNA-seq libraries were generated using VAHTSTM Small RNA Library Prep Kit for Illumina (Vazyme) according to the manufacturer’s protocol.

value: Drosha KD


title: 24 weeks old [F01]

status: Public on Apr 11 2020

type: SRA

city: Toronto

first: Bibaswan

last: Ghoshal

address: 600 University Avenue

country: Canada

institute: Lunenfeld Tanenbaum Research Institute

description: individual organoids

library_source: transcriptomic

data_processing:
Cellrangar 2.0 is run on the FASTQ files to generate matrix
Data is read into Seurat with 1 minimum cell and 200 minimum genes and subsequently converted in scater for quality control and filtering based on lirary size, feature size and percentage of mitochondrial genes. Furthermore, normalization steps are performed and then the normalized data is transported back to Seurat. In Seurat, data is scaled and dimesion reduction, cluster identification, PCA and tSNE are performed.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix in .mtx format generated by cellranger filtered_bc_matrices. The csv files contain normalized expression data from combined whole epithelium, crypts and 170 FACS sorted cells with indepth sequencing.

molecule: total RNA

organism: Homo sapiens

source_name: cerebral organoids

extract_protocol:
Cerebral organoids were cut and dissociated to isolate single cells and then subjected to 10X Genomics single cell RNA sequencing following manufacturer’s recommendations. Illumina HiSeq 3000 was used for deep sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: brain

tag: age

value: 24 weeks old


title: 12 weeks old [D12]

description: individual organoids

value: 12 weeks old


title: Hela_Drosha_KD

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

country: China

institute: Sun Yat-sen University

description:
Drosha-KDR1, Drosha-KDR2
Stranded RNA-seq for Drosha knockdown HeLa cells.
polyA RNA
processed data file: Hela_Drosha_KD_genes_FPKM_res.txt

data_processing:
RNA-seq: Adapter sequences, low-quality bases and Ns were first trimmed using cutadapt.
RNA-seq: RNA-seq data were mapped to the human reference genome (hg19) using tophat2 (TopHat v2.1.0).
RNA-seq: Gene expression levels were calculated by cufflinks (cufflinks v2.2.1).
Small RNA-seq: Adapter sequences, low-quality bases and Ns were first trimmed using cutadapt.
Small RNA-seq: Clean reads were next mapped to the human reference genome (hg19) with STAR (Version 2.5.2b).
Small RNA-seq: Read numbers were counted by featureCounts (Version 2.0.0) and the CPM values were calculated using a custom perl script.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Gene FPKM values produced by cufflinks.
Supplementary_files_format_and_content: miRNA counts produced by featureCounts.

source_name: HeLa cell line

extract_protocol:
Total RNA was extracted with TRIzol and Direct-zol RNA Kits (Zymo Research).
mRNA was selected using Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and then fragmented into 150~200 nt fragments by incubation at 94 °C for 8 minutes in fragmentation buffer (NEBNext Ultra II Directional RNA Library Prep Kit, NEB). The fragmented RNA was then used for library construction, following the manufacturer’s protocol (NEBNext Ultra II Directional RNA Library Prep Kit, NEB). Libraries were sequenced on Hiseq X10 (Illumina) to produce paired-end 150 bp reads.

tag: cell line

value: HeLa

tag: genotype/variation


title: CT12 WT Biological Replicate 1

city: New York

first: Rosemary

middle: V

last: Sampogna

state: NY

department: Medicine

country: USA

institute: Columbia University

description:
AR004
CT12-s004

data_processing:
Bases were called with RTA (Illumina), and bcl2fastq.gz2 (version 2.17) was used for converting BCL to fastq.gz format, with adaptor trimming.
Reads were mapped to UCSC/mm10 using STAR (2.5.2b), and summarized to gene-level counts with featureCounts (v1.5.0-p3). One sample at embryonic day 18 and 12hr (E18.5) was removed from the dataset due to poor quality.
Genes that were not represented by more than five counts in at least two replicates were filtered out of downstream analysis. To  correct for differences in sequencing depth, the data then underwent upper-quartile normalization by the betweenLaneNormalization function from the EDASeq package. Removal of unwanted variation (RUV) normalization was performed by the RUVg function from the RUVSeq package, which uses factor analysis and a list of in silico empirical negative control genes to reduce variation from unknown technical effects.
Empirical controls, which can be considered non-rhythmic transcripts, were obtained by first-pass meta2d analysis using MetaCycle on the upper-quartile-normalized dataset (settings: cycMethod = c("JTK", "LS"), minper = 20, maxper = 28).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including count values for each sample and rhythmic analysis of transcripts using MetaCycle (v.1.2.0). Results ranked by decreasing integrated q-value (FDR-adusted p-value).

organism: Mus musculus

source_name: Fetal Kidney

extract_protocol:
Fetal kidneys were extracted, stored in RNAlater, and RNA was isolated using the QIASymphony kit. Poly-A pull-down was used for mRNA enrichment. Libraries were prepared using Illumina TruSeq RNA Prep Kit, and sequenced on Illumina HiSeq2500/HiSeq4000.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: developmental stage

value: kidney


title: BL21(DE3)_heatshock_2min

status: Public on Apr 12 2020

type: RNA

city: Seoul

first: Sung Ho

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Konkuk University

hyb_protocol: The fragmented and labeled RNA was hybridized with the tiling array for 17 hours at 65°C.

scan_protocol: After the hybridization and wash steps described in the array manufacturer’s instructions, arrays were scanned using an Agilent DNA microarray Scanner (Agilent Technologies).

data_processing: Signal intensity and local background were determined using Feature Extraction software (Agilent Technologies).

organism: Escherichia coli BL21(DE3)

source_name: 42°C, time=2min

label_protocol: The resulting RNA was directly labeled with Cy3 using a Label IT µArray Labeling Kit (Mirus, Madison, WI, USA), per the manufacturer’s instruction.

growth_protocol: Chemostat cultures were grown in glucose-limited defined medium with the dilution rate of 0.1 h-1. The temperature was shifted from 37°C to 42°C within 3.5 min.

extract_protocol: Total RNA was prepared using a mirVana miRNA Isolation Kit (Thermo Fisher Scientific Inc., Waltham, MA, USA), per the manufacturer’s instruction. Any contaminating DNA was digested with Turbo DNase (Applied Biosystems, Austin, TX, USA) for 30 minutes at 37C and then removed using the filter cartridges supplied with the mirVana miRNA Isolation Kit.

treatment_protocol: Culture broth (4.0 × 10e8 cells) was immediately mixed with two volumes of RNAprotect Bacteria Reagent (Qiagen, Düsseldorf, Germany).

tag: culture medium

value: Modified R (minimal medium)

tag: cell density in od600

tag: temperature

tag: time


title: smRNA_Hela_Drosha_WT

description:
Small RNA-seq for Drosha knockdown HeLa cells.
small RNA
processed data file: smRNA_Hela_Drosha_WT_miRNA_counts.txt

value: Drosha WT


title: 12 weeks old [D11]

description: individual organoids


title: CT8 WT Biological Replicate 4

description:
AR033
CT08-s033

value: E18 + 8 HRS


title: 7_Ps2Ex3M1_Hom_6month_F3_83_Fem

city: Adelaide

first: Stephen

middle: Martin

last: Pederson

state: SA

address: North Terrace

department: Biological Sciences

country: Australia

institute: University of Adelaide

data_processing:
Illumina BaseSpace was used for basecalling
Reads were trimmed using cutadapt v1.14 with settings -m35 --trim-n --max-n 1 --nextseq-trim=30
Trimmed reads were aligned to GRCz11 (Ensembl Release 98) using STAR 2.7.0d with default settings
Reads were summarised at the gene level using featureCounts (Subread 1.5.2) using the file Danio_rerio.GRCz11.98.chr.gtf from Ensembl, with the settings -Q 10 -s 2 -p --fracOverlap 1
Genome_build: GRCz11
Supplementary_files_format_and_content: A counts matrix as output by featureCounts contains gene-levels counts from each sample

organism: Danio rerio

source_name: Brain

growth_protocol: All fish were raised together in the same tank until 6 months of age

extract_protocol:
Total RNA was extracted from pooled larvae using the mirVanaTM miRNA isolation Kit (Ambion, Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA).
rRNA was depleted from total RNA samples using the rRNAseH rRNA depletion method [Adiconis et al, Nat Methods 2013 Jul (10) 7 623-629] and a combination of human/rat/mouse sequences. 500ng of RNA was used for rNRA depletion, followed by the KAPA Hyper Library Prep kit, fragmentation at 85 degrees (C) for 6 mins and 11 PCR cycles. Sequencing was performed by the Australian Cancer Research Foundation Cancer Genomics Facility in Adelaide, South Australia

tag: genotype

value: Whole brain

value: 6 months


title: BL21(DE3)_heatshock_8h

source_name: 42°C, time=8h


title: 12 weeks old [D10]

description: individual organoids


title: HEK293_ADAR1_WT

description:
WT
Stranded RNA-seq for control HEK293 cells.
polyA RNA
processed data file: HEK293_ADAR1KO_genes_FPKM_res.txt

source_name: HEK293 cell line

value: ADAR1 WT


title: 12 weeks old [D09]

description: individual organoids


title: HEK293_ADAR1_KO

description:
ADAR1KO
Stranded RNA-seq for ADAR1 knockout HEK293 cells.
polyA RNA
processed data file: HEK293_ADAR1KO_genes_FPKM_res.txt

value: ADAR1 KO


title: CT8 WT Biological Replicate 3

description:
AR023
CT08-s023


title: 12 weeks old [D08]

description: individual organoids


title: CT8 WT Biological Replicate 2

description:
AR013
CT08-s013


title: 12 weeks old [D07]

description: individual organoids


title: TCR-668: RNAseq T cells sorted from rtTA-HER2d16 tumor #668 treated with Ad-HER2d16

city: Durham

first: Zachary

middle: Conrad

last: Hartman

state: NC

address: Research Drive MSRB rm 414

department: Surgery

institute: Duke University

description:
3000 live sorted single T cells used per sample
TCR-668

data_processing:
Fastq files for paired-end reads and the index file for each samples was procssed using 10X cellranger v 2.1.0 count program to generate an expression count matrix for each sample.
The raw counts were analzed with Seurat v 3.1.2
Seurat returned a corrected data matrix for all datasets, which was used for subsequent analyses.
We filtered out cells with UMI count aggregate falling outside of a minimum value of 200 and a maximum value not exceeding 99th percentile, and minimized doublet rate by trimming genes/features whose UMI counts exceeded 95th percentile
Genome_build: mm10

molecule: polyA RNA

source_name: TILS

growth_protocol: HER2 expression was induced in mammary tissues of one month old mice, spontaneous breast tumor growth were monitored weekly

extract_protocol:
Breast tumors were removed and processed into single cell suspensions as described in manuscript, and live single T cells were sorted.
10X Genomics gene expression libraries were generated using Chromium Single Cell 5’ Library Construction Kit (PN-1000020). A targeted cell recovery of 3000 cells were used for each sample.
scRNA seq (10X Genomics), Single Cell 5' Gene Expression Libraries, 26x8x98 single i7 index.

treatment_protocol: Vaccine, aPD1, and/or isotype control antibody were given weekly after a palable tumor was discovered.

tag: treatment

tag: cell type

value: Tumor-infiltrating lymphocytes

value: FVB/NJ

tag: mouse model


title: CT8 WT Biological Replicate 1

description:
AR003
CT08-s003


title: TCR-471A: RNAseq T cells sorted from rtTA-HER2d16 tumor #471 treated with Ad-HER2d16+aPD1

description:
3000 live sorted single T cells used per sample
TCR-471A


title: TCR-663: RNAseq T cells sorted from rtTA-HER2d16 tumor #663 treated with aPD1

description:
3000 live sorted single T cells used per sample
TCR-663


title: TCR-464A: RNAseq T cells sorted from rtTA-HER2d16 tumor #464 treated with Isotype

description:
3000 live sorted single T cells used per sample
TCR-464A

value: Isotype


title: CT4 WT Biological Replicate 4

description:
AR032
CT04-s032

value: E18 + 4 HRS


title: CT24 WT Biological Replicate 3

description:
AR027
CT24-s027


title: TCR-672: RNAseq T cells sorted from rtTA-HER2d16 tumor #672 treated with Isotype

description:
3000 live sorted single T cells used per sample
TCR-672


title: TCR-403B: RNAseq T cells sorted from rtTA-HER2d16 tumor #403B treated with aPD1

description:
3000 live sorted single T cells used per sample
TCR-403B


title: CT4 WT Biological Replicate 1

description:
AR002
CT04-s002


title: TCR-669: RNAseq T cells sorted from rtTA-HER2d16 tumor #669 treated with Ad-HER2d16+aPD1

description:
3000 live sorted single T cells used per sample
TCR-669


title: 18 weeks old [G12]

description: individual organoids

value: 18 weeks old


title: CT4 WT Biological Replicate 3

description:
AR022
CT04-s022


title: CT0 WT Biological Replicate 4

description:
AR031
CT00-s031


title: GEX-669: RNAseq T cells sorted from rtTA-HER2d16 tumor #669 treated with Ad-HER2d16+aPD1

description:
3000 live sorted single T cells used per sample
GEX-669


title: PBS High 6

first: Dave

last: Prescott

state: ON

address: 1 King's College Circle, Room 7336

department: Immunology

institute: University of Toronto

description: RNA pre-amplified by Affymetrix WT Plus Pico Kit

hyb_protocol: 5.5 ug of cDNA were hybridized for 16 hr at 45C on the GeneChip Mouse Gene 2.0 ST array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Data were analyzed in Expression Console and normalized using the RMA algorithm with a log2 transformation of the signal

label: Biotin Allonamide Triphosphate

source_name: CD205+CD8+CD103-High splenic DCs from PBS-treated Mouse

label_protocol: 400ng RNA was pre-amplified by the affymetrix WT Plus Pico kit, and Biotinylated cDNA was prepared according to affymetrix protocols

growth_protocol: Littermate mice were bred in-house, and injected with 5e6 FLT3L-secreting B16 melanoma cells subcutaneously at 6 weeks of age

extract_protocol: Total RNA was extracted from sorted DCs with Trizol according to the manufacturer's instructions.

