title: SRX1431480

value: dal|trained|lane|mapped|million|neuron


title: SRX1431481

status: Public on Jul 18 2018

type: SRA

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

country: USA

institute: NIDDK, NIH

library_source: transcriptomic

data_processing:
We created a pre-alignment pipeline to identify technical metadata and generate sample quality metrics. We downloaded FASTQs from SRA using fastq-dump (sra-tools v2.8.2) --split-files -M 0, and counted the number of reads and estimated average read lengths. A sample was considered paired end if two files were generated by fastq-dump and each file had an equal number of reads, ≥ 10,000 reads, and an average read length ≥ 10 bp. We filtered individual reads that were ≤ 25 bp using atropos (v1.1.18) with --minimum-length 25. We simultaneously verified samples were indeed Drosophila and estimated contamination with FastQ Screen (v0.11.3) and bowtie 2 (v2.3.3.1); by mapping 100,000 reads to 8 references (dm6, rRNA, wolbachia, human, yeast, e. coli, PhiX, ERCC-SRM2374). Next we aligned all reads with Hisat2 (v2.1.0) with --max_intronlen 300000 and --known-splicesite-file to the Drosophila melanogaster Release 6 plus ISO1 MT (GCA_000001215.4). This was followed with samtools (v1.7) and bamtools (v2.4.1) with default settings to generate summary statistics. We estimated various metrics with Picard CollectRNASeqMetrics (v2.15.0) using three separate parameters STRAND=NONE, STRAND=FIRST_READ_TRANSCRIPTION_STRAND, and STRAND=SECOND_READ_TRANSCRIPTION_STRAND. These metrics allowed us estimate library strandedness. Finally we identified duplicates using Picard MarkDuplicates (v2.15.0).
To generate counts tables and coverage tracks we used parameters discovered in the pre-alignment pipeline in our alignment pipeline. The alignment pipeline uses FASTQ file(s) downloaded by the pre-alignment pipeline, but trimms adapter sequence and low quality bases using atropos (v1.1.18) with -q 20 --minimum-length 25. The remaining reads were mapped using Hisat2 (v2.1.0) with --dta --max-intronlen 300000 --known-splicesite-infile and the --rna-strandedness using ‘F’, ‘R’, ‘FR’, or ‘RF’ depending on the strandedness. We merged alignments from individual SRA runs (SRRs) to the library level (SRX) and generated gene level, junction level, and intergenic coverage counts using FeatureCounts from the subread package (v1.5.3). Finally we created browser tracks using bamCoverage from the deeptools package (v2.5.4) using --binSize 1 --normalizeTo1x 129000000 --ignoreForNormalization chrX.
Genome_build: Drosophila melanogaster Release 6 plus ISO1 MT (GeneBank assembly accession: GCA_000001215.4)
Supplementary_files_format_and_content: Processed data files include:
*.bw are BigWig files generated using deeptools bamCoverage
*.counts are gene level coverage counts
*.jcounts are gene level junction counts
*.intergenic.counts are intergenic coverage counts
*.intergenic.jcounts are intergenic junction counts
Series level supplementary files:
dmel_r6-11.intergenic.gtf intergenic GTF generated by the pipeline for estimating intergenic coverage counts.
supplemental_metadata.tsv supplemental metadata file containing additional metadata for each sample including QC values and various flags generated by each pipeline
gene_counts.tsv supplemental file containing all gene counts as a single matrix
intergenic_counts.tsv supplemental file containing all intergenic counts as a single matrix

molecule: total RNA

organism: Drosophila melanogaster

extract_protocol: see original sample

tag: cell type

value: neuron

tag: attributes


title: SRX154748

source_name: wild type neuroblast 1

tag: tissue

value: brain

value: neuroblast

value: neuroblast|express|marker|nuclear


title: SRX3222460

source_name: HSD tissue, replicate 3

value: head

value: tissue|hsd|sugar|high|head


title: SRX3222457

source_name: HFD tissue, replicate 4

value: hfd|tissue|high|head|fat


title: SRX3222459

source_name: HSD tissue, replicate 2


title: SRX3222458

source_name: HSD tissue, replicate 1


title: SRX3222461

source_name: HSD tissue, replicate 4


title: SRX1431479

value: dal|lane|mapped|million|neuron|control


title: SRX149407

source_name: D. melanogaster OSS cell line

value: os|line|cell


title: SRX149408

source_name: D. melanogaster OSC cell line

value: osc|line|cell


title: SRX3222456

source_name: HFD tissue, replicate 3


title: SRX1431478


title: SRX3222455

source_name: HFD tissue, replicate 2


title: SRX148886

source_name: tj-piwi

value: ovary

value: ovary|driven|piwi|knockdown


title: SRX148885

source_name: tj-shu

value: ovary|shu|driven|knockdown


title: SRX3222454

source_name: HFD tissue, replicate 1


title: SRX1431477


title: SRX148887

value: OSS

value: sheet|somatic|ovarian|dsrna


title: SRX3222452

source_name: NMD tissue, replicate 3

value: nmd|tissue|normal|medium|head


title: SRX148883

source_name: nos-piwi


title: SRX1431475

value: dal|trained|lane|mapped|million|neuron


title: SRX3222453

source_name: NMD tissue, replicate 4


title: SRX148881

source_name: nos-w

value: ovary|driven|knockdown|white


title: SRX148884

source_name: tj-w


title: SRX1431474

value: neuron


title: SRX148882

source_name: nos-shu


title: SRX1431471

value: gamma kenyon


title: SRX143457

source_name: Small RNA from fly ovary of w1118: loqsf00791/CyO

tag: Sex

value: female


title: SRX3222450

source_name: NMD tissue, replicate 1

value: head


title: SRX3202734

value: male

value: whole body

value: body|whole|male


title: SRX3202735


title: SRX3202733


title: SRX1431472

value: dal|lane|mapped|million|neuron|control


title: SRX3222451

source_name: NMD tissue, replicate 2


title: SRX1431470


title: SRX1411409

source_name: D. melanogaster DOG

value: mixed

tag: developmental stage

value: third instar larval stage

value: dorsal organ ganglia

value: dog|orco|ganglion|organ|yfp|dorsal


title: SRX1431476


title: SRX143455

source_name: Small RNA from fly ovary of w1118: loqsKO/CyO

value: ovary


title: SRX1411408


title: SRX3202732


title: SRX1431473


title: SRX143454

source_name: Small RNA from fly ovary of w1118: loqsKO; loqs-PA, loqs-PB, loqs-PD/TM3


title: SRX1411407

source_name: D. melanogaster TOG

value: terminal organ ganglia

value: terminal|tog|ganglion|organ|yfp


title: SRX1411406


title: SRX3202730


title: SRX3202731


title: SRX143453

source_name: Small RNA from fly ovary of w1118: loqsKO; loqs-PB, loqs-PD/TM3


title: SRX143456

source_name: Small RNA from fly ovary of w1118: loqsf00791


title: SRX1411115


title: SRX143450

source_name: Small RNA from fly ovary of w1118: loqsKO; loqs-PB/TM3


title: SRX3202729


title: SRX3202728


title: SRX3202727


title: SRX143452

source_name: Small RNA from fly ovary of w1118: loqsKO; loqs-PA, loqs-PD/TM3


title: SRX143449

source_name: Small RNA from fly ovary of w1118: loqsKO; loqs-PA/TM3


title: SRX143447

source_name: Small RNA from female fly head of wIR: loqsf00791/CyO

value: wir|head


title: SRX1404123

value: embryonic stage 3-3.5 h (ael)


title: SRX143446

source_name: Small RNA from female fly head of wIR: loqsf00791


title: SRX1404124


title: SRX3202726


title: SRX1404121


title: SRX1411116


title: SRX143448

source_name: Small RNA from fly ovary of w1118


title: SRX3202724


title: SRX3202725


title: SRX143445

source_name: Small RNA from female fly head of wIR: loqsKO/CyO


title: SRX3202723


title: SRX3202722


title: SRX1404119


title: SRX143444

source_name: Small RNA from female fly head of wIR: loqsKO; loqs-PA, loqs-PB, loqs-PD/TM3


