title: PDX-C69 transduced with control shRNA

city: Stanford

first: Robert

middle: Wenchen

last: Hsieh

state: CA

address: 265 Campus Drive

department: Stem Cell Institute

institute: Stanford University

description: gene expression from PDX-C69 transduced with control shRNA

hyb_protocol: The fragmented and labeled targets were hybridized to the arrays per standard Affymetrix protocol, which includes 16hr (overnight) hybridization at 45degC at 60rpm in an Affymetrix GeneChip Hybridization Oven 645. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Affymetrix® Expression Console™ Software using Affymetrix default analysis settings.

source_name: breast cancer patient-derived xenograft

label_protocol: Affymetrix 3'IVT Plus protocol was used to generate biotinylated cRNA from 200 ngs of total RNA  was used to generate biotinylated  cRNA from 200 ngs of total RNA

growth_protocol: EpCAM enriched PDX-C69 cells were infected with shRNA targeting CDK19, shRNA targeting CDK8, control shRNA or not infected and grown in organoid culture conditions for 72 hours

extract_protocol: Total RNA was extracted from these cells by RNeasy plus micro kit (Qiagen) according to manufacturer’s instructions

value: breast cancer

tag: subtype

value: Triple-Negative

tag: host

value: mouse


title: 200550980035_R08C01

status: Public on Aug 01 2018

type: genomic

city: Atlanta

first: Sarah

middle: Whelan

last: Curtis

state: GA

address: 101 Woodruff Circle NE, Ste 42

country: USA

institute: Emory University

description: HumanMethylationEPIC BeadChip - standard protocol

hyb_protocol: HumanMethylationEPIC BeadChip

scan_protocol: BeadStudio

data_processing:
non-normalized, background subtracted
beta-values

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral Blood

label_protocol: not provided

extract_protocol:
AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA)
bisulfite conversion protocol: EZ DNA Methylation-GoldTM Kit (Zymo Research, Irvine, CA)

tag: tissue

value: Peripheral Blood

tag: gender

value: Male

tag: age

tag: ln(totalpbb)


title: 200550980035_R07C01

value: Female


title: 200550980035_R06C01


title: HPV 16 Negative and HIV positive cases Sample2

type: RNA

city: trivandrum

first: Radhakrishna

middle: Madhavan

last: Pillai

state: KERALA

address: poojappura

department: Cancer Research Program

country: India

institute: Rajiv Gandhi Centre for Biotechnology

description: microRNA expression from human cervical cells

hyb_protocol: The labeled RNA was quantified, fractionated and hybridized to the miRNA microarray according to the standard procedures provided by the manufacture.The chips were washed and stained using a Genechip Fluidics Station 450 (Affymetrix, Santa Clara, California, United States).

scan_protocol: The chips were then scanned with an Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, California, United States).

data_processing: The Data generated from the scan was then analyzed using the Affymetrix GeneChip® Command Console™ Software, v1.1, and the Affymetrix GeneChip® Expression Console software, v 1.1

label: biotin

molecule: total RNA

source_name: Human cervical smear collected with cyto brush

label_protocol: The RNA samples were labeled with the Genisphere FlashTag Biotin HSR RNA labeling kit (Genisphere, Hatfield, United Kingdom).

growth_protocol: The Cervical cells were collected from the subjects in preservecyt medium

extract_protocol: Total RNA was isolated using Ambion MiRVAna Kit according to the manufacturer's instructions.

treatment_protocol: The cervical cells were pelleted down at approximately 6000 rpm and used for isolating Total RNA

value: Cervical cells

value: female

value: 24 years


title: 200550980035_R01C01


title: 200550980035_R03C01


title: 200550980035_R04C01


title: 200550980035_R05C01


title: HPV 16 Negative and HIV positive cases Sample1

value: 37 years


title: 200550980034_R07C01


title: 200550980034_R06C01


title: PDX-C69 transduced with CDK19 shRNA

description: gene expression from PDX-C69 transduced with CDK19 shRNA


title: 200550980034_R05C01


title: PDX-C69 transduced with CDK8 shRNA

description: gene expression from PDX-C69 transduced with CDK8 shRNA


title: 200550980034_R04C01


title: 200550980034_R03C01


title: Healthy Population Control sample 2 (HIV and HPV Negative cases)

value: 36 years


title: Healthy Population Control sample 1 (HIV and HPV Negative cases)

value: 40 years


title: 200550980034_R02C01


title: 200550980035_R02C01


title: 200550980034_R01C01


title: 200550980025_R08C01


title: 200550980025_R07C01


title: 200550980025_R06C01


title: SHC_2

city: Seoul

first: DONG-MYUNG

last: SHIN

address: Pungnap-2 dong, Songpa-gu

department: Department of Biomedical Sciences

country: South Korea

institute: University of Ulsan College of Medicine

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC).

label: biotin-labeled with TdT

source_name: Human umbilical cord blood-derived mesenchymal stem cells(MSCs)

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Human UCB-MSCs used in the present study were grown in Minimum Essential Medium-a (MEM-a, Gibco, Carlsbad, Grand Island, NY)  supplemented with 2mM L-glutamine, 20mM 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES) (pH7.3), minimum essential medium(MEM) nonessential amino acid solution, penicillin/streptomycin(Corning Cellgro; Thermo Fisher Scientific, Inc., Waltham, MA, USA), 1mg/ml ascorbic acid (Sigma-Aldrich), 10% heat-inactivated fetal bovine serum(FBS) (Hyclone) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol: Total RNA from various cells was isolated using the RNeasy Mini Kit (QIAGEN, Valencia, CA), including treatment with DNase I (QIAGEN)

treatment_protocol: MSCs cultured under SHC procedure (SHC) were cultivated under 3 % hypoxic condition in MEM-a medium supplemented with 1.8 mM calcium and 10% fetal bovine serum (FBS, Gibco). For control, normally cultured naïve MSCs were used.

value: Umbilical cord blood

tag: cell type

value: Mesenchymal stem cell


title: SHC_1


title: NT_1

description: control replicate#1


title: NT_2

description: control replicate#2


title: 200550980025_R05C01


title: DU145

city: Shinjuku-ku

first: Hiroshi

last: Hongo

state: Tokyo

address: 35, Shinanomachi

department: Urology

country: Japan

institute: Keio University School of Medicine

description: SAMPLE 1

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized on the GeneChip Human Gene 2.0 ST Array using  the GeneChip Hybridization Oven 645. GeneChips were washed and stained in the  GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console v1.4(Affymetrix) and Transcriptome Analysis Console v3.1 (Affymetrix). RMA was used as summarization algorithm.

source_name: Prostate cancer

label_protocol: cDNA synthesis, amplification and labeling were performed with WT PLUS Reagent Kit (Affymetrix).

growth_protocol: DU145, and DU145CR were routinely maintained in RPMI-1640 (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (Dainippon Pharmaceutical, Tokyo, Japan) at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol: Total RNA was isolated purified using RNeasy Mini kit (Qiagen).

treatment_protocol: DU145CR cells were were grown and passaged upon reaching confluence in medium containing CBZ over a 18-month period. Examinations were performed after 3 months without CBZ exposure.

tag: cell line

value: Prostate cancer

value: prostate

tag: phenotype

value: control


title: 200550980025_R03C01


title: 80 (Invasive front adenocarcinoma)

city: Herlev

first: Rikke

middle: Karlin

last: Jepsen

state: Danmark

address: Herlev Ringvej 75

department: Dept. Pathology

country: Denmark

institute: University Hospital of Copenhagen, Herlev and Gentofte Hospital

description: miRNA expression data from invasive front of pT1pN+ colorectal cancer

hyb_protocol: and hybridized 17 hours at 48°C to GeneChip® miRNA 2.0 arrays (Affymetrix, CA).

scan_protocol: The arrays were washed and stained with Affymetrix Fluidics Station 450 and scanned on an Affymetrix G7 scanner

data_processing:
Initial data analysis was done using the justRMA function in the Bioconductor package (open source software for bioinformatics), based on R (R Development Core Team, Vienna, Austria, http://www.R-project.org)
Intensity measures were adjusted for background and normalized by the quantile method with the resulting expression levels on a log scale base 2

label: Biotin

source_name: Invasive front adenocarcinoma

label_protocol: 400 ng of miRNA was labeled using FlashTag HSR™ Biotin RNA Labeling Kit (Genisphere, PA)

extract_protocol: Total RNA was extracted using the FFPE miRNeasy Kit (Qiagen, Germany) according to manufacturer´s instructions and carried out in batches including both LNM positive and negative tumors

treatment_protocol: Invasive tumor front ares with tumor cellularity of at least 50%, was identified using hematoxylin and eosin stained tumor slides. Formalin fixed paraffin embedded CRC tissue was isolated using a 1-2 mm hollow needle.

tag: pt category according to uicc

tag: pn category (metastatic status according to uicc)

value: pN+

tag: risk-factor lymphovascular invasion (0=no, 1=yes)

tag: risk-factor venous invasion (0=no, 1=yes)

tag: risk factor

value: tumor budding, 1=low grade, 2=high grade:1


title: 79 (Invasive front adenocarcinoma)

value: tumor budding, 1=low grade, 2=high grade:2


title: DU145CR

description: SAMPLE 2

value: cabazitaxel-resistant


title: 77 (Invasive front adenocarcinoma)


title: 78 (Invasive front adenocarcinoma)


title: 81 (Invasive front adenocarcinoma)


title: 74 (Invasive front adenocarcinoma)


title: 72 (Invasive front adenocarcinoma)


title: 73 (Invasive front adenocarcinoma)


title: 69 (Invasive front adenocarcinoma)


title: 75 (Invasive front adenocarcinoma)


title: 71 (Invasive front adenocarcinoma)


title: 70 (Invasive front adenocarcinoma)


title: 200550980025_R01C01

value: Peripheral Blood

value: Male


title: 200550980010_R08C01

value: Female


title: 200550980010_R07C01


title: 200550980025_R04C01


title: 200550980010_R06C01


title: 200550980025_R02C01


title: 200550980010_R04C01


title: 200550980010_R05C01


title: 67 (Invasive front adenocarcinoma)


title: 68 (Invasive front adenocarcinoma)


title: 200550980010_R03C01


title: 200550980010_R01C01


title: 200550980002_R07C01


title: 200550980002_R06C01


title: 200550980002_R05C01


title: 65 (Invasive front adenocarcinoma)


title: 200550980002_R04C01


title: 200550980002_R08C01


title: 61 (Invasive front adenocarcinoma)


title: 62 (Invasive front adenocarcinoma)


title: 200550980002_R02C01


title: 64 (Invasive front adenocarcinoma)


title: 200550980002_R01C01


title: 60 (Invasive front adenocarcinoma)


title: 56 (Invasive front adenocarcinoma)

description: miRNA expression data from invasive front of pT3pN+ colorectal cancer