treatment_protocol: 5 days later mice were injected i.p. with either 100ul of PBS or 100ul of PBS containing 50ug of Muramyl Dipeptide (MDP).  24h later mice were euthanized, their spleens extracted and digested with 2mg/ml Collagenase D, and FACS-sorted to purify CD205+CD8+ Dendritic Cells and further subsorted into CD103 high and CD103 low expressing groups

tag: Sex

value: Male

value: 6 Weeks

tag: tumor status

value: Flt3L-secreting B16 melanoma - 5 days

value: Spleen

value: CD205+CD8+ Dendritic Cell

tag: cd103 expression

value: High

tag: agent

value: PBS i.p. 24h prior


title: 18 weeks old [H02]

description: individual organoids

tag: tissue

value: brain

tag: age


title: GEX-668: RNAseq T cells sorted from rtTA-HER2d16 tumor #668 treated with Ad-HER2d16

description:
3000 live sorted single T cells used per sample
GEX-668


title: CT4 WT Biological Replicate 2

description:
AR012
CT04-s012

value: kidney


title: PBS High 5


title: PBS High 4


title: 24 weeks old [F05]

description: individual organoids

value: 24 weeks old


title: MDP High 2

source_name: CD205+CD8+CD103-High splenic DCs from MDP-treated Mouse

value: 50ug MDP i.p. 24h prior


title: MDP High 3


title: MDP High 4


title: GEX-663: RNAseq T cells sorted from rtTA-HER2d16 tumor #663 treated with aPD1

description:
3000 live sorted single T cells used per sample
GEX-663


title: GEX-672: RNAseq T cells sorted from rtTA-HER2d16 tumor #672 treated with Isotype

description:
3000 live sorted single T cells used per sample
GEX-672


title: GEX-471: RNAseq T cells sorted from rtTA-HER2d16 tumor #471 treated with Ad-HER2d16+aPD1

description:
3000 live sorted single T cells used per sample
GEX-471


title: CT0 WT Biological Replicate 3

description:
AR021
CT00-s021


title: GEX-403B: RNAseq T cells sorted from rtTA-HER2d16 tumor #403B treated with aPD1

description:
3000 live sorted single T cells used per sample
GEX-403B
supplementary file on series record


title: CT0 WT Biological Replicate 1

description:
AR001
CT00-s001


title: CT0 WT Biological Replicate 2

description:
AR011
CT00-s011


title: TCR-403A: RNAseq T cells sorted from rtTA-HER2d16 tumor #403A treated with aPD1

description:
3000 live sorted single T cells used per sample
TCR-403A


title: GEX-403A: RNAseq T cells sorted from rtTA-HER2d16 tumor #403A treated with aPD1

description:
3000 live sorted single T cells used per sample
GEX-403A
supplementary file on series record


title: Breast-T9-mRNA

data_processing:
Merged all reads from technique replicates into a single fastq file
We trimmed the first 20 bp primer sequences and last 10bp of the reads using fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
We used BWA to align reads to the reference genome (bwa –n 6).
We took variant positions in which the mismatch was supported by at least two mismatch reads with base quality score ≥ 20 and located at targeted loci.
We further removed all known human genomic variants, including all SNPs present in dbSNP (except SNPs of molecular type “cDNA”; v138), the 1000 Genomes Project, and gDNA of the individuals used for editing call.
Genome_build: hg19
Supplementary_files_format_and_content: bed format of variant result.

source_name: Breast tumor tissue

extract_protocol:
Total RNA was extracted with TRIzol and Direct-zol RNA Kits (Zymo Research).
After two rounds of DNase I treatment, 1 ug of total RNA was used to synthesize the cDNA. cDNA was purified with Axygen AxyPrep Mag PCR clean-up beads (Axygen). Each cDNA library (300 - 500 ng) was preamplified using a primer pool (50 uM each) covering all human miRNAs. Preamplified product was purified using Axygen AxyPrep Mag PCR clean-up beads. Preamplified cDNAs and primer pools were loaded into the 48.48 Access Array IFC (Fluidigm) and amplified as described before22. PCR products of each sample were subject to 15 cycle barcoding PCR and pooled together. All pools were combined at equal volumes and purified via Axygen AxyPrep Mag PCR clean-up beads.

value: Breast

value: Adult

tag: tissue type

value: Tumor


title: X7_CC_PDL-1_L8.D707

city: San Diego

first: Rajkumar

last: Balakrishnan

state: California

address: 10300 Campus Point Drive, Suite 100,

department: Informatics & Predictive Sciences

institute: Bristol Myers Squibb

description:
Sample ID: 33219
processed data file: CountsSalmon.TPM.33185-33246.xls

data_processing:
FASTQ quality evaluated with FASTqQC (v 0.11.5).
FASTQ files aligned using Star (v2.5.2b) and Salmon (v0.7).
Alignment quality evaluated with Picard tools (v2.18).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: CountsSalmon.TPM.33185-33246.xls: Gene expression matrix (TPM).

source_name: T lymphocytes

extract_protocol:
Qiagen AllPrep extraction kit.
Illumina TruSeq Stranded mRNA library kit.

treatment_protocol: Patient CD3+ T cells (1 × 10e6) were plated (1 mL complete RPMI) with 1 μg/mL anti-CD28 Ab in 48-well plates previously coated with 1 μg/mL anti-CD3 Ab at 37°C, in the presence of avadomide (0.1 μM) and/or durvalumab or nivolumab (or vehicle treatments) for 18 h. Cells were then washed once with PBS, centrifuged at 250xg for 5 min and following removal of supernatant, snap-frozen in liquid nitrogen.

tag: patient

tag: disease diagnosis

value: Chronic lymphocytic leukemia (CLL)

value: CD3+ T cells

value: Avadomide+Durvalumab

tag: prognostic group

value: Poor

tag: igvh mutational status

value: Unmutated

tag: chromosomal abnormalities or subset

value: Trisomy 12


title: PBS Low 6

source_name: CD205+CD8+CD103-Low splenic DCs from PBS-treated Mouse

tag: strain

value: Male

value: 6 Weeks

value: Flt3L-secreting B16 melanoma - 5 days

value: Spleen

value: Low


title: WXS: tumor C rtTA-HER2d16 mouse on FVB background #555

data_processing:
Fastq files were aligned to mouse reference genome mm10 using STAR (PMID: 23104886) version 2.4.2a.
Quantification was done using Salmon version 0.6.0 (PMID: 28263959).
Gene-level data were normalized to the upper quartile for non-zero genes and log2 transformed.
Genes with zero reads in more than 80% of samples were excluded.
Mutational load was estimated using a calculated exome length of 209.6285 megabases and only non-synonymous mutations predicted to have a moderate or high impact
Genome_build: mm10

source_name: Whole tumor

extract_protocol:
SureSelect XT Mouse All Exon Kit (Agilent)
2x150 30M PE (27.7M each site) don eby Admera Health LLC

treatment_protocol: No treatment was given.

value: breast tumor

value: FVB/NJ

value: rtTA-HER2d16 mouse


title: GEX-401AB: RNAseq T cells sorted from rtTA-HER2d16 tumor #401 treated with Isotype

description:
3000 live sorted single T cells used per sample
GEX-401AB

value: Isotype

value: Tumor-infiltrating lymphocytes


title: WXS: tumor D rtTA-HER2d16 mouse on FVB background #555


title: X7_PDL-1_L7.D705

description:
Sample ID: 33229
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Durvalumab


title: X7_CC_PD-1_L8.D708

description:
Sample ID: 33235
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Chronic lymphocytic leukemia (CLL)

value: Avadomide+Nivolumab


title: PBS Low 4

value: CD205+CD8+ Dendritic Cell

value: PBS i.p. 24h prior


title: GEX-464: RNAseq T cells sorted from rtTA-HER2d16 tumor #464 treated with Isotype

description:
3000 live sorted single T cells used per sample
GEX-464


title: Breast-T8-mRNA

value: Breast

tag: developmental stage

value: Adult

value: Tumor


title: PBS Low 1

value: Male

value: 6 Weeks


title: PBS Low 3

value: Flt3L-secreting B16 melanoma - 5 days

value: Spleen


title: WXS: tumor B rtTA-HER2d16 mouse on FVB background #555

value: breast tumor


title: Breast-T7-mRNA


title: WXS: tumor A rtTA-HER2d16 mouse on FVB background #555

value: FVB/NJ


title: 24 weeks old [F07]

description: individual organoids

value: brain

value: 24 weeks old


title: X7_PD-1_L8.D706

description:
Sample ID: 33209
processed data file: CountsSalmon.TPM.33185-33246.xls

value: CD3+ T cells

tag: treatment

value: Nivolumab

value: Poor

value: Unmutated

value: Trisomy 12


title: Breast-T6-mRNA


title: WXS: tumor D rtTA-HER2d16 mouse on FVB background #531

value: rtTA-HER2d16 mouse


title: X7_CC_L7.D704

description:
Sample ID: 33203
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Chronic lymphocytic leukemia (CLL)

tag: cell type

value: Avadomide


title: shFTO_Rep3

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

institute: Beckman Research Institute of City of Hope

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
the TPM were calculated using RSEM 1.2.31 with default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: table delimited text file containing the expression of genes

source_name: AML cell line NOMO-1

growth_protocol: NOMO-1 cells were  routinely  kept in RPMI1640 mediun with 10% FBS at 0.5*10^6 cells/ml and were passeged every other day.

extract_protocol:
The total RNA were extracted with QIAzol lysis reagent.
FastTrack MAG Maxi mRNA isolation kit

treatment_protocol: About 1*10^6 cells were infected with lentivirus targeting FTO collected from 6 cm dish with existence of 1ug/ml polybrene for spinoculation (1,200 rpm, 32℃，1 hour). 48 hours later, the positive cells were selected with 1ug/ml puromucin for 1 week. As drug treatment, NOMO-1 cells were seed in 10 cm dishes at 0.5*10^6 cells/ml and treated with 100nM CS1, 500nM CS2 or DMSO for 72 hours.

value: Acute myeloid leukemia

tag: cell line


title: Breast-T10-mRNA

value: Breast

value: Adult

value: Tumor


title: MDP Low 2

source_name: CD205+CD8+CD103-Low splenic DCs from MDP-treated Mouse

tag: Sex

value: Male

value: 6 Weeks

value: Flt3L-secreting B16 melanoma - 5 days

value: Spleen

value: CD205+CD8+ Dendritic Cell

value: Low

value: 50ug MDP i.p. 24h prior


title: TCR-401AB: RNAseq T cells sorted from rtTA-HER2d16 tumor #401 treated with Isotype

description:
3000 live sorted single T cells used per sample
TCR-401AB

value: Isotype

value: Tumor-infiltrating lymphocytes

value: FVB/NJ

tag: mouse model


title: MDP Low 3

tag: tumor status

tag: cd103 expression


title: shFTO_Rep2


title: Breast-T5-mRNA

tag: tissue


title: MDP Low 1

tag: age

tag: agent


title: Breast-T4-mRNA

tag: tissue type


title: WXS: tumor C rtTA-HER2d16 mouse on FVB background #531

value: breast tumor

value: rtTA-HER2d16 mouse


title: X7_Veh_L7.D703

description:
Sample ID: 33192
processed data file: CountsSalmon.TPM.33185-33246.xls

tag: patient

tag: disease diagnosis

value: Chronic lymphocytic leukemia (CLL)

value: CD3+ T cells

value: Vehicle

value: Poor

value: Unmutated

value: Trisomy 12


title: 18 weeks old [H03]

description: individual organoids

value: brain

value: 18 weeks old


title: WXS: tumor B rtTA-HER2d16 mouse on FVB background #531


title: WXS: tumor A rtTA-HER2d16 mouse on FVB background #531


title: Breast-T3-mRNA

value: Breast

value: Adult

value: Tumor


title: shNS-Rep3

value: Acute myeloid leukemia


title: X3_CC_PD-1_L7.D702

description:
Sample ID: 33245
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Avadomide+Nivolumab