title: SRX1404122


title: SRX3202721


title: SRX3202720


title: SRX143441

source_name: Small RNA from female fly head of wIR: loqsKO; loqs-PA, loqs-PB/TM3


title: SRX143442

source_name: Small RNA from female fly head of wIR: loqsKO; loqs-PA, loqs-PD/TM3


title: SRX1404120


title: SRX1404117

value: stage|embryo|late|oregon


title: SRX1404118


title: SRX1388464


title: SRX143438

source_name: Small RNA from female fly head of wIR


title: SRX1388465


title: SRX143440

source_name: Small RNA from female fly head of wIR: loqsKO; loqs-PB/TM3


title: SRX142102


title: SRX143439

source_name: Small RNA from female fly head of wIR: loqsKO; loqs-PA/TM3


title: SRX3202714


title: SRX3202718


title: SRX1404116


title: SRX142100


title: SRX3202719


title: SRX1387030


title: SRX3202710


title: SRX1386954


title: SRX3202715


title: SRX142099


title: SRX1299428

source_name: rnai|tbph|total|brain|biological

value: brain

value: rnai|tbph|total|brain|biological


title: SRX143443

source_name: Small RNA from female fly head of wIR: loqsKO; loqs-PB, loqs-PD/TM3

value: female

value: head


title: SRX1388466


title: SRX3202709

value: male

value: whole body


title: SRX3202713

value: body|whole|male


title: SRX1299423

value: mixed


title: SRX142098


title: SRX1388463


title: SRX3202712


title: SRX142097


title: SRX3202707


title: SRX1299416

value: third instar larval stage


title: SRX142101


title: SRX1299415


title: SRX142096


title: SRX3202705


title: SRX3202706


title: SRX1299413


title: SRX3202703


title: SRX3202704


title: SRX1299405

source_name: hsromega|null|total|brain|biological

value: hsromega|null|total|brain|biological


title: SRX142093


title: SRX1299407


title: SRX1299406


title: SRX1299399


title: SRX1299397


title: SRX142090


title: SRX3202698


title: SRX142092


title: SRX3202708


title: SRX3202696


title: SRX142089


title: SRX142094


title: SRX141944


title: SRX1299303


title: SRX3202694


title: SRX142095


title: SRX3202695


title: SRX1299336


title: SRX141943


title: SRX3202693


title: SRX3202699


title: SRX142091


title: SRX1299292


title: SRX141942


title: SRX3202692


title: SRX1299078


title: SRX141940


title: SRX1218649

value: multi-dendritic sensory neurons

value: sensory|neuron|redstinger|md|uas


title: SRX141939


title: SRX3202691


title: SRX3202690


title: SRX1218648


title: SRX1218650


title: SRX1218647


title: SRX3202689


title: SRX3202687


title: SRX1158179

source_name: SIN3 187HA rep3


title: SRX3202688


title: SRX141937


title: SRX141936


title: SRX141938


title: SRX141935


title: SRX1158178

source_name: SIN3 187HA rep2


title: SRX3202684


title: SRX3202683


title: SRX1158176

source_name: S2 rep3


title: SRX141941


title: SRX3202682


title: SRX141933


title: SRX3202681


title: SRX141934


title: SRX1158175

source_name: S2 rep2


title: SRX135548

value: testis

value: testis|fly|day


title: SRX3202680


title: SRX1158174

source_name: S2 rep1


title: SRX1142519

source_name: Low Feeder Pop 2, G10 Males, Biological Rep 2


title: SRX3202679


title: SRX1142518

source_name: Low Feeder Pop 2, G10 Males, Biological Rep 1


title: SRX120139

value: ovary


title: SRX3202678


title: SRX1158177

source_name: SIN3 187HA rep1


title: SRX135547


title: SRX120137

value: oregon|ovary


title: SRX3202677


title: SRX1142516

source_name: Low Feeder Pop 2, G10 Females, Biological Rep 1


title: SRX1142517

source_name: Low Feeder Pop 2, G10 Females, Biological Rep 2


title: SRX120136

value: none|oregon|ovary


title: SRX120135


title: SRX3202674


title: SRX120138


title: SRX1142514

source_name: Low Feeder Pop 2, G9 Males, Biological Rep 1


title: SRX120134


title: SRX3202672


title: SRX120133


title: SRX3202671


title: SRX120132


title: SRX1142512

source_name: Low Feeder Pop 2, G9 Females, Biological Rep 1


title: SRX3202670


title: SRX1142513

source_name: Low Feeder Pop 2, G9 Females, Biological Rep 2


title: SRX1142511

source_name: Low Feeder Pop 1, G10 Males, Biological Rep 2


title: SRX3202675


title: SRX120131


title: SRX3202667


title: SRX3202668


title: SRX1142509

source_name: Low Feeder Pop 1, G10 Females, Biological Rep 2


title: SRX1142515

source_name: Low Feeder Pop 2, G9 Males, Biological Rep 2


title: SRX1142508

source_name: Low Feeder Pop 1, G10 Females, Biological Rep 1


title: SRX3202669


title: SRX3202664


title: SRX120127


title: SRX120129


title: SRX1142510

source_name: Low Feeder Pop 1, G10 Males, Biological Rep 1


title: SRX3202663


title: SRX120126


title: SRX1142507

source_name: Low Feeder Pop 1, G9 Males, Biological Rep 2


title: SRX120128


title: SRX1142506

source_name: Low Feeder Pop 1, G9 Males, Biological Rep 1


title: SRX1142504

source_name: Low Feeder Pop 1, G9 Females, Biological Rep 1


title: SRX3202661


title: SRX120124


title: SRX1142505

source_name: Low Feeder Pop 1, G9 Females, Biological Rep 2


title: SRX3202659


title: SRX120125


title: SRX3202658


title: SRX120123


title: SRX1142503

source_name: High Feeder Pop 2, G10 Males, Biological Rep 2


title: SRX120130


title: SRX1142502

source_name: High Feeder Pop 2, G10 Males, Biological Rep 1


title: SRX120122


title: SRX120121


title: SRX3202655


title: SRX1142500

source_name: High Feeder Pop 2, G10 Females, Biological Rep 1


title: SRX1142501

source_name: High Feeder Pop 2, G10 Females, Biological Rep 2


title: SRX1142499

source_name: High Feeder Pop 2, G9 Males, Biological Rep 2


title: SRX3202673


title: SRX119217

source_name: Total small RNAs from uap56 mutant, ovary, oxidized


title: SRX3202653


title: SRX119216

source_name: Total small RNAs from uap56 mutant, ovary, un-oxidized


title: SRX1142498

source_name: High Feeder Pop 2, G9 Males, Biological Rep 1


title: SRX3202654


title: SRX119215

source_name: Total small RNAs from w1118, ovary, un-oxidized


title: SRX118209

value: total|rna|old|embryo


title: SRX3202656


title: SRX118208

value: polysome|fraction|old


title: SRX1142496

source_name: High Feeder Pop 2, G9 Females, Biological Rep 1

value: female


title: SRX1142495

source_name: High Feeder Pop 1, G10 Males, Biological Rep 2


title: SRX3202650


title: SRX1142494

source_name: High Feeder Pop 1, G10 Males, Biological Rep 1


title: SRX1142493

source_name: High Feeder Pop 1, G10 Females, Biological Rep 2


title: SRX3202649


title: SRX3202657


title: SRX120120


title: SRX3202646


title: SRX3202647


title: SRX1142497

source_name: High Feeder Pop 2, G9 Females, Biological Rep 2


title: SRX118206


title: SRX3202645


title: SRX1142491

source_name: High Feeder Pop 1, G9 Males, Biological Rep 1


title: SRX118205

value: mrnp|fraction|old


title: SRX118210


title: SRX3202644

value: male


title: SRX3202651

value: whole body


title: SRX118204


title: SRX1142490

source_name: High Feeder Pop 1, G9 Females, Biological Rep 2


title: SRX3202643

value: body|whole|male


title: SRX1142489

source_name: High Feeder Pop 1, G9 Females, Biological Rep 1


title: SRX3202642


title: SRX118202


title: SRX114903

source_name: Genome-wide analysis of a reversible neurodegenerative process in Drosophila reveals the regulation of potential neuroprotective genes


title: SRX1142488

source_name: High Feeder Pop 1, G10 Females, Biological Rep 1


title: SRX3202641


title: SRX3202640


title: SRX1142492

source_name: High Feeder Pop 1, G9 Males, Biological Rep 2


title: SRX114902


title: SRX3202639


title: SRX1118825

source_name: wts149 d9 3b.RNAseq


title: SRX118207


title: SRX1118823

source_name: wts149 d9 2b.RNAseq


title: SRX3202638


title: SRX1118822

source_name: wts149 d9 2a.RNAseq


title: SRX118203


title: SRX1118821

source_name: wts149 d9 1b.RNAseq


title: SRX118201


title: SRX114900


title: SRX114901


title: SRX3202636


title: SRX1118820

source_name: wts149 d9 1a.RNAseq


title: SRX1118824

source_name: wts149 d9 3a.RNAseq


title: SRX3202635


title: SRX1118819

source_name: wts149 d5 3b.RNAseq


title: SRX1118818

source_name: wts149 d5 3a.RNAseq


title: SRX3202634


title: SRX114897


title: SRX114898


title: SRX114896


title: SRX114895


title: SRX3202633


title: SRX1118816

source_name: wts149 d5 2a.RNAseq


title: SRX1118817

source_name: wts149 d5 2b.RNAseq


title: SRX113899


title: SRX1118815

source_name: wts149 d5 1b.RNAseq


title: SRX3202631


title: SRX3202637


title: SRX1118814

source_name: wts149 d5 1a.RNAseq


title: SRX113893


title: SRX3202630


title: SRX3202629


title: SRX1118812

source_name: 82B d5 3a.RNAseq


title: SRX3202628


title: SRX113891


title: SRX1118813

source_name: 82B d5 3b.RNAseq


title: SRX3202627


title: SRX113890


title: SRX113892


title: SRX1118811

source_name: 82B d5 2b.RNAseq


title: SRX113887

value: sal


title: SRX3202652


title: SRX3202626


title: SRX3202625


title: SRX1118809

source_name: 82B d5 1b.RNAseq

value: third instar larval stage


title: SRX3202632


title: SRX113884


title: SRX113896


title: SRX113880


title: SRX113883


title: SRX1118808

source_name: 82B d5 1a.RNAseq


title: SRX3202624


title: SRX112023

source_name: Ovaries_3d_RH(high capacity to repress)

value: ovary|day


title: SRX1101053

source_name: Type II neuroblast replicate 3

value: neuroblast


title: SRX110215

source_name: GSM840649: Mutant IP RNA-seq


title: SRX1101051

source_name: Type II neuroblast replicate 1


title: SRX1118810

source_name: 82B d5 2a.RNAseq


title: SRX110214

source_name: GSM840648: Wild type IP RNA-seq


title: SRX1101050

source_name: Neuron replicate 2

value: neuron

value: neuron|wandering|brain|replicate


title: SRX1101049

source_name: Neuron replicate 1


title: SRX1101052

source_name: Type II neuroblast replicate 2


title: SRX1101048

source_name: Mushroom body neuroblast replicate 3

value: mushroom body


title: SRX1101047

source_name: Mushroom body neuroblast replicate 2


title: SRX1101046

source_name: Mushroom body neuroblast replicate 1


title: SRX101448

source_name: larval salivary gland rep 2

value: salivary gland

value: salivary|gland|larval


title: SRX3202618


title: SRX110212

source_name: GSM840646: Wild type total RNA-seq

value: ovary

value: wild|type|total|none|ovary


title: SRX3202619


title: SRX3202616


title: SRX3202623


title: SRX3202615


title: SRX3202622


title: SRX3202620


title: SRX101449

source_name: SuUR-/- larval salivary gland rep 2


title: SRX1101045

source_name: Mushroom body neuroblast 3 wash replicate 3


title: SRX3202621


title: SRX101447

source_name: SuUR-/- larval salivary gland rep1


title: SRX1101044

source_name: Mushroom body neuroblast 3 wash replicate 2


title: SRX3202614


title: SRX110213

source_name: GSM840647: Mutant total RNA-seq

value: null|piwi|mutant|total|none|ovary


title: SRX099112

value: fly


title: SRX101446

source_name: larval salivary gland rep 1


title: SRX1101042

source_name: Mushroom body neuroblast 2hr wait replicate 3


title: SRX1101043

source_name: Mushroom body neuroblast 3 wash replicate 1


title: SRX1101041

source_name: Mushroom body neuroblast 2hr wait replicate 2


title: SRX3202612


title: SRX099111


title: SRX3202611


title: SRX099110


title: SRX3202617


title: SRX099047

source_name: Drosophila melanogaster embryos

value: embryo


title: SRX3202613

value: male


title: SRX1101040

source_name: Mushroom body neuroblast 2hr wait replicate 1


title: SRX3202610

value: whole body


title: SRX3202351

value: body|whole|male


title: SRX092564

value: female

value: adult stage 0-10 days

value: mated|wholeflies|day|old|fly


title: SRX1101038

source_name: Glia replicate 1

value: glia

value: glia|wandering|brain


title: SRX092565

value: mated|wholeflies|day|old


title: SRX3202349


title: SRX1101039

source_name: Glia replicate 2


title: SRX3202350


title: SRX092563


title: SRX1101037

source_name: Antennal lobe neuroblast replicate 3

value: neuroblast


title: SRX3202348


title: SRX1101036

source_name: Antennal lobe neuroblast replicate 2


title: SRX1101035

source_name: Antennal lobe neuroblast replicate 1


title: SRX092562


title: SRX092561


title: SRX3202346


title: SRX3202347


title: SRX1101034

source_name: All neuroblast replicate 3


title: SRX3202345


title: SRX1101033

source_name: All neuroblast replicate 2


title: SRX092558

source_name: Wholeflies_w1118_Male_R2_Illumina (ln7)


title: SRX092559

source_name: Wholeflies_w1118_Male_R2_Illumina (ln8)


title: SRX1101032

source_name: All neuroblast replicate 1


title: SRX3202344


title: SRX3202343


title: SRX1101018

source_name: Mushroom body 36hr after pupae replicate 3

value: mushroom body


title: SRX087353


title: SRX3202342


title: SRX085349

source_name: small RNAs (18-29nt) from homozygotes of zuc mutants

value: zuc|mut|homozygote


title: SRX1101016

source_name: Mushroom body 36hr after pupae replicate 1


title: SRX3202341


title: SRX1101017

source_name: Mushroom body 36hr after pupae replicate 2


title: SRX3202340


title: SRX085348

source_name: small RNAs (18-29nt) from heterozygotes of zuc mutants

value: ovary

value: zuc|heterozygote|het


title: SRX1101014

source_name: Mushroom body 84hr after larva hatch replicate 2


title: SRX3202338


title: SRX3202339


title: SRX085347

source_name: small RNAs (18-29nt) from homozygotes of fs(1)yb mutants

value: mut|homozygote|small|mutant


title: SRX1101013

source_name: Mushroom body 84hr after larva hatch replicate 1


title: SRX1101012

source_name: Mushroom body 50hr after larva hatch replicate 3


title: SRX085345

source_name: small RNAs (18-29nt) from homozygotes of CG4771-delta1


title: SRX092560


title: SRX3202336


title: SRX3202337


title: SRX085344

source_name: small RNAs (18-29nt) from heterozygotes of CG4771-delta1


title: SRX1101011

source_name: Mushroom body 50hr after larva hatch replicate 2


title: SRX092557


title: SRX1101010

source_name: Mushroom body 50hr after larva hatch replicate 1


title: SRX1101009

source_name: Mushroom body 24hr after larva hatch replicate 3


title: SRX079960

source_name: Bam Mutant

value: bam|mutant


title: SRX3202335


title: SRX085342

source_name: small RNAs (18-29nt) from heterozygotes of armi mutants

value: armi|heterozygote|het


title: SRX1101015

source_name: Mushroom body 84hr after larva hatch replicate 3


title: SRX3202333

value: male


title: SRX079959

source_name: dSETDB1 Mutant

value: mutant


title: SRX085346

source_name: small RNAs (18-29nt) from heterozygotes of fs(1)yb mutants

value: heterozygote|het|small|mutant


title: SRX077889

source_name: Su(Hw)+CP190_RIP-seq_rep2 (EL21-4)


title: SRX1101008

source_name: Mushroom body 24hr after larva hatch replicate 2


title: SRX3202331

value: whole body

value: body|whole|male


title: SRX1101006

source_name: Antennal lobe 84hr after larva hatch replicate 3


title: SRX1101007

source_name: Mushroom body 24hr after larva hatch replicate 1


title: SRX3202330


title: SRX077887

source_name: Su(Hw)+CP190_RIP-seq_rep2 (EL21-2)


title: SRX077886

source_name: Su(Hw)+CP190_RIP-seq_rep2 (EL21)


title: SRX1101004

source_name: Antennal lobe 84hr after larva hatch replicate 1


title: SRX1101005

source_name: Antennal lobe 84hr after larva hatch replicate 2


title: SRX3202329


title: SRX3202328


title: SRX3202334


title: SRX3202326


title: SRX1101002

source_name: Antennal lobe 50hr after larva hatch replicate 2


title: SRX077885

source_name: input_rep2 (EL20-4)


title: SRX1101003

source_name: Antennal lobe 50hr after larva hatch replicate 3


title: SRX077884

source_name: input_rep2 (EL20-3)


title: SRX1101001

source_name: Antennal lobe 50hr after larva hatch replicate 1


title: SRX3202323


title: SRX077883

source_name: input_rep2 (EL20-2)


