title: Conditioned failed 2 RNA-seq

description: Con. unsuccessful extinction SFCpExtpminus-LS17


title: Conditioned successful 1 RNA-seq

status: Public on Nov 02 2021

type: SRA

city: Rehovot

first: Igor

last: Ulitsky

state: Central

address: 234 Hertzl St.

country: Israel

institute: Weizmann Institute of Science

description: Con. successful extinction SFCpExtpplus-LS5

library_source: transcriptomic

data_processing:
RNA-seq: Raw reads were aligned to the mouse genome (mm10) using HiSAT and StringTie (Pertea et al., 2016) for transcript-based analysis or STAR aligner for count based analysis (Dobin et al., 2013). The program Ballgown was used to perform differential expression analysis based on FPKM values. Two other count-based strategies were performed since count-based differential expression analysis is more robust. For the first strategy, count data was calculated from the Ballgown data using an additional pipeline available, prepDE.PY. For the second strategy, the whole mapping was repeated using RNA STAR and the count data calculated using the HTseq pipeline. Both these count-based data were used to calculate differential expression of genes as well as transcripts using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig read coverage files are provided for all samples

molecule: total RNA

organism: Mus musculus

source_name: brain septum

extract_protocol:
Total RNA and protein were isolated from mouse brain septum using the NucleoSpin miRNA kit (Macherey-Nagel GmbH & Co KG) according to the manufacturer’s protocol for animal tissues.
Libraries for total RNA-seq were prepared using the Ovation SoLo RNA-Seq System, Mouse (#0501-32, NuGEN Technologies) according to the manufacturer’s protocol with an RNA starting concentration of 0.8 ng/µl.

tag: tissue

value: brain septum

tag: aso

tag: histone mark


title: MONOCYTES_Gt020

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

description:
RNASeq_Counts
cohort details: Whole blood, peripheral blood (PBMC) and other immune subpopulations for this study were collected from healthy donors enrolled in the Genetic and Epigenetic Signatures of Translational Aging Laboratory Testing study (GESTALT) (Protocol# 15-AG-0063). GESTALT participants (age range 22-83 years) were selected to be free of major diseases, except for controlled hypertension or a history of cancer that had been clinically silent for at least 10 years, were not chronically on medications,had no  physical or cognitive impairment , weighed more than 110 lbs and had BMI less than 30 kg/m2, and were not professional athletes.

data_processing:
Single-read sequencing was performed for 138 cycles and Real-Time Analysis (RTA) v1.18.66.3 generated the base-call files (BCL files).
BCL files were demultiplexed and converted to standard FASTQ files using bcl2fastq program (v2.17.1.14).
After adapter removal and end trimming of raw FASTQ files using cutadapt program(Martin, 2011),the quality of reads was checked using FastQC software (Andrews, 2010). A quality threshold of Q30 was used in cutadapt for trimming low quality reads.
The reads were aligned to hg19 genome using STAR aligner (Dobin et al., 2013). STAR was used with default parameters (10 mismatches) in total. The output BAM files were then processed into read-count files using featureCounts tool.
Genes with low read counts (<10 reads in 4 or more samples) were filtered out and pseudogenes were further excluded from the analysis. Differentially expressed transcripts in each cell type were identified using the DESeq2 software package(Love et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: Text files containing gene counts

organism: Homo sapiens

source_name: Monocytes

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from cytapheresis packs by density gradient centrifugation using Ficoll-Paque Plus (GE Healthcare, NJ, USA). For isolation of specific immune cells, total B, CD4 and CD8 cells were enriched by negative selection using EasySep Negative Human kits specific for each cell type; monocytes were negatively enriched using “EasySep Human Monocyte Enrichment Kit w/o CD16” (StemCell Technologies, Vancouver, Canada) following the manufacturer’s instructions. Natural killer cells were negatively enriched by depleting PBMCs with antibodies directed against CD3, CD4, CD14, CD19 and Glycophorin-A in HBSS buffer. Enriched cell populations were further purified by flow cytometry following Human Immunophenotyping Consortium (HIPC) phenotyping panels (Maecker et al., 2012).  Gating strategies and post-sort purity were analyzed by FlowJo software. Granulocytes were positively selected from whole blood using EasySep™ Human Whole Blood CD66b Positive Selection Kit
Total RNA was prepared from 2 million cells using miRNeasy mini kit (Qiagen Inc, CA) according to the manufacturer’s recommendations. RNA quality and quantity were checked using RNA-6000 nano kits on the Agilent 2100-Bioanalyzer and 500ng of the total RNA was used for ribosomal RNA (rRNA) depletion using GeneRead rRNA Depletion Nano Kit (Qiagen Inc, CA). 50ng of the rRNA depleted RNA was used for cDNA synthesis followed by single primer isothermal amplification (SPIA) using Ovation RNA–Seq System V2 kits according to manufacturer’s protocol (Nugen Technologies Inc, CA). 375ng of amplified cDNA sheared to an average size of 150–250 bases, was used to prepare the libraries using Illumina ChIP-Seq kits (Illumina Inc, CA) according to the manufacturer’s protocol, followed by sequencing using Illumina Hiseq2500 sequencer with V4 reagents

tag: donor id

tag: phase


title: Uncoditioned with extintion training 3 RNA-seq

description: Uncon. extPlus SFCmExtp-LS6


title: MONOCYTES_Gt018


title: MONOCYTES_Gt017


title: MONOCYTES_Gt045


title: Uncoditioned with extintion training 2 RNA-seq

description: Uncon. extPlus SFCmExtp-LS3


title: MONOCYTES_Gt035


title: Uncoditioned with extintion training 1 RNA-seq

description: Uncon. extPlus SFCmExtp-LS1


title: MONOCYTES_Gt016


title: Shock control 2 RNA-seq

description: Shock control shock-control-LS16


title: MONOCYTES_Gt014


title: MONOCYTES_Gt015


title: MONOCYTES_Gt011


title: MONOCYTES_Gt013


title: Shock control 1 RNA-seq

description: Shock control shock-control-LS15


title: Context control 1 RNA-seq

description: Context control context-LS7


title: Context control 2 RNA-seq

description: Context control context-LS14


title: PBMC_Gt004

source_name: Peripheral Blood


title: MONOCYTES_Gt007


title: MONOCYTES_Gt005


title: Conditioned 2 RNA-seq

description: Con. day 1 SFCpExtm-LS11


title: Conditioned 3 RNA-seq

description: Con. day 1 SFCpExtm-LS12


title: Uncoditioned 2 RNA-seq

description: Uncon. day 1 SFCmExtm-LS10


title: Conditioned 1 RNA-seq

description: Con. day 1 SFCpExtm-LS8


title: MONOCYTES_Gt002


title: MONOCYTES_Gt003


title: MONOCYTES_Gt001


title: MONOCYTES_Gt004


title: GRANULOCYTES_Gt042

source_name: Granulocytes


title: Uncoditioned 3 RNA-seq

description: Uncon. day 1 SFCmExtm-LS13


title: GRANULOCYTES_Gt045


title: GRANULOCYTES_Gt035


title: 42FTS_2

city: Corvallis

first: Christopher

middle: Michael

last: Sullivan

state: OR

address: Sinnhuber Aquatic Research Laboratory, 28645 East HWY 34

department: Environmental & Molecular Toxicology

institute: Oregon State University

description: exposed to 47 uM 4:2 FTS at 8 hours post fertilization

data_processing:
SOAPnukes (version v1.5.2; parameters: -l 15 -q 0.2 -n 0.05) was used by BGI to filter sequencing data (reads with adapter sequences, low-quality base ratios > 20%, or unknown base ratios > 5% were removed).
Clean read FASTQ files were mapped to the Danio rerio GRCz11 genome using HISAT2 (version v2.0.4; parameters: --sensitive --no-discordant --no-mixed -l 1 -X 1000 -p 8).
BAM files provided by BGI were used to generate the PFAS_shortchain_series_Raw_ReadCounts.xlsx using HTSeq-count (-m intersection-nonempty -s no).
Clean reads were mapped to the transcriptome by BGI using Bowtie2 (version v2.2.5; parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200). Gene expression levels were calculated by BGI using RSEM (version v1.2.8; parameters: -p 8 --forward-prob 0.5 --paired-end).
Differential gene expression analysi was conducted by BGI using DESeq2 (q-value ≤ 0.05), producing PFAS_shortchain_series_Differential_Expression_and_ReadCounts.xlsx.
Gene ontology (GO) enrichment was conducted by BGI using Phyper (Hypergeometric test; q-value ≤ 0.05; Bonferroni). GO enriched biological pathways for the FBSA exposure group (the only group in this study with >14 differentially expressed genes) are in PFAS_shortchain_series_FBSA_GO_Biological_Pathway_Enrichment.xlsx.
Transcription factor analysis for the FBSA exposure group was conducted using GeneGo MetaCore software (version 21.3) following conversion of zebrafish genes to human orthologues using the Bioinformatics Resource Manager (leaving 1,366 genes). Results of this analysis are in PFAS_shortchain_series_Transcription_Factor_Enrichment.xlsx.
Genome_build: GRCz11

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish (Tropical 5D line) embryos were developmentally staged, dechorionated at 4 hours post fertilization (hpf), placed in 96-well plates in buffered embryo medium, and maintained at 28° ± 1°C.

extract_protocol:
10 embryos were pooled per replicate, ethanized via ice bath, homogenized in RNA-zol, and stored at -80°C until processing. Samples were then extracted using a Zymo Research Direct-zol RNA MiniPrep kit.
Libraries were prepared for sequencing using standard BGI protocols for sequencing on the BGISEQ-500 platform. Briefly, mRNA was purified using oligo(dT)-attached magnetic beads and fragmented, cDNA was synthesized, subjected to end-repair and 3' adenylated, adapters were ligated to cDNA fragments, and then fragments were amplified and purified. PCR products were circularized and formatted into the final library, which was amplified with phi29 to form DNA nanoballs to be loaded onto the patterned array and sequenced.

treatment_protocol: Embryos were statically exposed to chemical treatments beginning 8 hpf (0 or 47 uM PFAS, 0.5% methanol normalization). 96-well plates were then sealed and shaken overnight on an orbital shaker at 235 rpm. Embryos were sampled at 48 hpf.

tag: strain

value: Tropical 5D Wildtype

tag: age

value: 48 hours post fertilization

tag: pooled organisms

tag: treatment


title: GRANULOCYTES_Gt032


title: 42FTS_3

value: exposed to 47 uM 4:2 FTS at 8 hours post fertilization


title: Uncoditioned 1 RNA-seq

description: Uncon. day 1 SFCmExtm-LS9


title: 42FTS_1


title: GRANULOCYTES_Gt029


title: GRANULOCYTES_Gt027


title: PFPeA_3

description: exposed to 47 uM PFPeA at 8 hours post fertilization


title: GRANULOCYTES_Gt026


title: GRANULOCYTES_Gt030


title: PFPeA_1

value: exposed to 47 uM PFPeA at 8 hours post fertilization


title: PFBS_3

description: exposed to 47 uM PFBS at 8 hours post fertilization


title: PFPeA_2


title: PFBS_2

value: exposed to 47 uM PFBS at 8 hours post fertilization


title: FBSA_2

description: exposed to 47 uM FBSA at 8 hours post fertilization


title: FBSA_1

value: exposed to 47 uM FBSA at 8 hours post fertilization


title: CD8N_Gt045

source_name: Naïve CD8


title: PFBS_1


title: FBSA_3


title: GRANULOCYTES_Gt022


title: GRANULOCYTES_Gt020


title: PBMC_Gt013


title: CD8N_Gt030


title: CD8N_Gt029


title: CD8N_Gt027


title: GRANULOCYTES_Gt024


title: Control_3 (PFAS control)

description: untreated

value: untreated


title: Control_1 (PFAS control)

description: untreated


title: CD8N_Gt042


title: Control_2 (PFAS control)

description: untreated


title: CD8N_Gt024


title: CD8N_Gt022


title: CD8N_Gt035


title: CD8N_Gt033


title: CD8N_Gt017


title: CD8N_Gt032


title: GRANULOCYTES_Gt025


title: CD8N_Gt015


title: CD8N_Gt014


title: CD8N_Gt025


title: GRANULOCYTES_Gt018


title: CD8N_Gt020


title: CD8N_Gt018


title: CD8N_Gt013


title: CD8N_Gt026


title: CD8N_Gt016


title: CD8N_Gt011


title: CD8N_Gt005


title: CD8N_Gt007


title: CD8N_Gt004


title: CD8N_Gt003


title: CD8N_Gt002


title: CD8N_Gt001


title: SK-N-SH_no_treatment_rep3 [SHAP18]

type: genomic

city: Kumamoto

first: Kazuya

last: Iwamoto

address: 1-1-1 Honjo, Chuo-ku

department: Faculty of Life Sciences

country: Japan

institute: Kumamoto University

hyb_protocol: Bisulfite converted DNA was amplified, processed and hybridized to Illumina HumanMethylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
Illumina BeadStudio was used, according to the manufacturer's instructions.
Average Beta values (Beta value was calculated according to the ratio of intensities between methylated and unmethylated alleles, as in the following formula: beta value = methylated intensity/(methylated intensity + unmethylated intensity + 100) ).
Unmethylated and methylated signal intensities (same as signalA and signalB on BeadStudio output, respectively).

label: Cy5 and Cy13

molecule: genomic DNA

source_name: human neuroblastoma cells (SK-N-SH) without antipsychotics/DMSO

label_protocol: Standard Illumina Protocol was used.

