title: LoVo MEK inhibitor 100 nM rep3


title: YK-4-279_0.065_6 [CR1D04]

status: Public on Feb 25 2018

type: SRA

city: New York

first: Mariano

middle: Javier

last: Alvarez

state: NY

address: 1130 St. Nicholas ave.

department: Systems Biology

country: USA

institute: Columbia University

library_source: transcriptomic

data_processing:
Sequencing was performed in a Hi-Seq 2500 sequencer (Illumina) and base calling was performed with Illumina HCS software.
Single end reads were mapped to human reference genome HG19 using Bowtie v0.12.8, using default parameters.
Reads mapping to known transcripts were counted with GenomicFeatures v1.22.13 (Bioconductor) for R-system v3.2.3.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *txt: Tab-delimited matrix of raw counts for each known gene (EntrezID) in rows and sample in columns.

molecule: total RNA

organism: Homo sapiens

source_name: H-STS NET cell line, YK-4-279, 6h

growth_protocol: H-STS cells were maintained in 1:1 mix of M199 : Ham's F-12 containing 10% FBS and antibiotics (penicillin 100 IU/ml and streptomycin 100 ug/ml).

extract_protocol:
Cells were lysed and total RNA isolated. RNA integrity was evaluated with a 2100 Bioanalyzer.
Standard TruSeq protocols from Illumina.

treatment_protocol: Small molecule compounds were added to achieve a concentration corresponding to the ED20 and 1/10 of it, measured by cell viability at 60h after compound treatment. Vehicle control, including DMSO, ethanol and methanol were added in duplicate.

tag: cell line

value: H-STS NET

tag: compound

tag: concentration (um)

tag: time-point

tag: batch


title: LoVo MEK inhibitor 100 nM rep2

city: Fujisawa

first: Kanae

last: Gamo

state: Kanagawa

address: 26-1, Muraoka-higashi 2-chome

department: Immunology Unit, Research

country: Japan

institute: Takeda Pharmaceutical Company Limited

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer (Torrent suite ver.5.0.4.0).
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence, then mapped to hg19_AmpliSeq_Transcriptome_ERCC_v1 using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.0.4.0).
Count data were calculated using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.0.4.0).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (read count) for each sample.

source_name: LoVo treated with MEK inhibitor

growth_protocol: LoVo cells were cultured with F-12K in the presence of 10% FBS

extract_protocol:
Extraction of total RNA was performed according to the manufacturer's instructions (RNeasy, QIAGEN)
10 ng of total RNA from each dose and biological replicate were reverse transcribed to cDNA with SuperScript® VILO™ cDNA Synthesis Kit (Thermo Fisher Scientific). Then cDNA is amplified using Ion AmpliSeq™ technology (Thermo Fisher Scientific). After primer digestion, adapters and molecular barcodes were ligated to the amplicons followed by magnetic bead purification. Libraries were then diluted to 100 pM and pooled equally, with eighteen individual samples per pool.

treatment_protocol: Treatment with test article or DMSO for 24 hours

value: LoVo

tag: treatment

value: MEK inhibitor

tag: sample type

value: Colorectal cancer cell line


title: LoVo MEK inhibitor 30 nM rep1


title: LoVo MEK inhibitor 300 nM rep1


title: LoVo MEK inhibitor 30 nM rep3


title: LoVo MEK inhibitor 30 nM rep2


title: LoVo MEK inhibitor 10 nM rep3


title: MK-2206_0.684_6 [CR1C10]

source_name: H-STS NET cell line, MK-2206, 6h


title: Tivantinib_0.709_6 [CR1C11]

source_name: H-STS NET cell line, Tivantinib, 6h

value: Tivantinib


title: Topotecan_0.0138_24 [CR1E05]

source_name: H-STS NET cell line, Topotecan, 24h

value: Topotecan


title: LoVo MEK inhibitor 10 nM rep2


title: LoVo MEK inhibitor DMSO rep3 chip2

source_name: LoVo treated with DMSO

value: DMSO


title: LoVo MEK inhibitor 10 nM rep1


title: Imatinib_20_24 [CR1C07]

source_name: H-STS NET cell line, Imatinib, 24h

value: Imatinib


title: Imatinib_2_24 [CR1C08]


title: LoVo MEK inhibitor 300 nM rep2


title: LoVo MEK inhibitor DMSO rep1 chip2


title: Topotecan_0.0138_6 [CR1D01]

source_name: H-STS NET cell line, Topotecan, 6h


title: Entinostat_0.684_24 [CR1C06]

source_name: H-STS NET cell line, Entinostat, 24h

value: Entinostat


title: LoVo MEK inhibitor 3 nM rep2


title: Entinostat_6.84_24 [CR1C05]


title: LoVo MEK inhibitor 1 nM rep2


title: Belinostat_0.0325_24 [CR1C03]

source_name: H-STS NET cell line, Belinostat, 24h

value: Belinostat


title: Belinostat_0.00325_24 [CR1C04]


title: LoVo MEK inhibitor 1 nM rep3


title: LoVo MEK inhibitor 3 nM rep3


title: LoVo MEK inhibitor 1000 nM rep3


title: Imatinib_2_24 [CR1B12]


title: Entinostat_0.684_24 [CR1B10]


title: LoVo MEK inhibitor 3 nM rep1


title: MK-2206_6.84_6 [CR1C09]


title: LoVo MEK inhibitor 0.3 nM rep2


title: LoVo MEK inhibitor 1 nM rep1


title: LoVo MEK inhibitor 0.3 nM rep1


title: Imatinib_20_24 [CR1B11]


title: LoVo MEK inhibitor 0.3 nM rep3


title: LoVo MEK inhibitor 0.1 nM rep3


title: Entinostat_6.84_24 [CR1B09]


title: LoVo MEK inhibitor DMSO rep2 chip2


title: Belinostat_0.00325_24 [CR1B08]


title: LoVo MEK inhibitor 0.1 nM rep2


title: Belinostat_0.0325_24 [CR1B07]


title: LoVo MEK inhibitor 0.1 nM rep1


title: AZD8055_2_24 [CR1B06]

source_name: H-STS NET cell line, AZD8055, 24h


title: AZD8055_20_24 [CR1C01]


title: AZD8055_20_24 [CR1B05]


title: LoVo MEK inhibitor 0.03 nM rep2


title: Imatinib_2_6 [CR1B04]

source_name: H-STS NET cell line, Imatinib, 6h


title: LoVo MEK inhibitor 0.03 nM rep3


title: LoVo MEK inhibitor 0.03 nM rep1


title: AZD8055_2_6 [CR1A10]

source_name: H-STS NET cell line, AZD8055, 6h


title: Entinostat_6.84_6 [CR1B01]

source_name: H-STS NET cell line, Entinostat, 6h


title: LoVo MEK inhibitor DMSO rep2 chip1


title: Imatinib_20_6 [CR1B03]


title: Belinostat_0.00325_6 [CR1A12]

source_name: H-STS NET cell line, Belinostat, 6h


title: LoVo MEK inhibitor DMSO rep3 chip1


title: Belinostat_0.0325_6 [CR1A11]


title: AZD8055_20_6 [CR1A09]


title: Belinostat_0.00325_6 [CR1A04]


title: Entinostat_0.684_6 [CR1A06]


title: Imatinib_2_6 [CR1A08]


title: Belinostat_0.0325_6 [CR1A03]


title: Entinostat_6.84_6 [CR1A05]


title: Imatinib_20_6 [CR1A07]


title: hMeDIP-Seq Tet2 Overexpression Rep 3

city: San Francisco

first: Jeremy

middle: Michael

last: Shea

state: CA

address: 513 Parnassus Avenue

department: Anatomy

institute: University of California, San Francisco

library_source: genomic

data_processing:
Base calls performed using Real-Time Analysis v2
Samples were separated using Barcode Splitter (Galaxy Version 1.0.0). For paired-end samples, samples were combined matched using FASTQ joiner (Galaxy Version 2.0.1).
Reads were mapped to the mouse genome (mm9) using Bowtie2 with the following options: -x 750 --no-mixed TRUE --no-discordant TRUE -5 5.
Duplicate reads were removed using SAMtools RmDup
Peaks called using MACS2 with the following options: for aging comparisons, BAM files were combined prior to analsyis and --mfold 2 20; for OE comparisons --mfold 5 50
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files generated using MACS2; scores represent pooled count of sample biological replicates

molecule: genomic DNA

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
Hippocampi were subdissected following perfusion with PBS. Samples were snap frozen on dry ice. Tissues were homogenized with mortor and pestle on liquid nitrogen. Homogenized tissue was lysed using DNA lysis buffer. Phenol/chloroform extraction followed by ethanol precipitation was used to isolate genomic DNA.
For each library, 1.5ug of DNA was sonicated to 300-500 base pairs. DNA was precipitated, and resuspended in TE buffer. After end cleanup (Lucigen, ER81050) and A-tailing (Klenow Exo- NEB, M0212L), barcoded adapters were ligated onto the samples using T4 DNA ligase, followed by phenol/chloroform extraction and ethanol precipitation. Samples were then divided into input and immunoprecipitation samples. DNA was denatured by heating at 95°C for 10 minutes, followed by plunging the samples on ice. Ice-cold 10x hMeDIP buffer (100mM NaPO4 pH 7.0, 1.4mM NaCl, and 0.5% Triton X-100) was added to the immunoprecipitation sample to a final concentration of 1x. 2uL of 5-hmC DNA antibody (Active Motif, 39769) was added to the samples. The samples were rotated overnight at 4°C. Protein A magnetic beads (NEB, S1425S) were added to the reaction, and rotated at 4°C for 2 hours. The samples were collected on a magnetic rack, and the samples were washed three times (with 10 minute incubations) with 1x hMeDIP buffer.  DNA was eluted from the beads by shaking the samples in lysis buffer (50mM Tris pH 8.0, 10mM EDTA, and 0.5% SDS) with proteinase K (100ug/mL) at 55°C for 3+ hours. The DNA was purified by phenol/chloroform extraction followed by ethanol precipitation. After purification, the libraries were PCR amplified (KAPA HiFi, kk2602) for 14-16 cycles using paired-end primers. Libraries were pooled and purified with 1.8X Agencourt AMpure XP beads (Beckman Coulter, A63881). Pooled libraries were quantified with KAPA Library Quantification Kit (kk4824). Pooled hMeDIP libraries were sequenced on an Illumina HiSeq 2500.