tag: prognostic group

tag: igvh mutational status

value: TP53mutation, Complex karyotype


title: shNS-Rep2


title: X3_PDL-1_L7

description:
Sample ID: 33234
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Durvalumab

tag: chromosomal abnormalities or subset


title: WXS: tumor C rtTA-HER2d16 mouse on FVB background #527

value: breast tumor

tag: strain

value: FVB/NJ


title: WXS: tumor D rtTA-HER2d16 mouse on FVB background #527

value: rtTA-HER2d16 mouse


title: shNS-Rep1


title: Breast-T1-mRNA

tag: developmental stage


title: X3_PD-1_L8

description:
Sample ID: 33208
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Chronic lymphocytic leukemia (CLL)

tag: cell type

value: CD3+ T cells

tag: treatment

value: Nivolumab


title: Breast-N10-mRNA

source_name: Breast normal tissue

value: Normal


title: WXS: tumor A rtTA-HER2d16 mouse on FVB background #527


title: WXS: tumor B rtTA-HER2d16 mouse on FVB background #527


title: Breast-N9-mRNA


title: shFTO_Rep1

tag: cell line


title: CS2-Rep3


title: X2_CC_PDL-1_L6

description:
Sample ID: 33228
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Avadomide+Durvalumab

value: Good

value: Mutated


title: X3_Veh_L1.D709_501

description:
Sample ID: 33198
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Vehicle

value: Poor

value: Unmutated


title: CS2-Rep1

value: Acute myeloid leukemia


title: WXS: tumor D rtTA-HER2d16 mouse on FVB background #525

tag: mouse model


title: Breast-T2-mRNA

value: Breast

value: Adult

value: Tumor


title: X2_PDL-1_L1

description:
Sample ID: 33246
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Durvalumab


title: Breast-N7-mRNA


title: Breast-N8-mRNA


title: Breast-N6-mRNA


title: WXS: tumor B rtTA-HER2d16 mouse on FVB background #525

value: breast tumor

value: FVB/NJ


title: CS1-Rep3


title: X2_CC_L5

description:
Sample ID: 33217
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Chronic lymphocytic leukemia (CLL)

value: Avadomide


title: CS1-Rep1


title: CS2-Rep2


title: CS1-Rep2


title: WXS: tumor A rtTA-HER2d16 mouse on FVB background #525

value: rtTA-HER2d16 mouse


title: X3_CC_L1.D710_501

description:
Sample ID: 33202
processed data file: CountsSalmon.TPM.33185-33246.xls

value: CD3+ T cells

value: TP53mutation, Complex karyotype


title: Breast-N4-mRNA

value: Normal


title: X1_CC_PDL-1_L3

description:
Sample ID: 33227
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Avadomide+Durvalumab

value: Good

value: Mutated


title: DMSO-Rep3


title: Breast-N3-mRNA


title: WXS: tail rtTA-HER2d16 mouse on FVB background #298

source_name: tail clip

value: tail


title: DMSO-Rep4

value: Acute myeloid leukemia


title: WXS: tumor C rtTA-HER2d16 mouse on FVB background #525


title: DMSO-Rep2


title: Breast-N2-mRNA

value: Breast


title: WXS: tail rtTA-HER2d16 mouse on FVB background #297


title: X1_CC_L5.D702

description:
Sample ID: 33216
processed data file: CountsSalmon.TPM.33185-33246.xls


title: X1_PDL-1_L2

description:
Sample ID: 33244
processed data file: CountsSalmon.TPM.33185-33246.xls


title: WXS: tail rtTA-HER2d16 mouse on FVB background #295


title: DMSO-Rep1


title: X1_Veh_L1

description:
Sample ID: 33191
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Vehicle


title: Breast-N5-mRNA

value: Adult


title: RNA-Seq: tumor C rtTA-HER2d16 mouse on FVB background #525


title: Breast-T10-miRNA-rep2

value: Tumor


title: X2_Veh_L4

description:
Sample ID: 33201
processed data file: CountsSalmon.TPM.33185-33246.xls


title: Breast-T10-miRNA-rep1


title: C2_CC_PDL-1_L1.D701

description:
Sample ID: 33218
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Del13q, Subset 4


title: WT1_3165

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using inDrops pipeline (https://github.com/indrops/indrops). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Barcodes were filtered (Liu et al., 2018), resulting in the processed data table. Bcd code can be converted to sequence barcodes within the inDrops pipeline. An example is at https://www.dropbox.com/s/tm9ciucqwgunwip/20190419_2969_AS-1-GCCAAT_pickle_bcd.txt?dl=0
NextSeq:Technical read: read2 - UMI/cell barcode - the oligo barcodes are inDrop Version 2 which is positioned exactly as in (Klein et al. 2015) Biological read: read1 - 3' end
Genome_build: Human: GRCh38.85, Mouse: GRCm38.85 (mixed database)
Supplementary_files_format_and_content: Delimited tables, with cells and genes, as columns and rows

source_name: pancreatic islets

growth_protocol: primary cells

extract_protocol:
Viable single islet cells were dissociated and collected as stated in Liu et al., Developmental Cell, 2019. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015.
CEL-Seq linear amplification of RNA/cDNA followed by index primer-based amplification
RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths

tag: genotype

value: WT

value: pancreatic islets


title: WXS: tail rtTA-HER2d16 mouse on FVB background #954

value: FVB/NJ


title: C2_CC_PD-1_L1.D702

description:
Sample ID: 33243
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Chronic lymphocytic leukemia (CLL)

value: Avadomide+Nivolumab


title: RNA-Seq: tumor B rtTA-HER2d16 mouse on FVB background #525

value: breast tumor

value: rtTA-HER2d16 mouse


title: Sin3A mutant1_2426

value: Sin3A mutant


title: RNA-Seq: tumor A rtTA-HER2d16 mouse on FVB background #525


title: C2_PDL-1_L9

description:
Sample ID: 33189
processed data file: CountsSalmon.TPM.33185-33246.xls

value: CD3+ T cells

value: Durvalumab

value: Good


title: Breast-T9-miRNA-rep2


title: RNA-Seq: tumor D rtTA-HER2d16 mouse on FVB background #555


title: Breast-T9-miRNA-rep1


title: Breast-N1-mRNA

value: Normal


title: C2_PD-1_L1.D712

description:
Sample ID: 33213
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Nivolumab

value: Mutated


title: Breast-T8-miRNA-rep2

value: Breast

value: Adult


title: WT1_2426


title: C2_CC_L8.D710

description:
Sample ID: 33206
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Avadomide

value: Del13q, Subset 4


title: Breast-T8-miRNA-rep1

value: Tumor


title: RNA-Seq: tumor B rtTA-HER2d16 mouse on FVB background #555

value: FVB/NJ


title: Breast-T7-miRNA-rep2


title: RNA-Seq: tumor C rtTA-HER2d16 mouse on FVB background #555


title: C2_Veh_L8.D709

description:
Sample ID: 33190
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Chronic lymphocytic leukemia (CLL)

value: Vehicle


title: Sin3A mutant1_3165

value: pancreatic islets


title: RNA-Seq: tumor A rtTA-HER2d16 mouse on FVB background #555

value: breast tumor

value: rtTA-HER2d16 mouse


title: MDA-MB-231 xenograft rep1

city: Göteborg

first: Emma

last: Jonasson

address: Medicinaregatan 1F, floor 5

department: Sahlgrenska Center for Cancer Research

country: Sweden

institute: University of Gothenburg

description: Reads.xlsx

data_processing:
Alignment was performed using STAR (with ERCC spike-in sequences included) with splice junctions supplied from the GENCODE V17 annotation. The SortedByCoordinate option was included.
Gene expression was quantified using HTseq with the options “-s no” and “-m intersection-strict”
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Excel file containing matrix of unnormalized reads mapped to each transcript (including ERCC spike-ins) as a result from HTseq analysis

source_name: Breast cancer cell line

growth_protocol:
Cell lines were cultured under normal cell culture conditions, MCF7 cells in Dulbecco's modified Eagle's medium (DMEM) complete media and MDA-MB-231 in RPMI 1640 complete media.
For patient-derived scaffold (PDS) culture, tumor pieces were decellularized using detergent wash. The PDSs were cut into 3x3 mm pieces, maximum 2 mm thick, and added to 48-well culture plates. Cells were added onto the PDSs in complete media and cultured for 21 days before analysis. PDS pieces were regulalry transferred to new wells with fresh media.
For xenograft culture, cells were dissociated using Accutase and resuspended in DMEM media mixed 1:1 with matrigel. Cells were injected subcutaneously into flanks of NOG mice. Tumors were extraced after 32 days.

extract_protocol:
Samples were lyzed in either lysis buffer containing 1 µg/µl BSA and 2.5% glycerol or in QIAzol lysis reagent. PDS and xenograft samples were homogenized using a stainless steel bead in TissueLyzer II. RNA was extracted using Qiagen miRNeasy Mini Kit including DNase treatment. RNA concentration was measured with nanodrop and RNA quality was randomly assessed with Agilent RNA 6000 Nano Kit using Bioanalyser 2100.
The library was generated using the Smart-seq2 protocol (Picelli, Faridani et al. 2014) with some modifications.

tag: cell culture method

value: Xenograft culture


title: MDA-MB-231 xenograft rep3

description: Reads.xlsx


title: Breast-T7-miRNA-rep1

tag: tissue


title: C1_CC_PD-1_L8.D702

description:
Sample ID: 33242
processed data file: CountsSalmon.TPM.33185-33246.xls

value: CD3+ T cells

value: Avadomide+Nivolumab


title: Breast-T6-miRNA-rep2


title: RNA-Seq: tumor D rtTA-HER2d16 mouse on FVB background #531


title: MDA-MB-231 PDS rep3

description: Reads.xlsx

value: Patient-derived scaffold (PDS) culture


title: MDA-MB-231 xenograft rep2

description: Reads.xlsx


title: C1_CC_PDL-1_L8.D701

description:
Sample ID: 33188
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Avadomide+Durvalumab

value: Good


title: MDA-MB-231 PDS rep2

description: Reads.xlsx


title: C1_PDL-1_L19

description:
Sample ID: 33233
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Durvalumab

value: Mutated


title: Breast-T6-miRNA-rep1

value: Breast

value: Adult


title: RNA-Seq: tumor C rtTA-HER2d16 mouse on FVB background #531


title: RNA-Seq: tumor B rtTA-HER2d16 mouse on FVB background #531


title: C1_PD-1_L20

description:
Sample ID: 33212
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Nivolumab

value: Del13q, Subset 4


title: MDA-MB-231 2D rep6

description: Reads.xlsx

value: Adherent 2D culture


title: C1_CC_L8.D710

description:
Sample ID: 33205
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Chronic lymphocytic leukemia (CLL)

value: Avadomide


title: MDA-MB-231 2D rep5

description: Reads.xlsx


title: RNA-Seq: tumor A rtTA-HER2d16 mouse on FVB background #531

value: breast tumor

value: FVB/NJ


title: Breast-T5-miRNA-rep2

value: Tumor


title: RNA-Seq: tumor D rtTA-HER2d16 mouse on FVB background #527

value: rtTA-HER2d16 mouse


title: C1_Veh_L7.D709

description:
Sample ID: 33196
processed data file: CountsSalmon.TPM.33185-33246.xls

value: CD3+ T cells

value: Vehicle


title: MDA-MB-231 2D rep4

description: Reads.xlsx


title: C_CC_PDL-1_L4.D705

description:
Sample ID: 33226
processed data file: CountsSalmon.TPM.33185-33246.xls

value: C

value: Avadomide+Durvalumab

value: Poor

value: Unmutated

value: Subset 8


title: RNA-Seq: tumor C rtTA-HER2d16 mouse on FVB background #527


title: Breast-T4-miRNA-rep2

value: Breast

value: Adult


title: Breast-T4-miRNA-rep1


title: C_CC_PD-1_L4.D706

description:
Sample ID: 33240
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Avadomide+Nivolumab


title: RNA-Seq: tumor B rtTA-HER2d16 mouse on FVB background #527


title: MDA-MB-231 2D rep3

description: Reads.xlsx

value: Adherent 2D culture


title: C_PDL-1_L4.D703

description:
Sample ID: 33231
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Chronic lymphocytic leukemia (CLL)

value: Durvalumab


title: RNA-Seq: tumor A rtTA-HER2d16 mouse on FVB background #527

value: breast tumor


title: MDA-MB-231 2D rep2

description: Reads.xlsx


title: MDA-MB-231 PDS rep1

description: Reads.xlsx

value: Patient-derived scaffold (PDS) culture


title: Breast-T3-miRNA-rep1

value: Tumor


title: C_PD-1_L4.D704

description:
Sample ID: 33214
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Nivolumab


title: MCF7 xenograft rep3

description: Reads.xlsx

value: Xenograft culture


title: MDA-MB-231 2D rep1

description: Reads.xlsx


title: RNA-Seq: tumor D rtTA-HER2d16 mouse on FVB background #525

value: FVB/NJ

value: rtTA-HER2d16 mouse


title: Breast-T5-miRNA-rep1


title: MCF7 xenograft rep2

description: Reads.xlsx


title: C_CC_L4.D702

description:
Sample ID: 33207
processed data file: CountsSalmon.TPM.33185-33246.xls

