title: Head Kidney, stressed, sample 40

description: 40 I


title: Head Kidney, stressed, sample 42

status: Public on Feb 01 2021

type: RNA

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

description: 42 I

hyb_protocol: 600 ng of Cy3-cRNA was fragmented and hybridized on a sub-array. Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing.

scan_protocol: Microarrays were scanned with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3µm and 20bits)

data_processing: Data were then obtained with the Agilent Feature Extraction software (10.7.3.1) according to the appropriate GE protocol (GE1_107_Sep09). Normalization and statistical analysis were performed using GeneSpring software (Agilent). A t-test with a Benjamini-Hochberg correction (P < 0.05) was used as the criteria for defining genes differentially expressed between the control and stressed groups for each organ.

molecule: total RNA

organism: Oncorhynchus mykiss

source_name: Head Kidney, stressed

label_protocol: Pituitary and head kidney RNA from the fish sampled on day 21 (8 control (C) and 7-8 stressed (S) fish) were labelled and hybridized following the “One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling)”Agilent protocol.  Briefly, for each sample, 150 ng of total RNA was amplified and labeled using Cy3-CTP. Yield (>0.825µg cRNA) and specific activity (> 6pmol of Cy3 per µg of cRNA) of Cy3-cRNA produced were checked with the Nanodrop.

growth_protocol: Rainbow trout stress trials were performed at the facilities of PEIMA (INRA fish farming in Brittany, France) using fish hatched and reared in an open flow system. Immature rainbow trout (~ 118 g) were distributed into 6 tanks and acclimatized to a 50 kg/cm3 density (84-86 fishes/tank with 200 litres of water) for 2 weeks with 3 water renewals/h. During the 3-week experiment (deteriorated water quality stress), the photoperiod was maintained at 12:12 (Light: Dark) and the mean water temperature increased from 10.5 to 12.25°C. The fish were fed ad libitum 3 times per day.

extract_protocol: Total RNA from pituitary gland, and head kidney was extracted using TRIzol reagent according to the manufacturer's instruction (Promega). RNA was quantified by measuring the optical density at 260 nm. RNA integrity was checked using the Bioanalyzer 2100 Agilent and RNA 6000 LabChip® kits (Agilent Technologies, Waldbroon, Germany) according to the manufacturer’s instructions.

treatment_protocol: To obtain deteriorated water quality stress for 3 weeks, water renewal was modified to decrease the oxygen level to 3-4 mg/l (30-40% O2 saturation) during the day in 3 tanks for 3 weeks (Stress group = S) while the oxygen level was adjusted to 8-12 mg/l (70-110% O2 saturation) in the remaining 3 tanks (Control group = C). After 21 days under such deteriorated water quality conditions, the HPI axis response in the C and S groups was measured. The fish were not fed the day before sampling. For microarray, 8 fish of the C and S groups were caught, euthanized rapidly with a lethal dose of phenoxy-ethanol and weighed. The pituitary gland and interrenal were frozen in nitrogen liquid and stored at -80°C until use.

tag: stress

value: Stressed sample

tag: tissue

value: Head Kidney


title: RECQ1 siRNA_rep 2_mRNA seq

type: SRA

city: bethesda

first: Stefan

last: Ambs

state: md

address: 37 convent cir

country: USA

institute: NIH

library_source: transcriptomic

data_processing:
none provided by the submitter
Genome_build: hg19
Supplementary_files_format_and_content: counts

organism: Homo sapiens

source_name: Breast cancer cell line MCF7

growth_protocol: MCF7 cells were purchsed from ATCC and grown in complete medium as per the instructions from ATCC.

extract_protocol:
For RNA-seq, ~10 million MCF7 cells transfected with CTL siRNA, ESR1 siRNAs (smartpool) or RECQ1 siRNAs (smartpool) for 48 hr were harvested and total RNA was isolated with the use of the RNeasy plus micro kit (Qiagen). The mRNA-seq samples were pooled and sequenced on HiSeq using Illumina TruSeq mRNA Prep Kit RS-122-2101 and paired-end sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: treatment


title: Head Kidney, stressed, sample 37

description: 37 I


title: ESR1 siRNA_rep 3_mRNA seq


title: cjnw5krpf00983h5v4wkwpxb7

city: South San Francisco

first: Adam

last: Freund

state: CA

address: 1170 Veterans Blvd

institute: Calico Life Sciences LLC

data_processing:
Sequencing quality control was performed using FastQC (v0.11.5)
Transcript expression was then quantified using Salmon [1] (v0.9.1) in pseudo-alignment mode, without adapter trimming, producing per-gene count estimates, using the Ensembl mm10 transcriptome
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes counts for each gene for each sample, in long-format

organism: Mus musculus

source_name: Subscapular fat

growth_protocol: Mice were maintained on a 12:12 hour light:dark cycle at 22℃ with environmental enrichment (e.g., nesting material and/or huts) with access to water and food ad libitum.

extract_protocol:
RNA was extracted from whole tissues using the Qiagen RNeasy 96 Universal Tissue Kit (Qiagen, 74881) and was digested with DNAseI before preparation for RNA-seq
Lib Prep method: TruSeq® Stranded Total RNA Library Prep Human/Mouse/Rat, Input Total Conc: 100ng in 10ul. PCR 12 cycles. Sequencing  - 3nM on Hiseq 4000

treatment_protocol: Mice were treated with control or anti-PAPP-A antibody for 17 weeks, then sacrificied and nine tissues were harvested and processed for RNA-seq:  lung, liver, kidney, heart, spleen, bone marrow, gonadal fat, subscapular (subcutaneous) fat, skin

value: Subscapular fat

tag: strain

tag: Sex

value: male

value: aPAPPA


title: RECQ1 siRNA_rep 1_mRNA seq


title: CTL siRNA_rep 3_mRNA seq

value: CTL


title: ESR1 siRNA_rep 2_mRNA seq


title: cjnw5krpf00923h5vl0547xdk

source_name: Spleen

value: Spleen


title: cjnw5krpf00933h5vvmy2f41p

source_name: Heart

value: Heart


title: cjnw5krpf00943h5vk8grnujz

source_name: Liver

value: Liver


title: copperTreated_rep2

city: Aurora

first: Joshua

middle: C

last: Black

state: CO

address: 12801 East 17th Ave

department: Pharmacology

institute: University of Colorado

library_source: genomic

data_processing:
Library strategy: Rerep-seq
Fastq files were aligned to SacCer3 using BWA-mem
Sam files were transformed into bam files and blacklisted using samtools (v1.2, RRID:SCR_002105). Blacklists were the same as previously used for Rerep-seq analysis (Menzel et al., 2020). Bedtools (v2.26.0, RRID:SCR_006646) was used to generate bedGraphs
Bedgraphs were binned and normalized by RPM and mitochondrial reads using a custom R script
Replicates were then averaged
The CUP1 gene is exactly duplicated in the yeast genome, so we replaced the CUP1.1 gene copy with ambiguous nucleotides “N” to force alignment to CUP1.2 rather than allow for random alignment between the two copies.
Genome_build: SacCer3, with cup 1.1 removed
Supplementary_files_format_and_content: bedgraph

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: copperTreated

growth_protocol: Yeast strains and plasmids used in this study are listed in Table 1 and were grown according to standard procedures in YPD (yeast extract, peptone, and 2% dextrose) at 30°C for all experiments unless otherwise stated. To accommodate S. cerevisiae’s lack of the thymidine salvage pathway, yeast strains in this paper are all stably transformed with NheI linearized p403–BrdU–Inc HIS3, a reconstituted thymidine salvage pathway cassette, consisting of Herpes simplex virus thymidine kinase (HSV–TK) and human equilibrative nucleoside transporter (hENT1), that enables efficient cellular uptake and incorporation of the thymidine analogue BrdU into DNA . Inserts were confirmed by spot assays for sensitivity to 75 µg/ml FUDR and susceptibility to BrdU uptake and genomic fragmentation via Rerep-seq.

extract_protocol:
Rerep-seq was performed as described in . Briefly, In an 8 strip PCR tube 1 – 5 ug high molecular weight genomic DNA was mixed with 2.5uL 10X Hoechst 33258 (0.1mg/ml) and 2.5uL 10X NEB 4 (50 mM Potassium Acetate, 20 mM Tris-acetate , 10 mM Magnesium Acetate, 1 mM DTT pH 7.9@25°C) to a final volume of 24uL; open tubes placed upright in PCR tube rack, covered with a glass plate (3" x 3" glass plate from VWR Vertical Gel Electrophoresis Systems), exposed to 7.5 minutes of glass plate filtered (UVA only) from Stratalinker followed by addition of 0.5uL UDG (5 units of Uracil-DNA Glycosylase), 0.5uL APE1 (10 units of human apurinic/apyrimidinic endonuclease 1) for 2 hours at 37°C. The digested DNA was repaired with NEB’s FFPE DNA Repair Mix for 30 minutes; mixed with 10X loading dye then run on 0.8% agarose gel for 15 minutes. The fragmented DNA ranging from 0.1Kb to 3Kb was gel extracted with Wizard® SV Gel and PCR Clean-Up System with the purified DNA eluted in 50uL nuclease free water.
Sequencing libraries were constructed using the Illumina Nextera DNA Flex Library Prep Kit (catalog number 20018704) following the manufacturers’ protocol and using 14 cycles of amplification for final library construction. Libraries were constructed using dual index barcodes from the Nextera DNA CD Indexes (catalog number 20018707).

treatment_protocol: We developed a copper-resistant yeast strain by culturing cells in the presence of 6 mM copper for approximately 30 generations. Controls were cultured under normal conditions.

value: copper treated

tag: input or rerep

value: ReRep-Seq


title: copperTreated_rep1


title: ESR1 siRNA_rep 1_mRNA seq


title: CTL siRNA_rep 2_mRNA seq


title: cjnw5krpf00913h5va9bbj9n9

source_name: Kidney

value: Kidney


title: CTL siRNA_rep 1_mRNA seq


title: P203_1

city: Boston

first: Eriene-Heidi

last: Sidhom

state: MA

address: 4 Blackfan Circle HIM 536

institute: Harvard Medical School

description: bulk RNA

data_processing:
Reads were aligned to the mm10 mouse genome using STAR aligner
RSEM v1.3.0 was used to estimate gene expression.
FastQC used to evaluate the quality of raw reads.
Genome_build: mm10
Supplementary_files_format_and_content: .txt, RSEM estimated gene expression

source_name: Immortalized mouse podocytes

growth_protocol: Conditionally immortalized mouse podocytes (RRID:CVCL_AS86) were cultured under permissive conditions (33oC) in RPMI-1640 with 10% FBS, 100 U/ml penicillin and 100 mg/ml streptomycin and interferon- on type I collagen. Induction of differentiation is mediated by thermo-shift to 37oC without interferon-gamma.

extract_protocol:
Total RNA extraction was performed using RNeasy Mini Kit. RNA was eluted using Nuclease-Free water and total yield and purity of RNA were assessed using NanoDrop™ 2000 (Thermo Fisher).
RNA from cells quantified using the Quant-iTTM RiboGreen® RNA Assay Kit and normalized to 5 ng/μL. An automated variant of the Illumina TruSeqTM Stranded mRNA Sample Preparation Kit was used for library preparation from a 200 ng aliquot of RNA. This method preserves strand orientation of the RNA transcript and uses oligo dT beads to select mRNA from the total RNA sample. Following cDNA synthesis and enrichment, cDNA libraries were quantified with qPCR using KAPA Library Quantification Kit for Illumina Sequencing Platforms and then pooled equimolarly.

treatment_protocol: Podocytes were plated into 10-cm dishes (90K/plate) for differentiation, transduced with shRNA lentivirus on day 7 of differentiation and RNA was collected on day 14 of differentiation.

tag: shRNA

tag: cell type

value: podocyte


title: cjnw5krpf00903h5vlp5ikjy7

value: control


title: 111C [miRNA-Seq]

city: Poznań

first: Arkadiusz

last: Kajdasz

state: wielkopolskie

address: ul. Z. Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

description: library preparation kit: TruSeq Small RNA Library Preparation Kit (Illumina, San Diego)

data_processing:
raw reads were trimmed with cutadapt (untrimmed reads and reads shorter than 10 nt were discarded)
Reads were aligned to Ensembl GRCh38 human genome with bowtie2
Raw read counts were generated with featureCounts v1.6.3
Genome_build: GRCh38
Supplementary_files_format_and_content: Table with microRNA expression raw reads in txt format.

