title: C4-2 [RNA-seq]

status: Public on Oct 03 2018

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
processed data file:
DFCI_EpiCluster_RNA-Seq.reads.gct
C4-2_bam

data_processing:
RNA-Seq: Illumina Casava1.7 software used for basecalling.
RNA-seq: Quality check was performed using the Broad Firehose pipeline (screen data) and VIPER [https://bitbucket.org/cfce/viper/src/master/] (validation data).
RNA-Seq: The datasets were aligned to the human reference GRCh37/hg19 genome using the STAR RNA-Seq aligner in Firehose and VIPER using the default parameters.
RNA-Seq: The read counts for individual genes were generated using the 'RNASeqMetricsSetSummary' module of Firehose and VIPER using the default parameters and the hg19 Ensembl and RefSeq annotation files.
Genome_build: hg19
ChIP-Seq: Illumina Casava1.7 software used for basecalling
ChIP-Seq: Read quality check was performed using the chilin pipeline (https://github.com/cfce/chilin).
ChIP-Seq: Reads were aligned to GRCh37/hg19 using BWA in chilin.
ChIP-Seq: Peak calling was performed using MACS2 in chilin.
Supplementary_files_format_and_content: RNA-Seq: Tab-separated file of the raw read counts of the screened samples or each validation samples for each gene.
Supplementary_files_format_and_content: ChIP-Seq: Bigwig (bw) files generated using MACS2 in the chilin pipeline.

growth_protocol: HCC3153 cells were cultured in RPMI1640 supplemented with 10% FBS and 1% penicillin/streptomycin. MDA-IBC3 and SUM159 cells were cultured in a 1:1 mixture of DMEM/F12 supplemented with 10% FBS and 1% penicillin/streptomycin and Human Mammary Epithelial Cell Medium. For genomic profiling, 59 cell lines were grown in corresponding media described in Table S1.

extract_protocol:
For RNA-seq total RNA was extracted using the RNeasy Kit (Qiagen). For ChIP-seq 5-8 × 10^6 cells were fixed by adding 1:20 volume of fixing buffer (11% paraformaldehyde (Electron Microscopy Sciences, cat# 15714), 0.1M NaCl, 1mM EDTA pH 8.0, 50mM HEPES pH 8.0) directly to the tissue culture medium for 10 min at room temperature for histone modification ChIPs or at 37°C for transcription factor ChIPs and subsequently quenched by glycine. Cells were lysed in lysis buffer (50mM HEPES pH 8.0, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) for 10 min at 4°C. Nuclei were pelleted and washed in wash buffer (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) for 10 min at 4°C and then pelleted and resuspended shearing buffer (10mM Tris-HCl pH 7.4, 1mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate, 0.25% sarkosyl, 1mM DTT) and sonicated in a Covaris sonicator. Debris was removed by centrifugation (5 min at 10,000g) and 970µl of the lysate was mixed with 30µl of 5M NaCl. Chromatin was pre-cleared for 1 hr at 4°C with 40µl of Dynabeads Protein G (LifeTechnologies, cat# 10003D) washed in 0.5% BSA in PBS. Lysates were then incubated with corresponding primary antibody overnight at 4°C. Complexes were precipitated by incubation with 40µl of washed Dynabeads Protein G for 2 hrs at 4°C, washed with low salt wash buffer (20mM Tris-HCl pH 8.0, 150mM NaCl, 2mM EDTA pH 8.0, 1% Triton X-100, 0.1% SDS), high salt wash buffer (20mM Tris-HCl pH 8.0, 500mM NaCl, 2mM EDTA pH 8.0, 1% Triton X-100, 0.1% SDS), LiCl wash buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1mM EDTA pH 8.0, 1% NP40, 1% sodium deoxycholate), and twice with TE pH 8.0. DNA was eluted in elution buffer (100mM NaHCO3, 1% SDS) by incubating overnight at 65°C, followed by 30 min treatment with RNase A at 37°C and 2 hrs treatment with proteinase K at 55°C. DNA was purified with phenol-chloroform extraction and precipitated with isopropanol. For methylation analysis, DNA was isolated using QIAamp DNA Mini kit (QIAGEN, cat# 51304). DNA methylation profiling was carried out on Infinium HumanMethylation450K BeadChip arrays (Illumina, discontinued) at the Harvard Medical School-Partners HealthCare Center for Genetics and Genomics.
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols. ChIP-seq libraries were prepared using the Rubicon ThruPLEX DNA-seq Kit from purified ChIP DNA or input DNA according to the manufacturer’s protocol.

treatment_protocol: Were indicated as "dox+", cells were treated with 100 ng/ml of doxycycline.

tag: cell line


title: Za_Tumor

status: Public on Aug 01 2018

type: SRA

city: West Lafayette

first: Deborah

last: Knapp

address: 625 Harrison Street

country: USA

institute: Purdue University

description: Tumor

library_source: transcriptomic

data_processing:
Strand NGS (v3.1, Build 234566, Strand Life Sciences Pvt Ltd, Bangalore, India) was used to align the data to ENSEMBL. The raw reads were filtered by read metrics. After quantification, data were normalized using DESeq and TMM.
Data were base line transformed and filtered for expression. DESeq2 was performed on data normalized using DESeq and edge R was used on data normalized using TMM.  Only the genes with >2 fold change were considered significant (FDR correction, p<0.05).
Genome_build: CanFam3.1

Raw data has been submitted but is embargoed for 6 months (by submitter) to allow further analysis.

molecule: total RNA

organism: Canis lupus familiaris

source_name: Invasive urothelial carcinoma

extract_protocol:
Normal bladder was removed and bladder mucosa was separated using fine dissection. Bladder tumors were collected via cystoscopy. Tissues were stored directly in trizol and flash frozen. RNA was extracted and purified using RNAeasy (Qiagen).  Ribosomal RNA was removed and libraries constructed using ScriptSeqTM v2 RNA-Seq library preparation kit.
Following purification, di-tagged cDNA was amplified by limit-cycle PCR and purified using AMPure XP System (Beckman Coulter)
Paired-end 150 bp sequence reads were generated using Illumina HiSeq 4000 platform, to obtain an average of 50 million reads/sample. Raw reads were cleaned for PCR artifacts and adapter trimmed, then aligned to the canine genome (CanFam 3.1 reference genome) using COBWeb to obtain expression levels for annotated genes and isoforms (Strand NGS, v3.1, Build 234566, Strand Life Sciences Pvt Ltd, Bangalore, India)

tag: tissue

value: Bladder

tag: cell type

value: Invasive urothelial carcinoma


title: Ab_Tumor

description: Tumor


title: 7_733858_Tumor

description: Tumor


title: Sp_Tumor

description: Tumor


title: Po_Tumor

description: Tumor


title: Mi_Tumor

description: Tumor


title: Mis_Tumor

description: Tumor


title: Da6_Tumor

description: Tumor


title: prostate: PARCB8 RNA-seq

status: Public on Oct 05 2018

city: Los Angeles

first: Owen

middle: N

last: Witte

state: CA

address: 675 Charles E Young Dr S, 5720 MRL Bldg; MC 729022

department: MIMG

institute: UCLA

data_processing:
TOIL processing pipeline (https://github.com/BD2KGenomics/toil-rnaseq)
RNA-Seq measurements expressed as upper quartile normalized counts, log2 transformed, filtered for coding genes using HUGO
Genome_build: hg38 human genome
Supplementary_files_format_and_content: RSEM and Kallisto outputs

organism: Homo sapiens

source_name: prostate

extract_protocol: Library preparation performed by Techonology Center for Genomics & Bioinformatics (TCGB) at UCLA. Libraries for mRNA-Seq were prepared with KAPA Stranded RNA-Seq Kit.

value: prostate

value: transformed prostate basal epithelial

tag: transplant

value: NSG mice


title: 9_Tumor

description: Tumor


title: CH_Tumor

description: Tumor


title: prostate: PARCB3 RNA-seq


title: 5_Tumor

description: Tumor


title: 8_734_223_Tumor

description: Tumor


title: 4_Tumor

description: Tumor


title: 20_Tumor

description: Tumor


title: 19_Tumor

description: Tumor


title: 1_Tumor

description: Tumor


title: 2_Tumor

description: Tumor


title: 16_Tumor

description: Tumor


title: 15_Tumor

description: Tumor


title: 18_Tumor

description: Tumor


title: Sn_Tumor

description: Tumor


title: JE_Tumor

description: Tumor


title: Ja_Tumor

description: Tumor


title: 12_Tumor

description: Tumor


title: 7_Tumor

description: Tumor


title: C_Normal_Mucosa

description: Normal

source_name: Normal Urothelial cells

value: Normal Urothelial cells


title: 2_699898_Tumor

description: Tumor


title: B_Normal_Mucosa

description: Normal


title: A_Normal_Mucosa

description: Normal


title: 11_Tumor

description: Tumor


title: 10_Tumor

description: Tumor


title: 3_Tumor

description: Tumor


title: H. sal worker - fat body - rep2

status: Public on May 24 2018

city: Philadelphia

first: Roberto

last: Bonasio

state: PA

address: 3400 Civic Center Blvd - SCTR 9-111

department: Cell and Developmental Biology

institute: University of Pennsylvania

description:
180311.H2WV5BGX5.ND87
fatbody_rep2

data_processing:
reads were aligned to Hsal v8.5 with STAR (version 2.5.0b). Max intron length was set to 50 kb.
counts were assigned to gene models in Hsal OGS4.0 or Hsal lncRNA4.0 using the R package DEG-seq
RPKMs were calculated by DEG-seq
Differential expression was determined with the R package DESeq2 using variance stabilization models.
Genome_build: Hsal v8.5
Supplementary_files_format_and_content: Table of normalized RPKM values for all genes models in OGS4.0 and Hsal lncRNA4.0 for tissues and brain regions (ovary, fat body, antenna, non-visual brain, optic lobe, retina)

molecule: polyA RNA

organism: Harpegnathos saltator

source_name: worker_fat body

growth_protocol: Animals were housed in a plaster nest in a clean, temperature  (25°C) and humidity (50%) controlled ant facility on a 12-hour light/dark cycle and fed three times per week with live crickets.

