title: RNA-seq analysis of human differentiating macrophages treated with IL-4 (rep2)

city: Debrecen

first: Gergely

last: Nagy

address: Egyetem ter 1.

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

data_processing:
alignment with TopHat v2.0.7 using default parameters
calculating RPKM values by cufflinks v2.0.2 using default parameters
calculating raw count values by HTSeq 0.6.0 using default parameters
Genome_build: hg19
Supplementary_files_format_and_content: [RNA-Seq] raw tag count file

source_name: RNA-seq, differentiating macrophages treated with IL-4

extract_protocol:
Total RNA was isolated from cells using Tri Reagent (MRC) according to the manufacturer’s protocol.
Indexed cDNA libraries were prepared from 1 µg of total RNA following the TruSeq™ RNA Sample Preparation Kit (Illumina, Inc.) protocol. Briefly, the mRNA Poly-A was selected on oligo (dT) magnetic beads and fragmented by divalent cations at 94°C for 5 min. Reverse transcription was performed using SuperScript II reverse transcriptase (Life Technologies, Inc.) and random primers. After second strand cDNA synthesis, fragments were end repaired, A-tailed and ligated with indexed adapters. cDNA libraries were purified and size selected after PCR with AMPure XP beads (Beckman Coulter, Inc, Fullerton, C.A USA).

value: adult

value: blood

tag: treatment


title: RNA-seq analysis of human differentiating macrophages treated with IL-4 (rep1)

status: Public on Jul 07 2017

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: age

tag: tissue

tag: cell type


title: 178063390_HO_GPSM3

city: New York

first: Eric

last: Schadt

address: 1425 Madison Avenue

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: homozygous knockout

data_processing:
Illumina Casava1.82 software used for basecalling.
Short reads in fastQ format are processed using RAPiD, which is a RNA-Seq analysis framework developed and maintained by the Technology Development group at Icahn Institute for Genomics and MultiScale Biology. .
RAPiD uses STAR to map the short reads to the  [ MOUSE: mm10 ] reference and resultant alignment map in BAM format is quantified for gene level expression using featureCounts of the subreads package. Detailed QC metrics are generated using the RNASeQC package
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count number reads per gene for each Sample.

organism: Mus musculus

growth_protocol: mouse models

extract_protocol:
RNA was prepared using the KAPA Stranded RNA-Seq with RiboErase sample preparation kit (kapabiosystems) in accordance with the manufacturer’s instructions.
Briefly, 500ng of total RNA was ribo depleted, fragmented and went under first and second strand synthesis, A tailing, adapter ligation and PCR amplification (using 11 cycles).  Final libraries were quantified using the KAPA Library Quantification Kit (KAPA Biosystems), Qubit Fluorometer (Life Technologies) and Agilent 2100 BioAnalyzer.
Samples were sequenced on an Illumina HiSeq2500 sequencer (v4 chemistry) using 1 x 100bp cycles.

treatment_protocol: For each mouse line for: Gpsm3 (3% DSS), Aif1 (3% DSS), Nckap1l (Hem1), Dock2 (3% DSS), Dok3 (3.5% DSS) DSS treatment for five days followed by water for 5 days, (7 days for Nckap1l).  Tissue was collected at Day 10 (Day 12 for Nckap1l (HEM1))

tag: Sex

value: M

tag: genotype

value: HO

tag: strain


title: RNAseq-hNCC-ZIKVPR-2  [HiSeq 3000]

city: Atlanta

first: Peng

last: Jin

state: Georgia

address: 615 Michael St., Rm 325

department: Human Genetics

institute: Emory University

description: Illumina HiSeq3000

data_processing:
RNA-seq reads were aligned using tophat v2.0.8 and differential RPKM expression values were extracted using cuffdiff v2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: RNAseq gene expression value in cufflink fpkm_tracking file format

source_name: hNCC

extract_protocol:
RNA was extracted by Trizol.
RNA-seq libraries were constructed with Illumina True-seq kit

tag: virus infection


title: 178063639_WT_HEM1

description: wild type

value: WT


title: RNA-seq analysis of untreated human differentiating macrophages (rep1)

source_name: RNA-seq, untreated differentiating macrophages

value: untreated


title: STAT6 ChIP-seq analysis of human differentiating macrophages treated with IL-4 (rep2)

library_source: genomic

data_processing:
alignment with bwa v0.7.10 using default parameters
bam generation with samtools v0.1.19 using default parameters
tag directory generation with homer v4.2 makeTagDirectory using -checkGC parameter
peak/region calling with homer v4.2 findPeaks using -center or -region -size 1000 -minDist 2500 parameters, respectively
annotation with homer v4.2 annotatePeaks.pl using default parameters
Genome_build: hg19
Supplementary_files_format_and_content: [ChIP-seq] annotation file

molecule: genomic DNA

source_name: STAT6 ChIP-seq, differentiating macrophages treated with IL-4

extract_protocol:
Human CD14+ monocyte-derived differentiating macrophages at 24 hours following isolation were treated with IL-4 (20 ng/ml, 30 min) as indicated then harvested by scraping in medium followed by centrifugation at 4C for 10 min at 1000 g then cross-linked using DSG and formaldehyde-based double cross-linking method and processed for ChIP. Chromatin was immunoprecipitated with antibodies against PU.1 (sc-352), STAT6 (sc-981), RXR (sc-774) and H3K27Ac (ab4729).
Library preparation was performed as previously described (Nagy, Daniel, Jonas et al., 2013) with minor modifications. 1 ng (STAT6, PU.1, RXR) and 5 ng (H3K27Ac) DNA amounts were used for the library preparation.

tag: chip antibody


title: STAT6 ChIP-seq analysis of human differentiating macrophages treated with IL-4 (rep1)


title: 178063385_HO_GPSM3

description: homozygous knockout


title: 178063348_HO_GPSM3

description: homozygous knockout


title: 178063350_WT_GPSM3

description: wild type


title: 178063345_HO_GPSM3

description: homozygous knockout


title: STAT6 ChIP-seq analysis of untreated human differentiating macrophages (rep1)

source_name: STAT6 ChIP-seq, untreated differentiating macrophages


title: 178063372_HO_GPSM3

description: homozygous knockout


title: 178063344_HO_GPSM3

description: homozygous knockout


title: RXR ChIP-seq analysis of human differentiating macrophages treated with IL-4 (rep2)

source_name: RXR ChIP-seq, differentiating macrophages treated with IL-4


title: RXR ChIP-seq analysis of human differentiating macrophages treated with IL-4 (rep1)


title: 178063334_HO_AIF1

description: homozygous knockout


title: RXR ChIP-seq analysis of untreated human differentiating macrophages (rep2)

source_name: RXR ChIP-seq, untreated differentiating macrophages


title: 178063333_HO_AIF1

description: homozygous knockout


title: RXR ChIP-seq analysis of untreated human differentiating macrophages (rep1)


title: 178063332_HO_AIF1

description: homozygous knockout


title: PU.1 ChIP-seq analysis of human differentiating macrophages treated with IL-4 (rep2)

source_name: PU.1 ChIP-seq, differentiating macrophages treated with IL-4


title: 178063359_WT_GPSM3

description: wild type


title: 178063322_HO_AIF1

description: homozygous knockout


title: 178063323_HO_AIF1

description: homozygous knockout


title: RNA-seq analysis of untreated human differentiating macrophages (rep2)


title: H3K27ac ChIP-seq analysis of human differentiating macrophages treated with IL-4

source_name: H3K27ac ChIP-seq, differentiating macrophages treated with IL-4


title: PU.1 ChIP-seq analysis of untreated human differentiating macrophages (rep1)

source_name: PU.1 ChIP-seq, untreated differentiating macrophages


title: 178063321_HO_AIF1

description: homozygous knockout


title: STAT6 ChIP-seq analysis of untreated human differentiating macrophages (rep2)


title: 178063324_HO_AIF1

description: homozygous knockout


title: PU.1 ChIP-seq analysis of untreated human differentiating macrophages (rep2)


title: 178063320_HO_AIF1

description: homozygous knockout


title: 178063318_WT_AIF1

description: wild type


title: H3K27ac ChIP-seq analysis of untreated human differentiating macrophages

source_name: H3K27ac ChIP-seq, untreated differentiating macrophages


title: 178063315_WT_AIF1

description: wild type


title: 24h_P1

city: Dallas

first: Kishore

last: Annavarapu

state: TX

address: 5323 Harry Hines Blvd

department: Department of Obstetrics & Gynecology

institute: UT Southwestern Medical Center

data_processing:
Basecalls performed using casava/1.8.2
Reads were trimmed to remove adaptor sequences and low quality bases using fastq-mcf (v1.1.2-806)
RNAseq reads aligned to hg19 using TopHat v2.0.10
Raw read counts generated using featureCounts (package subread v1.4.6)
Normalized read counts and differential expression results were generated using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited txt files that include raw read counts for each sample

source_name: cervical stroma

growth_protocol: Cells grown in DMEM (Sigma # D6429) with 10% FBS (Atlanta Biologicals #S11150) at 37 C in 5% CO2

extract_protocol:
Total RNA extracted using kit (Invitrogen #AM1914)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: human cervical stromal cells were treated with DMSO (vehicle) or PGE2 (100 nM) for 1 h or 24 h followed by total RNA extraction and Sequencing

value: explant derived cells in culture

tag: agent

tag: time point


title: 178063314_WT_AIF1

description: wild type


title: 24h_D2

value: DMSO


title: 1h_P2


title: 1h_P1


title: 178063197_WT_DOCK2

description: wild type

value: F


title: 178063331_WT_AIF1

description: wild type


title: 24h_D1


title: 178063198_WT_DOCK2

description: wild type


title: 178063196_HO_DOCK2

description: homozygous knockout


title: 178063195_HO_DOCK2

description: homozygous knockout


title: 1h_D1


title: 1h_D2


title: 178063349_WT_GPSM3

description: wild type


title: 178063187_HO_DOCK2

description: homozygous knockout


title: 24h_P2


title: 178063181_WT_DOCK2

description: wild type


title: 178063183_HO_DOCK2

description: homozygous knockout


title: 178063180_WT_DOCK2

description: wild type


title: 178063186_WT_DOCK2

description: wild type


title: RNAseq-hNCC-ZIKVPR-2

description: Illumina HiSeq2500

value: neural crest cells


title: RNAseq-hPN-ZIKVPR-2

description: Illumina HiSeq2500

source_name: hPN

value: peripheral neurons


title: RNAseq-hNCC-mock-2

description: Illumina HiSeq2500

value: mock


title: 178063177_HO_DOCK2

description: homozygous knockout


title: RNAseq-hNCC-ZIKVPR-1

description: Illumina HiSeq2500


title: RNAseq-hPN-mock-2

description: Illumina HiSeq2500


title: 178063175_HO_DOCK2

description: homozygous knockout


title: 178063171_WT_DOCK2

description: wild type


title: 9V colon female control S134

description: 9V colon female control S134

data_processing:
Illumina Casava1.82 software used for basecalling.
Short reads in fastQ format are processed using RAPiD, which is a RNA-Seq analysis framework developed and maintained by the Technology Development group at Icahn Institute for Genomics and MultiScale Biology. .
RAPiD uses STAR to map the short reads to the  [hg19 ] reference and resultant alignment map in BAM format is quantified for gene level expression using featureCounts of the subreads package. Detailed QC metrics are generated using the RNASeQC package
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include fragment per kilobase per million (FPKM) for each gene

source_name: colon

growth_protocol: Inflammatory bowel disease and health control samples

treatment_protocol: A variety of clinical perturbation by following the clincal guildlines.