source_name: cancer kidney tissue

extract_protocol:
For the preservation of RNA, tissue fragments were collected into tubes containing RNAlater (Sigma Aldrich) and stored at -80°C for further processing. Next, fragments of tissue were transferred into a sterile mortar and grinded in liquid nitrogen. RNA was extracted with Trizol.
TruSeq Small RNA Library Preparation Kit (Illumina, San Diego)

tag: cancer type

value: clear cell renal cell carcinoma (ccRCC)

tag: fuhrman's grade

value: Male


title: 084C [miRNA-Seq]

value: Female


title: cjnw5krpf008z3h5vxuxwibrb

source_name: Gonadal fat

value: Gonadal fat


title: Patient 3, Gel

city: St Louis

first: Lori

last: Setton

state: MO

address: 1 Brookings Drive, Campus box 1097

department: Department of Biomedical Engineering

institute: Washington University in St. Louis

data_processing:
FASTQ files were read into Partek Flow software for analysis
Unaligned reads were trimmed based on quality score (minimum quality score, Phred, = 20, minimum read length = 25) before aligned to the whole human genome (hg19) using STAR 2.6.1d. The output of the alignment was quantified to the annotation model (Partek E/M; hg19_ensembl_release75_v2)
Within Partek Flow gene counts were calculated and filtered to exclude features where maximum <= 10.0.
Data were subjected to a normalization step per Partek Flow recommendations: counts per million (CPM) and add 1.0E-4
PCA was performed and GSA was conducted based on the factors of timepoint and treatment.  p-values and fold change values were calculated by comparing cells on gels to cells on TCPS (Gel/TCPS). Model selection criteria = AICc. Differentially expressed genes (fold change greater than or equal to 2 or less than or equal to -2 and with a p value less than or equal to 0.05) were analyzed using gene set enrichment. Hierarchical clustering was conducted as well (Cluster distance metric = average linkage; point distance metric = Euclidean; normalization mode = Standarize).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each sample
Supplementary_files_format_and_content: tab-deliminated text files showing the output of the GSA analysis for comparison of cells on gel to  cells on TCPS (Total counts, p-value, FDR-step up, Ratio, Fold Change, LSMean)

source_name: Nucleus Pulposus

growth_protocol: NP cells were enzymatically isolated from surgical waste tissue (exempt from IRB review, Washington University Institutional Review Board) as previously described in Gilchrist+, 2011, PLoS One (volume 6, no. 11). Isolated cells were maintained and expanded in tissue culture using Ham's F-12 media supplemented with 1% penicillin/streptomycin and 10% FBS under 5% CO2, atmospheric oxygen at 37 degrees C.

extract_protocol:
After  4 days, mRNA was extracted using the Rneasy mini kit with DNase I digestion (Qiagen). RNA quality was ensured to be greater than 8 using a Bioanalyzer (Agilent). Ds-cDNA was consructed using Clontech SMARTer Ultra Low RNA kit for Illumina Sequencing. cDNA was fragmented using a Covaris E220 sonicator. cDNA was blunt ended,  an A base added to 3' ends, and then Illumina sequencing adapters ligated to the ends. Ligated fragments were amplified for 12 cycles and run on an Illumina NovaSeq reading 150 bases from both ends to a depth of 30 million reads per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were cultured on either TCPS or gels for 4 days

value: nucleus pulposus

tag: age

value: GEL

tag: timepoint

value: 4 Days


title: P202_1

description: bulk RNA


title: 134N [miRNA-Seq]

source_name: normal adjacent kidney tissue

value: normal tissue


title: cjnw5krpf008y3h5v8dw68i21

source_name: Skin

value: Skin

value: male


title: 096C [miRNA-Seq]


title: P201_1

description: bulk RNA


title: Patient 3, TCPS

value: TCPS


title: 068C [miRNA-Seq]


title: cjnw5krpf008x3h5v2blhhx7g

source_name: Lung

value: Lung


title: Patient 2, Gel


title: Patient 2, TCPS


title: cjnw5krpf008w3h5vukytbhpp

value: Liver


title: 134C [miRNA-Seq]


title: P102_1

description: bulk RNA


title: cjnw5krpf008v3h5vvir4szhp

value: Heart


title: 059C [miRNA-Seq]


title: Patient 1, TCPS


title: Scr03_1

description: bulk RNA


title: Head Kidney, stressed, sample 46

description: 46 I

value: Stressed sample

value: Head Kidney


title: Scr02_1

description: bulk RNA

value: podocyte


title: Patient 1, Gel


title: SUIT-2_Reverse_Adapted_ATAC_clone5

first: Nada

middle: Y

last: Kalaany

address: 3 Blackfan Circle CLS 16067

institute: Boston Children's Hospital

data_processing:
RNA-seq: Data was aligned to the hg19 genome using STAR. Read counts were obtained using Salmon and analyzed using the tximport and DESeq2 packages in R.
ATAC-seq: Data was aligned to the hg19 genome using Bowtie2. Bigwigs were obtained using bamCoverage from the deeptools tool suite, normalized to 1X coverage
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-seq: bigwig files; RNA-seq: raw gene counts file

source_name: SUIT-2 cells

growth_protocol: Grown in RPMI medium with low glucose (0.5 mM) and low glutamine (0.1 mM). Then regrown in RPMI medium with high glucose (11 mM) and high glutamine (2 mM).

extract_protocol: Cells were resuspended in 50 ul ice-cold ATAC lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA-630) and centrifuged at 500 g at 4°C to isolate nuclear pellets that we treated in 50 ul reactions with Nextera Tn5 Transposase (Illumina, FC-121-1030) for 30 min at 37°C. Column-purified DNA (Qiagen) was stored at -20°C or amplified immediately in 50 ul reactions with high-fidelity 2X PCR Master Mix (New England Biolabs) using a common forward primer and different reverse primers with unique barcodes for each sample. From the reaction mix, 45 ul was kept on ice after 5 cycles of PCR, while 5 ul was amplified by qPCR for 20 additional cycles; the remaining 45 ul was then amplified for the 5-7 cycles required to achieve 1/3 of the maximum qPCR fluorescence intensity. Amplified DNA was purified over columns and primer dimers (<100 bp) were removed using AMPure beads (Beckman Coulter).

treatment_protocol: Cells were seeded overnight at 700,000 per 10 cm plate. The cells were then washed once with PBS and incubated in L-L medium for 24 h. L-L medium refers to customized RPMI medium with low glucose (0.5 mM) and low glutamine (0.1 mM).


title: cjnw5krpe008s3h5vq4k17pv4

value: Subscapular fat

value: aPAPPA


title: 067C [miRNA-Seq]

value: clear cell renal cell carcinoma (ccRCC)

value: Female


title: SUIT-2_Reverse_Adapted_ATAC_clone4


title: Scr01_1

description: bulk RNA


title: 050C [miRNA-Seq]


title: late ciCPC2

city: Cincinnati

first: JIALIANG

last: LIANG

address: 231 Albert Sabin Way

department: Department of Pathology and Laboratory Medicine

institute: University of Cincinnati

description: CRISPR-induced cardiac progenitors (Day-22) rep2

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
Genome_build: Mus musculus GRCm38 reference genome
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: tail tip skin

extract_protocol:
PureLink® RNA Mini Kit
cDNA synthesis via polyA selection

treatment_protocol: CRISPRa (SAM) vectors

value: progenitors

tag: genotype

value: wild type

value: CRISPRa vectors and colony isolation


title: SUIT-2_Adapted_ATAC_clone5

growth_protocol: Grown in RPMI medium with low glucose (0.5 mM) and low glutamine (0.1 mM).


title: cjnw5krpe008r3h5vwxojxmla

value: Gonadal fat


title: cjnw5krpe008q3h5vdre4fnwp

value: Skin


title: 058C [miRNA-Seq]


title: SUIT-2_Adapted_ATAC_clone4


title: cjnw5krpf008u3h5vpsjkaib5

value: Spleen

value: male

value: control


title: 120N [miRNA-Seq]

value: normal tissue

value: Male


title: cjnw5krpf008t3h5v9c9z57vj

value: Kidney


title: 083C [miRNA-Seq]


title: 045C [miRNA-Seq]


title: cjnw5krpe008o3h5v5qkbtcaj

value: Liver


title: late ciCPC1

description: CRISPR-induced cardiac progenitors (Day-22) rep1


title: cjnw5krpe008p3h5vkt1e9p83

value: Lung


title: SUIT-2_Non-Adapted_ATAC_clone2

growth_protocol: Grown in RPMI medium with high glucose (11 mM) and high glutamine (2 mM).


title: early ciCPC1

description: early reprogrammed cells  (Day-7)  rep-1

value: fibroblasts

value: CRISPRa vectors


title: cjnw5krpe008n3h5vk7epc854

value: Heart

value: aPAPPA


title: early ciCPC2

description: Partially reprogrammed cells  (Day-7) rep-2


title: TTF2

description: Fibroblasts  (Day-0)  rep-2

value: negetive lentiviral vectors


title: 118C [miRNA-Seq]

value: clear cell renal cell carcinoma (ccRCC)

value: Female


title: TTF1

description: Fibroblasts (Day-0) rep-1

value: wild type


title: cjnw5krpe008m3h5vbgek56v1


title: 024C [miRNA-Seq]


title: LNCaP_T_DHT2

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

data_processing:
Raw sequencing reads (in a FASTQ format) were trimmed of residual adaptor sequences using Scythe software. Low quality bases at the beginning or the end of sequencing reads were removed using sickle then the quality of remaining reads was confirmed with FastQC.
Reads were aligned to hg19 with STAR software then raw counts were computed with featureCounts for each gene in each sample.
Data normalization and selection of differentially expressed genes was performed according to DESeq2 methodology.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes  ENSEMBL id  and raw counts for each gene, in each sample

source_name: LNCaP cells

extract_protocol:
RNAeasy mini columns (from QIAGEN) following vendor instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: prostate; derived from metastatic site:left supraclavicular lymph node

tag: growth condition

value: vehicle


title: cjnw5krpe008l3h5vq2o0yg7q

value: male


title: SUIT-2_Non-Adapted_ATAC_clone1


title: 019C [miRNA-Seq]


title: cjnw5krpe008k3h5v4uf4dry8

value: Subscapular fat


title: LGB-25-3-2

city: København

first: Guangbin

last: Luo

state: Denmark

address: Strynøgade 5，Østerbro Kollegiet, 2, 208

country: China

institute: Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Obtained reads were trimmed for adaptor sequences. low-complexity or low-quality sequences were masked and then mapped to T, urartu genome sequence release 39  using bowtie v0.12.2.
The relative transcript abundance each gene were calculated using the unique aligned reads as the expected number of fragments per kilobase of the transcript sequence per million base pairs sequenced (FPKM).
Genome_build: ftp://ftp.ensemblgenomes.org/pub/plants/release3 9/fasta/triticum_urartu
Supplementary_files_format_and_content: Excel spreadsheet including the FPKM of each gene in the T. urartu endosperm throughout grain-filling.

organism: Triticum urartu

source_name: Endosperms at the stage of 25 days post anthesis

growth_protocol: The T. urartu accession PI 428198 was planted in three replications during the 2013-2014 growing season at the experimental station of the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences (IGDB, CAS), Beijing, China. In each replicate, 15 seeds were sown in one 1.5 m long row, and the rows were spaced 25 cm apart.

extract_protocol:
Endosperms (with the embryo, aleurone, seed coat and pericarp removed) at 5, 10, 15, 20 and 25 DPAs of the T. urartu accession PI 428198 were used for RNA-Seq analysis. Each sample had three independent biological replicates. The total RNA of endosperms was isolated using the standard Trizol reagent method.
A library with an insert length of ~350 bp was sequenced using the Illumina HiSeq 2000 (San Diego, CA, USA).