extract_protocol:
RNA was extracted from tissues with TRIzol. DNA was removed using Turbo DNAse.
RNA was fragmented by boiling in presence of divalent cations. RT was performed with random hexamers.
Unstranded RNA-seq

value: worker

value: fat body


title: H. sal worker - retina - rep2

description:
180311.H2WV5BGX5.b1111
retina_rep2

value: retina


title: H. sal worker - fat body - rep3

description:
180311.H2WV5BGX5.ND96
fatbody_rep3


title: H. sal worker - non-visual brain - rep3

description:
180311.H2WV5BGX5.b0606
nvbr_rep3

source_name: worker_non-visual brain

value: non-visual brain


title: H. sal worker - non-visual brain - rep1

description:
180311.H2WV5BGX5.b0404
nvbr_rep1


title: H. sal worker - retina - rep1

description:
180311.H2WV5BGX5.b1010
retina_rep1


title: H. sal worker - optic lobe - rep1

description:
180311.H2WV5BGX5.0707
optic_rep1

source_name: worker_optic lobe

value: optic lobe


title: H. sal worker - non-visual brain - rep2

description:
180311.H2WV5BGX5.b0505
nvbr_rep2


title: H. sal worker - antenna - rep2

description:
180311.H2WV5BGX5.b0202
antenna_rep2

value: antenna


title: H. sal worker - antenna - rep3

description:
180311.H2WV5BGX5.b0303
antenna_rep3


title: H. sal worker - fat body - rep1

description:
180311.H2WV5BGX5.ND78
fatbody_rep1


title: H. sal worker - optic lobe - rep3

description:
180311.H2WV5BGX5.0909
optic_rep3


title: H. sal worker - optic lobe - rep2

description:
180311.H2WV5BGX5.b0808
optic_rep2


title: H. sal worker - antenna - rep1

description:
180311.H2WV5BGX5.b0101
antenna_rep1


title: H. sal gamergate - ovary - rep2

description:
180311.H2WV5BGX5.ND60
ovary_rep2

value: gamergate

value: ovary


title: H. sal worker - retina - rep3

description:
180311.H2WV5BGX5.b1212
retina_rep3


title: H. sal gamergate - ovary - rep3

description:
180311.H2WV5BGX5.ND69
ovary_rep3


title: D_Normal_Mucosa

description: Normal


title: H. sal male - whole body - rep2

description:
HS.male.b2
internal reference: 160205.HL72VBGXX.b0204.R1.gz

data_processing:
reads were aligned to Hsal v8.5 with STAR (version 2.5.0b). 75 bp were clipped from the 3' end to produce 125 bp reads, and max intron length was set to 10,000 bp.
counts were assigned to gene models in Hsal OGS4.0 or Hsal lncRNA4.0 using the R package DEG-seq
RPKMs were calculated by DEG-seq
Differential expression was determined with the R package DESeq2 using variance stabilization models.
Genome_build: Hsal v8.5
Supplementary_files_format_and_content: Table of normalized RPKM values for all genes models in OGS4.0 and Hsal lncRNA4.0

source_name: H. sal male_whole body

extract_protocol:
RNA was extracted from full bodies with TRIzol. DNA was removed using Turbo DNAse.
RNA was fragmented by boiling in presence of divalent cations. RT was performed with random hexamers and dUTP was incorporated in the 2nd strand to retain strand information.
Strand-specific RNA-seq (dUTP)

tag: developmental stage

value: male

value: whole body


title: H. sal adult worker - whole body - rep2

description:
HS.worker.b2
internal reference: 160205.HL72VBGXX.H202.R1.gz

source_name: H. sal adult worker_whole body


title: H. sal male - whole body - rep1

description:
HS.male.b1
internal reference: 160205.HL72VBGXX.b0103.R1.gz


title: H. sal adult worker - whole body - rep1

description:
HS.worker.b1
internal reference: 160205.HL72VBGXX.H193.R1.gz


title: C. flo minor - whole body - rep1

description:
CF.minor.b1
internal reference: 160205.HL72VBGXX.b0305.R1.gz

data_processing:
reads were aligned to C. flo v7.4 with STAR (version 2.5.0b). 75 bp were clipped from the 3' end to produce 125 bp reads, and max intron length was set to 10,000 bp.
counts were assigned to gene models in Cflo OGS4.0 or Cflo lncRNA4.0 using the R package DEG-seq
RPKMs were calculated by DEG-seq
Differential expression was determined with the R package DESeq2 using variance stabilization models.
Genome_build: Cflo v7.4
Supplementary_files_format_and_content: Table of normalized RPKM values for all genes models in OGS4.0 and Cflo lncRNA4.0

organism: Camponotus floridanus

source_name: C. flo minor_whole body

growth_protocol: Animals were housed in a plaster nest in a clean, temperature  (25°C) and humidity (50%) controlled ant facility on a 12-hour light/dark cycle and fed twice weekly with excess supplies of water, 20% sugar water (sucrose cane sugar), and Bhatkar-Whitcomb diet.

value: minor


title: C. flo late pupae major - whole body - rep2

description:
CF.lpupMaj.b2
internal reference: 160205.HL72VBGXX.ND94.R1.gz

source_name: C. flo late pupae major_whole body

value: late pupa major


title: C. flo male - whole body

description:
CF.male.b1
internal reference: 160205.HL72VBGXX.b0608.R1.gz

source_name: C. flo male_whole body


title: H. sal late pupuae - whole body - rep2

description:
HS.lpup.b2
internal reference: 160205.HL72VBGXX.H094.R1.gz

source_name: H. sal late pupuae_whole body

value: late pupa


title: H. sal gamergate - ovary - rep1

description:
180311.H2WV5BGX5.ND51
ovary_rep1


title: C. flo minor - whole body - rep2

description:
CF.minor.b2
internal reference: 160205.HL72VBGXX.b0407.R1.gz


title: C. flo late pupae minor - whole body - rep2

description:
CF.lpupMin.b2
internal reference: 160205.HL72VBGXX.H192.R1.gz

source_name: C. flo late pupae minor_whole body

value: late pupa minor


title: C. flo early pupae - whole body - rep 1

description:
CF.epup.b1
internal reference: 160205.HL72VBGXX.H165.R1.gz

source_name: C. flo early pupae_whole body

value: early pupa


title: C. flo instar 1 larvae - whole body - rep2

description:
CF.inst1.b2
internal reference: 160205.HL72VBGXX.b1202.R1.gz

source_name: C. flo instar 1 larvae_whole body

value: instar 1 larva


title: H. sal early pupae - whole body - rep 2

description:
HS.epup.b2
internal reference: 160205.HL72VBGXX.H068.R1.gz

source_name: H. sal early pupae_whole body


title: H. sal embryo - whole body - rep2

description:
HS.embryo.b2
internal reference: 160205.HL72VBGXX.ND85.R1.gz

source_name: H. sal embryo_whole body

value: embryo


title: H. sal late pupuae - whole body - rep1

description:
HS.lpup.b1
internal reference: 160205.HL72VBGXX.H081.R1.gz


title: H. sal instar 1 larvae - whole body - rep1

description:
HS.inst1.b1
internal reference: 160205.HL72VBGXX.H003.R1.gz

source_name: H. sal instar 1 larvae_whole body


title: C. flo instar 4 larvae - whole body - rep 2

description:
CF.inst4.b2
internal reference: 160205.HL72VBGXX.H156.R1.gz

source_name: C. flo instar 4 larvae_whole body

value: instar 4 larva


title: C. flo instar 1 larvae - whole body - rep1

description:
CF.inst1.b1
internal reference: 160205.HL72VBGXX.b1101.R1.gz


title: C. flo late pupae minor - whole body - rep1

description:
CF.lpupMin.b1
internal reference: 160205.HL72VBGXX.H183.R1.gz


title: H. sal instar 4 larvae - whole body - rep 2

description:
HS.inst4.b2
internal reference: 160205.HL72VBGXX.H042.R1.gz

source_name: H. sal instar 4 larvae_whole body


title: H. sal instar 4 larvae - whole body - rep 1

description:
HS.inst4.b1
internal reference: 160205.HL72VBGXX.H029.R1.gz


title: C. flo late pupae major - whole body - rep1

description:
CF.lpupMaj.b1
internal reference: 160205.HL72VBGXX.b1006.R1.gz


title: H. sal instar 1 larvae - whole body - rep2

description:
HS.inst1.b2
internal reference: 160205.HL72VBGXX.H016.R1.gz


title: H. sal embryo - whole body - rep1

description:
HS.embryo.b1
internal reference: 160205.HL72VBGXX.ND07.R1.gz


title: H. sal early pupae - whole body - rep 1

description:
HS.epup.b1
internal reference: 160205.HL72VBGXX.H055.R1.gz


title: U-2932 Y691F - untreated - rep1

status: Public on Apr 27 2018

description:
polyA+ RNA
160505.HTTLKBGXX.b0803.gz

data_processing:
reads were aligned to GRCh38 & ENSEMBL release 83 with STAR (version 2.5.0b)
counts were assigned to gene models in ENSEMBL 83 using the R package DEG-seq and normalized with the RPKM method
Differential expression was determined with the R package DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: Table of counts and normalized RPKM values for all genes models in ENSEMBL 83

source_name: U-2932 cell line (DLBLC)

growth_protocol: RPMI + 10% FBS

extract_protocol:
Total RNA was extracted with TRI reagent. DNA was removed using Turbo DNAse.
RNA was chemically fragmented by heating in presence of divalent cations. RT was performed with random hexamers and dUTP was incorporated in the 2nd strand to retain strand information.
Strand-specific RNA-seq (dUTP)

treatment_protocol: When indicated, cells were treated with 10 µg/ml F(ab')2-IgM

tag: genotype

value: Roquin-2 Y691F

tag: treatment

value: NT


title: U-2932 Y691F - + IgM - rep1

description:
polyA+ RNA
160505.HTTLKBGXX.b0904.gz

value: IgM


title: U-2932 WT - + IgM - rep3

description:
polyA+ RNA
160505.HTTLKBGXX.ND21.gz

value: WT


title: U-2932 Y691F - + IgM - rep3

description:
polyA+ RNA
160505.HTTLKBGXX.ND39.gz


title: U-2932 WT - + IgM - rep1

description:
polyA+ RNA
160505.HTTLKBGXX.b0702.gz


title: U-2932 WT - + IgM - rep2

description:
polyA+ RNA
160505.HTTLKBGXX.b1106.gz


title: C. flo early pupae - whole body - rep 2

description:
CF.epup.b2
internal reference: 160205.HL72VBGXX.H174.R1.gz


title: U-2932 Y691F - untreated - rep3

description:
polyA+ RNA
160505.HTTLKBGXX.ND30.gz


title: C. flo instar 4 larvae - whole body - rep 1

description:
CF.inst4.b1
internal reference: 160205.HL72VBGXX.H147.R1.gz


title: C. flo embryo - whole body - rep1

description:
CF.embryo.b1
internal reference: 160205.HL72VBGXX.H107.R1.gz

source_name: C. flo embryo_whole body


title: U-2932 WT - untreated - rep1

description:
polyA+ RNA
160505.HTTLKBGXX.b0601.gz


title: C. flo embryo - whole body - rep2

description:
CF.embryo.b2
internal reference: 160205.HL72VBGXX.H120.R1.gz


title: U-2932 WT - untreated - rep2

description:
polyA+ RNA
160505.HTTLKBGXX.b1005.gz


title: U-2932 Y691F - + IgM - rep2

description:
polyA+ RNA
160505.HTTLKBGXX.ND03.gz


title: U-2932 Y691F - untreated - rep2

description:
polyA+ RNA
160505.HTTLKBGXX.b1207.gz


title: FUL IM, rep2

status: Public on Feb 13 2018

city: Berlin

first: Dijun

last: Chen

address: Philippstr. 13 (House 22)

department: Plant Cell and Molecular Biology

country: Germany

institute: Humboldt University

description:
processed data file:
FUL_IM.rpkm.bw
FUL_IM.narrowPeak.bed.gz

library_source: genomic

data_processing:
Reads were then mapped to the A.thaliana genome (TAIR10) using Bowtie (version 1.1.2) with parameters “--threads 8 -n 2 -m 3 -k 1 --best --chunkmbs 256 -q”.
Redundant reads were removed using Picard tools (v2.60; http://broadinstitute.github.io/picard/). Peak-calling was performed using MACS2 (version 2.1.0). Duplicated reads were not considered (--keep-dup=1) during peak calling in order to achieve a better specificity
The "--mfold" parameter was set as "2-20" to build the model.
Peaks across replicates with an IDR ≤ 0.05 (https://sites.google.com/site/anshulkundaje/projects/idr) were retained.
Wiggle tracks were generated by DeepTools with the command “bamCoverage”; read coverage was normalized as RPKM (Reads Per Kilobase per Million reads).
The above processing pipeline was implemented in (Chen and Kaufmann 2017, Methods in Molecular Biology (Clifton, NJ) 1629, 239-269)
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: inflorescence-like meristems

growth_protocol: All plants were grown on rock-wool at 21°C under long day conditions (16 h light, 8 h dark).