title: Saccharomyces_Li_K

type: SRA

city: Cambridge

first: Giovanni

last: Marsico

address: Robinson Way

country: United Kingdom

institute: CRUK Cambridge Institute

description: G4-seq protocol

library_source: genomic

data_processing:
library strategy: Other (G4-Seq2: modified DNA-Seq)
Fastq files (Read-1) containing 150 bp single-end reads were aligned to the humang genome (hg19) using bwa mem. Read-2 files were assigned to the same genomic location of the corresponding Read-1 files.
Bam alignment files were converted to bed files and processed with bedtools: 1) bamToBed conersion; 2) bed file expansion (slopBed -s -r 30); 3) grouping to keep only best alignments (groupBy -g 4 -c 5 -o max); 4) fasta sequence extraction (bedtools getfasta -s)
fasta sequence files and original fastq file were processed in R to compare Read-1 to Read-2 files: sequence tails beyond poly-A (>9) were trimmed; difference in quality score and base mismatches was calculated for each pair of reads; single-base mismatch values were averaged for all reads overlapping each aligned genomic location.
Genome_build: Genome sources;
Homo sapiens (hg19) from http://hgdownload.cse.ucsc.edu/downloads.html/
Mus Musculus (mm10) from http://hgdownload.cse.ucsc.edu/downloads.html/
Danio Rerio (danRer10) from http://hgdownload.cse.ucsc.edu/downloads.html/
Drosophila Melanogaster (dm6) from http://hgdownload.cse.ucsc.edu/downloads.html/
Caenorhabditis elegans (ce10) from http://www.wormbase.org/species/c_elegans/
Saccharomyces cerevisiae (sacCer3) from http://hgdownload.cse.ucsc.edu/downloads.html/
Leishmania major (LmjF_v6.1_all_20131105) from www.genedb.org/Homepage/Lmajor
Trypanosoma Brucei (TriTrypDB-9.0_TbruceiTREU927) from http://www.genedb.org/Homepage/Tbruceibrucei927
Plasmodium falciparum (PlasmoDB-28_Pfalciparum3D7) from http://plasmodb.org/
Arabidopsis thaliana (Arabidopsis_thaliana.TAIR10.31.dna.genome) from https://www.arabidopsis.org/
Escherichia coli (Ecoli_K12) from ftp://ftp.ensemblgenomes.org/pub/bacteria/release-34/
Rhodobacter sphaeroides from ftp://ftp.ensemblgenomes.org/pub/bacteria/release-30/. Annotation files sources: Arabidopsis thaliana (https://www.arabidopsis.org/download/index-auto.jsp?dir=%2Fdownload_files%2FGenes%2FTAIR10_genome_release%2FTAIR10_gff3)
Caenorhabditis elegans (ftp://ftp.wormbase.org/pub/wormbase/releases/WS220/species/c_elegans/)
Drosophila Melanogaster (ftp://ftp.ensembl.org/pub/release-87/gff3/drosophila_melanogaster/)
E. coli (ftp://ftp.ensemblgenomes.org/pub/bacteria/release-34/gff3/bacteria_0_collection/escherichia_coli_str_k_12_substr_mg1655/)
Homo sapiens (USCS annotation for genes:  http://emea.support.illumina.com/sequencing/sequencing_software/igenome.html
Gencode annotation for non-coding RNAs: https://www.gencodegenes.org/releases/19.html)
Leishmania major( ftp://ftp.sanger.ac.uk/pub/project/pathogens/gff3/CURRENT)
Mus musculus (ftp://ftp.ensembl.org/pub/release-87/gff3/mus_musculus/)
Plasmodium falciparum (http://plasmodb.org/common/downloads/release-28/Pfalciparum3D7/gff/data/)
Rhodobacter sphaeroides (ftp://ftp.ensemblgenomes.org/pub/bacteria/release-30/gff3/bacteria_0_collection/rhodobacter_sphaeroides_2_4_1/)
Saccharomyces cerevisiae (ftp://ftp.ensembl.org/pub/release-87/gff3/saccharomyces_cerevisiae/)
Trypanosoma brucei (ftp://ftp.sanger.ac.uk/pub/project/pathogens/gff3/CURRENT)
Danio rerio (ftp://ftp.ensembl.org/pub/release-87/gff3/danio_rerio/).
Supplementary_files_format_and_content: bedgraphs for coverage and mismatch levels; bed files for scoring G-quadruplexes (separated by strand)

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: Organisms were cultured in standard conditions, withouth any treatment.

extract_protocol:
DNA was extracted with standard phenol/chloroform extraction as previously described in Chambers et. al 2015 (doi: 10.1038/nbt.3295), except for samples where DNA was purchased from companies (see source and characteristics field).
Genomic DNA samples were  sonicated and the library prepared, as in Chambers et al. 2015 (doi: 10.1038/nbt.3295). Libraries were prepared using the TruSeq Nano DNA LT Library Prep Kit (Nano in each sample file name), or with PCR-Free Library Prep Kit (PCRFree or not specified in each sample file name).

treatment_protocol: All samples were untreated, wild type organisms.

value: whole cell


title: 59 (Invasive front adenocarcinoma)


title: 55 (Invasive front adenocarcinoma)


title: 53 (Invasive front adenocarcinoma)


title: 54 (Invasive front adenocarcinoma)


title: 200550980002_R03C01


title: 57 (Invasive front adenocarcinoma)


title: 58 (Invasive front adenocarcinoma)


title: Saccharomyces_Li_KPDS

description: G4-seq protocol


title: 51 (Invasive front adenocarcinoma)


title: 49 (Invasive front adenocarcinoma)


title: 50 (Invasive front adenocarcinoma)


title: HeLa 4MU-xyloside 16h rep3

city: Ako

first: Hiderou

last: Yoshida

state: Hyogo

address: Kamigori, Koto 3-2-1

department: Life Science

institute: University of Hyogo

description: Gene expression after 16hr in 4MU-xyloside-treated HeLa cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer (Gene Expression Hybridization Kit) was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K v2 Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffers Pack (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HeLa cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HeLa cells were cultured in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using Sepasol-RNAⅠSuper G (Nacalai, Japan) and purified through the RNeasy mini kit (QIAGEN, Valencia, CA) following the manufacturers' recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: HeLa cells were treated with DMSO or 4MU-xyloside for 16 h in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

value: HeLa cells (cervical cancer)

value: female

tag: treatment

value: 7.5mM 4MU-xyloside, 16h


title: HeLa control 16h rep3

description: Gene expression after 16hr in DMSO-treated HeLa cells

value: DMSO, 16h


title: HeLa 4MU-xyloside 16h rep2


title: 46 (Invasive front adenocarcinoma)


title: 48 (Invasive front adenocarcinoma)


title: HeLa control 16h rep2


title: HeLa 4MU-xyloside 16h rep1


title: Drosophila_Li_K

description: G4-seq protocol

organism: Drosophila melanogaster

source_name: whole organism

value: whole organism


title: 52 (Invasive front adenocarcinoma)


title: 47 (Invasive front adenocarcinoma)


title: HeLa control 16h rep1


title: Drosophila_Li_KPDS

description: G4-seq protocol


title: 44 (Normal colorectal stroma)

description: miRNA expression data from normal colorectal stroma

source_name: Normal colorectal stroma

value: not relevant

value: tumor budding, 1=low grade, 2=high grade:not relevant


title: Sigma IVS10  - W5 - sample 53521

city: Beerse

first: An

last: De Bondt

address: Turnhoutseweg 30

country: Belgium

institute: Janssen Pharmaceutica

hyb_protocol: Target hybridization was processed on the GeneTitan® Instrument according to the instructions provided in the User Guide for Expression Array Plates (P/N 702933).

scan_protocol: Images were analyzed using the GeneChip® Command Console Software (AGCC) (Affymetrix).

data_processing: All microarray data were processed using the statistical computing program R (R version 3.2.2) as well as Bioconductor tools. The gene expression values were normalized using RMA. Grouping of the individual probes into gene-specific probe sets was performed based on Entrez Gene using the metadata package hgu219hsentrezg (version 20.0.0).

source_name: hiPSC derived neurons

label_protocol: All microarray-related steps for target preparation, including the amplification of total RNA and labeling, were carried out as described in the GeneChip®3’ IVT Express Kit User Manual (Affymetrix 2004). Biotin-labeled target samples were hybridized to the GeneChip® HG-U219 containing probes for 18492 genes.

growth_protocol: Human iPSC’s were cultured feeder-free and fed daily with fresh mTeSR™1 medium (Stem Cell Technologies). Cells were passaged with EDTA (Gibco) at confluency and differentiation into neural progenitor cells (NPCs) and cortical neurons was performed using an adapted dual SMAD inhibition protocol. For functional calcium experiments, neurons were co-cultured with human primary astrocytes (ScienCell™) that were cultured and passaged per manufacturer’s instructions (in human astrocyte medium, ScienCell™). Control and ZFN gene edited lines are deposited in EBiSC (https://cells.ebisc.org) as SIGi001-A (parental control, female), SIGi001-A-9 (IVS10+16 bi-allelic + P301S bi-allelic), SIGi001-A-12 (IVS10+16 bi-allelic) and SIGi001-A-13 (IVS10+16 mono-allelic). Patient-derived lines (IVS10+16 mono-allelic) V97 and TSM were kindly provided by Dr. Selena Wray. Both female patients were pre-symptomatic at the time of biopsy.

extract_protocol: Cells were lysed using RLT buffer (Qiagen) and RNA extracted with the RNeasy 96 kit (p/n 74181 Qiagen).

treatment_protocol: Gene editing was performed by Sigma Aldrich on their in-house control human iPSC line (cat#IPSC0028).

value: hiPSC derived neurons

value: Sigma IVS10

tag: time (hours)


title: 66 (Invasive front adenocarcinoma)

value: pN+


title: 42 (Normal colorectal stroma)


title: Celegans_Li_KPDS

description: G4-seq protocol

organism: Caenorhabditis elegans

tag: strain or cell type

value: N2 strain


title: 45 (Invasive front adenocarcinoma)

value: tumor budding, 1=low grade, 2=high grade:1


title: 41 (Normal colorectal mucosa)

description: miRNA expression data from normal colorectal mucosa

source_name: Normal colorectal mucosa


title: Sigma CTR - W5 - sample 53519

value: Sigma CTR


title: RB16, Passage 5

city: Silver Spring

first: Ian

last: Bellayr

state: Maryland

address: 10903 New Hampshire Ave

institute: FDA

hyb_protocol: Assembled slide chambers were placed in the hybridization oven set to 55oC with a rotator speed of 20rpm for 20 hours.  See manuscript for more detailed description

scan_protocol: All images were produced using the DNA microarray scanner with surescan high-resolution technology (Agilent Technologies).  Slides were scanned at 446 nm for the Cy3 dye and a resolution of 2 µm double pass.  See manuscript for more detailed description

data_processing:
The spots were annotated through the Agilent Feature Extraction (AFE) 11.0 software.  All methods and analyses used in this study were implemented in JMP Genomics, which included normalization, principle component analysis, clustering, box plots and statistics.  See manuscript for more detailed description.
Data was normalized by the quantile normalization method.