title: SRX3202325


title: SRX077882

source_name: input_rep2 (EL20)


title: SRX1101000

source_name: Antennal lobe 36hr after larva hatch replicate 3


title: SRX1100999

source_name: Antennal lobe 36hr after larva hatch replicate 2


title: SRX3202332


title: SRX077888

source_name: Su(Hw)+CP190_RIP-seq_rep2 (EL21-3)


title: SRX3202322


title: SRX1100998

source_name: Antennal lobe 36hr after larva hatch replicate 1


title: SRX077881

source_name: unbound_fraction_rep2 (EL19)


title: SRX3202320


title: SRX3202321


title: SRX1100997

source_name: Antennal lobe 24hr after larva hatch replicate 3


title: SRX077880

source_name: Su(Hw)+CP190_RIP-seq_rep2 (EL18)


title: SRX1100996

source_name: Antennal lobe 24hr after larva hatch replicate 2


title: SRX077878

source_name: Su(Hw)+CP190_RIP-seq_rep2 (EL16)


title: SRX3202317

value: head

value: head|male


title: SRX1100995

source_name: Antennal lobe 24hr after larva hatch replicate 1


title: SRX3202316


title: SRX1085141


title: SRX077876

source_name: input_rep1 (EL14)


title: SRX3202315


title: SRX066235

source_name: 16C follicle cells replicate 2

value: follicle


title: SRX1085140


title: SRX3202314


title: SRX066234

source_name: 16C follicle cells replicate 1


title: SRX3202313


title: SRX1085138


title: SRX077879

source_name: unbound_fraction_rep2 (EL17)


title: SRX3202312


title: SRX1054694

value: uasp|tj|ovarian|tissue|ovary


title: SRX056911

value: adult stage

value: susceptible|genetics|line


title: SRX3202318


title: SRX1054693


title: SRX1054692


title: SRX056910

value: mutagenesis|resistant|screen


title: SRX054461

value: adult

value: post|eclosion|tissue|fly|whole|day


title: SRX1054691

value: ovary


title: SRX3202311


title: SRX077877

source_name: Su(Hw)+CP190_RIP-seq_rep1 (EL15)


title: SRX054459

value: female


title: SRX3202307


title: SRX1054690


title: SRX032590


title: SRX3202310


title: SRX032589


title: SRX1054689


title: SRX1085139


title: SRX3202306


title: SRX032588


title: SRX1054688

value: ovarian|tissue|ovary


title: SRX032591


title: SRX3202304

value: male


title: SRX3202302


title: SRX1054687


title: SRX3202300


title: SRX032586


title: SRX1054686


title: SRX3202299


title: SRX3202305


title: SRX1054685


title: SRX032585


title: SRX3202298


title: SRX032584


title: SRX3202296


title: SRX1054684


title: SRX032583


title: SRX3202293


title: SRX1045309

source_name: testis|male

value: testis

value: testis|male


title: SRX1045369


title: SRX032587


title: SRX032582


title: SRX032581


title: SRX1026294

source_name: rogers|rl|carcass|post|eclosion

value: carcass

value: rogers|rl|carcass|post|eclosion


title: SRX032580


title: SRX3202290

value: head


title: SRX032579


title: SRX3202294

value: head|male


title: SRX3202292


title: SRX1026313

source_name: rogers|rl|post|testis|eclosion

value: rogers|rl|post|testis|eclosion


title: SRX032578


title: SRX3202289


title: SRX1026263


title: SRX3202288


title: SRX1025980

source_name: rogers|rl|post|eclosion|virgin

value: rogers|rl|post|eclosion|virgin


title: SRX1054683


title: SRX032576


title: SRX1023913

source_name: SIN3 KD + LID KD + paraquat rep2


title: SRX1023914

source_name: SIN3 KD + LID KD + paraquat rep3


title: SRX3103165

value: transient|sorting|induced


title: SRX3103164


title: SRX3103163


title: SRX032574


title: SRX032575


title: SRX1023912

source_name: SIN3 KD + LID KD + paraquat rep1


title: SRX3103162


title: SRX1023911

source_name: LID KD + paraquat rep3


title: SRX032573


title: SRX3103161


title: SRX1023909

source_name: LID KD + paraquat rep1


title: SRX032571


title: SRX032577


title: SRX032572


title: SRX3103160


title: SRX1023910

source_name: LID KD + paraquat rep2


title: SRX1023908

source_name: SIN3 KD + paraquat rep3


title: SRX032569


title: SRX3103156


title: SRX032570


title: SRX1023907

source_name: SIN3 KD + paraquat rep2


title: SRX3103157


title: SRX1023906

source_name: SIN3 KD + paraquat rep1


title: SRX1023905

source_name: GFP RNAi + paraquat rep3


title: SRX3103155


title: SRX1023903

source_name: GFP RNAi + paraquat rep1


title: SRX1023904

source_name: GFP RNAi + paraquat rep2


title: SRX032567


title: SRX032566


title: SRX3103154


title: SRX3103153


title: SRX032565


title: SRX3103152


title: SRX1023902

source_name: SIN3 KD + LID KD rep3

value: applicable|lid|kd


title: SRX3103158


title: SRX3103150


title: SRX032564


title: SRX1023899

source_name: LID KD rep3

value: applicable|lid


title: SRX032562


title: SRX032563


title: SRX1023900

source_name: SIN3 KD + LID KD rep1


title: SRX032568


title: SRX032561


title: SRX3103147

value: sorting|induced|neuron


title: SRX3103146


title: SRX3103145


title: SRX032559


title: SRX1023896

source_name: SIN3 KD rep3


title: SRX1023901

source_name: SIN3 KD + LID KD rep2


title: SRX1023895

source_name: SIN3 KD rep2


title: SRX032558


title: SRX1023897

source_name: LID KD rep1


title: SRX1023894

source_name: SIN3 KD rep1


title: SRX032557


title: SRX1023893

source_name: GFP RNAi rep3

value: applicable|gfp|control|prior


title: SRX032555


title: SRX3103142


title: SRX3103143


title: SRX3103144


title: SRX1023892

source_name: GFP RNAi rep2

value: applicable|gfp|control|prior|gene


title: SRX3103141


title: SRX032560


title: SRX032554


title: SRX1023898

source_name: LID KD rep2


title: SRX1023891

source_name: GFP RNAi rep1


title: SRX3103148


title: SRX3103149


title: SRX3103139


title: SRX032553


title: SRX032552


title: SRX3103140


title: SRX1006725

source_name: Drosophila melanogaster Winters 76 Mated 0

value: female

value: adult

value: winter|mated


title: SRX032551


title: SRX3103137


title: SRX1006711

source_name: Drosophila melanogaster Winters 74 Mated 0


title: SRX1006724


title: SRX032556


title: SRX3059364

value: embryonic stage 1.5-3 h (ael)


title: SRX032550


title: SRX032549


title: SRX1006710


title: SRX3059363


title: SRX3059362


title: SRX1006693

source_name: Drosophila melanogaster Winters 68 Mated 0


title: SRX032548


title: SRX032547


title: SRX032546


title: SRX1006577

source_name: Drosophila melanogaster Winters 26 Mated 0


title: SRX3059360


title: SRX1006686

source_name: Drosophila melanogaster Winters 67 Mated 0


title: SRX3059359


title: SRX3059358


title: SRX032544


title: SRX032545


title: SRX1006576


title: SRX3059356


title: SRX032543


title: SRX1006545

source_name: Drosophila melanogaster Raleigh 900 Mated 0

value: mated|raleigh


title: SRX1006544


title: SRX3059361


title: SRX032541


title: SRX3059351


title: SRX1006495

source_name: Drosophila melanogaster Raleigh 850 Mated 0


title: SRX1006692


title: SRX3059354


title: SRX032539


title: SRX1006463

source_name: Drosophila melanogaster Raleigh 808 Mated 0


title: SRX3059349


title: SRX3059350


title: SRX1006687


title: SRX032538


title: SRX1006494


title: SRX032540


title: SRX1006462


title: SRX3059348


title: SRX032537


title: SRX032542


title: SRX1006426

source_name: Drosophila melanogaster Raleigh 790 Mated 0


title: SRX032536


title: SRX3059343


title: SRX3059355


title: SRX1006427


title: SRX3059347


title: SRX032535


title: SRX3059342


title: SRX1006353

source_name: Drosophila melanogaster Raleigh 535 Mated 0


title: SRX1006352


title: SRX3059341


title: SRX032534


title: SRX032533


title: SRX3059340


title: SRX1006333

source_name: Drosophila melanogaster Raleigh 502 Mated 0


title: SRX3059339


title: SRX1006332


title: SRX1006305

source_name: Drosophila melanogaster Raleigh 476 Mated 0


title: SRX1006304


title: SRX032530


title: SRX032529


title: SRX3020558


title: SRX1006279

source_name: Drosophila melanogaster Raleigh 440 Mated 0


title: SRX032528


title: SRX1006278


title: SRX3020559


title: SRX3020557


title: SRX1006243

source_name: Drosophila melanogaster Raleigh 392 Mated 0


title: SRX3020556


title: SRX032527


title: SRX032526


title: SRX032525


title: SRX3020555


title: SRX032532


title: SRX1006242


title: SRX1006231

source_name: Drosophila melanogaster Raleigh 391 Mated 0


title: SRX3020554


title: SRX032524


title: SRX3020560


title: SRX3020553


title: SRX032523


title: SRX1006230


title: SRX1006133

source_name: Drosophila melanogaster Raleigh 367 Mated 0


title: SRX032531


title: SRX032522


title: SRX3005922

source_name: ph505 mutant cells 6

value: eye-antennal disc


title: SRX3005919

source_name: ph505 mutant cells 4


title: SRX1006132


title: SRX032521


title: SRX3005918

source_name: control cells 3


title: SRX1006029

source_name: Drosophila melanogaster Raleigh 332 Mated 0


title: SRX1006028


title: SRX3005917

source_name: ph505 mutant cells 3


title: SRX3005916

source_name: control cells 2


title: SRX032519


title: SRX1005979

source_name: Drosophila melanogaster Raleigh 287 Mated 0


title: SRX1005978


title: SRX032517


title: SRX3005914

source_name: control cells 1


title: SRX032518


title: SRX3005913

source_name: ph505 mutant cells 1


title: SRX2982437

source_name: rna|ovary

value: ovary

value: rna|ovary


title: SRX032516


title: SRX1005934

source_name: Drosophila melanogaster Raleigh 217 Virgin 0

value: head

value: virgin|raleigh


title: SRX1005953

source_name: Drosophila melanogaster Raleigh 280 Mated 0


title: SRX032514


title: SRX2982435


title: SRX2982436


title: SRX1005933


title: SRX032515


title: SRX2934415

source_name: RNA-seq of Drosophila melanogaster: 4 weeks 3 replicate male fucoxanthin

value: male

value: collected|fucoxanthin|week


title: SRX1005952


title: SRX1005899

source_name: Drosophila melanogaster Raleigh 195 Mated 0


title: SRX1005900


title: SRX032520


title: SRX032513


title: SRX032512


title: SRX2934413

source_name: RNA-seq of Drosophila melanogaster: 2 weeks 3 replicate female fucoxanthin


title: SRX2934412

source_name: RNA-seq of Drosophila melanogaster: 4 weeks 3 replicate female fucoxanthin


title: SRX032510


title: SRX1005881

source_name: Drosophila melanogaster Raleigh 138 Mated 0


title: SRX2934411

source_name: RNA-seq of Drosophila melanogaster: 2 weeks 2 replicate male fucoxanthin


title: SRX1005856

source_name: Drosophila melanogaster Raleigh 109 Mated 0


title: SRX1005855


title: SRX2934410

source_name: RNA-seq of Drosophila melanogaster: 6 weeks 1 replicate female fucoxanthin


title: SRX032508


title: SRX032507


title: SRX2934414

source_name: RNA-seq of Drosophila melanogaster: 6 weeks 3 replicate male fucoxanthin


title: SRX1005842

source_name: Drosophila melanogaster Raleigh 101 Mated 0


title: SRX2934409

source_name: RNA-seq of Drosophila melanogaster: 4 weeks 1 replicate female fucoxanthin


title: SRX1005841


title: SRX2934408

source_name: RNA-seq of Drosophila melanogaster: 2 weeks 1 replicate female fucoxanthin


title: ERX455048


title: SRX032511


title: SRX031242


title: SRX032506


title: ERX455047


title: SRX031243


title: ERX455046


title: SRX031240


title: SRX1005882


title: SRX2934405

source_name: RNA-seq of Drosophila melanogaster: 6 weeks 2 replicate male fucoxanthin


title: SRX2934404

source_name: RNA-seq of Drosophila melanogaster: 4 weeks 2 replicate male fucoxanthin


title: SRX2934407

source_name: RNA-seq of Drosophila melanogaster: 4 weeks 2 replicate female fucoxanthin