extract_protocol:
ChIP-seq experiments were performed following a previously published protocol (van Mourik et al 2015. Book Chapter. Methods in Molecular Biology: Plant Functional Genomics. 1284:93-1210.). ChIP-seq experiment input samples were used as negative controls. For each tissue two biological replicates and one input sample were sequencing on the Illumina HiSeq.
ChIP-seq libraries as well as control libraries that were based on “input” DNA were prepared using ThruPLEX DNA-seq kit (RUBICON GENOMICS, USA) following the manufacturer.

treatment_protocol: No treatment

tag: ecotype

value: Ler/Col F2

tag: genotype/variation

value: pFUL:FUL-GFP 35S:AP1-GR ap1-1 cal-1

value: uninduced IM of plants

value: inflorescence meristem

tag: chip antibody

value: MACS anti-GFP microbeads (Miltenyi Biotec; Cat. # 130-091-125)


title: U-2932 WT - untreated - rep3

description:
polyA+ RNA
160505.HTTLKBGXX.ND12.gz


title: FUL pistil, rep2

description:
processed data file:
FUL_pistil.rpkm.bw
FUL_pistil.narrowPeak.bed.gz

source_name: pistils

value: pFUL:FUL-GFP ful-1

value: stage 12-16 pistils of plants

value: pistil


title: FUL pistil, rep1


title: FUL pistil, input

description: processed data file:


title: Thyroid_lymph_node_metastasis_from_patient_I1

status: Public on Mar 01 2018

type: RNA

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Standard Agilent scanning protocol with Agilent SureScan microarray scanner (G2505C).

data_processing: Scanned images were processed with Agilent Feature Extraction v10.7 with default parameters to obtain raw data. Raw data were imported in R and processed using the AgiMicroRna package. microRNA-level processed signals were obtained using the RMA algorithm with quantile normalization.

label_protocol: Total RNA from each sample was labeled according to the manufacturers recommendations.

extract_protocol: Total RNA, including the miRNA fraction, was extracted from the FFPE sections by using the miRNeasy FFPE kit (Qiagen, Valencia, CA, USA) according to the protocol provided by the manufacturer; RNA quality was assessed  by the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: sampleID

value: Thyroid

tag: disease state


title: Thyroid_primary_tumor_from_patient_I7


title: FUL IM, rep1


title: Thyroid_lymph_node_metastasis_from_patient_I2


title: Thyroid_lymph_node_metastasis_from_patient_I3_2


title: FUL IM, input

description: processed data file:


title: Thyroid_primary_tumor_from_patient_I4


title: Thyroid_primary_tumor_from_patient_I1


title: Thyroid_primary_tumor_from_patient_I5


title: Thyroid_primary_tumor_from_patient_I8


title: Thyroid_lymph_node_metastasis_from_patient_I4


title: Thyroid_lymph_node_metastasis_from_patient_I8


title: Thyroid_primary_tumor_from_patient_I2


title: Normal_thyroid_from_patient_I11


title: Thyroid_lymph_node_metastasis_from_patient_I3_1


title: Thyroid_lymph_node_metastasis_from_patient_I5


title: Normal_thyroid_from_patient_I9


title: Thyroid_lymph_node_metastasis_from_patient_I6


title: 72_sALS_Frontal Cortex

status: Public on Aug 14 2017

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

data_processing:
Bismark (v0.13.1)
Bowtie 2 (v2.2.3)
MethylKit
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited methylation counts

source_name: sALS_Frontal Cortex

extract_protocol:
DNA was isolated from 20–40 mg of sampled frontal cortex and cerebellum frozen tissue using the Wizard genomic DNA purification kit (Promega, Madison, WI, USA) as per manufacturers’ instructions, and re-suspended in TE buffer. Concentration was assessed using a Qubit 3.0 Fluorometer (ThermoFisher Scientific, Waltham, MA), and 50ng/ul of DNA in a 10ul volume was sent to the Mayo Clinic Medical Genome Facility in Rochester (Minnesota, USA) for processing and sequencing.
RRBS library construction and sequencing was conducted at the Mayo Clinic Medical Genome Facility in Rochester (Minnesota, USA). First, the concentration and size distribution of the libraries were determined using Agilent (Santa Clara, CA, USA) Bioanalyzer DNA 1000 chip, Qubit fluorometry (Invitrogen, Carlsbad, CA), and qPCR. Libraries were pooled at equimolar concentrations and loaded onto a paired end flow cell at concentrations of 7-8 pM to generate cluster densities of 600,000-700,000/mm2 following Illumina’s standard protocol, using the Illumina cBot and HiSeq Paired end cluster kit version 3 (San Diego, CA, USA). Because bisulfite treated samples are unbalanced due to an under representation of C bases, a lane of PhiX genomic DNA was run to allow the Illumina data collection software to call bases correctly. Each lane of a HiSeq flow cell produces 21-39 Gbases of sequence. The flow cells were sequenced as 51 X 2 paired end reads on an Illumina HiSeq 2000 using TruSeq SBS sequencing kit version 3 and HiSeq data collection version 2.0.12.0 software. Base-calling was performed using Illumina’s RTA version 1.17.21.3.

tag: subject status

value: sporadic amyotrophic lateral sclerosis (sALS)

value: brain

tag: tissue subtype

value: Frontal Cortex


title: Thyroid_primary_tumor_from_patient_I6


title: Thyroid_primary_tumor_from_patient_I3


title: Thyroid_lymph_node_metastasis_from_patient_I7


title: Nurse head - rep13

status: Public on Aug 10 2017

data_processing:
reads were aligned to Mpha v2.0 & gene annotation v100 with STAR (version 2.5.0b)
counts were assigned to gene models in Mpha annotation 100 using the R package DEG-seq
RPKMs were calculated by DEG-seq
Genome_build: M.pharaonis_V2.0
Supplementary_files_format_and_content: table of RPKM values for all genes models

organism: Monomorium pharaonis

source_name: head

growth_protocol: Colonies were maintained at 27 +/-1 C, 50% RH, 12:12 light:dark cycle, and fed twice weekly dried mealworms (Tenebrio molitor) and an agar-based synthetic diet (Dussutour and Simpson 2008)

extract_protocol:
Qiagen RNeasy mini kit
Nextera library prep kit
Unstranded RNA-seq

treatment_protocol: All samples were collected from colonies with 10 queens, ~300-400 workers, and ~300-400 brood

tag: task

value: nurse


title: Nurse head - rep14


title: E16.5_rep3

status: Public on May 17 2019

city: Pullman

first: Nathan

middle: C

last: Law

state: WA

address: 100 Dairy Road

department: School of Molecular Biology

institute: Washington State University

description: scRNA-seq data from isolated male germ cells at E16.5

data_processing:
Raw base call files were demultiplexed using the 10X Genomics Cell Ranger pipeline (v2.1.0) and aligned to the mouse mm10 transcriptome.
A total of 8 transcriptomes (n=3 for E16.5, n=2 for P0, n=2 for P3, and n=1 for P6) were merged in R using the Seurat package 1 (v2.3.2).
Low quality cell transcriptomes and doublets were assessed within each library and excluded using the following criteria: >1,300 genes for E16.5 #1; >1,900 genes and <80,000 UMI counts for E16.5 #2; >1,200 genes for P0 #1; >1,000 genes and <30,000 UMI counts for P0 #2; >1,500 genes and <70,000 UMI counts for P3 #1; <35,000 UMI counts for P3 #2; <40,000 UMI counts for P6. Filtering based on percent mitochondrial genes detected was conservatively set at <25% for all libraries based on visual inspection of overall distribution and the variability of mitochondrial gene content that occurs based on cell type, proliferation status, and developmental state.
Germ cells were isolated from a small number of contaminating cells in the dataset based on Dazl and Ddx4 transcript abundance before the entire dataset was normalized, scaled (“vars.to.regress” included number of genes, number of UMIs, percent mitochondrial transcripts, and age replicate), and dimensionally reduced using Seurat.
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: Gene-Cell Matrix filled with Raw Read/Expression Values

organism: Mus musculus

source_name: testicular germ cells

extract_protocol:
Single cell suspensions of E16.5, P0, P3, or P6 quadruple-transgenic testes were prepared and germ cells isolated using FACS with an SH800 machine (Sony Biotechnology) gating for tdTomato+ cells. Live cells were loaded into a Chromium Controller (10X Genomics, Inc.).
Single-cell cDNA libraries were generated using v2 chemistry according to the manufacturer’s protocol (10X Genomics, Inc.).

tag: strain

value: Mixed C57/B6 and 129

value: male germ cells


title: Nurse head - rep9


title: Nurse head - rep10


title: Nurse head - rep8


title: Nurse head - rep4


title: Nurse head - rep6


title: Nurse head - rep2


title: Nurse head - rep7


title: Nurse head - rep12


title: Nurse head - rep1


title: Forager head - rep8

value: forager


title: Nurse head - rep3


title: Nurse head - rep11


title: Forager head - rep3


title: Forager head - rep2


title: Nurse head - rep5


title: Forager head - rep7


title: Forager head - rep5


title: Forager head - rep6


title: d110 - rep5

description:
submitter provided internal reference: raw_data/FASTQ/2013/130610_RB_VN_RSM/RB.130514.A.VLB5.gz
d110.b5

data_processing:
Reads were aligned to Hsal v3.0 & OGS3.5 with STAR (version 2.5.0b)
Counts were assigned to gene models in Hsal OGS3.8 using the R package DEG-seq
RPKMs were calculated by only considering reads assigned to protein-coding genes
Assembly and annotation were described in Bonasio et al. Science 2010 (PMID: 20798317) and Bonasio et al. Current Biol 2012 (PMID: 22885060). Assembly and annotations can be downloaded from the Hymenoptera Genome Database, using the following links.
Genome_build: http://hymenopteragenome.org/harpegnathos/?q=genome_consortium_datasets
Genome_build: Hsal v3.0
Supplementary_files_format_and_content: Table of raw RNA-seq counts and normalized RPKM values for all genes models in OGS3.8

source_name: Whole brain (with optic lobes)

extract_protocol:
Three whole brains (including optic lobes) per replicate were dissected and pooled and RNA extracted with TRIzol. DNA was removed using Turbo DNAse.
RNA was fragmented by boiling in presence of divalent cations. RT was performed with random hexamers and dUTP was incorporated in the 2nd strand to retain strand information.
Strand-specific RNA-seq (dUTP)

treatment_protocol: We set up 5 adoptive colonies lacking dominant reproductives using 70–100 young (4–8 weeks) workers per colony. At the time of transfer, we removed 3 workers for baseline gene expression (“d0”). We monitored colonies each day until more than 8 workers in a colony were observed dueling, usually three days later. On the 3rd, and 10th day after the start of the tournament, we removed the three individuals (“d6” and “d13”) that had been observed to duel most frequently. Finally, three established gamergates were sampled between 104 and 110 days after transfer (“d110”). We identified their status on behavioral grounds (location next to cocoons, submissive response by subordinate workers, standing with high posture) and verified it by dissection and observation of their activated ovaries.