source_name: MSC Bone Marrow Derived_Passage 5

label_protocol: Individual RNA material was labeled with Cy3.

growth_protocol: MSCs were expanded at initial plating densities of ~60 cells/cm2 using standard MSC growth medium (alpha-minimum essential media (αMEM), 1% L-glutamine, 1% penicillin-streptomycin (PS), 16% fetal bovine serum (FBS)) following established protocols.

extract_protocol: Total RNA were isolated from samples using the RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer’s protocols.

treatment_protocol: Upon reaching ~80% confluence, cells were lifted and re-plated at their same initial plating densities, which is designated as one “passage”.

tag: donor id

tag: age (years)

value: Bone Marrow

value: mesenchymal stem cells (MSC)

tag: passage

value: Passage 5


title: Sigma IVS10  - W5 - sample 53520

tag: tissue


title: Celegans_Li_K

description: G4-seq protocol


title: 43 (Normal colorectal stroma)


title: 40 (Normal colorectal mucosa)


title: Sigma CTR - W5 - sample 53518


title: LM2 sh-hnRNPM

city: Houston

first: Samuel

middle: Emerson

last: Harvey

state: TEXAS

address: One Baylor Plaza

department: Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

description:
control_and_hnRNPM_KD_fpkm.txt
LM2_HNRNPM_KD

library_source: transcriptomic

data_processing:
Paired-end RNA-seq reads for each sample were mapped to the human genome (GRCh37) and transcriptome (Gencode v24 backmapped to GRCh37) using STAR v2.5.3a using the following command: STAR --runThreadN 16 --alignEndsType EndToEnd –outSAMtype BAM SortedByCoordinate --readFilesCommand zcat
Gene expression quantification and differential gene expression was conducted for all samples using cuffdiff v2.2.1 using the following command: cuffdiff -p 8 –max-bundle-frags 1000000000 --library-type fr-firststrand -o output_dir gencode.v24lift37.annotation.gtf
Alternative splicing quantification and differential analysis was conducted for all samples using rMATS v3.2.5 using the following command: python RNASeq-MATS.py -gtf gencode.v24lift37.annotation.gtf -o output_dir  -t paired -len 100 -analysis U -libType fr-firststrand
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited file with FPKM for each gene in each sample (file was filtered to remove any genes with zero values in all four samples)

source_name: MDA-MB-231 LM2 (4175) cells

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS, L-glutamine, Penicillin, and Streptomycin

extract_protocol:
Total RNA was extracted using standard Trizol extraction procedures
Stranded paired-end polyA-purified RNA sequencing libraries were prepared using Illumina TruSeq protocols

treatment_protocol: Cell lines stably expressing the relevant shRNA were generated using lentiviral vectors using standard infection protocols

value: Triple-negative human breast cancer cells, lung metastasis derivative

value: MDA-MB-231 LM2 (4175) cells

value: hnRNPM shRNA treated

tag: genotype

value: hnRNPM knockdown


title: LM2 control

description:
control_and_hnRNPM_KD_fpkm.txt
LM2_control

value: Non-specific shRNA treated

value: control


title: RB12, Passage 5

tag: gender

value: Male


title: RB16, Passage 2

source_name: MSC Bone Marrow Derived_Passage 2

value: Female

tag: cell type

value: Passage 2


title: Sigma IVS10  - W5 - sample 53522

value: hiPSC derived neurons

value: Sigma IVS10


title: 39 (Normal colorectal mucosa)

value: not relevant

value: tumor budding, 1=low grade, 2=high grade:not relevant


title: Sigma CTR - W5 - sample 53517

value: Sigma CTR


title: BM1 control

description:
control_and_hnRNPM_KD_fpkm.txt
BM1_control

source_name: MDA-MB-231 BM1 (1833) cells

value: Triple-negative human breast cancer cells, bone metastasis derivative

tag: cell line

value: MDA-MB-231 BM1 (1833) cells


title: RB12, Passage 2

value: Bone Marrow

value: mesenchymal stem cells (MSC)


title: RB14, Passage 5

value: Passage 5


title: RB14, Passage 2


title: 38 (Invasive front adenocarcinoma)

description: miRNA expression data from invasive front of pT1pN0 colorectal cancer

value: tumor budding, 1=low grade, 2=high grade:1


title: BM1 sh-hnRNPM

description:
control_and_hnRNPM_KD_fpkm.txt
BM1_HNRNPM_KD

value: hnRNPM shRNA treated

value: hnRNPM knockdown


title: 36 (Invasive front adenocarcinoma)


title: 37 (Invasive front adenocarcinoma)

value: tumor budding, 1=low grade, 2=high grade:2


title: Sigma CTR - NPC - sample 53513

value: NPC


title: PCBM1641, Passage 5

value: Female


title: Sigma IVS10  - NPC - sample 53516


title: 34 (Invasive front adenocarcinoma)


title: Sigma IVS10  - NPC - sample 53515


title: Sigma CTR - NPC - sample 53512


title: Sigma IVS10  - NPC - sample 53514


title: RB09, Passage 5

value: Male


title: 35 (Invasive front adenocarcinoma)


title: 33 (Invasive front adenocarcinoma)


title: RB09, Passage 2

value: Passage 2


title: PCBM1632, Passage 5


title: 32 (Invasive front adenocarcinoma)


title: PCBM1641, Passage 3

source_name: MSC Bone Marrow Derived_Passage 3

value: Passage 3


title: Patient IVS10 TSM - NPC - sample 53524

value: hiPSC derived neurons

value: Patient IVS10 TSM


title: PCBM1632, Passage 3


title: Patient IVS10 TSM - NPC - sample 53523


title: Patient IVS10 TSM - NPC - sample 52258


title: 31 (Invasive front adenocarcinoma)


title: 167696, Passage 3


title: Early morula_1

city: Storrs

first: Xiuchun

last: Tian

state: CT

address: 1390 Storrs Road, ABL220D

department: Animal Science

institute: University of connecticut

data_processing:
Multiplexed sequencing reads were first trimmed to remove low-quality bases and adaptor sequences using the Trim_galore tool. The clean reads were then aligned to the bisulfite-converted reference bovine genome UMD3.1.1 (bosTau8) using Bismark alignment tools (version 0.16.3) with default parameters. Once the alignment was completed, the sorted BAM files were generated by Picard toolkit and a pileup file of mapped data was created for DNA methylation calculation.
The methylation levels of each sampled cytosine were estimated as the number of reported C (‘methylated’ reads) divided by the sum of reported C (‘methylated’ reads) and T (‘unmethylated’ reads) at the same positions of the reference genome.
Genome_build: UMD3.1.1
Supplementary_files_format_and_content: text file with methlyation levels

organism: Bos taurus

source_name: Early morula

extract_protocol:
Individual gamtes and embryos were lysis in a single tubes to obtain DNA using protease.
We conducted DNA extraction, MspI digestion, end-repair, dA-tailing, adaptor ligation, bisulfite conversion, and PCR amplification libraries in single tubes to minimize DNA loss.

treatment_protocol: Frozen bovine sperm were collected from a bull with proven fertility; Germinal vesicle stage and in vitro matured oocytes were produced using slaughterhouse ovaries; For embryo collection, multiparous Holstein cows (n = 10) were synchronized and superovulated. Artificial insemination using semen from a bull with proven fertility was conducted at 12 and 24 hours post standing heat (Day 0). Donor animals were sacrificed at 30 hours, and 2-4 days after estrus to collect in vivo developed oocytes and embryos at the 2- to 8-cell stages by oviductal flushing. Early/compact morulae and blastocysts were collected by routine non-surgical uterine flushing on Days 5, 6 and 7.

tag: strain

value: Holstein

value: Early morula


title: 8-cell_3


title: 30 (Invasive front adenocarcinoma)

tag: pt category according to uicc


title: Sigma CTR - NPC - sample 53511

value: Sigma CTR


title: SMN HITS-CLIP, replicate 2

city: Ames

first: Ravindra

middle: N

last: Singh

state: IA

address: 2034 Veterinary Medicine

department: Biomedical Sciences

institute: Iowa State University

data_processing:
Adapter sequences were removed using cutadapt
Duplicate removal using fastx toolkit
Sequences were mapped using Tophat
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig file showing read depth. File is available on the series record.

source_name: SH-SY5Y cells

growth_protocol: Cells were grown in 150 mm dishes in 1:1 mixture of MEM and F12 growth media supplemented with 10% FBS

extract_protocol:
Custom
Illumina TruSeq small RNA with modifications

treatment_protocol: Cells were washed 2X in ice-cold PBS and exposed to 150 mJ/cm2 prior to collection

tag: clip antibody

value: SMN monoclonal clone 8

tag: antibody information

value: BD Transduction Laboratories, catalog number 610647


title: Early morula_2


title: SMN HITS-CLIP, replicate 1


title: SMN HITS-CLIP, replicate 3


title: In vitro_MII oocyte_1

source_name: MII oocyte

value: MII oocyte


title: In vitro_MII oocyte_3


title: Patient IVS10 V97 - NPC - sample 52256

value: Patient IVS10 V97


title: 29 (Invasive front adenocarcinoma)

tag: pn category (metastatic status according to uicc)

tag: risk-factor lymphovascular invasion (0=no, 1=yes)

tag: risk-factor venous invasion (0=no, 1=yes)

value: tumor budding, 1=low grade, 2=high grade:1


title: Immature oocyte_3

source_name: Immature oocyte

value: Immature oocyte


title: Patient IVS10 V97 - NPC - sample 52257

tag: treatment

tag: time (hours)


title: 26 (Invasive front adenocarcinoma)

tag: risk factor


title: 167696, Passage 5

tag: donor id

tag: age (years)

value: Bone Marrow

value: mesenchymal stem cells (MSC)

value: Passage 5


title: 63 (Invasive front adenocarcinoma)

value: pN+

value: tumor budding, 1=low grade, 2=high grade:2


title: 28 (Invasive front adenocarcinoma)


title: 27 (Invasive front adenocarcinoma)


title: 25 (Invasive front adenocarcinoma)


title: Patient IVS10 TSM - W5 - sample 52253

tag: tissue


title: Patient IVS10 TSM - W5 - sample 52254


title: 8F3560, Passage 5

value: Female

tag: passage


title: Patient IVS10 V97 - NPC - sample 52255

value: hiPSC derived neurons

value: NPC


title: 8F3560, Passage 3

tag: gender

value: Passage 3


title: 24 (Invasive front adenocarcinoma)


title: 23 (Invasive front adenocarcinoma)


title: Immature oocyte_1

value: Holstein


title: Patient IVS10 TSM - W5 - sample 52252

value: Patient IVS10 TSM


title: Sperm_3

source_name: Sperm

value: Sperm


title: 76 (Invasive front adenocarcinoma)

source_name: Invasive front adenocarcinoma


title: Immature oocyte_2


title: Sperm_2


title: Patient IVS10 V97 - W5 - sample 52251


title: Patient IVS10 V97 - W5 - sample 52250


title: Patient IVS10 V97 - W5 - sample 52249


title: 21 (Invasive front adenocarcinoma)


title: coculture vs monoculture Dh replicate 2 at 27 h

city: Thiverval Grignon

first: Reine

last: Malek

address: Avenue Lucien Brétignières

country: France

institute: INRA, UMR 1319 MICALIS

hyb_protocol: Hybridizations were performed for 17h at 65°C in dedicated micro-chambers with 300 ng of the different labelled samples.hybridization buffer was from Agilent (ref 5188-5242)

scan_protocol: Agilent G2565 Scanner in extended dynamic range with a resolution of 5nm per pixel

data_processing: Intensity-dependent normalization was performed with the LOESS procedure followed by subtraction of the log-ratio median calculated over the values for an entire block from each individual log-ratio using the anapuce package of R. Differential analysis was performed with the varmixt package of R. the raw P values were adjusted by the Bonferroni method

organism: Debaryomyces hansenii

source_name: growth on coculture with Yarrowia lipolytica

label_protocol: RNA was labeled using two different fluorescent dyes: cyanine 3-CTP and cyanine 5-CTP as described in the Agilent Low Input Quick Amp labeling Kit.