tag: gender

value: female

tag: age (yr)

tag: clinical condition

value: control


title: PU.1 ChIP-seq analysis of human differentiating macrophages treated with IL-4 (rep1)


title: RNAseq-hPN-mock-1

description: Illumina HiSeq2500


title: RNAseq-hPN-ZIKVPR-1

description: Illumina HiSeq2500


title: 9R rightcolon female control S132

description: 9R rightcolon female control S132

source_name: rightcolon


title: 9S smallbowel male control S133

description: 9S smallbowel male control S133

source_name: smallbowel

value: male


title: 178063172_WT_DOCK2

description: wild type


title: 178063167_WT_DOCK2

description: wild type


title: 178063319_WT_AIF1

description: wild type


title: 9O leftcolon male Crohn's disease S130

description: 9O leftcolon male Crohn's disease S130

source_name: leftcolon

value: Crohn's disease


title: 178063166_WT_DOCK2

description: wild type


title: 178063164_HO_DOCK2

description: homozygous knockout


title: 9Q sigmoid male Crohn's disease S131

description: 9Q sigmoid male Crohn's disease S131

source_name: sigmoid


title: 178063162_WT_DOCK2

description: wild type


title: 9N ileum_slightlyinflamed female Ulcerative Colitis S129

value: Ulcerative Colitis


title: 9L sigmoid male control S128

description: 9L sigmoid male control S128


title: 178063157_HO_DOCK2

description: homozygous knockout


title: 178063158_HO_DOCK2

description: homozygous knockout


title: RNAseq-hNCC-mock-1

description: Illumina HiSeq2500

source_name: hNCC


title: 9I_6I leftcolon male Ulcerative Colitis S127


title: 178063156_WT_DOCK2

description: wild type


title: 8W transversecolon female control S125

description: 8W transversecolon female control S125

source_name: transversecolon


title: 178063170_WT_DOCK2

description: wild type


title: 9F transversecolon female control S126

description: 9F transversecolon female control S126


title: 178063153_WT_DOCK2

description: wild type


title: 8V leftcolon male control S124

description: 8V leftcolon male control S124


title: 178063152_WT_DOCK2

description: wild type


title: 178063154_HO_DOCK2

description: homozygous knockout


title: 178063143_WT_DOCK2

description: wild type


title: 8S smallbowel male Crohn's disease S121

description: 8S smallbowel male Crohn's disease S121


title: 8L smallbowel female control S118

description: 8L smallbowel female control S118


title: 178063147_HO_DOCK2

description: homozygous knockout


title: 8Q rightcolon female control S120

description: 8Q rightcolon female control S120


title: 178063141_WT_DOCK2

description: wild type


title: 8U leftcolon female Ulcerative Colitis S123


title: 178063145_WT_DOCK2

description: wild type


title: 8M leftcolon male Ulcerative Colitis S119


title: 8K ileum female Crohn's disease S117

description: 8K ileum female Crohn's disease S117

source_name: ileum


title: 178063155_HO_DOCK2

description: homozygous knockout


title: 178063142_HO_DOCK2

description: homozygous knockout


title: 178063140_WT_DOCK2

description: wild type


title: 8J ileum male Crohn's disease S116

description: 8J ileum male Crohn's disease S116


title: 178063139_WT_DOCK2

description: wild type


title: 8I leftcolon female Ulcerative Colitis S115


title: 178063135_WT_DOCK2

description: wild type


title: 178063134_WT_DOCK2

description: wild type


title: 178063132_HO_DOCK2

description: homozygous knockout


title: 7W ileum male Crohn's disease S111

description: 7W ileum male Crohn's disease S111


title: 8C rightcolon female control S112

description: 8C rightcolon female control S112


title: 7V rectosigmoid female control S110

description: 7V rectosigmoid female control S110

source_name: rectosigmoid


title: 178063129_HO_DOCK2

description: homozygous knockout


title: 178063128_WT_DOCK2

description: wild type


title: 7 transversecolon male control S108

description: 7 transversecolon male control S108


title: 7U rectosigmoid female control S109

description: 7U rectosigmoid female control S109


title: 8F ileum male Crohn's disease S114

description: 8F ileum male Crohn's disease S114


title: 7T leftcolon female Ulcerative Colitis S107


title: 178063126_HO_DOCK2

description: homozygous knockout


title: 7S leftcolon female control S106

description: 7S leftcolon female control S106


title: 8 ileum male Crohn's disease S122

description: 8 ileum male Crohn's disease S122


title: 178063121_WT_DOCK2

description: wild type


title: 7M leftcolon male Ulcerative Colitis S104


title: 178062903_HO_HEM1

description: homozygous knockout


title: 7R rightcolon female control S105

description: 7R rightcolon female control S105


title: 178062907_WT_HEM1

description: wild type


title: 7L leftcolon male Crohn's disease S103

description: 7L leftcolon male Crohn's disease S103


title: 178062901_WT_HEM1

description: wild type


title: 7H leftcolon male Ulcerative Colitis S102


title: 7E ileum female Crohn's disease S101

description: 7E ileum female Crohn's disease S101


title: 178062896_WT_HEM1

description: wild type


title: 178063133_HO_DOCK2

description: homozygous knockout


title: 178062892_HO_HEM1

description: homozygous knockout


title: 178063169_HO_DOCK2

description: homozygous knockout


title: 6W leftcolon female Crohn's disease S99

description: 6W leftcolon female Crohn's disease S99


title: 178062890_HO_HEM1

description: homozygous knockout


title: 7C rectosigmoid female control S100

description: 7C rectosigmoid female control S100


title: 178062887_WT_HEM1

description: wild type


title: 6T sigmoid female control S97

description: 6T sigmoid female control S97


title: 6U ileum male Crohn's disease S98

description: 6U ileum male Crohn's disease S98


title: 178062880_HO_HEM1

description: homozygous knockout


title: 6S leftcolon male Crohn's disease S96

description: 6S leftcolon male Crohn's disease S96


title: 6P leftcolon female Ulcerative Colitis S94


title: 178062874_WT_HEM1

description: wild type


title: 6R colon male control S95

description: 6R colon male control S95


title: 178062902_WT_HEM1

description: wild type


title: 178062885_WT_HEM1

description: wild type


title: 6O rightcolon_noninflamed male Ulcerative Colitis S93


title: 178062884_HO_HEM1

description: homozygous knockout


title: 6H smallbowel male Crohn's disease S90

description: 6H smallbowel male Crohn's disease S90


title: 178063124_WT_DOCK2

description: wild type


title: 6N rectum male Ulcerative Colitis S92

description: 6N rectum male Ulcerative Colitis S92

source_name: rectum


title: S95

city: Princeton

first: Mike

last: Levine

state: NJ

address: South Dr

department: Lewis Sigler Institute

institute: Princeton University

data_processing:
Bases were called on Illumina Truseq 500
Sequences were aligned to mm10 genome using Bowtie2
Normalized abundance was generated by RSEM
Genome_build: mm10
Supplementary_files_format_and_content: Excel sheet includes TPM for all genes per sample

source_name: Embryo

growth_protocol: Embryos were cultured as described

extract_protocol:
Manufacturer's instructions
Manufacturer's instructions. SMART-seq v4.