treatment_protocol: No treatment

value: T. urartu accession PI 428198, wild type

tag: Stage

value: 25 days post anthesis

value: Endosperm


title: LGB-25-6-2

department: Institute of Genetics and Developmental Biology


title: LGB-20-7

source_name: Endosperms at the stage of 20 days post anthesis

value: 20 days post anthesis


title: liver MDA-MB-231 EV rep6

city: Duarte

first: wei

last: chen

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

data_processing:
Base calling was done using Illumina RTA and bcl2fastq v2.18.0.12
Sequences were aligned to mm9 using Tophat2 with default settings
Gene expression level of Refseq coding genes were quantified using in-house R scripts
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text file gene expression counts

source_name: liver tissue

growth_protocol: Eight-week old female NOD scid gamma (NSG) mice were maintained in a standard mouse facility in sterile conditions.

extract_protocol:
TRIZOL reagent (Invitrogen) was used to extract total RNA from tissue following the manufacturer’s protocols.  RNA pellet was dissolved in RNase-free water, and subjected to library construction and deep sequencing.
Kapa stranded mRNA-seq kit

treatment_protocol: Mice received tail-vein injection of EV or PBS twice a week for 5 weeks (~10 ug EV per injection).  Two days after the last injection, liver was collected for immediate RNA extraction.

value: liver

value: MDA-MB-231 EV


title: liver MDA-MB-231 EV rep5


title: 021C [miRNA-Seq]

value: Male


title: LGB-25-2


title: cjnw5krpe008i3h5vpoebte2c

value: Skin


title: liver MDA-MB-231 EV rep4


title: 016C [miRNA-Seq]


title: cjnw5krpe008j3h5vzvebytls

value: Gonadal fat

value: aPAPPA


title: LGB-20-6


title: LGB-20-3


title: liver MDA-MB-231 EV rep3


title: 091N [miRNA-Seq]

value: normal tissue


title: 036C [miRNA-Seq]

value: clear cell renal cell carcinoma (ccRCC)

value: Female


title: liver MDA-MB-231 EV rep2


title: 012C [miRNA-Seq]


title: LGB-15-5-2

source_name: Endosperms at the stage of 15 days post anthesis

value: 15 days post anthesis


title: 004C [miRNA-Seq]


title: LGB-15-4


title: liver MCF10A/miR-122 EV rep6

value: MCF10A/miR-122 EV


title: 003C [miRNA-Seq]


title: cjnw5krpe008e3h5vz7cmwhxx

source_name: Spleen

value: Spleen

value: male


title: liver MCF10A/miR-122 EV rep5


title: 185C [miRNA-Seq]


title: LGB-10L-2-2

source_name: Flag leaves at the stage of 10 days post anthesis

value: T. urartu accession PI 428198, wild type

value: 10 days post anthesis

value: Flag leaf


title: cjnw5krpe008d3h5vabzsplix

source_name: Kidney

value: Kidney


title: liver MCF10A/miR-122 EV rep4

value: liver


title: cjnw5krpe008c3h5v3d2stxua

source_name: Subscapular fat

value: Subscapular fat

value: control


title: LGB-10L-1-2


title: 179N [miRNA-Seq]

value: Male


title: liver MCF10A/miR-122 EV rep3


title: 179C [miRNA-Seq]

source_name: cancer kidney tissue


title: cjnw5krpe008f3h5vr0ij8cfb

source_name: Heart

value: Heart


title: liver MDA-MB-231 EV rep1

value: MDA-MB-231 EV


title: cjnw5krpe008a3h5v6ylkeb56

value: Skin


title: LGB-10-6

source_name: Endosperms at the stage of 10 days post anthesis

value: Endosperm


title: cjnw5krpe008b3h5v3rcp39bl

source_name: Gonadal fat

value: Gonadal fat


title: liver MCF10A/miR-122 EV rep1


title: 178N [miRNA-Seq]

source_name: normal adjacent kidney tissue

value: normal tissue


title: LGB-10-3


title: cjnw5krpe008h3h5vc1od9ti3

source_name: Lung

value: Lung

value: aPAPPA


title: liver MCF10A EV rep6

value: MCF10A EV


title: 178C [miRNA-Seq]

value: clear cell renal cell carcinoma (ccRCC)


title: LGB-15-1

value: T. urartu accession PI 428198, wild type

value: 15 days post anthesis


title: LGB-10-1

value: 10 days post anthesis


title: cjnw5krpe008g3h5vg9pbyzxz

source_name: Liver

value: Liver

value: male


title: LGB-10L-3-2

value: Flag leaf


title: cjnw5krpe00883h5ve07z48xc

value: control


title: 172N [miRNA-Seq]

value: Female


title: LGB-5-5

source_name: Endosperms at the stage of 5 days post anthesis

value: 5 days post anthesis


title: liver MCF10A EV rep5

value: liver


title: 153C [miRNA-Seq]

value: Male


title: cjnw5krpe00873h5vbp8osslb

value: Heart


title: LGB-5-3

value: Endosperm


title: liver MCF10A/miR-122 EV rep2

value: MCF10A/miR-122 EV


title: liver MCF10A EV rep4


title: cjnw5krpe00893h5vmsgw5z6d

value: Lung


title: 149C [miRNA-Seq]


title: cjnw5krpe00863h5vt4hr0pkk

value: Spleen


title: cjnw5krpd00853h5vjnagqg7l

value: Kidney


title: liver MCF10A EV rep3

value: MCF10A EV


title: 120C [miRNA-Seq]

value: clear cell renal cell carcinoma (ccRCC)


title: Day 3 worker Fat Body replicate 5 [d3_w5_fb]

city: Paris

first: NIKOLAOS

last: KONSTANTINIDES

address: 15 rue Helene Brion

institute: Institut Jacques Monod

description: H57W7BCX2_l01n01_d3_w5_fb.351000000b878b

data_processing:
The reads were trimmed for quality and adapter sequence using Trimmomatic (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Reads from both sample sets were mapped with STAR (v.2.5.3a) (Dobin et al. 2013) on the Harpegnathos genome version 8.5 (Shields et al. 2018)
The reads were counted using ht-seq union mode (Anders et al. 2015)
Genome_build: Harpegnathos genome version 8.5 (Shields et al 2018)
Supplementary_files_format_and_content: Htseq output for all samples are provided in the txt file.

molecule: polyA RNA

organism: Harpegnathos saltator

source_name: Day 3 worker Fat Body

extract_protocol:
For extracting RNA, a pipette was used to gently aspirate and agitate the tissue. After agitation, fresh Trizol was added to bring the volume to 1 ml. The mixture was placed into a new 1.5 mL microcentrifuge tube and 200 μl chloroform per 1ml Trizol was added. The tube was inverted repeatedly for 30 sec and left at room temperature for 5 min. The Trizol mixture was centrifuged for 15 min at 12,000x g at 4oC. The top clear aqueous phase (~500 μl) was transferred to a new microcentrifuge tube containing 1μl of Glycoblue (ThermoFisher, #AM9515) and 1x volume of isopropanol. The RNA/isopropanol/Glycoblue mix was then centrifuged for 30 min at 20,000x g at 4°C. The supernatant was removed and the pellet was washed twice with 70% and 80% ethanol, respectively and subsequently centrifuged for 10 min at 20,000x g at 4°C. The pellet was air dried for 5 min before dissolved in BTE buffer (10mM Bis-Tris pH 6.8, 1mM EDTA). RNA samples were treated by DNase I (Ambion, #2239) and DNase I was removed by phenol/choloform extraction and isopropanol precipitation.
For library preparation, polyA+ RNA was isolated from approximately 500 ng total RNA using NEBNext ® Poly(A) mRNA Magnetic Isolation (E7490). Libraries were prepared using NEBNext® Ultra II RNA library prep kit (E7770, E7335 and E7500), quantified before and after amplification using KAPA SYBR® Fast universal qPCR Kit (KK4854) and sequenced on Illumina Hiseq 2500.

tag: caste

value: worker

value: Fat body

tag: time point

value: Day 3


title: liver MCF10A EV rep2

tag: tissue


title: cjnw5krpd00833h5vru7zo873

value: Gonadal fat

value: male


title: Day 3 worker Ovary replicate 5 [d3_w5_ov]

description: H57W7BCX2_l01n01_d3_w5_ov.351000000b87a5

source_name: Day 3 worker Ovary

value: Ovary


title: cjnw5krpd00843h5vxy649ki8

value: Subscapular fat

value: control


title: liver MCF10A EV rep1

value: liver


title: LGB-5-1

value: T. urartu accession PI 428198, wild type

value: 5 days post anthesis


title: 183N

description: library preparation kit: TruSeq RNA Library Preparation Kit v2 (Illumina, San Diego)

data_processing:
RNA-Seq raw paired-end reads were trimmed with cutadapt
Trimmed reads were aligned to Ensembl GRCh38 human genome with STAR (v2.7)
Counts were obtained using featureCounts v1.6.3
Genome_build: GRCh38
Supplementary_files_format_and_content: Table with gene expression raw reads in txt format.

extract_protocol:
For the preservation of RNA, tissue fragments were collected into tubes containing RNAlater (Sigma Aldrich) and stored at -80°C for further processing. Next, fragments of tissue were transferred into a sterile mortar and grinded in liquid nitrogen. RNA was extracted with Trizol.
TruSeq RNA Library Preparation Kit v2 (Illumina, San Diego)

value: normal tissue

value: Male


title: 183C


title: liver PBS rep6

value: PBS


title: cjnw5krpd00823h5vn6ei0h0u

source_name: Skin

value: Skin


title: 185C

value: Female


title: liver PBS rep5

source_name: liver tissue


title: Day 3 worker Ovary replicate 4 [d3_w4_ov]

description: H57W7BCX2_l01n01_d3_w4_ov.351000000b8748


title: 182N


title: liver PBS rep4


title: 182C

value: clear cell renal cell carcinoma (ccRCC)


title: cjnw5krpd00803h5v1nip80cx

value: Liver


title: liver PBS rep3


title: cjnw5krpd007z3h5vf4s7jj73

value: Heart


title: Day 3 worker Ovary replicate 3 [d3_w3_ov]

description: H57W7BCX2_l01n01_d3_w3_ov.351000000b86dc

value: worker

value: Day 3


title: Day 3 worker Brain replicate 4 [d3_w4_br]

description: H57W7BCX2_l01n01_d3_w4_br.351000000b86f6

source_name: Day 3 worker Brain

value: Non-visual brain


title: Day 3 worker Brain replicate 5 [d3_w5_br]

description: H57W7BCX2_l01n01_d3_w5_br.351000000b8761


title: liver PBS rep2


title: 180C


title: cjnw5krpd007x3h5v1ypp71d9

value: Kidney

value: male


title: cjnw5krpd00813h5v3l4qouko

value: Lung

value: control


title: liver PBS rep1

value: liver


title: 178C


title: cjnw5krpd007w3h5vs8wnddzq

value: Subscapular fat

value: aPAPPA


title: 179N

value: normal tissue

value: Male


title: cjnw5krpd007y3h5v1vct4h78

source_name: Spleen

value: Spleen


title: Day 3 worker Fat Body replicate 3 [d3_w3_fb]

description: H57W7BCX2_l01n01_d3_w3_fb.351000000b86b2

value: Fat body


title: Day 3 worker Brain replicate 3 [d3_w3_br]

description: H57W7BCX2_l01n01_d3_w3_br.351000000b8699


title: cjnw5krpd007v3h5v0pwpxtj6

value: Gonadal fat


title: Week19_EGFR;p53;Cas9_osimertinib

city: Stanford

first: Chuan

last: Li

address: 327 Campus Drive

department: Biology

institute: Stanford University

data_processing:
Each read is expected to contain an 8-nucleotide sgID region followed by a 23-nucleotide barcode (BC) region (AANNNNNTTNNNNNAANNNNNAT), and each of the 15 Ns represent random nucleotides with roughly equal representation of A, T, G and C.
The sgID region identifies the putative tumour suppressor gene being targeted, for which we require perfect match between the sequence in the forward read and one of the 15 sgIDs with known sequences.
We require the forward and reverse read to agree completely within the 23 nucleotide sequence to be further processed. Any “tumours” that are within a Hamming distance of two from a larger tumour is assigned as “spurious tumours”, which are likely to be resulting from sequencing or PCR error, and are removed from subsequent analysis.
The tumour size (number of neoplastic cells) is calculated by normalizing the number of reads to the three benchmarks “spike-in” cell lines (5x10^5 cells for each benchmark cell line) added to each sample prior to lysis of the lung and DNA extraction step.
Supplementary_files_format_and_content: Txt files showing the tumor sgRNA, barcode and tumor size for each identified tumor.