growth_protocol: D. hansenii cells were grown up to 120h in pure culture or in coculture with Yarrowia lipolytica

extract_protocol: Total RNA was extracted by trizol treatment following manufacturer's instructions (Invitrogen, Carlsbad, CA, USA)

tag: growth

value: coculture with Yarrowia lipolytica

tag: time point

source_name: growth on pure culture

value: pure culture


title: coculture vs monoculture Dh replicate 4 at 27 h


title: 20 (Invasive front adenocarcinoma)


title: coculture vs monoculture Dh replicate 3 at 27 h


title: coculture vs monoculture Dh replicate 2 at 12 h


title: coculture vs monoculture Dh replicate 4 at 12 h


title: 19 (Invasive front adenocarcinoma)


title: 22 (Invasive front adenocarcinoma)


title: Sperm_1

tag: strain


title: MR2E3_A: Male WSR2 EtOH 3

city: Portland

first: Marina

last: Guizzetti

state: OR

address: 3710 SW US Veterans Hospital Rd

department: Behavioral Neuroscience

institute: Oregon Health & Science University; Portland VA Research Service

hyb_protocol: Hybridization with complex labeled RNA probe was performed overnight at 50° C with Microhyb hybridization buffer.

scan_protocol: Microarrays were exposed to storage phosphor screens for 2d and scanned at high resolution with a Cyclone phosphorimager and OptiQuant software (Perkin Elmer).

data_processing: Raw intensity values, determined with ArrayPro Analyzer 4.5 (MediaCybernetics) and were further processed and analyzed in R. Raw expression values were log2 transformed and normalized by quantiles. Clones with hybridization intensities below background on more than 10% of the arrays were excluded and batch effects were removed using the ‘sva’ package (Leek et al., 2012). Ethanol regulated genes were determined using the empirical Bayes function of the ‘LIMMA’ package (McCarthy and Smyth, 2009; Ritchie et al., 2015).

organism: Mus musculus

source_name: prefrontal cortex

label_protocol: DNase treated total RNA isolated from the PFC of two animals (2.5 micrograms each) was pooled for each complex probe labeling reaction.  For each array hybridization, 2.5 µg of total RNA from two animals from the same selected line and treatment group was pooled for a total of 5 µg and complex probe was generated by linear synthesis with 33P-dCTP using SuperScript II Reverse Transcriptase. Labeled probes were  purified using Biospin P-30 columns.

extract_protocol: Total RNA was extracted from the PFC using RNA  STAT-60 (Tel-Test, Inc.) according to the manufacturers protocol.  Contaminating genomic DNA was  removed by digestion with Rnase free Dnase followed by Zymo-spin column purification according to the manufacturer's recommendations (Zymo Research).

treatment_protocol: Two independently derived replicate Withdrawal-Seizure Resistant (WSR) were derived by selective breeding for divergent withdrawal severity from genetically heterogeneous HS/Ibg mice.  Male mice from both replicates were tested for expression differences.  Mice were maintained under a light/dark cycle of 0600-1800 light with water and Purina Lab Diet Chow available ad libitum.  Room temperatures were maintained at 22 +/- 1 degree celcius.  All animal procedures were approved by the Portland Oregon VA Medical Center Institutional Animal Care and Use committee and followed US National Institutes of Health animal welfare guidelines.  Mice were made dependent upon Ethanol (EtOH) using a method of vapor inhalation in chambers manufactured in-house, with modifications previously published (Beadles-Bohline and Wiren, 2006).  Drug-naive adult mice were used.  EtOH exposure was initiated at 0800 h.  On day one EtOH mice were weighed, injected i.p. with EtOH at 1.5 g/kg and 68.1 mg/kg pyrazole HCl.  Control animal were placed into air chambers and received pyrazole only.  All mice again received pyrazole (68.1 mg/kg) at 24 h and 48 h to reduce fluctuations in BEC.  EtOH exposed mice had 20 microliters of blood take from the tail for daily BEC determination.  Following 72 h of constant EtOH vapor exposure, all mice were removed from the chambers, weighed, and had tail blood samples drawn for BEC determination by gas chromatography as previously described.  Prefronal cortex (PFC) was isolated by dissection from whole brain by first discarding the olfactory bulb and making a coronal slice 2 mm into the frontal region of the cortex.  Lateral regions were removed by cutting the tissue at a 45 degree angle with the lobes facing upward.

value: prefrontal cortex

value: Ethanol vapor

tag: time

value: 21d withdrawal


title: WK7  -  IVS10+16/P301S  -  sample50282

tag: time (weeks)


title: 17 (Invasive front adenocarcinoma)

tag: pt category according to uicc

value: tumor budding, 1=low grade, 2=high grade:1


title: coculture vs monoculture Dh replicate 3 at 12 h


title: In vivo_MII oocyte_3

value: MII oocyte


title: 18 (Invasive front adenocarcinoma)

tag: pn category (metastatic status according to uicc)


title: WK7  -  IVS10+16/P301S  -  sample50283


title: In vitro_MII oocyte_2


title: 16 (Invasive front adenocarcinoma)

tag: risk-factor lymphovascular invasion (0=no, 1=yes)


title: In vivo_MII oocyte_2


title: 8-cell_2


title: In vivo_MII oocyte_1


title: 4-cell_3


title: 4-cell_2


title: MR2E2_A: Male WSR2 EtOH 2


title: coculture vs monoculture Dh replicate 1 at 27 h


title: 4-cell_1


title: WK7  -  IVS10+16 +/+  -  sample50272


title: coculture vs monoculture Dh replicate 1 at 12 h


title: WK7  -  IVS10+16/P301S  -  sample50281


title: WK7  -  IVS10+16 +/+  -  sample50274


title: 15 (Invasive front adenocarcinoma)

tag: risk-factor venous invasion (0=no, 1=yes)


title: MR1E2_A: Male WSR1 EtOH 2

tag: treatment


title: MR1E1_A: Male WSR1 EtOH 1


title: WK7  -  IVS10+16 +/+  -  sample50273


title: 2-cell_3


title: WK7  -  IVS10+16 +/-  -  sample50271


title: 14 (Invasive front adenocarcinoma)

description: miRNA expression data from invasive front of pT3pN0 colorectal cancer


title: MR2A2_A: Male WSR2 Air 2

value: Control


title: WK7  -  IVS10+16 +/-  -  sample50270


title: 2-cell_2


title: MR2A1_A: Male WSR2 Air 1


title: WK7  -  IVS10+16 +/-  -  sample50269


title: 10 (Invasive front adenocarcinoma)


title: WK7  -  CTR  -  sample50267

value: CTR


title: 13 (Invasive front adenocarcinoma)


title: WK7  -  CTR  -  sample50268


title: 12 (Invasive front adenocarcinoma)


title: 11 (Invasive front adenocarcinoma)


title: 9 (Invasive front adenocarcinoma)


title: 2-cell_1


title: 8 (Invasive front adenocarcinoma)


title: Early morula_3

value: Early morula


title: Bdellovibrio with S aureus biofilm 3

city: Ulsan

first: Hansol

last: Im

address: UNIST gil 50st

institute: Ulsan National Institute of Science and Technology

data_processing:
Base-calling using the CLRNASeqTM program (ChunLab, South Korea)
The RNA sequencing reads in each sample were normalized using the RPKM method
Genome_build: NCBI Reference Sequence: NC_005363.1, Bioproject name : PRJNA224116
Supplementary_files_format_and_content: The excel file which include whole information of total reads, RPKM, RLE, TMM normalization. Actual publication would be conducted with RPKM version

organism: Bdellovibrio bacteriovorus HD100

source_name: Bdellovibrio bacteriovorus HD100

growth_protocol: The predatory bacterium Bdellovibrio bacteriovorus was maintained using E. coli MG1655 as the prey in HEPES buffer with CaCl2 and MgCl2 salts added (4 mM and 2 mM, respectively) , as mentioned at previous report,  'Attack-Phase Bdellovibrio bacteriovorus Responses to Extracellular Nutrients Are Analogous to Those Seen During Late Intraperiplasmic Growth'

extract_protocol:
Overnight cultures of B. bacteriovorus grown on E. coli MG1655 were filtered (0.45 µM) to remove any residual prey or bdelloplasts. These cultures were mixed with either sterile HEPES or the S. aureus biofilm cultures. After 4 h at 30ºC, the B. bacteriovorus cells were filtered (0.45 µM) to remove any S. aureus, collected by centrifugation (16,000xg, 10 min) and the total cellular RNA extracted using ChargeSwitch Total RNA Cell Kits (Invitrogen) and thier manual
After qualification of RNA samples, library was constructed via Hiseq 2500 (Illumina).   Libraries for sequencing were made using the Truseq Standard mRNA sample preparation kit (Illumina, USA). The sequencing was done using single-end 50 bp sequencing on the Illumina Hiseq 2500 platform.