title: SRX2934403

source_name: RNA-seq of Drosophila melanogaster: 2 weeks 3 replicate male fucoxanthin


title: ERX455045


title: SRX031241


title: SRX031238


title: ERX455043


title: SRX2934402

source_name: RNA-seq of Drosophila melanogaster: 6 weeks 2 replicate female fucoxanthin


title: ERX455044


title: SRX031237


title: SRX2934401

source_name: RNA-seq of Drosophila melanogaster: 2 weeks 2 replicate female control

value: collected|week|control


title: ERX455042


title: SRX2934406

source_name: RNA-seq of Drosophila melanogaster: 2 weeks 2 replicate female fucoxanthin


title: SRX031236


title: SRX2934400

source_name: RNA-seq of Drosophila melanogaster: 4 weeks 2 replicate female control


title: SRX031235


title: ERX455040


title: SRX031239


title: ERX2252507

source_name: Female_Anal_Pad_3; FlyAtlas2

value: anal pad


title: SRX031234


title: SRX031233


title: SRX2934397

source_name: RNA-seq of Drosophila melanogaster: 2 weeks 1 replicate male control


title: SRX2934398

source_name: RNA-seq of Drosophila melanogaster: 4 weeks 1 replicate female control


title: SRX2934396

source_name: RNA-seq of Drosophila melanogaster: 4 weeks 1 replicate male control


title: ERX2252506

source_name: Female_Anal_Pad_2; FlyAtlas2


title: SRX2934395

source_name: RNA-seq of Drosophila melanogaster: 4 weeks 2 replicate male control


title: ERX2252505

source_name: Female_Anal_Pad_1; FlyAtlas2


title: SRX2934394

source_name: RNA-seq of Drosophila melanogaster: 6 weeks 2 replicate male control


title: SRX031232


title: SRX031230


title: SRX031229


title: SRX2934392

source_name: RNA-seq of Drosophila melanogaster: 2 weeks 2 replicate male control


title: SRX2934391

source_name: RNA-seq of Drosophila melanogaster: 4 weeks 1 replicate male fucoxanthin


title: ERX455041


title: ERX2252501

source_name: Male_Accessory_Glands_3; FlyAtlas2

value: accessory gland


title: ERX2252503

source_name: Male_Anal_Pad_2; FlyAtlas2


title: SRX2934390

source_name: RNA-seq of Drosophila melanogaster: 6 weeks 1 replicate male fucoxanthin


title: SRX027836

value: mace|line


title: ERX2252499

source_name: Male_Accessory_Glands_1; FlyAtlas2


title: SRX2934399

source_name: RNA-seq of Drosophila melanogaster: 2 weeks 1 replicate female control


title: ERX2252504

source_name: Male_Anal_Pad_3; FlyAtlas2


title: SRX2934389

source_name: RNA-seq of Drosophila melanogaster: 4 weeks 3 replicate male control


title: ERX2252500

source_name: Male_Accessory_Glands_2; FlyAtlas2


title: SRX031231


title: SRX026895

value: adult stage 0-10 days

value: immunoprecipitates|ovary|piwi|old


title: SRX2934388

source_name: RNA-seq of Drosophila melanogaster: 6 weeks 3 replicate male control


title: ERX2252498

source_name: Female_Brain_3; FlyAtlas2

value: female

value: brain


title: ERX2252496

source_name: Female_Brain_1; FlyAtlas2


title: ERX2252497

source_name: Female_Brain_2; FlyAtlas2


title: SRX2934386

source_name: RNA-seq of Drosophila melanogaster: 2 weeks 3 replicate male control


title: SRX026894


title: SRX026892


title: SRX2934387

source_name: RNA-seq of Drosophila melanogaster: 6 weeks 2 replicate female control


title: SRX026893


title: SRX027837

value: embryo

value: mace|embryo


title: ERX2252036

value: brain|male


title: SRX026891

value: ovary


title: ERX2252038


title: SRX026890


title: SRX2934384

source_name: RNA-seq of Drosophila melanogaster: 2 weeks 1 replicate male fucoxanthin


title: SRX2934382

source_name: RNA-seq of Drosophila melanogaster: 4 weeks 3 replicate female control


title: SRX026889

value: zuc|ovary|heterozygous


title: ERX2164671

value: larval stage

value: whole body

value: larval|larva|whole


title: ERX2164670


title: SRX019317

value: line|cell


title: ERX2164672


title: ERX2164669

value: tubule

value: tubule|malpighian|larval


title: SRX2902869

source_name: Tor-OE transcriptional profiling replicate 3

value: third instar larval stage

value: muscle

value: transcriptional|profiling|wall


title: SRX019236


title: ERX2164668


title: SRX2902863

source_name: GluRIIA transcriptional profiling replicate 3

value: gluriia|transcriptional|profiling|wall


title: ERX2164667


title: SRX019234


title: SRX019235


title: SRX2934385

source_name: RNA-seq of Drosophila melanogaster: 6 weeks 3 replicate female control

value: female

value: collected|week|control


title: SRX2934381

source_name: RNA-seq of Drosophila melanogaster: 6 weeks 3 replicate female fucoxanthin

value: collected|fucoxanthin|week


title: ERX2164666

source_name: Larval_Trachea_3; FlyAtlas2

value: trachea


title: SRX018876


title: SRX018875


title: SRX2902853

source_name: wild type transcriptional profiling replicate 2


title: SRX2902852

source_name: wild type transcriptional profiling replicate 1


title: ERX2164664

source_name: Larval_Trachea_1; FlyAtlas2


title: ERX2164665


title: SRX023847

value: adult stage 0-10 days

value: sechellia|strain|rt|size|selection|rna


title: SRX018874


title: ERX2164589

value: salivary gland

value: salivary|gland|larval


title: ERX2164588

source_name: Larval_Salivary_Gland_2; FlyAtlas2

value: larval stage


title: SRX2618543

value: wing disc


title: SRX2618542


title: SRX018873


title: SRX018872


title: SRX2902861

source_name: GluRIIA transcriptional profiling replicate 1


title: SRX018871


title: SRX2618540


title: SRX2618541


title: ERX2164585

value: midgut

value: midgut|larval|larva


title: SRX2618539


title: SRX2902854

source_name: wild type transcriptional profiling replicate 3


title: SRX018870


title: ERX2164584

source_name: Larval_Midgut_1; FlyAtlas2


title: ERX2163611

value: hindgut

value: hindgut|larval


title: SRX016672

value: whole body


title: ERX2163610


title: SRX2618535


title: SRX2618537


title: ERX2163609


title: SRX2618533


title: SRX016671


title: ERX2163002

value: fat body

value: fat|body|larval|larva


title: SRX2618534


title: SRX2618532


title: SRX016670

value: female


title: SRX017853

source_name: S2 RNA


title: ERX2163000


title: ERX2164587

source_name: Larval_Salivary_Gland_1; FlyAtlas2


title: SRX2618492

value: brain


title: SRX2618491


title: ERX2162997

value: CNS

value: cns|nervous|central|system|larval


title: ERX2162999


title: SRX2618490


title: SRX2618489


title: SRX2618488


title: SRX014984

source_name: Bam mutant testes

value: testis

value: testis|mutant|bam|mrna


title: SRX014987

source_name: Wild type ovaries

value: ovary

value: ovary|mrna


title: SRX014986

source_name: Bam mutant ovaries

value: ovary|mutant|bam|mrna


title: SRX014492


title: ERX2162972

value: larval stage

value: carcass

value: carcass|larval


title: SRX014985

source_name: Wild type testes

value: male

value: testis|mrna


title: ERX2162973


title: SRX014490


title: ERX2163001


title: ERX2162971


title: SRX014489


title: SRX2608939

value: embryonic stage

value: fixed|live|mixture|dissociated|mrnaseq


title: SRX2608938


title: ERX2162344

value: tubule

value: tubule|malpighian


title: SRX014488


title: SRX014491


title: SRX2585878

source_name: WT flies grown in 29C replica 3


title: ERX2162343


title: SRX014486


title: ERX2162341

value: testis|male


title: SRX2585877

source_name: WT flies grown in 29C replica 2


title: SRX014487


title: ERX2162339

source_name: Male_Testis_1; FlyAtlas2


title: SRX2585874

source_name: ADAR hypomorph flies grown in 29C replica 2


title: SRX2618487

value: brain


title: SRX2585873

source_name: ADAR hypomorph flies grown in 29C replica 1


title: SRX014485


title: ERX2162340


title: SRX014481


title: SRX2585870

source_name: WT flies grown in 18C replica 1


title: ERX2162334

value: hindgut

value: hindgut|male


title: SRX2585871

source_name: WT flies grown in 18C replica 2


title: ERX2162338

value: midgut

value: midgut|male


title: SRX014482


title: SRX014480


title: ERX2162336

source_name: Male_Midgut_1; FlyAtlas2


title: SRX014484


title: ERX2160993

value: whole body

value: male|fly|whole


title: SRX2464546

source_name: Low protein 1

value: adult

value: protein|low|applicable


title: SRX2585876

source_name: WT flies grown in 29C replica 1


title: SRX2585867

source_name: ADAR hypomorph flies grown in 18C replica 1


title: SRX014479


title: SRX2585869

source_name: ADAR hypomorph flies grown in 18C replica 3


title: ERX2162332


title: SRX2464544

source_name: High protein 2

value: protein|high|applicable


title: SRX2464545

source_name: High protein 1

value: male


title: SRX014477


title: ERX2160992


title: ERX2160991


title: SRX014475


title: SRX2464543

source_name: Low protein 2


title: SRX2348483

value: third instar larval stage

value: eye-antennal disc


title: ERX2160989

value: head

value: head|male


title: ERX2162333


title: ERX2162337


title: SRX014476


title: SRX2348481


title: SRX014471


title: SRX014473


title: ERX2160988


title: ERX2160990


title: SRX014478


title: SRX2348480


title: ERX2160986

value: carcass

value: carcass|male


title: SRX014470


title: ERX2160987


title: SRX2348482


title: SRX014472


title: ERX2160985

source_name: Male_Carcass_1; FlyAtlas2


title: SRX014469


title: SRX014474


title: SRX014483


title: ERX2160334

value: female

value: fly|female|whole


title: SRX014468


title: SRX014466


title: SRX2325630

source_name: dMi-2 ctrl testis (no driver) rep2

value: testis


title: SRX2325628

source_name: dMi-2 ctrl testis (no driver) rep1


title: ERX2160331

source_name: Female_Tubule_3; FlyAtlas2

value: tubule


title: SRX014467


title: ERX2160332

source_name: Female_Whole_1; FlyAtlas2


title: ERX2160330

value: tubule|malpighian


title: SRX2325629

source_name: dMi-2 KD testis rep1


title: SRX2325626

source_name: kmg KD testis rep2

value: testis|kmg|kd|post|eclosion


title: SRX014465


title: ERX2160333

value: whole body


title: SRX2325625

source_name: kmg ctrl testis (no driver) rep2


title: SRX2325624

source_name: wild-type head rep1


title: ERX2160327

value: hindgut


title: SRX014462


title: SRX2325622

source_name: kmg ctrl testis (no driver) rep1


title: SRX2325623

source_name: kmg KD testis rep1


title: SRX014460


title: ERX2159570

value: ovary

value: ovary|female


title: ERX2159571


title: SRX014461


title: SRX014459


title: SRX2053344

value: white|head|day


title: SRX2053345


title: SRX2325627

source_name: wild-type head rep2


title: ERX2156957

value: midgut

value: midgut|female


title: SRX2325631

source_name: dMi-2 KD testis rep2


title: SRX014458


title: SRX2053343

value: head


title: SRX014463


title: ERX2160329


title: ERX2156956


title: ERX2160326


title: ERX141790

source_name: source|female|adult

value: adult

value: source|female|adult


title: SRX2053342


title: SRX2053341


title: ERX141791


title: ERX2156390

value: head|female


title: SRX2053339


title: SRX2053340


title: ERX2156955

value: female


title: ERX141789

value: day|female|adult


title: ERX141787


title: ERX2156132

value: carcass


title: SRX2010815


title: ERX2156389


title: SRX2053338


title: ERX2156131


title: ERX2156130


title: ERX141784


title: ERX2159569


title: ERX2156129


title: SRX2010812


title: ERX141783


title: ERX141782


title: SRX2010811


title: ERX141781


title: SRX2010814


title: SRX2010813


title: ERX2156128


title: SRX014464


title: ERX1818307

value: embryonic stage 10-11 h (ael)

value: zga|cycle


title: ERX2156127


title: ERX141779


title: ERX141788


title: ERX141786


title: SRX2010810


title: ERX1818305


title: SRX2000504


title: ERX141780


title: SRX2000503


title: ERX1818306


title: ERX141785


title: ERX010179

source_name: E-MTAB-493:s4; Drosophila melanogaster; s4

value: mixed

value: canton|day|wild|type|head


title: ERX141778


title: SRX2000501


title: ERX1818301

value: embryonic stage 4-10 h (ael)