value: C

value: CD3+ T cells

value: Avadomide


title: MCF7 xenograft rep1

description: Reads.xlsx


title: C_Veh_L11

description:
Sample ID: 33197
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Vehicle

value: Poor

value: Unmutated

value: Subset 8


title: Breast-T2-miRNA-rep1

value: Breast

value: Adult


title: B_CC_PDL-1_L3.D711

description:
Sample ID: 33224
processed data file: CountsSalmon.TPM.33185-33246.xls

value: B

value: Chronic lymphocytic leukemia (CLL)

value: Avadomide+Durvalumab

value: Good

value: Mutated


title: Breast-T1-miRNA-rep2

value: Tumor


title: scRNA-seq_P30

city: Brussel

first: Cédric

last: Blanpain

address: 808 route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Read Alignment - CellRanger (version 3.0.2)
Cell-cycle assignment - Scran (1.10.1)
UMAP dimensionality reduction - Seurat (3.0.1)
Normalization - Seurat (3.0.1)
Gene regulatory network analysis - SCENIC (0.9.9+2.gcaded79)
Genome_build: mm10-1.2.0
Supplementary_files_format_and_content: R Rds objects; scRNAseq CellRanger output; SCENIC AUC Matrix; SCENIC regulon definitions

source_name: tail interfollicular epidermal basal cells at postnatal day 30

extract_protocol:
After incubation in HBSS (Gibco) 0,25% trypsin  (Gibco) at 4°C overnight, tail epidermis was separtaed from the dermis and cells were mechanically dissociated, stained with  PE-conjugated anti-a6-integrin (clone GoH3; 1:200, ebioscience) and bulge cells were stained with biotinylated CD34 (clone RAM34; 1:50, BD Biosciences) and APC-conjugated streptavidin (BD Biosciences). Basal cells were enriched using EGFP negative, CD34 negative and integrin a6 positive gating and FACS sorted. After sorting, 6000 cells were loaded onto each channel of the Chromium Single Cell 3’ microfluidic chips (V2-chemistry, PN-120232, 10X Genomics) and individually barcoded with a 10X Chromium controller according to the manufacturer’s recommendations (10X Genomics). RNA from the barcoded cells was reverse transcribed, followed by amplification, shearing 5′ adaptor and sample index attachment.
The libraries were prepared using the Chromium Single Cell 3’ Library Kit (V2-chemistry, PN-120233, 10X Genomics), quantified using a low coverage Illumina NextSeq 550 run and sequenced on an Illumina NovaSeq

treatment_protocol: no treatment

value: Lgr5DTR-EGFP mice (Tian et al., Nature, 2011)

tag: age

value: postnatal day 30

value: tail epidermis

value: FACS sorted basal cells


title: scRNA-seq_P7

source_name: tail interfollicular epidermal basal cells at postnatal day 7

value: postnatal day 7


title: scRNA-seq_Adult

value: postnatal day > 60


title: MCF7 PDS rep3

description: Reads.xlsx

value: Patient-derived scaffold (PDS) culture


title: Breast-T1-miRNA-rep1


title: clodronate female PBS3

city: Newark

first: Dane

last: Parker

state: NJ

address: 205 South Organge Ave, G-1208

department: Pathology, Immunology and Laboratory Medicine

institute: Rutgers New Jersey Medical School

data_processing:
Analysis was performed using Partek Flow
Reads were trimmed with Phred scores <30, 20bp minimum length and a maximum N of 10%, along with adaptor sequences removed
Trimmed reads were aligned using STAR and unaligned reads further aligned using TopHat2
Combined alignments were quantified to the annotation model
Filtered counts were normalized by adding 1 and using TMM
Differential analysis was conducted using ANOVA and Limma-voom, clodronate males and females were compared either before or after infection
Genome_build: mm9
Supplementary_files_format_and_content: xlsx

source_name: Lung homogenate

extract_protocol:
Lung homogenate was ressuspended in TRIZOL reageant. RNA was extracted from whole lungs using The Direct-zol™ RNA MiniPrep Kit (Zymo Research), following manufacturer's instructions
mRNA was purified from 1 μg of total RNA using poly-T oligo-attached magnetic beads and then fragmented using fragmentation buffer. The first strand of cDNA was synthesized using a random hexamer and M-MuLV reverse transcriptase with the second strand of cDNA synthesized using DNA polymerase I and RNase H. cDNA was purified using AMPure XP beads (Beckman Coulter), converted to blunt ends, adenylated and New England Biolabs (NEB) adaptors ligated.

treatment_protocol: Alveolar macrophages were depleted by inoculating intranasally anesthetized mice with 50 μl of either liposome containing clodronate (5 mg/mL) or liposome only controls (Encapsula NanoSciences) 24 h before intranasal infection with 10^7 cfu of  A. baumannii 5075.

value: lung

tag: Sex

value: female

value: uninfected


title: Breast-T2-miRNA-rep2

value: Breast

value: Adult

tag: tissue type


title: Breast-T3-miRNA-rep2


title: clodronate female PBS2


title: B_PDL-1_L3.D709

description:
Sample ID: 33230
processed data file: CountsSalmon.TPM.33185-33246.xls

tag: patient

value: B

value: Chronic lymphocytic leukemia (CLL)

value: CD3+ T cells

value: Durvalumab


title: Breast-N10-miRNA-rep1

value: Normal


title: Breast-N10-miRNA-rep2


title: MCF7 PDS rep1

description: Reads.xlsx


title: Breast-N9-miRNA-rep2


title: B_PD-1_L3.D710

description:
Sample ID: 33195
processed data file: CountsSalmon.TPM.33185-33246.xls

tag: disease diagnosis

value: Nivolumab

value: Good

value: Mutated


title: clodronate female PBS1


title: B_CC-122_L2.D708

description:
Sample ID: 33211
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Avadomide

tag: prognostic group


title: Breast-N9-miRNA-rep1


title: MCF7 2D rep6

description: Reads.xlsx

value: Adherent 2D culture


title: MCF7 2D rep5

description: Reads.xlsx


title: clodronate female Ab3

value: Acinetobacter baumannii Infected


title: clodronate female Ab2


title: B_Veh_L2.D707

description:
Sample ID: 33204
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Vehicle

tag: igvh mutational status


title: Breast-N8-miRNA-rep2


title: B_CC_PD-1_L3.D712

description:
Sample ID: 33239
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Avadomide+Nivolumab

tag: chromosomal abnormalities or subset


title: A_CC_PDL-1_L2.D706

description:
Sample ID: 33223
processed data file: CountsSalmon.TPM.33185-33246.xls

value: A

value: Avadomide+Durvalumab

value: Poor


title: MCF7 2D rep4

description: Reads.xlsx


title: MCF7 PDS rep2

description: Reads.xlsx

value: Patient-derived scaffold (PDS) culture


title: MCF7 2D rep3

description: Reads.xlsx


title: A_PDL-1_L2.D705

description:
Sample ID: 33238
processed data file: CountsSalmon.TPM.33185-33246.xls


title: clodronate male PBS2

value: lung

tag: strain

value: male

value: uninfected


title: A_CC-122_L10

description:
Sample ID: 33200
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Chronic lymphocytic leukemia (CLL)

value: CD3+ T cells


title: MCF7 2D rep1

description: Reads.xlsx


title: Breast-N7-miRNA-rep1

value: Breast

tag: developmental stage

value: Adult

value: Normal


title: clodronate male PBS1


title: A_Veh_L1.D703

description:
Sample ID: 33210
processed data file: CountsSalmon.TPM.33185-33246.xls

tag: cell type

value: Mutated


title: 4_PDL-1_L13

description:
Sample ID: 33222
processed data file: CountsSalmon.TPM.33185-33246.xls

tag: treatment

value: Durvalumab

value: Unmutated


title: clodronate male Ab4

value: Acinetobacter baumannii Infected


title: Breast-N7-miRNA-rep2


title: Breast-N6-miRNA-rep2


title: DPT46-adenosine treated replicate-2_L4

city: Houston

first: Arun

last: Sreekumar

state: Texas

address: One Baylor Plaza

department: Molecular and Cell Biology

institute: Baylor College of Medicine

data_processing:
Sequenced reads were checked for quality with illumina internal (Q30  with 93%) and fastqc.
Sequenced reads were mapped with tophat 2.1.0 and bowtie2 as hg19 genome build.
The aligned files were used with htseq 2.7 to count the probes.
The counts are used for quantile normalization and differential analysis
Genome_build: hg19
Supplementary_files_format_and_content: htseq counts in text format

source_name: DPT46-adenosine treated replicate-2_L4

growth_protocol: cells were maintained in RPMI media with 10% FBS and grown on collagen coated plates

extract_protocol:
After 48hrs, cells are trypsinzed and collected for RNA extraction via the Bio-Rad Aurum Total RNA Isolation kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells are starved for 24hrs with M20 media(DMEM-HG supplemented with 0.2% BSA, Insulin transferrin selenium, and penicillin / streptomycin).  A stock solution of 10mM adenosine is reconsituted in M20 media, and added to the stroma at a final concentration of 100uM.  Treated cells are incubated for 48hrs.

value: prostate stroma

tag: cell line


title: 4_CC_PDL-1_L14

description:
Sample ID: 33241
processed data file: CountsSalmon.TPM.33185-33246.xls


title: DPT46-adenosine treated replicate-2_L3

source_name: DPT46-adenosine treated replicate-2_L3


title: clodronate male Ab3


title: Breast-N6-miRNA-rep1


title: X3_CC_PDL-1_L7.D701

description:
Sample ID: 33225
processed data file: CountsSalmon.TPM.33185-33246.xls

value: TP53mutation, Complex karyotype


title: DPT46-adenosine treated replicate-2_L2

source_name: DPT46-adenosine treated replicate-2_L2


title: clodronate male Ab2


title: clodronate male PBS3


title: Breast-N5-miRNA-rep1


title: Breast-N8-miRNA-rep1


title: Breast-N4-miRNA-rep2


title: DPT46-adenosine treated replicate-2_L1

source_name: DPT46-adenosine treated replicate-2_L1


title: clodronate male Ab1


title: MCF7 2D rep2

description: Reads.xlsx

value: Adherent 2D culture


title: DPT46-adenosine treated replicate-1-L4

source_name: DPT46-adenosine treated replicate-1-L4


title: 4_Veh_L5.D707

description:
Sample ID: 33199
processed data file: CountsSalmon.TPM.33185-33246.xls

source_name: T lymphocytes

value: Vehicle

value: Poor


title: 3_CC_PDL-1_L16

description:
Sample ID: 33221
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Avadomide+Durvalumab

value: Trisomy 12


title: Breast-N4-miRNA-rep1


title: clodronate female Ab1

value: lung

value: female


title: Breast-N3-miRNA-rep2


title: 3_CC_PD-1_L17

description:
Sample ID: 33237
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Chronic lymphocytic leukemia (CLL)

value: CD3+ T cells

value: Avadomide+Nivolumab


title: MT_rep1

city: xuzhou

first: yao

last: chen

address: Shanghai Road 101

institute: Jiangsu normal university

description:
D5_M1
Wax apple
Melatonin treatment group

data_processing:
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) including the Q20, Q30 and GC-content of the clean data. All downstream analyses were based on clean data of high quality.
De novo assembly of the transcriptome was performed with Trinity 2.4.0. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene).
All assembled Unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/), Gene ontology (GO)(http://www.geneontology.org), SwissProt (http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG)(http://www.genome.jp/kegg/) and eggNOG (http://eggnogdb.embl.de/) databases using DIAMOND with a threshold of Evalue<0.00001.
Salmon was used to perform expression level for Unigenes by calculating TPM. The differentially expressed Unigenes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR. Next, GO and KEGG enrichment analysis were again performed on the differentially expressed Unigenes by perl scripts in house.
Genome_build: Trinity.gene.fasta, Trinity.trans.fasta
Supplementary_files_format_and_content: Trinity.gene.fasta is the assembled gene sequence, and Trinity.trans.fasta is the assembled transcriptome sequence.
Supplementary_files_format_and_content: clean_data_stat.xls is clean data.
Supplementary_files_format_and_content: gene_expression.xls: Excel file includes gene expression levels and gene annotation.
Supplementary_files_format_and_content: D5_M_vs_D5_C_diff_exp.xls: Excel file includes TPM values for each Sample and also shows differentially expressed genes.

organism: Syzygium samarangense

source_name: fruit

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number > 7.0. Poly(A) RNA is purified from total RNA (5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq RNA Sample Preparation v2 (Cat. RS-122-2001,RS-122-2002) (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina HiSeq 4000 at the (LC Sciences, USA) following the vendor’s recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Control and 800µM melatonin treatment groups.