treatment_protocol: Embryos were injected as described

value: NI

tag: developmental stage

value: Embryo


title: 178062871_WT_HEM1

description: wild type

value: M


title: 6E rectosigmoid female control S89

description: 6E rectosigmoid female control S89


title: S96


title: 5S smallbowel male Crohn's disease S88

description: 5S smallbowel male Crohn's disease S88


title: S86

value: Ctrl


title: 6J leftcolon male Ulcerative Colitis S91


title: S9


title: 5P smallbowel male Ulcerative Colitis S87


title: 5N ileum female Crohn's disease S86

description: 5N ileum female Crohn's disease S86


title: 5M leftcolon male Ulcerative Colitis S85


title: S8


title: S75


title: 5J leftcolon male Ulcerative Colitis S84


title: S91


title: S74


title: 5D ileum male Crohn's disease S83

description: 5D ileum male Crohn's disease S83


title: S7


title: 178062868_HO_HEM1

description: homozygous knockout

value: HO


title: S65


title: 4W leftcolon male Crohn's disease S81

description: 4W leftcolon male Crohn's disease S81


title: 4S smallbowel male Crohn's disease S80

description: 4S smallbowel male Crohn's disease S80


title: S61

value: KRAB


title: 4P leftcolon male Ulcerative Colitis S79


title: S63


title: S56


title: 4K leftcolon female Ulcerative Colitis S76


title: S6


title: S55


title: 4M ileum male control S78

description: 4M ileum male control S78


title: 4J smallbowel female Crohn's disease S75


title: 4L ileum female Crohn's disease S77

description: 4L ileum female Crohn's disease S77


title: 4E_9H ileum female Crohn's disease S73

description: 4E_9H ileum female Crohn's disease S73


title: S52


title: S44


title: 4Y ileum female Crohn's disease S82

description: 4Y ileum female Crohn's disease S82


title: S53


title: 4F rectum female control S74

description: 4F rectum female control S74


title: 4D rightcolon female control S72

description: 4D rightcolon female control S72


title: 3W rectum male control S71

description: 3W rectum male control S71


title: S43


title: S4


title: S67


title: 3S ileum male Crohn's disease S70

description: 3S ileum male Crohn's disease S70


title: S39


title: 3R sigmoid male control S69

description: 3R sigmoid male control S69


title: S32


title: 3N colon male Crohn's disease S68

description: 3N colon male Crohn's disease S68


title: 3M smallbowel male control S67

description: 3M smallbowel male control S67


title: S30


title: S37


title: 3K leftcolon female Ulcerative Colitis S66


title: S25


title: 2Y sigmoid male control S62

description: 2Y sigmoid male control S62


title: S31


title: S28


title: 3I leftcolon female Ulcerative Colitis S65


title: S27


title: 3G transversecolon female control S64

description: 3G transversecolon female control S64


title: 2R rightcolon female control S59

description: 2R rightcolon female control S59


title: 2T rightcolon female control S61

description: 2T rightcolon female control S61


title: 2S leftcolon female Crohn's disease S60

description: 2S leftcolon female Crohn's disease S60


title: 3B sigmoid male control S63

description: 3B sigmoid male control S63


title: S20


title: 2Q rightcolon_inflamed female Crohn's disease S58


title: S40


title: S19


title: 8E smallbowel male Crohn's disease S113

description: 8E smallbowel male Crohn's disease S113


title: 2N leftcolon female control S56

description: 2N leftcolon female control S56


title: 2M rectosigmoid female control S55

description: 2M rectosigmoid female control S55


title: S18


title: 2K ileum male Crohn's disease S53

description: 2K ileum male Crohn's disease S53


title: 2P ileum male Crohn's disease S57

description: 2P ileum male Crohn's disease S57


title: S14


title: 2D rightcolon male control S48

description: 2D rightcolon male control S48


title: 2J ileum male Crohn's disease S52

description: 2J ileum male Crohn's disease S52


title: S15


title: 1T colon female control S46

description: 1T colon female control S46


title: 2L smallbowel male Crohn's disease S54

description: 2L smallbowel male Crohn's disease S54


title: 1R colon male control S45

description: 1R colon male control S45


title: 2E smallbowel male control S49

description: 2E smallbowel male control S49


title: S16


title: 2F sigmoid male control S50

description: 2F sigmoid male control S50


title: 1D_7D sigmoid female control S39

description: 1D_7D sigmoid female control S39


title: 1M rectum male Ulcerative Colitis S42

description: 1M rectum male Ulcerative Colitis S42


title: 1Y colon male control S47

description: 1Y colon male control S47


title: 12T sigmoid female Ulcerative Colitis S35


title: 1P leftcolon male Ulcerative Colitis S44


title: 1I sigmoid male control S41

description: 1I sigmoid male control S41


title: 2I sigmoid male control S51

description: 2I sigmoid male control S51


title: 12U leftcolon female control S36

description: 12U leftcolon female control S36


title: 12R rightcolon female control S33

description: 12R rightcolon female control S33


title: 12O smallbowel female Crohn's disease S31


title: 12W smallbowel male control S37

description: 12W smallbowel male control S37


title: 12F_6M leftcolon male control S27

description: 12F_6M leftcolon male control S27


title: 11W rightcolon female control S26

description: 11W rightcolon female control S26


title: 11U smallbowel female control S25

description: 11U smallbowel female control S25


title: 12S rightcolon male control S34

description: 12S rightcolon male control S34


title: 11L leftcolon male Ulcerative Colitis S20


title: 1O smallbowel female Crohn's disease S43


title: 12P rightcolon male Ulcerative Colitis S32


title: 11T rightcolon female Crohn's disease S24


title: 1C sigmoid female control S38

description: 1C sigmoid female control S38


title: 12L rightcolon male Ulcerative Colitis S29


title: 11R rightcolon male control S22

description: 11R rightcolon male control S22


title: 11S rightcolon female control S23

description: 11S rightcolon female control S23


title: 11E smallbowel female control S18

description: 11E smallbowel female control S18


title: 1F ileum female control S40

description: 1F ileum female control S40


title: 11B ileocolic male control S17

description: 11B ileocolic male control S17

source_name: ileocolic


title: 12M leftcolon male Ulcerative Colitis S30


title: Scramble antagomiR-transfected  CD34+-ECs, Replicate 3

city: Philadelphia

first: Sezin

last: Aday

state: Pennsylvania

address: 210 South 33rd Street, Skirkanich Hall

institute: University of Pennsylvania

data_processing:
The data analysis pipeline is based on the Tuxedo software package, which is a combination of open-source software and implements peer-reviewed statistical methods. In addition, specialized software developed internally at Exiqon was exployed to interpret and improve the readability of the final results.
The components of NGS RNA seq analysis pipeline include Bowtie2 (v. 2.2.2), Tophat (v2.0.11) and Cufflinks (v2.2.1) and are described in detail below.
Tophat is a fast splice junction mapper for RNA-Seq reads. It aligns the sequencing reads to the reference genome using the sequence aligner Bowtie2. Tophat also uses the sequence alignments to identify splice junctions for both known and novel transcripts.
Cufflinks takes the alignment results from Tophat to assemble the aligned sequences into transcripts, constructing a map or a snapshot of the transcriptome. To guide the assembly process, an existing transcript annotation is used. In addition, fragment bias correction which seeks to correct for sequence bias during library preparation (see Kasper et al., 2010 and Adam et al., 2011) was performed. The Cufflinks assembles aligned reads into different transcript isoforms based on exon usage and also determines the transcriptional start sites (TSSs).
When comparing groups, Cuffdiff is used to calculate the FPKM (number of fragments per kilobase per million mapped fragments) and test for differential expression and regulation among the assembled transcripts across the submitted samples using the Cufflinks output. Cuffdiff can be used to test differential expression at different levels, from CDS and gene specific, down to the isoform and TSS transcript level. For more information on the Cuffdiff module, see Trapnell et al., (2013).
As a final step, CummeRbund, which is an open source R package, will be used in combination with in-house custom software for post processing of Cufflinks and Cuffdiff results.
genome build: hsa hg 19 (Gencode v11) genome build from Ensembl has been used for annotation.
Supplementary_files_format_and_content: Differential Expression (cuffdiff_data): Result files created by Cuffdiff (see http://cole-trapnell-lab.github.io/cufflinks/cuffdiff)

source_name: Endothelial cell

growth_protocol: Human CD34+ endothelial cells were expanded in 1% (w/v) gelatin-coated T75 flasks (BD Falcon) in EGM-2 medium (Lonza). The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2 and medium was refreshed every other day.

extract_protocol:
Total RNA was isolated using the miRVanaTM miRNA isolation kit from Ambion (Cat# AM1560) according to the manufacturer’s instructions. RNA sample quality control was performed by Exiqon (Vedbaek, Denmark).
Library quality control and quantification were performed by Exiqon (Vedbaek, Denmark). The library preparation was done using TruSeq® Stranded mRNA Sample preparation kit (Illumina inc). The starting material (500 ng) of total RNA was mRNA enriched using the oligodT bead system (manufacturer). The isolated mRNA was subsequently fragmented using enzymatic fragmentation. Then first strand synthesis and second strand synthesis were performed and the double stranded cDNA was purified (AMPure XP, Beckman Coulter). The cDNA was end repaired, 3’ adenylated and Illumina sequencing adaptors ligated onto the fragments ends, and the library was purified (AMPure XP). The mRNA stranded libraries were pre-amplified with PCR and purified (AMPure XP). The libraries size distribution was validated and quality inspected on a Bioanalyzer high sensitivity DNA chip (Agilent Technologies). High quality libraries were quantified using qPCR, the concentration normalized and the samples pooled according to the project specification (number of reads). The library pool(s) were re-quantified with qPCR and optimal concentration of the library pool used to generate the clusters on the surface of a flowcell before sequencing on Nextseq500 instrument using High Output sequencing kit (50 cycles) according to the manufacturer instructions (Illumina Inc.).

treatment_protocol: CD34+ endothelial cells differentiated from umbilical cord blood hematopoietic stem cells (CD34+) were treated with 50 nM antagomiR-17 (transfection group, AmiR; Dharmacon) or scrambled antagomiR (control group; Ambion) using Lipofectamine RNAiMAx (Life Technologies) for 48 h.

tag: passage number

value: Passage 5

tag: transfection

value: Scramble antagomiR

value: CD34+ endothelial cells


title: 12H ileum female Crohn's disease S28

description: 12H ileum female Crohn's disease S28


title: 10R sigmoid male control S12

description: 10R sigmoid male control S12


title: 10W rightcolon female control S16

description: 10W rightcolon female control S16


title: 10U sigmoid male Crohn's disease S14

description: 10U sigmoid male Crohn's disease S14


title: Scramble antagomiR-transfected  CD34+-ECs, Replicate 2


title: 10S ileum male Crohn's disease S13

description: 10S ileum male Crohn's disease S13


title: 10V rightcolon female control S15

description: 10V rightcolon female control S15


title: 10Q leftcolon male Crohn's disease S11

description: 10Q leftcolon male Crohn's disease S11


title: 11P rightcolon female Ulcerative Colitis S21


title: 10P rightcolon male control S10

description: 10P rightcolon male control S10


title: 10L leftcolon male Ulcerative Colitis S7


title: AntagomiR17-transfected CD34+-ECs, Replicate 1


title: AntagomiR17-transfected CD34+-ECs, Replicate 3


title: 10J ileumcecum female Crohn's disease S5

source_name: ileumcecum


title: 10M rightcolon_noninflamed  female Ulcerative Colitis S8


title: Scramble antagomiR-transfected  CD34+-ECs, Replicate 1


title: 10H leftcolon male Ulcerative Colitis S4


title: immature testis replicate 2

city: Huhhot

first: Bei

last: Li

address: Zhaowuda Rd.306

country: China

institute: Inner Mongolia Agriculture University

data_processing:
Illumina Hiseq 2500 platform
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing  reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw datas were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
The small RNA tags were mapped to reference sequence by Bowtie without mismatch to analyze their expression and distribution on the reference.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500 platform and 50bp single-end reads were generated.
Genome_build: EquCab2.0
Supplementary_files_format_and_content: novel_piRNA.txt reports abundance measurements

organism: Equus caballus

source_name: immature testis

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, NEB 3' SR Adaptor was directly, and specifically ligated to 3' end of miRNA, siRNA and piRNA. After the 3' ligation reaction, the SR RT Primer hybridized to the excess of 3' SR Adaptor (that remained free after the 3' ligation reaction) and transformed the single-stranded DNA adaptor into a double-stranded DNA molecule. This step is important to prevent adaptor-dimer formation, besides, dsDNAs are not substrates for ligation mediated by T4 RNA Ligase 1 and therefore do not ligate to the 5´ SR Adaptor in the subsequent ligation step. 5´ends adapter was ligated to 5´ends of miRNAs, siRNA and piRNA. Then first  strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H–).PCR amplification  was  performed  using LongAmp Taq 2X Master Mix, SR Primer for  illumina and index (X) primer. PCR products were purified on a 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140~160 bp (the length of small noncoding RNA plus the 3' and 5' adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.

tag: breed

value: Mongolian horse

value: immature testis


title: 11I leftcolon female Ulcerative Colitis S19


title: mature testis replicate 3

source_name: mature testis

value: mature testis


title: immature testis replicate 3


title: 10F rectum male Ulcerative Colitis S2

description: 10F rectum male Ulcerative Colitis S2


title: E6-1

city: Jena

first: Katrin

last: Krause

address: Neugasse 25

department: Institute of Microbiology

country: Germany

institute: Friedrich Schiller university of Jena

data_processing:
Preprocessing: Trimming of reads with a low quality window of length 5 and average quality phredscore smaller than 15, removal of adapter, qualitycheck with FatQC
Mapping: Using Tophat S. commune against genome from http://genomeportal.jgi-psf.org/Schco2/Schco2.home.html
Gene expression: RPKM values: Normalized (gene length and library size) expression of each gene
Differentially expressed genes (DEG): Defined using 4 different methods capturing different aspects of the statistics: DeSeq, EdgeR, BaySeq,Noiseq; adjusted p-value cutoff: 0.01
Statistics: Each file consists of three sheets comparing the condition A versus condition B
Genome_build: http://genomeportal.jgi-psf.org/Schco2/Schco2.home.html
Supplementary_files_format_and_content: RPKM values for each sample

organism: Schizophyllum commune

source_name: Mycelium

growth_protocol: The S. commune strains were grown on solid medium (CYM) at 28°C. Mycelium of a mating interaction was transferred onto a cellophane membrane onto fresh CYM plates and grown for 3 days.

extract_protocol:
RNA was isolated according to the protocol delivered with the kit (RNeasy Plant Mini Kit, Qiagen, Hilden, Germany).
RNA-sequencing was performed by LGC Genomics, Berlin (Germany). Therefore, a mRNA-based cDNA-library was created. Sequencing adaptors were ligated to cDNA fragments to result in 50 bp single reads of the expressed genes. After the run, adaptors were cut from the resulted reads.

treatment_protocol: Mycelium was harvested, frozen in liquid nitrogen and ground with mortar and pestle to a powder.