value: cycle|embryo


title: ERX1818302


title: SRX1973495

value: OSS


title: ERX1818299


title: SRX1973494


title: SRX2000502


title: SRX1973493


title: SRX1973496


title: ERX010180


title: ERX1818303


title: ERX1818300


title: SRX1973492


title: ERX010177

source_name: E-MTAB-493:s2; Drosophila melanogaster; s2


title: ERX1818298


title: ERX1730246

source_name: E-MTAB-5069:mutant 3; mutant 3

value: embryonic stage

value: mutant


title: ERX1818293


title: ERX1818297


title: SRX1973490


title: ERX1818296


title: ERX010178


title: ERX1730245

source_name: E-MTAB-5069:mutant 2; mutant 2


title: ERX1818294


title: SRX1973491


title: SRX1973489


title: SRX1973487


title: SRX1973488


title: ERX1730244

source_name: E-MTAB-5069:mutant 1; mutant 1


title: SRX1973486


title: ERX1730243

source_name: E-MTAB-5069:control 3; control 3

value: control|embryo


title: SRX1973482


title: SRX1973481


title: SRX1973485


title: ERX1818292


title: SRX1973484


title: ERX1605883


title: ERX1730242

source_name: E-MTAB-5069:control 2; control 2


title: ERX1605881


title: SRX1973483


title: SRX1837303

value: ovary


title: SRX312274

source_name: Generic sample from Drosophila melanogaster

value: no|generic|ovary|sample


title: ERX1428249

source_name: E-MTAB-4545:UAS-dis3L2RNAi 1

value: third instar larval stage


title: ERX1605886


title: ERX1605885


title: ERX1605884


title: SRX1884288

source_name: ribosomal RNA depleted total RNA from WRR-1 dsRED control knock-down cells, replicate 2

value: Ras[V12]; wts[RNAi]


title: ERX1605882


title: SRX1884283

source_name: ribosomal RNA depleted total RNA from WRR-1 cells, replicate 1


title: SRX1884284

source_name: ribosomal RNA depleted total RNA from WRR-1 cells, replicate 2


title: ERX1730241

source_name: E-MTAB-5069:control 1; control 1


title: SRX1837302


title: ERX1428250

source_name: E-MTAB-4545:UAS-dis3L2RNAi 2


title: SRX1837301

source_name: piwi-embKD


title: SRX1837300

source_name: white-embKD


title: ERX1428246


title: ERX1428248

source_name: E-MTAB-4545:Dis3L2 knockdown 2; Dis3L2 knockdown 2


title: SRX312271

value: female


title: DRX073132

source_name: DGRP RAL-852

value: adult

value: whole body


title: SRX1884287

source_name: ribosomal RNA depleted total RNA from WRR-1 dsRED control knock-down cells, replicate 1


title: ERX1428245


title: DRX073128

source_name: F1 hybrids between RAL-852 female and RAL-324 male


title: ERX1428247

source_name: E-MTAB-4545:Dis3L2 knockdown 1


title: DRX073131

source_name: DGRP RAL-324


title: DRX073127

source_name: F1 hybrids between RAL-324 female and RAL-852 male


title: SRX1753854


title: SRX1753848


title: SRX1753853


title: SRX1753850


title: SRX312273


title: SRX1753845


title: SRX1753847


title: DRX073125

source_name: F1 hybrids between RAL-799 female and RAL-820 male


title: DRX073130

source_name: DGRP RAL-820


title: SRX1753842


title: DRX073129

source_name: DGRP RAL-799


title: DRX073121


title: SRX1753839


title: DRX073126

source_name: F1 hybrids between RAL-820 female and RAL-799 male


title: SRX1753846


title: SRX1753844


title: DRX073120


title: DRX073124


title: SRX1753843


title: SRX1753852


title: SRX1753837


title: DRX073118


title: SRX1753851


title: SRX1753841


title: DRX073123


title: SRX1753835


title: SRX1753840


title: DRX045950

value: male


title: DRX073119


title: DRX045947


title: DRX045946


title: DRX073117


title: SRX1753833


title: SRX1753834


title: SRX1753836


title: SRX1753832


title: SRX1753849


title: SRX1753831


title: DRX045949


title: SRX1753838


title: DRX073122


title: DRX045944


title: SRX1753829


title: SRX1753828


title: DRX045941


title: SRX1753830


title: DRX045943


title: SRX1706927


title: DRX027373

value: female|whole|adult


title: SRX1706928


title: DRX045940


title: SRX1706925


title: DRX027370


title: SRX1706926


title: DRX027368


title: SRX1706922


title: SRX1706919


title: DRX027374


title: DRX045881

source_name: total mRNA sequences of delta-mbt-OSCs

value: mrna|total


title: DRX027369


title: SRX1663883

source_name: High detergent rep 2

value: head

value: detergent|high|fly


title: SRX1663882

source_name: High detergent rep 1


title: DRX027365


title: SRX1706921


title: DRX027371


title: DRX027366

value: oregon|female|whole|adult


title: DRX027372


title: SRX1706920


title: DRX027363


title: SRX1592065

source_name: neuron_GAD_FMR1_TRIBE_mRNA 35

value: gabaergic neuron


title: DRX027359


title: DRX027362


title: SRX1592068

source_name: neuron_Cha_FMR1_TRIBE_mRNA 38

value: cholinergic neuron


title: SRX1592067

source_name: neuron_Cha_FMR1_TRIBE_mRNA 37


title: SRX1204208


title: DRX027358


title: DRX027364


title: SRX1894119

value: mixed

value: brian

value: kcl|high|young|brain|canton|pooled


title: SRX1706923


title: DRX027357


title: SRX1204206


title: SRX1663881

source_name: low detergent rep 2

value: detergent|low|fly


title: DRX027367


title: SRX1894117


title: DRX027354


title: SRX1706924


title: SRX1894115

value: kcl|high|c|young|brain|canton|pooled


title: SRX1894114


title: SRX1894113


title: DRX027351


title: SRX1592066

source_name: neuron_GAD_FMR1_TRIBE_mRNA 36


title: DRX027361


title: SRX1204199


title: SRX1894112


title: DRX027360


title: SRX1204198


title: SRX1894116


title: SRX1204197


title: SRX1894109


title: SRX1204201


title: SRX1204202


title: SRX1204207


title: DRX027356


title: SRX1894118


title: SRX1204205


title: DRX027355


title: SRX1894107


title: SRX1204204


title: SRX1204194


title: DRX027353


title: SRX1894106


title: DRX027352


title: SRX1894104

source_name: elav-gal4 60' -3


title: SRX1894098

source_name: Elav-TRP 60'-3


title: SRX1204203


title: SRX1204200


title: SRX1894110

value: c|kcl|high|young|brain


title: SRX1894111


title: SRX1204196


title: SRX1098308

source_name: sug HSD 8h repC

value: third instar larval stage


title: SRX1894095

source_name: Elav-Trp 0'-3


title: SRX1204195


title: SRX1098305

source_name: control HSD 8h repB


title: SRX1204193


title: SRX1894105

source_name: 0' cs


title: SRX1098301

source_name: control HSD 8h repA


title: SRX1098309

source_name: control HSD 8h repC


title: SRX1894108


title: SRX1894103

source_name: elav-gal4 0' -3


title: SRX1098307

source_name: control LSD 1.5h repC


title: SRX1098299

source_name: sug LSD 1.5h repA


title: SRX1892933

source_name: 30' Mrna

value: mrna|blue|led|young


title: SRX1894097

source_name: Elav-TRP 30'-3


title: SRX1892932

source_name: 15' Mrna


title: SRX1894096

source_name: Elav-TRP 15'-3


title: SRX1892938

source_name: 60' NUN

value: nun|blue|led|young


title: SRX1098306

source_name: sug LSD 1.5h repC

value: whole body


title: SRX1892937

source_name: 30' NUN


title: SRX1011102

value: female

value: ovary


title: SRX1892930

value: light|blue|led|young


title: SRX1098303

source_name: control LSD 1.5h repB


title: SRX1098300

source_name: control LSD 1.5h repA


title: SRX1892936

source_name: 15' NUN

value: head


title: SRX1098302

source_name: sug LSD 1.5h repB


title: SRX1892935

source_name: 0' NUN


title: SRX1098298

source_name: sug HSD 8h repA


title: ERX2176064


title: ERX2176063


title: ERX2176062


title: SRX1892934

source_name: 60' Mrna


title: SRX1892925

value: blue|led|young|brain|pooled


title: SRX1892927


title: ERX2176061


title: SRX1098304

source_name: sug HSD 8h repB


title: SRX1892931

source_name: 0' Mrna


title: ERX2176065


title: SRX1892928


title: SRX1892929


title: ERX2176066


title: ERX2176060


title: SRX1011103

value: applicable


title: ERX2176057


title: SRX1892926


title: ERX2176058


title: SRX1892923


title: ERX2075312

source_name: A738_RNA_WT_st17_rep3; RNA_WT_st17_rep3

value: embryonic stage 15-21 h (ael)

value: st|embryo


title: SRX1892919

value: mixed

value: brian


title: ERX2176059


title: SRX1892918


title: SRX1892921


title: SRX1892922


title: ERX2075310


title: SRX1892917


title: ERX2075307


title: SRX1892924


title: ERX1918287

value: isogenic|infection|canton|line


title: SRX1892916


title: SRX1892899

source_name: TH-EGFP 29C-3

value: DA neuron


title: SRX1892920


title: ERX1918284


title: ERX1918283


title: SRX1892915


title: ERX1918286


title: ERX1883590


title: ERX1918285


title: ERX1883587


title: SRX1892912

source_name: PDF-EGFP 18C-3

value: neuron


title: ERX1883586


title: SRX1892898

source_name: TH-EGFP 18C-3


title: ERX1918280

value: inflammation|isogenic|infection|canton


title: ERX1918278


title: ERX1918279


title: ERX2075309


title: ERX1918274


title: ERX1883589


title: ERX1883588


title: ERX1918268

value: inflammation|isogenic|canton


title: ERX1918277


title: ERX1883579

value: third instar larval stage


title: ERX1918275


title: ERX1883585


title: ERX1883578


title: ERX1918273


title: ERX1813184

source_name: E-MTAB-5252:RUplus3; RUplus3


title: SRX1892913

source_name: PDF-EGFP 29C-3


title: ERX2075316


title: ERX1883583


title: ERX1883584


title: ERX1918272


title: ERX1883582


title: ERX1918271


title: ERX1883580


title: ERX2075313

value: embryonic stage 11-13 h (ael)


title: ERX1918267

value: female


title: ERX1787346

source_name: E-MTAB-4766_2:Sample 8; Sample 8

value: sample


title: ERX2075292


title: ERX1813183

source_name: E-MTAB-5252:RUplus2; RUplus2


title: ERX1883577


title: ERX1918276


title: ERX1883575


title: ERX1883576


title: ERX1813180


title: ERX2075291

source_name: A715_RNA_WT_st11_rep3; RNA_WT_st11_rep3

value: embryonic stage 5-7 h (ael)


title: ERX2075314


title: ERX1883571


title: ERX1813182


title: ERX1883570


title: ERX1883573


title: ERX1787347

source_name: E-MTAB-4766_2:Sample 9; Sample 9


title: ERX2075308


title: ERX2075288


title: ERX1883567


title: ERX1883572


title: ERX2075290


title: ERX1787345

source_name: E-MTAB-4766_2:Sample 7; Sample 7


title: ERX1883566


title: ERX1787344

source_name: E-MTAB-4766_2:Sample 6; Sample 6


title: ERX2075289

source_name: A715_RNA_WT_st11_rep1; RNA_WT_st11_rep1


title: ERX1787343

source_name: E-MTAB-4766_2:Sample 5; Sample 5


title: ERX2075285


title: ERX1787342

source_name: E-MTAB-4766_2:Sample 4; Sample 4


title: ERX2075286


title: ERX1787341

source_name: E-MTAB-4766_2:Sample 3; Sample 3


title: ERX1883569


title: ERX1787337

source_name: E-MTAB-4766_2:Sample 12; Sample 12


title: ERX1883561


title: ERX1787340

source_name: E-MTAB-4766_2:Sample 2; Sample 2


title: ERX1787339

source_name: E-MTAB-4766_2:Sample 14; Sample 14


title: ERX1787334

source_name: E-MTAB-4766_2:Sample 1; Sample 1


title: ERX2075283


title: SRX2997991

source_name: G1S RNA-seq rep2


title: ERX1787338

source_name: E-MTAB-4766_2:Sample 13; Sample 13


title: ERX1883562


title: DRX013094

source_name: Penicillium-fungus infected 3rd instar larvae of Drosophila melanogaster.