tag: strain

tag: tissue

value: Hippocampus

tag: age

value: 6 month

tag: antibody


title: AZD8055_20_6 [CR1A01]


title: hMeDIP-Seq Tet2 Overexpression Rep 2

value: 5-hmC DNA antibody (Active Motif, 39769)


title: hMeDIP-Seq Tet2 Overexpression Rep 1


title: hMeDIP-Seq Ctl Rep 3


title: CD34_shLuc_RPF_2

city: Cambridge

first: Vijay

middle: G

last: Sankaran

state: MA

address: 7 Cambridge Center

institute: Broad Institute

description: Ribosome profiling

data_processing:
(mRNA-seq and RPF-seq) Lysates were prepared as described under polysome profiling and partitioned for either ribosome footprint profiling or mRNA sequencing. Total RNA was extracted with the Direct-zol™ RNA MiniPrep Plus w/ TRI Reagent® Kit (Zymo Research) according to the manufacturer’s instructions. Total mRNA was poly-A selected using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) according to the manufacturer’s instructions. mRNA seq libraries were generated as described previously (Engreitz et al. 2013). Ribosome footprinting and subsequent library preparation of ribosome protected RNA fragments (RPFs) was performed with the Truseq Ribo Profile (Mammalian) Kit (Illumina) according to the manufacturer’s protocol. RNase I (Ambion) digestion was done at a concentration of 2.5 U/ul lysate. RPFs were purified with MicroSpin S-400 columns (GE Healthcare Life Sciences). All libraries were sequenced on a HiSeq 2500 system (Illumina). Raw reads were trimmed using cutadapt with the options “-q 5 -m 20 --discard-untrimmed -a AGATCGGAAGAGCACACGTCTG”. Bowtie2 was then used to align trimmed reads to rRNA, tRNA, and abundant noncoding RNAs. FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used to determine that adapters and other sequences had been removed and to calculate the fragment length distribution of RPFs. The remaining reads were then aligned to the human hg19 genome build allowing for junctions based upon ENSEMBL transcripts using Tophat with the options “--no-novel-juncs --library-type fr-unstranded”. Non-uniquely mapping reads were excluded using Samtools. RSeQC was used to determine calculate the percentage of reads mapping to 5’ UTRs, CDS, and 3’ UTRs. Triplet periodicity was assessed using RibORF. For RNA-seq, genes were quantified either using Cuffquant and Cuffnorm with the option “-max-bundle-frags 20000000” or using HTSeq-count in intersection-strict mode. Fragments per kilobase per million (FPKM) were subsequently transformed to transcripts per million (TPM). For RPFs, reads between 26 and 34 nucleotides in length were quantified in the CDSs of protein coding genes using HTSeq-count. Reads mapping to less than 45 nucleotides from the start codon or 15 nucleotides from the stop codon were not included in order to reduce read biases in the 5’ and 3’ ends of CDSs. To determine differentially expressed genes between control and RPH or IRB conditions, we used a negative binomial model (mean and variance of distribution estimated in DESeq2).
(See Khajuria et al., Under Review, for further details)
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts for RNA-seq (across the entire transcript) and for ribosome profiling (across the matching CDS exluding the first 45 nucleotides and last 15 nucleotides) are included in Counts.txt.

source_name: CD34+ hematopoietic cells

growth_protocol: (cell culture) CD34+ cells were obtained from magnetically sorted mononuclear samples of G-CSF–mobilized peripheral blood from donors and were frozen after isolation. Cells were obtained from the Fred Hutchinson Cancer Research Center, Seattle, USA or the Department of Hematology/Oncology Flow Cytometry Research Facility at Boston Children’s Hospital. Cells were thawed and washed into PBS with 1% human AB serum (Atlanta Biologicals), pelleted and then seeded in differentiation medium containing IMDM with 2% human AB plasma, 3% human AB serum, 1% P/S, 200 ug/mL holo-transferrin, 10 ng/mL SCF (PeproTech, Inc.), 1 ng/mL IL-3 (PeproTech, Inc.) and 3 U/mL erythropoietin (EPO) (Amgen). Cells were maintained in this differentiation medium at a density between 0.1 × 106 and 0.5 × 106 cells per milliliter, with medium changes every other day as necessary. Cells were incubated at 37 °C with 5% CO2.

extract_protocol:
RNA was extracted at day 7 of culture using phenol chloroform
rRNA was depleted using Ribo-Zero Gold (Illumina, Inc., San Diego, CA); ribosome profiling libraries were created using approximately 2 ug of RNA from each sample using the TruSeq Ribo Profile kit (Illumina, Inc., San Diego, CA)

tag: cell type

value: Erythroid cells

tag: day

tag: modulation

value: Luc knockdown (control)


title: CD34_shLuc_RPF_1

description: Ribosome profiling


title: CD34_shRPS19_RPF_2

description: Ribosome profiling

value: RPS19 knockdown


title: LoVo MEK inhibitor DMSO rep1 chip1


title: CD34_shRPS19_RPF_1

description: Ribosome profiling


title: hMeDIP-Seq Ctl Rep 1


title: hMeDIP-Seq 18 Month Rep 4

value: 18 month


title: CD34_shRPL5_RPF_2

description: Ribosome profiling

value: RPL5 knockdown


title: Entinostat_0.684_6 [CR1B02]

value: H-STS NET


title: hMeDIP-Seq Ctl Rep 2


title: hMeDIP-Seq 18 Month Rep 3


title: hMeDIP-Seq 18 Month Rep 1


title: Pooled Input


title: AZD8055_2_6 [CR1A02]


title: CD34_shLuc_RNA_2

molecule: polyA RNA

extract_protocol:
RNA was extracted at day 7 of culture using the Direct-zol™ RNA MiniPrep Kit (Zymo Research)
Approximately 1 ug of RNA from each sample was used to generate cDNA libraries for sequencing using the TruSeq RNA Sample Prep Kit v2 (Illumina, Inc., San Diego, CA)


title: CD34_shLuc_RNA_1


title: AZD8055_2_24 [CR1C02]


title: hMeDIP-Seq 18 Month Rep 2


title: CD34_shRPL5_RPF_1

description: Ribosome profiling


title: hMeDIP-Seq 3 Month Rep 3

value: 3 month


title: hMeDIP-Seq 3 Month Rep 2


title: CD34_shTSR2_RNA_2

value: TSR2 knockdown


title: hMeDIP-Seq 3 Month Rep 1


title: hMeDIP-Seq 3 Month Rep 4


title: CD34_shTSR2_RNA_1


title: CD34_shRPS19_RNA_2


title: CD34_shRPS19_RNA_1


title: CD34_shRPL5_RNA_2


title: AB_F_NB

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

country: United Kingdom

institute: University of Oxford

data_processing:
the original fastq files were converted to fasta format and reads without Ns were kept for further analysis
the 3' adapter and HD signatures [Sorefan et al 2012] were trimmed and the files were converted from redundant to non-redundant format
the reads were mapped to the reference genome, allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al 2008]
the reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
the abundances of the reads were normalized using the RPM method [Mortazavi et al 2008]
the differential expression was called on offset fold change on confidence intervals built on replicates, offset = 20
Genome_build: D. Melanogaster v 6.11
Supplementary_files_format_and_content: csv, raw abundances

organism: Drosophila melanogaster

source_name: abdomen

growth_protocol: Females were collected by placing grape juice and agar media in a large outbread population of flies for a few hours. 24h later 1st star larvae were placed at a density of 100 per vial on 7ml of SYA food. Upon eclosion, virgin females were collected on ice and stored at 10 per vial on 7ml of SYA food. 24h before matings females were placed individually in the same type of vial.

extract_protocol:
Standard total RNA extraction using the miRvana RNA extraction kit.
sRNA-seq using HD adaptors as described in Sorefan et al 2012, Xu et al 2015

tag: gender

value: female

value: abdomen

tag: library

value: not blocked


title: Accessory glands_M2

data_processing:
the original fastq files were converted to fasta format and reads without Ns were kept for further analysis
the 3' adapter and HD signatures [Sorefan et al 2012] were trimmed and the files were converted from redundant to non-redundant format
the reads were mapped to the reference genome, allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al 2008]
the reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
the abundances of the reads were normalized using the RPM method [Mortazavi et al 2008]
the differential expression was called on offset fold change on confidence intervals built on replicates, offset = 20
Genome_build: D. melanogaster v6.11
Supplementary_files_format_and_content: csv files, sRNA expression levels

source_name: accessory glands

growth_protocol: Wildtype males (derived from 1970s Dahomey lab population) were reared at 25°C, 50% humidity, 12:12 light:dark cycle on sugar, yeast, agar food.

extract_protocol:
RNA enriched for fragments <200nt was extracted from 50 pooled accesory glands, using the miRvana miRNA kit (Ambion). The RNA sample was split and subjected to two different library construction protocols - one multiple blocking oligos complentary to the contaminating rRNA fragments, and one without the blocking oligos.
HD sRNA-seq libraries, created using HiSeq2500 IL adapter
library sequenced at the Earlham Institute

value: male

value: accessory glands

value: blocked with multiple oligos

tag: replicate


title: HT_F_NB

source_name: head-thorax

value: head-thorax


title: Accessory glands_M1


title: Accessory glands_NB2

value: not-blocked


title: LungGOFF

city: La Jolla

first: Richard

last: Daneman

address: 9500 Gilman Drive

institute: UCSD

description: BGOFLungReplicates.xlsx

data_processing:
Sequenced reads were mapped to Ensembl mm9 v67 whole genome using tophat v2.0.11 and bowtie2 v2.2.1 with parameters --no-coverage-search -m 2 -a 5 -p 7
Alignment files were sorted using SAMtools v.0.1.19
Count tables were generated using HTSeq-0.6.1
Differential expression was analyzed using DESeq2.
Genome_build: Ensembl mm9 v67
Supplementary_files_format_and_content: .xls files with two tabs.  Tab one has the output of DESeq2 and tab 2 has the raw counts and counts per million (CPM) for each sample.

source_name: Lung

extract_protocol:
Liver or lung tissues were dissociated by trituration and labeled with anti-CD31-Alexa647 antibody for fluorescence-activated cell sorting. See Results section and Daneman et. al. 2010 for details
Libraries were prepared with Illumina TruSeq RNA V2 kit using the manufacturer’s instructions.
Sequencing was accomplished with the HiSeq4000 system using paired-end 100 base pair reads (PE100) to an average depth of 42 million reads. 2 ng of RNA was used as input.