value: mycelium

tag: mating type loci

value: wild type


title: immature testis replicate 1

tag: tissue


title: 12-43-2


title: AntagomiR17-transfected CD34+-ECs, Replicate 2

tag: cell type


title: 10O smallbowel male Crohn's disease S9

description: 10O smallbowel male Crohn's disease S9

value: male


title: E6-2


title: mature testis replicate 1


title: dhc2-2

value: mutant delta_dhc2


title: dhc2-1


title: 12-43-1


title: OC 10M cage_seq

status: Public on Jul 06 2017

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Raw reads were first discarded if containing more than 2-N bases, then reads were processed by clipping adaptor, removing low quality bases, and discarding too short reads (less than 16nt). FASTX-Toolkit (Version 0.0.13) was used to get the clean reads.
After that, clean reads were aligned to the Macaque genome (MMUL 1.0) by tophat2 (Kim et al., 2013). Aligned reads with more than one genome location were discarded due to their ambiguous location.
Uniquely localized reads were used to calculate reads number and RPKM value (RPKM represents reads per kilobase and per million) for each gene according to reads and genes genome location. Other statistical results, such as gene coverage and depth, reads distribution around start codon and stop codon, were also obtained.
The end first reads for paired sequencing was used to do alignment and transcription start site identification. After alignment 5 prime end of each reads was considered as the CAGE tag-defined transcription start sites (CTSSs). The number of CAGE tags mapping to each CTSS across different samples was normalized to obtain the normalized number of tags per million (tpm).
We then combined the TSSs to transcription clusters (TCs) according the known method (Nepal et al., 2013). Only CTSSs supported by a minimum of 0.5 tpm in at least one sample were used for a sample-specific clustering into transcript clusters (TCs). Neighboring CTSSs were clustered if they were <20 bp apart.
Genome_build: MMUL 1.0
Supplementary_files_format_and_content: tabular data of text format,the TSS TPM value of each sample

molecule: polyA RNA

organism: Macaca mulatta

source_name: 10-yr old male brain

extract_protocol:
For RNA-Seq library, total RNA was extracted from all the brain tissue samples by using TRIzol Reagent(Ambion) following the manufacturer’s instructions. Total RNA was treated with RQ1 DNase (promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using smartspec plus (BioRad).
Total RNA was treated with RQ1 DNase (promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at  260 nm/280 nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% Agrose gel electrophoresis. For each sample, 10μg of total RNA was used for CAGE-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (invitrogen) .In brief,  mRNA was treated with T4 polynucleotide kinase   (NEB) at 37℃ for 30min and purified with oligo(dT)-conjugated magnetic beads (invitrogen).  and subsequently degested with Terminator™ 5´-Phosphate-Dependent Exonuclease (Ambion) at 30℃ for 30min and purified with oligo(dT)-conjugated magnetic beads (invitrogen). The capped mRNA was performed with RT primer， then synthesized DNA with Terminal-Tagging oligo. The cDNAs were purified and amplified with PCR primers (illumina) and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80 ℃ until used for sequencing.

treatment_protocol:
animal protocol: Sixteen socially-housed healthy rhesus macaques used in this study were selected at random and were equally divided into four groups according to age (1, 4, 10 and 20 years respectively). Each group included 4 monkeys, with 2 males and 2 females. These four groups were euthanized by injected with excessive pentobarbital sodium (80 mg/kg, i.v.) and the monkeys’ carotid artery was cut to allow the blood drain. And then the whole brain was taken out and the corresponding brain tissue (4mm×2mm×2mm) was sampled with sterilized ophthalmic scissors and tweezers. According to a widely used macaque brain atlas and brainmaps (http://www. Brainmaps.org),the prefrontal cortex was sampled at the main sulci, the posterior cingulate cortex was sampled at the Brodmann’s area 23, the temporal cortex was sampled at the superior temporal gyrus, the parietal cortex was sampled at the middle sylvian fissure, the occipital cortex was sampled at the V1, and the cerebellar cortex was sampled at the cauda cerebelli. The hippocampus (including CA1 and dentate gyrus) was also sampled. All the collected samples were washed with RNA later solution (AM7021, Ambion, USA) and put in freezing tubes to store at liquid nitrogen temperature. All these operations above were completed inside one hour after the monkeys died. All animal procedures were in strict accordance with the guidelines for the National Care and Use of Animals approved by the National Animal Research Authority (P.R. China) and the Institutional Animal Care and Use Committee (IACUC) of the Kunming Institute of Zoology of Chinese Academy of Sciences.
All the collected samples were washed with RNA later solution (AM7021, Ambion, USA) and put in freezing tubes to store at liquid nitrogen temperature. All these operations above were completed inside one hour after the monkeys died. All animal procedures were in strict accordance with the guidelines for the National Care and Use of Animals approved by the National Animal Research Authority (P.R. China) and the Institutional Animal Care and Use Committee (IACUC) of the Kunming Institute of Zoology of Chinese Academy of Sciences.

value: occipital cortex

tag: age

value: 10 year old


title: 10K smallbowel female Crohn's disease S6

value: female

value: Crohn's disease


title: OC 20M cage_seq

source_name: 20-yr old male brain

value: 20 year old


title: OC 20F cage_seq

source_name: 20-yr old female brain


title: mature testis replicate 2


title: OC 4M cage_seq

source_name: 4-yr old male brain

value: 4 year old


title: 10G rightcolon female control S3

description: 10G rightcolon female control S3

source_name: rightcolon

value: control


title: CB 20F cage_seq

value: cerebellar cortex


title: OC 4F cage_seq

source_name: 4-yr old female brain


title: OC 1F cage_seq

source_name: 1-yr old female brain

value: 1 year old


title: CB 10M cage_seq


title: OC 1M cage_seq

source_name: 1-yr old male brain


title: CB 20M cage_seq


title: 10E smallbowel female control S1

description: 10E smallbowel female control S1

source_name: smallbowel


title: CB 1M cage_seq


title: CB 4M cage_seq


title: CB 4F cage_seq


title: DG 20M cage_seq

value: dentate gyrus


title: DG 10M cage_seq


title: CB 1F cage_seq


title: CB 10F cage_seq

source_name: 10-yr old female brain


title: DG 20F cage_seq


title: OC 10F cage_seq


title: DG 4M cage_seq


title: DG 10F cage_seq


title: DG 4F cage_seq


title: DG 1M cage_seq


title: CA1 10M cage_seq

value: hippocampus CA1


title: CA1 4M cage_seq


title: DG 1F cage_seq


title: CA1 10F cage_seq


title: CA1 1M cage_seq


title: CA1 4F cage_seq


title: CA1 20F cage_seq


title: PC 20M cage_seq

value: parietal cortex


title: PC 10F cage_seq


title: PC 10M cage_seq


title: PC 4M cage_seq


title: PC 4F cage_seq


title: PC 1M cage_seq


title: PC 20F cage_seq


title: TC 20F cage_seq

value: temporal cortex


title: TC 20M cage_seq


title: PC 1F cage_seq


title: TC 1F cage_seq


title: TC 4F cage_seq


title: TC 1M cage_seq


title: PCC 20M cage_seq

value: posterior cingulate cortex


title: TC 4M cage_seq


title: CA1 20M cage_seq


title: PCC 20F cage_seq


title: PCC 10M cage_seq


title: PCC 4M cage_seq


title: PCC 10F cage_seq


title: PCC 1M cage_seq


title: PFC 10F cage_seq

value: prefrontal cortex


title: PFC 10M cage_seq

value: male


title: PFC 4M cage_seq


title: PFC 20F cage_seq


title: PFC 20M cage_seq


title: TC 10M cage_seq


title: PFC 4F cage_seq


title: TC 10F cage_seq


title: PFC 1F cage_seq


title: DG 20M RNA_seq

data_processing:
Raw reads were first discarded if containing more than 2-N bases, then reads were processed by clipping adaptor, removing low quality bases, and discarding too short reads (less than 16nt). FASTX-Toolkit (Version 0.0.13) was used to get the clean reads.
After that, clean reads were aligned to the Macaque genome (MMUL 1.0) by tophat2 (Kim et al., 2013). Aligned reads with more than one genome location were discarded due to their ambiguous location.
Uniquely localized reads were used to calculate reads number and RPKM value (RPKM represents reads per kilobase and per million) for each gene according to reads and genes genome location. Other statistical results, such as gene coverage and depth, reads distribution around start codon and stop codon, were also obtained.
LncRNAs were predicted by Cufflinks V2.2 (Trapnell et al., 2012). First transcripts of protein coding and non-coding were identified by cufflinks, and then cuffcompare was used to compare the transcripts with macaque known gene and novel transcripts were reserved as the candidate lncRNAs. Transcripts adjacent to known genes within 2000 bp were regarded as UTRs and lncRNAs’ coding potential was evaluated by cpc softwares with the default parameters. Finally, lncRNAs with multiple exons obtained from different tissue were merged together as the final lncRNA set. LncRNA prediction pipeline was described in the Sup Figures.
After getting the Expression level of all genes in all samples, differentially expressed genes were analyzed by using edgeR(Robinson et al., 2010), one of R packages. 0.01 p-value and 2 fold change were set as the threshold to define DEGs.
Genome_build: MMUL 1.0
Supplementary_files_format_and_content: [.xlsx] tabular data reporting gene RPKMs for each sample

extract_protocol:
For RNA-Seq library, total RNA was extracted from all the brain tissue samples by using TRIzol Reagent(Ambion) following the manufacturer’s instructions. Total RNA was treated with RQ1 DNase (promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using smartspec plus (BioRad).
RNA integrity was further verified by 1.5% Agarose gel electrophoresis. For each sample, 10 μg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (invitrogen) before used for directional RNA-seq library preparation. Purified mRNAs were ion fragmented at 95℃ followed by end repair and 5' adaptor ligation. Then mRNA reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified. And products corresponding to 200-500 bps were purified, quantified and stored at -80 ℃ before sequencing.

treatment_protocol:
Animal protocol: Sixteen socially-housed healthy rhesus macaques used in this study were selected at random and were equally divided into four groups according to age (1, 4, 10 and 20 years respectively). Each group included 4 monkeys, with 2 males and 2 females. These four groups were euthanized by injected with excessive pentobarbital sodium (80 mg/kg, i.v.) and the monkeys’ carotid artery was cut to allow the blood drain. And then the whole brain was taken out and the corresponding brain tissue (4mm×2mm×2mm) was sampled with sterilized ophthalmic scissors and tweezers. According to a widely used macaque brain atlas and brainmaps (http://www. Brainmaps.org),the prefrontal cortex was sampled at the main sulci, the posterior cingulate cortex was sampled at the Brodmann’s area 23, the temporal cortex was sampled at the superior temporal gyrus, the parietal cortex was sampled at the middle sylvian fissure, the occipital cortex was sampled at the V1, and the cerebellar cortex was sampled at the cauda cerebelli. The hippocampus (including CA1 and dentate gyrus) was also sampled. All the collected samples were washed with RNA later solution (AM7021, Ambion, USA) and put in freezing tubes to store at liquid nitrogen temperature. All these operations above were completed inside one hour after the monkeys died. All animal procedures were in strict accordance with the guidelines for the National Care and Use of Animals approved by the National Animal Research Authority (P.R. China) and the Institutional Animal Care and Use Committee (IACUC) of the Kunming Institute of Zoology of Chinese Academy of Sciences.
All the collected samples were washed with RNA later solution (AM7021, Ambion, USA) and put in freezing tubes to store at liquid nitrogen temperature. All these operations above were completed inside one hour after the monkeys died. All animal procedures were in strict accordance with the guidelines for the National Care and Use of Animals approved by the National Animal Research Authority (P.R. China) and the Institutional Animal Care and Use Committee (IACUC) of the Kunming Institute of Zoology of Chinese Academy of Sciences.