tag: time


title: d110 - rep2

description:
submitter provided internal reference: raw_data/FASTQ/2012/120904_RB_SK/RB.120627.C.VLB3.gz
d110.b2


title: d110 - rep3

description:
submitter provided internal reference: raw_data/FASTQ/2013/130211_RB_AR_VN/RB.130124.B.VLB3.gz
d110.b3


title: Forager head - rep9


title: d110 - rep1

description:
submitter provided internal reference: raw_data/FASTQ/2012/120904_RB_SK/RB.120627.B.VLB1.gz
d110.b1


title: Forager head - rep1


title: d110 - rep4

description:
submitter provided internal reference: raw_data/FASTQ/2013/130211_RB_AR_VN/RB.130124.C.VLB1.gz
d110.b4


title: d13 - rep5

description:
submitter provided internal reference: raw_data/FASTQ/2013/130610_RB_VN_RSM/RB.130514.A.VLB3.gz
d13.b5


title: d13 - rep3

description:
submitter provided internal reference: raw_data/FASTQ/2013/130211_RB_AR_VN/RB.130124.A.VLB1.gz
d13.b3


title: d13 - rep2

description:
submitter provided internal reference: raw_data/FASTQ/2012/120904_RB_SK/RB.120627.C.VLB1.gz
d13.b2


title: d6 - rep4

description:
submitter provided internal reference: raw_data/FASTQ/2013/130211_RB_AR_VN/RB.130124.B.VLB2.gz
d6.b4


title: d13 - rep4

description:
submitter provided internal reference: raw_data/FASTQ/2013/130211_RB_AR_VN/RB.130124.C.VLB3.gz
d13.b4


title: d6 - rep5

description:
submitter provided internal reference: raw_data/FASTQ/2013/130610_RB_VN_RSM/RB.130514.A.VLB2.gz
d6.b5


title: d13 - rep1

description:
submitter provided internal reference: raw_data/FASTQ/2012/120904_RB_SK/RB.120627.A.VLB3.gz
d13.b1


title: d0 - rep4

description:
submitter provided internal reference: raw_data/FASTQ/2013/130211_RB_AR_VN/RB.130124.B.VLB1.gz
d0.b4


title: d0 - rep2

description:
submitter provided internal reference: raw_data/FASTQ/2012/120904_RB_SK/RB.120627.B.VLB3.gz
d0.b2


title: Worker - set 2, rep 1

description: submitter provided internal reference:RK-08

data_processing:
Reads were aligned to Cflo v3.0 & gene annotation OGS3.5 with STAR (version 2.5.0b)
Counts were assigned to gene models in OGS3.5 using the R package DEG-seq
RPKMs were calculated by DEG-seq
Assembly and annotation were described in Bonasio et al. Science 2010 (PMID: 20798317) and Bonasio et al. Current Biol 2012 (PMID: 22885060). Assembly and annotations can be downloaded from the Hymenoptera Genome Database, using the following links.
Genome_build: http://hymenopteragenome.org/camponotus/?q=genome_consortium_datasets
Genome_build: Cflo v3.0
Supplementary_files_format_and_content: RPKM table

source_name: whole body

growth_protocol: C. floridanus ants were housed plaster nests and maintained at 25ºC under 12 hours alternating cycles of light and darkness. Ants were fed twice a week with water, 30% sugar water solution, artificial diet and boiled pieces of beetle larvae (Zophobas morio)

extract_protocol:
RNA was extracted from whole homogenized bodies with TRIzol. DNA was removed using Turbo DNAse.
RNA was fragmented by boiling in presence of divalent cations. RT was performed with random hexamers and dUTP was incorporated in the 2nd strand to retain strand information.
Strand-specific RNA-seq (dUTP)

treatment_protocol: Samples were collected from queenright lab colonies without any treatment.

tag: caste

value: worker


title: d0 - rep5

description:
submitter provided internal reference: raw_data/FASTQ/2013/130610_RB_VN_RSM/RB.130514.A.VLB1.gz
d0.b5


title: Stable worker brain - d120 - rep3

description:
submitter supplied internal reference id: 160202.H2NVVBGXY.ND64.gz
stable.worker.d120.b3
Hsal.brains.transition.d120.RPKMs.gz

data_processing:
reads were aligned to Hsal v3.0 & OGS3.5 with STAR (version 2.5.0b)
counts were assigned to gene models in Hsal OGS3.8 using the R package DEG-seq
RPKMs were calculated by only considering reads assigned to protein-coding genes
Differential expression was determined with the R package DESeq2 using variance stabilization models that included samples sequenced in parallel but not described in the study.
Assembly and annotation were described in Bonasio et al. Science 2010 (PMID: 20798317) and Bonasio et al. Current Biol 2012 (PMID: 22885060). Assembly and annotations can be downloaded from the Hymenoptera Genome Database, using the following links.
Genome_build: http://hymenopteragenome.org/harpegnathos/?q=genome_consortium_datasets
Genome_build: Hsal v3.0
Supplementary_files_format_and_content: Table of normalized RPKM values for all genes models in OGS3.8
Supplementary_files_format_and_content: Output table from DESeq2 including maximum a posteriori log-fold-change, raw P-values, and adjusted P-values

source_name: brain (minus optic lobes)

extract_protocol:
Brains (minus optic lobes) were dissected and RNA extracted with TRIzol. DNA was removed using Turbo DNAse.
RNA was fragmented by boiling in presence of divalent cations. RT was performed with random hexamers and dUTP was incorporated in the 2nd strand to retain strand information.
Strand-specific RNA-seq (dUTP)

treatment_protocol: To induce worker–gamergate transitions we transferred 30 newly eclosed female ants (1–3 days old) from mature colonies to a new nest together with three males. Every ant was individually painted with a unique two-color combination. Ants were carefully observed for 1–2 hours every morning and evening in the following two weeks to monitor dueling activities. After 120 days, ants were scored for their hunting behavior and sacrificed.

tag: colony

value: stable


title: Stable worker brain - d120 - rep2

description:
submitter supplied internal reference id: 160202.H2NVVBGXY.ND55.gz
stable.worker.d120.b2
Hsal.brains.transition.d120.RPKMs.gz


title: d0 - rep1

description:
submitter provided internal reference: raw_data/FASTQ/2012/120904_RB_SK/RB.120627.A.VLB1.gz
d0.b1


title: d6 - rep2

description:
submitter provided internal reference: raw_data/FASTQ/2012/120904_RB_SK/RB.120627.B.VLB4.gz
d6.b2


title: d0 - rep3

description:
submitter provided internal reference: raw_data/FASTQ/2013/130211_RB_AR_VN/RB.130124.A.VLB3.gz
d0.b3


title: Queen - set 2, rep 1

description: submitter provided internal reference: RK-08

value: queen


title: d6 - rep1

description:
submitter provided internal reference: raw_data/FASTQ/2012/120904_RB_SK/RB.120627.A.VLB2.gz
d6.b1


title: Stable worker brain - d120 - rep1

description:
submitter supplied internal reference id: 160202.H2NVVBGXY.ND46.gz
stable.worker.d120.b1
Hsal.brains.transition.d120.RPKMs.gz


title: Transition worker brain - d120 - rep6

description:
submitter supplied internal reference id: 160202.H2NVVBGXY.b0905.gz
transition.worker.d120.b6
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz

value: transition


title: d6 - rep3

description:
submitter provided internal reference: raw_data/FASTQ/2013/130211_RB_AR_VN/RB.130124.A.VLB4.gz
d6.b3


title: Forager head - rep4


title: Gamergate brain - d120 - rep5

description:
submitter supplied internal reference id:  160202.H2NVVBGXY.b0703.gz
transition.gamergate.d120.b5
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz

value: gamergate


title: Transition worker brain - d120 - rep5

description:
submitter supplied internal reference id:  160202.H2NVVBGXY.b0804.gz
transition.worker.d120.b5
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz


title: Worker - set 2, rep 2


title: Transition worker brain - d120 - rep2

description:
submitter supplied internal reference id:  151203.HKKH7BGXX.ND10.R2.gz
transition.worker.d120.b2
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz


title: Transition worker brain - d120 - rep7

description:
submitter supplied internal reference id: 160202.H2NVVBGXY.b1208.gz
transition.worker.d120.b7
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz


title: Transition worker brain - d120 - rep3

description:
submitter supplied internal reference id:  160202.H2NVVBGXY.H035.gz
transition.worker.d120.b3
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz


title: Gamergate brain - d120 - rep2

description:
submitter supplied internal reference id:  151203.HKKH7BGXX.b1207.R2.gz
transition.gamergate.d120.b2
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz


title: Transition worker brain - d120 - rep4

description:
submitter supplied internal reference id:  160202.H2NVVBGXY.H048.gz
transition.worker.d120.b4
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz


title: Gamergate brain - d120 - rep7

description:
submitter supplied internal reference id:  160202.H2NVVBGXY.b1107.gz
transition.gamergate.d120.b7
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz


title: Corazonin injection - rep10

description:
Hsal.brains.injections.d1.RPKMs.gz
Hsal.brains.injections.d1.DESeq2.gz
submitter supplied internal reference id: 170511.H7FMMBGX2.b0610.R1.gz

data_processing:
Reads were aligned to Hsal v3.0 & OGS3.5 with STAR (version 2.5.0b)
Counts were assigned to gene models in Hsal OGS3.8 using the R package DEG-seq
RPKMs were calculated by only considering reads assigned to protein-coding genes
Differential expression was determined with the R package DESeq2 including all sequenced samples in the experiment for variance stabilization
Genome_build: Hsal v3.0
Supplementary_files_format_and_content: Table of raw RNA-seq counts and normalized RPKM values for all genes models in OGS3.8
Supplementary_files_format_and_content: Output table from DESeq2 including maximum a posteriori log-fold-change, raw P-values, and adjusted P-values

treatment_protocol: On the 6th day of transition, ants that had been dueling for three consecutive days were transferred to a new nest in groups of 6. Three were injected with synthetic corazonin and three with a controlled scrambled peptide. Each ant was injected with a calibrated glass capillary needle directly into the head, right behind the antennas, or into the gaster with 100 ng of peptide dissolved in 0.5 ml of ant saline.