treatment_protocol: Transgenic mice used: Control: Rosa-Bcat-GOF, Experimental: Rosa-Bcat-GOF; VE-Cadherin-CreERT2

tag: cells

value: endothelial

tag: genotype

value: Rosa-Bcat-GOF/+; VE-Cadherin-CreERT2


title: LungGOFD

description: BGOFLungReplicates.xlsx


title: LungGOFB

description: BGOFLungReplicates.xlsx


title: LungControlD

description: BGOFLungReplicates.xlsx

value: Rosa-Bcat-GOF/+


title: Activated T cell transfer colitis model_anti-TNFa rep1

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer (Torrent suite ver.5.0.4.0).
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence, then mapped to mm10 using software provided with the Ion Torrent Proton sequencer (RNASeqAnalysis v5.0.4.0).
Count data were calculated using software provided with the Ion Torrent Proton sequencer (RNASeqAnalysis v5.0.4.0).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (read count) for each sample.

source_name: Colon

growth_protocol: Female BALB/c mice (7 weeks of age) and C.B-17/Icr-scid/scid mice (SCID, 7 weeks of age) were purchased from Charles River Japan and CLEA Japan, respectively. All procedures were performed in accordance with the standards for humane care, and treatment of research animal was approved by Institutional Animal Care and Use Committee (IACUC) in Takeda Pharmaceutical Company, Ltd (Approval No. 10797).

extract_protocol:
Total RNA was prepared using Isogen II (Nippongene) and further purified by the aid of RNeasy Mini Kit column (Qiagen) and DNaseI (Qiagen) to avoid genomic DNA contamination, according to the manufacturer's instructions.
The polyA-RNA was isolated from 2 ug of total RNA using the Dynabeads mRNA Direct Purification Kit (Thermo Fisher Scientific). The mRNA fragmentation with RNaseIII and following steps were carried out according to Ion Total RNA-Seq Kit v2 recommendation (#4476286, Thermo Fisher Scientific).

treatment_protocol: Enteric MEK inhibitor MPs were orally administered once a day from day 17 to day 27. Isotype mAb and anti-TNFa mAb were intraperitoneally injected every 4 days from day 17 at 0.1 mg/mouse.

value: Anti-TNFa mAb

value: colon


title: Activated T cell transfer colitis model_isotype mAb control rep3

value: Isotype mAb


title: Activated T cell transfer colitis model_anti-TNFa rep2


title: Activated T cell transfer colitis model_anti-TNFa rep4


title: Activated T cell transfer colitis model_anti-TNFa rep3


title: LungControlB

description: BGOFLungReplicates.xlsx


title: Activated T cell transfer colitis model_isotype mAb control rep4


title: Activated T cell transfer colitis model_isotype mAb control rep2


title: LungControlE

description: BGOFLungReplicates.xlsx


title: LiverGOFG

description: BGOFLiverReplicates.xlsx

source_name: Liver


title: CD34_shRPL5_RNA_1

value: Erythroid cells

value: RPL5 knockdown


title: Activated T cell transfer colitis model_MEK inhibitor 1 mg/kg rep4

value: 1 mg/kg enteric MEK inhibitor microparticles


title: Activated T cell transfer colitis model_MEK inhibitor 1 mg/kg rep2


title: Activated T cell transfer colitis model_MEK inhibitor 1 mg/kg rep1


title: Activated T cell transfer colitis model_MEK inhibitor 1 mg/kg rep3


title: LiverGOFF

description: BGOFLiverReplicates.xlsx


title: Accessory glands_NB1


title: LungGOFE

description: BGOFLungReplicates.xlsx


title: Activated T cell transfer colitis model_MEK inhibitor 0.3 mg/kg rep2

value: 0.3 mg/kg enteric MEK inhibitor microparticles


title: Activated T cell transfer colitis model_MEK inhibitor 0.3 mg/kg rep3


title: LiverGOFE

description: BGOFLiverReplicates.xlsx


title: LungControlF

description: BGOFLungReplicates.xlsx


title: Activated T cell transfer colitis model_MEK inhibitor 0.3 mg/kg rep4


title: AB_unblocked

extract_protocol:
RNA enriched for fragments <200nt was extracted from 50 pooled male abdomens, using the miRvana miRNA kit (Ambion). The RNA sample was split and subjected to two different library construction protocols - one using a blocking oligo complentary to a contaminating 30mer rRNA sequence, and one without the blocking oligo.
HD sRNA-seq libraries, created using HiSeq2500 IL adapter; library sequenced by BaseClear provider.

value: abdomen

value: wildtype (derived from 1970s Dahomey lab population)


title: Activated T cell transfer colitis model_vehicle control rep4

value: Vehicle (0.5% methylcellulose)


title: Activated T cell transfer colitis model_isotype mAb control rep1


title: LiverGOFB

description: BGOFLiverReplicates.xlsx


title: AB_blocked

value: male

value: blocked


title: Activated T cell transfer colitis model_MEK inhibitor 0.3 mg/kg rep1


title: LiverControlG

description: BGOFLiverReplicates.xlsx


title: Activated T cell transfer colitis model_vehicle control rep1


title: LiverControlF

description: BGOFLiverReplicates.xlsx


title: LiverControlE

description: BGOFLiverReplicates.xlsx


title: Normal mouse rep4


title: Activated T cell transfer colitis model_vehicle control rep2


title: Normal mouse rep1


title: Activated T cell transfer colitis model_vehicle control rep3


title: Normal mouse rep3


title: Normal mouse rep2


title: LiverControlB

description: BGOFLiverReplicates.xlsx


title: Spaceflight, 8 days old, WS Rep2

status: Public on Feb 24 2018

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

description:
FLT 8d WS Rep2
processed data file:
FLT 8d WS to GC 8d WS.xlsx
FLT 4d WS to FLT 8d WS.xlsx

data_processing:
The data analysis was performed at the ICBR bioinformatics core, University of Florida. Input fastq files were trimmed to remove the adapters and low-quality bases using trimmomatic (version 0.36) with the following parameters: LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, MINLEN:50. Quality control on the trimmed reads was performed using FastQC version 0.11.2. Reads were aligned to the Col-0 TAIR10 genome or to the WS genome (Gan et al. Nature. 2011 Aug 28; 477(7365):419-23.) using the STAR aligner (version 2.5.1b), and duplicate reads due to PCR artifacts were removed using the Picard MarkDuplicates tool. In total, 502 million reads were aligned to the transcriptome.
Expression quantification and differential gene expression analysis were performed using cufflinks and cuffdiff respectively (version 2.2.1) with default parameters. The cuffdiff output files were parsed with custom scripts to generate the final annotated tables of differentially expressed genes.
Genome_build: Col-0 TAIR10 genome or to the WS genome (Gan et al. Nature. 2011 Aug 28; 477(7365):419-23.)
Supplementary_files_format_and_content: annotated tables of differentially expressed genes

organism: Arabidopsis thaliana

source_name: solid 0.5x MS media plates; grown in spaceflight, 8 days old plant harvested into KFT containing RNAlater fixative

growth_protocol: The laboratory preparations and launch conditions:   Dry, sterilized Arabidopsis seeds were planted aseptically on the surface of 10-cm2 solid media plates comprised of 0.5% Phytagel/0.5× MS media, and then immediately wrapped in light-tight black cloth (Duvetyne, SeattleFabrics.com) and transported to KSC (Kennedy Space Center), FL, USA. The wrapped plates were stored at temperatures between 4 and 10 °C until launch within a cold stowage bag nominally at 4 °C. The seeds remained dormant until removed from cold stowage and exposed to light at the initiation of the experiment on the ISS (International Space Station).   Plant growth on the ISS and ISSES:  The APEX03-2 experiment plates were grown in the Vegetable Production System (VPS/Veggie) hardware on the Columbus Module of the ISS. The 10-cm2 Petri plates were housed perpendicular (“vertical”) to the overhead LED lighting of the VPS. Plants received between 100–135 μmoles/m2/s PAR inside the VPS. Four and eight days after germination was initiated by unwrapping the plates and exposing them to light in the VPS. The ground control plates were grown inside the VPS ground unit within the ISSES (International Space Station Environment Simulator) chamber at KSC with the 48-h delay. The ISSES chamber replicated the temperature, CO2 levels and lighting that had been experienced by the spaceflight plants in the previous 48 h.

extract_protocol:
Sample preparation for transcriptomics:  Seedlings stored in RNAlater were recovered from -80°C freezer. Each tube containing the seedlings was allowed to thaw in the fridge overnight. After completely thawing the samples to room temperature, the seedlings were observed under the microscope. Roots of the preserved seedlings from the spaceflight and ground control harvests were dissected and the rest of the seedlings were saved in RNAlater and stored back to -80°C freezer.  For 4 day old roots 5-8 roots were combined to serve as one biological replica. For 8 day old roots 2-3 roots were used to form one biological replica. In each case the four biological replicas were used for the transcriptomic analysis.   Total RNA extraction: Total RNA was extracted using Qiashredder and RNAeasy™ kits from QIAGEN (QIAGEN Sciences, MD, USA) according to the manufacturer’s instructions. Residual DNA was removed by performing an on-column digestion using an RNase Free DNase (QIAGEN GmbH, Hilden, Germany). Integrity of the RNA was evaluated using the Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA).
Library preparation:  RNASeq Libraries Preparation using SMART-Seq V4 ultra low input RNA kit for sequencing combined with Illumina Nextera DNA Sample Preparation Kit  Ten ng of total RNA was used for cDNA library construction using CloneTech SMART-Seq V4 ultra low input RNA kit for sequencing (Clontech Laboratories, Inc, cat#: 634890) according to manufacturer's protocol. Briefly, 1st strand cDNA was primed by the SMART-Seq v4 oligonucleotide and then base-pairs with these additional nucleotides, creating an extended template. The reverse transcriptase then switches templates and continues transcribing to the end of the oligonucleotide, resulting full-length cDNA that contains an anchor sequence that serves as a universal priming site for second strand synthesis. cDNA was amplified with primer II A for 8 PCR cycles. Then Illumina sequencing libraries were generated with 150 pg of cDNA using Illumina Nextera DNA Sample Preparation Kit (Cat#: FC-131-1024) according to manufacturer’s instructions. Briefly, 150 pg of cDNA was fragmented by tagementation reaction and then adapter sequences added onto template cDNA by PCR amplification. Libraries were quantitated by Bioanalyzer and qPCR (Kapa Biosystems, catalog number: KK4824). Finally, the libraries were pooled equal molar concentration and sequenced by Illumina 2X75 NextSeq 500.
Illumina sequencing:  Sequencing experiments were performed at the Interdisciplinary Center for Biotechnology Research (ICBR) gene expression and sequencing core, University of Florida.  In preparation for sequencing, barcoded libraries were sized on the bioanalyzer, quantitated by QUBIT and qPCR (Kapa Biosystems, catalog number: KK4824). Individual samples were pooled equimolarly at 4 nM. This “working pool” was used as input in the NextSeq500 instrument sample preparation protocol (Illumina, Part # 15048776, Rev A). Typically, a 1.3 pM library concentration resulted in optimum clustering density in our instrument (i.e., ~200,000 clusters per mm2). Samples were sequenced on 5 flowcells (5 NextSeq 500 runs), using a 2x75 cycles (paired-end) configuration. A typical sequencing run in the NextSeq500 produced 750-800 million paired-end read with a Q30>=85%. For RNA seq, around 40 million reads provided sufficient depth for transcriptome analysis.