tag: protocol

value: Staphylococcus aureus biofilm


title: WK7  -  CTR  -  sample50266

source_name: hiPSC derived neurons


title: MR1A1_A: Male WSR1 Air 1


title: Blastocyst_3

source_name: Blastocyst

value: Blastocyst


title: 8-cell_1


title: Bdellovibrio with S aureus biofilm 1


title: WK5  -  IVS10+16/P301S  -  sample50262


title: Blastocyst_1


title: 6 (Invasive front adenocarcinoma)

tag: risk factor


title: Bdellovibrio with HEPES 3

value: HEPES


title: Bdellovibrio with HEPES 2


title: Compact morula_3

source_name: Compact morula

value: Compact morula


title: Bdellovibrio with HEPES 1


title: Blastocyst_2

value: Holstein


title: MR1A2_A: Male WSR1 Air 2


title: WK5  -  IVS10+16 +/+  -  sample50253


title: ES9: END_seq_aHCT116_8h_NT_rep1

city: Bethesda

first: Andre

last: Nussenzweig

state: MD

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

institute: National Institutes of Health

description: Control: N/A

data_processing:
Library strategy: END-seq
mouse and human reads were aligned to the GRCm38p2/mm10 and  GRCh37/hg19 genome assemblies,respectively.
Alignment done using bowtie version 0.12.7, with the parameters:   -l 25 -n 3 --best --all --strata -M 1 --tryhard –t
END-seq peaks were called using the parameters: --nolambda,-- nomodel and –keep-dup=all
Genome_build: GRCm38p2/mm10 for mouse and  GRCh37/hg19 for human
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

extract_protocol:
Single cell suspensions of B-cells (15 million per agarose plug), T-cells (15 million per agarose plug), MEFS (4 million per agarose plug), HCT116 (7.5 million per agarose plug)were washed in PBS, embedded in agarose and transferred into plug molds (Bio-Rad CHEF Mammalian Genomic DNA plug kit) and processed as previously described (Canela et al., 2016). Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads).
libraries were prepared and sequenced following standard Illumina protocols

tag: cell type

tag: genotype

value: WT


title: 5 (Invasive front adenocarcinoma)

value: tumor budding, 1=low grade, 2=high grade:2


title: Compact morula_1

tag: tissue


title: WK5  -  IVS10+16 +/+  -  sample50252


title: WK5  -  IVS10+16 +/+  -  sample50251


title: ES8: END_seq_aHCT116_8h_HU_8h_10mM_rep1

description: Control: END_seq_aHCT116_8h_NT_rep1


title: 4 (Invasive front adenocarcinoma)


title: 1 (Invasive front adenocarcinoma)


title: 7 (Invasive front adenocarcinoma)


title: WK5  -  IVS10+16 +/-  -  sample50250


title: WK5  -  IVS10+16/P301S  -  sample50260


title: Leishmania_Li_KPDS

description: G4-seq protocol

organism: Leishmania major

source_name: purified DNA from ATCC®

tag: strain or cell type

value: 30012DTM strain


title: 2 (Invasive front adenocarcinoma)


title: 3 (Invasive front adenocarcinoma)


title: WK5  -  IVS10+16/P301S  -  sample50261


title: WK5  -  IVS10+16 +/-  -  sample50248


title: WK5  -  CTR  -  sample50247


title: Compact morula_2


title: WK5  -  IVS10+16 +/-  -  sample50249


title: WK5  -  CTR  -  sample50246


title: Trypanosoma_Li_KPDS

description: G4-seq protocol

organism: Trypanosoma brucei

source_name: whole cell

value: whole cell


title: Spleens of BALB/c mouse, 28th day, OVA 2

city: Beijing

first: LI

middle: Yong

last: Ning

address: 7 Panjiayuan Nanli

country: China

institute: China National Center for Food Safety Risk Assessment

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to LncRNA+mRNA Mouse Gene Expression Microarray V1.0 for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

source_name: Spleens,28th day, OVA

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Six-week-old  female BALB/c mice were injected intraperitoneally with OVA or normal saline  at 2 mg/kg body weight for 3 times (days 1, 3, and 5). At the end of the experiment the animals were humanely sacrificed by pentobarbital anesthetization 2 hours at 14th and 28th day, separately.

extract_protocol: Total RNA containing small RNA was extracted from the snap-frozen spleens by using the Trizol reagent (Invitrogen, Carlsbad, CA, USA) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA) according to manufacturer’s  protocol.

treatment_protocol: Treatment groups of mice were injected intraperitoneally with OVA at 2 mg/kg body weight for 3 times (days 1, 3, and 5).The control groups were treated with the solvent vehicle (normal saline).

tag: gender

value: female

tag: age

value: six week

tag: sample type

value: OVA-induced allergic mouse


title: Spleens of BALB/c mouse, 28th day, OVA 3


title: Spleens of BALB/c mouse, 28th day, OVA 4


title: Trypanosoma_Li_K

description: G4-seq protocol


title: Leishmania_Li_K

description: G4-seq protocol


title: WJC3

city: New York

first: Li

last: Wang

address: 1 Gustave L. Levy Pl

institute: Icahn school of medicine at Mount Sinai

description:
processed data files:
humanBetter_count.txt; humanOnly_count.txt; mouseBetter_count.txt; mouseOnly_count.txt

data_processing:
Reads were first mapped to human and mouse genome separately using TopHat.
The Bamcmp algorithm was then used separate each read into human only, mouse only and both. The latter category was further categorized into reads aligning better to human or reads aligning better to mouse.
Genome_build: hg19,mm10
Supplementary_files_format_and_content: humanBetter_count.txt: reads mapped better to human genome; humanOnly_count.txt: reads only mapped to human genome; mouseBetter_count.txt: reads mapped better to mouse genome; mouseOnly_count.txt: reads only mapped to mouse genome;

organism:
Homo sapiens
Mus musculus

source_name: Urothelial Cancer

growth_protocol: 30 ml of peripheral blood was collected from patients with metastatic Urothelial Cancer prior to initiation of chemotherapy. Density gradient centrifugation was performed followed by isolation of circulating tumor cells through flow cytometry by depletion of CD45+ mononuclear cells and subsequent subcutaneous injection of CD45- cells into immunocompromised “NSG” mice. PDX that had undergone less than 5 passages were histologically confirmed and molecularly characterized by performing genome-wide transcriptome profiling using RNA-sequencing.

extract_protocol: Cell suspensions of tissue sections of bladder CTC PDX models were obtained from CTC-PDX tumors by mechanically triturating the sample with a sterile scalper and forceps, without enzymatic digestion. RNA was isolated using the RNeasy Mini kit (Qiagen) in accordance with manufacturer's instructions. High-quality total RNA samples (RNA Integrity score >7.7 by Agilent Bioanalyzer) were subjected to poly A-selected sequencing library preparation using TruSeq RNA Sample Prep Kit ver.2 (Illumina) following manufacturer's protocol. The libraries were sequenced by HiSeq 2500 genome sequencer (Illumina).

tag: xenograft host

value: immunocompromised NGS mice

tag: pdx model name

value: WJC

tag: tumor type

value: Urothelial Cancer


title: Microglia/Macrophages LPS rep 4

city: Montreal

first: Andrew

last: Greenhalgh

state: Quebec

address: Montreal General Hospital, 1650 Cedar Ave

country: Canada

institute: The Research Institute of the McGill University Health Center

description: Adult mouse microglia cultured for 7 days before treatments

hyb_protocol: After fragmentation and labeling, 3.5µg DNA target was hybridized on Mouse Clariom™ S Assay (ThermoFisher-Affymetrix) and incubated at 45C in the Genechip® Hybridization oven 640 (ThermoFisher-Affymetrix) for 17 hours at 60 rpm.

scan_protocol: The microarrays were finally scanned on a GeneChip® scanner 3000 (Affymetrix).

data_processing: Microarray data sets were normalized by the robust multiarray averaging (RMA) method in Affymetrix Expression Console (Affymetrix). To assess whether there were transcripts differentially expressed between activated microglia and activated microglia in the presence of macrophages, normalized data sets were compared in Affymetrix Transcriptome Analysis Console (TAC) Software.

source_name: Microglia/Macrophages LPS

label_protocol: Sense-strand cDNA was synthesized from 100 ng of total RNA, and fragmentation and labeling were performed to produce ss DNA with the Affymetrix GeneChip® WT Terminal Labeling Kit according to manufacturer’s instructions (ThermoFisher-Affymetrix)

growth_protocol: Adult microglia were re-suspended at 8x10^5 cell-mL (approximately two brains per mL) in media (DMEM F12, 10% FBS, 1% penicillin/streptomycin (P/S)) with 10% L-cell conditioned media, a source of M-CSF (or 10ng/ml recombinant mouse M-CSF [R&D cat no 416-ML-010/CF]), and 50ng/ml recombinant human TGF-β1 (Miltenyi cat no: 130-095-067)

extract_protocol: RNA was extracted using Qiagen Microkit according to manufactors instructions

treatment_protocol: Adult microglia and bone marrow-derived macrophges were cultured separately for 7 days, as described above; BMDMs were then re-plated on poly-L-lysine coated glass coverslips. Cells were plated at 2x10^5 per 25 mm coverslip (for insertion in 6 well plates) of 4x10^4 per 12 mm coverslip (for insertion in 24 well plates). Coverslips were pre-mounted with 3 small paraffin droplets on the same surface which the cells were plated, as previously described for neuron-astrocyte co-cultures (Jones et al., 2012). BMDMs were allowed to adhere overnight. Bilaminar culture experiments began by inserting coverslips containing BMDM and wax paraffin nodule face down, into culture plates containing adult microglia. All experiments were performed in DMEMF12 serum free media.

tag: strain

value: male

value: Adult  microglia

value: Macrophages, LPS


title: WJC2


title: WK3  -  IVS10+16/P301S  -  sample50241

tag: time (weeks)


title: Spleens of BALB/c mouse, 28th day, OVA 1


title: WJC1


title: WK5  -  CTR  -  sample50245

value: CTR


title: WK3  -  IVS10+16 +/+  -  sample50232


title: Microglia/Macrophages LPS rep 2


title: WK3  -  IVS10+16/P301S  -  sample50240


title: WK3  -  IVS10+16/P301S  -  sample50239


title: Microglia/Macrophages LPS rep 3


title: Microglia/Macrophages rep 4

source_name: Microglia/Macrophages

value: Macrophages


title: Spleens of BALB/c mouse, 14th day, OVA 3

source_name: Spleens,14th day, OVA


title: Microglia/Macrophages LPS rep 1


title: Spleens of BALB/c mouse, 14th day, OVA 4


title: Spleens of BALB/c mouse, 14th day, OVA 2


title: Spleens of BALB/c mouse, 14th day, OVA 1


title: WK3  -  IVS10+16 +/+  -  sample50231


title: MS2

value: MS


title: Spleens of BALB/c mouse, 28th day, control 2

source_name: Spleens,28th day, control

value: control


title: MS1


title: MS3


title: WK3  -  IVS10+16 +/+  -  sample50230


title: WK3  -  IVS10+16 +/-  -  sample50229


title: Spleens of BALB/c mouse, 28th day, control 1


title: Microglia/Macrophages rep 3


title: 187C3


title: WK3  -  IVS10+16 +/-  -  sample50228


title: WK3  -  IVS10+16 +/-  -  sample50227


title: MR2E1_A: Male WSR2 EtOH 1

value: prefrontal cortex

value: Ethanol vapor

tag: time

value: 21d withdrawal


title: 187C2


title: Microglia/Macrophages rep 1


title: Spleens of BALB/c mouse, 14th day, control 2

source_name: Spleens,14th day, control


title: Microglia/Macrophages rep 2


title: Microglia LPS rep 3

source_name: Microglia LPS

value: LPS


title: 187C1


title: Microglia LPS rep 4


title: Spleens of BALB/c mouse, 14th day, control 1

value: female


title: 173C3


title: β-TC3 H3K27ac Rep2

city: Edinburgh

first: nick

last: gilbert

address: Crewe Rd

department: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

description: Raw array files from slide scanner of Input and ChIP samples

hyb_protocol: ChIP samples (Cy5) and Input samples (Cy3) were hybridized using a NimbleGen Hybridization and Sample Tracking Control Kit (Roche Cat. 05993776001) according to the manufacturer’s instructions. Slides were washed (NimbleGen Wash Buffer Kit, Roche Cat. 0558450700).