value: corazonin


title: Transition worker brain - d120 - rep1

description:
submitter supplied internal reference id:  151203.HKKH7BGXX.ND01.R2.gz
transition.worker.d120.b1
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz


title: Control injection - rep9

description:
Hsal.brains.injections.d1.RPKMs.gz
Hsal.brains.injections.d1.DESeq2.gz
submitter supplied internal reference id: 170511.H7FMMBGX2.b0307.R1.gz

value: control


title: Control injection - rep8

description:
Hsal.brains.injections.d1.RPKMs.gz
Hsal.brains.injections.d1.DESeq2.gz
submitter supplied internal reference id: 170511.H7FMMBGX2.b0206.R1.gz


title: Corazonin injection - rep8

description:
Hsal.brains.injections.d1.RPKMs.gz
Hsal.brains.injections.d1.DESeq2.gz
submitter supplied internal reference id: 170511.H7FMMBGX2.H195.R1.gz


title: Corazonin injection - rep4

description:
Hsal.brains.injections.d1.RPKMs.gz
Hsal.brains.injections.d1.DESeq2.gz
submitter supplied internal reference id: 170106.HK2J7BGXY.H145.gz


title: Gamergate brain - d120 - rep4

description:
submitter supplied internal reference id:  160202.H2NVVBGXY.b0602.gz
transition.gamergate.d120.b4
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz


title: Gamergate brain - d120 - rep6

description:
submitter supplied internal reference id:  160202.H2NVVBGXY.b1006.gz
transition.gamergate.d120.b6
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz


title: Control injection - rep7

description:
Hsal.brains.injections.d1.RPKMs.gz
Hsal.brains.injections.d1.DESeq2.gz
submitter supplied internal reference id: 170511.H7FMMBGX2.b0105.R1.gz


title: Control injection - rep11

description:
Hsal.brains.injections.d1.RPKMs.gz
Hsal.brains.injections.d1.DESeq2.gz
submitter supplied internal reference id: 170511.H7FMMBGX2.b0509.R1.gz


title: Corazonin injection - rep9

description:
Hsal.brains.injections.d1.RPKMs.gz
Hsal.brains.injections.d1.DESeq2.gz
submitter supplied internal reference id: 170511.H7FMMBGX2.H204.R1.gz


title: Gamergate brain - d120 - rep3

description:
submitter supplied internal reference id:  160202.H2NVVBGXY.b0501.gz
transition.gamergate.d120.b3
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz


title: Corazonin injection - rep7

description:
Hsal.brains.injections.d1.RPKMs.gz
Hsal.brains.injections.d1.DESeq2.gz
submitter supplied internal reference id: 170511.H7FMMBGX2.H186.R1.gz


title: Corazonin injection - rep11

description:
Hsal.brains.injections.d1.RPKMs.gz
Hsal.brains.injections.d1.DESeq2.gz
submitter supplied internal reference id: 170511.H7FMMBGX2.b0711.R1.gz


title: Corazonin injection - rep12

description:
Hsal.brains.injections.d1.RPKMs.gz
Hsal.brains.injections.d1.DESeq2.gz
submitter supplied internal reference id: 170511.H7FMMBGX2.b0812.R1.gz


title: Control injection - rep4

description:
Hsal.brains.injections.d1.RPKMs.gz
Hsal.brains.injections.d1.DESeq2.gz
submitter supplied internal reference id: 170106.HK2J7BGXY.H154.gz


title: Stable worker brain - d120 - rep10 - tech1

description:
Hsal.brains.transition.d120.RPKMs.gz
submitter supplied internal reference id: 170412.H7NVFBGX2.H104.R2.gz
170807_1_GB_sample27

data_processing:
reads were aligned to Hsal v3.0 & OGS3.5 with STAR (version 2.5.0b)
counts were assigned to gene models in Hsal OGS3.8 using the R package DEG-seq
RPKMs were calculated by only considering reads assigned to protein-coding genes
Differential expression was determined with the R package DESeq2 using variance stabilization models that included samples sequenced in parallel but not described in the study.
Genome_build: Hsal v3.0
Supplementary_files_format_and_content: Table of normalized RPKM values for all genes models in OGS3.8
Supplementary_files_format_and_content: Output table from DESeq2 including maximum a posteriori log-fold-change, raw P-values, and adjusted P-values


title: Stable worker brain - d120 - rep9 - tech2

description:
Hsal.brains.transition.d120.RPKMs.gz
submitter supplied internal reference id: 170421.H7FMFBGX2.H093.gz
170807_1_GB_sample26


title: Stable worker brain - d120 - rep8 - tech1

description:
Hsal.brains.transition.d120.RPKMs.gz
submitter supplied internal reference id: 170412.H7NVFBGX2.H082.R2.gz
170807_1_GB_sample23


title: Control injection - rep6

description:
Hsal.brains.injections.d1.RPKMs.gz
Hsal.brains.injections.d1.DESeq2.gz
submitter supplied internal reference id: 170106.HK2J7BGXY.H172.gz


title: Gamergate brain - d120 - rep1

description:
submitter supplied internal reference id: 151203.HKKH7BGXX.b1108.R2.gz
transition.gamergate.d120.b1
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz


title: Corazonin injection - rep6

description:
Hsal.brains.injections.d1.RPKMs.gz
Hsal.brains.injections.d1.DESeq2.gz
submitter supplied internal reference id: 170106.HK2J7BGXY.H190.gz


title: Corazonin injection - rep5

description:
Hsal.brains.injections.d1.RPKMs.gz
Hsal.brains.injections.d1.DESeq2.gz
submitter supplied internal reference id: 170106.HK2J7BGXY.H181.gz


title: Stable worker brain - d120 - rep8 - tech2

description:
Hsal.brains.transition.d120.RPKMs.gz
submitter supplied internal reference id: 170421.H7FMFBGX2.H082.gz
170807_1_GB_sample24


title: Stable worker brain - d120 - rep10 - tech2

description:
Hsal.brains.transition.d120.RPKMs.gz
submitter supplied internal reference id: 170421.H7FMFBGX2.H104.gz
170807_1_GB_sample28


title: Stable worker brain - d120 - rep7 - tech2

description:
Hsal.brains.transition.d120.RPKMs.gz
submitter supplied internal reference id: 170421.H7FMFBGX2.H071.gz
170807_1_GB_sample22


title: Control injection - rep5

description:
Hsal.brains.injections.d1.RPKMs.gz
Hsal.brains.injections.d1.DESeq2.gz
submitter supplied internal reference id: 170106.HK2J7BGXY.H163.gz


title: Control injection - rep10

description:
Hsal.brains.injections.d1.RPKMs.gz
Hsal.brains.injections.d1.DESeq2.gz
submitter supplied internal reference id: 170511.H7FMMBGX2.b0408.R1.gz


title: Stable worker brain - d120 - rep7 - tech1

description:
Hsal.brains.transition.d120.RPKMs.gz
submitter supplied internal reference id: 170412.H7NVFBGX2.H071.R2.gz
170807_1_GB_sample21


title: Transition worker brain - d120 - rep11 - tech2

description:
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz
submitter supplied internal reference id: 170421.H7FMFBGX2.H205.gz
170807_1_GB_sample18


title: Transition worker brain - d120 - rep11 - tech1

description:
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz
submitter supplied internal reference id: 170412.H7NVFBGX2.H205.R2.gz
170807_1_GB_sample17


title: Transition worker brain - d120 - rep10 - tech2

description:
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz
submitter supplied internal reference id: 170421.H7FMFBGX2.H198.gz
170807_1_GB_sample16


title: Transition worker brain - d120 - rep10 - tech1

description:
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz
submitter supplied internal reference id: 170412.H7NVFBGX2.H198.R2.gz
170807_1_GB_sample15


title: Transition worker brain - d120 - rep9 - tech2

description:
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz
submitter supplied internal reference id: 170421.H7FMFBGX2.H191.gz
170807_1_GB_sample14


title: Transition worker brain - d120 - rep8 - tech2

description:
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz
submitter supplied internal reference id: 170421.H7FMFBGX2.H184.gz
170807_1_GB_sample12


title: Transition worker brain - d120 - rep9 - tech1

description:
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz
submitter supplied internal reference id: 170412.H7NVFBGX2.H191.R2.gz
170807_1_GB_sample13


title: Stable worker brain - d120 - rep9 - tech1

description:
Hsal.brains.transition.d120.RPKMs.gz
submitter supplied internal reference id: 170412.H7NVFBGX2.H093.R2.gz
170807_1_GB_sample25


title: Gamergate brain - d120 - rep12 - tech2

description:
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz
submitter supplied internal reference id: 170421.H7FMFBGX2.H115.gz
170807_1_GB_sample10


title: Gamergate brain - d120 - rep12 - tech1

description:
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz
submitter supplied internal reference id: 170412.H7NVFBGX2.H115.R2.gz
170807_1_GB_sample9


title: Transition worker brain - d120 - rep8 - tech1

description:
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz
submitter supplied internal reference id: 170412.H7NVFBGX2.H184.R2.gz
170807_1_GB_sample11


title: Gamergate brain - d120 - rep11 - tech2

description:
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz
submitter supplied internal reference id: 170421.H7FMFBGX2.b0401.gz
170807_1_GB_sample8


title: Gamergate brain - d120 - rep11 - tech1

description:
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz
submitter supplied internal reference id: 170412.H7NVFBGX2.b0401.R2.gz
170807_1_GB_sample7


title: Gamergate brain - d120 - rep10 - tech2

description:
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz
submitter supplied internal reference id: 170421.H7FMFBGX2.b0302.gz
170807_1_GB_sample6


title: Gamergate brain - d120 - rep10 - tech1

description:
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz
submitter supplied internal reference id: 170412.H7NVFBGX2.b0302.R2.gz
170807_1_GB_sample5


title: Gamergate brain - d120 - rep9 - tech2

description:
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz
submitter supplied internal reference id: 170421.H7FMFBGX2.b0203.gz
170807_1_GB_sample4


title: Gamergate brain - d120 - rep8 - tech2

description:
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz
submitter supplied internal reference id: 170421.H7FMFBGX2.b0104.gz
170807_1_GB_sample2


title: Gamergate brain - d120 - rep9 - tech1

description:
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz
submitter supplied internal reference id: 170412.H7NVFBGX2.b0203.R2.gz
170807_1_GB_sample3


title: Gamergate brain - d120 - rep8 - tech1

description:
Hsal.brains.transition.d120.RPKMs.gz
Hsal.brains.transition.d120.DESeq2.gz
submitter supplied internal reference id: 170412.H7NVFBGX2.b0104.R2.gz
170807_1_GB_sample1


title: Stable worker brain - d120 - rep6 - tech2

description:
Hsal.brains.transition.d120.RPKMs.gz
submitter supplied internal reference id: 170421.H7FMFBGX2.H060.gz
170807_1_GB_sample20