treatment_protocol: On Orbit Operations and harvest:  At four or for the second experimental set at eight days, seedlings were harvested by an astronaut into KFT (Kennedy Fixation Tube) containing RNAlater solutions. Once the plants were placed in the KFTs, the KFT was actuated with RNAlater to preserve the sample. At 24 hours post-harvest, KFTs were then transferred to MELFI freezer. Following Dragon Capsule splashdown in the Pacific Ocean, the KFTs transferred to the Cold Stowage charter plane at the Long Beach Airport, placed into an insulated shipper with dry ice, and flown to Johnson Space Center (JSC). The KFTs were then transferred via FedEx ground to the Kennedy Space Center. The KFTs were removed from dry ice and transferred to a -80°C freezer. The PIs retrieved the plant samples from the KFTs and transferred the samples back to the University of Florida.  The harvested material was used to compare the transcriptomes of each genotype. The patterns of gene expression was compared between treatments (spaceflight versus ground control) within each genotype of same age or between two ages within same genotype and within same treatment.

tag: cultivar

value: WS

tag: material type

value: Roots

tag: organism part

value: whole root of the 8 days old seedling

value: 8 days old plants, light grown

tag: biosource type

value: RNAlater fixed_sample


title: Spaceflight, 8 days old, Col-0 Rep4

description:
FLT 8d Col-0 Rep4
processed data file:
FLT 8d Col-0 to GC 8d Col-0.xlsx
FLT 4d Col-0 to FLT 8d Col-0.xlsx


title: Ground Control, 8 days old, WS Rep4

description:
GC 8d WS Rep4
processed data file:
FLT 8d WS to GC 8d WS.xlsx
GC 4d WS to GC 8d WS.xlsx

source_name: solid 0.5x MS media plates; grown on the ground, 8 days old plant harvested into KFT containing RNAlater fixative


title: Spaceflight, 8 days old, WS Rep3

description:
FLT 8d WS Rep3
processed data file:
FLT 8d WS to GC 8d WS.xlsx
FLT 4d WS to FLT 8d WS.xlsx


title: Ground Control, 8 days old, WS Rep1

description:
GC 8d WS Rep1
processed data file:
FLT 8d WS to GC 8d WS.xlsx
GC 4d WS to GC 8d WS.xlsx


title: Ground Control, 8 days old, Col-0 Rep3

description:
GC 8d Col-0 Rep3
processed data file:
FLT 8d Col-0 to GC 8d Col-0.xlsx
GC 4d Col-0 to GC 8d Col-0.xlsx


title: Spaceflight, 8 days old, WS Rep1

description:
FLT 8d WS Rep1
processed data file:
FLT 8d WS to GC 8d WS.xlsx
FLT 4d WS to FLT 8d WS.xlsx


title: Ground Control, 8 days old, WS Rep2

description:
GC 8d WS Rep2
processed data file:
FLT 8d WS to GC 8d WS.xlsx
GC 4d WS to GC 8d WS.xlsx


title: Spaceflight, 8 days old, WS Rep4

description:
FLT 8d WS Rep4
processed data file:
FLT 8d WS to GC 8d WS.xlsx
FLT 4d WS to FLT 8d WS.xlsx


title: Ground Control, 8 days old, Col-0 Rep4

description:
GC 8d Col-0 Rep4
processed data file:
FLT 8d Col-0 to GC 8d Col-0.xlsx
GC 4d Col-0 to GC 8d Col-0.xlsx


title: Spaceflight, 8 days old, Col-0 Rep3

description:
FLT 8d Col-0 Rep3
processed data file:
FLT 8d Col-0 to GC 8d Col-0.xlsx
FLT 4d Col-0 to FLT 8d Col-0.xlsx


title: Spaceflight, 8 days old, Col-0 Rep2

description:
FLT 8d Col-0 Rep2
processed data file:
FLT 8d Col-0 to GC 8d Col-0.xlsx
FLT 4d Col-0 to FLT 8d Col-0.xlsx


title: Ground Control, 8 days old, Col-0 Rep2

description:
GC 8d Col-0 Rep2
processed data file:
FLT 8d Col-0 to GC 8d Col-0.xlsx
GC 4d Col-0 to GC 8d Col-0.xlsx


title: Ground Control, 8 days old, WS Rep3

description:
GC 8d WS Rep3
processed data file:
FLT 8d WS to GC 8d WS.xlsx
GC 4d WS to GC 8d WS.xlsx


title: Spaceflight, 8 days old, Col-0 Rep1

description:
FLT 8d Col-0 Rep1
processed data file:
FLT 8d Col-0 to GC 8d Col-0.xlsx
FLT 4d Col-0 to FLT 8d Col-0.xlsx


title: Spaceflight, 4 days old, WS Rep3

description:
FLT 4d WS Rep3
processed data file:
FLT 4d WS to GC 4d WS.xlsx
FLT 4d WS to FLT 8d WS.xlsx

source_name: solid 0.5x MS media plates; grown in spaceflight, 4 days old plant harvested into KFT containing RNAlater fixative

value: whole root of the 4 days old seedling

value: 4 days old plants, light grown


title: Spaceflight, 4 days old, WS Rep4

description:
FLT 4d WS Rep4
processed data file:
FLT 4d WS to GC 4d WS.xlsx
FLT 4d WS to FLT 8d WS.xlsx


title: Spaceflight, 4 days old, WS Rep1

description:
FLT 4d WS Rep1
processed data file:
FLT 4d WS to GC 4d WS.xlsx
FLT 4d WS to FLT 8d WS.xlsx


title: Ground Control, 8 days old, Col-0 Rep1

description:
GC 8d Col-0 Rep1
processed data file:
FLT 8d Col-0 to GC 8d Col-0.xlsx
GC 4d Col-0 to GC 8d Col-0.xlsx


title: KD, rep1

city: Los Angeles

first: Yu-Ting

last: Tseng

state: California

address: 650 Charles E. Young Drive South

department: Department of Microbiology, Immunology, & Molecular Genetics

institute: University of California, Los Angeles

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to Ensembl transcript (release 72) then hg19 whole genome using tophat v1.4.1 with parameters -a 8 -m 0 -I 300000 -p 8 -g 20 --library-type fr-unstranded --initial-read-mismatches 3 --segment-mismatches 2
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using cuffdiff v2.2.0 with uniquely and properly mapped pairs.
Genome_build: hg19
Supplementary_files_format_and_content: an excel file includes FPKM values for each Sample …

source_name: Human choriocarcinoma

extract_protocol:
RNA from purified total placenta of human uterus were harvested by Trizol extraction. 1 ug of total RNA was used for  for RNA-seq library preparation using the TruSeq™ Stranded mRNA LT Sample Prep Kit (Illumina). 100x2 bp paired-end RNA-seq reads were generated on a HiSeq 2000 sequencer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Placenta

tag: genotyp/variation

value: PEG10 KD


title: CTRL, rep2

value: PEG10 CTRL


title: KD, rep2


title: Ground Control, 4 days old, WS Rep4

description:
GC 4d WS Rep4
processed data file:
FLT 4d WS to GC 4d WS.xlsx
GC 4d WS to GC 8d WS.xlsx

source_name: solid 0.5x MS media plates; grown on the ground, 4 days old plant harvested into KFT containing RNAlater fixative


title: KD, rep3


title: CTRL, rep3


title: Ground Control, 4 days old, WS Rep3

description:
GC 4d WS Rep3
processed data file:
FLT 4d WS to GC 4d WS.xlsx
GC 4d WS to GC 8d WS.xlsx


title: CTRL, rep1


title: Ground Control, 4 days old, WS Rep1

description:
GC 4d WS Rep1
processed data file:
FLT 4d WS to GC 4d WS.xlsx
GC 4d WS to GC 8d WS.xlsx


title: PbIP0d2(WT_0d_2)

status: Public on Feb 23 2018

city: Hefei

first: Kan

last: He

state: Anhui

address: 111 Jiulong Road

country: China

institute: Anhui University

data_processing:
Illumina Hiseq3000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using STAR software
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include the expression values of this transcript  for each Sample

extract_protocol:
RNA was harvested using Trizol reagent.TruSeq® RNA LT Sample Prep Kit v2  was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: time point

value: 0 day

value: wild type


title: Pbppary5d3(PPARγ/+_5d_3)

value: 5 day

value: PPAR<gamma>/+


title: PbIP5d2(WT_5d_2)


title: Spaceflight, 4 days old, WS Rep2

description:
FLT 4d WS Rep2
processed data file:
FLT 4d WS to GC 4d WS.xlsx
FLT 4d WS to FLT 8d WS.xlsx

tag: age


title: Pbppary5d2(PPARγ/+_5d_2)


title: Hyp1

first: Sangeeta

middle: N.