source_name: Lung epithelial cell

growth_protocol: All procedures were performed in accordance with protocols approved by the Yale University IACUC and in agreement with the NIH Guide for the Care and Use of Laboratory Animals.

extract_protocol:
Genomic DNA was isolated from bulk tumour-bearing lung tissue from each mouse. Three cell lines with a defined sgID-BC added at 5x10^5 cell/sample were added to each mouse lung sample prior to lysis to enable the calculation of the absolute number of neoplastic cells in each tumour from the number of sgID-BC reads.
Q5 High-Fidelity 2x Master Mix was used to amplify the sgID-BC region from 32 µg of genomic DNA using unique dual-indexed primers.

treatment_protocol: For analysis of tumor growth 11 weeks after tumor initiation, the Lenti-sgTSPool/Cre titer administered to EGFR;p53 mice was 2x10^6 infectious units (ifu)/mouse, while for EGFR;p53;Cas9 mice we used 1x10^6 ifu/mouse. For the 19-week time-point in EGFR;p53;Cas9 mice we initiated tumors with 1x10^5 ifu/mouse. Two weeks before collection, EGFR;p53;Cas9 mice were treated with either vehicle or osimertinib. For Kras;p53;Cas9 mice, we used 2.2x10^5 ifu/mouse.

tag: viral pool

value: Lenti-sgTSPool/Cre

tag: weeks after tumor initiation

tag: untreated

value: Osimertinib-treated tumors


title: 179C

value: clear cell renal cell carcinoma (ccRCC)

tag: Sex


title: Day 3 worker Fat Body replicate 4 [d3_w4_fb]

description: H57W7BCX2_l01n01_d3_w4_fb.351000000b872e

value: worker

value: Day 3


title: 180N


title: cjnw5krpd007u3h5vfovbna2i

value: Skin

tag: strain

tag: treatment


title: Day 3 worker Ovary replicate 2 [d3_w2_ov]

description: H57W7BCX2_l01n01_d3_w2_ov.351000000b868c

value: Ovary


title: Day 3 worker Brain replicate 2 [d3_w2_br]

description: H57W7BCX2_l01n01_d3_w2_br.351000000b8649

value: Non-visual brain


title: Week19_EGFR;p53;Cas9_vehicle

value: Vehicle-treated tumors


title: Day 3 worker Fat Body replicate 2 [d3_w2_fb]

description: H57W7BCX2_l01n01_d3_w2_fb.351000000b8656


title: 175C

value: Female


title: Week14_Kras;p53;Cas9

value: Untreated


title: 171N


title: cjnw5krpd007t3h5vqw9xd9xv

value: Lung

value: male

value: aPAPPA


title: Day 3 worker Ovary replicate 1[d3_w1_ov]

description: H57W7BCX2_l01n01_d3_w1_ov.351000000b8612


title: Week11_EGFR;p53;Cas9_osimertinib


title: Week11_EGFR;p53;Cas9_vehicle


title: 164C


title: cjnw5krpd007s3h5v3j0og8q2

value: Liver


title: Day 3 worker Fat Body replicate 1 [d3_w1_fb]

description: H57W7BCX2_l01n01_d3_w1_fb.351000000b85f7

value: Fat body


title: Week11_EGFR;p53


title: cjnw5krpd007r3h5v66604ix9

value: Heart


title: Day 3 worker Brain replicate 1 [d3_w1_br]

description: H57W7BCX2_l01n01_d3_w1_br.351000000b85dd


title: cjnw5krpd007q3h5vyo7m0soh

value: Spleen


title: cjnw5krpd007o3h5vhpnkf8t5

value: Subscapular fat

value: control


title: 153N

value: normal tissue

value: Male


title: cjnw5krpd007n3h5vs4nw6zru

value: Gonadal fat


title: Day 3 gamergate Brain replicate 5 [d3_g5_br]

description: H57W7BCX2_l02n01_d3_g5_br.351000000b8755

source_name: Day 3 gamergate Brain

value: gamergate

value: Day 3


title: 158N


title: cjnw5krpd007m3h5vx2b9ut4w

value: Skin


title: Day 3 gamergate Fat Body replicate 5 [d3_g5_fb]

description: H57W7BCX2_l02n01_d3_g5_fb.351000000b877e

source_name: Day 3 gamergate Fat Body


title: Day 3 gamergate Fat Body replicate 4 [d3_g4_fb]

description: H57W7BCX2_l02n01_d3_g4_fb.351000000b8711


title: 158C

description: library preparation kit: TruSeq RNA Library Preparation Kit v2 (Illumina, San Diego)

source_name: cancer kidney tissue

value: clear cell renal cell carcinoma (ccRCC)

value: Female


title: Day 3 gamergate Brain replicate 4 [d3_g4_br]

description: H57W7BCX2_l02n01_d3_g4_br.351000000b8704

value: Non-visual brain


title: cjnw5krpd007l3h5vym5kff18

value: Lung

value: male


title: cjnw5krpd007p3h5vcwr39cwg

source_name: Kidney

value: Kidney

value: aPAPPA


title: 152N


title: 153C


title: Day 3 gamergate Ovary replicate 4 [d3_g4_ov]

description: H57W7BCX2_l02n01_d3_g4_ov.351000000b873b

source_name: Day 3 gamergate Ovary

value: Ovary


title: cjnw5krpc007k3h5vdoltfn4b

value: Liver


title: Day 3 gamergate Ovary replicate 3 [d3_g3_ov]

description: H57W7BCX2_l02n01_d3_g3_ov.351000000b86e9


title: 149C


title: RNA-seq_SP8KO_limb_embryo_2

city: Santander

first: Marian

last: Ros

address: Albert Einstein, 22 (PCTCAN)

country: Spain

institute: Consejo Superior de Investigaciones Cientificas (CSIC) with Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC)

description:
sample name:
5.1_HO

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools
Reads were mapped to the mouse reference assembly, version GRCm38, using TopHat2
Read count means, fold-change (FC) and p-values were calculated with DEseq2
gene expression for the individual samples was calculated with Cufflinks as FPKMs.
Genome_build: GRCm38

source_name: Mouse embryo (E10.5) limb ectoderm

growth_protocol: For wild type embryos C57BL/6 inbred male and female mice were crossed. For Sp8 null embryos (Sp8-Cre-ERT2) heterozygous (Sp8+/-) male and female mice were crossed. E10.5 embryos were obtained from pregnant females by cesarean section. Genotype was performed by PCR from extraembryonic membranes.

extract_protocol:
Total RNA was extracted with RNeasy-Plus Micro Kit according to the manufacturer’s instructions (Qiagen). Libraries were prepared with the RNA sample preparation kit (TruSeq v2; Ilumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ectoderms were isolated with fine forceps from E10.5 forelimb buds after digestion with 0.25% trypsin for 20 min. on ince. The ectoderms of the two forelimbs of a single WT (C57Bl6J) or Sp8 null (Sp8-Cre-ERT2) embryo were used for each replicate.

value: limb ectoderm

tag: developmental stage

tag: mouse genotype

value: Sp8 KO

tag: background strain


title: 147N

source_name: normal adjacent kidney tissue

tag: cancer type

value: normal tissue


title: H3K4me2_ChIP-seq

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools
Reads were mapped to the mouse reference assembly, version GRCm38, using TopHat2
Normalized bedGraph files were generated using DeepTools
Peaks were called using MACS2
Genome_build: mm10

growth_protocol: Sp8-FLAG homozygous embryos male and female mice were crossed. E10.5 embryos were obtained from pregnant females by cesarean section. Genotype was confirmed by PCR from extraembryonic membranes.

extract_protocol:
ChIPmentation protocol was based on (Schmidl et al., 2015) with some modifications from A. Rada-Iglesias’s lab. Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the anti-FLAG M2 antibody (Sigma).
DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 100 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries.

treatment_protocol: Ectoderms were isolated with fine forceps from E10.5 forelimb buds of Sp8-FLAG homozygous embryos after digestion with 0.25% trypsin for 20 min. on ince. The ectoderms of 50 forelimb buds were used for each replicate.

value: WT

tag: chip antibody

value: Histone H3K4me2 antibody (pAb)- Active Motif- Catalog No:39141


title: H3K4me2_input


title: cjnw5krpc007j3h5vjzaiazwi

source_name: Heart

value: Heart

value: control


title: Day 3 gamergate Fat Body replicate 3 [d3_g3_fb]

description: H57W7BCX2_l02n01_d3_g3_fb.351000000b86cf

value: gamergate

value: Fat body

value: Day 3


title: 162C

value: clear cell renal cell carcinoma (ccRCC)

tag: fuhrman's grade

value: Male


title: 156N


title: Day 3 gamergate Ovary replicate 5 [d3_g5_ov]

description: H57W7BCX2_l02n01_d3_g5_ov.351000000b8798


title: cjnw5krpc007i3h5v01o9fiqd

value: Spleen

value: male


title: Day 3 gamergate Brain replicate 3 [d3_g3_br]

description: H57W7BCX2_l02n01_d3_g3_br.351000000b86a6

value: Non-visual brain


title: 147C


title: Day 3 gamergate Fat Body replicate 2 [d3_g2_fb]

description: H57W7BCX2_l02n01_d3_g2_fb.351000000b8662


title: 143N


title: cjnw5krpc007h3h5vuvldre9b

value: Kidney


title: Day 3 gamergate Ovary replicate 2 [d3_g2_ov]

description: H57W7BCX2_l02n01_d3_g2_ov.351000000b867f

value: Ovary


title: Day 3 gamergate Ovary replicate 1[d3_g1_ov]

description: H57W7BCX2_l02n01_d3_g1_ov.351000000b862f


title: SS_AT_MC_IFNg-2uM-Ox-2-10

city: Houston

first: Shabnam

last: Shalapour

state: TX

address: 1881 East Road

department: Cancer Biology

institute: MD Anderson Cancer Center

data_processing:
Base-calling was performed using Illumina Real Time Analysis RTA.2.7.7.0 with default parameters
Sequenced reads were trimmed for adaptor sequence and filtered for short and/or high-error sequences using cutadapt “-m 5 -e 0.10”,  then mapped to mm10 whole genome using bowtie2 v2.2.8 with parameters “-X2000 --mm -k 5”.
improper mapped, poorly mapped and unmated reads were filtered from the resultant raw bam files using samtools28 view with parameter “-F 1804 -q30”. Then, duplicates were marked by Picard28 “MarkDuplicate” and removed by samtools “-F 1804”. In the end, the final bam files were acquired after removing mitochondrial reads, sorted, and indexed with samtools.
Replicates were pooled then used MACS (v2.1.0) with “--shift -75 --extsize 150 -p 0.01 --nomodel --keep-dup all” to call the accessible regions with enriched ATAC-seq signals. Peaks were further filtered against the ENCODE blacklist regions.
Genome build: mm10
Supplementary_files_format_and_content: Processed data files represent narrowPeak calls from pooled replicates

source_name: PCa Cell Line

growth_protocol: Mammalian cells were all grown in a humidified incubator with 5% CO2 at 37°C. Myc-CaP  were grown in Dulbecco’s Modified Eagle Media (DMEM, Gibco) supplemented with 10% FBS, 1% L-glutamine, and 1% penicillin and streptomycin.