value: Pulp

value: 5th day after harvest

value: Melatonin


title: MT_rep3

description:
D5_M3
Wax apple
Melatonin treatment group


title: 3_PDL-1_L6.D701

description:
Sample ID: 33232
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Durvalumab

value: Unmutated


title: DPT46-adenosine treated replicate-1-L3

source_name: DPT46-adenosine treated replicate-1-L3

value: prostate stroma


title: Breast-N3-miRNA-rep1

value: Breast

value: Adult

value: Normal


title: DPT46-adenosine treated replicate-1-L2

source_name: DPT46-adenosine treated replicate-1-L2


title: DPT46-adenosine treated replicate-1-L1

source_name: DPT46-adenosine treated replicate-1-L1


title: 3_PD-1_L15

description:
Sample ID: 33194
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Nivolumab

value: Poor


title: CK_rep3

description:
D5_C3
Wax apple
CK

value: Control


title: Breast-N5-miRNA-rep2

source_name: Breast normal tissue


title: 4_CC_L12

description:
Sample ID: 33215
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Avadomide


title: CK_rep2

description:
D5_C2
Wax apple
CK


title: DPT46-untreated replicate-3-L4

source_name: DPT46-untreated replicate-3-L4


title: Breast-N2-miRNA-rep1


title: DPT46-untreated replicate-3-L3

source_name: DPT46-untreated replicate-3-L3


title: 3_Veh_L5.D711

description:
Sample ID: 33185
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Vehicle

value: Trisomy 12


title: CK_rep1

description:
D5_C1
Wax apple
CK


title: 3_CC-122_L6.D712

description:
Sample ID: 33187
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Chronic lymphocytic leukemia (CLL)

value: CD3+ T cells


title: DPT46-untreated replicate-3-L2

source_name: DPT46-untreated replicate-3-L2


title: 1_CC_PDL-1_L18

description:
Sample ID: 33220
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Avadomide+Durvalumab

value: Good

value: Mutated


title: KO PAB rep 4

city: Madison

first: Naomi

last: Chesler

state: Wisconsin

address: 2146 Engineering Centers Building, 1550 Engineering Drive

department: Biomedical Engineering

institute: University of Wisconsin-Madison

description:
10 weeks of pulmonary artery banding (pressure overload)
Sample 15

data_processing:
The trimming software skewer v0.1.123 (Jiang et al. 2014) was used to preprocess raw fastq files
Samples were normalized by the method of trimmed mean of M-values (TMM), where the product of this factor and the library sizes defines the effective library size (Robinson and Oshlack 2010).
The trimmed paired-end reads are aligned against the selected reference genome sequence using STAR v2.5.3a (Spliced Transcripts Alignment to a Reference) (Dobin et al. 2013).
Mapped paired-end reads for genes were counted in each sample using RSEM v1.3.0 (RNASeq by Expectation Maximization), described in Li and Dewey (2011).
Genome_build: Rattus norvegicus Rnor_6.0 genome (assembly accession GCA_000001895.4)
Supplementary_files_format_and_content: tab-delimited text files include TPM adjusted expected read counts for each Sample

organism: Rattus norvegicus

source_name: Right ventricle

extract_protocol:
Total RNA was extracted from 10 mg of RV using Qiagen RNeasy Fibrous Tissue Mini Kit (cat. # 74704). DNaseI treatment was performed in the column according to the manufacturer’s protocol. 60 uL of total RNA were recovered with concentrations ranging from 72.7 to 180.6 ng/μl and with A260/280 nm ranging from 1.89 to 2.11. RNA quality and integrity were evaluated by capillary electrophoresis on the Agilent 2100 Bioanalyzer platform (Agilent Technologies).
The sequencing library from mRNA was prepared using TruSeq Stranded mRNA Library Preparation Kit (Illumina; San Diego, CA)

value: Sprague Dawley

value: Right ventricle

value: Female

value: 20-21 weeks

value: ERalpha -/-

tag: stress induction

value: Stress


title: MT_rep2

description:
D5_M2
Wax apple
Melatonin treatment group

value: Pulp

value: 5th day after harvest

value: Melatonin


title: DPT46-untreated replicate-3-L1

source_name: DPT46-untreated replicate-3-L1

value: prostate stroma


title: DPT46-untreated replicate-2-L4

source_name: DPT46-untreated replicate-2-L4


title: Breast-N1-miRNA-rep1

value: Breast

value: Adult

value: Normal


title: 1_CC_L7.D706

description:
Sample ID: 33186
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Chronic lymphocytic leukemia (CLL)

value: CD3+ T cells

value: Avadomide


title: 1_Veh_L7.D705

description:
Sample ID: 33193
processed data file: CountsSalmon.TPM.33185-33246.xls

value: Vehicle

value: Good

value: Mutated


title: CD11b+_M

city: Jacksonville

first: Tae Hyun

last: Hwang

state: FL

address: 4500 San Pablo Rd S

department: Department of Artificial Intelligence and Informatics

institute: Mayo Clinic

data_processing:
Basecalls performed using CASAVA version 1.4
The Universal Adapter "AGATCGGAAGAGC" is trimmed by cutadapt
Kallisto (v0.44.0) quantifies the transcription abudnance with the program argument --bootstrap-samples 100 and the mouse GENCODE gene set M16 (release date Dec 2017)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample …

source_name: nonMDSC

growth_protocol: primary cells were isolated from femur and tibia

extract_protocol:
RNAeasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 2 x 10^6 bone marrow cells were co-cultured with 1 x 10^5 GL261 cells in the presence of 40 ng/ml GM-CSF and 80 ng/ml IL-13 in 2ml 10% RPMI in 6-well plates for 3 days. mMDSC, gMDSC and nonMDSC were sorted based on CD11b, Ly6C and Ly6G expression.

value: nonMDSC

tag: cell phenotype

value: Male


title: KO PAB rep 3

description:
10 weeks of pulmonary artery banding (pressure overload)
Sample 11

value: Sprague Dawley

value: Right ventricle

value: Female

value: 20-21 weeks

tag: genotype

value: ERalpha -/-


title: CD11b+_F2


title: DPT46-untreated replicate-2-L3

source_name: DPT46-untreated replicate-2-L3

tag: tissue

value: prostate stroma


title: Breast-N2-miRNA-rep2

value: Breast


title: CD11b+_F1


title: DPT46-untreated replicate-2-L2

source_name: DPT46-untreated replicate-2-L2


title: KO PAB rep 2

description:
10 weeks of pulmonary artery banding (pressure overload)
Sample 9

tag: age

value: Stress


title: KO PAB rep 1

description:
10 weeks of pulmonary artery banding (pressure overload)
Sample 7

tag: Sex


title: CD11b+_3


title: KO SHAM rep 4

description:
Sham for pulmonary artery banding
Sample 18

value: No stress


title: DPT46-untreated replicate-2-L1

source_name: DPT46-untreated replicate-2-L1


title: Breast-N1-miRNA-rep2

value: Adult

tag: tissue type

value: Normal


title: AeAeg_Ovary_TC_rr

city: BOSTON

first: NELSON

middle: C

last: LAU

state: MA

address: 72 E Concord St K219, Dept of Biochemistry

department: Biochemistry and Cell Biology

institute: Boston University Chobanian & Avedisian School of Medicine

data_processing:
Illumina Nextseq 500 on instrument base calling
FastX initial quality score trimming and filtering of reads against structural RNAs, microRNAs, viral RNAs
Mapped to the Aedes aegypti, Aedes albopictus, Anopheles gambiae, and Culex quinquefasciatus reference genome, with Bowtie, allowing up to 2 mismatches
SAM file of reads counted against RefSeq database of all  transcripts, counts per locus region and both strands measured
Genome_build: Aedes aegypti: AaegL5; Aedes albopictus: AalbF2; Anopheles gambiae: AgamP4; Culex quinquefasciatus: CpipJ2
Supplementary_files_format_and_content: text file tab-delimited tables of read counts mapped to refseq transcripts

organism: Aedes aegypti

growth_protocol: 6 mosquito cell lines (Sua5b, Mos55, Aag2, C7-10, U4-4, C636) were cultured in Shield and Sang M13 media with 10% FBS and bactopeptone and yeast extract additions.  2 mosquito cell lines (CCL-125 and Hsu) were cultured in Low Glucose DMEM with Nonessential Amino Acids and 20% FBS.  See the full protocol from Ma et al, 2020, Biorxiv submission

extract_protocol:
Total RNA from cell pellets and tissues were extracted with the Tri-reagent protocol of Chomzcynski and and Sacchi, 1987.
New Englad Bioloabs, NEBNext small RNA Library Prep Kit for Illumina.
8 to 20 libraries with different barcodes were multiplexed in each sequencing run.  Separation of sequences by different barcodes was conducted during the on-instrument base-calling.

treatment_protocol: Steady state cultures or cultures subjected to 7 days of treatment with an infection of Dengue or Zika virus were neutralized in the extraction protocol.  Adult males and females mosquitos either rased on a sugur diet, or fed rodent blood for 48 hours for females, were subjected to  euthanisia and then ovaries and testes were dissected under PBS solution.

value: Ovary


title: KO SHAM rep 3

description:
Sham for pulmonary artery banding
Sample 10


title: CD11b+_2


title: AeAeg_Ovary_GH


title: KO SHAM rep 2

description:
Sham for pulmonary artery banding
Sample 8


title: 1_PDL-1_L7.D707

description:
Sample ID: 33236
processed data file: CountsSalmon.TPM.33185-33246.xls

tag: patient

value: Chronic lymphocytic leukemia (CLL)

value: CD3+ T cells

value: Durvalumab


title: CD11b+_1

value: nonMDSC


title: AeAeg_Fcarc_TC

value: Female carcass


title: AeAeg_Fcarc_GH_rep3


title: KO SHAM rep 1

description:
Sham for pulmonary artery banding
Sample 6

value: Sprague Dawley


title: DPT46-untreated replicate-1-L3

source_name: DPT46-untreated replicate-1-L3


title: gMDSC_M

source_name: gMDSC

value: gMDSC

value: Male


title: DPT46-untreated replicate-1-L2

source_name: DPT46-untreated replicate-1-L2


title: gMDSC_F2

value: Female


title: WT PAB rep 4

description:
10 weeks of pulmonary artery banding (pressure overload)
Sample 19

value: Right ventricle

value: 20-21 weeks

value: WT


title: AeAeg_Fcarc_GH_rep2


title: WT PAB rep 3

description:
10 weeks of pulmonary artery banding (pressure overload)
Sample 16

value: Stress


title: gMDSC_F1


title: DPT46-untreated replicate-1-L1

source_name: DPT46-untreated replicate-1-L1

value: prostate stroma


title: WT PAB rep 2

description:
10 weeks of pulmonary artery banding (pressure overload)
Sample 13


title: gMDSC_3


title: AeAeg_Fcarc_GH_rep1


title: AeAeg_Aag2_Zika_PR_rep2


title: AeAeg_CCL-125_cells


title: Neu-NT7d-LH84

data_processing:
Resulting fastq files were aligned to the mouse mm10 reference genome using the STAR aligner algorithm
BAM files were sorted and indexed using Samtools and quality control was performed using Picard
Transcript read counts were determined using Salmon
Genome_build: mm10
Supplementary_files_format_and_content: Salmon quantified read-counts.

source_name: mammary tumor

growth_protocol: Tumors were orthotopically injected in sygeneic hosts. Tumors were allowed to progress to a 5mm diameter, then grew for 7 days withouth any treatment

extract_protocol:
RNA was extracted using Qiagen Rneasy kits. mRNA quality was assessed using the Agilent Bioanalyzer.
Libraries for mRNA-seq made using total RNA and the Illumina TruSeq mRNA sample preparation kit
Paired end (2x50bp) sequencing was performed on the Illumina HiSeq 2000/2500 sequencer at the UNC High Throughput Sequencing Facility

treatment_protocol: No Treatment

value: FVB-MMTV-Neu

value: mammary tumor


title: WT PAB rep 1

description:
10 weeks of pulmonary artery banding (pressure overload)
Sample 3


title: Neu-NT7d-LH73


title: DPT46-untreated replicate-1-L4

source_name: DPT46-untreated replicate-1-L4


title: Neu-NT7d-164606


title: gMDSC_2


title: AeAeg_Aag2_Zika_PR_rep1_rr


title: WT SHAM rep 3

description:
Sham for pulmonary artery banding
Sample 14

value: No stress


title: AeAeg_Aag2_Zika_OW_rep2


title: TAG RAS/DNP53 HAsiRNA rep3 [140219_SND393_A_L003_HBY-9_R1]

city: Montpellier

first: Frederic

middle: Emile

last: Bienvenu

address: 141 rue de la Cardonille

department: Cancer Biology

country: France

institute: CNRS-Institute of Functinal Genomics

description: MEFs RAS Ctag 14 siHA rep2

data_processing:
- HiSeq Control Software 2.2.38
- RTA 1.18.61.0
- CASAVA-1.8.2
TopHat 2.0.8b
Cufflinks 2.1.1
Genome_build: MGSCv37
Supplementary_files_format_and_content: Excel file include 3 sheets with 1-expression change call, 2-BiNGO analysis of enriched GO, 3-selected developmental GO

source_name: RAS tumor

growth_protocol: 0,5 million cells were implanted subcutaneously into immune compromised mice. Treatment was applied after tumors reached 500 mm3 in size.