last: Bhatia

state: Massachusetts

address: 500 Main Street Cambridge MA 02142

department: HST

institute: Massachusetts Institute of Technology

description: total RNA followed by P. vivax-specific RNA based capture

data_processing:
Reads were aligned against Plasmodium vivax PvP01 from PlasmoDB v. 34 (Sept 2017) using STAR v. 2.5.3a with flags -runThreadN 8 --runMode alignReads  --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM with --genomeDir pointing to a 75nt-junction PvivaxP01 STAR suffix array.
Gene expression was quantitated using RSEM v. 1.3.0 with the following flags for all libraries(Li and Dewey, 2011): rsem-calculate-expression --calc-pme --alignments -p 8  --forward-prob 0 against an annotation matching the STAR SA reference.
Posterior mean estimates (pme) of counts were used, reads mapping to rRNA subtracted and RPKMs and TPMs estimated for each sample.
Genome_build: PvP01 PlasmoDB v. 34 (Sept 2017)
Supplementary_files_format_and_content: Tab-delimited text files with rRNA subtracted TPM output

organism: Plasmodium vivax

source_name: hypnozoite enriched samples 1

growth_protocol: MPCCs were infected with P. vivax sporozoites. Cultures were kept for 5 days with daily media changes. Day 5 cultures were drug-treated until day 8 to enrich for hypnozoites. Cultures were kept for an additional day and on day 9, total RNA was extracted with TRIzol and processed for sequencing

extract_protocol:
Total RNA was extracted with TRIzol® (Invitrogen), DNAse treated and purified using the RNeasy MinElute Cleanup Kit (Qiagen). cDNA synthesis was performed using SuperScript II (Invitrogen).
RNA was quality controlled using an AATI Fragment Analyzer and 100ng was prepared following the SureSelectXT RNA Direct protocol version A0. Illumina libraries were quantitated using the Fragment Analyzer and by qPCR and sequenced as a single end 40nt read using a HiSeq2000.
SureSelectXT RNA Direct protocol version A0

treatment_protocol: Cultures were kept with daily media changes. For hypnozoite enriched cultures, drug treatment was performed from day 5 to day 8 with daily supplementation.

tag: developmental stage

value: P. vivax hypnozoites in primary human hepatocytes, with 3T3-J2s

tag: isolate

value: P. vivax (Thai isolate VK210)


title: Spaceflight, 4 days old, Col-0 Rep2

description:
FLT 4d Col-0 Rep2
processed data file:
FLT 4d Col-0 to FLT 8d Col-0.xlsx
FLT 4d Col-0 to GC 4d Col-0.xlsx


title: Mixed2

source_name: Schizont/hypnozoite mixed samples 2

growth_protocol: MPCCs were infected with P. vivax sporozoites. Cultures were kept for 9 days with daily media changes, allowing for development of parasites. On day 9 post infection, total RNA was extracted with TRIzol and processed for sequencing

value: P. vivax hypnozoites and schizonts in primary human hepatocytes, with 3T3-J2s


title: PbIP5d3(WT_5d_3)


title: Spaceflight, 4 days old, Col-0 Rep3

description:
FLT 4d Col-0 Rep3
processed data file:
FLT 4d Col-0 to FLT 8d Col-0.xlsx
FLT 4d Col-0 to GC 4d Col-0.xlsx


title: PND 14-1 H3K4me1

city: Beaverton

first: Hollis

last: Wright

state: OR

address: 505 NW 185th Avenue

department: DIvision of Neuroscience

institute: ONPRC/OHSU

description: ChIP seq for H3K4me1

data_processing:
Intial basecalling using Illumina RTA 1.18.64
Barcode and adapter sequence was removed using Trimmomatic v0.33 ILLUMINACLIP
TruSeq3-SE.fa:2:30:10 SLIDINGWINDOW:10:34 HEADCROP:13
Alignment using Tophat2 v2.1 to rat rn6

organism: Rattus norvegicus

source_name: MBH

extract_protocol:
MBH tissue was removed, flash frozen on dry ice and chromatin prepared for Chromatin immunoprecipitation using  the following antibodies from Active Motif: H3K4me1 (Cat # 61633), H3K27me3 (Cat # 39155) H3K27Ac (Cat # 39133).  Immunoprecipitated DNA was amplified using LinDA amplification technique before sending it to the OSU Center for genome Research and Biocomputing for library preparation and sequencing using a HiSeq 3000 instrument.  Six samples per lane were sequenced with a target density of 300 million reads per lane using a single-read 100 cycle protocol.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: sprague dawley

tag: tissue

value: MBH (Medial Basal hypothalamus)

value: 14 days


title: Pbppary5d1(PPARγ/+_5d_1)


title: Ground Control, 4 days old, Col-0 Rep3

description:
GC 4d Col-0 Rep3
processed data file:
FLT 4d Col-0 to GC 4d Col-0.xlsx
GC 4d Col-0 to GC 8d Col-0.xlsx

value: Roots


title: PND 21-4 H3K4me1

description: ChIP seq for H3K4me1

value: 21 days


title: Pbppary0d2(PPARγ/+_0d_2)


title: Spaceflight, 4 days old, Col-0 Rep4

description:
FLT 4d Col-0 Rep4
processed data file:
FLT 4d Col-0 to FLT 8d Col-0.xlsx
FLT 4d Col-0 to GC 4d Col-0.xlsx

value: whole root of the 4 days old seedling

value: RNAlater fixed_sample


title: Ground Control, 4 days old, Col-0 Rep4

description:
GC 4d Col-0 Rep4
processed data file:
FLT 4d Col-0 to GC 4d Col-0.xlsx
GC 4d Col-0 to GC 8d Col-0.xlsx

value: 4 days old plants, light grown


title: Ground Control, 4 days old, Col-0 Rep1

description:
GC 4d Col-0 Rep1
processed data file:
FLT 4d Col-0 to GC 4d Col-0.xlsx
GC 4d Col-0 to GC 8d Col-0.xlsx


title: Ground Control, 4 days old, Col-0 Rep2

description:
GC 4d Col-0 Rep2
processed data file:
FLT 4d Col-0 to GC 4d Col-0.xlsx
GC 4d Col-0 to GC 8d Col-0.xlsx


title: PbIP5d1(WT_5d_1)


title: Ground Control, 4 days old, WS Rep2

description:
GC 4d WS Rep2
processed data file:
FLT 4d WS to GC 4d WS.xlsx
GC 4d WS to GC 8d WS.xlsx

value: WS


title: Pbppary0d1(PPARγ/+_0d_1)


title: Spaceflight, 4 days old, Col-0 Rep1

description:
FLT 4d Col-0 Rep1
processed data file:
FLT 4d Col-0 to FLT 8d Col-0.xlsx
FLT 4d Col-0 to GC 4d Col-0.xlsx


title: Hyp2

source_name: hypnozoite enriched samples 2


title: PbIP0d3(WT_0d_3)


title: PND 28-5 H3K4me1

description: ChIP seq for H3K4me1

value: 28 days


title: Mixed1

source_name: Schizont/hypnozoite mixed samples 1


title: PbIP0d1(WT_0d_1)

value: 0 day


title: PND 21-5 H3K4me1

description: ChIP seq for H3K4me1


title: PND 28-3 H3K4me1

description: ChIP seq for H3K4me1


title: PND 28-3 H3K27me3

description: ChIP seq for H3K27me3


title: PND 14-4 H3K4me1

description: ChIP seq for H3K4me1


title: PND 14-1 H3K27me3

description: ChIP seq for H3K27me3


title: PND 14-4 H3K27me3

description: ChIP seq for H3K27me3


title: Pbppary0d3(PPARγ/+_0d_3)


title: PND 28-3 H3K27Ac

description: ChIP seq for H3K27Ac


title: PND 21-5 H3K27Ac

description: ChIP seq for H3K27Ac


title: PND 14-4 H3K27Ac

description: ChIP seq for H3K27Ac


title: PND 28-5 H3K27me3

description: ChIP seq for H3K27me3


title: PND 21-4 H3K27Ac

description: ChIP seq for H3K27Ac


title: PND 21-4 H3K27me3

description: ChIP seq for H3K27me3


title: PND 28-5 H3K27Ac

description: ChIP seq for H3K27Ac


title: PND 14-1 H3K27Ac

description: ChIP seq for H3K27Ac


title: PDGF-driven glioblastoma mouse model single cell 78

city: Tucson

first: Hongxu

last: Ding

state: AZ

address: The University of Arizona

institute: University of Arizona

description:
PS004-GGACTCCTAAGGAGTA-78
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt

data_processing:
After demultiplexing, the resulting raw reads were aligned to the murine genome and transcriptome annotation (mm10, UCSC annotation from Illumina iGenomes) with Tophat 2.
Uniquely aligned, exonic reads were then quantified for each gene using HTSeq.
Genome_build: mm10 (GRCm38), UCSC annotation from Illumina iGenomes.
Supplementary_files_format_and_content: counts.txt: Tab-delimited text file includes HTSeq counts for each cell. Column 1 includes Entrez Gene IDs.

source_name: de novo tumor-derived cell line from Canoll mouse glioblastoma model

growth_protocol: PDGFB-IRES-CRE expressing retrovirus was injected into the rostral subcortical white matter of adult Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice. Mice developed brain tumors with the histopathological features of glioblastoma by 28 days post injection with retrovirus. Following IACUC guidelines, animals were sacrificed at the first sign of morbidity. Ex-vivo gross total resection of the tumor was performed and tumor cells were isolated using enzymatic digestion. The isolated cells were cultured in a 2:1 ratio of basal media (DMEM, N2, T3, 0.5% FBS, and penicillin/streptomycin/amphotericin) in B104 conditioned media. This media was further supplemented with PDGF-AA (Sigma-Aldrich; St. Louis, MO) and FGFb (Gibco; Grand Island, NY) to a concentration of 10 ng/ml.

extract_protocol:
Cells were lysed and mRNA were first reverse transcribed into cDNA, and then pre-amplified full-length cDNA by PCR automatically using the Fluidigm C1 Autoprep instrument according to the manufacturer's instructions.
Individual cDNA libraries were harvested from the microfluidic device and converted into indexed, Illumina sequencing libraries by in vitro transposition and PCR using the Nextera system (Illumina). The pooled libraries were sequenced on a single lane of an Illumina HiSeq 2000 with single-end 100-bp reads.