title: DRX013093

source_name: Penicillium-fungus uninfected 3rd instar larvae of Drosophila melanogaster.


title: SRX2997990

source_name: G1S RNA-seq rep1


title: ERX1787336

source_name: E-MTAB-4766_2:Sample 11; Sample 11


title: SRX129243

source_name: Microarray-based Capture of Novel Expressed Cell type-specific Transcripts (CoNECT) to annotate tissue specific transcript isoforms in D. melanogaster


title: ERX1883574


title: IGTB481.48hr_activated T cells_RNA-seq

status: Public on Jul 12 2018

city: San Francisco

first: Rachel

last: Gate

state: CA

address: 533 Parnassus Ave

institute: UCSF

data_processing:
Used RSEM for alignment to hg19 transcriptome and quantification of isoforms and gene expected counts
Genome_build: hg19 transcriptome
Supplementary_files_format_and_content: Read abundances were calculated using RSEM for gene expression counts

organism: Homo sapiens

source_name: activated T cells

growth_protocol: Briefly, CD4+ T cells were isolated from whole blood by negative selection using RosetteSep human CD4+ T cell enrichment cocktail (STEMCELL Technologies Inc., Vancouver, BC) and RosetteSep density medium gradient centrifugation. Isolated CD4+ T cells were placed in freezing container at -80°C for overnight, and then moved into a liquid nitrogen tank for long-term storage. On the day of activation, CD4+ T cells were thawed in a 37°C water bath, counted and resuspended in RPMI- 1640 supplemented with 10% FCS, and plated at 50,000 cells per well in a 96 well round-bottom plate.

extract_protocol: RNA was isolated using Qiagen RNeasy Plus Mini Kit and RNA integrity was quantified by Agilent RNA 6000 Nano Kit using the Agilent Bioanalyzer. Purified RNA were converted to RNA-seq libraries using a previously published protocol in Satija  et.al, where reverse transcription was carried out based on the SMART template switching method and the resulting cDNA was further tagmented and PCR amplified using Nextera XT DNA Sample kit (Illumina) to add the Illumina sequencing adaptors. Samples were sequenced on Illumina HiSeq 2500 to an average depth of 16.9 million reads per sample (+/- 8.7 million).

treatment_protocol: Cells were either left untreated or stimulated for 48 hours with beads conjugated with anti-CD3 and anti-CD28 antibodies (Dynabeads, Invitrogen #11131D, Life Technologies) at a cell:bead ratio of 1:1. At each time point, cells were further purified by a second step positive selection with CD4+ Dynabeads (Invitrogen #11145D, Life Technologies).

value: blood

tag: activation

value: anti-CD3 and anti-CD28

value: Male

tag: age

tag: race

value: Caucasian

tag: ethnicity

value: Non-Hispanic

tag: bmi

tag: systolic

tag: diastolic


title: IGTB1424.0hr_unstimulated T cells_RNA-seq

source_name: unstimulated T cells

value: no stimulation

value: Female


title: IGTB1424.48hr_activated T cells_RNA-seq


title: IGTB495.0hr_unstimulated T cells_RNA-seq


title: IGTB481.0hr_unstimulated T cells_RNA-seq


title: IGTB1432.0hr_unstimulated T cells_RNA-seq


title: IGTB1372.48hr_activated T cells_RNA-seq


title: SRX129242


title: ERX1883565


title: IGTB1372.0hr_unstimulated T cells_RNA-seq


title: IGTB495.48hr_activated T cells_RNA-seq


title: ERX1883563


title: IGTB1432.48hr_activated T cells_RNA-seq


title: ERX1787335

source_name: E-MTAB-4766_2:Sample 10; Sample 10


title: IGTB1394.48hr_activated T cells_RNA-seq


title: IGTB1394.0hr_unstimulated T cells_RNA-seq


title: Aged Untreated Rep2

status: Public on Apr 01 2018

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: total RNA from liver of 20-22 months C57Bl6 mouse with no treatment

data_processing:
Raw data file is not unavailable for this sample/library

Pseudoalignment performed in Kallisto using annotations from UCSC for the mm10 mouse genome.
Reads thresholded to 1
Normalized using the quantile normalization procedure and filtered based on at least 2 reads in >50% of samples in at least one experimental condition.
Genome_build: mm10
Supplementary_files_format_and_content: gene symbol and TPM

organism: Mus musculus

source_name: liver

growth_protocol: C57Bl6 mice aged to 2 months and 20-22 months

extract_protocol:
Illumina TruSeq RNA preparation kit
standard illumina protocols, paired-end

treatment_protocol: Control young and aged mice fed either standard chow diet or chow + 450mg/k P-0332991 for 2 weeks prior to sacrifice.

value: 20-22 months

tag: treatment

value: no

tag: strain


title: Young Untreated Rep3

description: total RNA from liver of 2 months C57Bl6 mouse with no treatment

value: 2 months


title: Aged Untreated Rep3


title: Sample collected from patient 4C at 3 months after transplantation PRAGUE_control_8

status: Public on May 22 2018

type: RNA

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

country: Czech Republic

institute: Institute for Clinical and Experimental Medicine

description: RNA was extracted using RNeasy Micro Kit (QIAgen)

hyb_protocol: For all samples a total of 750 ng of labeled cRNA was hybridized at 58°C for 16 hours to the Illumina HumanHT-12 v4.0 Expression BeadChips (Illumina) and subsequently washed.

scan_protocol: Fluorescence signals of the hybridized IlLumina Microarrays were detected using BeadStation 500 instrument (Illumina Inc). The raw data were extracted with the BeadStudio Data Analysis Software (Illumina).

data_processing: Bead level data were summarized by Illumina BeadStudio Software v3, imported into R and normalized using the quantile method in the Lumi package. Only probes with detectable signal intensity in at least five samples were filtered. Thus matrix contains only these filtered probes.

source_name: renal graft biopsy

label_protocol: RNA was amplified and biotinylated  for hybridization using Ambion® Illumina® TotalPrep™ RNA Amplification Kit according to manufacturer´s instructions. For all samples 200 ng of total RNA was used for amplification. Yields of labeled cRNA were determined using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: The small portion (2mm) of the  the renal graft biopsy was immediately placed in RNA later (Ambion Corporation, Austin, TX), snap frozen and stored at -80 °C until RNA extraction. RNA was isolated from renal biopsies using the RNeasy Micro Kit (Qiagen, Hilden, Germany).Quality and integrity of PAXgene RNA were determined using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified by measuring absorbance at 260 nm on the ND-1000 Spectrophotometer (NanoDrop Technologies).

treatment_protocol: Intragraft transcriptome of early IV, T cell-mediated vascular rejection (TCMRV) and nonrejection histologic findings was compared using microarrays.

tag: patient id

tag: histopathological diagnosis (normal=0, isolated v lesion=1, t cell-mediated vascular rejection=2)


title: Sample collected from patient 3C at 3 months after transplantation PRAGUE_control_7


title: Sample collected from patient 6C at 3 months after transplantation PRAGUE_control_3


title: Sample collected from patient 1A at 6 posttransplantation day  PRAGUE_TCMRV_4


title: Sample collected from patient 6B at 15 posttransplantation day  PRAGUE_eIV_5


title: Sample collected from patient 1C at 3 months after transplantation PRAGUE_control_4


title: Sample collected from patient 1B at 8 posttransplantation day  PRAGUE_eIV_6


title: Sample collected from patient 2C at 3 months after transplantation PRAGUE_control_2


title: Sample collected from patient 4A at 9 posttransplantation day  PRAGUE_TCMRV_1


title: Sample collected from patient 5B at 10 posttransplantation day  PRAGUE_eIV_3


title: Sample collected from patient 2B at 7 posttransplantation day  PRAGUE_eIV_4


title: Sample collected from patient 8C at 3 months after transplantation PRAGUE_control_1


title: Aged PD-0332991 Rep2

description: total RNA from liver of 20-22 months C57Bl6 mouse with PD-0332991 treatment


title: Aged PD-0332991 Rep1


title: Aged PD-0332991 Rep3


title: Aged Untreated Rep1


title: Young Untreated Rep2


title: Sample collected from patient 3B at 6 posttransplantation day  PRAGUE_eIV_1


title: Young Untreated Rep1


title: Sample collected from patient 3A at 6 posttransplantation day  PRAGUE_TCMRV_2


title: patient 29, T-MSCs, passage 5

status: Public on Mar 31 2018

city: LAUSANNE

first: Mathieu

last: Quinodoz

state: Vaud

address: Rue du Bugnon 27

department: DBC

country: Switzerland

institute: Université de Lausanne

hyb_protocol: Affymetrix Human Gene 1.0 ST arrays were hybridized with 2.5mg of biotinylated target, at  45°C for 17 hours washed and stained according to the protocol described in Affymetrix GeneChip Expression Analysis Manual (Fluidics protocol FS450_0007)

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

data_processing: The data were analyzed with Affymetrix Expression Console version v 1.4.1 using Affymetrix default analysis settings and Robust Multi-array Average (RMA) as normalization method.

label: biotin

source_name: T-MSCs_passage 5

label_protocol: 100ng of total RNA were amplified using the WT Expression kit (Invitrogen). The resulting sense cDNA was fragmented using UDG and APE 1 and biotin-labeled with TdT using the GeneChip WT Terminal labeling kit (Affymetrix)

growth_protocol: T- and N-MSCs were isolated respectively from paired lung tumor tissues and normal adjacent tissues removed by surgical resection from lung carcinoma patients at Centre Universitaire Hospitalier Vaudois (CHUV) with the agreement of the Swiss ethic committee (project authorization n° 131/12). Tissues were mechanically disrupted and enzymatically dissociated in IMDM (Gibco) supplemented with Collagenase II and IV (0,5 mg/mL, Gibco) and DNAse (0,1 mg/mL, Roche). The resulting single cell bulk was cultured one night in MSC medium: IMDM+GlutaMAX (Gibco) supplemented with 10% fetal bovine serum (FBS, PAN Biotech), 1% penicillin streptomycin (PS, Gibco), 1% non essential amino acids (NEAA, Gibco) and 10 ng/mL platelet-derived growth factor (PDGF, Prospec). The next day, the whole medium was changed and only adherent cells were kept in culture in MSC medium. Upon reaching 80% confluence, cells were split 1:4 - 1:6 using trypsin-EDTA 0.25 mg/ml (Lonza, USA). At each passage, some cell aliquots were frozen in FBS-DMSO 10% and kept in liquid nitrogen.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNAs were then precipitated 2h at -20°C in isopropanol, washed in EtOH 75% and suspended in H2O.

treatment_protocol: Frozen MSC samples at culture passage 5 or 6 were thawed, washed once in ice-cold IMDM+PS1% and twice in ice-cold PBS1x. Cell pellets were then suspended in Trizol reagent (Ambion, Life Technologies)

tag: subject status

value: lung carcinoma patient

tag: subject id

value: patient 29

value: mesenchymal stem cells (MSCs)

tag: cell group

value: tumor-associated MSCs (T-MSCs)

tag: passage

value: passage 5


title: patient 29, N-MSCs, passage 5

source_name: N-MSCs_passage 5

tag: cell type

value: non tumor-associated MSCs (N-MSCs)


title: histone-input

status: Public on Mar 28 2018

city: Minhang

first: bing

last: zhang

state: Shanghai

address: 800 Dong Chuan Road

department: Shanghai Center for Systems Biomedicine

country: China

institute: Shanghai Jiao Tong University

description: histone input

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 human genome assembly using bowtie2 with the following configurations: -p 1
ChiP-seq Peaks were called using MACS with the following setting: -f BAM -g 2.45e9, and then peaks fall inside the blacklist of ChIP-seq regions were trimmed.
The reads density was calculated using Homer and displayed in tag heat map using JAVA Tree.
RNA-seq reads were aligned to the hg19 genome assembly using tophat2.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using a protocol from Trapnell, Cole, et al. , Nature protocols 7.3 (2012): 562-578. In short, cufflinks was used for transcript assembly supplying a set of gene model annotation from GENCODE 19, cuffmerge for assemblies merge, cuffdiff for differnetial analysis and CummeRbund for the following analysis.
Genome_build: hg19
Supplementary_files_format_and_content: fpkm, peaks.bed

molecule: genomic DNA

source_name: Human Endothlial cell line

growth_protocol: Primary HUVEC cells purchased from Lonza  within 3-6 passages were grown  in EBM2+1% FBS or EGM2 medium (Lonza)

extract_protocol:
ChiP-seq: Chromatin DNA was extracted from sonicated nuclei and further selectively accumulated by ChiP-specific antibody.  RNA-seq: total RNA were purified by Qiagen RNeasy column.
Illumina multiplex library protocol for ChiP-seq and mRNA seq of VEGF stimualtion is as described (Bing Zhang, et al. , 2013,Genome Res. 2013 Jun;23(6):917-27); Spike-in mRNA-seq protocol followed ScriptSeq v2 RNA-seq kit (Illumina)

treatment_protocol: 50ng/ml VEGFa was used to treat serum-starved HUVEC cells. For modified RNA experiments, 0.5ug/ml modified RNA expressing GFP and ETS1 was used. For siRNA experiment, 10ng/ml siRNA was used.