scan_protocol: Microarray slides were scanned at 2 µm resolution on a MS 200 Microarray Scanner (Nimblegen). Images were processed using Nimblescan version 2.5 and the Cy3 and Cy5 images were aligned with the NimbleGen design file (ndf) and a pair file generated of the intensity values.

data_processing: Ringo (Bioconductor) was used for pre-processing, normalisation, combining replicates and peak calling of ChIP-chip data. Ringo Probe annotation was performed on pair files using “posToProbeAnno” with following position file ("110505_AB_MM9_regions_ChIP.pos" provided, using mm9 genome. RG data was then background corrected using “minimum” method, and preprocessed using “loess” method and data normalised using “normalizedBetweenArrays” function.   Data was smoothed using “ computeRunningMedians” with winHalfSize=250, and min.probes=1, and replicates combined. Data was written out as a bedgraph file of log2 ratio ChIP/Input.

source_name: H3K27ac Input DNA β-TC3

label_protocol: ChIP and Input samples where whole genome amplified (GenomePlex, Sigma), purified (QIAquick, Qiagen) and labelled (NimbleGen Dual-Colour Labelling Kit, Roche Cat. 06370250001).

extract_protocol: H3K27ac ChIP was performed largely as described in Creyghton et al., 2010. One T75 flask was used per replicates with cells at ~80% confluency. Culture media was aspirated and replaced with 20 ml of fresh DMEM with no additives and 550 μl of 37% Formaldehyde was added to each flask for 10 min, before 2 ml of 2 M glycine solution was added to quench the formaldehyde and flasks were incubated at 4°C for 5 min. Flasks were washed with ice cold PBS twice, rocking for 10 min at 4 °C. A cell scrapper was used to remove the adherent cell layer in 10 ml cold PBS and the cells pooled in a 50 ml conical tube. Fixed cells were centrifuged for 5 min, supernatant removed and the pellet resuspended in 3 ml of cold Cell Lysis Buffer (50 mM HEPES pH 6.8, 140 mM NaCl, 10% (v/v) glycerol, 0.5% (v/v) IPEGAL, 0.25% (v/v) Triton X, 1mM EDTA, 0.25 mM PMSF) and a 21G needle and syringe used to resuspend completely before samples incubated on ice 10 min. Samples were centrifuged for 5 min, supernatant removed and the pellet resuspended in 3-10 ml Pre ChIP Wash buffer (200 mM NaCl, 10 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA, 0.25 mM PMSF) and incubated 5 min on ice. Samples were centrifuged and resuspended in ~2.5 ml of Sonication buffer (100 mM NaCl, 0.1% (v/v) Na deoxycholate, 0.5 % N-lauroylsarcosine 10 mM Tris pH8, 1 mM EDTA, 0.5 mM EGTA, 0.25 mM PMSF). Samples were sonicated for 13 min, 30 sec on, 30 sec off (rest 2 min after 8 min), at 50% amplitude with a Soniprep 150 probe sonicator, to achieve a size range of ~300-500 bp. 10 µl of H3K27ac antibody (Abcam Cat#ab4729) was used per sample, with Protein G Dyna beads (ThermoFisher Cat#10003D). IP bound beads were washed in 5x RIPA Buffer (50 mM HEPES (pH 7.6), 1 mM EDTA, 0.7% Na deoxycholate (v/v),1% (v/v) Nonidet P-40, and 0.5 M LiCl), and 2x ChIP Wash 4(TE, 50 mM NaCl). Chromatin was eluted from beads, in 400 µl elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS), shaking at 65°C overnight along with a 10% Input sample to reverse the cross-linking.  DNA was treated with RNaseA (0.2 μg/μl final) for 2 h at 37°C, followed by proteinase K (0.2 μg/μl final) for 2 h at 50°C. Two phenol chloroform extractions were performed with 2 ml Phase lock tubes (5 prime). Resulting DNA was purified using a PCR clean up kit (Qiagen), with a double 50 µl final elution and stored at -20°C. Two experimental replicates where performed for each ChIP.

treatment_protocol: Xlinked ChIP

tag: cell line

tag: antibody

value: input

source_name: H3K27ac ChIP DNA β-TC3


title: β-TC3 H3K27ac Rep1


title: Microglia LPS rep 2

tag: treatment


title: 173C2


title: WK3  -  CTR  -  sample50225


title: WK3  -  CTR  -  sample50226


title: WK3  -  CTR  -  sample50224


title: breast tissue_KO

city: Guangzhou

first: Xiaojia

last: Huang

address: 651 East Dongfeng Road

institute: Sun Yat-sen University Cancer Center

description: differentially expressed mRNAs and lncRNAs in female mice breast tissues  with miR-34a knockout

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: breast tissue with miR-34a knockout

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: The miR-34a floxed mice (miR-34a fl/fl) and the mammary gland specific Cre expressing mice were purchased from The Jackson Laboratory (Stock Numbers 018545 and 003553, Maine, USA). And the miR-34a fl/fl mice were crossed to Cre mice to obtain mammary gland specific miR-34a knock out mice (miR-34a -/-). Female miR-34a -/- mice (KO) were used for all experiments and miR-34a fl/fl mice (NC) were used as control.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Mammary glands from miR-34a -/- (KO) and miR-34a fl/fl (NC) mice were harvested and RNA were extracted.

tag: genotype/variation

value: breast


title: 173C1

value: immunocompromised NGS mice


title: Microglia LPS rep 1

tag: cell type


title: NPC  -  IVS10+16/P301S  -  sample50223

value: NPC


title: 163C3

value: Urothelial Cancer


title: microglia alone rep 3

source_name: microglia alone

value: male


title: NPC  -  IVS10+16/P301S  -  sample50222

source_name: hiPSC derived neurons


title: microglia alone rep 4

value: Adult  microglia


title: breast tissue_NC

description: differentially expressed mRNAs and lncRNAs in female mice breast tissues without miR-34a knockout

source_name: breast tissue without miR-34a knockout

value: miR-34a fl/fl (control)


title: microglia alone rep 2


title: microglia alone rep 1


title: 163C2


title: 163C1


title: NPC  -  IVS10+16/P301S  -  sample50221


title: NPC  -  IVS10+16 +/+  -  sample50217


title: Bdellovibrio with S aureus biofilm 2

source_name: Bdellovibrio bacteriovorus HD100

tag: protocol

value: Staphylococcus aureus biofilm


title: NPC  -  IVS10+16 +/+  -  sample50215


title: MR2E2_B: Male WSR2 EtOH 2

source_name: prefrontal cortex

tag: tissue


title: MR2E3_B: Male WSR2 EtOH 3


title: MR2A2_B: Male WSR2 Air 2

value: Control


title: NPC  -  IVS10+16 +/+  -  sample50216


title: NPC  -  IVS10+16 +/-  -  sample50214


title: MR1E2_B: Male WSR1 EtOH 2


title: MR1E1_B: Male WSR1 EtOH 1


title: NPC  -  CTR  -  sample50211

value: CTR


title: NPC  -  IVS10+16 +/-  -  sample50212


title: MR2E1_B: Male WSR2 EtOH 1


title: MR2A1_B: Male WSR2 Air 1


title: NPC  -  IVS10+16 +/-  -  sample50213


title: MR1A1_B: Male WSR1 Air 1


title: MR1A2_B: Male WSR1 Air 2


title: NPC  -  CTR  -  sample50210


title: Trachea (3'-droplet based RNAseq) - Mouse 4

status: Public on Jul 30 2018

city: Boston

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

data_processing:
3' polyA RNA-seq
CellRanger 1.0
PCA (prcomp in R)
kNN-based graph clustering (R code)
Genome_build: mm10
Supplementary_files_format_and_content: 10X genomics CellRanger output: UMI count expression values for each gene (rows) in each cell (columns)

source_name: WT Mouse airway (trachea) epithelial cells

extract_protocol:
3' polyA RNA seq
10X Genomics Chromium Prep

value: trachea epithelium

tag: genotype

value: Wild-type


title: Trachea (3'-droplet based RNAseq) - Mouse 3


title: Trachea (3'-droplet based RNAseq) - Mouse 5


title: Trachea (3'-droplet based RNAseq) - Mouse 6


title: 7 day postnatal, bio rep 3

status: Public on Jul 31 2018

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

hyb_protocol: Hybridization was perfromed at 45 degress C overnight with 60 rpm to Rat transcriptome arrays.  Wash Stain rx was done on an Affy Fluidics Station FS 450 using protocol FS450-0001

scan_protocol: Visualization utilized an Affy 3000 7G scanner

data_processing: Affymetrix Expression Console version 1.0, sst-RMA

organism: Rattus norvegicus

source_name: Liver

label_protocol: 100 ng total RNA input was used for the Rt reaction followed by second strand synthesis and ON IVT rx.  IVT cRNA was purified using magnetic beads and 15 ug IVT cRNA were reverse transcribed, and the resulting sscDNA was RNase treated to digest the RNA template and then bead purified. 5.5 ug sscDNA was fragmented and 5.15 ug fragmented cDNA were biotin end-labeled.  All reagents used were part of the Affy WT Plus amplification kit or Wash/Stain/ Hyb kit respectively.

growth_protocol: All animals were housed under standard conditions with access to food and water ad libitum. E21 fetuses were delivered by C-section & decapitated before drawing a breath.  Timed pregnant dams were monitored continuously to observe time of birth.

extract_protocol: RNA was extracted using the Rneasy kit according to the manufacturer's directions.

treatment_protocol: RNA was extracted from flash frozen liver.

value: Liver

value: Sprague Dawley

value: 7 days post-birth (direct observation)


title: Trachea (3'-droplet based RNAseq) - Mouse 2


title: 4 hr postnatal, bio rep 3

value: 4 hr post-birth (direct observation)


title: 1 day postnatal bio rep 1

value: 1 day post-birth (direct observation)


title: 12 hr postnatal, bio rep 2

value: 12hr post-birth (direct observation)


title: 4 hr postnatal, bio rep 2


title: 7 day postnatal, bio rep 2


title: NPC  -  CTR  -  sample50209


title: Trachea (3'-droplet based RNAseq) - Mouse 1


title: 7 day postnatal, bio rep 1


title: E21, bio rep 2

value: embryonic day 21 (C-section)


title: E21, bio rep 3


title: 30 min postnatal, bio rep 2

value: 30 minutes post-birth (direct observation)


title: 4 hr postnatal, bio rep 1


title: 30 min postnatal, bio rep 1


title: E21, bio rep 1


title: 1 day postnatal bio rep 3


title: 12 hr postnatal, bio rep 1


title: 1 day postnatal bio rep 2


title: 30 min postnatal, bio rep 3


title: 12 hr postnatal, bio rep 3


title: SM-GE8ZB_S135_E1-50

status: Public on Jul 13 2018

city: Seattle

first: Lucas

middle: T

last: Gray

state: WA

address: 615 Westlake Ave N

department: Molecular Genetics

institute: Allen Institute for Brain Science

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8ZB_E1-50_CTCCTAGA-AAGAGGCA

data_processing:
50-base pair paired-end reads were aligned to GRCm38 (mm10) using a RefSeq annotation gff file retrieved from NCBI on 01/18/2016 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/). Sequence alignment was performed using STAR v2.5.3 (Dobin et al., 2013) in twopassMode.
PCR duplicates were masked and removed using STAR option “bamRemoveDuplicates”. Only uniquely aligned reads were used for gene quantification.
Exon and intron counts were computed using the R GenomicAlignments package (Lawrence et al., 2013) sumarizeOverlaps function using “IntersectionNotEmpty”.
We mapped all non-genome-mapped reads to synthetic constructs, including ERCCs and transgene sequences using STAR v2.5.3 and a custom index built using supplementary files synthetic_constructs.gtf and synthetic_constructs.fa.
Genome_build: mm10
Supplementary_files_format_and_content: star_exon_counts.csv: Comma separated values matrix of count values for reads mapping to exons.
Supplementary_files_format_and_content: star_intron_counts.csv: Comma separated values matrix of count values for reads mapping to introns.
Supplementary_files_format_and_content: star_synthetic_counts.csv: Comma separated values matrix of count values for reads mapping to synthetic constructs and transgenes.

source_name: primary visual cortex (VISp)

growth_protocol: Both male and female transgenic mice ≥ P56 were utilized for all experiments.  All animals were housed 3-5 per cage and maintained on a 12-hour light/dark cycle, in a humidity- and temperature-controlled room with water and food available ad libitum.  All experimental procedures related to the use of mice were conducted with approved protocols in accordance with NIH guidelines, and were approved by the Institutional Animal Care and Use Committee (IACUC) of the Allen Institute for Brain Science.

extract_protocol:
Cells from transgenic mice or transgenic mice injected with AAV-pCAG-FLEX-EGFP-WPRE-pA were collected by microdissection, single-cell suspension, and single-cell FACS. Cells were then frozen at -80ºC.
Frozen cells were later processed for scRNA-seq using the SMART-Seq v4 method, as described in the Allen Institute Transcriptomics Technical Whitepaper (http://help.brain-map.org/download/attachments/8323525/CellTypes_Transcriptomics_Overview.pdf)

treatment_protocol: Induction of DHFR-domain containing dCre, dgCre or dgFlpO driver lines was done by administration via oral gavage (PO) of trimethoprim (TMP) at 0.3 mg/g body weight per day for 3 days. TMP working solution was diluted from a 10x stock in 100% DMSO with a 2% methylcellulose solution. Induction of CreERT2 driver lines was done by administration via oral gavage (PO) of tamoxifen (50 mg/ml in corn oil) at 0.2 mg/g body weight per day for 1-5 days. Mice can be used for experiments starting at 1-2 weeks after TMP or tamoxifen dosing.

tag: donor id

tag: donor genotype

tag: donor driver(s)

tag: donor reporter(s)

tag: donor sex

value: M

tag: dissected layer

tag: facs gating

value: GFP-positive

tag: facs container

tag: rna amplification set

tag: library preparation set

tag: library preparation date

tag: sequencing batch

tag: total sequenced reads

tag: genes detected

tag: cell class

value: GABAergic


title: SM-GE8ZC_S046_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8ZC_E1-50_ATCCGGTA-GCATTGGT


title: SM-GE8ZB_S142_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8ZB_E1-50_TGGATCAC-AACCAGAG


title: SM-GE8ZB_S143_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8ZB_E1-50_CCGGAATT-GAAGACTG


title: SM-GE8ZB_S132_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8ZB_E1-50_ACGACAGA-AAGGAAGG


title: SM-GE8ZB_S125_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8ZB_E1-50_AGTGTTGG-GTACGATC


title: SM-GE8ZB_S124_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8ZB_E1-50_AGCTTGAG-TATGCGGT


title: SM-GE8ZB_S043_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8ZB_E1-50_TTAGGTCG-CGAAGTCA


title: SM-GE8ZB_S122_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8ZB_E1-50_TGTTCGAG-TCTGGACA


title: SM-GE8ZB_S037_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8ZB_E1-50_AAGAGCCA-ATGCGTCA


title: SM-GE8ZB_S038_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8ZB_E1-50_GCTTCTTG-CACAGGAA


title: SM-GE8ZA_S152_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8ZA_E1-50_TCGAAGGT-CTACAAGG


title: SM-GE8ZB_S029_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8ZB_E1-50_ATGGAAGG-CAATGCGA


title: SM-GE8ZB_S032_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8ZB_E1-50_CAAGCAGT-ACAGAGGT


title: SM-GE8ZB_S033_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8ZB_E1-50_CATGGAAC-ACGGTACA


title: SM-GE8ZA_S145_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8ZA_E1-50_TGAGGTGT-ATCATGCG


title: SM-GE8Z9_S191_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8Z9_E1-50_CTTACCTG-ACAGTTCG


title: SM-GE66X_S141_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE66X_E1-50_TGCGTAGA-TACATCGG


title: SM-GE8Z9_S180_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8Z9_E1-50_GTGAGCTT-AACCTACG


title: SM-D9D7Q_S90_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7Q_E1-50_TCGACGTC-TTCTAGCT

source_name: anterior lateral motor cortex (ALM)

value: F

value: GFP-positive (RFP unknown)

tag: rna amplification date


title: SM-GE8Z9_S086_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8Z9_E1-50_CTGGTTCT-CCACAACA


title: SM-GE8Z9_S095_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8Z9_E1-50_CTGCGTAT-CGCCTTAT


title: SM-GE66X_S138_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE66X_E1-50_CATAACGG-CACGTCTA


title: SM-GE8Z9_S075_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8Z9_E1-50_AGGATGGT-AGCCAACT


title: SM-GE66X_S146_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE66X_E1-50_CAGTCTTC-AATTCCGG


title: SM-D9D7Q_S94_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7Q_E1-50_TCGACGTC-AAGGCTAT


title: SM-D9D7Q_S96_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7Q_E1-50_TCGACGTC-TTATGCGA


title: SM-GE8Z9_S084_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8Z9_E1-50_TCGAGTGA-AGATACGG


title: SM-GE8Z9_S088_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8Z9_E1-50_GTCTAGGT-CTATCCAC


title: SM-GE8Z9_S073_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8Z9_E1-50_TATCAGCG-AACTGAGG


title: SM-D9D7Q_S95_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7Q_E1-50_TCGACGTC-GAGCCTTA


title: SM-GE8Z9_S183_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8Z9_E1-50_CTCGATAC-AACTCGGA


title: SM-D9D7O_S48_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7O_E1-50_ATGCGCAG-TCTCTCCG


title: SM-GE66X_S140_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE66X_E1-50_TCTGCTCT-GTAAGCAC


title: SM-D9D7O_S46_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7O_E1-50_ATGCGCAG-CTAAGCCT


title: SM-D9D7O_S47_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7O_E1-50_ATGCGCAG-CGTCTAAT


title: SM-D9D7O_S45_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7O_E1-50_ATGCGCAG-AAGGAGTA


title: SM-GE8ZA_S129_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE8ZA_E1-50_TCTCTAGG-TCGACAAG


title: SM-D9D7Q_S89_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7Q_E1-50_TCGACGTC-TCGACTAG


title: SM-D9D7O_S44_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7O_E1-50_ATGCGCAG-ACTGCATA


title: SM-D9D7O_S42_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7O_E1-50_ATGCGCAG-TATCCTCT


title: SM-GE66X_S160_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-GE66X_E1-50_CGTGTACT-GTTGGCAT


title: SM-D9D7O_S39_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7O_E1-50_TACGCTGC-CGTCTAAT


title: SM-D9D7O_S41_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7O_E1-50_ATGCGCAG-CTCTCTAT


title: SM-D9D7O_S37_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7O_E1-50_TACGCTGC-AAGGAGTA


title: SM-D9D7O_S38_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7O_E1-50_TACGCTGC-CTAAGCCT


title: SM-D9D7O_S43_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7O_E1-50_ATGCGCAG-GTAAGGAG


title: SM-D9D7O_S36_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7O_E1-50_TACGCTGC-ACTGCATA


title: SM-D9D7O_S35_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7O_E1-50_TACGCTGC-GTAAGGAG


title: SM-D9D7O_S21_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7O_E1-50_GCGTAGTA-AAGGAGTA

value: Pvalb-IRES-Cre

value: RFP-positive


title: SM-D9D7M_S56_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7M_E1-50_TAGCGCTC-TCTCTCCG


title: SM-D9D7N_S55_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7N_E1-50_TAGCGCTC-CGTCTAAT


title: SM-D9D7N_S56_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7N_E1-50_TAGCGCTC-TCTCTCCG


title: SM-D9D7N_S51_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7N_E1-50_TAGCGCTC-GTAAGGAG


title: SM-D9D7N_S47_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7N_E1-50_ATGCGCAG-CGTCTAAT


title: SM-D9D7N_S26_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7N_E1-50_CGGAGCCT-TATCCTCT


title: SM-D9D7N_S49_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7N_E1-50_TAGCGCTC-CTCTCTAT


title: SM-D9D7O_S19_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7O_E1-50_GCGTAGTA-GTAAGGAG


title: SM-D9D7N_S54_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7N_E1-50_TAGCGCTC-CTAAGCCT


title: SM-D9D7M_S55_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7M_E1-50_TAGCGCTC-CGTCTAAT


title: SM-D9D7M_S54_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7M_E1-50_TAGCGCTC-CTAAGCCT


title: SM-D9D7M_S52_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7M_E1-50_TAGCGCTC-ACTGCATA


title: SM-D9D7M_S53_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7M_E1-50_TAGCGCTC-AAGGAGTA


title: SM-D9D7N_S52_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7N_E1-50_TAGCGCTC-ACTGCATA


title: SM-D9D7M_S50_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7M_E1-50_TAGCGCTC-TATCCTCT


title: SM-D9D7M_S51_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7M_E1-50_TAGCGCTC-GTAAGGAG


title: SM-D9D7M_S49_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7M_E1-50_TAGCGCTC-CTCTCTAT


title: SM-D9D7M_S48_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7M_E1-50_ATGCGCAG-TCTCTCCG