title: GFP KD control - rep8 (t1)

description:
submitter provided internal reference: 170412.H7NVFBGX2.H100.R2.gz
170519_GB_sample33
KD.GFP.b8 technical replicate 1

data_processing:
Reads were aligned to Hsal v3.0 & OGS3.5 with STAR (version 2.5.0b)
Counts were assigned to gene models in Hsal OGS3.8 using the R package DEG-seq
After verifying co-clustering, technical replicates were collapsed by summing their counts
RPKMs were calculated by only considering reads assigned to protein-coding genes
Differential expression was determined with the R package DESeq2 including all sequenced samples in the experiment for variance stabilization
Assembly and annotation were described in Bonasio et al. Science 2010 (PMID: 20798317) and Bonasio et al. Current Biol 2012 (PMID: 22885060). Assembly and annotations can be downloaded from the Hymenoptera Genome Database, using the following links.
Genome_build: http://hymenopteragenome.org/harpegnathos/?q=genome_consortium_datasets
Genome_build: Hsal v3.0
Supplementary_files_format_and_content: [Hsal.CrzR.KD.RPKMs.txt] Table of raw RNA-seq counts and normalized RPKM values for all genes models in OGS3.8 after collapsing the technical replicates (submitter provided internal id: BA85)
Supplementary_files_format_and_content: [Hsal.CrzR.KD.DESeq2.txt] Output table from DESeq2 including log-fold-change, raw P-values, and adjusted P-values (submitter provided internal id: BA85)

extract_protocol:
Brains (minus optic lobes) were dissected and RNA extracted with TRIzol. DNA was removed using Turbo DNAse. Each brain was used to construct a separate library (biological replicate).
RNA was fragmented by boiling in presence of divalent cations. RT was performed with random hexamers and dUTP was incorporated in the 2nd strand to retain strand information.
Strand-specific RNA-seq (dUTP)

treatment_protocol: On the 6th day of transition, ants that had been dueling for three consecutive days were transferred to a new nest in groups of 6. Three were injected with siRNAs targeting the corazonin receptor and three with a controlled siRNA targeting GFP. Each ant was injected with a calibrated glass capillary needle directly into the head, right behind the antennas with 0.5 µl of 5 µM Dicer-substrate siRNAs complexed with in vivo-jetPEI reagent.

value: GFP KD (Ctrl)

tag: tissue

value: brain (minus optic lobes)


title: Stable worker brain - d120 - rep6 - tech1

description:
Hsal.brains.transition.d120.RPKMs.gz
submitter supplied internal reference id: 170412.H7NVFBGX2.H060.R2.gz
170807_1_GB_sample19


title: GFP KD control - rep7 (t1)

description:
submitter provided internal reference: 170412.H7NVFBGX2.H089.R2.gz
170519_GB_sample31
KD.GFP.b7 technical replicate 1


title: GFP KD control - rep9 (t2)

description:
submitter provided internal reference: 170419.H7FMNBGX2.H111.gz
170519_GB_sample36
KD.GFP.b9 technical replicate 2


title: GFP KD control - rep5 (t1)

description:
submitter provided internal reference: 170412.H7NVFBGX2.H034.R2.gz
170519_GB_sample27
KD.GFP.b5 technical replicate 1


title: GFP KD control - rep7 (t2)

description:
submitter provided internal reference: 170419.H7FMNBGX2.H089.gz
170519_GB_sample32
KD.GFP.b7 technical replicate 2


title: GFP KD control - rep4 (t1)

description:
submitter provided internal reference: 170412.H7NVFBGX2.H023.R2.gz
170519_GB_sample25
KD.GFP.b4 technical replicate 1


title: GFP KD control - rep3 (t2)

description:
submitter provided internal reference: 170419.H7FMNBGX2.H187.gz
170519_GB_sample24
KD.GFP.b3 technical replicate 2


title: GFP KD control - rep6 (t1)

description:
submitter provided internal reference: 170412.H7NVFBGX2.H045.R2.gz
170519_GB_sample29
KD.GFP.b6 technical replicate 1


title: GFP KD control - rep9 (t1)

description:
submitter provided internal reference: 170412.H7NVFBGX2.H111.R2.gz
170519_GB_sample35
KD.GFP.b9 technical replicate 1


title: GFP KD control - rep2 (t1)

description:
submitter provided internal reference: 170412.H7NVFBGX2.H180.R2.gz
170519_GB_sample21
KD.GFP.b2 technical replicate 1


title: GFP KD control - rep3 (t1)

description:
submitter provided internal reference: 170412.H7NVFBGX2.H187.R2.gz
170519_GB_sample23
KD.GFP.b3 technical replicate 1


title: GFP KD control - rep1 (t1)

description:
submitter provided internal reference: 170412.H7NVFBGX2.H173.R2.gz
170519_GB_sample19
KD.GFP.b1 technical replicate 1


title: GFP KD control - rep8 (t2)

description:
submitter provided internal reference: 170419.H7FMNBGX2.H100.gz
170519_GB_sample34
KD.GFP.b8 technical replicate 2


title: GFP KD control - rep6 (t2)

description:
submitter provided internal reference: 170419.H7FMNBGX2.H045.gz
170519_GB_sample30
KD.GFP.b6 technical replicate 2


title: GFP KD control - rep4 (t2)

description:
submitter provided internal reference: 170419.H7FMNBGX2.H023.gz
170519_GB_sample26
KD.GFP.b4 technical replicate 2


title: GFP KD control - rep5 (t2)

description:
submitter provided internal reference: 170419.H7FMNBGX2.H034.gz
170519_GB_sample28
KD.GFP.b5 technical replicate 2


title: Corazonin receptor KD - rep6 (t1)

description:
submitter provided internal reference: 170412.H7NVFBGX2.H012.R2.gz
170519_GB_sample11
KD.CrzR.b6 technical replicate 1

value: CrzR KD


title: Corazonin receptor KD - rep9 (t1)

description:
submitter provided internal reference: 170412.H7NVFBGX2.H078.R2.gz
170519_GB_sample17
KD.CrzR.b9 technical replicate 1


title: Corazonin receptor KD - rep8 (t2)

description:
submitter provided internal reference: 170419.H7FMNBGX2.H067.gz
170519_GB_sample16
KD.CrzR.b8 technical replicate 2


title: Corazonin receptor KD - rep7 (t1)

description:
submitter provided internal reference: 170412.H7NVFBGX2.H056.R2.gz
170519_GB_sample13
KD.CrzR.b7 technical replicate 1


title: Corazonin receptor KD - rep5 (t1)

description:
submitter provided internal reference: 170412.H7NVFBGX2.H201.R2.gz
170519_GB_sample9
KD.CrzR.b5 technical replicate 1


title: Corazonin receptor KD - rep5 (t2)

description:
submitter provided internal reference: 170419.H7FMNBGX2.H201.gz
170519_GB_sample10
KD.CrzR.b5 technical replicate 2


title: GFP KD control - rep1 (t2)

description:
submitter provided internal reference: 170419.H7FMNBGX2.H173.gz
170519_GB_sample20
KD.GFP.b1 technical replicate 2


title: Corazonin receptor KD - rep7 (t2)

description:
submitter provided internal reference: 170419.H7FMNBGX2.H056.gz
170519_GB_sample14
KD.CrzR.b7 technical replicate 2


title: Corazonin receptor KD - rep4 (t1)

description:
submitter provided internal reference: 170412.H7NVFBGX2.H194.R2.gz
170519_GB_sample7
KD.CrzR.b4 technical replicate 1


title: Corazonin receptor KD - rep3 (t2)

description:
submitter provided internal reference: 170419.H7FMNBGX2.H166.gz
170519_GB_sample6
KD.CrzR.b3 technical replicate 2


title: Corazonin receptor KD - rep9 (t2)

description:
submitter provided internal reference: 170419.H7FMNBGX2.H078.gz
170519_GB_sample18
KD.CrzR.b9 technical replicate 2


title: GFP KD control - rep2 (t2)

description:
submitter provided internal reference: 170419.H7FMNBGX2.H180.gz
170519_GB_sample22
KD.GFP.b2 technical replicate 2


title: Corazonin receptor KD - rep4 (t2)

description:
submitter provided internal reference: 170419.H7FMNBGX2.H194.gz
170519_GB_sample8
KD.CrzR.b4 technical replicate 2


title: Corazonin receptor KD - rep6 (t2)

description:
submitter provided internal reference: 170419.H7FMNBGX2.H012.gz
170519_GB_sample12
KD.CrzR.b6 technical replicate 2


title: Corazonin receptor KD - rep2 (t2)

description:
submitter provided internal reference: 170419.H7FMNBGX2.H159.gz
170519_GB_sample4
KD.CrzR.b2 technical replicate 2


title: Corazonin receptor KD - rep3 (t1)

description:
submitter provided internal reference: 170412.H7NVFBGX2.H166.R2.gz
170519_GB_sample5
KD.CrzR.b3 technical replicate 1


title: Corazonin receptor KD - rep1 (t2)

description:
submitter provided internal reference: 170419.H7FMNBGX2.H152.gz
170519_GB_sample2
KD.CrzR.b1 technical replicate 2


title: Corazonin receptor KD - rep1 (t1)

description:
submitter provided internal reference: 170412.H7NVFBGX2.H152.R2.gz
170519_GB_sample1
KD.CrzR.b1 technical replicate 1


title: Corazonin injection - rep3

description:
corazonin.injection.d1.b3
submitter provided internal id: raw_data/FASTQ/2015/151203_NS500234_0155_AHKKH7BGXX/151203.HKKH7BGXX.ND28.R2.gz

data_processing:
Reads were aligned to Hsal v3.0 & OGS3.5 with STAR (version 2.5.0b)
Counts were assigned to gene models in Hsal OGS3.8 using the R package DEG-seq
RPKMs were calculated by only considering reads assigned to protein-coding genes
Differential expression was determined with the R package DESeq2 including all sequenced samples in the experiment for variance stabilization
Assembly and annotation were described in Bonasio et al. Science 2010 (PMID: 20798317) and Bonasio et al. Current Biol 2012 (PMID: 22885060). Assembly and annotations can be downloaded from the Hymenoptera Genome Database, using the following links.
Genome_build: http://hymenopteragenome.org/harpegnathos/?q=genome_consortium_datasets
Genome_build: Hsal v3.0
Supplementary_files_format_and_content: Table of raw RNA-seq counts and normalized RPKM values for all genes models in OGS3.8
Supplementary_files_format_and_content: Output table from DESeq2 including maximum a posteriori log-fold-change, raw P-values, and adjusted P-values


title: Corazonin receptor KD - rep8 (t1)

description:
submitter provided internal reference: 170412.H7NVFBGX2.H067.R2.gz
170519_GB_sample15
KD.CrzR.b8 technical replicate 1


title: Control injection - rep3

description:
control.injection.d1.b3
submitter provided internal id: raw_data/FASTQ/2015/151203_NS500234_0155_AHKKH7BGXX/151203.HKKH7BGXX.ND19.R2.gz