extract_protocol:
Permeabilized nuclei were obtained by resuspending cells in 250µL Nuclear Permeabilization Buffer [0.2% IGEPAL-CA630 (I8896, Sigma), 1mM DTT (D9779, Sigma), Protease inhibitor (05056489001, Roche), 5% BSA (A7906, Sigma) in PBS (10010-23, Thermo Fisher Scientific)], and incubating for 10 min on a rotator at 4°C. Nuclei were then pelleted by centrifugation for 5 min at 500 xg at 4°C. The pellet was resuspended in 25µL ice-cold Tagmentation Buffer [33 mM Tris-acetate (pH = 7.8) (BP-152, Thermo Fisher Scientific), 66 mM K-acetate (P5708, Sigma), 11 mM Mg-acetate (M2545, Sigma), 16 % DMF (DX1730, EMD Millipore) in Molecular biology water (46000-CM, Corning)]. An aliquot was then taken and counted by hemocytometer to determine nuclei concentration. Approximately 50,000 nuclei were resuspended in 20µL ice-cold Tagmentation Buffer, and incubated with 1mL Tagmentation enzyme (FC-121-1030; Illumina) at 37 °C for 30 min with shaking 500 rpm. The tagmentated DNA was purified using MinElute PCR purification kit (28004, Qiagen).
The libraries were amplified using NEBNext High-Fidelity 2X PCR Master Mix (M0541, NEB) with primer extension at 72°C for 5 min, denaturation at 98°C for 30s, followed by 8 cycles of denaturation at 98°C for 10 s, annealing at 63°C for 30 s and extension at 72°C for 60 s. Amplified libraries were then purified using MinElute PCR purification kit (28004, Qiagen), and two size selection steps were performed using SPRIselect bead (B23317, Beckman Coulter) at 0.55X and 1.5X bead-to-sample volume rations, respectively. Each library was then sequenced on an Illumina NextSeq500 or HiSeq4000 to a depth of >= 25 million usable reads pairs (i.e. after mapping, filtering, and elimination of PCR duplicates as described in the data processing section).

treatment_protocol: Cells were treated with or without indicated concentration of Oxaliplatin (2uM), Cisplatin (2uM), IFNg (1000pg), or a combination of Oxali (2uM) + IFNg (1000pg) for 48h.

value: FVB/NJ

tag: gender

tag: agent

value: Oxali 2uM + IFNg 1000pg

tag: cell line

value: Myc-CaP


title: 132C


title: Day 3 gamergate Brain replicate 2 [d3_g2_br]

description: H57W7BCX2_l02n01_d3_g2_br.351000000b863c

tag: caste

tag: time point


title: 143C


title: SS_AT_MC_IFNg-2uM-Ox-1-9


title: Input_TN

city: Mainz

first: Abhijeet

last: Pataskar

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

description:
Input_CHIP_seq
Input genomic DNA
Peaks_enrichment.xls

data_processing:
RNAseq alignment was undertaken using TopHat v2.0.8. Tag counts were calculated by HTSeq v0.5.4p1. Differential gene expression analysis was done using EdgeR.
ChIP-seq data samples were aligned using Bowtie v-0.12.9.
Peaks were called using MACS2 2.0.10.20120913
Read counts per genomic features (promoters, length stabilized enhancers) were calculated by QuasR package.
WIG file were generated by QuasR package
Genome_build: mm9
Supplementary_files_format_and_content: WIG file were generated by QuasR package using command qExportWig.

source_name: TN

growth_protocol: Pregnant mice were kept until E12.5 of offspring, opened and electroporation was performed. Animals were sacrifized at E.16.5 of offspring.

extract_protocol:
E 16.5 embryonic brains were isolated and downstream processing was done in cold HBSS. Cortical region of brains were micro dissected and processed for single cell dissociation using Neural Tissue Dissociation Kit (P) (130-092-628) following the manufacturer's instructions. GFP positive live cells were FACS sorted directly into RLT lysis buffer and RNA was isolated using RNeasy Micro Kit (Qiagen, 74004) following the manufacturer's instructions.
For RNA-seq samples, PolyA library type was used.

treatment_protocol: Mouse embryos were electroporated at E12.5 and analysed at E16.5.

tag: molecule

value: HAChIP

tag: sample type

value: Invitro ChIP-seq

tag: cell type

value: brain cell


title: 132N

value: normal tissue

tag: Sex


title: SS_AT_MC_I1000pg-IFNg-1-7

tag: strain

value: IFNg 1000pg


title: SS_AT_MC_1000pg-IFNg-2-8


title: ST18_ChIPseq_rep1

description:
St18_ChIP-seq
ChIP-seq for ST18 in TN
ST18.wig


title: Day 3 gamergate Brain replicate 1 [d3_g1_br]

description: H57W7BCX2_l02n01_d3_g1_br.351000000b85ea

value: gamergate

tag: tissue


title: 126C


title: 126N


title: NTC_rep4

description:
RNASeq
RNASeq in NTC
NormalizedTagCounts.xlsx

source_name: brain cells

value: PolyA

value: GFP FACS sorted

tag: treatment

value: control


title: SS_AT_MC_2uM-Cis-2_6

value: Cis 2uM


title: Day 3 gamergate Fat Body replicate 1 [d3_g1_fb]

description: H57W7BCX2_l02n01_d3_g1_fb.351000000b8605

value: Fat body

value: Day 3


title: 125C

value: clear cell renal cell carcinoma (ccRCC)

value: Female


title: Day 10 worker Ovary replicate 5 [d10_w5_ov]

description: H57VTBCX2_l01n01_d10_w5_ov.351000000b8a6e

source_name: Day 10 worker Ovary

value: worker

value: Ovary

value: Day 10


title: SS_AT_MC_2uM-Cis-1_5

value: FVB/NJ

value: male

value: Myc-CaP


title: NTC_rep3

value: brain cell


title: 124C

description: library preparation kit: TruSeq RNA Library Preparation Kit v2 (Illumina, San Diego)


title: Day 10 worker Fat Body replicate 5 [d10_w5_fb]

description: H57VTBCX2_l01n01_d10_w5_fb.351000000b8a45

source_name: Day 10 worker Fat Body


title: SS_AT_MC_2uM-Ox-2_4

value: Oxali 2uM


title: 123N

value: normal tissue


title: NTC_rep2

value: PolyA


title: SS_AT_MC_2uM-Ox-1_3


title: ST18_ChIPseq_rep2

description:
St18_ChIP-seq
ChIP-seq for ST18 in TN
NormalizedEnrichment_Promoter_st18.txt

value: HAChIP

value: Invitro ChIP-seq


title: Day 10 worker Brain replicate 5 [d10_w5_br]

description: H57VTBCX2_l01n01_d10_w5_br.351000000b8a2b

source_name: Day 10 worker Brain

value: Non-visual brain


title: 123C


title: SS_AT_MC_Ctrl-2_2

value: Control, none


title: ST18_early_rep4

description:
RNASeq
RNASeq in ST18 KD
EdgeR_St18.xlsx

value: GFP FACS sorted

value: ST18 KD


title: NTC_rep1

value: control


title: Day 10 worker Ovary replicate 4 [d10_w4_ov]

description: H57VTBCX2_l01n01_d10_w4_ov.351000000b8a01

value: worker


title: 119N

value: Male


title: SS_AT_MC_Ctrl-1_1


title: MC.48h.2000pg.IFNg.2uM.Ox.3

data_processing:
Base-calling was performed using Illumina Real Time Analysis RTA.2.7.7.0 with default parameters
Sequencing reads were aligned to the mouse genome build GRCm38 using annotations from GENCODE (vm12) with the splice-aware RNA-seq aligner STAR (v2.7.3a)
Read quantification was performed with RSEM v1.3.0 and Ensembl annotation Mus_musculus.GRCm38.68.gtf
GRCm38.vm12
Supplementary_files_format_and_content: processed data is in supplementary file, which is a comma-separated text file containing a matrix of read counts for each gene accession number and sample

source_name: PCa cell line

growth_protocol: Mammalian cells were all grown in a humidified incubator with 5% CO2 at 37°C. Myc-CaP were grown in Dulbecco’s Modified Eagle Media (DMEM, Gibco) supplemented with 10% FBS, 1% L-glutamine, and 1% penicillin and streptomycin.

extract_protocol:
Total RNA were extracted using an RNeasy Mini Kit (Qiagen).
Sequencing libraries were prepared from 100 ng of total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's protocol.

treatment_protocol: Cells were treated with or without indicated concentration of Oxaliplatin (2uM), IFNg (200pg or 2000pg), or a combination of Oxaliplatin (2uM) + IFNg (200pg or 2000pg) for 48 hr.

value: Oxali 2uM + IFNg 2000pg


title: Day 10 worker Brain replicate 4 [d10_w4_br]

description: H57VTBCX2_l01n01_d10_w4_br.351000000b89d9

value: Day 10


title: 119C

value: clear cell renal cell carcinoma (ccRCC)


title: 118C

value: Female


title: Day 10 worker Fat Body replicate 4 [d10_w4_fb]

description: H57VTBCX2_l01n01_d10_w4_fb.351000000b89e6

value: Fat body


title: ST18_early_rep3

value: brain cell


title: MC.48h.2000pg.IFNg.2uM.Ox.2

value: FVB/NJ

value: male

value: Myc-CaP


title: Day 10 worker Ovary replicate 3 [d10_w3_ov]

description: H57VTBCX2_l01n01_d10_w3_ov.351000000b89bf

value: Ovary


title: Day 10 worker Fat Body replicate 3 [d10_w3_fb]

description: H57VTBCX2_l01n01_d10_w3_fb.351000000b8996


title: ST18_early_rep1

value: PolyA


title: 107C


title: MC.48h.200pg.IFNg.2uM.Ox.3

value: Oxali 2uM + IFNg 200pg


title: MC.48h.200pg.IFNg.2uM.Ox.2


title: Day 10 worker Brain replicate 3 [d10_w3_br]

description: H57VTBCX2_l01n01_d10_w3_br.351000000b896f

value: Non-visual brain


title: MC.48h.2uM.Ox.2

value: IFNg 2000pg


title: 106N

value: normal tissue


title: MC.48h.2uM.Ox.1


title: 106C


title: Day 10 worker Ovary replicate 2 [d10_w2_ov]

description: H57VTBCX2_l01n01_d10_w2_ov.351000000b8946

value: worker


title: Day 10 worker Brain replicate 2 [d10_w2_br]

description: H57VTBCX2_l01n01_d10_w2_br.351000000b8902


title: MC.48h.2000pg.IFNg.3

value: IFNg 200pg


title: 117C

value: Male


title: ST18_early_rep2

value: GFP FACS sorted

value: ST18 KD


title: MC.48h.2000pg.IFNg.2


title: 096C

value: clear cell renal cell carcinoma (ccRCC)


title: 104C

value: Female


title: liver_KO_18weeks_sample-d

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

description: Gene expression data from liver of a male Glmp KO mouse of age 18 weeks

hyb_protocol: 250 ng of total RNA was used for hybridization of Affymetrix Gene Chip Mouse 2.0 ST Arrays according to the manufacturer’s instructions (Genechip® Whole Transcript (wt) PLUS Reagent Kit User Manual – P/N 703174 Rev 2). Labeled samples were injected into Affymetrix arrays and hybridized at 45°C and 60 rpm for 16 h in an Affymetrix Hybridization Oven. Arrays were stained and washed in the Affymetrix GeneChip Fluidic Station 450.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000 7G.

data_processing:
GeneChip data was processed and analyzed using R/Bioconductor packages. Data were summarized and quantile-normalized using RMA algorithm from oligo package.
MoGene-2_0-st.pgf
MoGene-2_0-st.mps

label: biotin

source_name: Mus musculus, male, genotype Glmp KO, age 18 weeks

label_protocol: Total RNA was used to synthesize double-stranded cDNA with random hexamer primers tagged with a T7 promoter sequence. The double-stranded cDNA was subsequently used as a template and amplified by T7 RNA polymerase producing cRNA. In the second cycle of cDNA synthesis, random hexamers were used to prime reverse transcription of the cRNA and dUTP was incorporated to produce single-stranded DNA. This single-stranded DNA samples were then treated with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognized the unnatural dUTP residues and broke the DNA strand. DNA was labeled by terminal eoxynucleotidyl transferase (TdT) with the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin. All steps were done according to the manufacturer’s instructions  for Genechip® Whole Transcript (wt) PLUS Reagent Kit User Manual – P/N 703174 Rev 2.