value: Primary Human Umbilical Vein Endothelial Cells

tag: agent

value: VEGF


title: Sample collected from patient 4B at 7 posttransplantation day  PRAGUE_eIV_2


title: EZH2-1hour

description: EZH2 ChIP-seq after VEGF stimulation for 1hour

tag: antibody

value: EZH2, Cell Signaling

tag: time point


title: Sample collected from patient 7C at 3 months after transplantation PRAGUE_control_6


title: patient 28, N-MSCs, passage 5

value: patient 28


title: patient 28, T-MSCs, passage 5


title: Sample collected from patient 5C at 3 months after transplantation PRAGUE_control_5


title: Sample collected from patient 2A at 7 posttransplantation day  PRAGUE_TCMRV_3


title: p300-1hour

description: p300 ChIP-seq after VEGF stimulation for 1hour

value: EP300, Santa Cruz


title: p300-4hour

description: p300 ChIP-seq after VEGF stimulation for 4hour


title: p300-0hour

description: p300 ChIP-seq after VEGF stimulation for 0hour


title: GATA2-0hour

description: GATA2 ChIP-seq after VEGF stimulation for 0hour

value: GATA2, Gift from Emery H.Bresnick


title: GATA2-12hour

description: GATA2 ChIP-seq after VEGF stimulation for 12hour


title: EZH2-0hour

description: EZH2 ChIP-seq after VEGF stimulation for 0hour


title: p300-12hour

description: p300 ChIP-seq after VEGF stimulation for 12hour


title: RBPJ-12hour

description: RBPJ ChIP-seq after VEGF stimulation for 12hour

value: RBPJ, Cell Signaling


title: EZH2-12hour

description: EZH2 ChIP-seq after VEGF stimulation for 12hour


title: RBPJ-4hour

description: RBPJ ChIP-seq after VEGF stimulation for 4hour


title: EZH2-4hour

description: EZH2 ChIP-seq after VEGF stimulation for 4hour


title: patient 27, T-MSCs, passage 5

value: patient 27


title: RBPJ-0hour

description: RBPJ ChIP-seq after VEGF stimulation for 0hour


title: JUN-12hour

description: JUN ChIP-seq after VEGF stimulation for 12hour

value: JUN, Cell Signaling


title: JUN-0hour

description: JUN ChIP-seq after VEGF stimulation for 0hour


title: RBPJ-1hour

description: RBPJ ChIP-seq after VEGF stimulation for 1hour


title: JUN-4hour

description: JUN ChIP-seq after VEGF stimulation for 4hour


title: JUN-1hour

description: JUN ChIP-seq after VEGF stimulation for 1hour


title: GATA2-4hour

description: GATA2 ChIP-seq after VEGF stimulation for 4hour


title: FLI-4hour

description: FLI ChIP-seq after VEGF stimulation for 4hour

value: FLI, Santa Cruz


title: FLI-12hour

description: FLI ChIP-seq after VEGF stimulation for 12hour


title: FLI-1hour

description: FLI ChIP-seq after VEGF stimulation for 1hour


title: FLI-0hour

description: FLI ChIP-seq after VEGF stimulation for 0hour


title: ERG-4hour

description: ERG ChIP-seq after VEGF stimulation for 4hour

value: ERG, Santa Cruz


title: patient 27, N-MSCs, passage 5

value: lung carcinoma patient


title: ERG-12hour

description: ERG ChIP-seq after VEGF stimulation for 12hour


title: GATA2-1hour

description: GATA2 ChIP-seq after VEGF stimulation for 1hour


title: ERG-1hour

description: ERG ChIP-seq after VEGF stimulation for 1hour


title: ETS1 - 12hour

description: ETS1 ChIP-seq after VEGF stimulation for 12hour

value: ETS1, Santa Cruz


title: RNAPII-1hour

description: RNAPII ChIP-seq after VEGF stimulation for 1hour

value: RNAPII, Millipore


title: ETS1 - 1hour

description: ETS1 ChIP-seq after VEGF stimulation for 1hour


title: ETS1 - 0hour

description: ETS1 ChIP-seq after VEGF stimulation for 0hour


title: RNAPII-12hour

description: RNAPII ChIP-seq after VEGF stimulation for 12hour


title: RNAPII-4hour

description: RNAPII ChIP-seq after VEGF stimulation for 4hour


title: ETS1 - 4hour

description: ETS1 ChIP-seq after VEGF stimulation for 4hour


title: H3K27ac-12hour

description: H3K27ac ChiP-seq after VEGF stimulation for 12hour

value: H3K27ac, Abcam


title: H3K27ac-4hour

description: H3K27ac ChiP-seq after VEGF stimulation for 4hour


title: RNAPII-0hour

description: RNAPII ChIP-seq after VEGF stimulation for 0hour


title: H3K27ac-1hour

description: H3K27ac ChiP-seq after VEGF stimulation for 1hour


title: H3K27me3-1hour

description: H3K27me3 ChiP-seq after VEGF stimulation for 1hour

value: H3K27me3, Millipore


title: H3K27me3-4hour

description: H3K27me3 ChiP-seq after VEGF stimulation for 4hour


title: H3K27me3-12hour

description: H3K27me3 ChiP-seq after VEGF stimulation for 12hour


title: H3K4me3-4hour

description: H3K4me3 ChiP-seq after VEGF stimulation for 4hour

value: H3K4me3, Actice Motif


title: H3K27me3-0hour

description: H3K27me3 ChiP-seq after VEGF stimulation for 0hour

value: Primary Human Umbilical Vein Endothelial Cells


title: H3K4me3-0hour

description: H3K4me3 ChiP-seq after VEGF stimulation for 0hour

value: VEGF


title: H3K4me2-12hour

description: H3K4me2 ChiP-seq after VEGF stimulation for 12hour

value: H3K4me2, Abcam


title: H3K4me2-4hour

description: H3K4me2 ChiP-seq after VEGF stimulation for 4hour


title: H3K4me2-0hour

description: H3K4me2 ChiP-seq after VEGF stimulation for 0hour


title: H3K4me2-1hour

description: H3K4me2 ChiP-seq after VEGF stimulation for 1hour


title: H3K4me3-1hour

description: H3K4me3 ChiP-seq after VEGF stimulation for 1hour


title: ERG-0hour

description: ERG ChIP-seq after VEGF stimulation for 0hour


title: H3K4me1-4hour

description: H3K4me1 ChiP-seq after VEGF stimulation for 4hour

value: H3K4me1, Abcam


title: H3K4me1-12hour

description: H3K4me1 ChiP-seq after VEGF stimulation for 12hour


title: H3K4me1-0hour

description: H3K4me1 ChiP-seq after VEGF stimulation for 0hour


title: Mouse H3K27me3 (16 tissues)

status: Public on Mar 06 2018

city: Freiburg

first: Thomas

last: Manke

address: Stuebeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: RELACS-barcoded nuclei extracted from each tissues have been pooled before ChIP; two biological replicates per tissue

data_processing:
ChIP-seq reads were aligned to the mm10 and hs37d5 genome assembly using Bowtie2-2.2.8 with the following configuration: -X 1000 --local --fr --rg CN:mpi-ie_deep_sequencing_unit --rg PL:ILLUMINA
Data were sorted and indexed using samtools-1.3.1, then filtered with deeptools3 in all downstrean analysis using the following specifications: --ignoreDuplicates --blackListFileName
Reads different quality measurments were assesed using FastaQC/0.11.3, fastq_screen/0.5.1, and MultiQC/1.3
Chips were explored using different tools within deeptools3: bamCoverage, bamCompare, multiBigwigSummary, plotCorrelation, computeMatrix, plotEnrichment, plotProfile, plotFingerprint, plotHeatmap
Peaks were called using MACS2-2.1.0 callpeak with the following configurations: -f BAM -g 2900338458 --keep-dup all --nomodel; and using histoneHMM/histone_call_regions.R  -b 750 -P 0.1
Genome_build: mouse: mm10, human: hs37d5
Supplementary_files_format_and_content: txt,bed,gff,bigwig

source_name: whole organ

growth_protocol: HepG2 (ATCC, HB-8065TM) were culture in EMEM (Lonza, 06-174) supplemented with 10% FBS, 2 mM L-Glutamine, 1.8 mM CaCl2, 1mM sodium pyruvate and penicillin-streptomycin mixture (100 units/ml, Lonza), at 37 ˚C at 5% CO2. S2 cells were cultured in Express Five SFM (Thermo Fisher Scientific) supplemented with glutamax, at 27°C. Mouse experiments were performed on 9 weeks-old wild-type (WT) FVB/NJ littermate male mice fed chow diet and maintained on a 12h light cycle (lights on at 7 am).

extract_protocol:
RELACS: nuclei have been extracted, permeabilized and barcoded following RELACS protocol. Nuclei labeled with distinct barcodes have been pooled and lysed to complete chromatin preparation. Traditional ChIP-seq: after nuclei extraction chromatin has been fragmented by sonication. Immunoprecipitation has been performed using the antibody of interest.
RELACS libraries: as described in the paper, using A-tailing strategy and ligation of adapters containing nuclear barcodes. After ChIP and DNA purification library preparation has been completed by PCR amplification using NEB workflow (NEBNext Ultra II DNA library preparation kit (E7645L, NEB)). Traditional ChIP-seq libraries: NEBNext Ultra II DNA library preparation kit (E7645L, NEB)

value: brain, skeletal muscle, duodenum, pancreas, lungs, liver, heart, spleen

tag: provider/strain

value: wild-type (WT) FVB/NJ; 9 weeks old, male

tag: chip antibody


title: Mouse input (16 tissues)


title: H3K4me1-1hour

description: H3K4me1 ChiP-seq after VEGF stimulation for 1hour


title: RELACS HepG2 input 100

description: each ChIP contains 7 technical replicates identified by separated RELACS barcodes. Chromatin amount per input: same as used for ChIP

value: liver hepatocellular carcinoma

value: ATCC, HB-8065


title: Mouse H3K27ac (16 tissues)


title: RELACS HepG2 H3K27me3 1000

description: each ChIP contains 7 technical replicates (1,000 cells/replicate) identified by separated RELACS barcodes


title: RELACS HepG2 H3K27me3 100

description: each ChIP contains 7 technical replicates (100 cells/replicate) identified by separated RELACS barcodes


title: H3K27ac-0hour

description: H3K27ac ChiP-seq after VEGF stimulation for 0hour


title: RELACS HepG2 CTCF 100

value: CTCF (Abcam, ab70303)


title: RELACS HepG2 H3K4me3 100


title: H3K4me3-12hour

description: H3K4me3 ChiP-seq after VEGF stimulation for 12hour


title: RELACS HepG2 H3K4me3 1000


title: RELACS HepG2 CTCF 1000


title: RELACS HepG2 H3K4me3 10,000

description: each ChIP contains 7 technical replicates (10,000 cells/replicate) identified by separated RELACS barcodes


title: Traditional HepG2 input

description: chromatin prepared using traditional protocol for ChIP-seq (doi: 10.1093/nar/gkv1495); cell number per input: 1,000


title: RELACS HepG2 CTCF 10,000


title: RELACS HepG2 input 10,000

description: each ChIP contains 7 technical replicates identified by separated RELACS barcodes. Chromatin amount per input: 1% of ChIP volume


title: Traditional HepG2 p300

description: chromatin prepared using traditional protocol for ChIP-seq (doi: 10.1093/nar/gkv1495); cell number per ChIP: 100,000

value: p300 (Santa Cruz biotechnology, sc-585)


title: Traditional HepG2 CTCF


title: RELACS HepG2 H3K27me3 10,000


title: Traditional HepG2 H3K27me3


title: Traditional HepG2 H3K4me3


title: RELACS HepG2 p300

description: each ChIP contains 20 technical replicates (5,000 cells each) identified by different RELACS barcodes


title: Traditional HepG2 H3K27ac


title: RELACS HepG2 input

description: each ChIP contains 20 technical replicates identified by different RELACS barcodes. Chromatin amount per input: 1% of ChIP volume


title: Mouse H3K36me3 (16 tissues)


title: RELACS HepG2 input 1000

description: each ChIP contains 7 technical replicates identified by separated RELACS barcodes. Chromatin amount per input: 10% of ChIP volume


title: TraditionalHepG2 H3K4me1


title: RELACS HepG2 H3K27me3


title: RELACS HepG2 H3K9me3


title: RELACS HepG2 H3K27ac


title: RELACS HepG2 H3K4me3


title: RELACS HepG2 H3K36me3


title: Cross contamination control

description: Barcoded nuclei from each species (4 replicates each) were pooled before input preparation

organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

source_name: HepG2 + Mouse liver + Drosophila

value: HepG2 + Mouse liver + S2 cells


title: RELACS HepG2 H3K4me1


title: RELACS HepG2 CTCF


title: Traditional HepG2 H3K9me3


title: Traditional HepG2 H3K36me3


title: Pubertal Day9 Vehicle3

status: Public on Feb 21 2018

city: Boston

first: Lester

last: Kobzik

state: MA

address: 665 Huntington Ave

department: Environmental Health

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

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: Using Partek Genomics Suite Software, RMA Background Correction with Quantile Normalization, Probeset Summarization using Median Polish

source_name: Male Bl/6 mice

label_protocol: Standard Affymetrix procedure

extract_protocol: Whole lungs were isolated after euthanasia on days 3, 6 or 9 after infection or vehicle treatment.