title: Corazonin injection - rep2

description:
corazonin.injection.d1.b2
submitter provided internal id: raw_data/FASTQ/2015/151031_NS500234_0147_AHFG7YBGXX/151031.HFG7YBGXX.H022.R2.gz


title: Corazonin injection - rep1

description:
corazonin.injection.d1.b1
submitter provided internal id: raw_data/FASTQ/2015/151031_NS500234_0147_AHFG7YBGXX/151031.HFG7YBGXX.H009.R2.gz


title: Control injection - rep1

description:
control.injection.d1.b1
submitter provided internal id: raw_data/FASTQ/2015/151031_NS500234_0147_AHFG7YBGXX/151031.HFG7YBGXX.ND55.R2.gz


title: Corazonin receptor KD - rep2 (t1)

description:
submitter provided internal reference: 170412.H7NVFBGX2.H159.R2.gz
170519_GB_sample3
KD.CrzR.b2 technical replicate 1


title: Stable worker brain - d120 - rep5

description:
submitter supplied internal reference id: 160202.H2NVVBGXY.H022.gz
stable.worker.d120.b5
Hsal.brains.transition.d120.RPKMs.gz


title: Stable worker brain - d120 - rep4

description:
submitter supplied internal reference id: 160202.H2NVVBGXY.H009.gz
stable.worker.d120.b4
Hsal.brains.transition.d120.RPKMs.gz


title: BPC+ZnF KD-bioRep 3

status: Public on Jul 31 2017

data_processing:
reads were aligned to the genome using bowtie2
reads were extended to 200 bp using bedtools
coverage was calculated using bedtools
coverage was normalized to 10 million reads mapped per million reads sequenced (10RPM) using a custom script
mean coverage from replicates was calculated using wiggleTools
in some tracks (input-corrected) mean input noise was subtracted from the mean ChIP signal using wiggleTool (diff command)
Genome_build: TAIR10 release 31 (ftp://ftp.ensemblgenomes.org/pub/plants/release-31/fasta/arabidopsis_thaliana/dna/)
Supplementary_files_format_and_content: bigwig normalized to 10RPKM for single replicates
Supplementary_files_format_and_content: bigwig normalized to 10RPKM for the mean of three replicates for each sample
Supplementary_files_format_and_content: bigwig normalized to 10RPKM for the mean of three replicates for each sample after subtracting the relevant background sample
Supplementary_files_format_and_content: bed file (narrowPeak format) containing peaks called by MACS v2.1.0.20151222 filtered by Q-value < 1e-10

source_name: 30 hr old plants

growth_protocol: Plants were grown in long day (16 hr light/ 8 hr dark, light intensity: ~110 μMol/m2s1) on standard growth plates (1/2 Murashige and Skoog (MS) medium)

extract_protocol:
ChIP assay was performed according to Yamaguchi et al., 2014. N. Yamaguchi et al., PROTOCOLS: Chromatin Immunoprecipitation from Arabidopsis Tissues. Arabidopsis Book 12, e0170 (2014).
DNA libraries were generated using the ThruPLEX DNA-seq kit (RUBICON GENOMICS, cat. R400406),and quantification by the NEBNext Library Quant Kit (cat. E7630L) , equal amounts of DNA were pooled from each library with different dual indexing primers and sequenced

value: Ws

tag: transgene

value: pRNAi-BPC; pRNAi-ZnF

tag: ip antibody

value: anti-FIE

tag: antibody source

value: Wood et al. 2006

tag: antibody lot


title: Input chromatin from Ws - bioRep 2

value: No transgene


title: Input chromatin from Ws - bioRep 3


title: Input chromatin from Ws - bioRep 1


title: WT-FIE - bioRep 3


title: WT-FIE - bioRep 2


title: BPC+ZnF KD-bioRep 1


title: Hnf1b_chIP-seq

status: Public on Aug 01 2017

city: Nijmegen

first: Andreas

last: Kompatscher

state: Gelderland

address: Geert Grooteplein Zuid 30

department: Physiology

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences

description: Sample 1

data_processing:
Base calling was performed with CASAVA version 1.4
burrows-wheeler transformation, 0.710 -r789 , default
Peak calling was executed with Macs2, q-value (False discovery rate, FDR) 0.001
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files were generated using a custom bam to bigwig script

growth_protocol: mpkDCT cells were cultured on 14 cm petri-dishes. Convulent plates (15 x10^6 cells) were used for chromatin isolation. Cells were cultured in DMEM/HAMF12 medium supplemented with 2% FCS, glutamine, insulin, dexamethasone, selenium, transferrin, Triiodothyronine, HEPES pH 7.5, D-Glucose, EGF.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: strain background

tag: cell line

tag: cell type

value: immortalized mouse DCT cells

tag: passages

value: rabbit anti-Hnf1β  (Santa Cruz, H-85, SC-22840)


title: WT-FIE - bioRep 1


title: BPC1 ChIP from Col - bioRep 2

description:
Col.BPC1.merge.bw
Col.BPC1.minus.input.bw

data_processing:
reads were aligned to the genome using bowtie2
reads were extended to 200 bp using bedtools
coverage was calculated using bedtools
coverage was normalized to 10 million reads mapped per million reads sequenced (10RPM) using a custom script
mean coverage from replicates was calculated using wiggleTools
in some tracks (input-corrected) mean input noise was subtracted from the mean ChIP signal using wiggleTool (diff command)
Genome_build: TAIR10 release 31 (ftp://ftp.ensemblgenomes.org/pub/plants/release-31/fasta/arabidopsis_thaliana/dna/)
Supplementary_files_format_and_content: bigwig normalized to 10RPKM for single replicates
Supplementary_files_format_and_content: bigwig normalized to 10RPKM for the mean of three replicates for each sample
Supplementary_files_format_and_content: bigwig normalized to 10RPKM for the mean of three replicates for each sample after subtracting the relevant background sample
Supplementary_files_format_and_content: peaks were called using MACS version 2.1.1.20160309 using default parameters for AZF, BPC, and FIE, and the broad peaks option for H3K27me3; peak lists were filtered for Q-value < 1e-10

source_name: 30 hrs old plants

extract_protocol:
ChIP assay is performed according to Yamaguchi et al., 2014. N. Yamaguchi et al., PROTOCOLS: Chromatin Immunoprecipitation from Arabidopsis Tissues. Arabidopsis Book 12, e0170 (2014).
DNA was end repaired, A-tailed, and ligated to universal PE adapters using reagents from enzymatics. Libraries were amplified using custom-designed dual-indexed oligos.

tag: ecotype

value: Col

value: gBPC1-Myc in Col

value: anti-Myc

value: Sigma


title: BPC1 ChIP from Col - bioRep 1


title: AZF1 ChIP from Col - bioRep 3

description:
Col.AZF1.merge.bw
Col.AZF1.minus.input.bw

value: gAZF1-Myc in Col


title: Input chromatin from Col - bioRep 2

description: Col.input.merge.bw


title: AZF1 ChIP from Col - bioRep 2


title: AZF1 ChIP from Col - bioRep 1


title: Input chromatin from Col - bioRep 3

description: Col.input.merge.bw


title: FIE ChIP from C24 - bioRep 3

description:
C24.FIE.merge.bw
C24.FIE.minus.input.bw

value: pFIE:FIE-HA in fie-11

value: anti-HA

value: Roche


title: FIE ChIP from C24 - bioRep 1

description:
C24.FIE.merge.bw
C24.FIE.minus.input.bw


title: Input chromatin from Col - bioRep 1

description: Col.input.merge.bw


title: Input chromatin from C24 - bioRep 2


title: FIE ChIP from C24 - bioRep 2

description:
C24.FIE.merge.bw
C24.FIE.minus.input.bw


title: Input chromatin from C24 - bioRep 3


title: H3K27me3 ChIP from Col - bioRep 3

description:
Col.H3K27me3.merge.bw
Col.H3K27.minus.H3.bw

value: Millipore


title: H3K27me3 ChIP from Col - bioRep 1


title: BPC+ZnF KD-bioRep 2


title: H3K27me3 ChIP from Col - bioRep 2


title: Input chromatin from C24 - bioRep 1


title: Histone H3 ChIP from Col - bioRep 3


title: BPC1 ChIP from Col - bioRep 3


title: Histone H3 ChIP from Col - bioRep 2


title: Histone H3 ChIP from Col - bioRep 1


title: RHa10_T2

status: Public on Feb 28 2017

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina Casava1.8.2 software used for basecalling and demultiplexing.
Reads were mapped to Macaca_mulatta UNMC_v7.6 genome assembly with the STAR (v2.3.0e) aligner args: --outFileterMultimapNmax 1 --outFilterType BySJout --outSJfilterReads Unique --sjdbGTFfile UNMC_rhesus_annotation_v7.6 --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Per sample annotated transcript models were quantitated with Cufflinks (v2.1.1) args: -G UNMC_rhesus_annotation_v7.6.gtf
Sample transcript models were merged with Cuffmerge (v2.1.1)
FPKM (Fragments per kilobase of exon per million reads mapped) abundance estimates and differential expression was caluclated with Cuffdiff (v2.1.1)
Genome_build: UNMC_v7.6 is a presubmission version of the MacaM GCA_000772875.1 assembly. (MaSuRCA_Rhesus_Genome_v7_20130927.fasta, UNMC_rhesus_annotation_v7.6.gtf)
Supplementary_files_format_and_content: tab delimited text file containing FPKM for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
Total RNA was prepared using the QIAGEN RNEasy Micro Kit.
Libraries were generated using the CLONTECH SMARTer HV kit, barcoding and sequencing primers were added using NexteraXT DNA kit.  Libraries were validated by microelectrophoresis, quantified, pooled and clustered on Illumina TruSeq v3 flowcell.  Clustered flowcell was sequenced on an Illumina HiSeq 1000 in 100-base single-read reactions.

tag: subjectid

tag: treatment

tag: processinggroup

tag: processday

tag: time point


title: RPy8_T2

value: Control


title: RPu12_T2


title: RKd12_T2


title: RKg11_T2


title: RTb12_T2


title: RJp11_T2


title: RGe12_T2


title: RJw12_T2


title: RBt12_T2


title: RLm12_T2


title: RVt10_T2


title: RGv10_T2


title: ROe12_T2


title: RHa10_T1


title: RPu12_T1


title: RPy8_T1


title: RKd12_T1


title: RCb12_T2


title: RTb12_T1


title: RJw12_T1


title: RVt10_T1


title: RCb12_T1


title: ROc10_T1


title: RJp11_T1


title: RBt12_T1


title: RGv10_T1


title: RGe12_T1


title: ROe12_T1


title: RPy8_Pre-ART

value: Pre-ART


title: RHa10_Pre-ART


title: ROc10_Pre-ART


title: RTb12_Pre-ART


title: RKg11_Pre-ART


title: RVt10_Pre-ART


title: RKg11_T1


title: RPu12_Pre-ART


title: RGe12_Pre-ART


title: RCb12_Pre-ART


title: RJp11_Pre-ART


title: ROe12_Pre-ART


title: RGv10_Pre-ART


title: RLm12_Pre-ART


title: RBt12_Pre-ART


title: SeaUrchin_48hpf (18)

status: Public on May 18 2015

city: Seville

first: Carlos

last: Gómez

state: Seville

address: Crta Utrera  km 1

country: Spain

institute: Centro Andaluz de Biologia del Desarrollo

data_processing:
library strategy: 4C-Seq
Demultiplexing: different samples were demultiplexed using the primer sequences
Mapping: reads were mapped to the Mus musculus (mm9 assembly) , Danio rerio (danRer7 assembly) or S.purpuratus (StrPur4 assembly) genomes using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept. Reads located in fragments flanked by two restriction sites of the same enzyme, or in fragments smaller than 40 bp were filtered out
Mapped reads were then converted to reads-per-first-enzyme-fragment-end units, and smoothed using a 30 DpnII fragments mean running window algorithm.
Data visualization: data were uploaded to UCSC Browser for visualization.
Genome_build: mm9/danRer7/StrPur4
Supplementary_files_format_and_content: bedGraph, they contain smoothed data of 4Cseq of  viewpoint that can be directly uploaded to UCSC for visualization.