value: 20-year old


title: DG 20F RNA_seq


title: DG 10M RNA_seq

value: 10-year old


title: DG 10F RNA_seq


title: CA1 1F cage_seq


title: DG 4F RNA_seq

value: 4-year old


title: DG 4M RNA_seq


title: DG 1F RNA_seq

value: 1-year old

value: female


title: CA1 20F RNA_seq


title: CA1 10M RNA_seq


title: CA1 4M RNA_seq


title: PCC 1F cage_seq


title: CA1 4F RNA_seq


title: CA1 1M RNA_seq


title: CA1 10F RNA_seq


title: PCC 4F cage_seq


title: CA1 1F RNA_seq


title: PC 20M RNA_seq


title: PC 20F RNA_seq


title: CA1 20M RNA_seq


title: PC 10F RNA_seq


title: PC 4M RNA_seq


title: TC 10F RNA_seq


title: TC 20M RNA_seq


title: TC 20F RNA_seq


title: DG 1M RNA_seq


title: PC 1M RNA_seq


title: PFC 1M cage_seq


title: PC 1F RNA_seq


title: TC 4M RNA_seq


title: PC 4F RNA_seq


title: TC 10M RNA_seq


title: TC 1M RNA_seq


title: PCC 10M RNA_seq


title: TC 1F RNA_seq


title: PCC 20F RNA_seq


title: PCC 20M RNA_seq


title: PCC 4M RNA_seq


title: PCC 1F RNA_seq


title: PFC 20F RNA_seq


title: PFC 20M RNA_seq


title: PCC 1M RNA_seq


title: PFC 4M RNA_seq


title: PFC 10F RNA_seq


title: PC 10M RNA_seq


title: PFC 10M RNA_seq


title: PCC 4F RNA_seq


title: PFC 4F RNA_seq


title: TC 4F RNA_seq


title: Sample Kidney 25 kidney dose 2 rep 1

city: College Station

first: Ivan

last: Rusyn

address: 4458 TAMU

department: Department of Veterinary Integrative Biosciences

institute: Texas A&M University

description: kidney.GEO.csv

data_processing:
Data preprocessing was performed following a standard CASAVA v.1.8.2 pipeline, providing FASTQ output. Overall expression was quantified using a TopHat2 mapping pipeline. For primary expression calling, each read was aligned to the mm10 mouse reference sequence using TopHat v2.0.10 (Trapnell et al., 2009).
A maximum of one match per read was used in the alignments, and the mouse genome mm10 RefSeq annotations downloaded from UCSC Genomes were used as a guide for the alignments. The resulting .bam files were sorted and converted to .sam for use with HTSeq (Anders et al., 2015) with the options for no-stranded sequencing and intersection-nonempty, which calls the best (or longest) match to a gene as the gene being counted when there was more than one gene overlapped by a given read.
A set of customized Perl scripts were written to aggregate the counts results into a single file with 24,602 genes, and to add the ENSEMBL ID(s) associated with the RefSeq ID, where possible. The mapping between RefSeq ID and ENSEMBL ID was also obtained from UCSC Genomes browser files.
comma delimited .CSV files include counts for each sample
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: kidney

growth_protocol: Adult (5-6 weeks of age) male B6C3F1/J mice were obtained from the Jackson Laboratory (Bar Harbor, ME). All mice were housed in polycarbonate cages on Sani-Chips (P.J. Murphy Forest Products, Montville, NJ) irradiated hardwood bedding. Animals were fed NTP-2000 (Zeigler Brothers, Gardners, PA) wafer diet and water ad libitum on a 12 h light-dark cycle. All studies were approved by the Institutional Animal Care and Use Committee at the University of North Carolina at Chapel Hill.

extract_protocol:
Total RNA was extracted from liver or kidney samples using miRNEasy kits (Qiagen, Valencia, CA). RNA integrity was determined using Bioanalyzer (Agilent, Santa Clara, CA). cDNA libraries were constructed using TruSeq Total RNA kits (Illumina, San Diego, CA) following the manufacturer's instructions. Library quality was assessed on a Bioanalyzer and sequenced on an Illumina HiSeq-2000 (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols
Whole transcriptome RNA-Seq

treatment_protocol: After a week-long acclimatization period, mice were intragastrically administered a single dose of TCE, PCE, or vehicle (5% Alkamuls El-620 in saline, 5 mL/kg). All dosing occurred between the hours of 07:00 and 09:00. In addition to vehicle-only treated animals (0 dose), the following doses were used for TCE (24, 80, 240, 800 mg/kg), or PCE (30, 100, 300, 1,000 mg/kg). These approximate to 0.22, 0.67, 2.0, and 6.0 mmol/kg for each of TCE and PCE.

value: kidney

tag: chemical (mmol/kg )

value: PCE

tag: dose


title: Sample Kidney 28 kidney dose 6 rep 1

description: kidney.GEO.csv

tag: strain


title: Sample Kidney 29 kidney dose 6 rep 2

description: kidney.GEO.csv


title: Sample Kidney 30 kidney dose 6 rep 3

description: kidney.GEO.csv


title: Sample Kidney 24 kidney dose 0.67 rep 3

description: kidney.GEO.csv


title: Sample Kidney 21 kidney dose 0.22 rep 3

description: kidney.GEO.csv


title: Sample Kidney 20 kidney dose 0.22 rep 2

description: kidney.GEO.csv


title: Sample Kidney 23 kidney dose 0.67 rep 2

description: kidney.GEO.csv


title: Sample Kidney 27 kidney dose 2 rep 3

description: kidney.GEO.csv


title: PFC 1M RNA_seq


title: PCC 10F RNA_seq


title: Sample Kidney 17 kidney dose 0 rep 2

description: kidney.GEO.csv


title: Sample Kidney 12 kidney dose 2 rep 3

description: kidney.GEO.csv

value: TCE


title: Sample Kidney 11 kidney dose 2 rep 2

description: kidney.GEO.csv


title: Sample Kidney 22 kidney dose 0.67 rep 1

description: kidney.GEO.csv


title: Sample Kidney 19 kidney dose 0.22 rep 1

description: kidney.GEO.csv


title: Sample Kidney 15 kidney dose 6 rep 3

description: kidney.GEO.csv


title: Sample Kidney 10 kidney dose 2 rep 1

description: kidney.GEO.csv


title: Sample Kidney 14 kidney dose 6 rep 2

description: kidney.GEO.csv


title: Sample Kidney 16 kidney dose 0 rep 1

description: kidney.GEO.csv


title: Sample Kidney 9 kidney dose 0.67 rep 3

description: kidney.GEO.csv


title: Sample Kidney 13 kidney dose 6 rep 1

description: kidney.GEO.csv


title: Sample Kidney 7 kidney dose 0.67 rep 1

description: kidney.GEO.csv


title: Sample Kidney 6 kidney dose 0.22 rep 3

description: kidney.GEO.csv


title: Sample Kidney 5 kidney dose 0.22 rep 2

description: kidney.GEO.csv


title: Sample Kidney 4 kidney dose 0.22 rep 1

description: kidney.GEO.csv


title: Sample Kidney 3 kidney dose 0 rep 3

description: kidney.GEO.csv


title: Sample Kidney 1 kidney dose 0 rep 1

description: kidney.GEO.csv


title: Sample Liver 30 liver dose 6 rep 3

description: liver.GEO.csv

source_name: liver

value: liver


title: Sample Liver 29 liver dose 6 rep 2

description: liver.GEO.csv


title: Sample Kidney 2 kidney dose 0 rep 2

description: kidney.GEO.csv


title: Sample Liver 27 liver dose 2 rep 3

description: liver.GEO.csv


title: Sample Liver 28 liver dose 6 rep 1

description: liver.GEO.csv


title: Sample Liver 23 liver dose 0.67 rep 2

description: liver.GEO.csv


title: Sample Kidney 8 kidney dose 0.67 rep 2

description: kidney.GEO.csv


title: Sample Liver 26 liver dose 2 rep 2

description: liver.GEO.csv


title: Sample Liver 21 liver dose 0.22 rep 3

description: liver.GEO.csv


title: Sample Liver 22 liver dose 0.67 rep 1

description: liver.GEO.csv


title: Sample Liver 16 liver dose 0 rep 1

description: liver.GEO.csv


title: Sample Liver 25 liver dose 2 rep 1

description: liver.GEO.csv


title: Sample Liver 20 liver dose 0.22 rep 2

description: liver.GEO.csv


title: Sample Liver 11 liver dose 2 rep 2

description: liver.GEO.csv


title: Sample Liver 14 liver dose 6 rep 2

description: liver.GEO.csv


title: Sample Liver 17 liver dose 0 rep 2

description: liver.GEO.csv


title: Sample Liver 18 liver dose 0 rep 3

description: liver.GEO.csv


title: Sample Liver 15 liver dose 6 rep 3

description: liver.GEO.csv


title: Sample Liver 19 liver dose 0.22 rep 1

description: liver.GEO.csv


title: Sample Liver 10 liver dose 2 rep 1

description: liver.GEO.csv


title: Sample Liver 13 liver dose 6 rep 1

description: liver.GEO.csv


title: Sample Liver 8 liver dose 0.67 rep 2

description: liver.GEO.csv


title: Sample Liver 9 liver dose 0.67 rep 3

description: liver.GEO.csv


title: Sample Liver 7 liver dose 0.67 rep 1

description: liver.GEO.csv


title: Sample Liver 6 liver dose 0.22 rep 3

description: liver.GEO.csv


title: Sample Liver 5 liver dose 0.22 rep 2

description: liver.GEO.csv


title: Sample Liver 1 liver dose 0 rep 1

description: liver.GEO.csv


title: Sample Liver 2 liver dose 0 rep 2

description: liver.GEO.csv


title: Sample Liver 3 liver dose 0 rep 3

description: liver.GEO.csv


title: Sample Liver 4 liver dose 0.22 rep 1

description: liver.GEO.csv


title: Sample Liver 12 liver dose 2 rep 3

description: liver.GEO.csv


title: PFC 1F RNA_seq


title: MLL4KD_JM8A-9234-2_GAGTGG_L001_R1_001

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human genome assembly hg19 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Genome_build: mm9
Supplementary_files_format_and_content: raw counts

source_name: mESC

growth_protocol: Male mouse ESCs were grown on 0.2% gelatinized tissue-culture plates and cultured in complete ESC growth medium supplemented with LIF (Knock-out DMEM (ThermoFisher Sci., 10829-018) containing with 2 mM L-glutamine (ThermoFisher Sci., 25030-081), 0.1 mM 2-mercaptoethanol (ThermoFisher Sci., 21985-023), 0.1 mM nonessential amino acids (ThermoFisher Sci., 11140-050), 50 units/mL penicillin/streptomycin (Sigma), and 15% (vol/vol) ES cell-qualified FBS (ThermoFisher Sci., 10439-024)).

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit

treatment_protocol: No treatment

tag: genotype

value: MLL4 Knockdown


title: UTXWT_JM8A-2_TTAGGC_L001_R1_001

value: UTX Wildtype


title: MLL4KD_JM8A_9234-1_GGCTAC_L002_R1_001


title: UTXKO_A6-3_GCCAAT_L002_R1_001

value: UTX Knockout


title: UTXWT_JM8A-1_ATCACG_L002_R1_001


title: Sample_mESC_UTXWT_H3K27ac

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse assembly mm9 using bowtie2 (v2.2.2) with default parameters.
To create density files, the reads were extended to 200 bp, the signal was then normalized to ten million mapped reads and converted to BigWig using BEDTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads

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

tag: chip antibody

value: Anti-H3K27ac (Abcam, ab4729)


title: MLL4KD_JM8A-9234-3_AGTCAA_L002_R1_001


title: Sample_mESC_UTXWT_H3K27me3

value: Anti-H3K27me3 (Upstate, 07-449)


title: Sample_mESC_UTXKO_H3K4me1

value: Anti-H3K4me1 (Abcam, ab8895)


title: Sample_mESC_UTXWT_UTX

value: Anti-UTX (Bethyl laboratories, A302-374A)


title: Sample_mESC_UTXWT_H3K4me1


title: Sample_mESC_UTXKO_H3K27me3


title: 3_24E

city: Adelaide

first: Justine

last: Smith

address: Bedford Park

country: Australia

institute: Flinders University

data_processing:
The quality and number of reads for each sample were assessed with FastQC v0.11.3 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Adaptors were trimmed from reads, and low quality bases with Phred scores under 28 were trimmed from ends of reads, using Trimgalore v0.4.0 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Trimmed reads of less than 20 nucleotides were discarded. Reads passing all quality control steps were aligned to the hg38 assembly of the human genome using TopHat v2.1.0, allowing for up to two mismatches. Reads not uniquely aligned to the genome were discarded. HTSeq-count v0.6.0 was used in the union model to assign uniquely aligned reads to UCSC hg38-annotated genes.
Genome_build: UCSC HG38
Supplementary_files_format_and_content: Non-normalized read counts for each gene in each of the 6 samples

source_name: ARPE-19 cell

growth_protocol: The ARPE-19 human retinal pigment epithelial cell line (American Type Culture Collection [ATCC], Manassas, VA) was cultured in 1:1 Dulbecco’s modified Eagle’s medium (DMEM):F12 medium (Thermo Fisher Scientific-GIBCO, Grand Island, NY) supplemented with heat-inactivated 10% fetal bovine serum (FBS) (GE Healthcare-Hyclone, Logan, UT)  at 37 °C and 5% CO2 in air. Ebola virus (Zaire ebolavirus, EBOV variant Mayinga) was amplified in Vero C1008 cells (European Collection of Authenticated Cell Cultures [ECACC], Salisbury, United Kingdom), cultured with DMEM supplemented with 10% FBS at 37 °C and 5% CO2 in air, and titrated by end-point dilution of culture supernatant in fresh Vero C1008 cell monolayers.

extract_protocol:
Total RNA was extracted from TRIzol Reagent-lysed ARPE-19 cells, according to the manufacturer’s instructions, and stored at -80 °C ahead of use for RNA-seq. RNA concentration was determined by spectrophotometry on the Qubit 2.0 Fluorometer (Thermo Fisher Scientific-Invitrogen) for RNA-seq. RNA integrity was confirmed on the 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).
Total RNA was depleted of ribosomal RNA and converted to cDNA libraries, using the TruSeq Stranded Total RNA kit with Ribo-Zero Gold (Illumina, San Diego, CA), strictly in accordance with the manufacturer’s instructions. RNA samples were diluted to 1.3 pM ahead of sequencing on the Illumina NextSeq 500, which was performed with NextSeq 500/550 High Output Kits (Illumina) for 2 x 75 cycles of sequencing. The PhiX Control v3 library (Illumina) was used as a sequencing control.

treatment_protocol: Confluent monolayers of ARPE-19 cells were inoculated with EBOV at a multiplicity of infection of 5, or mock-infected, in minimum volumes of DMEM:F12 medium with 10% FBS for 30-40 minutes, subsequently washed twice with fresh medium, and finally returned to standard volumes of medium, all at 37 °C and 5% CO2 in air. Infected cell monolayers were incubated for 24 hours. After 24 hours, supernatant was collected and frozen at -80 °C, and cells were lysed with TRIzol Reagent (Thermo Fisher Scientific-Invitrogen, Carlsbad, CA) and stored at -80 °C ahead of RNA extraction for RNA-seq.

tag: cell line

tag: infection

value: EBOV


title: Sample_mESC_UTXWT_p300

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


title: UTXWT_JM8A-3_ACAGTG_L002_R1_001


title: UTXKO_A6-1_ACTTGA_L002_R1_001


title: 2_24E

value: human retinal pigment epithelial cell line


title: 2_24C

value: Mock


title: 3_24C


title: 1_24E


title: 1_24C


title: UTXKO_A6-2_GATCAG_L001_R1_001


title: Sample_mESC_UTXKO_H3K27ac


title: OC 10M RNA_seq

growth_protocol: Sixteen socially-housed healthy rhesus macaques used in this study were selected at random and were equally divided into four groups according to age (1, 4, 10 and 20 years respectively). Each group included 4 monkeys, with 2 males and 2 females. These four groups were euthanized by injected with excessive pentobarbital sodium (80 mg/kg, i.v.) and the monkeys’ carotid artery was cut to allow the blood drain. And then the whole brain was taken out and the corresponding brain tissue (4mm×2mm×2mm) was sampled with sterilized ophthalmic scissors and tweezers. According to a widely used macaque brain atlas and brainmaps (http://www. Brainmaps.org), the occipital cortex was sampled at the V1.

value: occipital cortex

value: 10-year old

tag: gender

value: male


title: OC 4M RNA_seq

value: 4-year old


title: OC 20F RNA_seq

value: 20-year old

value: female


title: OC 10F RNA_seq


title: OC 4F RNA_seq


title: OC 1F RNA_seq

value: 1-year old


title: OC 20M RNA_seq


title: pgrn.ko SAM21131490

city: South San Francisco

first: Brad

middle: A

last: Friedman

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

data_processing: Reads were aligned to the NCBIM37 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: RNA from whole cortex

extract_protocol: RNA was extracted from cortex of 1 year old wildtype, heterozygous or homozygous PGRN knockout mice.

value: whole cortex


title: pgrn.het SAM21131484


title: wt SAM21131478

value: wt


title: pgrn.ko SAM21131491


title: pgrn.ko SAM21131489


title: pgrn.het SAM21131483


title: pgrn.het SAM21131485


title: pgrn.ko SAM21131492


title: CB 20M RNA_seq

value: cerebellar cortex


title: CB 20F RNA_seq


title: wt SAM21131479


title: CB 10M RNA_seq


title: wt SAM21131482


title: pgrn.ko SAM21131488


title: pgrn.het SAM21131486


title: wt SAM21131481


title: pgrn.het SAM21131487


title: CB 10F RNA_seq


title: CB 4M RNA_seq


title: CB 4F RNA_seq


title: wt SAM21131480


title: CB 1M RNA_seq


title: 5641-404 CD11b

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: RNA from sorted brain cells

extract_protocol: Cells were centrifuged at 2,600 rcf for 7 minutes (neurons) or 6,600 rcf for 7 minutes (other cell types) and the supernatant was discarded. RNA was extracted from the cell pellet using Qiagen RNeasy Plus Micro kit in a final volume of 25 μl. We typically obtained 200-300 ng RNA from neurons, 10-20 ng from microglia, and 2-5 ng from astrocytes. RNA quality was quantified using the Bioanalyzer.

value: brain

tag: sort

tag: Sex

value: Male


title: 5641-342 GFAP

value: GFAP


title: OC 1M RNA_seq


title: YAP1 biological replication 1

city: Kunming

first: Yong-Gang

last: Yao

state: Yunnan

address: 32 Jiaochang Donglu

department: Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province

institute: Kunming Institute of Zoology

description: U251-APP cells overexpressing YAP1

data_processing:
The processed final library was sequenced on an IlluminaHiseq 4000 platform, and 150 bp paired-ends reads were generated.
Raw RNA-seq reads were trimmed to remove sequencing adapters and low quality reads by Trimmomatic 0.33.
The clean reads were then aligned to the reference genome (GRCh38.p7) sequence using Tophat.
HTSeq-count (0.6.1p1) was used to count aligned reads that mapped to the annotated human genes (GRCh38.p7).
Gene-level differential expression analyses were performed using DESeq2.
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: Processed datafiles were provided in TXT format, which contains rlog transformed gene expression levels by DESeq2.

source_name: U251 cell with a stably expression of mutant APP 128 (M671L)

growth_protocol: U251 cells with stable expression of mutant APP (M671L) were cultured in Roswell RPMI-1640 medium (HyClone, C11875500BT) supplemented with 10% fetal bovine serum at 37 °C in a humidified atmosphere incubator with 5% CO2.

extract_protocol:
Cells were harvested at 72 h after transfection. Total RNA was extracted by using the RNAeasy kit (TianGen, co.td.) according to the manufacturer’s instructions.
1.5 μg total RNA per sample was used to prepare library for RNA-seq. Sequencing libraries were generated using the NEBNextUltraTM RNA Library Prep kit for Illumina (NEB, USA) following the manufacturer’s recommendation and index codes were added to attribute sequence to each sample.

treatment_protocol: Transfection with siRNA or plasmid DNA was performed using an electroporator (CUY21EDIT, Nepa gene, Japan) and electroporation cuvettes (EC-002S, Nepa gene, Japan) following manufactures’ instructions. U251 cells were harvested by trypsinization and washed three times with Opti-MEM medium. After cell counting, 1×10E6 cells were resuspended in 100 μL Opti-MEM medium, then added 2.5 μL siRNA (20 μM) or 10 μg plasmid DNA. After dispensing 100 μL mixture into a cuvette, electroporation was carried out. After electroporation, cells were seeded in pre-warmed growth medium in 6-well plates. Supernatant in each well was replaced with equal volume of new growth medium after 24 h, and 1 μg/mL doxycycline (Sigma; D9891) was added to induce APP expression.

tag: treatment

value: overexpression of YAP1


title: 5641-429 CD11b


title: 5641-346 CD11b


title: 5641-342 CD11b


title: CB 1F RNA_seq


title: vector biological replication 2

description: U251-APP cells overexpressing pCMV-HA vector

value: empty vector


title: vector biological replication 3


title: si-YAP1 biological replication 3

description: U251-APP cells with YAP1 siRNA interference

value: siRNA interference of YAP1


title: si-YAP1 biological replication 2


title: vector biological replication 1


title: si-YAP1 biological replication 1


title: 5641-385 NeuN

value: NeuN

value: Female


title: siNC biological replication 1

description: scramble U251-APP cells with control siRNA

value: control siRNA


title: 5641-337 GFAP


title: 5641-351 CD11b


title: siNC biological replication 3


title: 5641-350 NeuN


title: 5641-353 GFAP


title: Sample Kidney 26 kidney dose 2 rep 2

description: kidney.GEO.csv

value: kidney

value: PCE


title: 5641-353 CD11b


title: siNC biological replication 2


title: 5641-350 GFAP


title: 5641-351 NeuN


title: NPC_ZHH

first: Shuibing

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina bcl2fastq v2.17 was used for base calling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt with parameters "-O 5 -m 45 -q 10"; then mapped to the UCSC hg19 human reference genome using tophat v2.0.11.
Gene abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: hg19
Supplementary_files_format_and_content: excel file including gene name, RefSeq id, locus, RPKM values of each sample, for each gene

source_name: ZIKA infection, HH drug

growth_protocol: Cells were maintained on growth factor reduced Matrigel (BD Biosciences) coated plates in NPC media, including Dulbecco’s Modiﬁed Eagle Medium/Ham’s F12 Nutrient Mixture (ThermoFisher Scientific), 1xN2 (ThermoFisher Scientific), 1xB27minus RA (ThermoFisher Scientific) and 20 ng/ml recombinant human basic FGF (Peprotech), and split at 1:3 ratio every week with Accutase (Millipore).

extract_protocol:
Total RNA was extracted with Rneasy plus mini kit (Qiagen) according to the user manual provided by the vendor.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hNPCs were plated on 6-well plates at 8.5x104/cm2. After overnight incubation, hNPCs were treated with 6 different conditions, including: Mock infection; 25 µM HH treatment; 15 µM AQ treatment; ZIKV MR 766 (MOI=0.125) infection with DMSO treatment; ZIKV MR 766 (MOI=0.125) infection with 25 µM HH treatment or ZIKV MR 766 (MOI=0.125) infection with 15 µM AQ treatment, and the cells in each condition were collected after 72 hours treatment.