growth_protocol: Glmp KO model was described in Kong XY, Kase ET, Herskedal A, Schjalm C, Damme M, Nesset CK, et al. (2015). Lack of the Lysosomal Membrane Protein, GLMP, in Mice Results in Metabolic Dysregulation in Liver. PLoS ONE 10(6): e0129402. doi:10.1371/journal.pone.0129402

extract_protocol: Biological samples were collected at design age points (Kong Y.X. et al, 2016). Mice were weighed, organs (liver, spleen, epididymal fat pads) were removed and patho-morphologically examined. The material was fresh frozen and stored at – 80 °C for subsequent analysis. Livers were pulverized and the RNA was isolated using TRI Reagent according to the manufacturer’s instructions. RNA quantity and quality were assessed with NanoDrop-1000 and Agilent 2100 Bioanalyzer instruments, respectively. All samples were of sufficient purity and integrity for microarray hybridization.

treatment_protocol: not applicable

value: liver

tag: age

value: 18 weeks

tag: genotype

value: Glmp KO

tag: animal


title: MC.48h.200pg.IFNg.2

value: FVB/NJ

value: male

value: Oxali 2uM

value: Myc-CaP


title: Day 10 worker Fat Body replicate 1 [d10_w1_fb]

description: H57VTBCX2_l01n01_d10_w1_fb.351000000b88da

value: Fat body

value: Day 10


title: Day 10 worker Ovary replicate 1[d10_w1_ov]

description: H57VTBCX2_l01n01_d10_w1_ov.351000000b88f4

value: Ovary


title: liver_KO_18weeks_sample-c


title: liver_KO_18weeks_sample-b


title: 091C

tag: cancer type


title: Day 10 worker Brain replicate 1 [d10_w1_br]

description: H57VTBCX2_l01n01_d10_w1_br.351000000b88b0

value: worker

value: Non-visual brain


title: MC.48h.200pg.IFNg.1


title: 090C

description: library preparation kit: TruSeq RNA Library Preparation Kit v2 (Illumina, San Diego)

tag: fuhrman's grade


title: MC.48h.Ctrl.2

tag: gender

value: Control, none


title: Day 10 worker Fat Body replicate 2 [d10_w2_fb]

description: H57VTBCX2_l01n01_d10_w2_fb.351000000b892c


title: liver_WT_18weeks_sample-b

description: Gene expression data from liver of a male Glmp WT mouse of age 18 weeks

source_name: Mus musculus, male, genotype Glmp WT, age 18 weeks

value: Glmp WT


title: 084C


title: liver_KO_18weeks_sample-a


title: liver_WT_18weeks_sample-c


title: Day 10 gamergate Fat Body replicate 5 [d10_g5_fb]

description: H57VTBCX2_l02n01_d10_g5_fb.351000000b8a52

source_name: Day 10 gamergate Fat Body

value: gamergate


title: Day 10 gamergate Ovary replicate 5 [d10_g5_ov]

description: H57VTBCX2_l02n01_d10_g5_ov.351000000b8a7b

source_name: Day 10 gamergate Ovary


title: MC.48h.Ctrl.1

tag: agent


title: Day 10 gamergate Brain replicate 5 [d10_g5_br]

description: H57VTBCX2_l02n01_d10_g5_br.351000000b8a38

source_name: Day 10 gamergate Brain


title: E1_6_TRAMP_c2_cis_2uM_24h_2

data_processing:
Base-calling was performed using Illumina Real Time Analysis RTA.2.7.7.0 with default parameters
Sequenced reads were mapped to the Gencode GRCm38.p6.genome.fa reference genome using STAR v2.5.3a with default parameters
Read quantification was performed with RSEM v1.3.0 and Gencode annotation gencode.vM19.annotation.gtf
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: processed data is in supplementary file, which is a comma-separated text file containing a matrix of read counts for each gene accession number and sample

growth_protocol: Mammalian cells were all grown in a humidified incubator with 5% CO2 at 37°C. Myc-CaP  were grown in Dulbecco’s Modified Eagle Media (DMEM, Gibco) supplemented with 10% FBS, 1% L-glutamine, and 1% penicillin and streptomycin. TRAMP-C2 cells were grown in DMEM supplemented with 5% FBS, 0.2% L-glutamine, 1% penicillin and streptomycin (Gibco), 5% NuSerum IV (Corning), 0.005 mg/ml bovine insulin (Sigma-Aldrich, Darmstadt, Germany), and 10nM dehydroisoantrosterone (Acros Organics)

treatment_protocol: Cells were treated with or without indicated concentration of Oxaliplatin (2 or 20 uM) or Cisplatin (2 or 20 uM) for 24 hr.

value: Cis 2uM

tag: cell line


title: 091N

value: normal tissue

value: Female


title: E1_5_TRAMP_c2_cis_2uM_24h_1


title: Day 10 gamergate Ovary replicate 4 [d10_g4_ov]

description: H57VTBCX2_l02n01_d10_g4_ov.351000000b8a1e

tag: caste


title: 083C

source_name: cancer kidney tissue

value: clear cell renal cell carcinoma (ccRCC)

value: Male


title: E1_4_TRAMP_c2_oxa_2uM_24h_2


title: 075C


title: E1_3_TRAMP_c2_oxa_2uM_24h_1


title: 081C


title: Day 10 gamergate Brain replicate 4 [d10_g4_br]

description: H57VTBCX2_l02n01_d10_g4_br.351000000b89cc

tag: time point


title: liver_WT_18weeks_sample-d

value: liver

value: 18 weeks


title: 074C


title: liver_KO_08weeks_sample-d

description: Gene expression data from liver of a male Glmp KO mouse of age 8 weeks

source_name: Mus musculus, male, genotype Glmp KO, age 8 weeks

value: 8 weeks

value: Glmp KO

value: male


title: E1_2_TRAMP_c2_ctrl_24h_2


title: liver_KO_08weeks_sample-c


title: liver_KO_08weeks_sample-b


title: Day 10 gamergate Ovary replicate 3 [d10_g3_ov]

description: H57VTBCX2_l02n01_d10_g3_ov.351000000b89a3

value: Day 10


title: 073C


title: Day 10 gamergate Fat Body replicate 3 [d10_g3_fb]

description: H57VTBCX2_l02n01_d10_g3_fb.351000000b8989

value: Fat body


title: liver_WT_18weeks_sample-a


title: 082C


title: 069C


title: E2_10_Myc_CaP_cis_20uM_24h_2

data_processing:
Base-calling was performed using Illumina Real Time Analysis RTA.2.7.7.0 with default parameters
Sequenced reads were mapped to the Mouse Genomes Project GRCm38_68.fa reference genome using STAR v2.5.1a with default parameters
Read quantification was performed with RSEM v1.3.0 and Ensembl annotation Mus_musculus.GRCm38.68.gtf
Genome_build: GRCm38.68
Supplementary_files_format_and_content: processed data is in supplementary file, which is a comma-separated text file containing a matrix of read counts for each gene accession number and sample

value: Myc-CaP

value: FVB/NJ

value: Cis 20uM


title: Day 10 gamergate Brain replicate 3 [d10_g3_br]

description: H57VTBCX2_l02n01_d10_g3_br.351000000b897c

value: Non-visual brain


title: Day 10 gamergate Fat Body replicate 4 [d10_g4_fb]

description: H57VTBCX2_l02n01_d10_g4_fb.351000000b89f3

value: gamergate


title: E2_9_Myc_CaP_cis_20uM_24h_1


title: 068C


title: 067C


title: liver_KO_08weeks_sample-a


title: E2_8_Myc_CaP_oxa_20uM_24h_2

value: Oxali 20uM


title: liver_WT_08weeks_sample-d

description: Gene expression data from liver of a male Glmp WT mouse of age 8 weeks

source_name: Mus musculus, male, genotype Glmp WT, age 8 weeks

value: Glmp WT


title: E1_1_TRAMP_c2_ctrl_24h_1

value: Control, none


title: E2_7_Myc_CaP_oxa_20uM_24h_1


title: liver_WT_08weeks_sample-c


title: Day 10 gamergate Brain replicate 2 [d10_g2_br]

description: H57VTBCX2_l02n01_d10_g2_br.351000000b891f


title: Day 10 gamergate Ovary replicate 2 [d10_g2_ov]

description: H57VTBCX2_l02n01_d10_g2_ov.351000000b8953

value: Ovary


title: Day 10 gamergate Ovary replicate 1[d10_g1_ov]

description: H57VTBCX2_l02n01_d10_g1_ov.351000000b88e7


title: E2_6_Myc_CaP_cis_2uM_24h_2

value: Cis 2uM


title: 062C

description: library preparation kit: TruSeq RNA Library Preparation Kit v2 (Illumina, San Diego)

value: clear cell renal cell carcinoma (ccRCC)

value: Female


title: 065C


title: Day 10 gamergate Fat Body replicate 2 [d10_g2_fb]

description: H57VTBCX2_l02n01_d10_g2_fb.351000000b8939


title: E2_5_Myc_CaP_cis_2uM_24h_1


title: Day 10 gamergate Fat Body replicate 1 [d10_g1_fb]

description: H57VTBCX2_l02n01_d10_g1_fb.351000000b88cd


title: 058C


title: E2_4_Myc_CaP_oxa_2uM_24h_2

value: Oxali 2uM


title: liver_WT_08weeks_sample-b

value: liver

value: 8 weeks


title: 050C


title: E2_3_Myc_Cap_oxa_2uM_24h_1

value: male


title: Day 10 gamergate Brain replicate 1 [d10_g1_br]

description: H57VTBCX2_l02n01_d10_g1_br.351000000b88a4

value: Day 10


title: Day 0 Ovary replicate 5 [d0_5_ov]

source_name: Day 0 Ovary

value: worker

value: Day 0


title: 045C

value: Male


title: 059C


title: 035C


title: Day 0 Brain replicate 5 [d0_5_br]

source_name: Day 0 Brain

value: Non-visual brain


title: HUVEC_ATPT_replicate_3

first: Guillermo

last: Garcia-Cardena

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School / Brigham and Women's Hospital

description: Gene expression data from HUVEC cultures exposed to atheroprotective flow for 48 hours

hyb_protocol: Following labeling, 3.5 ug of ssDNA were hybridized for 16 hr at 45C on GeneChip Human Gene ST 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix Expression Console(Build 1.3.1.187) using Affymetrix default RMA analysis settings.

source_name: ATPT Flow

label_protocol: Biotinylated ssDNA were prepared according to the standard GeneChip WT Plus Reagents Kit Affymetrix protocol from 500ng total RNA (User manual P/N 703174 Rev 1, 2013, Affymetrix)

growth_protocol: HUVEC were cultured in Medium-199 with or without Doxorubicin at 250 ng/mL (431 nM) while exposed to an atheroprotective shear stress waveform, or cultured under static (no flow) conditions.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini kit according to manufacturer's protocol.

treatment_protocol: HUVEC were washed with PBS and lysed with Qiagen buffer RLT

value: HUVEC


title: HUVEC_ATPT_DOX_replicate_3

description: Gene expression data from HUVEC cultures exposed to atheroprotective flow for 48 hours, of which 24 hours with Doxorubicin

source_name: ATPT Flow + DOX


title: HUVEC_ATPT_DOX_replicate_2


title: Sample_LS_sRNA

city: Vasant Kunj

first: Neeti

last: Sanan-Mishra

state: Delhi

address: Aruna Asaf Ali Marg

department: Plant RNAi Biology

country: India

institute: ICGEB

data_processing:
Quality filtereing  and adapter trimming was done by NGStool kit
Abundance was calculated for unique reads

organism: Oryza sativa

source_name: Flag leaf

growth_protocol: The seeds were grown under controlled temperature (28 ± 2 °C), relative air humidity (70%) and 16/8-h light/dark cycle conditions.

extract_protocol:
Total RNA was isolated using Trizol reagent and enriched with 50% PEG and 0.1% NaCl for small RNA isolation. The RNA bands of corresponding size ranging between 15-30 nucleotides were gel purified
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Heat stress was given at 42°C for 6 hours.