extract_protocol:
Animals were sacrificed 30 minutes after the last siRNA injection, tumors were dissected and RNA was extracted using Trizol reagent.
The libraries were prepared with the TruSeq Stranded mRNA sample prep kit from illumina according to the manufacture's instructions. After oligo d(T) purification, mRNA was fragmented by zinc. cDNA was synthesized using random primer. Adapters are then ligated and PCR cycles were performed to enrich the library. The libraries were sequenced on a HiSeq 2500 instrument (from illumina) in a single read 1x100bp. The v3 chemistry was used according to manufacture's instructions.

treatment_protocol: Animals carrying tumors were treated by rectal route with Aonys siRNA formulation (mg/mL) for 5 times per day every other hour.

tag: tumor type

value: Tagged-Cyclin D1 RAS/DNP53-driven tumor

tag: tumor treatment

value: HA-siRNA


title: WT SHAM rep 4

description:
Sham for pulmonary artery banding
Sample 17


title: WT SHAM rep 2

description:
Sham for pulmonary artery banding
Sample 12


title: gMDSC_1


title: mMDSC_M

source_name: mMDSC

value: mMDSC


title: AeAeg_Aag2_Zika_OW_rep1


title: WT SHAM rep 1

description:
Sham for pulmonary artery banding
Sample 4


title: mMDSC_F2


title: mMDSC_F1


title: AeAeg_Aag2_Qmatrix_rep1


title: TAG RAS/DNP53 HAsiRNA rep2 [140521_SND393_B_L002_HBY-18_R1]

description: MEFs RAS Ctag 14 siHA


title: AeAeg_Aag2_NL_cells


title: TAG RAS/DNP53 HAsiRNA rep1 [140521_SND393_B_L003_HBY-17_R1]

description: MEFs RAS Ctag 12 siHA


title: mMDSC_3


title: mMDSC_2


title: TAG RAS/DNP53 HAsiRNA rep1 [140521_SND393_B_L002_HBY-17_R1]

description: MEFs RAS Ctag 12 siHA


title: AeAeg_Aag2_NL_Dmem


title: R_NahG_shPti5_pvy1

city: Ljubljana

first: Marko

last: Petek

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

description:
Solanum tuberosum cv. Rywal: genotype NahG_shPti5 PVY_GFP-treated 1
ExpressionBrowser_TotalCounts.txt

data_processing:
Trim Sequences 1.13 (CLC Genomics Server 9.1): trimming of polyA tails and residual Illumina adaptors identified using FastQC; Ambiguous limit 2, Quality limit 0.05.
RNA-Seq Analysis 2.15 (CLC Genomics Server 9.1): Reference type Genome annotated with genes and transcripts, Mismatch cost 2, Insertion cost 3, Deletion cost 3, Length fraction 0.9, Similarity fraction 0.9, Global alignment No, Auto-detect paired distances Yes, Strand specific Reverse, Maximum number of hits for a read 10, Count paired reads as two No, Expression value Total counts.
Create Expression Browser 1.0 (CLC Genomics Server 10.1.1): gene expression (GE) count results from RNA-Seq Analysis were used, resulting total counts table was exported as txt files.
Genome_build: PGSC Solanum tuberosum pureja DM v4.04, Solanum tuberosum tuberosum RH mitochondrion genome (Genbank ID: JF772173.1), Solanum tuberosum tuberosum cv. Desiree chloroplast genome (Genbank ID: DQ386163.2), potato_rRNAs, PVY-Wilga (Genbank ID: AJ889867), PVY-NTN, NIB isolate (AJ585342)
Supplementary_files_format_and_content: tab-delimited text file includes total count values for all samples

organism: Solanum tuberosum

source_name: leaf

growth_protocol: Potato cv. Rywal plants (transgenic NahG line) were grown in stem node tissue culture. Two weeks after node segmentation they were transferred to soil and kept in growth chambers under controlled environmental conditions at  22/20 °C with a long-day (16-h) photoperiod of light (light intensity 4000 lm/m2) and 60%-70% relative humidity.

extract_protocol:
Potato leaf samples (~150 mg) were homogenized using FastPrep instrument (MP Biomedicals). The total RNA was extracted using RNeasy Plant Mini kits (Qiagen) according to manufacturer’s instructions and treated with DNase (Qiagen; 1.3U DNase/ug RNA).
RNA libraries for sequencing were prepared at SeqMatic LLC using standard Illumina protocols.

treatment_protocol: PVY N605-GFP infective clone (Rupar et al., 2015) was propagated and maintain in Nicotiana tabacum cv. Xanthi. PVY inoculation was performed on 4 week-old plants as described by (Rupar et al., 2015). In brief, to prepare the inoculum, systemically infected leaves from N. tabacum cv. Xanthi were grinded in phosphate buffer.  The presence of PVY-GFP was previously confirmed by confocal microscopy. The inoculum was used to infect three bottom leaves of plants using mechanically inoculation with carborundum.  Control plants were mock inoculated with healthy N. tabacum cv. Xanthi plant sap. The inoculum was washed with tap water after 10 min.

tag: cultivar

value: Rywal

tag: line


title: R_NahG_shPti5_pvy2

description:
Solanum tuberosum cv. Rywal: genotype NahG_shPti5 PVY_GFP-treated 2
ExpressionBrowser_TotalCounts.txt


title: mMDSC_1

tag: strain


title: R_NahG_shPti5_mock3

description:
Solanum tuberosum cv. Rywal: genotype NahG_shPti5 mock-treated 3
ExpressionBrowser_TotalCounts.txt

value: Mock


title: TAG RAS/DNP53 HAsiRNA rep3 [140219_SND393_A_L002_HBY-9_R1]

description: MEFs RAS Ctag 14 siHA rep2


title: AeAeg_Aag2_NL-M3


title: CS1-2

description: MA9 mouse model with CS1 treatment 2

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were mapped to the  mouse mm10 using the STAR aligner. The aligned reads were then assigned to genes using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: table delimited text file containing the expression of genes

source_name: Spleen mononuclear cells isolated from MLL-AF9 mouse

extract_protocol: The total RNA were extracted with QIAzol lysis reagent.

treatment_protocol: The cells were isolated from speen of PBS- and FTO inhibitor (CS1)-treated MA9 mice and CD45.2 cells were enriched.

tag: tumor

value: Acute myeloid leukemia

value: spleen


title: WT RAS/DNP53 HAsiRNA rep2 [140219_SND393_A_L002_HBY-5_R1]

description: MEFs RAS WT 25 siHA

value: Cyclin D1 RAS/DNP53-driven tumor


title: WT RAS/DNP53 HAsiRNA rep2 [140219_SND393_A_L003_HBY-5_R1]

description: MEFs RAS WT 25 siHA


title: AeAeg_Aag2_DENV4_rep1


title: CS1-1

description: MA9 mouse model with CS1 treatment 1


title: R_NahG_shPti5_mock2

description:
Solanum tuberosum cv. Rywal: genotype NahG_shPti5 mock-treated 2
ExpressionBrowser_TotalCounts.txt


title: WT RAS/DNP53 HAsiRNA rep1 [140521_SND393_B_L003_HBY-15_R1]

description: MEFs RAS WT 18 siHA


title: R_NahG_shPti5_mock1

description:
Solanum tuberosum cv. Rywal: genotype NahG_shPti5 mock-treated 1
ExpressionBrowser_TotalCounts.txt


title: WT RAS/DNP53 HAsiRNA rep1 [140521_SND393_B_L002_HBY-15_R1]

description: MEFs RAS WT 18 siHA


title: R_NahG_shPti5_pvy3

description:
Solanum tuberosum cv. Rywal: genotype NahG_shPti5 PVY_GFP-treated 3
ExpressionBrowser_TotalCounts.txt


title: PBS-2

description: MA9 mouse model with PBS treatment 2

value: PBS


title: AeAeg_Aag2_DENV3_rep2


title: AeAeg_Aag2_DENV3_rep1


title: R_NahG_pvy3

description:
Solanum tuberosum cv. Rywal: genotype NahG PVY_GFP-treated 3
ExpressionBrowser_TotalCounts.txt

value: NahG


title: R_NahG_pvy2

description:
Solanum tuberosum cv. Rywal: genotype NahG PVY_GFP-treated 2
ExpressionBrowser_TotalCounts.txt


title: AeAeg_Aag2_DENV2NGC_rep2


title: PBS-1

description: MA9 mouse model with PBS treatment 1


title: CHLA9 scRNA-Seq

city: San Antonio

first: Henry

last: Miller

state: TX

address: 8403 Floyd Curl Drive

department: Cell Systems and Anatomy

institute: UT Health San Antonio

data_processing:
Fastq files were processed with cellranger v3.1.0 using the 'count' function. For CHLA9 and CHLA10, fastq files from NovaSeq and HiSeq were entered as a comma-separated list as recommended by 10X genomics.
Genome_build: hg38
Supplementary_files_format_and_content: cellranger count output (filtered feature bc matrices)

source_name: Ewing sarcoma cell line

growth_protocol: Ewing Sarcoma cell lines CHLA-9 and CHLA-10 were maintained in in Iscove’s Modified Dulbecco’s Medium (IMDM, Gibco) supplemented with 20% heat-inactivated Fetal Bovine Serum (FBS, ATLANTA biologicals), 1% Insulin-transferrin-sodium selenite (ITS, Corning) and 1X Antibiotic Antimycotic Solution (Corning). Ewing Sarcoma TC-71 cell line was maintained in RPMI-1640 Medium (Gibco) supplemented with 10% FBS (ATLANTA biologicals) and 1X Antibiotic Antimycotic Solution (Corning). All cell lines were culture at 37 °C in a humidified incubator containing 95% room air plus 5% CO2 atmosphere.

extract_protocol:
When the cells were around 70-80% confluent, the cells were washed twice with HBSS (Corning), recollected using 0.25% Trypsin, 2.21mM EDTA, 1X sodium bicarbonate solution (Corning) and centrifuged for 5 minutes at 300 rcf at 4 °C. Cell pellets were then resuspended in cold DPBS (containing no calcium and no magnesium) (Corning) supplemented with 0.04% Bovine Serum Albumin (BSA) to minimize cell sticking. Viable cells were consequently counted using an automated cell counter (Nexcelom), centrifuged as above described and resuspended at the desired final concentration in cold DPBS (containing no calcium and no magnesium) - 0.04% BSA. Finally, single cell suspensions were strain through a 70 um cell sieve and processed for sequencing. Immediatly prior to processing on the 10X single cell controller, cell density and viability were checked one last time by BioRad TC20 Automated Cell Counter by mixing 10ul cells and 10ul 0.4% trypan blue stian and also reviewed under microscope
10X Genomics Chromium Single Cell 3' V3.1 kit


title: R_NahG_pvy1

description:
Solanum tuberosum cv. Rywal: genotype NahG PVY_GFP-treated 1
ExpressionBrowser_TotalCounts.txt


title: AnGam_Testis_TN

organism: Anopheles gambiae

value: Testis


title: AnGam_Testes_BetaE

value: Testes


title: AeAeg_Aag2_DENV4_rep2


title: AnGam_Sua5bcells_BetaE


title: AeAeg_Aag2_DENV2NGC_rep1


title: AeAeg_Aag2_DENV2K0048_rep2


title: R_NahG_mock3

description:
Solanum tuberosum cv. Rywal: genotype NahG mock-treated 3
ExpressionBrowser_TotalCounts.txt


title: AnGam_Sua5b_NL_cells_rep2


title: AeAeg_Aag2_DENV2K0048_rep1


title: AeAlbo_Testis_OA

organism: Aedes albopictus


title: AeAlbo_Ovary_OA

value: Ovary


title: AeAlbo_U4_4_NL_cells


title: AnGam_Ovary_TN


title: AeAeg_Aag2_DENV1_rep2


title: R_NahG_mock1

description:
Solanum tuberosum cv. Rywal: genotype NahG mock-treated 1
ExpressionBrowser_TotalCounts.txt


title: AeAlbo_Larv_OA

value: Larvae


title: AnGam_Ovary_BetaE


title: AnGam_Mos55_NL_cells


title: AeAlbo_Mcarc_OA

value: Male  carcass


title: AeAeg_Aag2_DENV1_rep1


title: DJ

city: pingdingshan

first: shiping

last: cheng

address: weilai road

institute: pingdingshan university

data_processing:
Basecalls performed using CASAVA version 1.7
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Raw reads after quality control testing were then assembled using trinity software
count counting
Assemble Genome
Genome_build: Unigene.fa
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Rhododendron simsii

source_name: Fresh roots, leaves, flowers and stem tissues

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: AeAlbo_Fcarc_OA

value: Female carcass


title: CuQuin_Testes_NL

organism: Culex quinquefasciatus


title: AeAeg_Aag2_Ctrl_rep1


title: R_NahG_mock2

description:
Solanum tuberosum cv. Rywal: genotype NahG mock-treated 2
ExpressionBrowser_TotalCounts.txt