treatment_protocol: Dissociated cells were loaded into a Fluidigm Integrated Fluidic Circuit with capture sites designed for 10-17 μm diameter cells after staining the single cell suspension with Calcein AM (Life Technologies). Cells that had been captured were then imaged on-chip with both bright field and fluorescence microscopy using an inverted Nikon Eclipse Ti-U epifluorescence microscope with a 20x, 0.75 NA air objective (Plan Apo λ, Nikon), a 473 nm diode laser (Dragon Lasers), and an electron multiplying charge coupled device (EMCCD) camera (iXON3, Andor Technologies). By doing this, capture sites with zero, one, and more than one cell, as well as capture sites containing living cells, were identified.

tag: cell type

value: PDGF-driven glioblastoma single cell


title: PDGF-driven glioblastoma mouse model single cell 77

description:
PS004-CGTACTAGACTGCATA-77
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 82

description:
PS004-AGGCAGAAAGAGTAGA-82
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 80

description:
PS004-TAGGCATGACTGCATA-80
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 75

description:
PS004-AAGAGGCACTAAGCCT-75
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 71

description:
PS004-GTAGAGGATATCCTCT-71
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 73

description:
PS004-TCCTGAGCTAGATCGC-73
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 72

description:
PS004-TCCTGAGCAAGGAGTA-72
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 81

description:
PS004-CAGAGAGGTAGATCGC-81
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 70

description:
PS004-AGGCAGAAGTAAGGAG-70
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 84

description:
PS004-GTAGAGGACTAAGCCT-84
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PND 21-5 H3K27me3

description: ChIP seq for H3K27me3


title: PDGF-driven glioblastoma mouse model single cell 83

description:
PS004-GTAGAGGAAAGGAGTA-83
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 79

description:
PS004-CAGAGAGGAGAGTAGA-79
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 65

description:
PS004-CGAGGCTGAAGGAGTA-65
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 74

description:
PS004-CGTACTAGTAGATCGC-74
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 69

description:
PS004-TCCTGAGCTATCCTCT-69
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 64

description:
PS004-GGACTCCTTAGATCGC-64
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 63

description:
PS004-CGTACTAGCTCTCTAT-63
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 62

description:
PS004-TCCTGAGCAGAGTAGA-62
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 59

description:
PS004-GCTACGCTTATCCTCT-59
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 60

description:
PS004-GGACTCCTTATCCTCT-60
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 54

description:
PS004-TCCTGAGCGTAAGGAG-54
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 51

description:
PS004-TCCTGAGCCTAAGCCT-51
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 50

description:
PS004-GCTACGCTACTGCATA-50
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 57

description:
PS004-AAGAGGCATAGATCGC-57
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 61

description:
PS004-TAGGCATGTAGATCGC-61
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 56

description:
PS004-CGTACTAGCTAAGCCT-56
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 49

description:
PS004-AAGAGGCAAGAGTAGA-49
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 67

description:
PS004-GGACTCCTAGAGTAGA-67
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 66

description:
PS004-CGTACTAGAAGGAGTA-66
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 53

description:
PS004-CAGAGAGGCTAAGCCT-53
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 52

description:
PS004-CGTACTAGTATCCTCT-52
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 47

description:
PS004-TCCTGAGCACTGCATA-47
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 46

description:
PS004-GGACTCCTCTAAGCCT-46
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 55

description:
PS004-TCCTGAGCCTCTCTAT-55
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 68

description:
PS004-TAGGCATGTATCCTCT-68
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 44

description:
PS004-CGTACTAGGTAAGGAG-44
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 43

description:
PS004-CTCTCTACCTAAGCCT-43
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 76

description:
PS004-CTCTCTACTAGATCGC-76
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 41

description:
PS004-GTAGAGGATAGATCGC-41
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 58

description:
PS004-AGGCAGAATAGATCGC-58
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 40

description:
PS004-TAGGCATGAGAGTAGA-40
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 39

description:
PS004-AGGCAGAACTCTCTAT-39
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 38

description:
PS004-CTCTCTACCTCTCTAT-38
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 37

description:
PS004-GGACTCCTCTCTCTAT-37
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 36

description:
PS004-TAGGCATGAAGGAGTA-36
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 35

description:
PS004-AAGAGGCAGTAAGGAG-35
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 33

description:
PS004-CAGAGAGGAAGGAGTA-33
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 28

description:
PS004-CGTACTAGAGAGTAGA-28
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 27

description:
PS004-CAGAGAGGCTCTCTAT-27
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 30

description:
PS004-CGAGGCTGGTAAGGAG-30
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 26

description:
PS004-CAGAGAGGACTGCATA-26
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 29

description:
PS004-TAGGCATGCTAAGCCT-29
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 48

description:
PS004-CGAGGCTGCTCTCTAT-48
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 34

description:
PS004-GGACTCCTGTAAGGAG-34
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 24

description:
PS004-AGGCAGAAACTGCATA-24
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 22

description:
PS004-GTAGAGGAGTAAGGAG-22
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 20

description:
PS004-CTCTCTACAAGGAGTA-20
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 19

description:
PS004-AGGCAGAACTAAGCCT-19
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 45

description:
PS004-GCTACGCTAAGGAGTA-45
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 25

description:
PS004-AAGAGGCAAAGGAGTA-25
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 18

description:
PS004-GCTACGCTGTAAGGAG-18
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 17

description:
PS004-GGACTCCTACTGCATA-17
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 16

description:
PS004-AAGAGGCATATCCTCT-16
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 14

description:
PS004-GTAGAGGAACTGCATA-14
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 42

description:
PS004-CGAGGCTGCTAAGCCT-42
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 11

description:
PS004-CTCTCTACACTGCATA-11
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 13

description:
PS004-TAGGCATGCTCTCTAT-13
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 12

description:
PS004-TAGGCATGGTAAGGAG-12
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 31

description:
PS004-AGGCAGAATATCCTCT-31
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 32

description:
PS004-CGAGGCTGACTGCATA-32
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 8

description:
PS004-GTAGAGGAAGAGTAGA-8
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 7

description:
PS004-GCTACGCTTAGATCGC-7
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 9

description:
PS004-AGGCAGAAAAGGAGTA-9
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 6

description:
PS004-CGAGGCTGTAGATCGC-6
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 23

description:
PS004-AAGAGGCAACTGCATA-23
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 3

description:
PS004-CTCTCTACGTAAGGAG-3
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 1

description:
PS004-CTCTCTACAGAGTAGA-1
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 0

description:
PS004-CAGAGAGGTATCCTCT-0
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 21

description:
PS004-AAGAGGCACTCTCTAT-21
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 4

description:
PS004-GCTACGCTCTCTCTAT-4
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 2

description:
PS004-CGAGGCTGAGAGTAGA-2
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 5

description:
PS004-CTCTCTACTATCCTCT-5
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: PDGF-driven glioblastoma mouse model single cell 15

description:
PS004-GCTACGCTAGAGTAGA-15
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: Ugt8WT5FC

first: Yongzhong

last: Zhao

state: New York

address: 1470 Madison Avenue btw. 101st and 102nd Streets

department: Genetics

institute: Mount Sinai Medical Center

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were mapped to mm10
alignment with bowtie2 -k 60 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 4 --sam-no-hd -x
number counts of reads with tophat2
segment_juncs --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include number counts of reads for each Sample

source_name: brain

extract_protocol:
Brain regions were isloated and RNA was isolated using Trizol reagent and processed using Ribo-Zero rRNA removal.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: frontal cortex

tag: genotype/variation


title: Ugt8WT5CBM

value: cerebellum


title: Ugt8WT3FC


title: Ugt8WT4CBM


title: Ugt8WT3CBM


title: Ugt8WT4FC


title: Ugt8WT2FC


title: Ugt8WT2CBM


title: PDGF-driven glioblastoma mouse model single cell 10

description:
PS004-CAGAGAGGGTAAGGAG-10
The cells are derived from Pten lox/lox /p53 lox/lox /luciferase- stop-lox transgenic mice.
PolyA RNA
Processed data file: counts.txt


title: Ugt8WT1FC


title: Ugt8KO5FC


title: Ugt8WT1CBM


title: Ugt8KO4CBM


title: Ugt8KO3CBM


title: Ugt8KO4FC


title: Ugt8KO3FC


title: Ugt8KO2FC


title: Ugt8KO1CBM


title: PLPWT5FC


title: PLPWT4CBM


title: PLPWT5CBM


title: PLPWT3FC


title: PLPWT3CBM


title: PLPWT2FC


title: PLPWT4FC


title: PLPWT2CBM


title: PLPWT1FC


title: PLPWT1CBM


title: PLPKO4FC


title: PLPKO5CBM


title: PLPKO3FC


title: PLPKO5FC


title: PLPKO3CBM


title: PLPKO2FC


title: Ugt8KO5CBM


title: PLPKO1FC


title: PLPKO1CBM


title: Ugt8KO2CBM


title: Cnp_WT_5_FC


title: Cnp_WT_5_CBM


title: Cnp_WT_4_FC


title: Ugt8KO1FC


title: Cnp_WT_3_CBM


title: Cnp_WT_3_FC


title: Cnp_WT_4_CBM


title: Cnp_WT_2_FC


title: Cnp_WT_1_FC


title: Cnp_KO_5_FC


title: Cnp_KO_2_FC


title: Cnp_KO_4_FC


title: Cnp_KO_5_CBM


title: Cnp_KO_4_CBM


title: Cnp_KO_1_FC


title: Cnp_KO_2_CBM


title: Cnp_KO_1_CBM


title: PLPKO4CBM


title: adr_rrf3_rde4_4

city: Salt Lake City

first: Brenda

middle: L

last: Bass

state: Utah

address: 15 N Medical Drive East, Rm 4800

department: Biochemistry

institute: University of Utah

description:
Poly(A)+ RNA from adr-1;adr-2;rrf-3;rde-4 mixed embryos
gene_counts.txt
gene_normalized_coverage.txt

data_processing:
All reads were aligned to the C. elegans genome (version WS220/ce10) using Novoalign. Novoalign was run with arguments “ [ -o SAM -r All 10000 -i PE 320,40 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT ] -g ce10WBTransRad97Num100kMin10AdaptPhiX -i *.gz -gzip”
Alignments were parsed to .bam files using the Useq (version 8.8.2) application SamTranscriptomeParser, with the parameters "-a 120 -n 1 -d -p -r -b ".
Alignment files were used to compute relative transcript abundance using the Useq (Version 8.8.2) application DefinedRegionDifferentialSeq with the following parameters: "-g C_elegans_Oct_2010 -p -e 1"
Genome_build: ce10
Supplementary_files_format_and_content: gene_counts.txt; tab-delimited text file containing raw read counts for all samples in Ensembl genes.
gene_normalized_coverage.txt;  tab-delimited text file containing normalized read counts (fragments per kilobase-million reads) for all samples in Ensembl genes.