tag: stress

value: Heat Stress

tag: cultivar

value: Pusa basmati

tag: physiological character

value: Susceptible


title: E2_2_Myc_CaP_ctrl_24h_2

source_name: PCa Cell Line

value: Myc-CaP

value: FVB/NJ

value: Control, none


title: E2_1_Myc_CaP_ctrl_24h_1


title: Sample_L1_sRNA

value: Normal (control for stress)


title: 030C

value: clear cell renal cell carcinoma (ccRCC)

tag: Sex


title: HUVEC_static_replicate_3

description: Gene expression data from static (no flow) HUVEC cultures

source_name: Static (no flow)

tag: cell type


title: Trec_pooled

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, unique molecular identifier (UMI) counting and aggregating sequencing runs were performed using Cell Ranger software v.2.1.0 (10x Genomics).
Downstream analysis was performed using Seurat v2.3 (Butler, et. al. 2018). Briefly, individual library outputs from the Cell Ranger pipeline were loaded, and cells with fewer than 200 detected genes were excluded from downstream analysis. Genes detected in fewer than three cells across the dataset were also excluded. Raw UMI counts were normalized by total expression in the corresponding cell and multiplied by a scaling factor of 10,000 to give UMI count per million total counts and then log-transformed
Variable genes were selected based on average expression and dispersion. Linear dimensional reduction (PCA) was performed using variable genes and the first 7 principal components were determined to be significant using the jackstraw method. tSNE was performed on these significant principle components using default parameters for 1,000 iterations for visualization in two dimensions. Unsupervised clustering was performed using a shared nearest neighbor modularity optimization-based algorithm. Optimal number of clusters was chosen using Identifying K mAjor cell Population groups (IKAP) algorithm
Differential expression analysis was performed between each cluster and all other cells using a Wilcoxon rank sum test. Marker genes were identified by the Seurat function FindAllMarkers,Scaled expression data of these marker genes were used for creating the heatmaps. Normalized data are shown in the form of feature plots or violin plots. Trajectory analysis was performed with Monocle v.2 conducted using Monocle 2 v2.10.1 .
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Filtered gene-barcode matrices containing only cellular barcodes

source_name: CD8 T cells

growth_protocol: LCMV-specific P14 cells were sorted from mice infected with LCMV-Arm or LCMV-Cl13, as well as mice that received donor P14 TEX or TMEM

extract_protocol:
Cells were loaded onto the Chromium Controller (10x Genomics) for a target recovery of 5,000 single cells. The scRNAseq libraries were generated using Chromium Single Cell 3′ Library and Gel Bead Kit v2 (10x Genomics) according to the manufacturer’s protocol.
Briefly, emulsions were created and, after reverse transcription, gel-beads in emulsion were disrupted. Barcoded complementary DNA was isolated and amplified by PCR (12 cycles). Following fragmentation, end repair and A-tailing, sample indexes were added during index PCR (8 cycles). Samples were pooled and quantified using a KAPA Library Quantification Kit (Kapa Biosystems) prior to sequencing

treatment_protocol: Live CD8+ congenic (CD45.1+ or CD45.1/2+) LCMV-GP33-tetramer+ P14 cells were FACS-sorted (1.18–2.4 x104 cells), used to generate single-cell gel-beads in emulsion, and counted using a Countess II Automated Cell Counter (Thermo Fisher Scientific) prior to library preparation

tag: background strain

value: LCMV Clone13 infection


title: Tex_pooled

tag: treatment


title: liver_WT_08weeks_sample-a

tag: strain

tag: tissue

value: liver

tag: age

value: 8 weeks

value: Glmp WT


title: HUVEC_ATPT_replicate_2


title: HUVEC_static_replicate_2


title: Sample_s4_8_sRNA

source_name: Leaf

growth_protocol: Rice seeds were grown under green house conditions at temperature (28±2°C), relative air humidity (70%), and 16/8‐h light/dark cycle.


title: 028C

tag: cancer type


title: HUVEC_ATPT_replicate_1


title: Day 0 Brain replicate 4 [d0_4_br]

value: worker


title: Day 0 Fat Body replicate 4 [d0_4_fb]

source_name: Day 0 Fat Body

value: Fat body

value: Day 0


title: Tmem_pooled

value: LCMV Armstrong infection


title: HUVEC_ATPT_DOX_replicate_1

value: HUVEC


title: Sample_s4_1b_sRNA


title: HUVEC_static_replicate_1


title: Day 0 Fat Body replicate 5 [d0_5_fb]


title: 034C

tag: fuhrman's grade

value: Male


title: Trec_rep2

data_processing:
fastq files were aligned to GRCm38/mm10 reference  genome using bowtie2
Samtools/bedtools were used to process and filter mitochondrial reads and to remove duplicates.Peak calling was performed using MACS v2 (FDR q-value 0.01).
differential expression analysis was run using DESeq 2 package and data normalized
Differentially  accessible regions were identified following DESeq2 normalization using an FDR cut-off < 0.05 or 0.01 or otherwise indicated
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text file with normalized counts

growth_protocol: For acute viral infections, mice were injected intraperitoneally (i.p) with 2x105 plaque-forming units (PFU) of LCMV-Armstrong (LCMV-Arm). For chronic viral infections, mice were injected intravenously (i.v.) with LCMV-Cl13 (4x106 PFU). Mice were infected one day post adoptive transfer of P14 cells

extract_protocol:
Lysates were centrifuge (750xg,  10min, 4oC) and nuclei were resuspended in 50μl of transposition reaction mix (TD  buffer [25μl], Tn5 Transposase [2.5μl], nuclease-free water [22.5μl]; (Illumina)) and  incubated for 30min at 37oC.
Transposed DNA fragments were purified using a  Qiagen Reaction MiniElute Kit, barcoded with NEXTERA dual indexes (Illumina)  and amplified by PCR for 11 cycles using NEBNext High Fidelity 2x PCR Master  Mix (New England Biolabs). PCR products were purified using a PCR Purification  Kit (Qiagen) and amplified fragments size was verified on a 2200 TapeStation  (Agilent Technologies) using High Sensitivity D1000 ScreenTapes (Agilent  Technologies). Libraries were quantified by qPCR using a KAPA Library Quant Kit  (KAPA Biosystems).

treatment_protocol: P14 cells per replicate were sorted from spleens of mice into RPMI medium with 50% FBS (1–1.2x104 cells for REC-TEX, and 4–5x104 for other cell types).Sorted cells (2.5-to-5x104) were washed  twice in cold PBS and resuspended in 50μl of cold lysis buffer (10nM Tris-HCl, pH  7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween).

value: LCMV Clone 13 infection


title: 024C


title: Sample_s4_1_sRNA

value: Pusa basmati

value: Susceptible


title: Day 0 Ovary replicate 3 [d0_3_ov]

value: Ovary


title: Day 0 Ovary replicate 4 [d0_4_ov]


title: Sample_s11_sRNA

source_name: Root


title: Tex_rep2


title: Trec_rep1


title: 016C

value: Female


title: Day 0 Fat Body replicate 3 [d0_3_fb]


title: Day 0 Brain replicate 3 [d0_3_br]

value: Non-visual brain


title: Sample_s_7_sRNA

treatment_protocol: For salt treatment, seedlings were transferred to plastic containers containing 200 mM NaCl for definite time.

value: Salt Stress


title: Day 0 Fat Body replicate 2 [d0_2_fb]


title: Tex_rep1


title: Day 0 Ovary replicate 2 [d0_2_ov]


title: Tmem_rep3


title: 012C

value: clear cell renal cell carcinoma (ccRCC)


title: Sample_s_6_sRNA


title: Sample_s_5_sRNA

source_name: Flower

value: Normal (control for stress) (Pre-pollinated flower)


title: Tmem_rep2


title: Day 0 Brain replicate 2 [d0_2_br]


title: 009C


title: Sample_D2_sRNA

description: Glyoxalase over expressed lines


title: Day 0 Ovary replicate 1 [d0_1_ov]


title: 006C


title: Sample_D1_sRNA

description: Glyoxalase over expressed lines


title: Tmem_rep1


title: 019C


title: 005C


title: Day 0 Fat Body replicate 1 [d0_1_fb]


title: Naive_rep2


title: 011C


title: Naive_rep1


title: 001C


title: E1

status: Public on Jan 31 2021

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

description: Mixed mouse and human sample1

data_processing:
We performed basecalling on the raw fast5 data using Guppy (v) (guppy_basecaller –compress-fastq -c dna_r9.4.1_450bps_hac.cfg -x “cuda:1”) in GPU mode from Oxford Nanopore Technologies running on a GTX 1080 Ti graphics card. For each read we identify the barcode and UMI sequence by searching for the polyA region and flanking regions before and after the barcode/UMI. Accurately sequenced barcodes were identified based on their dual nucleotide complementarity. Unambiguous barcodes were then used as a guide to error correct the ambiguous barcodes in a second pass correction analysis approach. We performed fuzzy searching using a Levenshtein distance of 4 (unless otherwise stated in the figure legend) and replaced the original ambiguous barcode with the unambiguous sequence. A whitelist of barcodes was then generated using UMI-tools whitelist (umi_tools whitelist --bc-pattern=CCCCCCCCCCCCCCCCCCCCCCCCNNNNNNNNNNNNNNNN --set-cell-number=1000) [3]. This whitelist was used to assess the quality of our cells to read count ratio and used as an input for UMI-tools extract. Next the barcode and UMI sequence of each read was extracted and placed within the read2 header file using UMI-tools extract (umi_tools extract --bc-pattern=CCCCCCCCCCCCCCCCCCCCCCCCNNNNNNNNNNNNNNNN --whitelist=whitelist.txt). Reads were then aligned to the transcriptome using minimap2 [10] (-ax splice -uf --MD --sam-hit-only --junc-bed) using the reference transcriptome for human hg38 and mouse mm10. The resulting sam file was converted to a bam file and then sorted and indexed using samtools [11]. The transcript name was then added as a XT tag within the bam file using pysam. Finally, UMI-tools count (umi_tools count –per-gene –gene-tag=XT –per-cell –double-barcode) was used to count features to cells before being converted to a market matrix format. We modified UMI-tools count to handle the double nucleotide UMIs as defined below. This counts matrix was then used as an input into the standard Seurat pipeline.
Genome_build: hg38/mm10
Supplementary_files_format_and_content: mtx

organism:
Homo sapiens
Mus musculus

source_name: 3T3/HEK (1000 cells)

extract_protocol:
Samples were processed using the Drop-seq DolomiteBio Nadia encapsulator system.
For nanopore sequencing, cDNA was amplified with 25 SMART PCR reactions and sequencing libraries were prepared using the Oxford Nanopore LSK-109 library preperation kit.