title: CuQuin_Mcarc_NL

value: Male carcass


title: AeAeg_Aag2-TC-M3


title: AnGam_Mos55-JRcells_BetaE


title: AeAlbo_C636_cells_rep1


title: CuQuin_Hsu_NL

value: Hsu


title: AnGam_Fcarc_TN_rerun


title: AeAlbo_C636_NL_cells_rep_3


title: CuQuin_Fcarc_NL


title: AnGam_Mcarc_TN


title: DNA_ChIRP_LacZ_set_3

status: Public on Apr 10 2020

city: Deutschland

first: Raza

middle: Ur

last: Rahman

address: Falkenried, 94

country: Germany

institute: Systembiologie Bonnlab

library_source: genomic

data_processing:
Library strategy: ChIRP-seq
RNA-seq analysis: Quality assessment was based on the raw reads using the FASTQC (v0.10.1). The sequence reads (single-end 50 bp) were aligned to the rat reference genome (Rnor_6.0) with Bowtie2 (v2.0.2) using RSEM (v1.2.29) with default parameters. First, the rat reference genome was indexed using the Ensembl annotations (v83.6) with rsem-prepare-reference from RSEM software. Next, rsem-calculate-expression was used to align the reads and quantify the gene and isoform abundance. The output of rsem-calculate-expression gives separately the read count and TPM (transcripts per million) value for each gene and isoform.
ChIRP DNA analysis: Reads were aligned to the rat reference genome (Rnor_6.0) using Bowtie (v2.0.2) with default parameters allowing for 2 mismatches using seed alignment. Subsequently, aligned reads were filtered for high quality uniquely and multi-mapped reads (MAPQ ! = [0, 2, 3, 4]). Peaks were assigned to the genes if they are located within 5 kb upstream of the TSS or in the transcribed region or within 1 kb downstream of the transcription end site.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: bigWig files: location of the genome where the read aligned to
Supplementary_files_format_and_content: bedGraph files were generated with MACS2. Then, bedGraph files were converted to bigWig format using bedGraphToBigWig UCSC tools.
Supplementary_files_format_and_content: 22_DNA_ChIRP_pileup_controls.bw is created from:
Supplementary_files_format_and_content: 12_DNA_ChIRP_no_probe.fastq.gz
Supplementary_files_format_and_content: 14_DNA_ChIRP_LacZ_set_1.fastq.gz
Supplementary_files_format_and_content: 17_DNA_ChIRP_LacZ_set_2.fastq.gz
Supplementary_files_format_and_content: 20_DNA_ChIRP_LacZ_set_3.fastq.gz
Supplementary_files_format_and_content: 21_DNA_ChIRP_pileup_enriched.bw is created from:
Supplementary_files_format_and_content: 13_DNA_ChIRP_odd_set_1.fastq.gz
Supplementary_files_format_and_content: 15_DNA_ChIRP_odd_set_2.fastq.gz
Supplementary_files_format_and_content: 16_DNA_ChIRP_even_set_2.fastq.gz
Supplementary_files_format_and_content: 18_DNA_ChIRP_odd_set_3.fastq.gz
Supplementary_files_format_and_content: 19_DNA_ChIRP_even_set_3.fastq.gz

molecule: genomic DNA

source_name: Brain cortex

extract_protocol:
for RNA samples miRNeasy Mini Kit (Qiagen) or for DNA samples as described in Chu, C., Quinn, J. & Chang, H.Y. J. Vis. Exp. (2012).doi:10.3791/3912
Library preparation for mRNA sequencing was performed according to Illumina standard protocols using the TruSeq RNA Sample Prep Kit v2. Library preparation for ChIRP-seq was performed according to the NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs)

tag: animal age

value: Postnatal day 2

tag: enrichment method

value: Biotinylated oligonucleotides

value: Brain cortex


title: DNA_ChIRP_odd_set_3


title: DNA_ChIRP_even_set_3


title: DNA_ChIRP_LacZ_set_2


title: DNA_ChIRP_even_set_2


title: DNA_ChIRP_odd_set_2


title: DNA_ChIRP_odd_set_1


title: AeAeg_Aag2_Ctrl_rep2

tag: cell line


title: RNA_interactome_LacZ_set_3

data_processing:
RNA-seq analysis: Quality assessment was based on the raw reads using the FASTQC (v0.10.1). The sequence reads (single-end 50 bp) were aligned to the rat reference genome (Rnor_6.0) with Bowtie2 (v2.0.2) using RSEM (v1.2.29) with default parameters. First, the rat reference genome was indexed using the Ensembl annotations (v83.6) with rsem-prepare-reference from RSEM software. Next, rsem-calculate-expression was used to align the reads and quantify the gene and isoform abundance. The output of rsem-calculate-expression gives separately the read count and TPM (transcripts per million) value for each gene and isoform.
ChIRP DNA analysis: Reads were aligned to the rat reference genome (Rnor_6.0) using Bowtie (v2.0.2) with default parameters allowing for 2 mismatches using seed alignment. Subsequently, aligned reads were filtered for high quality uniquely and multi-mapped reads (MAPQ ! = [0, 2, 3, 4]). Peaks were assigned to the genes if they are located within 5 kb upstream of the TSS or in the transcribed region or within 1 kb downstream of the transcription end site.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: bigWig files: location of the genome where the read aligned to
Supplementary_files_format_and_content: bedGraph files were generated with MACS2. Then, bedGraph files were converted to bigWig format using bedGraphToBigWig UCSC tools.
Supplementary_files_format_and_content: 22_DNA_ChIRP_pileup_controls.bw is created from:
Supplementary_files_format_and_content: 12_DNA_ChIRP_no_probe.fastq.gz
Supplementary_files_format_and_content: 14_DNA_ChIRP_LacZ_set_1.fastq.gz
Supplementary_files_format_and_content: 17_DNA_ChIRP_LacZ_set_2.fastq.gz
Supplementary_files_format_and_content: 20_DNA_ChIRP_LacZ_set_3.fastq.gz
Supplementary_files_format_and_content: 21_DNA_ChIRP_pileup_enriched.bw is created from:
Supplementary_files_format_and_content: 13_DNA_ChIRP_odd_set_1.fastq.gz
Supplementary_files_format_and_content: 15_DNA_ChIRP_odd_set_2.fastq.gz
Supplementary_files_format_and_content: 16_DNA_ChIRP_even_set_2.fastq.gz
Supplementary_files_format_and_content: 18_DNA_ChIRP_odd_set_3.fastq.gz
Supplementary_files_format_and_content: 19_DNA_ChIRP_even_set_3.fastq.gz


title: DNA_ChIRP_no_probe


title: DNA_ChIRP_LacZ_set_1


title: CuQuin_Ovary_NL


title: AnGam_Mos55_JR_cellls


title: RNA_interactome_LacZ_set_2


title: AeAlbo_C7-10_NL_cells


title: RNA_interactome_even_set_2


title: AeAeg_Aag2-TC-Dmem


title: RNA_interactome_even_set_1


title: RNA_interactome_odd_set_1


title: RNA_interactome_odd_set_2


title: RNA_interactome_LacZ_set_1


title: RNA_interactome_no_probe


title: RNA_interactome_input


title: 31_ad_Cb2_f

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

description: counts.txt

data_processing:
Basecalling was performed using RTA 1.18.61
bcl files were converted to fastq using CASAVA 1.8.2
fastq files were aligned to the mouse genome (Gencode M10) using the Star aligner (version STAR_2.5.2b)
Gene counts were generated using featureCounts from the Subread package (featureCounts v1.6.2)
Prior to differential gene expression analysis low gene counts were removed with the lowest 32% of genecounts (sums of all samples) being removed.
Count normalization and differential gene expression analysis was performed using the limma/voom pipeline (limma version 3.38).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text files with raw transcript counts ("counts.txt")

source_name: Brain microglia

growth_protocol: All animals were maintained in SPF condition

extract_protocol:
Animals were killed by transcardial perfusion in anasthesia. Microglia cells were isolated from the brain by FACS sorting. Total RNA was extracted from sorted microglia by Pico Pure RNA extraction kit (Life Technologies) according to manufacturer’s protocol.
The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 1 ng total-RNA. Double stranded cDNA was amplified by LD PCR (11 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA).

treatment_protocol: No treatment prior to cell isolation was performed.

tag: region

value: cerebellum

tag: gender

value: female


title: 32_ad_Cb3_m

description: counts.txt

value: male


title: 33_ad_Cb4_m

description: counts.txt


title: 29_ad_Cx4_m

description: counts.txt


title: 28_ad_Cx3_m

description: counts.txt


title: RNA_interactome_even_set_3


title: 27_ad_Cx2_f

description: counts.txt


title: RNA_interactome_odd_set_3


title: 24_ad_CC3_m

description: counts.txt


title: 25_ad_CC4_m

description: counts.txt


title: 21_Cb3_3_P7_f

description: counts.txt


title: 19_Cb1_1_P7_m

description: counts.txt


title: 18_Cx3_3_P7_f

description: counts.txt


title: 22_ad_CC1_f

description: counts.txt


title: 16_CX1_1_P7_m

description: counts.txt


title: 15_CC3_3_P7_f

description: counts.txt


title: 26_ad_Cx1_f

description: counts.txt


title: 14_CC2_2_P7_m

description: counts.txt


title: 17_Cx2_2_P7_m

description: counts.txt


title: 13_CC_1_P7_m

description: counts.txt


title: 12_Cb4_P10_m

description: counts.txt


title: 20_Cb2_2_P7_m

description: counts.txt


title: 30_ad_Cb1_f

description: counts.txt


title: 10_Cb2_P10_f

description: counts.txt


title: 09_Cb1_P10_f

description: counts.txt


title: 11_Cb3_P10_m

description: counts.txt


title: 07_CX3_P10_m

description: counts.txt


title: TAG RAS/DNP53 HAsiRNA rep2 [140521_SND393_B_L003_HBY-18_R1]

description: MEFs RAS Ctag 14 siHA

value: Tagged-Cyclin D1 RAS/DNP53-driven tumor

value: HA-siRNA


title: 06_CX2_P10_f

description: counts.txt


title: 04_CC4_P10_m

description: counts.txt


title: 23_ad_CC2_f

description: counts.txt


title: 03_CC3_P10_m

description: counts.txt


title: 01_CC1_P10_f

description: counts.txt


title: 02_CC2_P10_f

description: counts.txt


title: 05_CX1_P10_f

description: counts.txt


title: 08_CX4_P10_m

description: counts.txt


title: LAPC4_R1881_Daro_0.5uM_8h_rep4

city: Berlin

first: Bernard

last: Haendler

address: Muellerstrasse 178

department: Preclinical Research

institute: Bayer AG

data_processing:
Illumina bcl2fastq v2.17 was used to convert bcl to fastqs.
RNA-seq reads were aligned to GRCh38 using STAR aligner.
featureCounts from subread package was used to quantify reads in genes
Counts data was further analyzed in R, DESeq2 was used for differential gene expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes counts in genes (obtained with featureCounts) for all samples

source_name: LAPC-4 (prostate)

growth_protocol: Cells were routinely grown in the recommended medium in the presence of 10% (v/v) fetal bovine serum (Life Technologies, Carlsbad, CA) at 37°C and 5% CO2. Authentication was performed by the DSMZ using short tandem repeat DNA typing analysis.

extract_protocol:
Cells were lyzed and RNA was isolated using RNeasy columns with on-column DNA digestion, as described by the manufacturer (Qiagen, Hilden, Germany). RNA integrity was measured and samples with values above 8 were further processed.
Libraries were prepared using Illumina TruSeq Stranded mRNA Kit and sequenced on Illumina HiSeq2500 HTv4 (single-end, dual-indexing, 50 Cycles).

treatment_protocol: Cells were stimulated with the synthetic androgen R1881 at a concentration of 1 nM after two days of starvation in medium supplemented with 10% charcoal-stripped fetal calf serum (cFCS). Darolutamide was added at a final concentration of 500 nM (low) or 2 µM (high), and the cells were harvested 8 h or 22 h post-treatment.

tag: agent 1

tag: concentration 1

tag: agent 2

value: Daro

tag: concentration 2

tag: duration


title: LAPC4_R1881_Daro_0.5uM_8h_rep5


title: LAPC4_R1881_Daro_0.5uM_8h_rep2


title: LAPC4_R1881_Daro_2uM_22h_rep1


title: LAPC4_R1881_Daro_2uM_22h_rep2


title: LAPC4_R1881_Daro_0.5uM_8h_rep3


title: LAPC4_R1881_Daro_0.5uM_22h_rep5


title: 0001156551N

city: Guangzhou

first: neng

last: jiang

state: Guangdong

address: No. 58, ZhongShan Second Road

department: Department of Pathology

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

description: Agilent Whole Genome Oligo Microarrays (one-color): Prepare the RNA Sample; Total RNA Clean-up and RNA QC; Prepare labeling reaction; Purify the labeled/amplified RNA and labeled cRNA QC; Hybridization; Microarray Wash; Scanning; Extract data using Agilent Feature Extraction Software;

hyb_protocol: After stopping the labeling procedure, Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) was used for mRNAs hybridization according to the manufacturer’s instructions. Hybridize at 65°C for 17 hours.

scan_protocol: The hybridized chips were scanned with an Agilent Microarray Scanner (Agilent p/n G2565BA).

data_processing:
Agilent Feature Extraction Software is used to read the raw intensity of the image. Add the images (.tif) to be extracted to the FE Project; Set FE Project Properties; Check the Extraction Set Configuration; Save the FE Project (.fep) by selecting File > Save As and browse for desired location; Select Project > Start Extracting and export data to txt.
Normalized intensity was regarded as mRNA expression level according to the recommended calculation methods.

source_name: non-tumor lung tissue specimen

label_protocol: mRNAs were labeled with the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442), according to the manufacturer’s guidelines.

extract_protocol: Total RNA was extracted from fresh tissue samples by TRIzol Reagent (Invitrogen life technologies) according to the recommended protocols.

tag: tissue

value: non-tumor lung tissue

tag: status after 5 years

value: Dead

tag: histology

value: AD

tag: age

value: 65 years

value: Female

tag: Stage

value: IA


title: LAPC4_R1881_Daro_0.5uM_22h_rep4


title: LAPC4_R1881_Daro_2uM_22h_rep4


title: 0001162111N

value: Alive

value: 60 years

value: IIB


title: 001156551T

source_name: fresh lung cancer tissue specimen

value: primary lung adenocarcinoma


title: LAPC4_R1881_Daro_0.5uM_22h_rep3


title: 001162111T


title: 568386N

value: 57 years

value: Male

value: IIIA


title: 0001164948N

value: 52 years

value: IB


title: LAPC4_R1881_Daro_0.5uM_22h_rep1


title: LAPC4_DMSO_DMSO_8h_rep9

value: DMSO


title: LAPC4_DMSO_DMSO_8h_rep10


title: 0030348590T


title: 0030338793T

value: 54 years


title: LAPC4_DMSO_DMSO_8h_rep8


title: LAPC4_R1881_Daro_0.5uM_22h_rep2

value: Daro


title: 0030338793N

value: non-tumor lung tissue


title: LAPC4_DMSO_DMSO_8h_rep7


title: LAPC4_DMSO_DMSO_8h_rep6


title: 0030340180T

value: Dead

value: AD


title: LAPC4_R1881_Daro_2uM_22h_rep3


title: LAPC4_R1881_Daro_0.5uM_8h_rep1


title: LAPC4_DMSO_DMSO_8h_rep5


title: LAPC4_DMSO_DMSO_8h_rep4


title: LAPC4_DMSO_DMSO_22h_rep6


title: LAPC4_DMSO_DMSO_8h_rep1


title: LAPC4_DMSO_DMSO_8h_rep3


title: LAPC4_DMSO_DMSO_8h_rep2


title: LAPC4_DMSO_DMSO_22h_rep7


title: LAPC4_DMSO_DMSO_22h_rep4


title: LAPC4_DMSO_DMSO_22h_rep3


title: VCaP_R1881_DMSO_8h_rep7

source_name: VCaP (prostate)

value: VCaP


title: VCaP_R1881_DMSO_8h_rep8


title: VCaP_R1881_DMSO_8h_rep10


title: LAPC4_DMSO_DMSO_22h_rep2


title: LAPC4_DMSO_DMSO_22h_rep1


title: VCaP_R1881_DMSO_8h_rep1


title: VCaP_R1881_DMSO_8h_rep4


title: VCaP_R1881_DMSO_8h_rep5


title: VCaP_R1881_DMSO_8h_rep9


title: VCaP_R1881_DMSO_8h_rep2


title: VCaP_R1881_DMSO_8h_rep6


title: VCaP_R1881_DMSO_8h_rep3


title: VCaP_R1881_DMSO_22h_rep8


title: VCaP_R1881_DMSO_22h_rep4


title: VCaP_R1881_DMSO_22h_rep6


title: VCaP_R1881_DMSO_22h_rep7


title: VCaP_R1881_DMSO_22h_rep5


title: VCaP_R1881_DMSO_22h_rep2


title: VCaP_R1881_DMSO_22h_rep3


title: VCaP_R1881_DMSO_22h_rep1


title: LAPC4_DMSO_DMSO_22h_rep5


title: VCaP_R1881_Daro_2uM_8h_rep4


title: VCaP_R1881_Daro_2uM_8h_rep5


title: VCaP_R1881_Daro_2uM_8h_rep3


title: VCaP_R1881_Daro_2uM_8h_rep1


title: VCaP_R1881_Daro_2uM_8h_rep2


title: VCaP_R1881_Daro_2uM_22h_rep5


title: VCaP_R1881_Daro_0.5uM_8h_rep3


title: VCaP_R1881_Daro_2uM_22h_rep1


title: VCaP_DMSO_DMSO_8h_rep10


title: VCaP_R1881_Daro_2uM_22h_rep3


title: VCaP_R1881_Daro_0.5uM_8h_rep4


title: VCaP_DMSO_DMSO_8h_rep9


title: VCaP_R1881_Daro_2uM_22h_rep2


title: VCaP_DMSO_DMSO_8h_rep3


title: VCaP_R1881_Daro_0.5uM_22h_rep4


title: VCaP_R1881_Daro_0.5uM_8h_rep1


title: VCaP_R1881_Daro_0.5uM_8h_rep2


title: VCaP_DMSO_DMSO_8h_rep1


title: VCaP_R1881_Daro_2uM_22h_rep4


title: VCaP_DMSO_DMSO_8h_rep8


title: VCaP_R1881_Daro_0.5uM_22h_rep1


title: VCaP_R1881_Daro_0.5uM_22h_rep2


title: VCaP_DMSO_DMSO_8h_rep7


title: VCaP_DMSO_DMSO_8h_rep4


title: VCaP_DMSO_DMSO_8h_rep2


title: VCaP_DMSO_DMSO_22h_rep8


title: VCaP_R1881_Daro_0.5uM_22h_rep3


title: VCaP_R1881_DMSO_22h_rep9


title: VCaP_DMSO_DMSO_22h_rep5


title: VCaP_DMSO_DMSO_22h_rep4


title: VCaP_DMSO_DMSO_22h_rep3


title: VCaP_DMSO_DMSO_22h_rep7


title: VCaP_DMSO_DMSO_8h_rep5


title: VCaP_DMSO_DMSO_22h_rep6


title: VCaP_DMSO_DMSO_8h_rep6


title: VCaP_DMSO_DMSO_22h_rep1


title: VCaP_DMSO_DMSO_22h_rep2


title: AR_LAPC4_Control_Rep3

data_processing:
Illumina bcl2fastq v2.17 was used to convert bcl to fastqs.
Sequencing reads were mapped to human genome hg19 using the BWA aligner with default settings.
Duplicate reads were marked with Picard tools and filtered out together with multi-mapping reads (MAPQ score below 30).
Narrow peaks were called by MACS2 with default parameters and a q-value cutoff of 0.05.
Human genome blacklisted regions (ENCODE consortium) were excluded.
Genome_build: hg19
Supplementary_files_format_and_content: narrowpeak files with genome regions

source_name: LAPC4 (prostate)

extract_protocol:
For chromatin immunoprecipitation experiments with subsequent sequencing (ChIP-seq), three replicates of eight million cells were seeded in 15-cm plates and treated with 2 µM darolutamide plus 1 nM R1881 for 22 h, subsequently fixed for ten minutes with 1% formaldehyde and processed as described previously (Baumgart et al. Nucleic Acids Res. 2017 Jul 27;45(13):7722-7735)
Library preparation was done as described by the manufacturer (MicroPlex Library Preparation Kit v2; Diagenode SA, Seraing, Belgium). The libraries were sequenced on a HiSeq2500 Illumina machine with 50 base pair, single-end reads to an average depth of 25–30 million reads per sample.

treatment_protocol: Cells were stimulated with the synthetic androgen R1881 at a concentration of 1 nM after two days of starvation in medium supplemented with 10% charcoal-stripped fetal calf serum (cFCS). Darolutamide was added at a final concentration of 2 µM and the cells were harvested 22 h post-treatment.

tag: chip antibody

value: AR

tag: treatment

value: Control


title: H3K4me1_LAPC4_Daro_Rep1

value: Darolutamide


title: H3K27ac_LAPC4_Control_Rep3


title: H3K27ac_LAPC4_R1881_Rep1


title: H3K27ac_LAPC4_R1881_Rep3


title: AR_LAPC4_Daro_Rep3


title: AR_LAPC4_Daro_Rep1


title: H3K4me1_LAPC4_Control_Rep3


title: AR_LAPC4_Daro_Rep2


title: H3K4me1_LAPC4_Control_Rep2


title: AR_LAPC4_R1881_Rep2


title: H3K4me1_LAPC4_R1881_Rep3


title: H3K27ac_LAPC4_Daro_Rep1


title: H3K4me1_LAPC4_Daro_Rep2


title: H3K4me1_LAPC4_R1881_Rep2


title: H3K27ac_LAPC4_Control_Rep1


title: H3K4me1_LAPC4_Daro_Rep3


title: AR_LAPC4_R1881_Rep1


title: H3K27ac_LAPC4_Daro_Rep3


title: AR_LAPC4_R1881_Rep3


title: H3K27ac_LAPC4_R1881_Rep2


title: AR_LAPC4_Control_Rep2


title: H3K27ac_LAPC4_Daro_Rep2


title: H3K4me1_LAPC4_R1881_Rep1


title: RNAPII_VCaP_R1881_Rep3

value: RNAPII


title: H3K4me1_LAPC4_Control_Rep1


title: RNAPII_VCaP_R1881_Rep2


title: RNAPII_VCaP_R1881_Rep1


title: H3K27ac_LAPC4_Control_Rep2


title: AR_LAPC4_Control_Rep1


title: RNAPII_VCaP_Daro_Rep3


title: Med1_VCAP_R1881_Rep1


title: Med1_VCAP_R1881_Rep2


title: Med1_VCAP_Control_Rep1


title: Med1_VCAP_Daro_Rep2


title: RNAPII_VCaP_Daro_Rep1


title: Med1_VCAP_Control_Rep2


title: RNAPII_VCaP_Daro_Rep2


title: Med1_VCAP_R1881_Rep3


title: RNAPII_VCaP_Control_Rep2


title: RNAPII_VCaP_Control_Rep3


title: Med1_VCAP_Control_Rep3


title: Med1_VCAP_Daro_Rep3


title: H3K4m1_VCaP_Control_Rep2


title: H3K4m1_VCaP_Control_Rep4


title: H3K27ac_VCaP_R1881_Rep1


title: H3K27ac_VCaP_Daro_Rep2


title: H3K4m1_VCaP_Daro_Rep1


title: H3K4m1_VCaP_R1881_Rep2


title: H3K4m1_VCaP_Daro_Rep2


title: H3K4m1_VCaP_Control_Rep3


title: H3K27ac_VCaP_R1881_Rep2


title: RNAPII_VCaP_Control_Rep1


title: H3K4m1_VCaP_R1881_Rep1


title: H3K4m1_VCaP_Daro_Rep3


title: H3K27ac_VCaP_Control_Rep3


title: H3K27ac_VCaP_Daro_Rep1


title: Med1_VCAP_Daro_Rep1


title: H3K4m1_VCaP_Control_Rep1


title: H3K27ac_VCaP_Daro_Rep3


title: H3K27ac_VCaP_Control_Rep2


title: H3K18ac_VCaP_R1881_Rep1


title: H3K18ac_VCaP_R1881_Rep2


title: H3K18ac_VCaP_Daro_Rep3


title: H3K27ac_VCaP_Control_Rep1


title: H3K18ac_VCaP_Control_Rep3


title: H3K18ac_VCaP_Daro_Rep2


title: H2Bk15ac_VCAP_R1881_Rep3


title: H3K18ac_VCaP_R1881_Rep3


title: H3K18ac_VCaP_Daro_Rep1


title: H2Bk15ac_VCAP_Control_Rep3


title: H2Bk15ac_VCAP_Daro_Rep1


title: H2Bk15ac_VCAP_Control_Rep1


title: H3K18ac_VCaP_Control_Rep2


title: FOXA1_VCaP_R1881_Rep1


title: H2Bk15ac_VCAP_Control_Rep2


title: FOXA1_VCaP_R1881_Rep2


title: FOXA1_VCaP_Daro_Rep2


title: FOXA1_VCaP_Control_Rep3


title: FOXA1_VCaP_Daro_Rep1


title: FOXA1_VCaP_Control_Rep2


title: H2Bk15ac_VCAP_R1881_Rep1


title: FOXA1_VCaP_R1881_Rep3


title: BRD4_VCaP_R1881_Rep3


title: H2Bk15ac_VCAP_Daro_Rep2


title: FOXA1_VCaP_Daro_Rep3


title: H3K18ac_VCaP_Control_Rep1


title: BRD4_VCaP_R1881_Rep2


title: FOXA1_VCaP_Control_Rep1


title: H2Bk15ac_VCAP_Daro_Rep3


title: BRD4_VCaP_R1881_Rep1


title: BRD4_VCaP_Daro_Rep3


title: BRD4_VCaP_Daro_Rep2


title: BRD4_VCaP_Daro_Rep1


title: BRD4_VCaP_Control_Rep1


title: BRD4_VCaP_Control_Rep3


title: BRD4_VCaP_Control_Rep2


title: AR_VCAP_R1881_Rep3


title: AR_VCAP_R1881_Rep1


title: AR_VCAP_R1881_Rep2


title: AR_VCAP_Daro_Rep3