organism: Caenorhabditis elegans

source_name: Mixed-stage embryos

growth_protocol: For each sample, worms were grown on 4 60 mm OP50 NGM plates until most, but not all, food was exhausted, and then washed into a culture of 200 mL S-complete liquid medium  with 5 mL of HB101 E. coli as food. Worms were grown in liquid culture 3 days at 20C, shaking 200 rpm. Mixed worms were then collected and embryos were isolated by sodium hypochlorite treatment and washed 3x in M9 buffer.

extract_protocol:
RNA was extracted using TRIzol reagent, depleted of DNA using TURBO-DNase, and extracted with phenol-chloroform followed by precipitation with ethanol.
Poly(A)+ selection on oligo-d(T) beads, RNA fragmentation (to an average size of 300-400 nts), and cDNA library preparation were performed using the Illumina TruSeq Stranded mRNA Library Preparation Kit with polyA selection according to manufacturer's instructions.

value: Mixed-stage embryos


title: PLPKO2CBM


title: adr_rrf3_rde1_4

description:
Poly(A)+ RNA from adr-1;adr-2;rrf-3;rde-1 mixed embryos
gene_counts.txt
gene_normalized_coverage.txt


title: rrf3_4

description:
Poly(A)+ RNA from rrf-3 mixed embryos
gene_counts.txt
gene_normalized_coverage.txt


title: adr_rrf3_4

description:
Poly(A)+ RNA from adr-1;adr-2;rrf-3 mixed embryos
gene_counts.txt
gene_normalized_coverage.txt


title: N2_4

description:
Poly(A)+ RNA from wildtype mixed embryos
gene_counts.txt
gene_normalized_coverage.txt

value: Bristol N2


title: adr_4

description:
Poly(A)+ RNA from adr-1;adr-2 mixed embryos
gene_counts.txt
gene_normalized_coverage.txt


title: adr_rrf3_3


title: adr_rrf3_rde4_3


title: rrf3_3


title: N2_3


title: adr_rrf3_rde4_2


title: adr_rrf3_rde1_2


title: rrf3_2


title: adr_rrf3_rde1_3


title: adr_3


title: Cnp_KO_3_FC


title: adr_rrf3_2


title: Cnp_KO_3_CBM


title: adr_1


title: rrf3_1


title: N2_2


title: adr_rrf3_1


title: N2_1


title: Input control H3K27ac ChIP

last: Koche

institute: Memorial Sloan Kettering Cancer Center

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human genome assembly hg19 using bowtie2 (v2.2.2) with default parameters.
To create density files, the reads were extended to 200 bp, the signal was then normalized to ten million mapped reads and converted to BigWig using BEDTools.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads.

growth_protocol: MV-411 cells were cultured in 5% CO2 in a humidified atmosphere at 37˚C in RPMI medium supplemented with 10% FBS (FBS) and antibiotics (100U/mL penicillin and 100 µg/mL streptomycin).

extract_protocol: ChIP-seq libraries were constructed with the NEBNext ChIP-seq library prep kit following the manufacturer’s recommended protocol (New England Biolabs, Ipswich, MA, USA).

treatment_protocol: Treatment protocol for cells: MV-411 cells were resuspended to a concentration of 10 million cells/5mL of working media. A peptide suspension was made in PBS of each TG3 and MYBMIM peptides from the lyophilized product. Peptide suspension was added directly to tissue culture media to a final concentration of 20μM. Cells were incubated with peptide for 12h at 37°C and then resuspended in PBS for Chromatin Immunoprecipitation and Sequencing.

value: leukemia cell line

tag: treatment

tag: chip antibody


title: L3-L4 total RNA

description:
processed data file:
all_input_505EERs.bed
l34_354EERs.bed,ce10_L3L4_Minus.bw
ce10_L3L4_Plus.bw

data_processing:
All reads were aligned to the C. elegans genome (version WS220/ce10) using Novoalign. Novoalign was run with arguments “ -g ce10WBTransRad32Num100kMin10AdaptPhiX -i *.txt.gz -gzip -novoalign [-r All].”
All alignments for a given biological sample were merged into one alignment file and filtered using the Useq (Version 8.8.2) application SamTranscriptomParser. For GNUMAP alignments, the following command options were used: -a 120 -n 1 -p -r -b
All parsed alignment files were intersected with a bed file of C. elegans ribosomal RNA gene loci to remove reads mapping in rRNA loci using the bedtools2 (version 2.19.0) application intersectBed with the following parameters: "-abam *.bam -b rRNA.bed -ubam -wa -s"
Alignment files were used to compute relative transcript abundance using the Useq (Version 8.8.2) application DefinedRegionDifferentialSeq with the following parameters: "-g C_elegans_Oct_2010 -p -e 1"
Alignments were converted to pileup format using samtools (Version 0.1.19) mpileup with the command options "-A -B -Q 13".
Pileup files were parsed using the Useq (Version 8.8.2) application RNAEditingPileupParser with the command options "-t -m -v C_elegans_Oct_2010"
The USeq (Version 8.8.2) application RNAEditingScanSeqs with command options "-m 5 -t" was used to detect editing enriched windows from RNAEditingPileupParser point data
The USeq (Version 8.8.2) application EnrichedRegionMaker with command options "-i 0 -s 3 -g 1000" generated initial lists of editing-enriched regions. All regions with less than 2 editing-enriched windows were discarded.
Genome_build: ce10
Supplementary_files_format_and_content:
all_1523EERs.bed; BED file of EERs defined in all samples
all_input_505EERs.bed; BED file of EERs defined in all input samples
all_j2_1148EERs.bed; BED file of EERs defined in all dsRIP samples
emb_566EERs.bed; BED file of EERs defined in embryo samples
112_460EERs.bed; BED file of EERs defined in L1/L2 samples
134_354EERs.bed; BED file of EERs defined in L3/L4 samples
ya_133EERs.bed; BED file of EERs defined in young adult samples
Cel_gene_EER_normalized_counts.txt; tab-delimited text file contains FPKM values for all samples for Ensembl genes and all defined EERs.
ce10_all_samples_Minus.bw; BigWig file displaying minus strand RNA editing sites in all samples
ce10_all_samples_Plus.bw; BigWig file displaying plus strand RNA editing sites in all samples
ce10_embryo_Minus.bw; BigWig file displaying minus strand RNA editing sites in embryo samples
ce10_embryo_Plus.bw; BigWig file displaying plus strand RNA editing sites in embryo samples
ce10_L1L2_Minus.bw; BigWig file displaying minus strand RNA editing sites in L1/L2 samples
ce10_L1L2_Plus.bw; BigWig file displaying plus strand RNA editing sites in L1/L2 samples
ce10_L3L4_Minus.bw; BigWig file displaying minus strand RNA editing sites in L3/L4 samples
ce10_L3L4_Plus.bw; BigWig file displaying plus strand RNA editing sites in L3/L4 samples
ce10_young_adult_Minus.bw; BigWig file displaying minus strand RNA editing sites in young adult samples
ce10_young_adult_Plus.bw; BigWig file displaying plus strand RNA editing sites in young adult samples

source_name: Whole worms

growth_protocol: Synchronized populations of C. elegans were obtained by sodium hypochlorite treatment of well-fed mixed stage Bristol N2 worms grown for 4-5 days in S-Complete liquid medium. After hypochlorite treatment, eggs were washed three times in M9 buffer and either collected for embryo samples or allowed to hatch overnight on a nutator at 20°C in M9 without food. On the next day, synchronized worms were filtered over two layers of Miracloth (Calbiochem) and subsequently cultured in S-Complete liquid medium to mid-L1 (6-8 hrs), the L1/L2 molt (12-14 hrs), mid-L2 (18-20 hrs), mid-L3 (28-30 hrs), the L3/L4 molt (34-36 hrs), mid-L4 (40-42 hrs), or young adulthood (50-54 hrs). Early larva samples were prepared by mixing L1, L2, and L1/L2 molt populations at a 5:5:2 volumetric ratio respectively. Late larval samples were similarly prepared with L3, L4, and L3/L4 molt populations.

extract_protocol:
RNA was extracted using TRIzol reagent, depleted of DNA using TURBO-DNase, and extracted with phenol-chloroform followed by precipitation with ethanol. For dsRIP samples, dsRNA was then immunoprecipitated with the J2 dsRNA antibody from English and Scientific Consulting.
RNAs were fragmented to an average size of 200-300 nts prior to library preparation. cDNA libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Kit according to manufacturer's instructions, except for the inclusion of additional DMSO for the reverse transcription reaction.