treatment_protocol: Mice received 50 uL of vehicle (PBS) or influenza ( A/Puerto Rico/8/1934 (PR8)) by intranasal insufflation at age 25 or 28.

tag: Sex

value: male

tag: age at infection

value: 28 days

tag: tissue

value: lung

tag: harvest day after infection

value: day 9


title: Pubertal Day9 Vehicle2

tag: strain


title: Pubertal Day9 Influenza3


title: Prepubertal Day9 Vehicle1

value: 25 days


title: Pubertal Day9 Influenza1


title: Pubertal Day6 Influenza4

value: day 6


title: Pubertal Day6 Influenza3


title: Prepubertal Day6 Influenza1


title: Prepubertal Day9 Vehicle2


title: Prepubertal Day3 Influenza4

value: day 3


title: Prepubertal Day9 Vehicle3


title: Prepubertal Day3 Influenza3


title: Prepubertal Day9 Vehicle4


title: Pubertal Day9 Vehicle4


title: Prepubertal Day9 Influenza2


title: Pubertal Day9 Influenza4


title: Prepubertal Day6 Influenza2


title: Pubertal Day3 Influenza4


title: Pubertal Day3 Influenza3


title: Prepubertal Day6 Influenza4


title: Prepubertal Day9 Influenza4


title: Prepubertal Day9 Influenza3


title: Pubertal Day9 Vehicle1


title: Prepubertal Day3 Influenza2


title: Pubertal Day6 Influenza1


title: Pubertal Day0 Vehicle3

value: day 0


title: Pubertal Day0 Vehicle4


title: Pubertal Day3 Influenza2


title: 236p

status: Public on Dec 01 2017

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced clean reads were mapped to Homo sapiens (hg19) whole genome using tophat v1.4.1 with parameters -i 10 -I 80000 --solexa1.3-quals --min-coverage-intron 20 --max-coverage-intron 11000 --min-segment-intron 10 --max-segment-intron 81000 --segment-length 20
Gene annotation and calculation of FPKM values was carried out using Cufflinks (v2.0.2) with the provision of a GTF annotation file (hg19).
Gene expression differences were assessed by Cuffdiff use upper-quartile normalization, with false discovery rate correction for multiple testing.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

source_name: normal lung

extract_protocol:
Tumor and adjacent tissues were ground into powder in liquid nitrogen; total RNA was harvested using RNeasy Plant Mini Kit (QIAGEN); then total RNA samples were treated with DNase I and the mRNA is enriched by using the oligo(dT) magnetic beads.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age (yrs)

tag: gender

value: female

tag: survival time

value: 9 months

value: normal lung


title: 236c

source_name: adenocarcinoma

value: adenocarcinoma

tag: tumor grade

value: Intermediate grade

tag: tumor stage


title: Prepubertal Day0 Vehicle3


title: Prepubertal Day3 Influenza1


title: Pubertal Day0 Vehicle1


title: Pubertal Day0 Vehicle2


title: Sample5_Control

status: Public on Oct 21 2015

type: genomic

city: Baltimore

first: Andrew

last: Jaffe

address: 855 N Wolfe St, Ste 300

department: Clinical Sciences

institute: Lieber Institute for Brain Development

description:
Human DLPFC DNA methylation sample
The negative ages refer to fetal/pre-birth samples

hyb_protocol: Following manufacturer's protocol

scan_protocol: Following manufacturer's protocol

data_processing:
idat files were read in using the minfi Bioconductor package and processed using the preprocessQuantile approach
GEO_procData.csv: the resulting Illumina "Beta" matrix (proportion methylation) after stratified quantile normalization.
GEO_rawData.csv: Unmethylated and methylated signal intensities
suppTable9_meQTLs_allPairs.csv: all significant SNP-CpG pairs for meQTLs with FDR < 0.01, with corresponding annotation.

source_name: DLPFC

label_protocol: Following manufacturer's protocol

extract_protocol: Genomic DNA was extracted from 100 mg of pulverized dorsolateral prefrontal cortex (DLPFC) tissue with the phenol-chloroform method.

treatment_protocol: Bisulfite conversion of 600 ng genomic DNA was performed with the EZ DNA methylation kit (Zymo Research).

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: dropsample (whether to remove the sample for failing quality control)

value: FALSE

tag: sex (clinical gender)

value: M

tag: race

value: AA

tag: group

value: Control

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

value: TRUE

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample4_Control

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

value: F


title: Sample8_Control

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)


title: Sample7_Control

tag: race

tag: group


title: Sample6_Control

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)


title: Prepubertal Day0 Vehicle2

tag: strain

tag: Sex

value: male

tag: age at infection

tag: tissue

value: lung

tag: harvest day after infection


title: Sample3_Control

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample2_Control

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample1_Control

tag: race

tag: group

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)


title: Prepubertal Day0 Vehicle1

tag: strain

tag: Sex

tag: age at infection

value: 25 days

tag: tissue

tag: harvest day after infection


title: Pubertal Day3 Influenza1

value: 28 days


title: CT6

status: Public on Mar 31 2015

city: Miami

first: John

last: Gilbert

state: FL

address: 1535 NW 10th Ave

department: John P. Hussman Institute for Human Genomics

institute: University of Miami

description: post-mortem brain tissue

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner setting

data_processing: Sample analysis was done according to the Illumina protocol; The unmethylated and methylated signal intensities are located on the series level and in the .idat files.

label: Cy3 and Cy5

source_name: temporal pole_no_disease

label_protocol: Sample preparation were done according to the Illumina protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: disease

value: brain

tag: brain region

value: temporal pole

tag: gender

value: Male


title: C1571-F

status: Public on Nov 24 2015

city: SYDNEY

first: Irina

last: VOINEAGU

address: High ST

country: Australia

institute: UNSW

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw expression data was log2 transformed and quantile normalized using the Lumi Bioconductor package.

label: Biotin

source_name: Frontal Cortex

label_protocol: Standard Illumina labeling protocol

extract_protocol: Total RNA was extracted from around 100mg of brain tissue using the Qiagen miRNEasy kit following the manufacturer’s protocol, including an on-column DNase I treatment. An additional DNase I (New England Biolabs) treatment was carried out in solution, in order to eliminate any contaminating genomic DNA.

value: Female

tag: age (y-years; d-days)

value: Postmortem Brain Tissue

tag: disease state


title: Prepubertal Day0 Vehicle4

value: day 0


title: CT9

description: post-mortem brain tissue


title: CT10

description: post-mortem brain tissue


title: CT8

description: post-mortem brain tissue


title: CT5

description: post-mortem brain tissue


title: CT3

description: post-mortem brain tissue


title: CT1

description: post-mortem brain tissue


title: CT2

description: post-mortem brain tissue


title: hESC-MasterShef10

status: Public on May 05 2015

city: Edinburgh

first: Tilo

last: Kunath

address: 5 LIttle France Drive

department: Centre for Regenerative Medicine

country: United Kingdom

institute: University of Edinburgh

description: Genomic DNA extracted from hES cells was genotyped using Illumina HumanCytoSNP-12 v2.1 BeadChip arrays

hyb_protocol: Labelled fragments were hybridized to Multi BeadChips as per the Infinium HD Assay Ultra Protocol Guide

scan_protocol: Hybridized beads were scanned with the iScan system and the BeadArray Reader

data_processing: Illumina GenomeStudio (v1.94)

label: C/G-biotin and A/T-DNP

source_name: Human embryonic stem cells

label_protocol: 200ng of genomic DNA (quantified by the PicoGreen assay) was labelled as per the Infinium HD Assay Ultra Protocol Guide

growth_protocol: Various self-renewing media and matrices. Media included Essential 8, StemPro, or NutriStem, and matrices included CellStart or Laminin-521.

extract_protocol: Genomic DNA was isolated from cell pellets using the MasterPure™ Complete DNA and RNA Purification Kit (Epicentre). Briefly, hES cell pellets were lysed with Tissue and Cell Lysis Solution, followed by Proteinase K and RNase A treatment. Proteins were precipitated with MPC Protein Precipitation Reagent and removed by centrifugation. Genomic DNA was precipitated with isopropanol, pelleted by centrifugation and then resuspended in TE buffer to a final concentration of 50 ng/μl. Purity was checked by spectrophotometry using the NanoDrop 1000 spectrophotometer (Thermo Fisher).

treatment_protocol: Self-renewing conditions.

tag: cell type

value: embryonic stem cells

tag: passage

value: passage 22


title: genomic DNA from OC52

status: Public on Sep 06 2014

city: TOLEDO

first: Barbara

last: Melendez

address: AVDA. BARBER 30

department: UNIDAD DE INVESTIGACION DE PATOLOGIA MOLECULAR

country: Spain

institute: HOSPITAL VIRGEN DE LA SALUD

description: normal brain tissue

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2, Raw data are available in IDAT files on each sample record and on series record in the file: Unmethylated_and_methylated_signal_intensities.txt

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using phenol-cloroform based methods according to standard conditions

value: Non tumoral brain tissue


title: genomic DNA from OC50

description: normal brain tissue


title: genomic DNA from OC49

description: normal brain tissue


title: 4137

status: Public on Sep 05 2014

city: Kelvin Grove

first: Joanne

last: Voisey

state: Queensland

address: 60 Musk Ave

department: IHBI

institute: Queensland University of Technology

description: genomic DNA from frontal cortex

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

scan_protocol: standard Illumina scan settings

data_processing: GenomeStudio v2011.1 with Methylation module 1.9.0 softward

label: cy3, cy5

source_name: frontal cortex

label_protocol: Standard Illumina protocol

extract_protocol: genomic DNA was extracted using the Roche MagNa Pure Compact

tag: disease status (1=control, 2=scz patient)

tag: age

tag: pmi (hours)

value: M

tag: sample well

tag: sentrix id

tag: sentrix position


title: 3280

description: genomic DNA from frontal cortex


title: genomic DNA from Craniotomy for Epilepsy NTB-1780

status: Public on Jan 06 2015

city: Acton

first: Sebastian

last: Kurscheid

state: ACT

address: 57 Garran Road

department: JCSMR

institute: Australian National University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

data_processing: BeadStudio software v3.2 was used for primary data acqusition. Raw data was imported into R and further processed using R/Bioconductor package “methylumi”. The raw pre-processing (Illumina method) was used for data normalization.

source_name: Craniotomy for Epilepsy NTB-1780

extract_protocol: Genomic DNA was isolated using Qiagen AllPrep DNA/RNA Kit (Qiagen, 80204).

value: U

value: Non-tumor brain

tag: geo expression data

tag: os


title: 3221

description: genomic DNA from frontal cortex


title: 3590

description: genomic DNA from frontal cortex


title: genomic DNA from Craniotomy for Epilepsy NTB-2903

source_name: Lobectomy NTB-2903

value: F


title: 3216

description: genomic DNA from frontal cortex


title: genomic DNA from OC51

description: normal brain tissue

tag: tissue


title: 3565

description: genomic DNA from frontal cortex


title: genomic DNA from Craniotomy for Epilepsy NTB-2901

source_name: Craniotomy for Epilepsy NTB-2901


title: 4064

description: genomic DNA from frontal cortex


title: genomic DNA from Craniotomy for Epilepsy NTB-1076

source_name: Craniotomy for Epilepsy NTB-1076


title: genomic DNA from Craniotomy for Epilepsy NTB-2900

source_name: Craniotomy for Epilepsy NTB-2900


title: 3545

description: genomic DNA from frontal cortex


title: 3611

description: genomic DNA from frontal cortex


title: 3589

description: genomic DNA from frontal cortex


title: 3276

description: genomic DNA from frontal cortex


title: 3603

description: genomic DNA from frontal cortex


title: genomic DNA from OC48

description: normal brain tissue


title: 3606

description: genomic DNA from frontal cortex


title: 3236

description: genomic DNA from frontal cortex


title: 3543

description: genomic DNA from frontal cortex


title: 4135

description: genomic DNA from frontal cortex


title: 3602

description: genomic DNA from frontal cortex


title: 3558

description: genomic DNA from frontal cortex