growth_protocol: Human neuroblastoma SK-N-SH cells were cultured with Eagle’s minimal essential medium with 10% fetal bovine serum containing antipsychotics for 8 days.

extract_protocol: Genomic DNA was extracted via standard phenol:chloroform methods. The DNA samples were subjected to bisulfite modification by the EZ DNA Methylation Kit D500 (Zymo Research,).

treatment_protocol: We used low and high concentrations of haloperidol (1 uM and 10 uM) and risperidone (3 uM and 30 uM) based on their effective blood concentrations. The antipsychotics were dissolved in dimethyl sulfoxide (DMSO). Final concentrations of DMSO were 0.001% to 0.06%, depending on the dose of antipsychotics. The cells were cultured with or without 0.06% of DMSO as a control.

tag: cell type

value: human neuroblastoma cells (SK-N-SH)

value: NT


title: mitotane treatment primary melanoma cell culture, biological rep 2

type: RNA

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized to Affymterix GeneChip Human Genome U219 ArrayStrip (16 h, 45°C).

scan_protocol: The array strips were scanned using an Imaging Station of GeneAtlas System (Thermo Fisher Scientific, MA, USA). The preliminary analysis of the scanned chips was carried out by means of Affymetrix GeneAtlas Operating Software (Affymetrix, Santa Clara, CA, USA).

data_processing: Obtained CEL files were subjected for background correction and normalization using RobustMultiarrayAveraging (RMA) algorithm implemented in affy package of BioConductor.

label: biotin

source_name: Human primary melanoma cell culture

label_protocol: The protocol involving transcription in vitro, biotin labelling and cDNA fragmentation for further hybridization was carried out using the Affymetrix GeneChip IVT Express Kit (Affymetrix, Santa Clara, CA, USA)

growth_protocol: Cell culture of metastatic melanoma in the left adrenal gland of unknown primary origin. Fresh melanoma tumour samples obtained during surgery were cut into several small pieces and the fragments were further dissociated enzymatically in in a DMEM F12 (Thermo Fisher Scientific, MA, USA) medium (25 ml) containing 0.1% type I collagenase (17018029; ThermoFisher Scientific, MA, USA) for 45 min in a 37°C water bath with intermittent mixing. After digestion, the mixture was filtered through a 70 μM sieve. Then, the tissue was centrifuged at 4°C, 1200 rpm for 7 min. The cell pellet was resuspended in the DMEM F12 medium in which antibiotic-antimycotic solution and 10% fetal bovine serum (FBS) (Hyclone, GE Healthcare, MA USA) were added. The primary cell culture was cultivated at 37°C and 5% CO2 in the humidified atmosphere up to 70% confluence. The cells demonstrated crucial melanoma markers The HAC15 cell line (ATCC® CRL-3301TM, VA, USA) was cultured in a defined medium consisting of DMEM/F-12 without phenol red (Thermo Fisher Scientific, Waltham, MA, USA), 10% Cosmic Calf Serum (Hyclone, GE Healthcare, MA USA), 1% ITS + Premix (Corning, NY, USA), and 1% P/S (Merck Millipore, Darmstadt, Germany). The WM266-4 cell line was cultured in high-glucose DMEM (Biowest, MO, USA) supplemented with 10% FBS (Hyclone, GE Healthcare, MA USA) and 1% P/S (Merck Millipore, Darmstadt, Germany). The metastatic human melanoma cell line - WM266-4 (Rockland Immuno-chemicals, Inc. Limerick, PA, USA) was cultured in medium consisting of DMEM High Glucoes (Thermo Fisher Scientific, Waltham, MA, USA), 10% Fetal Bovine Serum (Hyclone, GE Healthcare, MA USA) and 1% P/S (Merck Millipore, Darmstadt, Germany).

extract_protocol: Total RNA isolation was performed using the modified Chomczynski method with the use of TRI Reagent (Sigma, St Louis, MO, USA) and the RNeasy Mini Elute Cleanup Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions

treatment_protocol: HAC15, 266-4, and primary melanoma cell lines treatment. The cells were incubated with mitotane 50 μM for 24 h and then subjected to further analyses

value: mitotane treatment

value: Human primary melanoma cell culture


title: mitotane treatment HAC15 cell line, biological rep 1

source_name: Human Adrenal Carcinoma

value: Human Adrenal Carcinoma


title: CD4N_Gt045

source_name: Naïve CD4


title: mitotane treatment WM266-4 cell line, biological rep 1

source_name: Metastatic human melanoma cell line

value: Metastatic human melanoma cell line


title: SK-N-SH_DMSO_control_rep1 [SHAP13]

label: Cy5 and Cy8

source_name: human neuroblastoma cells (SK-N-SH) with 0.06% DMSO

value: DMSO


title: mitotane treatment HAC15 cell line, biological rep 2


title: mitotane treatment WM266-4 cell line, biological rep 2


title: SK-N-SH_DMSO_control_rep2 [SHAP14]

label: Cy5 and Cy9


title: mitotane treatment primary melanoma cell culture, biological rep 1


title: CD4N_Gt035


title: CD4N_Gt042


title: SK-N-SH_no_treatment_rep2 [SHAP17]

label: Cy5 and Cy12


title: CD4N_Gt033


title: CD4N_Gt032


title: SK-N-SH_risperidone_high_rep3 [SHAP09]

label: Cy5 and Cy4

source_name: human neuroblastoma cells (SK-N-SH) with 30 uM risperidone


title: CD4N_Gt029


title: SK-N-SH_haloperidol_low_rep3 [SHAP06]

label: Cy5 and Cy3

source_name: human neuroblastoma cells (SK-N-SH) with 1 uM haloperidol


title: SK-N-SH_DMSO_control_rep3 [SHAP15]

label: Cy5 and Cy10


title: CD4N_Gt026


title: control HAC15 cell line, biological rep 1

value: control


title: control primary melanoma cell culture, biological rep 1


title: control WM266-4 cell line, biological rep 1


title: CD4N_Gt027


title: CD4N_Gt025


title: control primary melanoma cell culture, biological rep 2


title: P31_V5_HDM

city: Nedlands

first: Anya

last: Jones

state: Western Australia

address: Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue

country: Australia

institute: Telethon Kids Institute, The University of Western Australia

hyb_protocol: Hybridisation was carried at the core facility according to the manufacturers instructions.

scan_protocol: cDNA was hybridised to Affymetrix PrimeView.

data_processing: The raw expression data was analysed in the R statistical programming language version 3.4.4. The robust multi-array average (RMA) algorithm was used for background correction, log2 transformation and quantile normalisation. A custom chip description file (primeviewhsentrezgcdf, Version 22) was employed to annotate probe sets to genes based on updated genome and transcriptome information. The data was filtered with the PVAC algorithm and probe sets of low quality were removed. Differentially expressed genes were identified employing moderated t-statistics LIMMA with a false discovery rate (FDR) control for multiple testing.

source_name: CD4+ Tcells

label_protocol: Total RNA samples (n=198) were labelled according to the manufacturers instructions at the core facility.

extract_protocol: CD4+ T cells were harvested from cultures using positive isolation with Dynabeads (ThermoFisher) and total RNA was extracted with TRIzol followed by RNAeasy.

treatment_protocol: PBMC from visits V1, V2, and V4 were thawed and cultured together in the presence of HDM extract (0.5mg/ml) or medium control for 24h in Gibco AIM-V medium + 2-Mercaptoethanol (ThermoFisher, Sigma Aldrich), whilst V5 was cultured as a standalone experiment.

tag: subjectid

tag: visit

tag: condition

value: HDM

tag: gender

value: F

tag: age at visit

tag: respiratory symptom score


title: SK-N-SH_no_treatment_rep1 [SHAP16]

label: Cy5 and Cy11


title: control HAC15 cell line, biological rep 2


title: P31_V4_HDM


title: control WM266-4 cell line, biological rep 2


title: SK-N-SH_risperidone_high_rep2 [SHAP08]


title: CD4N_Gt022


title: P31_V4_CTR

value: CTR


title: SK-N-SH_risperidone_low_rep3 [SHAP12]

label: Cy5 and Cy7

source_name: human neuroblastoma cells (SK-N-SH) with 3 uM risperidone


title: CD4N_Gt024


title: SK-N-SH_risperidone_high_rep1 [SHAP07]


title: P31_V2_CTR


title: SK-N-SH_risperidone_low_rep1 [SHAP10]

label: Cy5 and Cy5


title: P31_V2_HDM


title: CD4N_Gt018


title: P31_V5_CTR


title: CD4N_Gt020


title: SK-N-SH_risperidone_low_rep2 [SHAP11]

label: Cy5 and Cy6


title: CD4N_Gt017


title: P31_V1_HDM


title: SK-N-SH_haloperidol_high_rep3 [SHAP03]

source_name: human neuroblastoma cells (SK-N-SH) with 10 uM haloperidol


title: SK-N-SH_haloperidol_low_rep1 [SHAP04]


title: CD4N_Gt015


title: SK-N-SH_haloperidol_high_rep2 [SHAP02]


title: SK-N-SH_haloperidol_high_rep1 [SHAP01]


title: CD4N_Gt016


title: CD4N_Gt007


title: P31_V1_CTR


title: SK-N-SH_haloperidol_low_rep2 [SHAP05]


title: CD4N_Gt011


title: CD4N_Gt013


title: CD4N_Gt014


title: CD4N_Gt005


title: P30_V5_HDM

value: M


title: CD4N_Gt004


title: P30_V2_HDM


title: P30_V1_HDM


title: P30_V4_HDM


title: P30_V2_CTR


title: CD4N_Gt002


title: P30_V5_CTR


title: P30_V4_CTR


title: CD4N_Gt001


title: BN_Gt045

source_name: Naïve B


title: BN_Gt033


title: P29_V5_HDM


title: P30_V1_CTR


title: BN_Gt035


title: P29_V4_HDM


title: BN_Gt027


title: BN_Gt032


title: BN_Gt030


title: P29_V2_HDM


title: CD4N_Gt003


title: BN_Gt024


title: BN_Gt022


title: BN_Gt017


title: P29_V5_CTR


title: P28_V5_CTR


title: BN_Gt018


title: P28_V5_HDM


title: BN_Gt029


title: P29_V1_HDM


title: P29_V1_CTR


title: BN_Gt020


title: P29_V4_CTR


title: P28_V2_HDM


title: BN_Gt026


title: BN_Gt014


title: BN_Gt025


title: BN_Gt015


title: P29_V2_CTR


title: P28_V4_HDM


title: CD4N_Gt030


title: P28_V1_CTR


title: P28_V1_HDM


title: BN_Gt013


title: P27_V5_CTR


title: P27_V5_HDM


title: P27_V4_CTR


title: P28_V4_CTR


title: P27_V2_HDM


title: P27_V4_HDM


title: P28_V2_CTR


title: BN_Gt007


title: BN_Gt005


title: BN_Gt011


title: BN_Gt016


title: P27_V2_CTR


title: BN_Gt004


title: BN_Gt003


title: C14orf159-KO HCT116 cells_rep2

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: hg19

source_name: C14orf159 knockout (KO) cells of HCT-116 cells

extract_protocol:
Total RNA was extracted from EV cells and C14orf159-KO cells of HCT116 cells using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

tag: cell line

tag: genotype

value: C14orf159 knockout (KO)


title: P27_V1_HDM


title: BN_Gt001


title: control HCT116 cells_rep2

source_name: empty vector-transfected control (EV) cells of HCT-116 cells

value: empty vector-transfected control (EV)


title: C14orf159-KO HCT116 cells_rep1


title: BN_Gt002


title: control HCT116 cells_rep1


title: P26_V4_CTR


title: P26_V2_CTR


title: P26_V4_HDM


title: P26_V2_HDM


title: 853-855-619-BxD73a-RwwJ-FsalinePfc.

city: Los Angeles

first: Desmond

middle: J

last: Smith

state: CA

address: 650 Charles E Young Drive South

institute: UCLA

description: Cocaine study in HMDP mouse strains

data_processing:
Basecalls performed
Genome_build: GRCm38.95
Supplementary_files_format_and_content: text file with information features counts for each samples in a dataframe

source_name: prefrontal cortex

extract_protocol:
RNA-seq was performed as described, with minor variations (Hasin-Brumshtein et al., 2016). NAc and mFC from cocaine and saline treated male and female mice of each HMDP strain were punch dissected. After freezing at -80 degree C and storage with RNAlater (ThermoFisher), samples were homogenized using 1 ml of QIAzol reagent (Qiagen). RNA was extracted using the RNeasy Mini Kit (Qiagen) and quantitated using NanoDrop (ThermoFisher). Following quantification, samples were pooled by sex (3 samples per pool for each infusate/strain condition), except for 4 strains (A/J, LP/J, AKR/J and NOD/ShiLtJ40) where individual mice were analyzed. Sequencing employed 25 ul of each RNA sample at 40 ng/ul concentration.
Libraries were prepared using TruSeq Stranded RNA kits and 100 ng of RNA following standard protocols provided by Illumina. A total of 392 samples from 41 HMDP strains  were analyzed. Samples were barcoded and sequenced using 75 bp paired-ends on an Illumina HiSeq3200 machine. Ten samples per lane were used, with each sample distributed round robin style over multiple lanes to minimize variation.

value: prefrontal cortex

tag: Sex

value: female

value: Saline


title: 854-618-620-BxD73a-RwwJ-FcocainePfc.

description: Cocaine study in HMDP mouse strains

value: Cocaine


title: P26_V5_CTR


title: 851-621-623-BxD73a-RwwJ-MsalinePfc.

description: Cocaine study in HMDP mouse strains

value: male


title: P26_V5_HDM


title: P27_V1_CTR


title: P25_V5_HDM


title: P25_V4_HDM


title: P25_V5_CTR


title: P25_V2_HDM


title: P25_V2_CTR


title: 850-852-622-BxD73a-RwwJ-McocainePfc.

description: Cocaine study in HMDP mouse strains


title: 850-852-622-BxD73a-RwwJ-McocaineNac.

description: Cocaine study in HMDP mouse strains

source_name: nucleus accumben

value: nucleus accumben


title: 851-621-623-BxD73a-RwwJ-MsalineNac.

description: Cocaine study in HMDP mouse strains


title: 733-640-642-BXD61-RwwJ-FcocaineNac.

description: Cocaine study in HMDP mouse strains


title: P25_V4_CTR


title: 854-618-620-BxD73a-RwwJ-FcocaineNac.

description: Cocaine study in HMDP mouse strains


title: P25_V1_HDM


title: P26_V1_CTR


title: 853-855-619-BxD73a-RwwJ-FsalineNac.

description: Cocaine study in HMDP mouse strains


title: P25_V1_CTR


title: 732-734-641-BXD61-RwwJ-FsalinePfc.

description: Cocaine study in HMDP mouse strains


title: P24_V4_HDM


title: 729-731-644-BXD61-RwwJ-McocainePfc.

description: Cocaine study in HMDP mouse strains


title: 730-643-645-BXD61-RwwJ-MsalineNac.

description: Cocaine study in HMDP mouse strains


title: 729-731-644-BXD61-RwwJ-McocaineNac.

description: Cocaine study in HMDP mouse strains


title: 732-734-641-BXD61-RwwJ-FsalineNac.

description: Cocaine study in HMDP mouse strains


title: P24_V5_HDM


title: 733-640-642-BXD61-RwwJ-FcocainePfc.

description: Cocaine study in HMDP mouse strains


title: 730-643-645-BXD61-RwwJ-MsalinePfc.

description: Cocaine study in HMDP mouse strains


title: 655-572-574-NZB-BINJ-MsalinePfc.

description: Cocaine study in HMDP mouse strains

value: NZB/BINJ


title: 652-569-571-NZB-BINJ-FcocaineNac.

description: Cocaine study in HMDP mouse strains


title: 836-837-654-NZB-BINJ-McocaineNac.

description: Cocaine study in HMDP mouse strains


title: 651-653-570-NZB-BINJ-FsalinePfc.

description: Cocaine study in HMDP mouse strains


title: 652-569-571-NZB-BINJ-FcocainePfc.

description: Cocaine study in HMDP mouse strains


title: 655-572-574-NZB-BINJ-MsalineNac.

description: Cocaine study in HMDP mouse strains


title: 836-837-654-NZB-BINJ-McocainePfc.

description: Cocaine study in HMDP mouse strains


title: 558-647-831-PL-J-FcocaineNac.

description: Cocaine study in HMDP mouse strains

value: PL/J


title: 558-647-831-PL-J-FcocainePfc.

description: Cocaine study in HMDP mouse strains


title: 557-646-832-PL-J-FsalinePfc.

description: Cocaine study in HMDP mouse strains


title: 651-653-570-NZB-BINJ-FsalineNac.

description: Cocaine study in HMDP mouse strains


title: 557-646-832-PL-J-FsalineNac.

description: Cocaine study in HMDP mouse strains


title: 555-650-830-PL-J-MsalinePfc.

description: Cocaine study in HMDP mouse strains


title: 554-556-649-PL-J-McocaineNac.

description: Cocaine study in HMDP mouse strains


title: 555-650-830-PL-J-MsalineNac.

description: Cocaine study in HMDP mouse strains


title: 550-600-602-NZO-HlLtJE-FsalineNac.

description: Cocaine study in HMDP mouse strains

value: NZO/HlLtJE


title: 554-556-649-PL-J-McocainePfc.

description: Cocaine study in HMDP mouse strains


title: P24_V5_CTR


title: P24_V2_HDM


title: P20_V2_HDM


title: P20_V4_CTR


title: P20_V5_HDM


title: P19_V5_HDM


title: P19_V1_CTR


title: P20_V5_CTR


title: P19_V5_CTR


title: 550-600-602-NZO-HlLtJE-FsalinePfc.

description: Cocaine study in HMDP mouse strains


title: P18_V5_HDM


title: P19_V4_CTR


title: P19_V4_HDM


title: P20_V4_HDM


title: P24_V4_CTR


title: P20_V1_CTR


title: P24_V1_CTR


title: P18_V5_CTR


title: P26_V1_HDM


title: P20_V2_CTR


title: P19_V2_CTR


title: 549-551-601-NZO-HlLtJE-FcocainePfc.

description: Cocaine study in HMDP mouse strains


title: P24_V2_CTR


title: P19_V2_HDM


title: 549-551-601-NZO-HlLtJE-FcocaineNac.

description: Cocaine study in HMDP mouse strains


title: P19_V1_HDM


title: P20_V1_HDM


title: 548-604-833-NZO-HlLtJE-MsalinePfc.

description: Cocaine study in HMDP mouse strains


title: P24_V1_HDM


title: 543-603-605-NZO-HlLtJE-McocainePfc.

description: Cocaine study in HMDP mouse strains


title: 548-604-833-NZO-HlLtJE-MsalineNac.

description: Cocaine study in HMDP mouse strains


title: 543-603-605-NZO-HlLtJE-McocaineNac.

description: Cocaine study in HMDP mouse strains


title: 568-327-844-BXD62-RwwJ-McocainePfc.

description: Cocaine study in HMDP mouse strains


title: 515-517-326-BXD62-RwwJ-MsalinePfc.

description: Cocaine study in HMDP mouse strains


title: 568-327-844-BXD62-RwwJ-McocaineNac.

description: Cocaine study in HMDP mouse strains


title: 512-323-325-BXD62-RwwJ-FcocainePfc.

description: Cocaine study in HMDP mouse strains


title: 513-322-324-BXD62-RwwJ-FsalinePfc.

description: Cocaine study in HMDP mouse strains


title: P18_V4_CTR


title: 515-517-326-BXD62-RwwJ-MsalineNac.

description: Cocaine study in HMDP mouse strains


title: 513-322-324-BXD62-RwwJ-FsalineNac.

description: Cocaine study in HMDP mouse strains


title: P18_V2_HDM


title: P17_V5_HDM


title: P18_V1_CTR


title: P18_V1_HDM


title: 512-323-325-BXD62-RwwJ-FcocaineNac.

description: Cocaine study in HMDP mouse strains


title: 553-482-484-MA-MyJ-FcocainePfc.

description: Cocaine study in HMDP mouse strains

value: MA/MyJ


title: 553-482-484-MA-MyJ-FcocaineNac.

description: Cocaine study in HMDP mouse strains


title: 488-490-492-MA-MyJ-MsalinePfc.

description: Cocaine study in HMDP mouse strains


title: 488-490-492-MA-MyJ-MsalineNac.

description: Cocaine study in HMDP mouse strains


title: P18_V4_HDM


title: P18_V2_CTR


title: P17_V4_HDM


title: P17_V5_CTR


title: 487-489-491-MA-MyJ-McocainePfc.

description: Cocaine study in HMDP mouse strains


title: P17_V4_CTR


title: P17_V2_HDM


title: P17_V1_CTR


title: P17_V2_CTR


title: P16_V4_CTR


title: P16_V5_HDM


title: P16_V5_CTR


title: P16_V2_HDM


title: P16_V2_CTR


title: 483-485-486-MA-MyJ-FsalinePfc.

description: Cocaine study in HMDP mouse strains


title: 487-489-491-MA-MyJ-McocaineNac.

description: Cocaine study in HMDP mouse strains


title: 483-485-486-MA-MyJ-FsalineNac.

description: Cocaine study in HMDP mouse strains


title: P17_V1_HDM


title: 493-457-290-DBA-1J-FcocaineNac.

description: Cocaine study in HMDP mouse strains


title: 493-457-290-DBA-1J-FcocainePfc.

description: Cocaine study in HMDP mouse strains


title: 459-287-289-DBA-1J-McocainePfc.

description: Cocaine study in HMDP mouse strains


title: 458-286-288-DBA-1J-MsalinePfc.

description: Cocaine study in HMDP mouse strains


title: 458-286-288-DBA-1J-MsalineNac.

description: Cocaine study in HMDP mouse strains


title: P16_V1_CTR


title: 456-815-291-DBA-1J-FsalineNac.

description: Cocaine study in HMDP mouse strains


title: P15_V5_HDM


title: P15_V2_CTR


title: P16_V1_HDM


title: P16_V4_HDM


title: P15_V4_CTR


title: 408-187-189-BXD32-TyJ-FsalinePfc.

description: Cocaine study in HMDP mouse strains


title: P15_V4_HDM


title: 408-187-189-BXD32-TyJ-FsalineNac.

description: Cocaine study in HMDP mouse strains


title: P15_V5_CTR


title: 552-184-186-BXD32-TyJ-McocaineNac.

description: Cocaine study in HMDP mouse strains


title: 407-188-190-BXD32-TyJ-FcocainePfc.

description: Cocaine study in HMDP mouse strains


title: P15_V1_HDM


title: 459-287-289-DBA-1J-McocaineNac.

description: Cocaine study in HMDP mouse strains


title: P14_V5_HDM


title: 407-188-190-BXD32-TyJ-FcocaineNac.

description: Cocaine study in HMDP mouse strains


title: 456-815-291-DBA-1J-FsalinePfc.

description: Cocaine study in HMDP mouse strains


title: 552-184-186-BXD32-TyJ-McocainePfc.

description: Cocaine study in HMDP mouse strains


title: 252-254-509-BXD40-TyJ-FsalinePfc.

description: Cocaine study in HMDP mouse strains


title: P14_V5_CTR


title: 406-183-185-BXD32-TyJJ-MsalineNac.

description: Cocaine study in HMDP mouse strains


title: P14_V2_HDM


title: P14_V4_CTR


title: P14_V4_HDM


title: P14_V2_CTR


title: 252-254-509-BXD40-TyJ-FsalineNac.

description: Cocaine study in HMDP mouse strains


title: P15_V1_CTR


title: 251-253-422-BXD40-TyJ-FcocainePfc.

description: Cocaine study in HMDP mouse strains


title: 251-253-422-BXD40-TyJ-FcocaineNac.

description: Cocaine study in HMDP mouse strains


title: 406-183-185-BXD32-TyJ-MsalinePfc.

description: Cocaine study in HMDP mouse strains


title: 248-250-420-BXD40-TyJ-MsalinePfc.

description: Cocaine study in HMDP mouse strains


title: 248-250-420-BXD40-TyJ-MsalineNac.

description: Cocaine study in HMDP mouse strains


title: 247-421-510-BXD40-TyJ-McocaineNac.

description: Cocaine study in HMDP mouse strains


title: 247-421-510-BXD40-TyJ-McocainePfc.

description: Cocaine study in HMDP mouse strains


title: 244-246-499-SM-J-FsalinePfc.

description: Cocaine study in HMDP mouse strains

value: SM/J


title: P13_V5_HDM

value: HDM


title: 244-246-499-SM-J-FsalineNac.

description: Cocaine study in HMDP mouse strains


title: 243-500-523-SM-J-FcocainePfc.

description: Cocaine study in HMDP mouse strains


title: 243-500-523-SM-J-FcocaineNac.

description: Cocaine study in HMDP mouse strains


title: 241-501-524-SM-J-McocainePfc.

description: Cocaine study in HMDP mouse strains


title: P14_V1_CTR

value: F


title: P13_V4_CTR

value: CTR


title: P13_V1_HDM


title: P15_V2_HDM


title: 241-501-524-SM-J-McocaineNac.

description: Cocaine study in HMDP mouse strains


title: P14_V1_HDM


title: 240-242-502-SM-J-MsalinePfc.

description: Cocaine study in HMDP mouse strains


title: P13_V2_CTR


title: P13_V5_CTR


title: 240-242-502-SM-J-MsalineNac.

description: Cocaine study in HMDP mouse strains


title: P13_V1_CTR


title: P13_V2_HDM


title: 403-180-182-BPL-1J-FcocainePfc.

description: Cocaine study in HMDP mouse strains


title: P13_V4_HDM


title: P12_V4_HDM


title: 403-180-182-BPL-1J-FcocaineNac.

description: Cocaine study in HMDP mouse strains


title: P12_V2_HDM


title: P12_V5_HDM


title: P12_V1_HDM


title: P12_V5_CTR


title: P12_V4_CTR


title: P12_V1_CTR


title: P11_V5_HDM


title: P12_V2_CTR


title: 402-175-177-BPL-1J-MsalinePfc.

description: Cocaine study in HMDP mouse strains


title: 402-175-177-BPL-1J-MsalineNac.

description: Cocaine study in HMDP mouse strains


title: 401--176-178-BPL-1J-McocainePfc.

description: Cocaine study in HMDP mouse strains


title: P11_V5_CTR


title: 401--176-178-BPL-1J-McocaineNac.

description: Cocaine study in HMDP mouse strains


title: 179-181-572-BPL-1J-FsalinePfc.

description: Cocaine study in HMDP mouse strains


title: 179-181-572-BPL-1J-FsalineNac.

description: Cocaine study in HMDP mouse strains


title: P11_V4_HDM


title: CBA-J-283-285-398-FcocainePfc.

description: Cocaine study in HMDP mouse strains

value: CBA/J


title: P11_V4_CTR


title: P11_V2_HDM


title: CBA-J-282-284-399-FsalinePfc.

description: Cocaine study in HMDP mouse strains


title: P11_V2_CTR


title: CBA-J-282-284-399-FsalineNac.

description: Cocaine study in HMDP mouse strains


title: CBA-J-283-285-398-FcocaineNac.

description: Cocaine study in HMDP mouse strains


title: CBA-J-279-281-495-McocainePfc.

description: Cocaine study in HMDP mouse strains


title: CBA-J-278-280-397-MsalineNac.

description: Cocaine study in HMDP mouse strains


title: CBA-J-279-281-495-McocaineNac.

description: Cocaine study in HMDP mouse strains


title: P11_V1_HDM


title: CBA-J-278-280-397-MsalinePfc.

description: Cocaine study in HMDP mouse strains


title: C57BLKS-J-139-349-412-FcocainePfc.

description: Cocaine study in HMDP mouse strains


title: P11_V1_CTR


title: P09_V5_HDM


title: P09_V5_CTR


title: P09_V4_HDM


title: C57BLKS-J-139-349-412-FcocaineNac.

description: Cocaine study in HMDP mouse strains


title: P09_V4_CTR


title: C57BLKS-J-138-350-442-FsalinePfc.

description: Cocaine study in HMDP mouse strains


title: C57BLKS-J-138-350-442-FsalineNac.

description: Cocaine study in HMDP mouse strains


title: C57BLKS-J-136-382-497-MsalineNac.

description: Cocaine study in HMDP mouse strains


title: P08_V4_HDM


title: C57BLKS-J-135-137-351-McocainePfc.

description: Cocaine study in HMDP mouse strains


title: P08_V5_HDM


title: P08_V5_CTR


title: P09_V2_HDM


title: C57BLKS-J-135-137-351-McocaineNac.

description: Cocaine study in HMDP mouse strains


title: P09_V1_HDM


title: P09_V2_CTR


title: P09_V1_CTR


title: C57Bl-10J-62-64-308-MsalinePfc.

description: Cocaine study in HMDP mouse strains


title: P08_V2_HDM


title: P08_V1_HDM


title: C57BLKS-J-136-382-497-MsalinePfc.

description: Cocaine study in HMDP mouse strains


title: C57Bl-10J-60-305-496-FsalinePfc.

description: Cocaine study in HMDP mouse strains


title: C57Bl-10J-61--63-307-McocaineNac.

description: Cocaine study in HMDP mouse strains


title: C57Bl-10J-61--63-307-McocainePfc.

description: Cocaine study in HMDP mouse strains


title: P07_V5_HDM

value: M


title: C57Bl-10J-60-305-496-FsalineNac.

description: Cocaine study in HMDP mouse strains


title: P08_V4_CTR


title: P07_V5_CTR


title: P07_V4_CTR


title: P07_V4_HDM


title: C57Bl-10J-57-59-306-FcocainePfc.

description: Cocaine study in HMDP mouse strains


title: P07_V2_CTR


title: C57BL-6J-131-133-404-FsalinePfc.

description: Cocaine study in HMDP mouse strains


title: C57BL-6J-130-132-134-FcocainePfc.

description: Cocaine study in HMDP mouse strains


title: P08_V2_CTR


title: C57Bl-10J-57-59-306-FcocaineNac.

description: Cocaine study in HMDP mouse strains


title: C57BL-6J-131-133-404-FsalineNac.

description: Cocaine study in HMDP mouse strains


title: C57BL-6J-130-132-134-FcocaineNac.

description: Cocaine study in HMDP mouse strains


title: C57BL-6J-126-128-519-MsalineNac.

description: Cocaine study in HMDP mouse strains


title: C57BL-6J-125-127-129-McocaineNac.

description: Cocaine study in HMDP mouse strains


title: C57BL-6J-125-127-129-McocainePfc.

description: Cocaine study in HMDP mouse strains


title: BXD65-RwwJ-471-473-475-FsalinePfc.

description: Cocaine study in HMDP mouse strains


title: BXD65-RwwJ-471-473-475-FsalineNac.

description: Cocaine study in HMDP mouse strains


title: P08_V1_CTR


title: P07_V1_CTR


title: P05_V5_HDM


title: P05_V5_CTR


title: P07_V2_HDM


title: BXD65-RwwJ-470-472-474-FcocainePfc.

description: Cocaine study in HMDP mouse strains


title: P05_V4_HDM


title: P05_V2_HDM


title: P07_V1_HDM


title: P05_V1_HDM


title: BXD65-RwwJ-470-472-474-FcocaineNac.

description: Cocaine study in HMDP mouse strains


title: P05_V4_CTR


title: BXD65-RwwJ_121-123-476-McocainePfc.

description: Cocaine study in HMDP mouse strains


title: P05_V1_CTR


title: BXD65-RwwJ-121-123-476-McocaineNac.

description: Cocaine study in HMDP mouse strains


title: P04_V4_HDM


title: P05_V2_CTR


title: C57BL-6J-126-128-519-MsalinePfc.

description: Cocaine study in HMDP mouse strains


title: BXD65-RwwJ_120-122-477-MsalinePfc.

description: Cocaine study in HMDP mouse strains


title: P04_V5_CTR


title: P04_V2_CTR


title: P04_V4_CTR


title: P04_V1_HDM


title: NzW_LacJ_MSaline372_374_435PFC.

description: Cocaine study in HMDP mouse strains

value: NzW/LacJ


title: P04_V2_HDM


title: P04_V5_HDM


title: NzW_LacJ_MCocaine371_373_436NAC.

description: Cocaine study in HMDP mouse strains


title: NzW_LacJ_MCocaine371_373_436PFC.

description: Cocaine study in HMDP mouse strains

value: prefrontal cortex


title: P02_V5_HDM


title: NzW_LacJ_MSaline372_374_435NAC.

description: Cocaine study in HMDP mouse strains


title: P04_V1_CTR


title: NzW_LacJ_FSaline368_370_433PFC.

description: Cocaine study in HMDP mouse strains

value: female


title: NzW_LacJ_FCocaine367_369_434NAC.

description: Cocaine study in HMDP mouse strains


title: NzW_LacJ_FSaline368_370_433NAC.

description: Cocaine study in HMDP mouse strains

value: Saline


title: NzW_LacJ_FCocaine367_369_434PFC.

description: Cocaine study in HMDP mouse strains

value: Cocaine


title: BXD65-RwwJ_120-122-477-MsalineNac.

description: Cocaine study in HMDP mouse strains

value: male


title: P02_V4_HDM


title: KK_HiJ_MCocaine365_440_441PFC.

description: Cocaine study in HMDP mouse strains

value: KK/HiJ


title: P02_V5_CTR


title: KK_HiJ_MSaline364_366_439NAC.

description: Cocaine study in HMDP mouse strains

value: nucleus accumben


title: KK_HiJ_MCocaine365_440_441NAC.

description: Cocaine study in HMDP mouse strains


title: P02_V2_HDM


title: KK_HiJ_FSaline360_362_437PFC.

description: Cocaine study in HMDP mouse strains


title: KK_HiJ_MSaline364_366_439PFC.

description: Cocaine study in HMDP mouse strains


title: P02_V1_HDM


title: P02_V4_CTR


title: KK_HiJ_FCocaine361_363_438PFC.

description: Cocaine study in HMDP mouse strains


title: KK_HiJ_FSaline360_362_437NAC.

description: Cocaine study in HMDP mouse strains


title: KK_HiJ_FCocaine361_363_438NAC.

description: Cocaine study in HMDP mouse strains


title: P02_V2_CTR


title: P02_V1_CTR


title: C58_J_MSaline170_425_427NAC.

description: Cocaine study in HMDP mouse strains


title: C58_J_MCocaine171_424_426PFC.

description: Cocaine study in HMDP mouse strains


title: P01_V4_HDM


title: HCN, 24 h, biological rep4

city: Aberdeen Proving Ground

first: Ki

middle: Hwan

last: Ma

state: MD

address: 8350 Ricketts Point Road

department: Medical Toxicology

institute: US Army Medical Research Institute of Chemical Defense

description:
CN-317
Gene expression data from the heart of a mouse exposed to inhaled hydrogen cyanide (nose only, 327 ppm).

hyb_protocol: Following fragmentation, 7.9 ug of cRNA were hybridized for 16 hours at 45C to GeneChip HT MG-430 PM Array Plates (Affymetrix). Arrays were washed and stained in the Affymetrix GeneTitan System.

scan_protocol: Arrays were scanned following Affymetrix scanning protocol in the GeneTitan System.

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

source_name: heart harvested 24 h after nose-only exposure to inhaled HCN (327 ppm)

label_protocol: Biotinylated cRNA were prepared by reverse transcription, second-strand cDNA, and in vitro transcription/biotin labeling reaction from 100 ng total RNA according to the Affymetrix 3’ IVT PLUS Kit instruction.

extract_protocol: Total RNA was isolated using RNeasy Plus Mini Kits (QIAGEN; Germantown, MD, USA). RNA quality and quantity were determined using an Agilent 2100 Bioanalyzer (Agilent Technologies; Santa Clara, CA, USA) and a NanoDrop ND-1000 UV-Vis spectrophotometer (Thermo Fisher Scientific; Waltham, MD, USA), respectively.

value: Male

value: Adult

tag: tissue

value: Heart

tag: exposure

value: HCN (327 ppm)

tag: exposure route

value: Inhalation

tag: harvest time after exposure


title: C58_J_MCocaine171_424_426NAC.

description: Cocaine study in HMDP mouse strains

tag: strain


title: P01_V2_HDM

value: HDM

value: F


title: C58_J_FSaline172_174_429PFC.

description: Cocaine study in HMDP mouse strains


title: HCN, 4 h, biological rep3

description:
CN-284
Gene expression data from the heart of a mouse exposed to inhaled hydrogen cyanide (nose only, 327 ppm).

source_name: heart harvested 4 h after nose-only exposure to inhaled HCN (327 ppm)

tag: age

value: 4 h


title: HCN, 4 h, biological rep4

description:
CN-285
Gene expression data from the heart of a mouse exposed to inhaled hydrogen cyanide (nose only, 327 ppm).


title: HCN, 24 h, biological rep2

description:
CN-315
Gene expression data from the heart of a mouse exposed to inhaled hydrogen cyanide (nose only, 327 ppm).


title: HCN, 24 h, biological rep3

description:
CN-316
Gene expression data from the heart of a mouse exposed to inhaled hydrogen cyanide (nose only, 327 ppm).


title: HCN, 24 h, biological rep1

description:
CN-314
Gene expression data from the heart of a mouse exposed to inhaled hydrogen cyanide (nose only, 327 ppm).


title: C58_J_FSaline172_174_429NAC.

description: Cocaine study in HMDP mouse strains

tag: treatment


title: C58_J_MSaline170_425_427PFC.

description: Cocaine study in HMDP mouse strains

tag: cell type


title: C58_J_FCocaine173_428_430PFC.

description: Cocaine study in HMDP mouse strains


title: C57Br_cdJ_MSaline232_234_453PFC.

description: Cocaine study in HMDP mouse strains


title: C58_J_FCocaine173_428_430NAC.

description: Cocaine study in HMDP mouse strains


title: C57Br_cdJ_FCocaine237_449_451PFC.

description: Cocaine study in HMDP mouse strains


title: C57Br_cdJ_MCocaine231_233_452NAC.

description: Cocaine study in HMDP mouse strains


title: C57Br_cdJ_FSaline236_238_450PFC.

description: Cocaine study in HMDP mouse strains


title: C57Br_cdJ_FSaline236_238_450NAC.

description: Cocaine study in HMDP mouse strains


title: P01_V1_HDM

tag: subjectid


title: PDL1_3

city: Boston

first: Alex Chang-Yu

last: Chen

state: MA

address: 149 13th Street, 7th floor, Room 7103

department: Krantz Family Center for Cancer Research

institute: Massachusetts General Hospital

data_processing:
Adapter trimming and quality filtering of sequencing data were performed by using Cutadpat-v2.4 (Martin, 2011), Trimommatic-v0.36 (Bolger et al., 2014). The filtered reads were mapped on Refseq mm10 using Bowtie2-2.2.5 (parameters: -t -p 11 -N 1 -D 200 -R 20 -L 20 -i S,1,0.50 --nofw).
The mapped reads per gene (raw tag counts) were be quantified as gene expression. Between-sample normalization of gene expression was performed against raw count data by using R 3.6.1 (https://cran.r-project.org/) with DESeq2 (Love et al., 2014) and pheatmap (Kolde, 2015) packages. Genes with adjusted p value less than 0.05 and a fold-change of  2 between at least three samples were identified as statistically significant differentially expressed genes (DEGs).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized tag-count values for each sample

molecule: polyA RNA

source_name: total cells of tumor tissue

extract_protocol:
Tumor were cut into small pieces with a razor blade and digested enzymatically using 0.2% collagenase (Wako, Osaka, Japan) and 20 kU/mL DNase I (Sigma-Aldrich, St Louis, MO) for 60 min at 37°C. Tumor cell and dead cell were removed by 40% Percoll (GE Healthcare, Buckinghamshire, UK) density separation.
PolyA RNAs were isolated and amplified from total cells of tumor tissue. 5'SAGE-seq libraries were constructed. The sequencing was performed by using an Ion 540 Chef kit, an Ion 540 Chip kit, and an Ion S5 Sequencer (Thermo Fisher Scientific) according to the manufacturer’s instructions except the input library concentration was 65 pM.
5'SAGE-seq

treatment_protocol: Colon26 (2 x 10^5 cells / mouse) were subcutaneously inoculated into the right flank of BALB/c mice. The HMGN1 immunostimulatory peptide (minP1, at a dose of 0.08 microgram per mouse per injection, unless otherwise noted) was administered intraperitoneally on day 9 after tumor inoculation. Anti-PD-L1 antibody (clone 10F.9G2; BioXcell, USA) was injected intraperitoneally on days 4 and 8 after tumor inoculation (at a dose of 200 microgram per mouse per injection). On day 10, total cells of tumor tissue from each implanted mouse were used as transcriptome analysis sample.

value: Anti-PD-L1 antibody

value: total cell

value: BALB/c

value: tumor

value: wild type


title: minP1_PDL1_3

value: + Anti-PD-L1 antibody


title: minP1_PDL1_1


title: C57Br_cdJ_FCocaine237_449_451NAC.

description: Cocaine study in HMDP mouse strains

value: female

value: Cocaine


title: BXD98_RwwJ_MSaline270_272_393PFC.

description: Cocaine study in HMDP mouse strains

value: prefrontal cortex

value: male

value: Saline


title: minP1_PDL1_2


title: C57Br_cdJ_MSaline232_234_453NAC.

description: Cocaine study in HMDP mouse strains

value: nucleus accumben


title: C57Br_cdJ_MCocaine231_233_452PFC.

description: Cocaine study in HMDP mouse strains


title: P01_V4_CTR

tag: visit

value: CTR


title: HCN, 2 h, biological rep4

description:
CN-253
Gene expression data from the heart of a mouse exposed to inhaled hydrogen cyanide (nose only, 327 ppm).

source_name: heart harvested 2 h after nose-only exposure to inhaled HCN (327 ppm)

value: Male

value: Adult

value: Heart

value: HCN (327 ppm)

value: Inhalation

value: 2 h


title: PDL1_1

value: Anti-PD-L1 antibody

value: total cell

value: BALB/c


title: BXD98_RwwJ_MCocaine271_273_392PFC.

description: Cocaine study in HMDP mouse strains


title: BXD98_RwwJ_MSaline270_272_393NAC.

description: Cocaine study in HMDP mouse strains


title: P01_V2_CTR

tag: condition

value: F


title: P01_V1_CTR

tag: gender


title: HCN, 4 h, biological rep2

description:
CN-283
Gene expression data from the heart of a mouse exposed to inhaled hydrogen cyanide (nose only, 327 ppm).

value: 4 h


title: HCN, 2 h, biological rep3

description:
CN-252
Gene expression data from the heart of a mouse exposed to inhaled hydrogen cyanide (nose only, 327 ppm).


title: HCN, 1 h, biological rep4

description:
CN-220
Gene expression data from the heart of a mouse exposed to inhaled hydrogen cyanide (nose only, 327 ppm).

source_name: heart harvested 1 h after nose-only exposure to inhaled HCN (327 ppm)

value: 1 h


title: HCN, 4 h, biological rep1

description:
CN-282
Gene expression data from the heart of a mouse exposed to inhaled hydrogen cyanide (nose only, 327 ppm).


title: HCN, 2 h, biological rep1

description:
CN-250
Gene expression data from the heart of a mouse exposed to inhaled hydrogen cyanide (nose only, 327 ppm).


title: HCN, 2 h, biological rep2

description:
CN-251
Gene expression data from the heart of a mouse exposed to inhaled hydrogen cyanide (nose only, 327 ppm).


title: HCN, 1 h, biological rep2

description:
CN-218
Gene expression data from the heart of a mouse exposed to inhaled hydrogen cyanide (nose only, 327 ppm).


title: HCN, 1 h, biological rep3

description:
CN-219
Gene expression data from the heart of a mouse exposed to inhaled hydrogen cyanide (nose only, 327 ppm).


title: PDL1_2

value: tumor

value: wild type


title: minP1_2

value: MGN1 immunostimulatory peptide


title: BXD98_RwwJ_FSaline274_276_395NAC.

description: Cocaine study in HMDP mouse strains

value: nucleus accumben

value: female

value: Saline


title: BXD98_RwwJ_MCocaine271_273_392NAC.

description: Cocaine study in HMDP mouse strains

value: male

value: Cocaine


title: BXD98_RwwJ_FCocaine275_277_394NAC.

description: Cocaine study in HMDP mouse strains


title: BXD98_RwwJ_FSaline274_276_395PFC.

description: Cocaine study in HMDP mouse strains

value: prefrontal cortex


title: BXD98_RwwJ_FCocaine275_277_394PFC.

description: Cocaine study in HMDP mouse strains


title: minP1_3


title: BXD84_RwwJ_MSaline161_163_416NAC.

description: Cocaine study in HMDP mouse strains


title: BXD84_RwwJ_MCocaine162_164_415PFC.

description: Cocaine study in HMDP mouse strains


title: BXD84_RwwJ_MSaline161_163_416PFC.

description: Cocaine study in HMDP mouse strains


title: minP1_1


title: BXD84_RwwJ_MCocaine162_164_415NAC.

description: Cocaine study in HMDP mouse strains


title: HCN, 1 h, biological rep1

description:
CN-217
Gene expression data from the heart of a mouse exposed to inhaled hydrogen cyanide (nose only, 327 ppm).

value: Male

value: Adult

value: Heart

value: HCN (327 ppm)

value: Inhalation


title: BXD84_RwwJ_FSaline165_167_418PFC.

description: Cocaine study in HMDP mouse strains


title: Ct_3

value: control

value: total cell

value: BALB/c


title: C57Bl-10J-62-64-308-MsalineNac.

description: Cocaine study in HMDP mouse strains


title: Ct_2

value: tumor


title: BXD84_RwwJ_FSaline165_167_418NAC.

description: Cocaine study in HMDP mouse strains


title: BXD84_RwwJ_FCocaine166_168_417PFC.

description: Cocaine study in HMDP mouse strains


title: BXD77_RwwJ_MSaline100_102_320PFC.

description: Cocaine study in HMDP mouse strains


title: BXD84_RwwJ_FCocaine166_168_417NAC.

description: Cocaine study in HMDP mouse strains


title: Air, 24 h, biological rep4

description:
CN-301
Gene expression data from the heart of a mouse exposed to air.

source_name: heart harvested 24 h after nose-only exposure to air

value: Air


title: Air, 24 h, biological rep3

description:
CN-300
Gene expression data from the heart of a mouse exposed to air.


title: Air, 4 h, biological rep4

description:
CN-269
Gene expression data from the heart of a mouse exposed to air.

source_name: heart harvested 4 h after nose-only exposure to air

value: 4 h


title: Air, 24 h, biological rep1

description:
CN-298
Gene expression data from the heart of a mouse exposed to air.


title: Air, 24 h, biological rep2

description:
CN-299
Gene expression data from the heart of a mouse exposed to air.


title: BXD77_RwwJ_MSaline100_102_320NAC.

description: Cocaine study in HMDP mouse strains

value: nucleus accumben


title: BXD77_RwwJ_MCocaine99_101_391PFC.

description: Cocaine study in HMDP mouse strains


title: BXD77_RwwJ_MCocaine99_101_391NAC.

description: Cocaine study in HMDP mouse strains


title: BXD77_RwwJ_FSaline96_98_318PFC.

description: Cocaine study in HMDP mouse strains

value: female


title: BXD77_RwwJ_FSaline96_98_318NAC.

description: Cocaine study in HMDP mouse strains

value: Saline


title: Air, 4 h, biological rep2

description:
CN-267
Gene expression data from the heart of a mouse exposed to air.


title: Air, 4 h, biological rep3

description:
CN-268
Gene expression data from the heart of a mouse exposed to air.


title: BXD48a_RwwJ_MSaline356_358_447NAC.

description: Cocaine study in HMDP mouse strains

value: male


title: BXD48a_RwwJ_MSaline356_358_447PFC.

description: Cocaine study in HMDP mouse strains


title: BXD48a_RwwJ_MCocaine357_359_448PFC.

description: Cocaine study in HMDP mouse strains

value: Cocaine


title: Ct_1

value: wild type


title: BXD77_RwwJ_FCocaine95_97_319PFC.

description: Cocaine study in HMDP mouse strains

value: prefrontal cortex


title: BXD48a_RwwJ_MCocaine357_359_448NAC.

description: Cocaine study in HMDP mouse strains


title: BXD77_RwwJ_FCocaine95_97_319NAC.

description: Cocaine study in HMDP mouse strains


title: BXD48a_RwwJ_FSaline352_354_445PFC.

description: Cocaine study in HMDP mouse strains


title: Air, 4 h, biological rep1

description:
CN-266
Gene expression data from the heart of a mouse exposed to air.

value: Male

value: Adult


title: BXD48a_RwwJ_FSaline352_354_445NAC.

description: Cocaine study in HMDP mouse strains


title: BXD48a_RwwJ_FCocaine353_355_446PFC.

description: Cocaine study in HMDP mouse strains


title: BXD48a_RwwJ_FCocaine353_355_446NAC.

description: Cocaine study in HMDP mouse strains


title: BXD42_TyJ_MSaline262_264_410PFC.

description: Cocaine study in HMDP mouse strains


title: BXD42_TyJ_MSaline262_264_410NAC.

description: Cocaine study in HMDP mouse strains


title: BXD42_TyJ_MCocaine263_265_409PFC.

description: Cocaine study in HMDP mouse strains


title: BXD42_TyJ_FSaline266_268_414PFC.

description: Cocaine study in HMDP mouse strains


title: Air, 2 h, biological rep2

description:
CN-235
Gene expression data from the heart of a mouse exposed to air.

source_name: heart harvested 2 h after nose-only exposure to air

value: Heart

value: 2 h


title: BXD42_TyJ_MCocaine263_265_409NAC.

description: Cocaine study in HMDP mouse strains


title: BXD42_TyJ_FSaline266_268_414NAC.

description: Cocaine study in HMDP mouse strains


title: BXD42_TyJ_FCocaine267_269_413NAC.

description: Cocaine study in HMDP mouse strains


title: BXD42_TyJ_FCocaine267_269_413PFC.

description: Cocaine study in HMDP mouse strains


title: BXD38_TyJ_MSaline338_340_462PFC.

description: Cocaine study in HMDP mouse strains


title: Air, 2 h, biological rep4

description:
CN-237
Gene expression data from the heart of a mouse exposed to air.

value: Inhalation


title: Air, 2 h, biological rep3

description:
CN-236
Gene expression data from the heart of a mouse exposed to air.


title: Air, 2 h, biological rep1

description:
CN-234
Gene expression data from the heart of a mouse exposed to air.


title: Air, 1 h, biological rep4

description:
CN-204
Gene expression data from the heart of a mouse exposed to air.

source_name: heart harvested 1 h after nose-only exposure to air

value: 1 h


title: BXD38_TyJ_MSaline338_340_462NAC.

description: Cocaine study in HMDP mouse strains


title: BXD38_TyJ_MCocaine339_341_463PFC.

description: Cocaine study in HMDP mouse strains


title: BXD38_TyJ_FSaline334_336_460PFC.

description: Cocaine study in HMDP mouse strains


title: Air, 1 h, biological rep3

description:
CN-203
Gene expression data from the heart of a mouse exposed to air.


title: BXD38_TyJ_FSaline334_336_460NAC.

description: Cocaine study in HMDP mouse strains


title: BXD38_TyJ_FCocaine335_337_461PFC.

description: Cocaine study in HMDP mouse strains


title: Air, 1 h, biological rep1

description:
CN-201
Gene expression data from the heart of a mouse exposed to air.


title: Air, 1 h, biological rep2

description:
CN-202
Gene expression data from the heart of a mouse exposed to air.


title: KCN, 24 h, biological rep2

description:
CN-182
Gene expression data from the heart of a mouse subcutaneously injected with KCN (8.0 mg/kg).

source_name: heart harvested 24 h after subcutaneous injection of KCN (8.0 mg/kg)

value: KCN (8.0 mg/kg)

value: Subcutaneous injection


title: BXD31_TyJ_MSaline157_159_387NAC.

description: Cocaine study in HMDP mouse strains


title: BXD31_TyJ_MSaline157_159_387PFC.

description: Cocaine study in HMDP mouse strains


title: KCN, 24 h, biological rep4

description:
CN-184
Gene expression data from the heart of a mouse subcutaneously injected with KCN (8.0 mg/kg).


title: BXD38_TyJ_MCocaine339_341_463NAC.

description: Cocaine study in HMDP mouse strains


title: BXD31_TyJ_MCocaine158_388_389NAC.

description: Cocaine study in HMDP mouse strains


title: BXD31_TyJ_MCocaine158_388_389PFC.

description: Cocaine study in HMDP mouse strains


title: BXD38_TyJ_FCocaine335_337_461NAC.

description: Cocaine study in HMDP mouse strains


title: BALB_cJ_MSaline224_226_378PFC.

description: Cocaine study in HMDP mouse strains

value: BALB/cJ


title: BXD31_TyJ_FCocaine160_383_385PFC.

description: Cocaine study in HMDP mouse strains


title: BXD31_TyJ_FCocaine160_383_385NAC.

description: Cocaine study in HMDP mouse strains


title: KCN, 8 h, biological rep3

description:
CN-143
Gene expression data from the heart of a mouse subcutaneously injected with KCN (8.0 mg/kg).

source_name: heart harvested 8 h after subcutaneous injection of KCN (8.0 mg/kg)

value: 8 h


title: BXD31_TyJ_FSaline384_443_444NAC.

description: Cocaine study in HMDP mouse strains

value: nucleus accumben


title: BALB_cJ_FSaline228_230_431NAC.

description: Cocaine study in HMDP mouse strains

value: female


title: BALB_cJ_MCocaine223_225_400NAC.

description: Cocaine study in HMDP mouse strains


title: BALB_cJ_MCocaine223_225_400PFC.

description: Cocaine study in HMDP mouse strains


title: BALB_cJ_MSaline224_226_378NAC.

description: Cocaine study in HMDP mouse strains

value: Saline


title: KCN, 8 h, biological rep4

description:
CN-144
Gene expression data from the heart of a mouse subcutaneously injected with KCN (8.0 mg/kg).


title: BALB_cJ_FCocaine227_229_377PFC.

description: Cocaine study in HMDP mouse strains


title: BALB_cJ_FCocaine227_229_377NAC.

description: Cocaine study in HMDP mouse strains


title: SJL_J_MSaline13_214_343PFC.

description: Cocaine study in HMDP mouse strains

value: male

value: SJL/J


title: KCN, 24 h, biological rep3

description:
CN-183
Gene expression data from the heart of a mouse subcutaneously injected with KCN (8.0 mg/kg).


title: BXD31_TyJ_FSaline384_443_444PFC.

description: Cocaine study in HMDP mouse strains


title: KCN, 8 h, biological rep1

description:
CN-141
Gene expression data from the heart of a mouse subcutaneously injected with KCN (8.0 mg/kg).


title: KCN, 8 h, biological rep2

description:
CN-142
Gene expression data from the heart of a mouse subcutaneously injected with KCN (8.0 mg/kg).


title: KCN, 4 h, biological rep3

description:
CN-104
Gene expression data from the heart of a mouse subcutaneously injected with KCN (8.0 mg/kg).

source_name: heart harvested 4 h after subcutaneous injection of KCN (8.0 mg/kg)

value: 4 h


title: KCN, 4 h, biological rep1

description:
CN-101
Gene expression data from the heart of a mouse subcutaneously injected with KCN (8.0 mg/kg).


title: SJL_J_MSaline13_214_343NAC.

description: Cocaine study in HMDP mouse strains


title: SJL_J_MCocaine12_14_213PFC.

description: Cocaine study in HMDP mouse strains

value: prefrontal cortex

value: Cocaine


title: KCN, 4 h, biological rep2

description:
CN-103
Gene expression data from the heart of a mouse subcutaneously injected with KCN (8.0 mg/kg).

value: Male

value: Adult


title: BALB_cJ_FSaline228_230_431PFC.

description: Cocaine study in HMDP mouse strains


title: KCN, 2 h, biological rep4

description:
CN-64
Gene expression data from the heart of a mouse subcutaneously injected with KCN (8.0 mg/kg).

source_name: heart harvested 2 h after subcutaneous injection of KCN (8.0 mg/kg)

value: Heart

value: 2 h


title: KCN, 24 h, biological rep1

description:
CN-181
Gene expression data from the heart of a mouse subcutaneously injected with KCN (8.0 mg/kg).


title: SJL_J_MCocaine12_14_213NAC.

description: Cocaine study in HMDP mouse strains


title: SJL_J_FSaline8_10_217NAC.

description: Cocaine study in HMDP mouse strains


title: KCN, 2 h, biological rep2

description:
CN-62
Gene expression data from the heart of a mouse subcutaneously injected with KCN (8.0 mg/kg).


title: SJL_J_FSaline8_10_217PFC.

description: Cocaine study in HMDP mouse strains


title: SJL_J_FCocaine9_216_218PFC.

description: Cocaine study in HMDP mouse strains


title: NOD_ShiLtJ_MSaline152PFC.

description: Cocaine study in HMDP mouse strains

value: NOD/ShiLtJ


title: SJL_J_FCocaine9_216_218NAC.

description: Cocaine study in HMDP mouse strains


title: NOD_ShiLtJ_MSaline151NAC.

description: Cocaine study in HMDP mouse strains


title: NOD_ShiLtJ_MSaline149PFC.

description: Cocaine study in HMDP mouse strains


title: KCN, 1 h, biological rep4

description:
CN-24
Gene expression data from the heart of a mouse subcutaneously injected with KCN (8.0 mg/kg).

source_name: heart harvested 1 h after subcutaneous injection of KCN (8.0 mg/kg)

value: KCN (8.0 mg/kg)

value: 1 h


title: KCN, 2 h, biological rep1

description:
CN-61
Gene expression data from the heart of a mouse subcutaneously injected with KCN (8.0 mg/kg).

value: Subcutaneous injection


title: KCN, 1 h, biological rep3

description:
CN-23
Gene expression data from the heart of a mouse subcutaneously injected with KCN (8.0 mg/kg).


title: KCN, 2 h, biological rep3

description:
CN-63
Gene expression data from the heart of a mouse subcutaneously injected with KCN (8.0 mg/kg).


title: NOD_ShiLtJ_MCocaine303NAC.

description: Cocaine study in HMDP mouse strains


title: KCN, 1 h, biological rep2

description:
CN-22
Gene expression data from the heart of a mouse subcutaneously injected with KCN (8.0 mg/kg).


title: KCN, 1 h, biological rep1

description:
CN-21
Gene expression data from the heart of a mouse subcutaneously injected with KCN (8.0 mg/kg).


title: Saline, 24 h, biological rep4

description:
CN-164
Gene expression data from the heart of a mouse subcutaneously injected with saline.

source_name: heart harvested 24 h after subcutaneous injection of saline


title: NOD_ShiLtJ_MCocaine150PFC.

description: Cocaine study in HMDP mouse strains

source_name: prefrontal cortex


title: NOD_ShiLtJ_MCocaine150NAC.

description: Cocaine study in HMDP mouse strains

source_name: nucleus accumben


title: NOD_ShiLtJ_MCocaine303PFC.

description: Cocaine study in HMDP mouse strains


title: Saline, 24 h, biological rep3

description:
CN-163
Gene expression data from the heart of a mouse subcutaneously injected with saline.


title: NOD_ShiLtJ_MSaline149NAC.

description: Cocaine study in HMDP mouse strains


title: NOD_ShiLtJ_MCocaine148PFC.

description: Cocaine study in HMDP mouse strains


title: NOD_ShiLtJ_FSaline302PFC.

description: Cocaine study in HMDP mouse strains


title: NOD_ShiLtJ_MSaline152NAC.

description: Cocaine study in HMDP mouse strains


title: NOD_ShiLtJ_MCocaine148NAC.

description: Cocaine study in HMDP mouse strains


title: NOD_ShiLtJ_FSaline302NAC.

description: Cocaine study in HMDP mouse strains


title: NOD_ShiLtJ_FSaline156PFC.

description: Cocaine study in HMDP mouse strains


title: NOD_ShiLtJ_FSaline156NAC.

description: Cocaine study in HMDP mouse strains


title: NOD_ShiLtJ_FSaline154PFC.

description: Cocaine study in HMDP mouse strains


title: NOD_ShiLtJ_MSaline151PFC.

description: Cocaine study in HMDP mouse strains


title: Saline, 24 h, biological rep2

description:
CN-162
Gene expression data from the heart of a mouse subcutaneously injected with saline.


title: Saline, 8 h, biological rep3

description:
CN-123
Gene expression data from the heart of a mouse subcutaneously injected with saline.

source_name: heart harvested 8 h after subcutaneous injection of saline

value: 8 h


title: NOD_ShiLtJ_FCocaine155PFC.

description: Cocaine study in HMDP mouse strains


title: NOD_ShiLtJ_FSaline154NAC.

description: Cocaine study in HMDP mouse strains

value: nucleus accumben


title: Saline, 24 h, biological rep1

description:
CN-161
Gene expression data from the heart of a mouse subcutaneously injected with saline.


title: Saline, 8 h, biological rep4

description:
CN-124
Gene expression data from the heart of a mouse subcutaneously injected with saline.


title: NOD_ShiLtJ_FCocaine196PFC.

description: Cocaine study in HMDP mouse strains

value: female


title: Saline, 8 h, biological rep1

description:
CN-121
Gene expression data from the heart of a mouse subcutaneously injected with saline.

value: Saline


title: NOD_ShiLtJ_FCocaine155NAC.

description: Cocaine study in HMDP mouse strains


title: NOD_ShiLtJ_FCocaine153PFC.

description: Cocaine study in HMDP mouse strains


title: MRL_MpJ_MCocaine72_297_299PFC.

description: Cocaine study in HMDP mouse strains

value: male

value: MRL/MpJ


title: MRL_MpJ_MSaline69_71_298NAC.

description: Cocaine study in HMDP mouse strains


title: MRL_MpJ_FSaline65_67_301NAC.

description: Cocaine study in HMDP mouse strains


title: MRL_MpJ_FSaline65_67_301PFC.

description: Cocaine study in HMDP mouse strains


title: NOD_ShiLtJ_FCocaine153NAC.

description: Cocaine study in HMDP mouse strains


title: MRL_MpJ_FCocaine66_68_300PFC.

description: Cocaine study in HMDP mouse strains


title: MRL_MpJ_MCocaine72_297_299NAC.

description: Cocaine study in HMDP mouse strains


title: Saline, 4 h, biological rep3

description:
CN-84
Gene expression data from the heart of a mouse subcutaneously injected with saline.

source_name: heart harvested 4 h after subcutaneous injection of saline

value: 4 h


title: MRL_MpJ_MSaline69_71_298PFC.

description: Cocaine study in HMDP mouse strains

value: prefrontal cortex


title: Saline, 4 h, biological rep2

description:
CN-82
Gene expression data from the heart of a mouse subcutaneously injected with saline.


title: MRL_MpJ_FCocaine66_68_300NAC.

description: Cocaine study in HMDP mouse strains

value: Cocaine


title: LP_J_MSaline293PFC.

description: Cocaine study in HMDP mouse strains

value: LP/J


title: NOD_ShiLtJ_FCocaine196NAC.

description: Cocaine study in HMDP mouse strains


title: LP_J_MSaline293NAC.

description: Cocaine study in HMDP mouse strains


title: LP_J_MSaline56PFC.

description: Cocaine study in HMDP mouse strains


title: LP_J_MSaline56NAC.

description: Cocaine study in HMDP mouse strains


title: LP_J_MSaline54NAC.

description: Cocaine study in HMDP mouse strains


title: LP_J_MSaline54PFC.

description: Cocaine study in HMDP mouse strains


title: LP_J_MCocaine294PFC.

description: Cocaine study in HMDP mouse strains


title: single-cell HLHS2_d14 CMs_4

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

country: Germany

institute: Klinikum rechts der Isar – Technical University Munich

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for low-quality using Trimmomatic (default parameters)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat2 (default parameters)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include HTSeq-count values for each Sample, TPM matrix for single cell RNA-seq

source_name: hiPSC-derived cardiomyocytes

growth_protocol: Control and HLHS iPSCs were subjected to cardiac differentiation to generate early cardiac progenitors (Cao et al., Cell Research (2013) 23:1119-1132) and cardiomyocytes  (Burridge et al., Curr Protoc Hum Genet. ; 87: 21.3.1–21.3.15). Samples were collected at d0, d1, d2, d3, d6, d8, and d14 and processed for RNA-Seq.

extract_protocol:
Total RNA from 3 independent differentiations was extracted using the Stratagene Absolutely RNA Micro kit according to the manufacturer's instructions and pooled.
RNA libraries for sequencing were prepared from 1 µg RNA using standard Illumina protocols.

treatment_protocol: RNA samples were collected from 3 independent differentiations in triplicates at d0, d1, d2, d3, d6, d8, and d14.

value: hiPSC-derived cardiomyocytes

tag: diagnosis

value: HLHS


title: Saline, 2 h, biological rep3

description:
CN-43
Gene expression data from the heart of a mouse subcutaneously injected with saline.

source_name: heart harvested 2 h after subcutaneous injection of saline

value: Male

value: Adult

value: Heart

value: 2 h


title: Saline, 4 h, biological rep1

description:
CN-81
Gene expression data from the heart of a mouse subcutaneously injected with saline.

value: Subcutaneous injection


title: Saline, 1 h, biological rep4

description:
CN-4
Gene expression data from the heart of a mouse subcutaneously injected with saline.

source_name: heart harvested 1 h after subcutaneous injection of saline

value: 1 h


title: Saline, 2 h, biological rep1

description:
CN-41
Gene expression data from the heart of a mouse subcutaneously injected with saline.


title: Saline, 8 h, biological rep2

description:
CN-122
Gene expression data from the heart of a mouse subcutaneously injected with saline.

value: 8 h


title: LP_J_MCocaine294NAC.

description: Cocaine study in HMDP mouse strains

value: nucleus accumben


title: Saline, 2 h, biological rep2

description:
CN-42
Gene expression data from the heart of a mouse subcutaneously injected with saline.

value: Saline


title: Saline, 1 h, biological rep2

description:
CN-2
Gene expression data from the heart of a mouse subcutaneously injected with saline.


title: Saline, 1 h, biological rep3

description:
CN-3
Gene expression data from the heart of a mouse subcutaneously injected with saline.


title: LP_J_MCocaine53PFC.

description: Cocaine study in HMDP mouse strains

value: male


title: LP_J_MCocaine53NAC.

description: Cocaine study in HMDP mouse strains


title: LP_J_FSaline295PFC.

description: Cocaine study in HMDP mouse strains

value: female


title: single-cell CTRL1_d14 CMs_2

value: healthy control


title: MDA-MB-468_gRNA2+dox

city: Hong Kong

first: Rebecca Y. M.

last: Chin

address: To Yuen Street

department: BMS

country: Hong Kong

institute: City University of Hong Kong

data_processing:
RNA-seq raw reads  were mapped to the UCSC human reference genome (hg38) and calculation of gene counts using STAR mapping with gene quantification mode.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: MDA-MB-468 breast carcinoma cell line

extract_protocol:
RNA Isolation with TRIzol (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Knockout of TCOF1

value: doxycyline to induce TCOF1 knockout

value: breast cancer cell derived mammosphere


title: HLHS3_606 d14 CMs

value: hiPSC-derived cardiomyocytes


title: LP_J_MCocaine55PFC.

description: Cocaine study in HMDP mouse strains

value: prefrontal cortex

value: LP/J

value: Cocaine


title: MDA-MB-468_CTL+dox

value: wild type

value: doxycyline


title: single-cell HLHS2_d14 CMs_3

value: HLHS


title: LP_J_MCocaine55NAC.

description: Cocaine study in HMDP mouse strains


title: MDA-MB-468_gRNA2

value: no treatment


title: single-cell CTRL1_d14 CMs_1


title: HLHS3_606 d8 early CMs

source_name: hiPSC-derived early cardiomyocytes

value: hiPSC-derived early cardiomyocytes


title: Saline, 1 h, biological rep1

description:
CN-1
Gene expression data from the heart of a mouse subcutaneously injected with saline.

value: Male

value: Adult

value: Heart

value: Subcutaneous injection

value: 1 h


title: MDA-MB-468_CTL


title: LP_J_FSaline295NAC.

description: Cocaine study in HMDP mouse strains

value: nucleus accumben

value: female

value: Saline


title: HLHS3_606 d6 early CMs


title: HLHS3_606 d0 iPSCs

source_name: hiPSCs

value: hiPSCs


title: HLHS2_612 d14 CMs

value: hiPSC-derived cardiomyocytes


title: LP_J_FSaline52NAC.

description: Cocaine study in HMDP mouse strains

value: LP/J


title: LP_J_FSaline50PFC.

description: Cocaine study in HMDP mouse strains

value: prefrontal cortex


title: HLHS2_612 d8 early CMs


title: LP_J_FSaline50NAC.

description: Cocaine study in HMDP mouse strains


title: LP_J_FCocaine296NAC.

description: Cocaine study in HMDP mouse strains

value: Cocaine


title: LP_J_FCocaine51PFC.

description: Cocaine study in HMDP mouse strains


title: HLHS1_375 d14 CMs


title: HLHS2_612 d0 iPSCs


title: HLHS1_375 d8 early CMs


title: LP_J_FCocaine296PFC.

description: Cocaine study in HMDP mouse strains


title: LP_J_FSaline52PFC.

description: Cocaine study in HMDP mouse strains


title: HLHS1_375 d6 early CMs


title: LP_J_FCocaine49PFC.

description: Cocaine study in HMDP mouse strains


title: HLHS2_612 d6 early CMs


title: LP_J_FCocaine51NAC.

description: Cocaine study in HMDP mouse strains


title: LP_J_FCocaine49NAC.

description: Cocaine study in HMDP mouse strains


title: HLHS1_375 d0 iPSCs


title: CTR3 d14 CMs

value: healthy control


title: FVB_NJ_MSaline38_40_381NAC.

description: Cocaine study in HMDP mouse strains

value: male

value: FVB/NJ


title: CTR3 d8 early CMs

value: hiPSC-derived early cardiomyocytes


title: RMPI_C_3

city: Pamplona

first: Aintzane

last: Zabaleta

state: Navarra

address: Avda. Pío XII 55

country: Spain

institute: FOUNDATION FOR APPLIED MEDICAL RESEARCH

description: Gene expression data from FACS sorted RPMI 8226 cell line

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix HuGene-2_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: Data was normalized using Bioconductor software and RMA algorithm.

label: Biotin

source_name: RPMI 8226 multiple myeloma (MM) cell line cultured alone (Analysis of FACS sorted RPMI 8226 cell line)

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: RPMI 8226 MM cell line was cultured in RPMI medium supplemented with 10% FBS, 1% L-glutamine and 1% streptomycin/penicilin. Fresh PBLs were obtained form healthy volunteers and used the same day it was drawn.

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: RPMI 8226 cells were incubated in the presence of human PBL at a 10:1 effector to target ratio (E:T) with or without isatuximab. After 24 hrs cells were harvested and CD3-, CD56+, CD45+ NK cells and CD38+, CD138+, CD45- RPMI 8226 MM cell line were FACS sorted. Apoptotic cells were discarded based on anexinn-V staining. Transcriptome analysis was performed on purified cells.

tag: protocol

value: control

value: FACS sorted RPMI 8226 cell line


title: RMPI_PBLS_SAR_2

description: Gene expression data from FACS sorted RPMI 8226 cell line and NK cells from healthy donor´s PBMCs

source_name: RPMI 8226 MM cell line co-cultured with PBLs from healthy donors at a 10:1 effector to target ratio in the presence of isatuximab (Analysis of FACS sorted RPMI 8226 cell line and NK cells)

tag: cell line

value: RPMI 8226 multiple myeloma (MM) cell line


title: FVB_NJ_MCocaine37_39_192PFC.

description: Cocaine study in HMDP mouse strains


title: RMPI_C_2


title: RMPI_SAR_2

source_name: RPMI 8226 MM cell line cultured in the presence of 10 µg/ml isatuximab for 24 hrs (Analysis of FACS sorted RPMI 8226 cell line)


title: RMPI_SAR_3

value: cultured in the presence of 10 µg/ml isatuximab for 24 hrs


title: RMPI_PBLS_2

source_name: RPMI 8226 MM cell line co-cultured with PBLs from healthy donors at a 10:1 effector to target ratio (Analysis of FACS sorted RPMI 8226 cell line and NK cells)


title: CTR3 d0 iPSCs


title: sample_51 (PEP2_14)

city: Marseille

first: Thibaud

last: Parpaite

address: 51 Bd Pierre Dramard

department: Neural basis of the Somatosensory System

country: France

institute: Aix-Marseille University

data_processing:
cDNAds libraries were sequenced either in a NextSeq 500 (Illumina) using paired-end reads (76 pb) with an average depth of 29 million reads per cell. The raw reads (FastQ files) were cleaned by removing adaptor sequences, short sequences (length < 25 bp), low-quality bases (quality score < 30) and ambiguous sequences (i.e., reads with more than 30% unknown bases ‘N’) using CutAdapt 1.9.1 software.
TopHat-2 v2.1.0 was used to map the cleaned RNA-seq reads to the mouse genome (mm10 / GRCm38.90) with two mismatches, two gaps and one multihit allowed. TopHat-2 splicing algorithm was used to map reads covering splice junctions, thereby improving the utilization of reads.
After genome mapping, gene counts matrix was determined using GenomicAlignment (version 1.24.0) using GTF annotation. A set of mitochondrial genes (mt-Atp6, mt-Atp8, mt-Co1, mt-Co2, mt-Co3, mt-Cytb, mt-Nd1, mt-Nd2, mt-Nd3, mt-Nd4, mt-Nd4l, mt-Nd5, mt-Nd6) were used to check viability of each sample: the sample is considered as non-apoptotic if the expression of these genes is less than 10% of total count in the same cell.
Read counts were analyzed in the R/Bioconductor environment (version 3.12) with the R package edgeR. The gene expression value was normalized between samples by TMM with a gene detection threshold of 20 counts in at least two cells.
Relative abundance were obtained by sample normalization using TPM (transcripts per kilobase million).
Genome_build: mm10
Supplementary_files_format_and_content: Text file containing tab-delimited matrices of Transcripts Per Million (TPM) transformed values.

source_name: sensory neuron

growth_protocol: DRG were isolated and incubated in enzyme solution containing 2 mg.ml-1 of collagenase 1A (Sigma-Aldrich) and 5 mg.ml-1 of dispase II (ThermoFisher) for 45 min at 37 °C. The tissue was washed several times and triturated in Hanks’ balanced salt solution (HBSS, Gibco). The resulting suspension was centrifuged (300×g for 5 min) in 1 ml HBSS and 1 ml Bovine Serum Albumin (BSA, 15%, Sigma-Aldrich). The pellet was rinsed with Dulbecco’s Phosphate Buffered Saline (DPBS, Gibco) and centrifuged (300×g for 2 min). Cells were then plated onto poly-D-lysine-coated 12-mm round glass coverslips (Corning) in 24-well plates and were grown in Dulbecco’s modified Eagle’s medium (DMEM, High glucose, pyruvate, ThermoFisher) supplemented with 10% heat-inactivated Fetal Bovine Serum (FBS, Gibco), 100 U.ml-1 (1%) penicillin–streptomycin (Gibco), 100 ng.ml-1 nerve growth factor (NGF, Merk Millipore), and 50 ng.ml-1 glial-derived neurotrophic factor (GDNF, ThermoFisher).

extract_protocol:
After electrophysiological recording, the cytoplasmic content of the neuron was harvested into the patch pipette, transferred into lysis solution (RNaseOUT 8 U.µl-1, 2% Triton X-100) and flash frozen. Reverse transcription was performed using a SMART-seq v4 Low Input Kit (Clontech) directly on the cell lysate according to the manufacturer’s protocol.
After cDNAds amplification, 50 μl of the sample were subjected to cDNA purification on AMPure XP beads. 0.5 ng of each purified cDNAds were used to construct the sequencing library using Nextera XT kit (Illumina) with fragments over 300-bp length from each neuron.

treatment_protocol: Patch-clamp experiments were performed under whole-cell configuration using an Axopatch 200B amplifier (Axon Instruments). Patch pipettes had resistances of 2-3 MΩ when filled with an internal solution consisting of (in mM) 140 CsCl, 10 Hepes, 5 EGTA, 1 CaCl2, 1 MgCl2, 4 MgATP and 0.4 Na2GTP (pH adjusted to 7.3 with CsOH). Internal solution was supplemented with 0.4 U/µl of RNaseOUT (Invitrogen). The extracellular solution consisted of (in mM) 133 NaCl, 3 KCl, 1 MgCl2, 10 Hepes, 2.5 CaCl2, 10 glucose (pH adjusted to 7.3 with NaOH).

tag: genotype

value: wild type

value: dorsal root ganglion

value: 10-12 weeks

value: YES

value: SA

value: RA


title: sample_52 (PEP2_15)

tag: Sex

value: NO

value: US


title: FVB_NJ_FSaline34_36_380NAC.

description: Cocaine study in HMDP mouse strains

value: nucleus accumben

value: female

value: Saline


title: RMPI_C_1


title: RMPI_PBLS_SAR_1

value: co-cultured with PBLs from healthy donors at a 10:1 effector to target ratio in the presence of isatuximab

value: FACS sorted RPMI 8226 cell line and NK cells


title: FVB_NJ_FCocaine33_35_194PFC.

description: Cocaine study in HMDP mouse strains

value: prefrontal cortex

value: FVB/NJ

value: Cocaine


title: sample_50 (PEP2_13)

value: male

tag: tissue


title: Macrosomic, rep 4

city: Columbia

first: Julia

last: Taylor

state: MO

address: University Avenue

institute: University of Missouri

description: Gene expression data from adult male mouse adipose tissue

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 7G.  Software: GCOS 1.4, chip processing protocol (fluidics protocol):EukGE-WS2v5_450

data_processing: We used GCOS 1.4 software with the default setting (alpha1: 0.05, alpha2: 0.065, tau: 0.015, TGT Value: 500, Normalization factor (NF): 1.000) to generate the CHP files.

source_name: Epididymal fat pad

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Animals were the offspring of hemiovariectomized female mice. The resulting hyperovulation results in a crowded uterine horn. Embryo growth is affected, and pups born have a wide range of body weights.

extract_protocol: Tri Reagent extraction of total RNA was performed according to the manufacturer's instructions, with further cleanup on Qiagen Rneasy columns.

treatment_protocol: No treatment other than maternal hemiovariectomy prior to pregnancy.

tag: tag


title: RMPI_SAR_1

value: RPMI 8226 multiple myeloma (MM) cell line

value: cultured in the presence of 10 µg/ml isatuximab for 24 hrs

value: FACS sorted RPMI 8226 cell line


title: FVB_NJ_MCocaine37_39_192NAC.

description: Cocaine study in HMDP mouse strains


title: CTR2 d14 CMs

value: hiPSC-derived cardiomyocytes

value: healthy control


title: FVB_NJ_MSaline38_40_381PFC.

description: Cocaine study in HMDP mouse strains


title: CTR2 d8 early CMs

value: hiPSC-derived early cardiomyocytes


title: CTR2 d6 early CMs


title: RMPI_PBLS_1

value: co-cultured with PBLs from healthy donors at a 10:1 effector to target ratio


title: sample_49 (PEP2_12)

value: wild type

value: dorsal root ganglion

value: 10-12 weeks

value: YES

value: US

value: RA


title: CTR2 d0 iPSCs

value: hiPSCs


title: FVB_NJ_FCocaine33_35_194NAC.

description: Cocaine study in HMDP mouse strains

value: nucleus accumben

value: female

value: FVB/NJ


title: sample_53 (PEP2_16)

value: male

value: NO


title: DBA_2J_MSaline46_48_345PFC.

description: Cocaine study in HMDP mouse strains

value: prefrontal cortex

value: Saline


title: CTR1 d14 CMs

value: hiPSC-derived cardiomyocytes

value: healthy control


title: sample_47 (PEP2_10)


title: CTR3 d6 early CMs

value: hiPSC-derived early cardiomyocytes


title: FVB_NJ_FSaline34_36_380PFC.

description: Cocaine study in HMDP mouse strains


title: sample_45 (PEP2_08)

value: wild type

value: SA


title: CTR1 d8 early CMs


title: DBA_2J_MSaline46_48_345NAC.

description: Cocaine study in HMDP mouse strains


title: CTR1 d6 early CMs


title: DBA_2J_MCocaine45_47_207PFC.

description: Cocaine study in HMDP mouse strains

value: Cocaine


title: sample_48 (PEP2_11)

value: dorsal root ganglion

value: 10-12 weeks


title: sample_43 (PEP2_06)

value: YES

value: IA

value: US


title: DBA_2J_FSaline42_444_210PFC.

description: Cocaine study in HMDP mouse strains

value: female


title: DBA_2J_MCocaine45_47_207NAC.

description: Cocaine study in HMDP mouse strains

value: nucleus accumben


title: CTR1 d0 iPSCs

value: hiPSCs


title: HLHS2_612 d3 CPCs

source_name: hiPSC-derived cardiac progenitors

value: hiPSC-derived cardiac progenitors

value: HLHS


title: HLHS2_612 d2 CPCs


title: HLHS2_612 d1 CPCs


title: sample_44 (PEP2_07)

value: male

value: NO


title: sample_42 (PEP2_05)

value: RA


title: sample_39 (PEP2_02)


title: DBA_2J_FSaline42_444_210NAC.

description: Cocaine study in HMDP mouse strains

value: Saline


title: DBA_2J_FCocaine41_43_209NAC.

description: Cocaine study in HMDP mouse strains


title: sample_41 (PEP2_04)

value: wild type


title: C3HeB_FeJ_MSaline27_28_220PFC.

description: Cocaine study in HMDP mouse strains

source_name: prefrontal cortex

value: prefrontal cortex


title: sample_40 (PEP2_03)

value: SA


title: HLHS3_606 d2 CPCs


title: DBA_2J_FCocaine41_43_209PFC.

description: Cocaine study in HMDP mouse strains

value: Cocaine


title: HLHS3_606 d1 CPCs


title: sample_46 (PEP2_09)

value: dorsal root ganglion

value: 10-12 weeks


title: sample_37 (PEP1_09)

value: NR


title: C3HeB_FeJ_MSaline27_28_220NAC.

description: Cocaine study in HMDP mouse strains

source_name: nucleus accumben


title: C3HeB_FeJ_MCocaine30_29_219PFC.

description: Cocaine study in HMDP mouse strains


title: sample_38 (PEP2_01)


title: sample_36 (PEP1_08)


title: HLHS1_375 d3 CPCs


title: C3HeB_FeJ_MCocaine30_29_219NAC.

description: Cocaine study in HMDP mouse strains


title: HLHS1_375 d2 CPCs


title: sample_35 (PEP1_07)


title: C3HeB_FeJ_FSaline24_23_222PFC.

description: Cocaine study in HMDP mouse strains


title: HLHS3_606 d3 CPCs


title: sample_34 (PEP1_06)


title: HLHS1_375 d1 CPCs


title: C3HeB_FeJ_FSaline24_23_222NAC.

description: Cocaine study in HMDP mouse strains


title: CTR3 d3 CPCs

value: healthy control


title: CTR3 d2 CPCs


title: CTR2 d3 CPCs


title: sample_31 (PEP1_03)

value: YES

value: IA

value: US


title: C3H_HeJ_MSaline141_143_347PFC.

description: Cocaine study in HMDP mouse strains


title: C3HeB_FeJ_FCocaine25_26-221NAC.

description: Cocaine study in HMDP mouse strains

value: nucleus accumben

value: female


title: C3H_HeJ_MSaline141_143_347NAC.

description: Cocaine study in HMDP mouse strains

value: male


title: CTR2 d1 CPCs

value: hiPSC-derived cardiac progenitors


title: sample_29 (PEP1_01)

value: NO


title: CTR2 d2 CPCs


title: sample_27 (TH_01)

value: TH

value: RA


title: CTR1 d3 CPCs


title: C3H_HeJ_MCocaine140_142_313PFC.

description: Cocaine study in HMDP mouse strains

value: prefrontal cortex


title: C3H_HeJ_MCocaine140_142_313NAC.

description: Cocaine study in HMDP mouse strains


title: sample_28 (TH_02)

value: wild type


title: C3H_HeJ_FSaline145_147_346PFC.

description: Cocaine study in HMDP mouse strains

value: Saline


title: CTR1 d2 CPCs


title: CTR1 d1 CPCs


title: sample_26 (NP3_01)

value: dorsal root ganglion


title: sample_33 (PEP1_05)

value: 10-12 weeks


title: sample_25 (NP2_11)


title: C3HeB_FeJ_FCocaine25_26-221PFC.

description: Cocaine study in HMDP mouse strains

value: Cocaine


title: Germ free (Sample 4)

city: Edmonton

first: Edan

last: Foley

state: Alberta

address: 116 st and 85 ave

department: Medical Microbiology and Immunology

country: Canada

institute: University of Alberta

data_processing:
Cell Ranger v3.0 (10X Genomics) was used to demultiplex raw base call files from Illumina sequencing and to align reads to the Zebrafish reference genome
Genome_build: Ensembl GRCz11.96
Supplementary_files_format_and_content: TSV/MTX files

source_name: Dissociated intestines from germ-free fish

extract_protocol:
Cellular RNA extracted and barcoded with 10X Genomics Chromium Controller
Chromium Single Cell 3′ Library & Gel Bead Kit v3

value: TL

value: Intestinal and associated tissue

tag: developmental stage

value: 6 dpf larvae

value: germ-free


title: Conventially reared (Sample 3)

source_name: Dissociated intestines from conventionally reared fish

value: conventionally reared


title: sample_32 (PEP1_04)

value: YES

value: IA

value: US


title: sample_24 (NP2_10)

value: male


title: sample_30 (PEP1_02)


title: C3H_HeJ_FCocaine144_146_312PFC.

description: Cocaine study in HMDP mouse strains

value: female


title: Eye lrpap1-KO rep6 [LRPAP1-6]

city: Guangzhou

first: Jiali

last: Li

address: 253 Gongye Middle Avenue

country: China

institute: Zhujiang Hosptial

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-seq reads were aligned to the zebrafish genome(Ensembl, GRCz11) using HISAT2(version 2.1.0), and TPM was used to further normalize gene expression counts between 12 samples.
Genome_build: GRCz11
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Eyeball

growth_protocol: All animals were raised in laboratory practice

extract_protocol:
A total of 12 samples(six wild type zebrafish and six mutant) were used for PolyA sequencing. Each sample included a pair of eyeballs from the same zebrafish.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A stable lrpap1 knockout zebrafish line was obtained via several rounds of crossing and screening through Sanger sequencing.

value: Eyeball

tag: Stage

value: post natal month three


title: BALB_cByJ_MSaline116_257_259PFC.

description: Cocaine study in HMDP mouse strains

value: prefrontal cortex

tag: strain

value: BALB/cByJ


title: Eye lrpap1-KO rep5 [LRPAP1-5]


title: Eye lrpap1-KO rep4 [LRPAP1-4]


title: sample_22 (NP2_08)

value: wild type

value: dorsal root ganglion

tag: age


title: sample_21 (NP2_07)

value: 10-12 weeks

value: NO


title: Eye lrpap1-KO rep3 [LRPAP1-3]


title: BALB_cByJ_MCocaine115_117_375PFC.

description: Cocaine study in HMDP mouse strains

tag: treatment

value: Cocaine


title: BALB_cByJ_MCocaine115_117_375NAC.

description: Cocaine study in HMDP mouse strains

tag: cell type

value: nucleus accumben


title: BALB_cByJ_FSaline112_114_260PFC.

description: Cocaine study in HMDP mouse strains

value: Saline


title: sample_19 (NP2_05)

value: RA

value: SA


title: sample_18 (NP2_04)

value: YES


title: Eye lrpap1-KO rep1 [LRPAP1-1]


title: C3H_HeJ_FSaline145_147_346NAC.

description: Cocaine study in HMDP mouse strains


title: BALB_cByJ_FSaline112_114_260NAC.

description: Cocaine study in HMDP mouse strains


title: Eye WT rep6 [CONTROL-6]


title: sample_20 (NP2_06)

value: IA


title: BALB_cByJ_FCocaine111_113_261PFC.

description: Cocaine study in HMDP mouse strains


title: sample_23 (NP2_09)

value: male

value: US


title: sample_16 (NP2_02)


title: Eye WT rep4 [CONTROL-4]

value: Eyeball


title: BALB_cByJ_FCocaine111_113_261NAC.

description: Cocaine study in HMDP mouse strains

value: female


title: Eye WT rep3 [CONTROL-3]

value: post natal month three


title: AKR_J_MSaline204PFC.

description: Cocaine study in HMDP mouse strains

value: prefrontal cortex

value: AKR/J


title: BALB_cByJ_MSaline116_257_259NAC.

description: Cocaine study in HMDP mouse strains

value: BALB/cByJ


title: sample_17 (NP2_03)

value: wild type

value: dorsal root ganglion

value: 10-12 weeks


title: Eye WT rep5 [CONTROL-5]


title: C3H_HeJ_FCocaine144_146_312NAC.

description: Cocaine study in HMDP mouse strains

value: nucleus accumben

value: Cocaine


title: sample_15 (NP2_01)

value: NO

value: RA


title: sample_14 (NP1_06)

value: YES

value: SA


title: sample_13 (NP1_05)

value: male


title: Eye WT rep1 [CONTROL-1]


title: AKR_J_MSaline20PFC.

description: Cocaine study in HMDP mouse strains

value: Saline


title: sample_12 (NP1_04)

value: US

value: IA


title: Eye lrpap1-KO rep2 [LRPAP1-2]

value: Eyeball

value: post natal month three


title: AKR_J_MSaline20NAC.

description: Cocaine study in HMDP mouse strains

value: AKR/J


title: sample_10 (NP1_02)


title: sample_11 (NP1_03)


title: AKR_J_MSaline19PFC.

description: Cocaine study in HMDP mouse strains

value: prefrontal cortex


title: AKR_J_MSaline19NAC.

description: Cocaine study in HMDP mouse strains


title: sample_09 (NP1_01)

value: wild type


title: AKR_J_MCocaine203PFC.

description: Cocaine study in HMDP mouse strains


title: PTm_CMT3

city: Frederiksberg C

first: Andrew

last: Williams

state: --- Select One ---

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

data_processing:
Adaptor sequences and low quality reads removed
Mapped to Mus musculus (mm39) using HISAT
DEG assessed using DeSeq2
Genome_build: mm39
Supplementary_files_format_and_content: Excel file with count data for each sample.

source_name: CMT-93 intestinal epithelial cells

growth_protocol: Cells were treated with PSTO (20 uM) or vehicle control for 30 minutes prior to T. muris treament (100 ug/mL), and harvested after 6 hours.

extract_protocol:
Total RNA was extracted using mRNAeasy kits (Qiagen).
Standard Illumina

value: CMT-93 intestinal epithelial cells

value: PTSO + T. muris


title: PTm_CMT2


title: sample_08 (NF_08)

value: dorsal root ganglion

value: 10-12 weeks

value: NF


title: PTm_CMT1


title: sample_07 (NF_07)

value: NO

value: RA


title: AKR_J_MCocaine203NAC.

description: Cocaine study in HMDP mouse strains

value: nucleus accumben

value: Cocaine


title: AKR_J_MCocaine22PFC.

description: Cocaine study in HMDP mouse strains

value: male


title: AKR_J_MSaline204NAC.

description: Cocaine study in HMDP mouse strains

value: Saline


title: sample_06 (NF_06)


title: Eye WT rep2 [CONTROL-2]


title: Tm_CMT3

value: T. muris


title: Tm_CMT2


title: Tm_CMT1


title: AKR_J_MCocaine21PFC.

description: Cocaine study in HMDP mouse strains


title: sample_04 (NF_04)


title: AKR_J_MCocaine22NAC.

description: Cocaine study in HMDP mouse strains


title: sample_05 (NF_05)


title: AKR_J_MCocaine21NAC.

description: Cocaine study in HMDP mouse strains


title: AKR_J_FSaline205NAC.

description: Cocaine study in HMDP mouse strains

value: female


title: sample_02 (NF_02)


title: AKR_J_FSaline205PFC.

description: Cocaine study in HMDP mouse strains


title: sample_03 (NF_03)


title: P_CMT2

value: PTSO


title: P_CMT1


title: sample_01 (NF_01)


title: AKR_J_FSaline16PFC.

description: Cocaine study in HMDP mouse strains

value: AKR/J