value: mixture of 3T3 and HEK cells

tag: cell number


title: Mix2_2

description: Myeloma cells

data_processing:
We performed basecalling on the raw fast5 data using Guppy (v) (guppy_basecaller –compress-fastq -c dna_r9.4.1_450bps_hac.cfg -x “cuda:1”) in GPU mode from Oxford Nanopore Technologies running on a GTX 1080 Ti graphics card. For each read we identify the barcode and UMI sequence by searching for the polyA region and flanking regions before and after the barcode/UMI. Accurately sequenced barcodes were identified based on their dual nucleotide complementarity. Unambiguous barcodes were then used as a guide to error correct the ambiguous barcodes in a second pass correction analysis approach. We performed fuzzy searching using a Levenshtein distance of 4 (unless otherwise stated in the figure legend) and replaced the original ambiguous barcode with the unambiguous sequence. A whitelist of barcodes was then generated using UMI-tools whitelist (umi_tools whitelist --bc-pattern=CCCCCCCCCCCCCCCCCCCCCCCCNNNNNNNNNNNNNNNN --set-cell-number=1000) [3]. This whitelist was used to assess the quality of our cells to read count ratio and used as an input for UMI-tools extract. Next the barcode and UMI sequence of each read was extracted and placed within the read2 header file using UMI-tools extract (umi_tools extract --bc-pattern=CCCCCCCCCCCCCCCCCCCCCCCCNNNNNNNNNNNNNNNN --whitelist=whitelist.txt). Reads were then aligned to the transcriptome using minimap2 [10] (-ax splice -uf --MD --sam-hit-only --junc-bed) using the reference transcriptome for human hg38 and mouse mm10. The resulting sam file was converted to a bam file and then sorted and indexed using samtools [11]. The transcript name was then added as a XT tag within the bam file using pysam. Finally, UMI-tools count (umi_tools count –per-gene –gene-tag=XT –per-cell –double-barcode) was used to count features to cells before being converted to a market matrix format. We modified UMI-tools count to handle the double nucleotide UMIs as defined below. This counts matrix was then used as an input into the standard Seurat pipeline.
Genome_build: hg38
Supplementary_files_format_and_content: mtx

source_name: Myeloma cell lines (1200 cells)

value: Myeloma cell lines

tag: sample


title: E3

description: Myeloma cells

source_name: Myeloma cell lines (500 cells)


title: E2

description: Mixed mouse and human sample1

source_name: 3T3/HEK (500 cells)


title: STA-ST-1

description: Ewings cells

source_name: Ewings cells (500 cells)

value: Ewings cells


title: Sample_s_8_sRNA

data_processing:
Quality filtering  and adapter trimming was done by NGStool kit
Abundance was calculated for unique reads

value: Pokkali

value: Naturally Salt Tolerant


title: Day 0 Brain replicate 1 [d0_1_br]

data_processing:
The reads were trimmed for quality and adapter sequence using Trimmomatic (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Reads from both sample sets were mapped with STAR (v.2.5.3a) (Dobin et al. 2013) on the Harpegnathos genome version 8.5 (Shields et al. 2018)
The reads were counted using ht-seq union mode (Anders et al. 2015)
Genome_build: Harpegnathos genome version 8.5 (Shields et al 2018)
Supplementary_files_format_and_content: Htseq output for all samples are provided in the txt file.

value: worker

value: Day 0


title: 004C

first: Arkadiusz

last: Kajdasz

address: ul. Z. Noskowskiego 12/14

institute: Institute of Bioorganic Chemistry PAS

data_processing:
RNA-Seq raw paired-end reads were trimmed with cutadapt
Trimmed reads were aligned to Ensembl GRCh38 human genome with STAR (v2.7)
Counts were obtained using featureCounts v1.6.3
Genome_build: GRCh38
Supplementary_files_format_and_content: Table with gene expression raw reads in txt format.

source_name: cancer kidney tissue

value: Male


title: Sample_s_3_sRNA

value: Normal (control for stress)


title: E4

description: Myeloma cells


title: V3-skin_OS_rep3

city: LONGJUMEAU

first: Angela

last: PATATIAN

address: 1CHEMIN DE SAULXIER

department: ESSONNE

institute: GENEX

hyb_protocol: All cRNAs were hybridized to human whole genome oligo microarrays (Agilent Technologies V3 AMADID072363) which contains 60.000 probes, derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq.

scan_protocol: Slides were scanned on the Agilent Technologies Scanner G2505C(Agilent Technologies)

data_processing: Microarray data were quantified (GeneExtraction Feature V10.7) and normalized with R tools (Bioconductor).

source_name: Treated skin explants by organic solvent

label_protocol: RNAs (70ng) of each explant from 4 donors (V1 to V4 i) were used for reverse transcription, amplification and Cy3 labeling, using the Low Input Labeling kit, one-color (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Full-thickness human skin biopsies were obtained from abdomen of healthy female donors who had undergone plastic surgery. The hypodermis was removed from the skin and circular explants were excised using a sample punch. The samples were placed immediately in BIO-EC’s Explant Medium (BEM) for 5 days and were cultured under classical cell culture conditions (37°C in 5% CO2).

extract_protocol: Total RNAs were extracted using the ReliaPrep Tissue Miniprep kit  from Promega after disruption and homogenization using the TissueLyser Kit.

treatment_protocol: On day 5 (D5), the explants of the concerned batches were placed in the exposure system Pollubox® and treated with a solution containing heavy metals, hydrocarbons and fine particulate matters for 1h30 min. Some of these compounds were solubilized in an organic solvent (OS) which was also evaluated on the skin explants. On D6 and D7 respectively 24 and 48 hours after pollutants exposure, skin explants were harvested and were cut in half for storage in RNAlater (Qiagen) or fixation in buffered formol.

tag: source

value: tissue from abdominoplasty

value: skin explant


title: V4-skin_PO_rep1

source_name: Treated skin explants by pollutant Mix


title: V4-skin_PO_rep2


title: V4-skin_PO_rep3


title: PeritonealLavage_OVA+AEPS_2hr

city: Hangzhou

first: Xiangfeng

last: Chen

state: Zhejiang

address: Yuhangtang Road

institute: Zhejiang University

description: Gene expression of peritoneal cells from female BALB/c mice 2 hours after intraperitoneal injection with OVA(25 μg) and AEPS(50 μg).

hyb_protocol: The labeled cRNAs were hybridized onto the microarray. The Agilent SurePrint G3  8 × 60 k Mouse Gene Expression Microarray was used for the analysis.

scan_protocol: Hybridized microarrays were scanned with Agilent C scanner using Agilent’s Scan Control software, version A.8.4.1.

data_processing: The features were extracted with the Feature Extraction software. Data pre-processing and differential expression analysis were done in R software. Data were normalized between arrays using the quantile method (GENESPRING12.0).

source_name: Peritoneal lavage, 2hr

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

extract_protocol: Total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction.

treatment_protocol: BALB/c mice were injected intraperitoneally with PBS, AEPS(50 μg), OVA(25 μg), OVA(25 μg)+AEPS(50 μg), or OVA(25 μg)+Alum(200 μg). The peritoneal cells were harvested 2 h after injection.

value: peritoneal lavage

value: female

value: BALB/c

value: OVA(25 μg) and AEPS(50 μg)


title: PeritonealLavage_AEPS_2hr

description: Gene expression of peritonealcells from female BALB/c mice 2 hours after intraperitoneal injection with AEPS(50 μg).

value: AEPS(50 μg)


title: V3-skin_PO_rep2


title: PeritonealLavage_PBS_2hr

description: Gene expression of peritoneal cells from female BALB/c mice 2 hours after intraperitoneal injection with PBS.

value: PBS


title: V3-skin_OS_rep2


title: PeritonealLavage_OVA_2hr

description: Gene expression of peritoneal cells from female BALB/c mice 2 hours after intraperitoneal injection with OVA(25 μg).

value: OVA(25 μg)


title: V4-skin_OS_rep1


title: PeritonealLavage_OVA+Alum_2hr

description: Gene expression of peritoneal cells from female BALB/c mice 2 hours after intraperitoneal injection with OVA(25 μg) and Alum(200 μg).

value: OVA(25 μg) and Alum(200 μg)


title: V3-skin_untreated_rep2

source_name: untreated skin explants


title: V3-skin_OS_rep1


title: V3-skin_PO_rep1


title: V4-skin_untreated_rep3


title: V2-skin_PO_rep3


title: V4-skin_untreated_rep2


title: V2-skin_PO_rep1


title: V3-skin_untreated_rep1


title: V4-skin_untreated_rep1


title: V2-skin_OS_rep1


title: V2-skin_PO_rep4


title: V4-skin_OS_rep3


title: V2-skin_PO_rep2


title: V2-skin_untreated_rep2


title: V2-skin_OS_rep3


title: V2-skin_OS_rep2


title: V2-skin_untreated_rep3


title: TDF cells WT biological replicate 2 (RNA-seq)

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

institute: Francis Crick Institute

description:
RNA-Seq
WT_R2

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin M, 2011) with parameters “--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC”.
The RSEM package (version 1.3.0) (Li and Dewey, 2011) in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to hg19 RefSeq genes downloaded from the UCSC Table Browser (Karolchik et al., 2004) on 7th June 2017. The parameters used were “--star-output-genome-bam --forward-prob 0”.
Differential expression analysis was performed with the DESeq2 package (version 1.12.3) (Love et al., 2014) within the R programming environment (version 3.3.1). An adjusted p-value of <= 0.01 was used as the significance threshold for the identification of differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study

source_name: Transformed Dermal Fibroblast cells

growth_protocol: Cells were grown in MEM medium containing Tet-free 15% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, at 37 °C in 5% CO2.

extract_protocol:
Total cell RNA was prepared from the cells using RNAeasy reagents (Qiagen).
The total RNA samples were quality controlled (QC) using the 6000 Nano RNA Chip on the BioAnalyser 2100 (Agilent, Santa Clara, CA, USA) to insure RNA integrity and concentration before starting the procedure.  mRNA libraries were generated using the KAPA mRNA Hyper Prep Kit (Roche) following manufacturer’s instructions. Library QC was reperformed on the BioAnalyser 2100 followed by sequencing on the Illumina HiSeq 4000 to generate 76bp strand-specific single-end reads.

treatment_protocol: Cells were treated with 1µg/ml Doxycicline (dox) for 14 days to induce target gene KO.

value: Transformed Dermal Fibroblast cells

tag: genotype

value: WT


title: TDF cells WT biological replicate 3 (RNA-seq)

description:
RNA-Seq
WT_R3


title: TDF cells GFP KO biological replicate 3 (RNA-seq)

description:
RNA-Seq
GFP_R3

value: GFP KO


title: TDF cells WT biological replicate 1 (RNA-seq)

description:
RNA-Seq
WT_R1


title: TDF cells GFP KO biological replicate 2 (RNA-seq)

description:
RNA-Seq
GFP_R2


title: TDF cells GFP KO biological replicate 1 (RNA-seq)

description:
RNA-Seq
GFP_R1


title: TDF cells MSL3 KO biological replicate 3 (RNA-seq)

description:
RNA-Seq
MSL3_R3

value: MSL3 KO


title: V2-skin_untreated_rep1


title: TDF cells MSL3 KO biological replicate 2 (RNA-seq)

description:
RNA-Seq
MSL3_R2


title: TDF cells MSL2 KO biological replicate 3 (RNA-seq)

description:
RNA-Seq
MSL2_R3

value: MSL2 KO


title: TDF cells MSL3 KO biological replicate 1 (RNA-seq)

description:
RNA-Seq
MSL3_R1


title: V1-skin_OS_rep3


title: V1-skin_PO_rep3


title: V1-skin_OS_rep1


title: V1-skin_OS_rep2


title: V1-skin_PO_rep1


title: V1-skin_PO_rep2


title: V1-skin_untreated_rep2


title: TDF cells MSL2 KO biological replicate 2 (RNA-seq)

description:
RNA-Seq
MSL2_R2


title: TDF cells MSL1 KO biological replicate 3 (RNA-seq)

description:
RNA-Seq
MSL1_R3

value: MSL1 KO


title: TDF cells MSL1 KO biological replicate 1 (RNA-seq)

description:
RNA-Seq
MSL1_R1


title: V1-skin_untreated_rep1


title: LNCaP_305 PAX5_3

city: Tianjin

first: Zhe

last: LIU

address: 22 Qixiangtai Road

department: Department of Immunology

institute: TIanjin Medical University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Hisat2 v2.0
FeatureCounts v1.5 and stringtie v1.3 for RNA quantification and qualification
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: LNCaP cell

growth_protocol: LNCap cell line was obtained from the American Type Culture Collection (ATCC) and cultured as recommended by ATCC.

extract_protocol:
totoal RNAs from LNCaP-305 empty-1/2/3  and LNCaP-305PAX5-1/2/3 were extracted by Trizol Reagent according to the manufacturer`s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: LNCap cells were transfected with 305 empty or 305 PAX5 lentivirus for 8h per day and change with normal medium, repeat 4 days.

value: Prostate

tag: tumor stage

value: metastatic prostate carcinom

tag: cell line

value: LNCaP clone FGC

tag: genotype/variation

value: vector overexpressing PAX5


title: LNCaP_305 PAX5_2


title: LNCaP_305 PAX5_1


title: TDF cells MSL1 KO biological replicate 2 (RNA-seq)

description:
RNA-Seq
MSL1_R2


title: TDF cells MSL2 KO biological replicate 1 (RNA-seq)

description:
RNA-Seq
MSL2_R1


title: LNCaP_305 empty_2

value: vector control


title: LNCaP_305 empty_1


title: LNCaP_305 empty_3