value: neural progenitor cells (NPCs)

tag: infection status

value: ZIKA-infected

tag: drug treatment

value: HH


title: NPC_ZAQ

source_name: ZIKA infection, AQ drug

value: AQ


title: NPC_HH

source_name: mock infection, HH drug

value: mock


title: YAP1 biological replication 3

description: U251-APP cells overexpressing YAP1


title: 5641-341 GFAP


title: NPC_AQ

source_name: mock infection, AQ drug


title: NPC_M

source_name: mock infection, DMSO vehicle

value: none (DMSO vehicle)


title: NPC_ZIKA

source_name: ZIKA infection, DMSO vehicle


title: 5641-387 CD11b

value: brain


title: 5641-342 NeuN

value: Male


title: ATO 2

city: shanghai

first: XiangZhen

last: Liu

address: 197, rui-jin 2nd Road

institute: Shanghai institute of hematology

data_processing:
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to hg19 using STAR
Read counts were calculated by using htseq-count
Differential gene expression analysis was done using R package DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: excel file generated by Deseq2. gene_id,baseMean, log2FoldChange,lfcSE,stat,pvalue,padj

source_name: Leukemia cells

growth_protocol: GFP-labled APL cells were expanded in vivo via transplantation into syngeneic mice.

extract_protocol:
Total RNA was extracted with AMBION AM1560 kit.
Following "TruSeq RNA Sample Preparation Guide".

treatment_protocol: ATRA (10mg/kg) and ATO (4mg/kg) were given by daily intraperitoneal injection for 6 days

value: FVB N/J


title: 5641-387 GFAP

value: GFAP


title: ATO 3


title: 5641-352 CD11b


title: 5641-346 NeuN


title: 5641-387 NeuN


title: 5641-385 CD11b


title: 5641-337 NeuN


title: ATRA 3


title: ATRA 2


title: ATRA 1


title: 5641-353 NeuN


title: CON 3


title: A673/TR/shEF transfected with pooled si-TEAD1+si-TEAD2+si-TEAD3+si-TEAD4 no dox_replicate 1

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

description:
batch 3
replicate 1: transfected with pooled si-TEAD1+si-TEAD2+si-TEAD3+si-TEAD4
ASP14_siTEAD_1

data_processing:
HiSeq Control Software, VN:2.2.58, Basecalling Package, VN:1.18.64.0
The STAR aligner was used for alignment of reads to human genome build HsGRCh37.75 downloaded from ensembl with settings: --outFilterMultimapNmax 2 --outFilterMismatchNoverLmax 0.05
read counting in genes was performed with "featureCount" function of the Rsubread R-package
batch 1, 2 and 3 were analyzed separately for differential expression
Genome_build: HsGRCh37.75
Supplementary_files_format_and_content: read counts in Ensemble ENSG genes

source_name: Ewing Sarcoma cell line

growth_protocol: A clone of the EwS cell line A673 (A673/TR/shEF) with a stably transfected construct harbouring a doxycyclin inducible sh-RNA against the EWS-FLI1 fusion protein as previously described (Carrillo, Garcia-Aragoncillo et al. 2007). SK-N-MC EwS cell line was kindly provided by J. Biedler (Memorial Sloan-Kettering Cancer Center, New York, USA). Cells were transfected using the Lipofectamine Plus reagent or Oligofectamine (Invitrogen, Groningen, the Netherlands) according to manufacter´s instructions

extract_protocol:
Qiagen RNeasy-kit
RNA-Seq, New England Biolab kit with polyA enrichment

treatment_protocol: For efficient knockdown of MRTFA and MRTFB 4 µg of the pLKO shMKL-1/2 plasmid (Addgene, #27161)and as a control the sh-NS pLKO plasmid containing an inert sh-RNA (CAACAAGATGAAGAGCACCAA) (Addgene) were transfected into the cells. To transiently knockdown EWS-FLI1 in SK-N-MC cells the sh-EF30 pSUPER based plasmid and as a control the same vector containing a scrambled-shRNA (Ban, Bennani-Baiti et al. 2008) were used. Transfections were carried out using 3µg of the sh-EF30 or sh-scambled pSUPER and 2µg of sh-MKL-1/2 or sh-NS pLKO plasmids to a total DNA concentration of 5µg per transfection (per 10cm2 cell culture dish). Cells were puromycine selected for 72 hours. To separately knockdown MRTFA (MKL-1) the si-RNA 5’-GUGUCUUGGUGUAGUGUAA-3’ (Fang, Yang et al. 2011) sequence was ordered from Dharmacon (Dharmacon/GE Healthcare, Lafayette, CO, USA). To knockdown MRTFB (MKL-2) the ON-TARGETplus Human MKL2 (57496) si-RNA SMARTpool (Dharmacon/GE Healthcare, Lafayette, CO, USA) was used. Transfections with si-RNA were carried out using oligofectamine reagent (Invitrogen, Groningen, the Netherlands) according to the manufacturer’s instructions. Cells were cultivated under standard-serum conditions (10% FBS-DMEM).


title: CON 2


title: WT.UVC SAM24323232

first: Sarah

middle: K

last: Kummerfeld

institute: Genentech

data_processing: Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: sample_treatment: WT.UVC

extract_protocol:
HeLa cells (CL132529) were subjected to genome editing using the Cas9 technology to abrogate expression of the chromatin regulator BAZ1A. Lentiviral transduction was then used to re-express either BAZ1A wild-type or the BAZ1A* mutant in BAZ1A knockout cells. All genome edited cell lines have been cloned and passed in-house QC (mycoplasma-free and cell line authenticated).Cells were grown in standard conditions to 50% confluence. Cells were either unchallenged or subjected to UVC irradiation (200 J/m2) to cause DNA damage. One hour after irradiation, total RNA was extracted from 1×106
cells using the RNeasy Mini Kit (QIAGEN) including the on-column DNase digestion.  RNA extractions was performed in triplicates.

value: HeLa cells


title: 5641-404 NeuN


title: ATO 1


title: A673/TR/shEF transfected with si-Control + dox (48 h)_replicate 2

description:
batch 3
replicate 2: transfected with  non-targeting control si-RNA  + 1µg/ml doxycycline (48 h)
ASP14_siCtrldox_2

value: clone of the EwS cell line A673 (A673/TR/shEF) with a stably transfected construct harbouring a doxycyclin inducible sh-RNA against the EWS-FLI1 fusion protein


title: 5641-337 CD11b


title: BAZ1A_KO_KK_a3.UVC SAM24323237

source_name: sample_treatment: BAZ1A_KO_KK_a3.UVC


title: 5641-346 GFAP


title: A673/TR/shEF transfected with si-Control no dox_replicate 1

description:
batch 3
replicate 1: transfected with  non-targeting control si-RNA
ASP14_siCtrl_1


title: 5641-385 GFAP


title: A673/TR/shEF transfected with pooled si-TEAD1+si-TEAD2+si-TEAD3+si-TEAD4 no dox_replicate 2

description:
batch 3
replicate 2: transfected with pooled si-TEAD1+si-TEAD2+si-TEAD3+si-TEAD4
ASP14_siTEAD_2


title: BAZIA_KO_WT_d11.Control SAM24323248


title: 5641-352 NeuN

value: NeuN


title: A673/TR/shEF transfected with si-Control no dox_replicate 2

description:
batch 3
replicate 2: transfected with  non-targeting control si-RNA
ASP14_siCtrl_2


title: A673/TR/shEF transfected with si-Control + dox (48 h)_replicate 1

description:
batch 3
replicate 1: transfected with  non-targeting control si-RNA  + 1µg/ml doxycycline (48 h)
ASP14_siCtrldox_1


title: CON 1


title: BAZIA_KO_WT_d11.Control SAM24323247


title: BAZIA_KO_WT_d11.UVC SAM24323251

source_name: sample_treatment: BAZIA_KO_WT_d11.UVC


title: 5641-352 GFAP


title: A673/TR/shEF transfected with pooled si-TEAD1+si-TEAD2+si-TEAD3+si-TEAD4 + dox (48 h)_replicate 1

description:
batch 3
replicate 1: transfected with pooled si-TEAD1+si-TEAD2+si-TEAD3+si-TEAD4+ 1µg/ml doxycycline (48 h)
ASP14_siTEADdox_1


title: BAZ1A_KO_KK_a3.Control SAM24323234


title: SK-N-MC transfected with sh-MKL-1/2_replicate 2

description:
batch 2
replicate 2: transfected with (2µg) sh-MKL-1/2 pLKO+ (3µg) sh-scrambled pSUPER
SKNMC_MKL_2

value: SK-N-MC EwS


title: A673/TR/shEF transfected with pooled si-TEAD1+si-TEAD2+si-TEAD3+si-TEAD4 + dox (48 h)_replicate 2

description:
batch 3
replicate 2: transfected with pooled si-TEAD1+si-TEAD2+si-TEAD3+si-TEAD4+ 1µg/ml doxycycline (48 h)
ASP14_siTEADdox_2


title: SK-N-MC transfected with sh-EF30_replicate 2

description:
batch 2
replicate 2: transfected with (3µg) sh-EF30 pSUPER+ (2µg) sh-NS pLKO
SKNMC_EF1_2


title: SK-N-MC transfected with sh-MKL-1/2_replicate 1

description:
batch 2
replicate 1: transfected with (2µg) sh-MKL-1/2 pLKO+ (3µg) sh-scrambled pSUPER
SKNMC_MKL_1


title: SK-N-MC transfected with shControl_replicate 2

description:
batch 2
replicate 2: transfected with (2µg) sh-NS pLKO+ (3µg) sh-scrambled pSUPER
SKNMC_control_2


title: WT.Control SAM24323230

source_name: sample_treatment: WT.Control


title: SK-N-MC co-transfected with sh-MKL-1/2 and sh-EF30_replicate 2

description:
batch 2
replicate 2: transfected with (2µg) sh-MKL-1/2 pLKO+ (3µg) sh-EF30 pSUPER
SKNMC_MKLEF1_2


title: BAZ1A_KO.UVC SAM24323245

source_name: sample_treatment: BAZ1A_KO.UVC


title: SK-N-MC transfected with shControl_replicate 1

description:
batch 2
replicate 1: transfected with (2µg) sh-NS pLKO+ (3µg) sh-scrambled pSUPER
SKNMC_control_1


title: WT.UVC SAM24323233


title: A673/TR/shEF transfected with siMKL-1+si-MKL-2_+ dox_replicate 2

description:
batch 1
replicate 2: transfected with pooled si-MKL-1 (MRTFA)+si-MKL-2 (MRTFB) + 1µg/ml doxycycline treatment (48 h)
ASP14_siMKL12_dox_2


title: A673/TR/shEF transfected with si-MKL-2_+ dox_replicate 2

description:
batch 1
replicate 2: transfected with si-MKL-2 (MRTFB) + 1µg/ml doxycycline treatment (48 h)
ASP14_siMKL2_dox_2


title: A673/TR/shEF transfected with si-MKL-1_+ dox_replicate 2

description:
batch 1
replicate 2: transfected with si-MKL-1 (MRTFA) + 1µg/ml doxycycline treatment (48 h)
ASP14_siMKL1_dox_2


title: BAZ1A_KO_KK_a3.UVC SAM24323239


title: WT.Control SAM24323229


title: BAZ1A_KO.UVC SAM24323243


title: BAZ1A_KO_KK_a3.UVC SAM24323238


title: SK-N-MC co-transfected with sh-MKL-1/2 and sh-EF30_replicate 1

description:
batch 2
replicate 1: transfected with (2µg) sh-MKL-1/2 pLKO+ (3µg) sh-EF30 pSUPER
SKNMC_MKLEF1_1


title: BAZ1A_KO.Control SAM24323240

source_name: sample_treatment: BAZ1A_KO.Control


title: A673/TR/shEF transfected with si-Control_+ dox_replicate 2

description:
batch 1
replicate 2: transfected with non-targeting control si-RNA + 1µg/ml doxycycline treatment (48 h)
ASP14_siControl_dox_2


title: A673/TR/shEF transfected with siMKL-1+si-MKL-2_no dox_replicate 2

description:
batch 1
replicate 2: transfected with pooled si-MKL-1 (MRTFA)+si-MKL-2 (MRTFB)
ASP14_siMKL12_2