title: SM-D9D7M_S47_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7M_E1-50_ATGCGCAG-CGTCTAAT


title: SM-D9D7M_S45_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7M_E1-50_ATGCGCAG-AAGGAGTA


title: SM-D9D7O_S33_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7O_E1-50_TACGCTGC-CTCTCTAT


title: SM-D9D7M_S44_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7M_E1-50_ATGCGCAG-ACTGCATA


title: SM-D9D7M_S42_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7M_E1-50_ATGCGCAG-TATCCTCT


title: SM-D9CYP_S86_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9CYP_E1-50_GCTCATGA-CTAAGCCT


title: SM-D9D7O_S25_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7O_E1-50_CGGAGCCT-CTCTCTAT


title: SM-D9D7N_S50_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7N_E1-50_TAGCGCTC-TATCCTCT


title: SM-D9CYP_S84_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9CYP_E1-50_GCTCATGA-ACTGCATA


title: SM-D9CYP_S85_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9CYP_E1-50_GCTCATGA-AAGGAGTA


title: SM-D9D7N_S25_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9D7N_E1-50_CGGAGCCT-CTCTCTAT


title: SM-D9CYP_S82_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9CYP_E1-50_GCTCATGA-TATCCTCT


title: SM-D9CYP_S83_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9CYP_E1-50_GCTCATGA-GTAAGGAG


title: SM-D9CYH_S32_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9CYH_E1-50_TCCTGAGC-TCTCTCCG


title: SM-D9CYH_S30_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9CYH_E1-50_TCCTGAGC-CTAAGCCT


title: SM-D9CYH_S31_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9CYH_E1-50_TCCTGAGC-CGTCTAAT


title: SM-D9CYP_S81_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9CYP_E1-50_GCTCATGA-CTCTCTAT


title: SM-D9CYH_S28_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9CYH_E1-50_TCCTGAGC-ACTGCATA


title: SM-D9CYH_S29_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9CYH_E1-50_TCCTGAGC-AAGGAGTA


title: SM-D9CXX_S87_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9CXX_E1-50_GCTCATGA-CGTCTAAT


title: SM-D9CXX_S86_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9CXX_E1-50_GCTCATGA-CTAAGCCT


title: SM-D9EOT_S94_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EOT_E1-50_ATCTCAGG-CTAAGCCT


title: SM-D9EOT_S93_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EOT_E1-50_ATCTCAGG-AAGGAGTA


title: SM-D9EOT_S92_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EOT_E1-50_ATCTCAGG-ACTGCATA


title: SM-D9EOT_S91_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EOT_E1-50_ATCTCAGG-GTAAGGAG


title: SM-D9EOT_S84_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EOT_E1-50_GCTCATGA-ACTGCATA


title: SM-D9EOT_S83_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EOT_E1-50_GCTCATGA-GTAAGGAG


title: SM-D9EOT_S88_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EOT_E1-50_GCTCATGA-TCTCTCCG


title: SM-D9EPH_S95_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_ATCTCAGG-CGTCTAAT


title: SM-D9CYH_S27_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9CYH_E1-50_TCCTGAGC-GTAAGGAG


title: SM-D9EPH_S91_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_ATCTCAGG-GTAAGGAG


title: SM-D9EOT_S82_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EOT_E1-50_GCTCATGA-TATCCTCT


title: SM-D9EOT_S86_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EOT_E1-50_GCTCATGA-CTAAGCCT


title: SM-D9EOT_S81_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EOT_E1-50_GCTCATGA-CTCTCTAT


title: SM-D9EOT_S87_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EOT_E1-50_GCTCATGA-CGTCTAAT


title: SM-D9CYH_S26_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9CYH_E1-50_TCCTGAGC-TATCCTCT


title: SM-D9CYH_S25_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9CYH_E1-50_TCCTGAGC-CTCTCTAT


title: SM-D9CXX_S85_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9CXX_E1-50_GCTCATGA-AAGGAGTA


title: SM-D9EPH_S87_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_GCTCATGA-CGTCTAAT


title: SM-D9EPH_S86_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_GCTCATGA-CTAAGCCT


title: SM-D9EOT_S96_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EOT_E1-50_ATCTCAGG-TCTCTCCG


title: SM-D9EPH_S89_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_ATCTCAGG-CTCTCTAT


title: SM-D9EPH_S85_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_GCTCATGA-AAGGAGTA


title: SM-D9EPH_S83_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_GCTCATGA-GTAAGGAG


title: SM-D9EPH_S82_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_GCTCATGA-TATCCTCT


title: SM-D9EOT_S90_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EOT_E1-50_ATCTCAGG-TATCCTCT


title: SM-D9EOT_S89_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EOT_E1-50_ATCTCAGG-CTCTCTAT


title: SM-D9EPH_S80_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_GTAGAGGA-TCTCTCCG


title: SM-D9EPH_S78_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_GTAGAGGA-CTAAGCCT


title: SM-D9EPH_S79_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_GTAGAGGA-CGTCTAAT


title: SM-D9EPH_S74_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_GTAGAGGA-TATCCTCT


title: SM-D9EPH_S90_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_ATCTCAGG-TATCCTCT


title: SM-D9EPH_S61_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_CGAGGCTG-AAGGAGTA


title: SM-D9EPH_S70_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_AAGAGGCA-CTAAGCCT


title: SM-D9EPH_S66_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_AAGAGGCA-TATCCTCT


title: SM-D9EPH_S60_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_CGAGGCTG-ACTGCATA


title: SM-D9EPH_S65_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_AAGAGGCA-CTCTCTAT


title: SM-D9EPH_S63_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_CGAGGCTG-CGTCTAAT


title: SM-D9EPH_S68_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_AAGAGGCA-ACTGCATA


title: SM-D9EPH_S57_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_CGAGGCTG-CTCTCTAT


title: SM-D9EPH_S62_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_CGAGGCTG-CTAAGCCT


title: SM-D9EPH_S72_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_AAGAGGCA-TCTCTCCG


title: SM-D9EPH_S84_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_GCTCATGA-ACTGCATA


title: SM-D9EPH_S59_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_CGAGGCTG-GTAAGGAG


title: SM-D9EPH_S77_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_GTAGAGGA-AAGGAGTA


title: SM-D9EPH_S76_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_GTAGAGGA-ACTGCATA


title: SM-D9EPH_S56_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_CTCTCTAC-TCTCTCCG


title: SM-D9EPG_S96_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_ATCTCAGG-TCTCTCCG


title: SM-D9EPH_S44_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_TAGGCATG-ACTGCATA


title: SM-D9EPH_S55_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_CTCTCTAC-CGTCTAAT


title: SM-D9EPH_S43_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_TAGGCATG-GTAAGGAG


title: SM-D9EPH_S45_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_TAGGCATG-AAGGAGTA


title: SM-D9EPH_S52_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_CTCTCTAC-ACTGCATA


title: SM-D9EPH_S46_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_TAGGCATG-CTAAGCCT


title: SM-D9EPH_S49_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_CTCTCTAC-CTCTCTAT


title: SM-D9EPH_S42_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_TAGGCATG-TATCCTCT


title: SM-D9EPG_S93_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_ATCTCAGG-AAGGAGTA


title: SM-D9EPH_S73_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPH_E1-50_GTAGAGGA-CTCTCTAT


title: SM-D9EPG_S92_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_ATCTCAGG-ACTGCATA


title: SM-D9EPG_S95_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_ATCTCAGG-CGTCTAAT


title: SM-D9EPG_S91_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_ATCTCAGG-GTAAGGAG


title: SM-D9EPG_S85_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_GCTCATGA-AAGGAGTA


title: SM-D9EPG_S88_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_GCTCATGA-TCTCTCCG


title: SM-D9EPG_S81_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_GCTCATGA-CTCTCTAT


title: SM-D9EPG_S75_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_GTAGAGGA-GTAAGGAG


title: SM-D9EPG_S76_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_GTAGAGGA-ACTGCATA


title: SM-D9EPG_S73_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_GTAGAGGA-CTCTCTAT


title: SM-D9EPG_S82_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_GCTCATGA-TATCCTCT


title: SM-D9EPG_S70_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_AAGAGGCA-CTAAGCCT


title: SM-D9EPG_S71_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_AAGAGGCA-CGTCTAAT


title: SM-D9EPG_S65_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_AAGAGGCA-CTCTCTAT


title: SM-D9EPG_S66_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_AAGAGGCA-TATCCTCT


title: SM-D9EPG_S94_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_ATCTCAGG-CTAAGCCT


title: SM-D9EPG_S79_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_GTAGAGGA-CGTCTAAT


title: SM-D9EPG_S56_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_CTCTCTAC-TCTCTCCG


title: SM-D9EPG_S51_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_CTCTCTAC-GTAAGGAG


title: SM-D9EPG_S78_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_GTAGAGGA-CTAAGCCT


title: SM-D9EPG_S55_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_CTCTCTAC-CGTCTAAT


title: SM-D9EPG_S54_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_CTCTCTAC-CTAAGCCT


title: SM-D9EPG_S57_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_CGAGGCTG-CTCTCTAT


title: SM-D9EPG_S60_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_CGAGGCTG-ACTGCATA


title: SM-D9EPG_S64_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_CGAGGCTG-TCTCTCCG


title: SM-D9EPG_S90_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_ATCTCAGG-TATCCTCT


title: SM-D9EPG_S48_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_TAGGCATG-TCTCTCCG


title: SM-D9EPG_S50_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_CTCTCTAC-TATCCTCT


title: SM-D9EPG_S67_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_AAGAGGCA-GTAAGGAG


title: SM-D9EPG_S44_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_TAGGCATG-ACTGCATA


title: SM-D9EPG_S58_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_CGAGGCTG-TATCCTCT


title: SM-D9EPG_S41_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_TAGGCATG-CTCTCTAT


title: SM-D9EPG_S43_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_TAGGCATG-GTAAGGAG


title: SM-D9EPG_S35_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_GGACTCCT-GTAAGGAG


title: SM-D9EPG_S40_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_GGACTCCT-TCTCTCCG


title: SM-D9EPG_S33_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_GGACTCCT-CTCTCTAT


title: LS-15383_S28_E2-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
LS-15383_E2-50_TCCTGAGC-ACTGCATA

value: Glutamatergic


title: SM-D9EPG_S36_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_GGACTCCT-ACTGCATA


title: SM-D9EPG_S63_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_CGAGGCTG-CGTCTAAT


title: LS-15383_S36_E2-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
LS-15383_E2-50_GGACTCCT-ACTGCATA


title: SM-D9EPG_S62_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_CGAGGCTG-CTAAGCCT


title: SM-D9EPG_S34_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_GGACTCCT-TATCCTCT


title: SM-D9EPG_S46_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
SM-D9EPG_E1-50_TAGGCATG-CTAAGCCT


title: LS-15383_S34_E2-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
LS-15383_E2-50_GGACTCCT-TATCCTCT