value: L3-L4 larvae

tag: molecule subtype

value: total RNA


title: L4-L4 dsRIP

description:
processed data file:
all_j2_1148EERs.bed
l34_354EERs.bed,ce10_L3L4_Minus.bw
ce10_L3L4_Plus.bw

value: dsRNA purified by immunoprecipitation with the J2 dsRNA antibody


title: L1-L2 dsRIP

description:
processed data file:
all_j2_1148EERs.bed
l12_460EERs.bed,ce10_L1L2_Minus.bw
ce10_L1L2_Plus.bw

value: L1-L2 larvae


title: Young adult dsRIP

description:
processed data file:
all_j2_1148EERs.bed
ya_133EERs.bed,ce10_young_adult_Minus.bw
ce10_young_adult_Plus.bw

value: Young adults


title: Young adult total RNA

description:
processed data file:
all_input_505EERs.bed
ya_133EERs.bed,ce10_young_adult_Minus.bw
ce10_young_adult_Plus.bw


title: L1-L2 total RNA

description:
processed data file:
all_input_505EERs.bed
l12_460EERs.bed,ce10_L1L2_Minus.bw
ce10_L1L2_Plus.bw


title: Embryo total RNA

description:
processed data file:
all_input_505EERs.bed
emb_566EERs.bed,ce10_embryo_Minus.bw
ce10_embryo_Plus.bw

value: mixed-stage embryos


title: Embryo dsRIP

description:
processed data file:
all_j2_1148EERs.bed
emb_566EERs.bed,ce10_embryo_Minus.bw
ce10_embryo_Plus.bw


title: H3K27ac ChIP MYBMIM replicate 3

value: MYBMIM peptide

value: H3K27ac Rabbit polyclonal antibody (Abcam, #4729)


title: H3K27ac ChIP MYBMIM replicate 2


title: H3K27ac ChIP TG3 peptide control replicate 2

value: TG3 control peptide


title: H3K27ac ChIP TG3 peptide control replicate 1


title: H3K27ac ChIP TG3 peptide control replicate 3


title: H3K27ac ChIP MYBMIM replicate 1


title: H3K27ac ChIP control replicate 2


title: adr_rrf3_rde4_1

tag: genotype


title: adr_2


title: H3K27ac ChIP control replicate 1


title: H3K27ac ChIP control replicate 3


title: adr_rrf3_rde1_1


title: Nac_wt_3_Heavy

city: Montpellier

first: Emmanuel

last: Valjent

address: 141, rue de la cardonille

department: Neurobiology

country: France

institute: INSERM

description:
wild-type littermates
Stranded RNA-seq
Processed data file: Raw_Counts_RNA-Seq_Puighermanal.txt

data_processing:
Image analyses and basecalling were performed using the HiSeq Control Software and Real-Time Analysis component.
Demultiplexing was performed using Illumina's sequencing analysis software (CASAVA 1.8.2). The quality of the data was assessed using FastQC and Fastq Screen from the Babraham Institute and the Illumina software SAV (Sequence Analysis Viewer).
Alignment was performed with TopHat 2.0.13 (with Bowtie 2.2.3) to the mm10 version of the Mus musculus genome. The transcript annotation was retrieved from UCSC on May 23, 2014.
Counting of reads aligned to a gene was performed with HTSeq-count 0.6.1p1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Raw_Counts_RNA-Seq_Puighermanal.txt: Tab-separated text file. First column is the gene identifier (Gene symbol|Entrez Gene ID), the following columns are the raw counts (non-normalized) for each sample.

source_name: Nucleus accumbens, wild-type, heavy

extract_protocol:
Nac and DStr were removed and homogenized in polysome lysis buffer. Fifty microliters of the initial lysate were used for RNA extraction using Trizol protocol according to manufacturer's instructions (here referred as 'Total') and the rest of the lysate was then centrifuged in 10-50% sucrose density gradients. Ribosome profiling was then performed, samples were fractionated and RNA was isolated from heavy polysomal fractions (>4 ribosomes) using Trizol protocol (here referred as 'Heavy').
RNA-Seq libraries were prepared with the 'TruSeq Stranded RNA sample preparation Kit' (Illumina) according to the manufacturer's instructions.

value: wild-type

value: Brain

tag: brain region

value: Nucleus accumbens

tag: source

value: RNA-bound to heavy polysomes


title: Nac_wt_2_Total

source_name: Nucleus accumbens, wild-type, total

value: total cytosolic RNA


title: 3234-1-4N

first: Gabriel

middle: E

last: Hofman

address: 1 Gustave L Levy Plaza

department: Department of Genetics and Genomics Sciences

institute: Icahn School of Medicine at Mount Sinai

description:
RNA-seq from hiPSC-derived cell culture
NSB3234

data_processing:
RNA-Seq reads were aligned to GRCh37 with STAR v2.4.0g1. Uniquely mapping reads overlapping genes were counted with featureCounts v1.4.4 using annotations from ENSEMBL v70.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts are reported

source_name: HiPSC-derived cell line

growth_protocol: HFs were cultured on 0.1% (w/v) gelatin coated plates in HF medium (DMEM (ThermoFisher Scientific), 20% (v/v) FBS (Corning)). Replicating 90% confluent HFs were reprogrammed using a modified protocol; briefly, HFs were transduced with Cytotune® Sendai viruses (ThermoFisher Scientific) expressing OCT4, SOX2, KLF4 and c-MYC, as per lot specifications. Cells from a single well of a six-well plate were split 1:2, 1:3 and 1:10 onto 10-cm plates containing 1 x 106 mouse embryonic fibroblasts (mEFs; GlobalStem). Cells were switched to hiPSC media (DMEM/F12, 20% KO-Serum Replacement (v/v), 1% (v/v) GlutaMAX, 1% (v/v) nonessential amino acids (NEAA), 55 μM β‐mercaptoethanol (β‐me) (all ThermoFisher Scientific) and 20 ng ml-1 FGF2 (R & D Systems, 233-FB-10)) and fed daily. hiPSC colonies were manually picked and clonally plated onto 24-well mEF-coated plates. hiPSC lines were maintained on mEFs in hiPSC media; at early passages, hiPSCs were split using manual passaging and at higher passages, hiPSC were enzymatically passaged with Collagenase (1mg/ml in DMEM) (Sigma) until cryopreservation in cold freezing media (hiPSC media containing 10% DMSO). Individual hiPSC lines were validated using TRA-1-60 and SSEA-4 flow cytometry and NANOG, TRA-1-60, SOX2 and OCT4 immunocytochemistry. G-banded karyotyping was performed by WiCell Cytogenetic Services. The differentiation potential of the hiPSCs derived in this study was confirmed by RT-PCR for markers of the three germ layers following spontaneous differentiation of a subset of the lines into embryoid bodies. Routine (every 2 to 4 weeks) mycoplasma testing was conducted using the MycoAlert Mycoplasma detection kit (Lonza); all cells used in this study and were found to be negative.

extract_protocol: RNA Sequencing libraries were prepared using the Kapa Total RNA library prep kit with ribo-depletion and strand specific cDNA library construction (Kappa Biosystems). Paired-end sequencing reads (125bp) were generated on an Illumina HiSeq2500 platform (New York Genome Center).

treatment_protocol: NPCs were generated from unique hiPSC lines with had normal karyotypes, and then passed NPC quality control based on immunocytochemistry and FACS for SOX2 and NESTIN levels. NPCs were derived as previously described and maintained at high density, grown either growth factor reduced Matrigel (BD Biosciences) coated plates in NPC media (Dulbecco’s Modiﬁed Eagle Medium/Ham’s F12 Nutrient Mixture (ThermoFisher Scientific), 1x N2, 1x B27-RA (ThermoFisher Scientific) and 20 ng ml−1 FGF2 and split 1:3 every week with Accutase (Millipore, Billerica, MA, USA). NPCs were dissociated with Accutase and plated at 2.0 x 105 cells per cm-2 in NPC media onto growth factor reduced Matrigel-coated plates. For neuronal differentiation, media was changed to neural differentiation medium (DMEM/F12, 1xN2, 1xB27-RA, 20 ng ml-1 BDNF (Peprotech), 20 ng ml-1 GDNF (Peprotech), 1 mM dibutyryl-cyclic AMP (Sigma), 200nM ascorbic acid (Sigma) and 1 g ml-1  laminin (ThermoFisher Scientific) 1-2 days later.  NPC-derived neurons were differentiated for 6 weeks.

tag: diagnosis

value: control

tag: Sex

value: Male

value: NPC

tag: rna purification method

value: Qiagen miRNAeasy column

tag: rin

tag: library prep method

value: KAPA Total Kit

tag: cnv

tag: affected gene

tag: age of onset

value: caucasian

tag: iq

tag: developmental history

value: clean

tag: clozapine response

tag: family history

tag: reprogramming method

value: Sendai Virus

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

value: Kristen Brennand

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

value: NPC lot8

tag: npc technician

value: Ian Ladran

tag: npc thaw

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: Nac_wt_3_Total

tag: genotype/variation

tag: tissue

tag: brain region

tag: source


title: 3234-3-4F

tag: diagnosis

tag: Sex

tag: cell type

value: 6 wk FB neuron

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

value: 46,XY  - Nonclonal finding:47,XY,+20

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 3234-3-4FR

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 3234-1-4F

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 3234-3-4NR

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 3234-3-4N

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: Nac_wt_1_Total

tag: genotype/variation

value: wild-type

tag: tissue

value: Brain

tag: brain region

tag: source


title: Nac_wt_2_Heavy

value: Nucleus accumbens

value: RNA-bound to heavy polysomes


title: 3188-2A-4F

description:
RNA-seq from hiPSC-derived cell culture
NSB3188

tag: diagnosis

value: control

tag: Sex

value: Female

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 3183-3-2F

description:
RNA-seq from hiPSC-derived cell culture
NSB3183

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: Nac_wt_1_Heavy

tag: genotype/variation

tag: tissue

tag: brain region

tag: source


title: 3188-2A-4N

tag: diagnosis

tag: Sex

tag: cell type

value: NPC

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 3183-1-4F

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

value: Qiagen miRNAeasy column

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 3183-1-4N

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

value: KAPA Total Kit

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 3182-3-1N

description:
RNA-seq from hiPSC-derived cell culture
NSB3182

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

value: caucasian

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 3182-3-1FR

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: iq

tag: developmental history

value: clean

tag: clozapine response

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: Nac_KI_2_Total

description:
rpS6 knockin mice
Stranded RNA-seq
Processed data file: Raw_Counts_RNA-Seq_Puighermanal.txt

source_name: Nucleus accumbens, rpS6 knockin, total

tag: genotype/variation

value: rpS6 knockin

tag: tissue

tag: brain region

tag: source

value: total cytosolic RNA


title: 3182-3-1NR

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: reprogramming method

value: Sendai Virus

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

value: Kristen Brennand

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

value: NPC lot8

tag: npc technician

tag: npc thaw


title: Nac_KI_3_Heavy

source_name: Nucleus accumbens, rpS6 knockin, heavy

tag: genotype/variation

tag: tissue

tag: brain region

tag: source


title: Nac_KI_2_Heavy


title: 3182-3-1F

tag: diagnosis

tag: Sex

tag: cell type

value: 6 wk FB neuron

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

value: Ian Ladran

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: Nac_KI_3_Total

tag: genotype/variation

tag: tissue

value: Brain

tag: brain region

tag: source


title: 3182-1-2F

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 3130-4-21N

description:
RNA-seq from hiPSC-derived cell culture
NSB3130

tag: diagnosis

tag: Sex

value: Male

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

value: Sanford Consortium

value: NPC lot5

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 3182-1-2N

tag: diagnosis

value: control

tag: Sex

value: Female

tag: cell type

tag: rna purification method

tag: rin

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw