title: EBs.index07.BC_191

description: Transcriptome measurement of sample EBs.index07.BC_191


title: EBs.index07.BC_225

status: Public on Apr 01 2021

type: SRA

city: Utrecht

first: Isabel

last: Guerreiro

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Transcriptome measurement of sample EBs.index07.BC_225

library_source: transcriptomic

data_processing:
Demultiplexing of raw data (previously demultiplexed on Illumina index) was done using barcodes. Read1 measurements contain in read1, from 5’ to 3’: a 6nt UMI, an 8nt barcode, followed by unalignable sequence, usually polyT. Read2 of the transcriptomic measurements contains the mRNA sequence.
mRNA reads (in read2) were aligned using tophat2 (v2.1.1) using parameters ‘--segment-length 22 --read-mismatches 4 --read-edit-dist 4 --min-anchor 6 --min-intron-length 25 --max-intron-length 25000 --no-novel-juncs --no-novel-indels --no-coverage-search --b2-very-sensitive --b2-N 1 --b2-gbar 200’ to a transcriptome (options ‘--GTF’ and ‘--transcriptome-index’) obtained from GENCODE (v26) supplemented with ERCC mRNA spike-in sequences.
Reads and unique UMIs were counted per gene (according to the “intersection-strict” algorithm of `htseq-count` [http://htseq.readthedocs.io/en/master/count.html]). For each gene, the number of unique observed UMIs was trimmed by starting at the UMI with highest read count and setting UMIs with Hamming distance of 1 to zero, and iteratively filtering all UMI sequences (in case of equal read counts for a UMI, ties were broking by lexicographic sorting of the UMIs). The number of observed distinct UMIs after trimming was taken as the transcript count for that gene.
Genome_build: mm10
Supplementary_files_format_and_content: Tables are provided with the number of transcripts per gene.

molecule: polyA RNA

organism: Mus musculus

source_name: embryoid bodies from mouse ESCs

growth_protocol: Expansion medium: ESC were expanded for minimally 2 passages on gelatin-coated tissue-culture plastic in B27N2 medium supplemented with 3 μM CHIR99021 (AxonMed 1386), 1 μM 10 ng/mL Lif (Merck Millipore ESG1106), PD0325901 (1 μM, AxonMed 1408). PrE-induction medium: An average of 10 ESC per microwell was seeded in high-glucose DMEM containing sodium pyruvate and Glutamax (Thermo Fisher, 10569010), supplemented with 10% serum, 10 mM Non-essential amino acids, 10 mM HEPES and penicillin/streptomycin. This medium was supplemented with 10 ng/mL Lif (Merck Millipore ESG1106) and 2 µM Y27632 (AxonMed 1683). PrE-induction supplements were 3 μM CHIR99021 (AxonMed 1386), 50 ng/mL Fgf4 (RnD systems, 5846-F4-025), 10 nM RA (Sigma R2625), 1 mM 8Br-cAMP (Biolog, B007-50E), 1 µg/mL heparin (Sigma) and 50 µM 2-mercaptoethanol (Gibco 11528926).

extract_protocol:
EBs were washed twice in PBS-0 and collagenase IV (600U/ml) was added. Plates were shaken at 350RPM for 30 minutes. EBs were then transferred to TrypleE 10X (no dilution) and shaken for 20 minutes. EBs were dissociated into single cell suspensions using a small capillary. The resulting suspension was quenched using PBS with 50% FBS, centrifuged and resuspended in 230 ul of PBS0 with 10% FBS. Cells were stained with PDGFRA antibody (1:150 dilution) for 30 min at 4°C followed by three PBS (+10%FBS) washes, secondary antibody incubation (1:400) for 30 min. Cells were washed three times in PBS0 and sorted for further processing.
Library construction was done following the Sort-seq protocol as previously described [Muraro, T. et al. A Single-Cell Transcriptome Atlas of the Human Pancreas. Cell Systems 3, 385–394.e3 (2016).]
Library preparation was done as previously described[Hashimshony, T. et al. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome biology 17, 77, (2016).] using 5 μL of aRNA and 8 PCR cycles. Libraries were run on the Illumina NextSeq platform with high output 75 bp paired-end sequencing.

tag: tissue

value: embryoid bodies from mouse ESCs

tag: celseq2 adapter

tag: pdgfra staining

value: negative


title: Sham_O3 rep6

city: RTP

first: John

middle: S.

last: House

state: NC

address: 111 TW Alexander Drive

department: Biostatistics & Computational Biology Branch

country: USA

institute: National Instititute of Environmental Health Sciences

data_processing:
Reads Trimmed, aligned with STAR default parameters, and quantified to the PARTEK E/M Annotation model at the GENE level
Extracted Gene Counts rounded to nearest Integer for DESeq Analysis
Removed Genes without at least 1 count in at least 10 of the samples
Removed Two samples from Analysis (not uploaded) with abberant PCA clustering of top 500 expressed genes
DESeq2 Normalization provided in processed files
Genome_build: Rattus norvegicus rn6 with Annotation = Ensembl Transcripts Release 90
Supplementary_files_format_and_content: normalized count matrix from DESeq2

molecule: total RNA

organism: Rattus norvegicus

source_name: Liver

growth_protocol: 10-11 Week old purchased and housed hardwood chip bedding under controlled conditions (21°C, 50-65% relative humidity and 12h light/dark cycle); Rats were provided with standard Purina (5001) rat chow (Brentwood, MO) and water ad libitum

extract_protocol:
10-20mg similar location liver  extracted with Rneasy minikit (Qiagen, Valencia, CA)
hepatic RNA samples were indexed using the PrepXTM RNA-Seq for Illumina Library Kit (Takara Bio Inc.; Kusatsu, Japan) with SuperScript III Reverse Transcriptase (ThermoFisher) and AMPure XP beads (Agilent) on the Apollo324 system (Takara Bio Inc.) using the recommended protocols developed by Takara Bio.

treatment_protocol:
12wk old rats underwent either Sham or Hepatic Vagotomy surgery and were allowed to recover 5-6 days
Air or Ozone (1.0ppm) for 4 hours, for 1 or 2 days and necropsied within 2 hours after exposure

tag: treatment


title: HepV_O3 rep2


title: Sham_O3 rep5


title: HepV_O3 rep1


title: Sham_O3 rep3


title: Sham_O3 rep4


title: HepV_Air rep6

value: Air


title: Sham_O3 rep1


title: EBs.index07.BC_277

description: Transcriptome measurement of sample EBs.index07.BC_277


title: Sham_O3 rep2


title: HepV_Air rep4


title: HepV_Air rep5


title: EBs.index07.BC_187

description: Transcriptome measurement of sample EBs.index07.BC_187


title: HepV_Air rep3


title: HepV_Air rep1


title: EBs.index07.BC_143

description: Transcriptome measurement of sample EBs.index07.BC_143


title: EBs.index07.BC_181

description: Transcriptome measurement of sample EBs.index07.BC_181


title: HepV_Air rep2


title: Sham_Air rep5


title: EBs.index07.BC_141

description: Transcriptome measurement of sample EBs.index07.BC_141


title: Sham_Air rep4


title: Sham_Air rep3


title: Sham_Air rep2


title: EBs.index07.BC_185

description: Transcriptome measurement of sample EBs.index07.BC_185


title: EBs.index07.BC_183

description: Transcriptome measurement of sample EBs.index07.BC_183


title: Sham_Air rep1


title: EBs.index07.BC_137

description: Transcriptome measurement of sample EBs.index07.BC_137


title: miRNA EtOH_24h-2

city: Beijing

first: Xu

middle: Zhao

last: Gao

state: Beijing

address: The Summer Palace Road No. 5

department: College of Biological Sciences

country: China

institute: Peking University

data_processing:
The reads generated from RNA-seq were initially tested by fastQC and processed to remove the low-quality (Q value < 30 ) reads and adapter sequences. To get the high-quality reads, we cut the first 9bp from each read by perl script. Secondly, the high-quality reads left were mapped to the TAIR10 reference using the STAR (Spliced Transcripts Alignment to a Reference) tool (77). STAR can map the reads faster. The parameters were default, and the mapping rates was greater than 90%.
Genome_build: Tair 10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: plant

growth_protocol: The wild type plant used was Arabidopsis thaliana ecotype Col-0. The seedlings were separated into two classes for hormone processing. Half seedlings were incubated under ABA for 0.5h, 1h, 3h, 6h, 9h, 12h, and 24h time points. Simultaneously, the mock processed seedlings were curated for the same seven time points.

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the seedlings were collected separately for next sequencing

value: seedling

tag: genotype

value: wild type


title: EBs.index07.BC_133

description: Transcriptome measurement of sample EBs.index07.BC_133


title: EBs.index07.BC_123

description: Transcriptome measurement of sample EBs.index07.BC_123


title: miRNA EtOH_24h-1


title: miRNA EtOH_9h-2


title: miRNA EtOH_6h-2


title: miRNA EtOH_9h-1


title: miRNA EtOH_6h-1


title: EBs.index07.BC_095

description: Transcriptome measurement of sample EBs.index07.BC_095


title: EBs.index07.BC_091

description: Transcriptome measurement of sample EBs.index07.BC_091


title: miRNA EtOH_3h-2


title: EBs.index07.BC_093

description: Transcriptome measurement of sample EBs.index07.BC_093


title: EBs.index07.BC_089

description: Transcriptome measurement of sample EBs.index07.BC_089


title: miRNA EtOH_3h-1


title: EBs.index07.BC_139

description: Transcriptome measurement of sample EBs.index07.BC_139


title: miRNA EtOH_1h-2


title: miRNA EtOH_0.5h-2


title: EBs.index07.BC_085

description: Transcriptome measurement of sample EBs.index07.BC_085


title: miRNA EtOH_0.5h-1


title: EBs.index07.BC_079

description: Transcriptome measurement of sample EBs.index07.BC_079


title: miRNA EtOH_12h-2


title: EBs.index07.BC_077

description: Transcriptome measurement of sample EBs.index07.BC_077


title: EBs.index07.BC_073

description: Transcriptome measurement of sample EBs.index07.BC_073


title: miRNA EtOH_12h-1


title: miRNA ABA_9h-2


title: miRNA ABA_24h-1


title: miRNA ABA_9h-1


title: miRNA ABA_12h-1


title: miRNA ABA_6h-2


title: EBs.index07.BC_047

description: Transcriptome measurement of sample EBs.index07.BC_047


title: miRNA ABA_3h-2


title: EBs.index07.BC_045

description: Transcriptome measurement of sample EBs.index07.BC_045


title: miRNA ABA_24h-2


title: EBs.index07.BC_043

description: Transcriptome measurement of sample EBs.index07.BC_043


title: EBs.index07.BC_041

description: Transcriptome measurement of sample EBs.index07.BC_041


title: miRNA ABA_0.5h-2


title: miRNA ABA_1h-1


title: miRNA EtOH_1h-1


title: miRNA ABA_1h-2


title: miRNA ABA_0.5h-1


title: miRNA ABA_12h-2


title: EBs.index07.BC_039

description: Transcriptome measurement of sample EBs.index07.BC_039


title: 24HR_T3_ATAC_rep1

city: Minneapolis

first: Noelle

middle: E

last: Gillis

state: Minnesota

address: 2231 6th ST SE, CCRB

institute: University of Minnesota

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.7
illumina adapters were removed with TrimGalore
trimmed reads were mapped to hg38 using bowtie2
peaks were called with MACS2
differential accessibilty was called using DiffBind
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak

molecule: genomic DNA

organism: Homo sapiens

source_name: normal thyroid epithelial cell line Nthy-ORI

growth_protocol: Cells were hormone starved in phenol-red free culture media with charcoal stripped FBS for 24 hours, followed by the addition of  10nM T3 or vehicle (NaOH) treatment for 6 or 24 hours.

extract_protocol:
nuclei from 50,000 cells were extracted and incubated with Tn5 transposase
Illumina Nextera Library prep kit (ATAC-seq)

treatment_protocol: Cells were treated with 10nM T3 or vehicle (NaOH) treatment for 6 or 24 hours.

tag: time

value: 24 hours

value: 10nM T3

tag: data type

value: ATAC-seq


title: miRNA ABA_3h-1


title: 6HR_T3_ATAC_rep2

value: 6 hours


title: 24HR_T3_ATAC_rep2


title: EBs.index07.BC_033

description: Transcriptome measurement of sample EBs.index07.BC_033


title: 6HR_T3_ATAC_rep1


title: EBs.index07.BC_027

description: Transcriptome measurement of sample EBs.index07.BC_027


title: 24HR_T3_RNA_rep2

data_processing:
Basecalls performed using CASAVA version 1.7
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Fastq Quality Trimmer
STAR 2.7 was used to align fastq files to hg38
Htseq was used to count aligned reads
SARTools/DESeq2 was used for differential expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text files with raw counts values for each sample
Supplementary_files_format_and_content: matrix table with normalized counts; DESeq2 output

extract_protocol:
cells were lysed in Trizol reagent, RNA was extracted, followed by BioAnalyzer analysis and all RIN values were  >8
KAPA Hyperprep Total RNA kit with Ribo Depeltion Kit, 1ug of total RNA

value: RNA-seq


title: 24HR_T3_RNA_rep1


title: 24HR_vehicle_RNA_rep2

value: vehicle


title: vehicle_ATAC_rep1


title: EBs.index06.BC_356

description: Transcriptome measurement of sample EBs.index06.BC_356

value: positive


title: miRNA ABA_6h-1


title: 6HR_T3_RNA_rep1


title: EBs.index06.BC_350

description: Transcriptome measurement of sample EBs.index06.BC_350


title: vehicle_ATAC_rep2


title: EBs.index06.BC_354

description: Transcriptome measurement of sample EBs.index06.BC_354


title: 6HR_T3_RNA_rep2


title: 24HR_vehicle_RNA_rep1


title: 6HR_vehicle_RNA_rep2


title: 6HR_vehicle_RNA_rep1


title: EBs.index06.BC_346

description: Transcriptome measurement of sample EBs.index06.BC_346


title: EBs.index06.BC_344

description: Transcriptome measurement of sample EBs.index06.BC_344


title: PBRM1_CUTRUN_T3_rep1

data_processing:
Library strategy: CUT&RUN
Basecalls performed using CASAVA version 1.7
illumina adapters were removed with TrimGalore
trimmed reads were mapped to hg38 using bowtie2
peaks were called with MACS2
consensus peak sets were generated using IDR
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak file, consensus peaks dervied from two replicates

extract_protocol:
nuclei from 500,000 cells were extracted and subjected to CUT&RUN protocol using the indicated antibody.
NEB Next Ultra II FS DNA Library Kit (CUT&RUN)

tag: cell line

value: Nthy-ORI

tag: cell type

value: normal thyroid epithelial cell

value: CUT&RUN


title: IGG_CUTRUN


title: PBRM1_CUTRUN_T3_rep2


title: PBRM1_CUTRUN_vehicle_rep2


title: ARID1A_CUTRUN_T3_rep1


title: PBRM1_CUTRUN_vehicle_rep1


title: EBs.index06.BC_338

description: Transcriptome measurement of sample EBs.index06.BC_338


title: ARID1A_CUTRUN_T3_rep2


title: EBs.index06.BC_310

description: Transcriptome measurement of sample EBs.index06.BC_310


title: BRG1_CUTRUN_T3_rep2


title: BRG1_CUTRUN_vehicle_rep1


title: EBs.index06.BC_312

description: Transcriptome measurement of sample EBs.index06.BC_312


title: TRb_CUTRUN_T3_rep2


title: BRG1_CUTRUN_vehicle_rep2


title: BRG1_CUTRUN_T3_rep1


title: EBs.index06.BC_302

description: Transcriptome measurement of sample EBs.index06.BC_302


title: TRb_CUTRUN_T3_rep1


title: EBs.index06.BC_300

description: Transcriptome measurement of sample EBs.index06.BC_300


title: EBs.index06.BC_308

description: Transcriptome measurement of sample EBs.index06.BC_308


title: EBs.index06.BC_296

description: Transcriptome measurement of sample EBs.index06.BC_296


title: TRb_CUTRUN_vehicle_rep1


title: transposon mutant library subjected to carbon starvation in the absence of pyocyanin, replicate2

city: Pasadena

first: Dianne

last: Newman

state: CA

address: 1200 E California Blvd, MC 147-75

institute: Caltech

description:
pre-growth and out-growth medium: SMM=40 mM sodium succinate, 50 mM KH2PO4/K2HPO4 (pH 7), 42.8 mM NaCl, 1 mM MgSO4, 9.35 mM NH4Cl,  trace elements
survival medium: minimal phosphate buffer=50 mM KH2PO4/ K2HPO4 (pH 7), 42.8 mM NaCl
PCR-enriched dsDNA from transposon-genome boundary
transposon insertion site reads from library incubated in the absence of pyocyanin, replicate2
rep2_26noPYO

data_processing:
Library strategy: TnSeq
Image analysis, base calling, de-multiplexing, and conversion of sequencing to fastq format were carried out by HiSeq Control Software (HCS) on the Illumina HiSeq 2500 machine.
Transposon sequence (TATAAGAGTCAG) was identified and trimmed from reads using a custom perl script. Reads that did not include an exact match to the transposon sequence were discarded.
Trimmed reads were mapped to the Pseudomonas aeruginosa UCBPP-PA14 genome using bowtie2 with default options except -N set to 1(Langmead and Salzberg. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.)
To produce the processed data files, read counts per gene were summarized using the featueCounts program of the Subread package, using the “--read2pos” option to precisely map the transposon insertion site (Liao et al. featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7):923-30, 2014)
To produce the supplemental file, in which the robustness of the differences in read counts per gene to possible genetic bottlenecks of the experiment was assessed, the ARTIST package was used. The “Con-Artist” pipeline without HMM refinement was used as described by authors, with a window size of 100bp and 100 simulations (Pritchard et al. ARTIST: High-Resolution Genome-Wide Assessment of Fitness Using Transposon-Insertion Sequencing. PLOS Genetics 10(11): e1004782, 2014)
Genome_build: gi|116048575|ref|NC_008463.1|
Supplementary_files_format_and_content: Raw counts per gene are supplied as individual tab-delimited text files, one per sample. Genomic loci for each feature and aggregated ratios and p-values determined by ARTIST pipeline analysis are supplied as a supplemental file.

organism: Pseudomonas aeruginosa

source_name: planktonic cells

growth_protocol: An aliquot of the Pseudomonas aeruginosa (PA) PA14 transposon library generated by Basta et al. (Basta et al. Identification of Fitness Determinants during Energy-Limited Growth Arrest in Pseudomonas aeruginosa. mBio, 8(6):e01170-17, 2017) was thawed on ice for 15 min, diluted to a starting optical density (OD500) of 0.05 and grown aerobically under shaking conditions (250 rpm) at 37 ºC for ~ 4-5 generations to an OD500  of 0.8-1 in SMM.

extract_protocol:
Genomic DNA (gDNA) was extracted from the pelleted samples using the DNeasy Blood & Tissue kit (Qiagen) according to the manufacturer’s directions.
All the steps for sequencing library preparation followed exactly the protocol used by Basta et al. (mBio, 2017), including (i) DNA shearing by sonication (to produce 200-500 bp fragments), (ii) end-repair, (iii) addition of poly(C) tail and (iv) enrichment of transposon-genome junctions and addition of adapter for Illumina sequencing by PCR

treatment_protocol: Cells were pelleted, washed and resuspended (5 mL, OD500 = 2) in minimal phosphate buffer with or without 100 µM PYO. Cells were then incubated for 26 hrs under shaking conditions at 37º C. After the incubation, cultures from all treatments were pelleted, washed, and resuspended in fresh SMM. Immediately, an aliquot of each sample was diluted to an OD500 of ~ 0.05 in 25 mL SMM, followed by outgrowth for ~ 4-5 generations to an OD500 of 0.8-1. After outgrowth, 2.5 mL of each sample was pelleted and stored at -80 ºC.

tag: strain

value: Tn5 transposon insertion library constructed in WT background


title: EBs.index06.BC_342

description: Transcriptome measurement of sample EBs.index06.BC_342


title: transposon mutant library subjected to carbon starvation in the presence of pyocyanin, replicate2

description:
pre-growth and out-growth medium: SMM=40 mM sodium succinate, 50 mM KH2PO4/K2HPO4 (pH 7), 42.8 mM NaCl, 1 mM MgSO4, 9.35 mM NH4Cl,  trace elements
survival medium: minimal phosphate buffer=50 mM KH2PO4/ K2HPO4 (pH 7), 42.8 mM NaCl, 100 µM pyocyanin
PCR-enriched dsDNA from transposon-genome boundary
transposon insertion site reads from library incubated in the presence of pyocyanin, replicate2
rep2_26+PYO


title: transposon mutant library subjected to carbon starvation in the presence of pyocyanin, replicate1

description:
pre-growth and out-growth medium: SMM=40 mM sodium succinate, 50 mM KH2PO4/K2HPO4 (pH 7), 42.8 mM NaCl, 1 mM MgSO4, 9.35 mM NH4Cl,  trace elements
survival medium: minimal phosphate buffer=50 mM KH2PO4/ K2HPO4 (pH 7), 42.8 mM NaCl, 100 µM pyocyanin
PCR-enriched dsDNA from transposon-genome boundary
transposon insertion site reads from library incubated in the presence of pyocyanin, replicate1
rep1_26+PYO


title: ARID1A_CUTRUN_vehicle_rep2


title: EBs.index06.BC_294

description: Transcriptome measurement of sample EBs.index06.BC_294


title: EBs.index06.BC_264

description: Transcriptome measurement of sample EBs.index06.BC_264


title: ARID1A_CUTRUN_vehicle_rep1


title: EBs.index06.BC_256

description: Transcriptome measurement of sample EBs.index06.BC_256


title: dlPFC tissue_Normal Control [202817030020_R04C01]

type: genomic

city: Baltimore

first: Brion

middle: S

last: Maher

state: MD

address: 624 N. Broadway

department: Mental Health

institute: Johns Hopkins Bloomberg School of Public Health

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using standard recommended Illumina scanner settings.

data_processing:
R Statistical Stoftware v3.6.1
M_final.txt : log-transformed beta (i.e., M value)

label: Cy5 and Cy3

source_name: dlPFC tissue

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted and purified from tissue samples using Qiagen DNeasy Kit according to standard instructions.

tag: gender

value: M

tag: age of death

tag: postmortem interval

tag: race

value: AA

tag: group

value: Normal Control


title: dlPFC tissue_Pysch Control [202817030020_R02C01]

value: F

value: CAUC

value: Pysch Control


title: transposon mutant library subjected to carbon starvation in the absence of pyocyanin, replicate1

description:
pre-growth and out-growth medium: SMM=40 mM sodium succinate, 50 mM KH2PO4/K2HPO4 (pH 7), 42.8 mM NaCl, 1 mM MgSO4, 9.35 mM NH4Cl,  trace elements
survival medium: minimal phosphate buffer=50 mM KH2PO4/ K2HPO4 (pH 7), 42.8 mM NaCl
PCR-enriched dsDNA from transposon-genome boundary
transposon insertion site reads from library incubated in the absence of pyocyanin, replicate1
rep1_26noPYO


title: dlPFC tissue_Pysch Control [202817030020_R03C01]


title: dlPFC tissue_Opioids [202817030020_R05C01]

value: Opioids


title: dlPFC tissue_Normal Control [202817030020_R01C01]


title: EBs.index06.BC_254

description: Transcriptome measurement of sample EBs.index06.BC_254

value: embryoid bodies from mouse ESCs


title: dlPFC tissue_Pysch Control [202817030175_R07C01]


title: EBs.index06.BC_246

description: Transcriptome measurement of sample EBs.index06.BC_246


title: dlPFC tissue_Normal Control [202817030175_R06C01]


title: TRb_CUTRUN_vehicle_rep2


title: dlPFC tissue_Pysch Control [202817030175_R05C01]


title: dlPFC tissue_Opioids [202817030175_R04C01]


title: dlPFC tissue_Pysch Control [202817030175_R08C01]


title: EBs.index06.BC_216

description: Transcriptome measurement of sample EBs.index06.BC_216


title: EBs.index06.BC_214

description: Transcriptome measurement of sample EBs.index06.BC_214


title: EBs.index06.BC_212

description: Transcriptome measurement of sample EBs.index06.BC_212


title: dlPFC tissue_Pysch Control [202817030122_R08C01]


title: dlPFC tissue_Opioids [202817030175_R01C01]


title: dlPFC tissue_Pysch Control [202817030122_R07C01]


title: dlPFC tissue_Opioids [202817030122_R06C01]


title: dlPFC tissue_Pysch Control [202817030122_R04C01]


title: EBs.index06.BC_208

description: Transcriptome measurement of sample EBs.index06.BC_208


title: dlPFC tissue_Pysch Control [202817030122_R02C01]


title: dlPFC tissue_Pysch Control [202817030122_R03C01]


title: dlPFC tissue_Pysch Control [202817030122_R05C01]


title: EBs.index06.BC_206

description: Transcriptome measurement of sample EBs.index06.BC_206


title: EBs.index06.BC_202

description: Transcriptome measurement of sample EBs.index06.BC_202


title: dlPFC tissue_Opioids [202817030122_R01C01]


title: dlPFC tissue_Pysch Control [202817030078_R08C01]


title: dlPFC tissue_Opioids [202817030078_R07C01]


title: dlPFC tissue_Opioids [202817030078_R06C01]


title: dlPFC tissue_Opioids [202817030078_R05C01]


title: dlPFC tissue_Normal Control [202817030078_R03C01]


title: dlPFC tissue_Opioids [202817030078_R04C01]


title: dlPFC tissue_Pysch Control [202817030078_R02C01]


title: dlPFC tissue_Opioids [202817030078_R01C01]


title: dlPFC tissue_Opioids [202817030062_R08C01]


title: dlPFC tissue_Pysch Control [202817030062_R04C01]


title: EBs.index06.BC_164

description: Transcriptome measurement of sample EBs.index06.BC_164


title: EBs.index06.BC_160

description: Transcriptome measurement of sample EBs.index06.BC_160


title: EBs.index06.BC_194

description: Transcriptome measurement of sample EBs.index06.BC_194


title: EBs.index06.BC_168

description: Transcriptome measurement of sample EBs.index06.BC_168


title: EBs.index06.BC_158

description: Transcriptome measurement of sample EBs.index06.BC_158


title: EBs.index06.BC_162

description: Transcriptome measurement of sample EBs.index06.BC_162


title: dlPFC tissue_Opioids [202816900113_R06C01]


title: dlPFC tissue_Opioids [202817030062_R07C01]


title: EBs.index06.BC_210

description: Transcriptome measurement of sample EBs.index06.BC_210


title: dlPFC tissue_Opioids [202817030062_R06C01]


title: dlPFC tissue_Pysch Control [202817030175_R03C01]


title: dlPFC tissue_Opioids [202817030062_R05C01]


title: EBs.index06.BC_156

description: Transcriptome measurement of sample EBs.index06.BC_156


title: dlPFC tissue_Pysch Control [202817030175_R02C01]


title: dlPFC tissue_Opioids [202816900113_R05C01]


title: dlPFC tissue_Normal Control [202816900113_R07C01]


title: EBs.index06.BC_154

description: Transcriptome measurement of sample EBs.index06.BC_154


title: dlPFC tissue_Opioids [202817030062_R03C01]


title: EBs.index06.BC_146

description: Transcriptome measurement of sample EBs.index06.BC_146


title: dlPFC tissue_Normal Control [202816900113_R03C01]


title: dlPFC tissue_Opioids [202816900113_R01C01]


title: dlPFC tissue_Pysch Control [202816900049_R06C01]


title: dlPFC tissue_Opioids [202816900113_R02C01]


title: dlPFC tissue_Opioids [202816900049_R04C01]


title: dlPFC tissue_Opioids [202816900049_R05C01]


title: EBs.index06.BC_120

description: Transcriptome measurement of sample EBs.index06.BC_120


title: EBs.index06.BC_116

description: Transcriptome measurement of sample EBs.index06.BC_116


title: EBs.index06.BC_118

description: Transcriptome measurement of sample EBs.index06.BC_118


title: dlPFC tissue_Pysch Control [202817030062_R02C01]


title: EBs.index06.BC_114

description: Transcriptome measurement of sample EBs.index06.BC_114


title: EBs.index06.BC_112

description: Transcriptome measurement of sample EBs.index06.BC_112


title: EBs.index06.BC_108

description: Transcriptome measurement of sample EBs.index06.BC_108


title: dlPFC tissue_Pysch Control [202817030044_R08C01]


title: dlPFC tissue_Pysch Control [202817030044_R07C01]


title: dlPFC tissue_Opioids [202817030044_R05C01]


title: dlPFC tissue_Normal Control [202816900113_R04C01]


title: EBs.index06.BC_106

description: Transcriptome measurement of sample EBs.index06.BC_106


title: dlPFC tissue_Opioids [202817030044_R06C01]


title: dlPFC tissue_Opioids [202817030044_R04C01]


title: EBs.index06.BC_072

description: Transcriptome measurement of sample EBs.index06.BC_072


title: dlPFC tissue_Normal Control [202817030044_R01C01]


title: dlPFC tissue_Pysch Control [202817030044_R02C01]


title: dlPFC tissue_Opioids [202817030044_R03C01]


title: EBs.index06.BC_068

description: Transcriptome measurement of sample EBs.index06.BC_068


title: dlPFC tissue_Opioids [202816900049_R07C01]


title: dlPFC tissue_Pysch Control [202817030019_R07C01]


title: dlPFC tissue_Opioids [202817030019_R05C01]


title: dlPFC tissue_Opioids [202816900049_R03C01]


title: dlPFC tissue_Pysch Control [202816900049_R02C01]


title: dlPFC tissue_Opioids [202816900049_R01C01]


title: EBs.index06.BC_066

description: Transcriptome measurement of sample EBs.index06.BC_066


title: EBs.index06.BC_064

description: Transcriptome measurement of sample EBs.index06.BC_064


title: EBs.index06.BC_060

description: Transcriptome measurement of sample EBs.index06.BC_060


title: EBs.index06.BC_024

description: Transcriptome measurement of sample EBs.index06.BC_024


title: Sa_J1074/R2_DbkdR_Val_late_C

city: Bielefeld

first: Christian

last: Ruckert-Reed

address: Sequenz 1

department: Medical School OWL

country: Germany

institute: Bielefeld University

data_processing:
Basecalls were performed using RTA v 1.18.66.3.
Sequenced reads were mapped to the CP071123.1 whole genome using bowtie2 v2.3.2 with parameters -X 600.
Raw read counts per gene were calculated using featureCounts v2.0.0 with parameters -O -M -t gene -g locus_tag -s 1.
Read count normalization and data analysis were performed using DESeq2.
Genome_build: CP059254.1
Supplementary_files_format_and_content: *.txt: Tab-delimited text files contain normalized read counts derived via DESeq2 for each gene.
Supplementary_files_format_and_content: Raw_Read_Count_Matrix.txt: Tab-delimited matrix table with raw read counts for every gene and every sample.

organism: Streptomyces albidoflavus

source_name: cell culture grown in CDM with added valine (3mM)

growth_protocol: Liquid cultures were incubated in baffled shake flasks (500 mL, 10% filling volume) on an orbital shaker (Multitron, Infors AG, Bottmingen, Switzerland, 5 cm shaking diameter, 230 rpm, 75 % relative humidity), and at 28°C. S. albus was incubated on MS agar at 28 °C for three days until sporulation occurred. Spores of a single colony were collected to inoculate the pre-culture, which was incubated overnight in LB medium. Afterwards, cells were collected (5,000 xg, 25 °C, 6 min), resuspended in main culture medium (per liter: 10g mannitol, 200 mM potassium phosphate buffer (pH 7.8), 15 g (NH4)2SO4, 1 g NaCl, 550 mg MgCl2*7H2O, 200 mg CaCl2, 30 mg 3,4-dihydroxybenzoic acid, 20 mg FeSO4, 2 mg FeCl3*6H2O, 2 mg MnSO4*H2O, 0.5 mg ZnSO4*H2O, 0.2 mg CuCl2*2H2O, 0.2 mg Na2B4O7*10H2O, 0.1 mg (NH4)6Mo7O24*4H2O, 1 mg nicotinamide, 1 mg riboflavin, 0.5 mg thiamine hydrochloride, 0.5 mg pyridoxine hydrochloride, 0.2 mg biotin, and 0.1 mg p-aminobenzoic acid, in addition to 30 g L-1 glass beads (soda-lime glass, 5 mm, Sigma-Aldrich) to avoid cell agglomeration), and used to inoculate the main culture.

extract_protocol:
Total RNA was isolated using the Quick-RNA Miniprep Plus kit (Zymo Research, Freiburg, Germany). After DNase treatment, the obtained RNA was purified (RNA Clean & Concentrator-5 kit, Zymo Research) and quantified (DropSense 16, Trinean NV, Gent, Belgium).
To construct whole transcriptome cDNA libraries, 2.5 μg of total RNA each was depleted of rRNA (Ribo-Zero rRNA Removal Kit (Bacteria), Illumina, San Diego, CA, USA). Successful rRNA removal was validated (Agilent RNA Pico 6000 kit, Agilent 2100 Bioanalyzer, Agilent Technologies). The obtained mRNA was converted into a cDNA library according to the TruSeq Stranded mRNA Sample Preparation guide (Illumina). Appropriate cDNA quality and quantity was validated (Agilent High Sensitivity DNA kit, Agilent 2100 Bioanalyzer, Agilent Technologies). Sequencing was performed on an Illumina NextSeq 500 instrument using 75 bases read length (Illumina).

treatment_protocol: The control culture was grown in pure CDM medium. As treatment, 3mM L-valine was added to the sterile medium prior to inoculation. Samples were taken during growth phase (5h after inoculation) and main production phase (20 to 30 hours after inoculation).

value: Delta-bkdR

value: 3mM L-valine

tag: time point

value: production phase (30h after inoculation)


title: dlPFC tissue_Normal Control [202817030019_R03C01]


title: dlPFC tissue_Opioids [202817030019_R04C01]


title: Sa_J1074/R2_DbkdR_Val_late_B


title: Sa_J1074/R2_DbkdR_Val_late_A


title: dlPFC tissue_Normal Control [202817030019_R01C01]


title: dlPFC tissue_Opioids [202816900027_R08C01]


title: dlPFC tissue_Opioids [202817030019_R02C01]


title: EBs.index06.BC_022

description: Transcriptome measurement of sample EBs.index06.BC_022


title: Sa_J1074/R2_DbkdR_Val_early_C

value: growth phase (5h after inoculation)


title: Sa_J1074/R2_DbkdR_Val_early_A


title: EBs.index06.BC_100

description: Transcriptome measurement of sample EBs.index06.BC_100

value: positive


title: Sa_J1074/R2_DbkdR_Val_early_B


title: EBs.index06.BC_020

description: Transcriptome measurement of sample EBs.index06.BC_020


title: dlPFC tissue_Pysch Control [202816900027_R07C01]


title: dlPFC tissue_Pysch Control [202816900027_R06C01]


title: EBs.index06.BC_014

description: Transcriptome measurement of sample EBs.index06.BC_014


title: EBs.index06.BC_016

description: Transcriptome measurement of sample EBs.index06.BC_016


title: Sa_J1074/R2_WT_Val_late_C

value: wildtype


title: dlPFC tissue_Opioids [202816900027_R05C01]


title: Sa_J1074/R2_WT_Val_late_B


title: Sa_J1074/R2_WT_Val_late_A


title: dlPFC tissue_Pysch Control [202816900027_R04C01]


title: Sa_J1074/R2_WT_Val_early_C


title: dlPFC tissue_Pysch Control [202816900027_R03C01]


title: EBs.index05.BC_359

description: Transcriptome measurement of sample EBs.index05.BC_359


title: dlPFC tissue_Pysch Control [202816900027_R02C01]


title: Sa_J1074/R2_WT_Val_early_A


title: EBs.index06.BC_006

description: Transcriptome measurement of sample EBs.index06.BC_006


title: EBs.index05.BC_357

description: Transcriptome measurement of sample EBs.index05.BC_357


title: dlPFC tissue_Opioids [202816900026_R07C01]


title: EBs.index05.BC_353

description: Transcriptome measurement of sample EBs.index05.BC_353


title: dlPFC tissue_Normal Control [202816900027_R01C01]


title: EBs.index05.BC_355

description: Transcriptome measurement of sample EBs.index05.BC_355


title: Sa_J1074/R2_WT_Val_early_B


title: EBs.index05.BC_351

description: Transcriptome measurement of sample EBs.index05.BC_351


title: dlPFC tissue_Normal Control [202816900026_R08C01]


title: dlPFC tissue_Pysch Control [202816900026_R06C01]


title: Sa_J1074/R2_WT_CDM_late_A

source_name: cell culture grown in pure CDM

value: untreated control

value: production phase (20h after inoculation)


title: EBs.index05.BC_349

description: Transcriptome measurement of sample EBs.index05.BC_349


title: dlPFC tissue_Opioids [202816900026_R03C01]


title: dlPFC tissue_Pysch Control [202816900026_R05C01]


title: Sa_J1074/R2_WT_CDM_early_B


title: EBs.index05.BC_347

description: Transcriptome measurement of sample EBs.index05.BC_347


title: dlPFC tissue_Opioids [202816900026_R04C01]


title: Sa_J1074/R2_WT_CDM_early_A


title: EBs.index06.BC_010

description: Transcriptome measurement of sample EBs.index06.BC_010


title: dlPFC tissue_Pysch Control [202816900026_R02C01]


title: dlPFC tissue_Pysch Control [202816900026_R01C01]


title: EBs.index05.BC_339

description: Transcriptome measurement of sample EBs.index05.BC_339


title: EBs.index05.BC_341

description: Transcriptome measurement of sample EBs.index05.BC_341


title: EBs.index05.BC_337

description: Transcriptome measurement of sample EBs.index05.BC_337


title: EBs.index05.BC_345

description: Transcriptome measurement of sample EBs.index05.BC_345


title: dlPFC tissue_Opioids [202816900015_R08C01]


title: Sa_J1074/R2_WT_CDM_late_B


title: Sa_J1074/R2_WT_CDM_early_C


title: MDA-MB-231 IFNγ treated replicate 1

city: Clayton

first: Gabriel

last: Goncalves

state: VICTORIA

address: 15 Innovation walk

country: Australia

institute: Monash University

description: NonStrandedCounts-withNames.txt

data_processing:
BGI normalised the sequence fastaq data to the 1% ERCC spike in control
raw fastq files were processed from alignment to raw count files using RNAsik software on Massive 3 that wrapped aroudn the following tools/packages: STAR 2.5.2b, qualimap v2.2.1, BigDataScript 0.99999g, bwa v0.7.15, samtools v1.4.1, RNAsik-pipe 1.5.0, subread/1.5.2, bedtools2 v2.25.0, python v3.6.2, picard v2.18.0, multiqc v1.4, gcc v4.9.3, fastqc v0.11.5 and java v8u144
Raw count files were filltered and QC using the following steps… :
removal of 0 counts, prinicple component analysis (outliers were removed if >3SD), removal of genes were the average <10 counts across the samples.
filtered counts were normalised using EdgeR TMM
Genome_build: GRCh37 homo sapian
Supplementary_files_format_and_content: raw count file created using RNAsik pipeline (.txt)
Supplementary_files_format_and_content: Differential gene expression of all genes that passed filltering (.csv)

source_name: Breast carcinoma

growth_protocol: MDA-MB-231 cells were cultured in DMEM supplemented with 10% fetal bovine serum, 1% Penicillin/streptomycin and L-glutamine (2 mM) (Gibco) at 37°C with 5% CO2. Total RNA was extracted from 1x10^5 MDA-MB-231 cells in three biological replicates of IFNγ treated and untreated conditions using RNeasy mini kit (Qiagen).

extract_protocol:
Qiagen RNeasy mini kit to extract the RNA and QC on nanodrop to determine concentration.
Library construct was done by BGI (Paired-end, 30 million bp with 1% ERCC spike in control).

treatment_protocol: 50IU of IFNγ

value: IFNy treatment (50IU, 48 hrs)


title: MDA-MB-231 IFNγ treated replicate 2

description: NonStrandedCounts-withNames.txt


title: EBs.index05.BC_311

description: Transcriptome measurement of sample EBs.index05.BC_311


title: MDA-MB-231 IFNγ treated replicate 3

description: NonStrandedCounts-withNames.txt


title: dlPFC tissue_Pysch Control [202816900015_R07C01]

value: M


title: MDA-MB-231 untreated replicate 3

description: NonStrandedCounts-withNames.txt

value: No treatment


title: MDA-MB-231 untreated replicate 2

description: NonStrandedCounts-withNames.txt


title: Sa_J1074/R2_WT_CDM_late_C


title: dlPFC tissue_Normal Control [202816900015_R06C01]

value: AA

value: Normal Control


title: MDA-MB-231 untreated replicate 1

description: NonStrandedCounts-withNames.txt


title: EBs.index05.BC_309

description: Transcriptome measurement of sample EBs.index05.BC_309


title: dlPFC tissue_Pysch Control [202816900015_R04C01]

value: F


title: dlPFC tissue_Pysch Control [202816900015_R05C01]

value: CAUC

value: Pysch Control


title: EBs.index05.BC_305

description: Transcriptome measurement of sample EBs.index05.BC_305

value: embryoid bodies from mouse ESCs


title: T-ALL cell line - CCRF-CEM/WT

city: Amsterdam

first: Ittai

middle: Bernardo

last: Muller

address: De Boelelaan 1118

institute: Amsterdam UMC

data_processing:
Basecalling was performed by Illumina CASAVA 1.8.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then aligned to the human genome hg38 using STAR (version 2.5.4a) using the following parameters: --sjdbOverhang 100 --alignEndsType EndToEnd
Simulated datasets were constructed using Flux Simulator 1.2.1
Differential splicing was calculated using rMATS 4.0.2, MISO 0.5.4 and SUPPA2 2.2
Genome_build: hg38
Supplementary_files_format_and_content: bam files
Supplementary_files_format_and_content: txt files containing rMATS output
Supplementary_files_format_and_content: miso_bf files containing MISO output
Supplementary_files_format_and_content: dpsi.temp.0 files containing SUPPA2 output

source_name: T-ALL cells

growth_protocol: CCRF-CEM cells were routinely cultured and expanded at 2–3 × 10e6 cells into a T75 flask in RPMI Medium (Gibco) supplemented with 10%  FCS and L-glutamine

extract_protocol:
RNA was extracted according to manufacturer's protocol with RNEasy Mini Kit (Qiagen)
Library's were constructed using the Illumina Truseq Stranded mRNA kit according to manufacturer's protocol

value: T-acute lymphoid leukemia cell line

value: CCRF-CEM

value: WT

value: untreated


title: EBs.index05.BC_303

description: Transcriptome measurement of sample EBs.index05.BC_303

value: positive


title: dlPFC tissue_Opioids [202816900015_R03C01]

value: Opioids


title: kmt2cko.3

city: St Louis

first: Todd

last: Druley

state: Missouri

address: 660 South Euclid Ave

department: Department of Pediatrics

institute: Washington University In St Louis

description:
undifferentiated cells, 75% confluency
kmt2cko.3

data_processing:
The resulting sequencing reads were demultiplexed by index with a custom Python demultiplexing script and further demultiplexed by barcode with a custom Perl demultiplexing script.
The RNA-Seq reads were then aligned to the Homo sapiens Ensembl release 72 top-level assembly with STAR version 2.4.0b
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount.
Sailfish was used to produce isoform estimated counts.
Genome_build: Ensemble R72
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: human induced pluripotent stem cells

extract_protocol:
Qiagen RNAeasy micro plus
Clontech SMRTr

value: human induced pluripotent stem cells

value: KMT2C Knock out


title: dlPFC tissue_Normal Control [202816900015_R01C01]


title: EBs.index05.BC_295

description: Transcriptome measurement of sample EBs.index05.BC_295


title: dlPFC tissue_Pysch Control [202816900013_R08C01]


title: dlPFC tissue_Opioids [202816900015_R02C01]


title: kmt2cko.1

description:
undifferentiated cells, 75% confluency
kmt2cko.1


title: kmt2cko.2

description:
undifferentiated cells, 75% confluency
kmt2cko.2


title: EBs.index05.BC_299

description: Transcriptome measurement of sample EBs.index05.BC_299


title: dlPFC tissue_Normal Control [202816900013_R06C01]


title: EBs.index05.BC_263

description: Transcriptome measurement of sample EBs.index05.BC_263


title: dlPFC tissue_Opioids [202816900013_R05C01]


title: bjff.3

description:
undifferentiated cells, 75% confluency
bjff.3

value: Wild type


title: EBs.index05.BC_289

description: Transcriptome measurement of sample EBs.index05.BC_289


title: bjff.1

description:
undifferentiated cells, 75% confluency
bjff.1


title: T-ALL cell line - CCRF-CEM/R30DM


title: bjff.2

description:
undifferentiated cells, 75% confluency
bjff.2


title: EBs.index05.BC_261

description: Transcriptome measurement of sample EBs.index05.BC_261


title: dlPFC tissue_Opioids [202816900013_R04C01]


title: dlPFC tissue_Opioids [202816900013_R03C01]

value: M


title: EBs.index05.BC_259

description: Transcriptome measurement of sample EBs.index05.BC_259


title: NB4-RNA-KO1

city: Philadelphia

first: Siqing

last: Wang

state: PENNSYLVANIA

address: 3401 Civic Center Blvd

department: Department of Pediatrics, Division of Hematology

institute: Children’s Hospital of Philadelphia

description:
diff_NB4_KDM5A-KO_WSQ_homer.txt
diffExp_KDM5A-KO_vs_SCR_NB4_homer.xlsx

data_processing:
The FASTQ data were trimmed adaptor by trim_galore (bioinformatics.babraham.ac.uk)
ChIP-seq data mapped to human genome hg19 with Bowtie  in single-end mode.
ChIP-seq peaks were called by MACS2 .
RNA-seq data were mapped to human genome hg19 using STAR  (020201) and assembled by Homer get Homer tags.
Use Homer to get RNA-seq raw counts, counts per million (CPM), and differential expressed genes were generated by DEseq2 size-factor normalized log2(CPM), with fold change > 2 and p < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files for ChIP-seq peaks in sample 1 to sample 6. An Excel file for H3K4me2 ChIP-seq up-regulated peaks in KDM5A-KO vs scramble (sample 4 vs sample 3). A tab-delimited text file and an excel file for RNA-seq log2(CPM), log2(fold change) and p value for sample 7 to sample 10.

growth_protocol: Human AML cell lines, NB4 (kindly provided by Dr. Kankan Wang, Ruijin Hospital), THP-1 (American Type Culture Collection, Manassas, VA, USA), HL-60 (American Type Culture Collection, Manassas, VA, USA), MV4-11(American Type Culture Collection, Manassas, VA, USA) were cultured in RPMI 1640 supplemented with 10% FBS (Sigma), penicillin (100 U/ml) and streptomycin (10 mg/ml) at 37C in a 5% CO 2 humidified atmosphere.

extract_protocol:
For histone modification, 3 × 10 6 cells per IP and primary antibody (4 mg/ml) were used; for KMD5A ChIP, 40 × 10 6 cells per IP were used (10 mg/ml). The obtained DNA was then quantified by PicoGreen and processed for ChIP-seq library preparation (as described for the Illumina protocol) or used for qPCR.
For libraries preparation, 2 ng of immunoprecipitated DNA was used. Antibodies used for ChIP are as follows:  H3K4me2 (Abcam, no. 32356), H3K4me3 (Active Motif, no. 39159), KDM5A (Bethyl Laboratories, A300-897A), and immuno-globulin G rabbit (Jackson ImmunoResearch, lot no. 134230).

treatment_protocol: CRISPR-Cas9 gene knockout was carried out using lentiCRISPR V2 system  and acted as protocol recommended. sgRNAs target KDM5A were designed as followed: KDM5A-sgRNA1: TATCGGCCGCATCCGGCCTT, KDM5A-sgRNA2: GGCCTTTGGCGGAGAAAAC. GFP-control-sgRNA1: AGCTGGACGGCGACGTAAA, GFP-control-sgRNA2: GTGAACCGCATCGAGCTGA. The lentiCRISPR v2 was a gift from Feng Zhang (Addgene plasmid # 52961; http://n2t.net/addgene:52961; RRID: Addgene_52961).

value: leukemia

tag: wt or kdm5a ko

value: KDM5A KO


title: EBs.index05.BC_257

description: Transcriptome measurement of sample EBs.index05.BC_257

tag: tissue


title: NB4-RNA-KO2


title: NB4-RNA-SCR2

value: CRISPR scramble


title: EBs.index05.BC_255

description: Transcriptome measurement of sample EBs.index05.BC_255

tag: celseq2 adapter


title: EBs.index05.BC_307

description: Transcriptome measurement of sample EBs.index05.BC_307

tag: pdgfra staining


title: dlPFC tissue_Pysch Control [202816900013_R01C01]


title: EBs.index05.BC_293

description: Transcriptome measurement of sample EBs.index05.BC_293


title: EBs.index05.BC_253

description: Transcriptome measurement of sample EBs.index05.BC_253


title: dlPFC tissue_Normal Control [202816900124_R08C01]

value: F

value: Normal Control


title: dlPFC tissue_Opioids [202816900013_R02C01]

value: AA


title: dlPFC tissue_Pysch Control [202816900124_R07C01]

value: CAUC

value: Pysch Control


title: NB4-RNA-SCR1


title: dlPFC tissue_Normal Control [202816900124_R06C01]


title: EBs.index05.BC_245

description: Transcriptome measurement of sample EBs.index05.BC_245

value: embryoid bodies from mouse ESCs


title: EBs.index05.BC_249

description: Transcriptome measurement of sample EBs.index05.BC_249


title: MitoStress stimulated cells rep2

city: Vienna

first: Christoph

middle: J

last: Binder

address: Lazarettgasse 14

department: Laboratory Medicine

country: Austria

institute: Medical University of Vienna

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquistion on the sequencing instrument.
Basecalling was performed with the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing was performed with Illumina2bam tools 1.17 (https://github.com/wtsi-npg/illumina2bam)
The transcriptome analysis was performed using the Tuxedo suite. TopHat2 (v2.1.1, http://genomebiology.com/2013/14/4/R36/abstract) was supplied with reads passing vendor quality filtering (PF reads) and the Ensembl transcript set (Homo sapiens, e87, December 2016) as reference. TopHat2 analyses were run independently for each replicate.
Cufflinks (v2.2.1, http://www.nature.com/nbt/journal/v31/n1/full/nbt.2450.html) was then used to assemble transcripts from spliced read alignments, again using the Ensembl e87 transcriptome as the reference, allowing also de novo assembly of transcript models.
Transcriptome sets of all replicates for each sample group were combined with Cuffmerge.
Differential expression was assessed with Cuffdiff v2.2.1 (http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html).
cummeRbund (http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html) and biomaRt (http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html) were used in combination with custom R scripts to perform quality assessment and further refine analysis results.
Genome_build: GRCh38 (UCSC hg38)

source_name: human umbilical vein endothelial cells (HUVEC)

growth_protocol: HUVECs were grown in complete EBM-2 media (Lonza)

extract_protocol:
Total RNA was isolated by using Rneasy Mini Kit (Qiagen)
RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amounts were quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using Experion Automated Electrophoresis System (Bio-Rad). For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 3000 instrument using 50 bp single-read chemistry.

treatment_protocol: Cells were stimulated for 6 hours with MitoCo or MitoStress for 6 hours in FBS-free EBM-2 media.


title: dlPFC tissue_Opioids [202816900124_R05C01]


title: EBs.index05.BC_215

description: Transcriptome measurement of sample EBs.index05.BC_215


title: dlPFC tissue_Opioids [202816900124_R04C01]


title: dlPFC tissue_Opioids [202816900124_R03C01]


title: EBs.index05.BC_209

description: Transcriptome measurement of sample EBs.index05.BC_209


title: MitoCo stimulated cells rep3

value: human umbilical vein endothelial cells (HUVEC)


title: EBs.index05.BC_207

description: Transcriptome measurement of sample EBs.index05.BC_207


title: dlPFC tissue_Opioids [202816900124_R02C01]


title: MitoCo stimulated cells rep2


title: dlPFC tissue_Pysch Control [202816900124_R01C01]


title: EBs.index05.BC_201

description: Transcriptome measurement of sample EBs.index05.BC_201


title: MitoCo stimulated cells rep1


title: EBs.index05.BC_213

description: Transcriptome measurement of sample EBs.index05.BC_213


title: EBs.index05.BC_195

description: Transcriptome measurement of sample EBs.index05.BC_195


title: dlPFC tissue_Opioids [202816900099_R08C01]


title: dlPFC tissue_Normal Control [202816900099_R07C01]


title: 81L: Otocyst DMSO RNA-seq

city: London

first: Magdalena

last: Zak

address: 332 Grays Inn Road

country: United Kingdom

institute: UCL Ear Institute

data_processing:
Run data were demultiplexed and converted into fastq files using Illumina’s bcl2fastq Conversion Software v2.19
Kallisto package was used to map reads to a chicken reference genome (Gallus_gallus-GRCg6a) and to quantifying abundances of transcripts using default settings
Genome_build: Gallus_gallus-GRCg6a

organism: Gallus gallus

source_name: otocyst

extract_protocol:
Total RNA was extracted from each individual otocysts using the RNAqueous™-Micro Total RNA Isolation Kit (Ambion) according to the manufacturers protocol. The quality of isolated RNA was tested using Agilent 2200 Tapestation and only samples with RIN of at least 9 were used for library
Libraries were made using NEBNext Single Cell/Low Input RNA Library Prep Kit (New England Biolabs, Inc. ): cDNA was generated using the SMART (Switching Mechanism at 5' End of RNA Template) technology during 9 cycles of PCR. cDNA was then enzymatically sheared, end-repaired and A-tailed before ligation of an indexed adaptor containing a Unique Molecular Identfier (IDT). Dual ligated fragments were enriched with a limited cycle PCR (9 cycles) and R5 Primers (Swift BioScience).
Samples were sequenced on a NextSeq High Output flow-cell (Illumina) using a 75bp single-end read with >40M reads generated for every sample with 93% of bases called >Q30

treatment_protocol: Both left and right otocyst were dissected from chicken embryos aged E2.5, cleaned from surrounding mesenchyme and individually incubated free floating in IWR-1-enriched (300µM, right otocyst) or control (DMSO, left otocyst) media for 24h.

value: White Leghorn

tag: age

value: embryonic day 2.5

tag: treatment

value: DMSO

tag: duration of treatment


title: 79L: Otocyst DMSO RNA-seq


title: 77L: Otocyst DMSO RNA-seq


title: dlPFC tissue_Opioids [202816900099_R06C01]

value: Opioids


title: EBs.index05.BC_193

description: Transcriptome measurement of sample EBs.index05.BC_193

value: positive


title: MitoStress stimulated cells rep3


title: 76L: Otocyst DMSO RNA-seq


title: MitoStress stimulated cells rep1


title: dlPFC tissue_Normal Control [202816900099_R05C01]


title: dlPFC tissue_Pysch Control [202816900099_R04C01]


title: EBs.index05.BC_165

description: Transcriptome measurement of sample EBs.index05.BC_165


title: EBs.index05.BC_151

description: Transcriptome measurement of sample EBs.index05.BC_151


title: 82R: Otocyst IWR-1 RNA-seq

value: 300uM IWR-1


title: 81R: Otocyst IWR-1 RNA-seq


title: EBs.index05.BC_149

description: Transcriptome measurement of sample EBs.index05.BC_149


title: 79R: Otocyst IWR-1 RNA-seq


title: dlPFC tissue_Opioids [202816900099_R02C01]

value: M


title: EBs.index05.BC_119

description: Transcriptome measurement of sample EBs.index05.BC_119


title: 77R: Otocyst IWR-1 RNA-seq


title: dlPFC tissue_Pysch Control [202816900007_R08C01]


title: EBs.index05.BC_117

description: Transcriptome measurement of sample EBs.index05.BC_117


title: EBs.index05.BC_115

description: Transcriptome measurement of sample EBs.index05.BC_115


title: 76R: Otocyst IWR-1 RNA-seq


title: EBs.index05.BC_167

description: Transcriptome measurement of sample EBs.index05.BC_167


title: dlPFC tissue_Opioids [202816900007_R06C01]


title: EBs.index05.BC_161

description: Transcriptome measurement of sample EBs.index05.BC_161


title: dlPFC tissue_Opioids [202816900007_R05C01]


title: EBs.index05.BC_113

description: Transcriptome measurement of sample EBs.index05.BC_113


title: EBs.index05.BC_111

description: Transcriptome measurement of sample EBs.index05.BC_111


title: dlPFC tissue_Opioids [202816900007_R04C01]


title: EBs.index05.BC_109

description: Transcriptome measurement of sample EBs.index05.BC_109


title: dlPFC tissue_Pysch Control [202816900099_R03C01]


title: 82L: Otocyst DMSO RNA-seq


title: EBs.index05.BC_107

description: Transcriptome measurement of sample EBs.index05.BC_107


title: dlPFC tissue_Opioids [202816900007_R02C01]


title: dlPFC tissue_Pysch Control [202816900007_R01C01]


title: dlPFC tissue_Normal Control [202816900011_R08C01]


title: dlPFC tissue_Pysch Control [202816900099_R01C01]


title: EBs.index05.BC_103

description: Transcriptome measurement of sample EBs.index05.BC_103


title: mrn1D respiratory rep2

city: Berkeley

first: Nicholas

middle: T

last: Ingolia

email: ingolia@berkeley.edu, nick@ingolia.org

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

institute: University of California, Berkeley

data_processing:
Quantification with Kallisto v0.44.0 "--single -l 50 -s 5"
Genome_build: R64-2-1
Supplementary_files_format_and_content: read count and abundance estimates

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: log-phase growth to OD600 0.6 in YEPD 2% glucose followed by 20 minutes in YEPEG 2% ethanol and 2% glycerol

extract_protocol:
Phenol-chloroform total RNA extraction
rRNA depletion with QIAseq FastSelect followed by NEBNext Ultra II RNA Library Prep Kit

tag: genotype

tag: Stage

value: respiratory (ethanol + glycerol)


title: mrn1D respiratory rep3


title: EBs.index05.BC_101

description: Transcriptome measurement of sample EBs.index05.BC_101


title: dlPFC tissue_Pysch Control [202816900011_R06C01]


title: Wild-type respiratory rep3

value: wild-type


title: dlPFC tissue_Opioids [202816900011_R07C01]


title: EBs.index05.BC_097

description: Transcriptome measurement of sample EBs.index05.BC_097


title: dlPFC tissue_Opioids [202816900011_R05C01]


title: dlPFC tissue_Opioids [202816900011_R04C01]


title: EBs.index05.BC_071

description: Transcriptome measurement of sample EBs.index05.BC_071


title: Wild-type respiratory rep2


title: EBs.index05.BC_067

description: Transcriptome measurement of sample EBs.index05.BC_067


title: EBs.index05.BC_069

description: Transcriptome measurement of sample EBs.index05.BC_069


title: Wild-type respiratory rep1


title: dlPFC tissue_Normal Control [202816900011_R03C01]


title: mrn1D respiratory rep1


title: EBs.index05.BC_065

description: Transcriptome measurement of sample EBs.index05.BC_065


title: mrn1D fermentative rep3

growth_protocol: log-phase growth to OD600 0.6 in YEPD 2% glucose

value: fermentative (glucose)


title: EBs.index05.BC_105

description: Transcriptome measurement of sample EBs.index05.BC_105


title: mrn1D fermentative rep2


title: dlPFC tissue_Opioids [202816900011_R02C01]


title: dlPFC tissue_Opioids [202816900011_R01C01]


title: mrn1D fermentative rep1


title: dlPFC tissue_Pysch Control [202816900153_R07C01]

value: F


title: Wild-type fermentative rep3


title: dlPFC tissue_Pysch Control [202816900153_R06C01]


title: EBs.index05.BC_061

description: Transcriptome measurement of sample EBs.index05.BC_061


title: dlPFC tissue_Pysch Control [202816900153_R05C01]


title: dlPFC tissue_Pysch Control [202816900007_R03C01]


title: Wild-type fermentative rep1


title: EBs.index05.BC_057

description: Transcriptome measurement of sample EBs.index05.BC_057


title: Wild-type fermentative rep2


title: dlPFC tissue_Pysch Control [202816900153_R03C01]


title: dlPFC tissue_Normal Control [202816900153_R04C01]

value: Normal Control


title: model_WTE_390

first: kun

last: luo

address: Haidian district

institute: Tsinghua university

description: db/db mice treated with white tea extract

data_processing:
Demultiplexing and basecalling performed using CASAVA version 1.8.2.
QC was performed on the FASTQ files using FastQC(v0.11.5) software.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mice whole genome using HISAT2 (v2.1.0).
Sequence reads aligned to the mice genome were imported into StringTie(v1.3.3b) for sequence read counting.
Sequence reads mapped to different isoforms of individual genes were pooled together, and then were input into the DESeq2(v1.28.0) differential expression analysis program to normalize and determine expression levels and differentially expressed genes.
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each gene per sample

source_name: db/db mice liver

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen, Carlsbad, CA) and purified by an RNase-free DNase kit (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The C57BL/6J mice (normal group) were treated with saline. The T2DM db/db mice were treated with saline, DLE (200 mg/kg), white tea extract (WTE) or pioglitazone (PGZ, 20 mg/kg) for 12 weeks

value: liver

value: db/db mice

value: WTE


title: dlPFC tissue_Normal Control [202816900153_R02C01]

value: AA


title: EBs.index05.BC_017

description: Transcriptome measurement of sample EBs.index05.BC_017

data_processing:
Demultiplexing of raw data (previously demultiplexed on Illumina index) was done using barcodes. Read1 measurements contain in read1, from 5’ to 3’: a 6nt UMI, an 8nt barcode, followed by unalignable sequence, usually polyT. Read2 of the transcriptomic measurements contains the mRNA sequence.
mRNA reads (in read2) were aligned using tophat2 (v2.1.1) using parameters ‘--segment-length 22 --read-mismatches 4 --read-edit-dist 4 --min-anchor 6 --min-intron-length 25 --max-intron-length 25000 --no-novel-juncs --no-novel-indels --no-coverage-search --b2-very-sensitive --b2-N 1 --b2-gbar 200’ to a transcriptome (options ‘--GTF’ and ‘--transcriptome-index’) obtained from GENCODE (v26) supplemented with ERCC mRNA spike-in sequences.
Reads and unique UMIs were counted per gene (according to the “intersection-strict” algorithm of `htseq-count` [http://htseq.readthedocs.io/en/master/count.html]). For each gene, the number of unique observed UMIs was trimmed by starting at the UMI with highest read count and setting UMIs with Hamming distance of 1 to zero, and iteratively filtering all UMI sequences (in case of equal read counts for a UMI, ties were broking by lexicographic sorting of the UMIs). The number of observed distinct UMIs after trimming was taken as the transcript count for that gene.
Genome_build: mm10
Supplementary_files_format_and_content: Tables are provided with the number of transcripts per gene.

extract_protocol:
EBs were washed twice in PBS-0 and collagenase IV (600U/ml) was added. Plates were shaken at 350RPM for 30 minutes. EBs were then transferred to TrypleE 10X (no dilution) and shaken for 20 minutes. EBs were dissociated into single cell suspensions using a small capillary. The resulting suspension was quenched using PBS with 50% FBS, centrifuged and resuspended in 230 ul of PBS0 with 10% FBS. Cells were stained with PDGFRA antibody (1:150 dilution) for 30 min at 4°C followed by three PBS (+10%FBS) washes, secondary antibody incubation (1:400) for 30 min. Cells were washed three times in PBS0 and sorted for further processing.
Library construction was done following the Sort-seq protocol as previously described [Muraro, T. et al. A Single-Cell Transcriptome Atlas of the Human Pancreas. Cell Systems 3, 385–394.e3 (2016).]
Library preparation was done as previously described[Hashimshony, T. et al. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome biology 17, 77, (2016).] using 5 μL of aRNA and 8 PCR cycles. Libraries were run on the Illumina NextSeq platform with high output 75 bp paired-end sequencing.

value: embryoid bodies from mouse ESCs


title: model_WTE_381


title: EBs.index05.BC_015

description: Transcriptome measurement of sample EBs.index05.BC_015


title: model_WTE_382


title: model_WTE_325


title: EBs.index05.BC_055

description: Transcriptome measurement of sample EBs.index05.BC_055


title: Exon UMUC3_BCG-resistant_1

type: RNA

city: Rochester

first: Taichi

last: Mizushima

state: NY

address: 601 Elmwood

institute: University of Rochester

hyb_protocol: standard Affymetrix protocol

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: RMA

label: biotin

source_name: UMUC3; Bladder cancer cell line

label_protocol: standard Affymetrix protocol

extract_protocol: RNA was isolated from UMUC3 and its subline with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. Inclusion of RNase inhibitor in the lysis buffer.

value: BCG-resistant


title: EBs.index05.BC_021

description: Transcriptome measurement of sample EBs.index05.BC_021


title: EBs.index05.BC_053

description: Transcriptome measurement of sample EBs.index05.BC_053


title: Exon UMUC3_BCG-resistant_2


title: Exon UMUC3_Control_2

value: Control


title: dlPFC tissue_Opioids [202816900153_R01C01]

value: CAUC


title: Exon UMUC3-AR-konck-down_2

value: AR-konck down


title: model_DLE_401

description: db/db mice treated with Dendrocalamus latiflorus leaf extract

value: DLE


title: Exon UMUC3_AR-konck-down_1


title: model_DLE_378


title: model_DLE_373


title: dlPFC tissue_Normal Control [202817030052_R05C01]


title: model_DLE_361


title: EBs.index04.BC_378

description: Transcriptome measurement of sample EBs.index04.BC_378

value: negative


title: dlPFC tissue_Normal Control [202817030052_R04C01]


title: EBs.index04.BC_374

description: Transcriptome measurement of sample EBs.index04.BC_374


title: dlPFC tissue_Opioids [202817030052_R03C01]

value: M

value: Opioids


title: EBs.index04.BC_376

description: Transcriptome measurement of sample EBs.index04.BC_376


title: dlPFC tissue_Normal Control [202817030052_R02C01]


title: EBs.index05.BC_013

description: Transcriptome measurement of sample EBs.index05.BC_013

value: positive


title: EBs.index04.BC_382

description: Transcriptome measurement of sample EBs.index04.BC_382


title: dlPFC tissue_Opioids [202817030052_R07C01]


title: EBs.index04.BC_372

description: Transcriptome measurement of sample EBs.index04.BC_372


title: model_PGZ_404

description: db/db mice treated with pioglitazone

value: PGZ


title: dlPFC tissue_Opioids [202817030052_R06C01]


title: model_PGZ_360

description: db/db mice treated with pioglitazone


title: model_PGZ_328

description: db/db mice treated with pioglitazone


title: dlPFC tissue_Opioids [202817030052_R01C01]


title: dlPFC tissue_Opioids [202831040046_R07C01]


title: EBs.index04.BC_370

description: Transcriptome measurement of sample EBs.index04.BC_370


title: dlPFC tissue_Opioids [202831040046_R08C01]


title: model_407

description: db/db mice treated with saline

value: model


title: EBs.index04.BC_368

description: Transcriptome measurement of sample EBs.index04.BC_368


title: EBs.index04.BC_362

description: Transcriptome measurement of sample EBs.index04.BC_362


title: dlPFC tissue_Pysch Control [202831040046_R06C01]

value: F

value: Pysch Control


title: model_329

description: db/db mice treated with saline

value: liver

value: db/db mice


title: model_387

description: db/db mice treated with saline


title: model_327

description: db/db mice treated with saline


title: EBs.index04.BC_334

description: Transcriptome measurement of sample EBs.index04.BC_334


title: EBs.index04.BC_380

description: Transcriptome measurement of sample EBs.index04.BC_380


title: EBs.index04.BC_326

description: Transcriptome measurement of sample EBs.index04.BC_326


title: dlPFC tissue_Normal Control [202831040046_R04C01]

value: AA

value: Normal Control


title: dlPFC tissue_Pysch Control [202831040046_R02C01]


title: normal_376

description: wild type mice treated with saline

source_name: C57BL/6J mice liver

value: C57BL/6J wild type

value: normal


title: normal_409

description: wild type mice treated with saline


title: EBs.index04.BC_324

description: Transcriptome measurement of sample EBs.index04.BC_324

source_name: embryoid bodies from mouse ESCs

value: embryoid bodies from mouse ESCs


title: normal_349

description: wild type mice treated with saline


title: dlPFC tissue_Opioids [202831040046_R03C01]

value: CAUC


title: dlPFC tissue_Pysch Control [202831040046_R01C01]


title: EBs.index04.BC_318

description: Transcriptome measurement of sample EBs.index04.BC_318


title: dlPFC tissue_Opioids [202817030028_R08C01]


title: normal_346

description: wild type mice treated with saline


title: dlPFC tissue_Opioids [202817030028_R06C01]


title: DJT24 dLN-Mouse04

city: South San Francisco

first: Dev

last: Bhatt

address: 1120 Veterans Blvd

institute: Amgen

description: paired scTCR library of dLN-Mouse04

data_processing:
Sequences were aligned to the Ensembl mouse reference transcriptome using the 10X genomics CellRanger pipeline (version 2.1.0). QC and transcriptome analysis of the single cell datasets were performed using the R package Seurat (version 2.3.0)
The TCR library sequences were processed using the CellRanger vdj function supplied with mouse TCR gene annotations and reference sequence files acquired from IMGT and prepared using the mkvdjref function.
Genome_build: mm10-1.2.0
Supplementary_files_format_and_content: cell.counts.txt contain the raw UMI count matrix of all samples with genes in rows and cells in columns, celll.metadata.csv contains metainformation of all samples with cells in rows and labels in columns. For each sample, the cell ranger output filtered matrix files including  barcodes.tsv, features.tsv and matrix.mtx were included as processed data files as well.

source_name: T cells

extract_protocol:
Samples were pre-enriched for total T cells by immunomagnetic negative selection using the StemCell Technologies EasySep Mouse T Cell Isolation Kit (19851) following the manufacturer protocols for all three peripheral tissue suspensions, with minor modifications for processing of tumor suspensions. The negative selection antibody cocktail for tumor samples were supplemented with 15ug/ml anti-CD34-biotin (eBioscience, 13-0341-82) to deplete MC38 tumor cells. After labeling, the tumor-cocktail suspension was washed once with 5 mL MACS buffer prior to a 10-minute incubation with eBioscience MagniSort Streptavidin Negative Selection Beads (Invitrogen, MSNB600274) at 20 μL beads/100 mL sample. All sample volumes were brought up to 2.5 mL with additional MACS Buffer. Samples were then placed on a StemCell Technologies magnet for 10 minutes, and T cells were subsequently collected. All enriched mouse single T cell samples were stained for viability (Sytox Red) and with antibodies against CD45, TCRβ, and CD90.2 and sorted via Aria sorters prior to loading onto the 10X genomics single cell platform according to the manufacturer protocol.
Libraries were prepared using the 10X Chromium Single Cell 3' v3 Gene Expression Kit.

tag: animal number

value: dLN


title: DJT23 dLN-Mouse03

description: paired scTCR library of dLN-Mouse03


title: dlPFC tissue_Opioids [202817030028_R07C01]


title: EBs.index04.BC_284

first: Isabel

last: Guerreiro

address: Uppsalalaan 8

institute: Hubrecht Institute

description: Transcriptome measurement of sample EBs.index04.BC_284

value: negative


title: dlPFC tissue_Opioids [202831040046_R05C01]

value: M


title: EBs.index04.BC_314

description: Transcriptome measurement of sample EBs.index04.BC_314


title: EBs.index04.BC_336

description: Transcriptome measurement of sample EBs.index04.BC_336


title: EBs.index04.BC_282

description: Transcriptome measurement of sample EBs.index04.BC_282


title: DJT22 Spleen-Mouse04

description: paired scTCR library of Spleen-Mouse04

value: Spleen


title: EBs.index04.BC_280

description: Transcriptome measurement of sample EBs.index04.BC_280


title: dlPFC tissue_Normal Control [202817030028_R05C01]


title: dlPFC tissue_Opioids [202817030028_R04C01]

value: Opioids


title: EBs.index04.BC_322

description: Transcriptome measurement of sample EBs.index04.BC_322


title: EBs.index04.BC_278

description: Transcriptome measurement of sample EBs.index04.BC_278


title: DJT21 Spleen-Mouse03

description: paired scTCR library of Spleen-Mouse03


title: T48A_Genomic DNA from Buccal cells

city: Phoenix

first: Ignazio

middle: Stefano

last: Piras

state: Arizona

address: 445 N. Fifth Street, Phoenix

institute: Translational Genomic Research Institute

hyb_protocol: DNA methylation was quantified using the Infinium MethylationEPIC BeadChip

scan_protocol: Scanning was conducted on a Illumina iScanSystem

data_processing:
Raw IDAT files were exported for preprocessing in R with the minfi package and standard quality control analyses were performed, including quantile normalization, checking for sex mismatches, and excluding low-intensity samples (p detection < .01)(Aryee et al. 2014). Three samples did not pass our quality control pipeline due to low-intensity. Using the R package EpiDISH (Epigenetic Dissection of Intra-Sample Heterogeneity, 3.8) RPC method, we included the proportion of estimated epithelial cells as a covariate in our statistical models (m = 69%). Array was included as a covariate in all analyses to control for batch (Houseman et al. 2012; Teschendorff et al. 2017).
raw_matrix.txt contains:  unmethylated and methylated signal intensities
processed_matrix.txt contains: Beta normalized values (Quantile normalization)

label: Biotin

source_name: Buccal cells

label_protocol: Biotin

extract_protocol: DNA was extracted with a standard isolation kit (Qiagen, Hilden, Germany). Sample yield and purity were assessed spectrophotometrically using a NanoDrop ND-1000 (ThermoScientific, Wilmington, DE) and using Qubit fluorometric methods. DNA was treated with sodium bisulfite using the EZ-96 DNA Methylation Kit (Zymo Research, Irvine, CA).

treatment_protocol: Buccal cells were collected with Mawi iSWAB DNA collection tubes (Mawi DNA Technologies LLC, Hayward, CA) during the eight-year home visit.

value: buccal cells

tag: Sex

value: Male


title: T48B_Genomic DNA from Buccal cells


title: DJT20 Blood-Mouse04

description: paired scTCR library of Blood-Mouse04

value: Blood


title: EBs.index04.BC_272

city: Utrecht

description: Transcriptome measurement of sample EBs.index04.BC_272


title: DJT17 Tumor-Mouse03

description: paired scTCR library of Tumor-Mouse03

value: Tumor


title: DJT19 Blood-Mouse03

description: paired scTCR library of Blood-Mouse03


title: T47A_Genomic DNA from Buccal cells


title: T46B_Genomic DNA from Buccal cells


title: T46A_Genomic DNA from Buccal cells


title: DJT13 dLN-Mouse02

description: paired scTCR library of dLN-Mouse02


title: model_PGZ_408

description: db/db mice treated with pioglitazone

value: liver

tag: strain

value: PGZ


title: EBs.index04.BC_266

description: Transcriptome measurement of sample EBs.index04.BC_266


title: DJT12 dLN-Mouse01

description: paired scTCR library of dLN-Mouse01


title: EBs.index04.BC_240

description: Transcriptome measurement of sample EBs.index04.BC_240


title: T45B_Genomic DNA from Buccal cells

value: Female


title: DJT10 Spleen-Mouse02

description: paired scTCR library of Spleen-Mouse02


title: DJT09 Spleen-Mouse01

description: paired scTCR library of Spleen-Mouse01


title: T45A_Genomic DNA from Buccal cells


title: EBs.index04.BC_228

description: Transcriptome measurement of sample EBs.index04.BC_228


title: EBs.index04.BC_276

description: Transcriptome measurement of sample EBs.index04.BC_276


title: T44B_Genomic DNA from Buccal cells


title: EBs.index04.BC_224

description: Transcriptome measurement of sample EBs.index04.BC_224


title: T47B_Genomic DNA from Buccal cells


title: EBs.index04.BC_222

description: Transcriptome measurement of sample EBs.index04.BC_222


title: DJT18 Tumor-Mouse04

description: paired scTCR library of Tumor-Mouse04


title: EBs.index04.BC_192

description: Transcriptome measurement of sample EBs.index04.BC_192


title: DJT04 Blood-Mouse01

description: paired scTCR library of Blood-Mouse01


title: T44A_Genomic DNA from Buccal cells


title: EBs.index04.BC_270

description: Transcriptome measurement of sample EBs.index04.BC_270


title: DJT02 Tumor-Mouse02

description: paired scTCR library of Tumor-Mouse02


title: T43B_Genomic DNA from Buccal cells


title: EBs.index04.BC_268

description: Transcriptome measurement of sample EBs.index04.BC_268


title: EBs.index04.BC_190

description: Transcriptome measurement of sample EBs.index04.BC_190


title: DJT01 Tumor-Mouse01

description: paired scTCR library of Tumor-Mouse01


title: T43A_Genomic DNA from Buccal cells


title: T42B_Genomic DNA from Buccal cells


title: DJC23 dLN-Mouse03


title: EBs.index05.BC_063

description: Transcriptome measurement of sample EBs.index05.BC_063

value: positive


title: DJC24 dLN-Mouse04


title: EBs.index04.BC_170

description: Transcriptome measurement of sample EBs.index04.BC_170


title: T42A_Genomic DNA from Buccal cells


title: EBs.index04.BC_182

description: Transcriptome measurement of sample EBs.index04.BC_182


title: DJT05 Blood-Mouse02

description: paired scTCR library of Blood-Mouse02


title: EBs.index04.BC_178

description: Transcriptome measurement of sample EBs.index04.BC_178


title: DJC22 Spleen-Mouse04


title: T41B_Genomic DNA from Buccal cells


title: DJC21 Spleen-Mouse03


title: EBs.index04.BC_140

description: Transcriptome measurement of sample EBs.index04.BC_140


title: T41A_Genomic DNA from Buccal cells


title: T40B_Genomic DNA from Buccal cells


title: DJC20 Blood-Mouse04


title: T40A_Genomic DNA from Buccal cells


title: EBs.index04.BC_142

description: Transcriptome measurement of sample EBs.index04.BC_142


title: DJC19 Blood-Mouse03


title: DJC18 Tumor-Mouse04


title: EBs.index04.BC_138

description: Transcriptome measurement of sample EBs.index04.BC_138


title: T39B_Genomic DNA from Buccal cells


title: EBs.index04.BC_132

description: Transcriptome measurement of sample EBs.index04.BC_132


title: T39A_Genomic DNA from Buccal cells


title: EBs.index04.BC_134

description: Transcriptome measurement of sample EBs.index04.BC_134


title: DJC17 Tumor-Mouse03


title: EBs.index04.BC_122

description: Transcriptome measurement of sample EBs.index04.BC_122


title: T38B_Genomic DNA from Buccal cells


title: DJC13 dLN-Mouse02


title: EBs.index04.BC_094

description: Transcriptome measurement of sample EBs.index04.BC_094


title: T38A_Genomic DNA from Buccal cells


title: T37B_Genomic DNA from Buccal cells


title: DJC10 Spleen-Mouse02


title: EBs.index04.BC_092

description: Transcriptome measurement of sample EBs.index04.BC_092


title: DJC12 dLN-Mouse01


title: T37A_Genomic DNA from Buccal cells


title: DJC09 Spleen-Mouse01


title: EBs.index04.BC_090

description: Transcriptome measurement of sample EBs.index04.BC_090


title: T36B_Genomic DNA from Buccal cells


title: T36A_Genomic DNA from Buccal cells


title: DJC05 Blood-Mouse02


title: EBs.index04.BC_086

description: Transcriptome measurement of sample EBs.index04.BC_086


title: EBs.index04.BC_088

description: Transcriptome measurement of sample EBs.index04.BC_088


title: EBs.index04.BC_080

description: Transcriptome measurement of sample EBs.index04.BC_080


title: T35B_Genomic DNA from Buccal cells


title: DJC02 Tumor-Mouse02


title: DJC04 Blood-Mouse01


title: T35A_Genomic DNA from Buccal cells


title: EBs.index04.BC_074

description: Transcriptome measurement of sample EBs.index04.BC_074


title: EBs.index04.BC_076

description: Transcriptome measurement of sample EBs.index04.BC_076


title: I19R013a08: NBN Kir2.1-overexpressed rep2

city: Tuebingen

first: Olga

last: Garaschuk

state: BW

address: Keplerstraße 15

department: Neurophysiology Department

institute: University of Tuebingen

data_processing:
Quality control of reads (data in fastq files) was assessed with ReadQC (ngs-bits version 2019_09). Raw reads were filtered to remove sequencing adapters and for quality trimming using SeqPurge (ngs-bits version 2019_09).
Alignment of filtered reads was performed against the reference mouse genome of the Ensembl Mus Musculus GRCm38 using STAR (v2.7.0f). Reads with low mapping quality, mispairing, or multi-mapping were removed using Samtools (v1.9) and visually inspected in the Integrative Genome Viewer (v2.4.19).
A matrix of raw counts was built using subread (v1.6.4). Low expressed transcripts were filtered out to minimize the false-positive rate. Transcripts with less than 1 count per million in at least two samples were excluded, leaving 11,611 genes for further differential expression analysis.
Differentially expressed genes (DEGs) were identified using edgeR (v.3.24.3) with R (v3.5.2) (https://www.R-project.org/) following the standard workflow. Genes with an absolute >2-times-fold change and p<0.05 were considered as DEGs.
Detected DEGs were then imported to the online portal Metascape (https://metascape.org/gp/index.html#/main/step1) to run GO biological processes, cell components, molecular functions, and KEGG pathway enrichment analyses.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab-delimited text files include raw count, cpm, fpkm and tpm values for each sample
Supplementary_files_format_and_content: matric containing raw count, cpm, fpkm and tpm values for all samples
Supplementary_files_format_and_content: matric containing logFC and Pvalue for genotype effect

source_name: adult newborn neurons

growth_protocol: Mice were kept in the SPF (specified pathogen-free) area of the animal facility, with food and water ad libitum

extract_protocol:
Olfactory bulbs were dissected and the cellular component was isolated using Percoll. Adult newborn neurons were isolated by cell sorting using the fluorescence signal of Twitch2B. NBNs were flash-frozen on liquid nitrogen. A minimum of 3,000 cells was subjected to cDNA synthesis using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio).
Next-generation sequencing (NGS) libraries were prepared using 150 pg of cDNA input in the Nextera XT DNA Library Preparation Kit (Illumina), followed by 12 cycles of PCR. Libraries were sequenced as paired-end reads (100 bp read length) on a NovaSeq6000 (Illumina) with a depth of >20 million reads.

treatment_protocol: Mice were injected into the RMS (rostral migratory stream) with a lentiviral suspension expressing either the calcium sensor Twitch2B alone (control) or in combination with the potassium channel Kv1.2 (Kv1.2 overexpression) or Kir2.1 (Kir2.1 overexpression).

tag: gender

value: male

value: olfactory bulb

value: 3  months-old

tag: cell type

value: neurons

tag: genotype/variation

value: Lentivirus expressing Twitch2B and the potassium channel Kir2.1


title: DJC01 Tumor-Mouse01


title: T34B_Genomic DNA from Buccal cells


title: EBs.index04.BC_048

description: Transcriptome measurement of sample EBs.index04.BC_048

value: embryoid bodies from mouse ESCs

value: negative


title: I19R013a06: NBN Kir2.1-overexpressed rep1


title: EBs.index04.BC_046

description: Transcriptome measurement of sample EBs.index04.BC_046


title: T33B_Genomic DNA from Buccal cells


title: EBs.index04.BC_044

description: Transcriptome measurement of sample EBs.index04.BC_044


title: T33A_Genomic DNA from Buccal cells


title: T32B_Genomic DNA from Buccal cells


title: T32A_Genomic DNA from Buccal cells


title: EBs.index04.BC_042

description: Transcriptome measurement of sample EBs.index04.BC_042


title: EBs.index04.BC_036

description: Transcriptome measurement of sample EBs.index04.BC_036


title: I19R013a02: NBN control rep2

value: Lentivirus expressing Twitch2B


title: EBs.index04.BC_032

description: Transcriptome measurement of sample EBs.index04.BC_032


title: I19R013a03: NBN Kv1.2-overexpressed rep1

value: Lentivirus expressing Twitch2B and the potassium channel Kv1.2


title: T31B_Genomic DNA from Buccal cells

value: buccal cells


title: T31A_Genomic DNA from Buccal cells

value: Male


title: EBs.index04.BC_028

description: Transcriptome measurement of sample EBs.index04.BC_028


title: Hypothalamus - total RNA - SFI-213

city: Fermoy

first: Kanishka

last: Nilaweera

state: Co. Cork

address: Moorepark

department: Food Biosciences

country: Ireland

institute: Teagasc Food Research Centre

data_processing:
FASTQ files were trimmed for quality and the removal of adaptors using the Cutadapt and FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) programs as implemented by Trim Galore! (V.0.61)
High-quality trimmed reads mapped to Mus musculus reference genome assembly GRCm38 using STAR RNA-seq aligner (V.2.6.1)
Gene differential expression identified with the Bioconductor R package DeSeq2 (V.1.24.0)
Genome_build: Mus musculus reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files describing sample subsetting
Supplementary_files_format_and_content: tab-delimited tables of raw gene counts for all genes and samples

source_name: Hypothalamus tissue

extract_protocol:
Tri-reagent (Sigma, 93289)
Total RNA extracted using QIAGEN Rneasy Mini Kit (74104) following manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hypothalamus


title: Hypothalamus - total RNA - SFI-214


title: Hypothalamus - total RNA - SFI-215


title: EBs.index03.BC_383

description: Transcriptome measurement of sample EBs.index03.BC_383


title: T34A_Genomic DNA from Buccal cells


title: EBs.index03.BC_381

description: Transcriptome measurement of sample EBs.index03.BC_381


title: T30B_Genomic DNA from Buccal cells


title: I19R013a05: NBN Kv1.2-overexpressed rep2


title: Hypothalamus - total RNA - SFI-211


title: EBs.index03.BC_379

description: Transcriptome measurement of sample EBs.index03.BC_379


title: Hypothalamus - total RNA - SFI-210


title: T29B_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-209


title: I19R013a01: NBN control rep1


title: EBs.index03.BC_375

description: Transcriptome measurement of sample EBs.index03.BC_375


title: T30A_Genomic DNA from Buccal cells


title: EBs.index03.BC_371

description: Transcriptome measurement of sample EBs.index03.BC_371


title: Hypothalamus - total RNA - SFI-212


title: T28A_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-208


title: EBs.index03.BC_373

description: Transcriptome measurement of sample EBs.index03.BC_373


title: T29A_Genomic DNA from Buccal cells


title: EBs.index03.BC_369

description: Transcriptome measurement of sample EBs.index03.BC_369


title: Hypothalamus - total RNA - SFI-207


title: T27B_Genomic DNA from Buccal cells


title: T28B_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-206


title: T27A_Genomic DNA from Buccal cells


title: T26B_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-204


title: Hypothalamus - total RNA - SFI-205


title: EBs.index03.BC_331

description: Transcriptome measurement of sample EBs.index03.BC_331


title: Hypothalamus - total RNA - SFI-143


title: EBs.index03.BC_327

description: Transcriptome measurement of sample EBs.index03.BC_327


title: EBs.index03.BC_335

description: Transcriptome measurement of sample EBs.index03.BC_335


title: T26A_Genomic DNA from Buccal cells


title: T25B_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-142


title: T25A_Genomic DNA from Buccal cells


title: EBs.index03.BC_325

description: Transcriptome measurement of sample EBs.index03.BC_325


title: T24B_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-141


title: Hypothalamus - total RNA - SFI-140


title: T24A_Genomic DNA from Buccal cells


title: T23B_Genomic DNA from Buccal cells


title: EBs.index03.BC_367

description: Transcriptome measurement of sample EBs.index03.BC_367


title: Hypothalamus - total RNA - SFI-139


title: T23A_Genomic DNA from Buccal cells


title: EBs.index03.BC_319

description: Transcriptome measurement of sample EBs.index03.BC_319


title: EBs.index03.BC_317

description: Transcriptome measurement of sample EBs.index03.BC_317


title: EBs.index03.BC_321

description: Transcriptome measurement of sample EBs.index03.BC_321


title: EBs.index03.BC_315

description: Transcriptome measurement of sample EBs.index03.BC_315


title: T22B_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-137


title: Hypothalamus - total RNA - SFI-138


title: EBs.index03.BC_287

description: Transcriptome measurement of sample EBs.index03.BC_287


title: Hypothalamus - total RNA - SFI-136


title: Hypothalamus - total RNA - SFI-134


title: EBs.index03.BC_285

description: Transcriptome measurement of sample EBs.index03.BC_285


title: T22A_Genomic DNA from Buccal cells


title: T21B_Genomic DNA from Buccal cells


title: EBs.index03.BC_283

description: Transcriptome measurement of sample EBs.index03.BC_283


title: T21A_Genomic DNA from Buccal cells


title: EBs.index03.BC_281

description: Transcriptome measurement of sample EBs.index03.BC_281


title: Hypothalamus - total RNA - SFI-132


title: T20A_Genomic DNA from Buccal cells


title: EBs.index03.BC_313

description: Transcriptome measurement of sample EBs.index03.BC_313


title: EBs.index03.BC_277

description: Transcriptome measurement of sample EBs.index03.BC_277


title: T18B_Genomic DNA from Buccal cells


title: T19A_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-70


title: Hypothalamus - total RNA - SFI-67


title: Hypothalamus - total RNA - SFI-71


title: EBs.index03.BC_271

description: Transcriptome measurement of sample EBs.index03.BC_271


title: EBs.index03.BC_267

description: Transcriptome measurement of sample EBs.index03.BC_267


title: T17B_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-66


title: EBs.index03.BC_265

description: Transcriptome measurement of sample EBs.index03.BC_265


title: T18A_Genomic DNA from Buccal cells


title: EBs.index03.BC_237

description: Transcriptome measurement of sample EBs.index03.BC_237


title: Hypothalamus - total RNA - SFI-65


title: T17A_Genomic DNA from Buccal cells


title: T20B_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-69


title: T16B_Genomic DNA from Buccal cells


title: EBs.index03.BC_279

description: Transcriptome measurement of sample EBs.index03.BC_279


title: Hypothalamus - total RNA - SFI-72


title: T16A_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-63


title: Hypothalamus - total RNA - SFI-133


title: EBs.index03.BC_235

description: Transcriptome measurement of sample EBs.index03.BC_235


title: Hypothalamus - total RNA - SFI-64


title: T15B_Genomic DNA from Buccal cells


title: EBs.index03.BC_231

description: Transcriptome measurement of sample EBs.index03.BC_231


title: T19B_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-62


title: T15A_Genomic DNA from Buccal cells


title: EBs.index03.BC_275

description: Transcriptome measurement of sample EBs.index03.BC_275


title: EBs.index03.BC_223

description: Transcriptome measurement of sample EBs.index03.BC_223


title: Hypothalamus - total RNA - SFI-61


title: EBs.index03.BC_191

description: Transcriptome measurement of sample EBs.index03.BC_191


title: T14B_Genomic DNA from Buccal cells


title: EBs.index03.BC_183

description: Transcriptome measurement of sample EBs.index03.BC_183


title: Hypothalamus - total RNA - SFI-185


title: T14A_Genomic DNA from Buccal cells


title: T13A_Genomic DNA from Buccal cells


title: EBs.index03.BC_233

description: Transcriptome measurement of sample EBs.index03.BC_233


title: EBs.index03.BC_179

description: Transcriptome measurement of sample EBs.index03.BC_179


title: Hypothalamus - total RNA - SFI-184


title: Hypothalamus - total RNA - SFI-183


title: EBs.index03.BC_177

description: Transcriptome measurement of sample EBs.index03.BC_177


title: Hypothalamus - total RNA - SFI-178


title: Hypothalamus - total RNA - SFI-179


title: Hypothalamus - total RNA - SFI-177


title: T11B_Genomic DNA from Buccal cells


title: EBs.index03.BC_143

description: Transcriptome measurement of sample EBs.index03.BC_143


title: Hypothalamus - total RNA - SFI-176


title: T12A_Genomic DNA from Buccal cells


title: EBs.index03.BC_171

description: Transcriptome measurement of sample EBs.index03.BC_171


title: T12B_Genomic DNA from Buccal cells


title: T10B_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-174


title: Hypothalamus - total RNA - SFI-175


title: EBs.index03.BC_137

description: Transcriptome measurement of sample EBs.index03.BC_137


title: T11A_Genomic DNA from Buccal cells


title: EBs.index03.BC_139

description: Transcriptome measurement of sample EBs.index03.BC_139


title: T10A_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-172


title: T13B_Genomic DNA from Buccal cells


title: EBs.index03.BC_123

description: Transcriptome measurement of sample EBs.index03.BC_123


title: EBs.index03.BC_175

description: Transcriptome measurement of sample EBs.index03.BC_175


title: EBs.index03.BC_133

description: Transcriptome measurement of sample EBs.index03.BC_133


title: Hypothalamus - total RNA - SFI-99


title: T9A_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-97


title: T8A_Genomic DNA from Buccal cells


title: T8B_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-98


title: T7B_Genomic DNA from Buccal cells


title: EBs.index03.BC_091

description: Transcriptome measurement of sample EBs.index03.BC_091


title: EBs.index03.BC_141

description: Transcriptome measurement of sample EBs.index03.BC_141


title: EBs.index03.BC_095

description: Transcriptome measurement of sample EBs.index03.BC_095


title: T7A_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-107


title: EBs.index03.BC_085

description: Transcriptome measurement of sample EBs.index03.BC_085


title: Hypothalamus - total RNA - SFI-173


title: T6B_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-106


title: T6A_Genomic DNA from Buccal cells


title: T9B_Genomic DNA from Buccal cells


title: EBs.index03.BC_077

description: Transcriptome measurement of sample EBs.index03.BC_077


title: Hypothalamus - total RNA - SFI-105


title: EBs.index03.BC_045

description: Transcriptome measurement of sample EBs.index03.BC_045


title: T5B_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-103


title: EBs.index03.BC_121

description: Transcriptome measurement of sample EBs.index03.BC_121


title: T5A_Genomic DNA from Buccal cells


title: EBs.index03.BC_041

description: Transcriptome measurement of sample EBs.index03.BC_041


title: T4B_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-102


title: Hypothalamus - total RNA - SFI-101


title: T4A_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-96


title: EBs.index02.BC_360

description: Transcriptome measurement of sample EBs.index02.BC_360


title: EBs.index03.BC_089

description: Transcriptome measurement of sample EBs.index03.BC_089


title: EBs.index03.BC_027

description: Transcriptome measurement of sample EBs.index03.BC_027


title: T3B_Genomic DNA from Buccal cells


title: T3A_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-100


title: EBs.index02.BC_354

description: Transcriptome measurement of sample EBs.index02.BC_354


title: Hypothalamus - total RNA - SFI-36


title: EBs.index02.BC_356

description: Transcriptome measurement of sample EBs.index02.BC_356


title: T2B_Genomic DNA from Buccal cells


title: EBs.index02.BC_358

description: Transcriptome measurement of sample EBs.index02.BC_358


title: Hypothalamus - total RNA - SFI-104


title: EBs.index02.BC_352

description: Transcriptome measurement of sample EBs.index02.BC_352


title: Hypothalamus - total RNA - SFI-35


title: T2A_Genomic DNA from Buccal cells


title: T1B_Genomic DNA from Buccal cells


title: EBs.index02.BC_350

description: Transcriptome measurement of sample EBs.index02.BC_350


title: Hypothalamus - total RNA - SFI-34


title: EBs.index02.BC_348

description: Transcriptome measurement of sample EBs.index02.BC_348


title: Hypothalamus - total RNA - SFI-33


title: Hypothalamus - total RNA - SFI-32


title: T1A_Genomic DNA from Buccal cells


title: Hypothalamus - total RNA - SFI-31


title: EBs.index02.BC_340

description: Transcriptome measurement of sample EBs.index02.BC_340


title: Hypothalamus - total RNA - SFI-28


title: Hypothalamus - total RNA - SFI-27


title: Hypothalamus - total RNA - SFI-26


title: Hypothalamus - total RNA - SFI-25


title: EBs.index02.BC_346

description: Transcriptome measurement of sample EBs.index02.BC_346


title: EBs.index02.BC_308

description: Transcriptome measurement of sample EBs.index02.BC_308


title: EBs.index02.BC_310

description: Transcriptome measurement of sample EBs.index02.BC_310


title: Liver - total RNA - LV-KN-214

source_name: Liver tissue

extract_protocol:
Rneasy mini kit (Qiagen,74104)
Total RNA extracted using QIAGEN Rneasy Mini Kit (74104) following manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver


title: Liver - total RNA - LV-KN-215


title: Liver - total RNA - LV-KN-213


title: Liver - total RNA - LV-KN-212


title: E0771_pRetrox_MRTFB_Rep3

city: CHICAGO

first: Ekrem Emrah

last: Er

state: IL

address: 909 S  WOLCOTT AVE

department: Physiology and Biophysics

institute: The University of Illinois at Chicago

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s no -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, which is used to both normalize the full dataset and analyze differential expression between sample groups.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file containing normalized counts

source_name: E0771 cells

growth_protocol: RPMI with 10% FBS, L-Glut P/S 10mM HEPES

extract_protocol:
Qiagen RNeasy
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 500ng/mL Doxycycline for 48 hours to induce transgene expression

value: Mammary tumor cell

tag: cell line

value: MRTFB


title: E0771_pRetrox_MRTFB_Rep2


title: E0771_pRetrox_MRTFB_Rep1


title: E0771_pRetrox_MRTFA_Rep2

value: MRTFA


title: Liver - total RNA - LV-KN-211


title: E0771_pRetrox_MRTFA_Rep1


title: EBs.index02.BC_300

description: Transcriptome measurement of sample EBs.index02.BC_300

value: positive


title: E0771_pRetrox_MRTFA_Rep3


title: EBs.index02.BC_298

description: Transcriptome measurement of sample EBs.index02.BC_298


title: EBs.index02.BC_290

description: Transcriptome measurement of sample EBs.index02.BC_290


title: EBs.index02.BC_264

description: Transcriptome measurement of sample EBs.index02.BC_264