title: A673/TR/shEF transfected with si-MKL-2_no dox_replicate 2

description:
batch 1
replicate 2: transfected with si-MKL-2 (MRTFB)
ASP14_siMKL2_2

value: transfected with si-MKL-2 (MRTFB)


title: SK-N-MC transfected with sh-EF30_replicate 1

description:
batch 2
replicate 1: transfected with (3µg) sh-EF30 pSUPER+ (2µg) sh-NS pLKO
SKNMC_EF1_1


title: A673/TR/shEF transfected with si-MKL-1_no dox_replicate 2

description:
batch 1
replicate 2: transfected with si-MKL-1 (MRTFA)
ASP14_siMKL1_2

value: transfected with si-MKL-1 (MRTFA)


title: BAZ1A_KO_KK_a3.Control SAM24323236


title: WT.Control SAM24323228


title: A673/TR/shEF transfected with si-Control_no dox_replicate 2

description:
batch 1
replicate 2: transfected with non-targeting control si-RNA
ASP14_siControl_2


title: BAZ1A_KO_KK_a3.Control SAM24323235


title: WT.UVC SAM24323231


title: A673/TR/shEF transfected with si-MKL-2_+ dox_replicate 1

description:
batch 1
replicate 1: transfected with si-MKL-2 (MRTFB) + 1µg/ml doxycycline treatment (48 h)
ASP14_siMKL2_dox_1


title: BAZIA_KO_WT_d11.Control SAM24323246


title: A673/TR/shEF transfected with si-MKL-1_+ dox_replicate 1

description:
batch 1
replicate 1: transfected with si-MKL-1 (MRTFA) + 1µg/ml doxycycline treatment (48 h)
ASP14_siMKL1_dox_1


title: A673/TR/shEF transfected with si-Control_+ dox_replicate 1

description:
batch 1
replicate 1: transfected with non-targeting control si-RNA + 1µg/ml doxycycline treatment (48 h)
ASP14_siControl_dox_1


title: BAZ1A_KO.Control SAM24323241


title: BAZIA_KO_WT_d11.UVC SAM24323250


title: A673/TR/shEF transfected with siMKL-1+si-MKL-2_no dox_replicate 1

description:
batch 1
replicate 1: transfected with pooled si-MKL-1 (MRTFA)+si-MKL-2 (MRTFB)
ASP14_siMKL12_1


title: BAZ1A_KO.UVC SAM24323244


title: A673/TR/shEF transfected with si-MKL-2_no dox_replicate 1

description:
batch 1
replicate 1: transfected with si-MKL-2 (MRTFB)
ASP14_siMKL2_1


title: A673/TR/shEF transfected with si-MKL-1_no dox_replicate 1

description:
batch 1
replicate 1: transfected with si-MKL-1 (MRTFA)
ASP14_siMKL1_1


title: A673/TR/shEF transfected with si-Control_no dox_replicate 1

description:
batch 1
replicate 1: transfected with non-targeting control si-RNA
ASP14_siControl_1


title: BAZ1A_KO.Control SAM24323242


title: A673/TR/shEF_MRTFB_ChIP_48hdox_rep1

description:
ChIP antibody: MKL-2 A302-767A (Bethly laboratories)
MRTFB (MKL-2) ChIP-seq under serum-induced + 1µg/ml dox conditions
MRTFB_SI dox_1

data_processing:
HiSeq Control Software, VN:2.2.58, Basecalling Package, VN:1.18.64.0
reads were aligned to the hs37d5 (ftp://ftp.1000genomes.ebi.ac.uk/) genome assembly using the bwa aligner
ChIP-seq peaks were identified with MACS2
Genome_build: hs37d5 (ftp://ftp.1000genomes.ebi.ac.uk/)
Supplementary_files_format_and_content: output from MACS2 (*peaks.xls)

growth_protocol: The A673/TR/shEF cell line (Carrillo, Garcia-Aragoncillo et al. 2007), stable carrying a sh-EWS-Fli1 construct under a doxycycline-inducible promoter to induce efficient knockdown of the EWS-FLI1 protein was kindly provided by Javier Alonso (Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain) and cultivated in DMEM+Glutamax (Gibco by Life Technologies, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS) (10270) (Gibco by Life Technologies, Carlsbad, CA, USA), 100 U/mL penicillin, and 100 µg/mL streptomycin (Gibco by Life Technologies, Carlsbad, CA, USA) with the addition of blastizidin (2µg/ml) and zeocin (50µg/ml) (InvivoGen, San Diego, CA, USA) at 37°C and 5% CO2.

extract_protocol:
Approximately 10 million cells were harvested and double crosslinked using disuccinimidyl glutarate (DSG) (16434) and formaldehyde (FA) (28906) (Thermo Fisher Scientific, Waltham, MA, USA). ChIP was performed as described previously (Nowak, Tian et al. 2005), with some adaptations. Briefly, cells were harvested and crosslinked with 0.5M DSG for 20 minutes at room temperature. Pellets were washed twice and cells were crosslinked for 5 minutes with 1% FA. Cells were washed and subsequently lysed in the lysis buffers described in the reference above previously to sonication with Covaris ultrasonicator  for 15 minutes. Sheared chromatin was incubated with 5µg of the respective antibody over-night. For immunoprecipitation 50µl/ChIP of the Protein G Dynabeads (10004D) (Thermo Fisher Scientific, Waltham, MA, USA) was used.
Approximately 5ng ChIP-DNA was used for library prep with the NEBNext® Ultra™ DNA Library Prep Kit for Illumina (#E7370S) and the NEBNext® Multiplex Oligos for Illumina®  (Index Primers Set 1) (NEB #E7335) (New England Biolabs, Frankfurt, Germany) were used for adapter labelling in a multiplex sample preparation. The NEBNext Q5 Hot Start HIFI PCR Master mix was used and no size-selection of adapter-ligated DNA was performed. Library preparation was accomplished according to the the manufacturer’s instructions.

treatment_protocol: To efficiently knockdown EWS-FLI1 1µg/ml doxycycline (dox) was added to the medium for 48 h. For serum-induction cells were washed twice with 1Xphosphate-buffered saline (PBS) (14190) (Gibco by Life Technologies, Carlsbad, CA, USA) and starved over-night in medium containing 0.2% FBS. The next day cells were treated for 60 minutes with the respective medium containing 20% FBS.

value: doxycycline induction:48 h; serum-induction


title: A673/TR/shEF_MRTFB_ChIP_nodox_rep2

description:
ChIP antibody: MKL-2 A302-767A (Bethly laboratories)
MRTFB (MKL-2) ChIP-seq under serum-induced and no-dox conditions
MRTFB_SI no dox_2

value: no doxycyclin, serum-induction


title: A673/TR/shEF_SRF_ChIP_nodox_rep1

description:
ChIP antibody: SRF G20 (sc-335X) (Santa Cruz)
SRF ChIP-seq under serum-induced conditions
SRF_SI no dox_1

value: no doxycycline, serum-induction


title: A673/TR/shEF_MRTFB_ChIP_nodox_rep1

description:
ChIP antibody: MKL-2 A302-767A (Bethly laboratories)
MRTFB (MKL-2) ChIP-seq under serum-induced and no-dox conditions
MRTFB_SI no dox_1


title: A673/TR/shEF_FLI1_ChIP_nodox_rep1

description:
ChIP antibody: Fli1 ChIP grade (ab15289) (Abcam)
EWS-FLI1 ChIP-seq under serum-induced conditions
FLI1_SI_no_dox_rep1


title: A673/TR/shEF_SRF_ChIP_nodox_rep2

description:
ChIP antibody: SRF G20 (sc-335X) (Santa Cruz)
SRF ChIP-seq under serum-induced conditions
SRF_SI no dox_2


title: A673/TR/shEF_FLI1_ChIP_nodox_rep2

description:
ChIP antibody: Fli1 ChIP grade (ab15289) (Abcam)
EWS-FLI1 ChIP-seq under serum-induced conditions
FLI1_SI_no_dox_rep2


title: A673/TR/shEF_MRTFA_ChIP_nodox_rep2

description:
ChIP antibody: MKL-1 (sc-32909) (Santa Cruz)
MRTFA (MKL-1) ChIP-seq under serum-induced conditions
MKL1_SI_no_dox_rep2


title: A673/TR/shEF_MRTFA_ChIP_nodox_rep1

description:
ChIP antibody: MKL-1 (sc-32909) (Santa Cruz)
MRTFA (MKL-1) ChIP-seq under serum-induced conditions
MKL1_SI_no_dox_rep1


title: A673/TR/shEF transfected with siMKL-1+si-MKL-2_+ dox_replicate 1

description:
batch 1
replicate 1: transfected with pooled si-MKL-1 (MRTFA)+si-MKL-2 (MRTFB) + 1µg/ml doxycycline treatment (48 h)
ASP14_siMKL12_dox_1


title: BAZIA_KO_WT_d11.UVC SAM24323249


title: Yersinia pestis transposon mutant library cultured at 28ºC (replicate 3)

city: Exeter

first: ZhengRong

last: Yang

address: Prince of Wales Road

country: United Kingdom

institute: University of Exeter

description: Yersinia pestis mutant library cultured at 28ºC (replicate 3)

data_processing:
BWA was used to align the data
RD values - Relative distance to distal ends for each transposon insertion in genes
Supplementary_files_format_and_content: RD
Genome_build: Yersinia pestis CO92 complete genome - AL590842

organism: Yersinia pestis

growth_protocol: Grown in blood agar base (BAB) broth

extract_protocol:
genomic DNA extracted using the Gentra Puregene kit (Qiagen)
The gDNA was fragmented to <500 base pairs (bp) using 2 x 15 minute cycles at 4ºC in a BioRuptor sonicator (medium intensity, 30s on/90s off).  A NEBNext DNA library preparation for Illumina kit (NEB) was used according to the manufacturer’s instructions, to end repair, A-tail and ligate adapters to the fragments.  Parallel polymerase chain reaction (PCR) samples were set up with 10 μl JumpStart 10x buffer, 6 μl MgCl2, 2 μl 10mM nucleoside triphosphates (dNTPs), 0.6 μl 100 μM PE_PCR_V3.3 primer, 0.6 μl 100 μM Yp_EzTn_PCR primer, 1 μl JumpStart Taq DNA polymerase and 28.8 μl nuclease-free water per reaction.  Primer sequences are listed in Additional file 2, Table S2.  The reactions were amplified at 94oC for 2 minutes, (94oC for 30 seconds, 60oC for 20 seconds, 72oC for 30 seconds) for 22 cycles, 72oC for 10 minutes, then held at 12oC.  PCR products were pooled and ethanol precipitated before being size selected on a 2% (w/v) agarose tris-borate-EDTA (TBE) gel.  Agarose blocks corresponding to 350-500 bp were excised, and the DNA extracted using a Qiagen MinElute Gel Extraction kit as per the manufacturer’s instructions
The DNA was quantified by qPCR and on an Agilent BioAnalyzer before being submitted for sequencing as 100 bp single end reads on an Illumina HiSeq 2500 standard model.

treatment_protocol: Growth at 28ºC or 37ºC

tag: growth conditions

value: cultured at 28ºC


title: Yersinia pestis transposon mutant library cultured at 37ºC (replicate 1a)

description: Yersinia pestis mutant library cultured at 37ºC (replicate 1a)

value: cultured at 37ºC


title: Yersinia pestis transposon mutant library cultured at 37ºC (replicate 1b)

description: Yersinia pestis mutant library cultured at 37ºC (replicate 1c)


title: Yersinia pestis transposon mutant library cultured at 28ºC (replicate 2)

description: Yersinia pestis mutant library cultured at 28ºC (replicate 2)