organism: Strongylocentrotus purpuratus

source_name: 48hpf sea urchins embryos

growth_protocol: Embryos were raised at 12ºC untill they reached the desired developmental stage. They were cellularised before fixation.

extract_protocol:
Chromatin was extracted from single cells preparations from different samples. DNA was digested with DpnII and ligated. Then sample was de-crosslinked, digested with Csp6I and ligated again.
Primers with Illumina adaptors were used to amplify the library. Different samples were multiplexed for sequencing.

tag: developmental stage

value: whole embryos


title: RLm12_T1


title: RKd12_Pre-ART


title: 293Trex_NFH-SNRNP70.input

status: Public on Oct 24 2014

data_processing:
reads were trimmed to 36 nts
mapped to hg19 with BOWTIE -m40 -v2
reads were assigned to gene model in ENSEMBL v65 using the R package DEG-seq
Genome_build: hg19
Supplementary_files_format_and_content: table of raw RNA-seq counts and normalized RPKM values for all genes models in ENSEMBL v65

growth_protocol: 293T-REx were grown in DMEM containing 10% fetal bovine serum, 1% penicillin 1% streptomycin, and 1% streptomycin

extract_protocol:
After photolabeling, RNA was isolated with TRIzol (Invitrogen, CA) and biotinylated species were precipitated with MyOne Streptavidin C1 dynabeads (Invitrogen, CA) in RIP buffer (10 mM Tris, 200 mM KCl, 10 mM EDTA, 0.05% IGEPAL-630) with 3 washes in RIP-W buffer (10 mM Tris, 200 mM KCl, 0.1 mM EDTA, 0.05% IGEPAL-630, 1 mM MgCl2).
RNA was fragmented by boiling in presence of divalent cations. RT was performed with random hexamers and dUTP was incorporated in the 2nd strand to retain strand information. Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with LigaFast (Promega, city, state #M8225). Fragments of 300±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530) after treatment with UDG to remove the second strand.

treatment_protocol: 293T-REx cell lines were induced to express transgenes by treatment with 1 µg/ml doxycycline for 24 hours. Photo-activatable compounds were added to fresh complete medium at a concentration of 10 µM when not specified otherwise. Cells were incubated with full medium containing photo-activatable compounds for 2 hours at 37°C. After incubation, cells were washed once in ice-cold PBS, and left in a small volume of PBS for irradiation. Photolabeling was induced with 500 mJ/cm2 UVA (365 nm) in a Stratalinker irradiator (Stratagene, CA) while cells were kept on ice.

value: input


title: 293Trex_NFH-SNRNP70.IPL

value: IPL


title: RJw12_Pre-ART


title: E14.ND.JARID2.b1

status: Public on Sep 18 2014

data_processing:
3' adapter (TTGATATAAATAGTGCCCATGGATC) trimmed with fastx_clipper collapsed with fast fastx_collapser to 25 nts
mapped to the mm9 genome using BOWTIE -v2 -m40 --best --strata
putative RNA-binding sites identified with PARalyzer software (Corcoran et al., 2011) requiring at least two T->C conversions per RCS (RNA contact site)
Genome_build: mm9
Supplementary_files_format_and_content: BED files containing all unfiltered RCSs

source_name: E14 embyonic stem cells

growth_protocol: E14 cells were grown in standard ESC conditions including 15% ESC certified serum and LIF

extract_protocol:
Whole cell extracts were obtained by incubating the cells for 10 min at 37C in an appropriate volume of CLIP buffer (20 mM HEPES pH 7.4, 5 mM EDTA, 150 mM NaCl, 2% lauryldimethylbetaine) supplemented with protease inhibitors, 20 U/ml Turbo DNase (Life technologies), and 200 U/ml murine RNase inhibitor (New England Biolabs).
immunoprecipitation and size selection protocol: After clearing the lysate by centrifugation, immunoprecipitations were carried out in the same CLIP buffer for 1 hour at 4C, after which, when required, the extracts were treated with various concentration of RNAse A + T1 cocktail (Ambion) for 5’ at 37C. Immunocomplexes were recovered by adding protein G-coupled dynabeads (Life technologies) for 45 min at 4C. Contaminating DNA was removed by treating the beads with Turbo DNase (2U in 20 μl). Crosslinked RNA was labeled by successive incubation with 5U Antarctic phosphatase (New England Biolabs) and 5U T4 PNK (New England Biolabs) in presence of 10 μCi [γ-32P] ATP (PerkinElmer, MA). Labeled material was resolved on 8% bis-tris gels, transferred to nitrocellulose membranes and exposed to autoradiography films for 1–24 hours.
100 pmol of a 3’-blocked DNA adapter were ligated to the RNA after dephosphorylation and before 5’ labeling by incubating the beads with T4 RNA ligase 1 (New England Biolabs) for 1 hour at 25C. After autoradiography, bands of interest were excised and the RNA eluted from the membrane by treating with proteinase K for 30’ at 37C and then proteinase K in presence of 3.5M urea for 30’ at 55C. Custom designed 5’ RNA adapters were ligated, the products size-selected on polyacrylamide or agarose gels.

treatment_protocol: Cells were pulsed with 500 µM 4-SU for 2h and irradiated with 400 mJ/cm2 UVB (312 nm)

value: control

value: in-house

tag: antibody lot #


title: E14.RA.1d.JARID2.b1

value: 2 µM RA, 24 hrs


title: E14.RA.1d.JARID2.b3


title: E14.RA.1d.JARID2.b2


title: E14.ND.JARID2.b2


title: E14.ND.JARID2.b3


title: SeaUrchin_48hpf (14)

tag: tissue


title: 293Trex_N3-SCML2AdRBR.HA.PA

status: Public on Jul 02 2014

data_processing:
Trimmed (3') sequences to 35 nts
Mapped to hg19 using bowtie -v2 -m40
Counts and RPKMs for lincRNAs were calculated using the R package DEGseq and the lincRNA catalog found at http://www.broadinstitute.org/genome_bio/human_lincrnas/
Counts and RPKMs for mRNAs were calculated using the R package DEGseq and ENSEMBL annotation version 70
Genome_build: hg19
Supplementary_files_format_and_content: TXT files for RPKM tables

growth_protocol: 293T-REx stable lines transfected with HA-tagged PRC1 subunits or an empty vector were grown in standard conditions (DMEM 10% FBS) and kept in selection with zeocin

extract_protocol: After polyA+ RNA isolation, libraries were prepared with the dUTP strand-specific protocol. After RT and second-strand synthesis, cDNA was end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with T4 ligase (Enzymatics). Fragments of 200±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530) after removal of the 2nd strand with heat-labile UDG (Roche).

treatment_protocol: Expression of the transgenes was induced by doxycycline treatment for 48 hours

tag: transgene

tag: antibody

value: HA (abcam ab9110)


title: 293Trex.NE400.PA


title: 293Trex_N3-SCML2AdRBR.HA.b4

data_processing:
mapped to mm9 with BOWTIE -m4 -v2 --best
1nt resolution bedgraphs were generated with the BEDtools bamToBed and genomeCoverageBed utilities after extending each read to 200
coverage was normalized to FP10M (fragments per 10 million reads sequenced)
bigWig files were generated with bedGraphToBigWig
Genome_build: mm9
Supplementary_files_format_and_content: FP10M-normalized bigWigs

growth_protocol:
293T-REx stable lines transfected with HA-tagged PRC1 subunits or an empty vector were grown in standard conditions (DMEM 10% FBS) and kept in selection with zeocin
K562 cells were grown in standard conditions (RPMI 10% FBS)

extract_protocol: Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with LigaFast (Promega, city, state #M8225). Fragments of 300±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530).

tag: epitope tag

value: Flag-HA-OneSTrEP (N-terminal)

value: HA - Abcam ab9110


title: 293Trex_N3.HA.PA

value: N3 (empty vector)


title: 293Trex_N3-SCML2AdRBR.input.b4


title: 293Trex_N3-SCML2A.BMI1.b4

value: PCGF4 - Bethyl A301-694A


title: 293Trex_MSA-SNRNP70.input


title: 293Trex_N3-SCML2A.input.b4


title: 293Trex_N3-SCML2AdRBR.SCML2.b4

value: SCML2 (in-house)


title: 293Trex_MSA-SNRNP70.IPL


title: 293Trex_N3.BMI1.b4

value: N3 (empty vector), no dox


title: 293Trex_N3-SCML2A.SCML2.b4


title: 293Trex_N3m.input.b4


title: 293Trex_N3-SCML2A.HA.PA


title: 293Trex_N3.HA.b4


title: 293Trex_N3-SCML2AdRBR.BMI1.b3


title: 293Trex_N3-SCML2AdRBR.BMI1.b4


title: 293Trex_N3.SCML2.b4


title: 293Trex_N3-SCML2AdRBR.SCML2.b3


title: 293Trex_N3-SCML2A.HA.b4


title: 293Trex_N3-SCML2AdRBR.input.b3


title: 293Trex_N3-SCML2A.SCML2.b3


title: Control injection - rep2

description:
control.injection.d1.b2
submitter provided internal id: raw_data/FASTQ/2015/151031_NS500234_0147_AHFG7YBGXX/151031.HFG7YBGXX.ND64.R2.gz


title: 293Trex_N3-SCML2A.BMI1.b3


title: 293Trex_N3.HA.b3


title: 293Trex_N3.BMI1.b3


title: 293Trex_N3-SCML2A.HA.b3


title: 293Trex_N3m.input.b3


title: K562.PMA.input.PA

data_processing:
Library strategy: RIP-Seq
Trimmed (3') sequences to 35 nts
Mapped to hg19 using bowtie -v2 -m40
Duplicates were removed with samtools rmdup
Wig coverage was calculated separately on the minus and plus strand a custom script
Wigs were normalized to 10,000,000 sequenced reads using a custom script
Counts and RPKMs for lincRNAs was calculated using the R package DEGseq and the lincRNA catalog found at http://www.broadinstitute.org/genome_bio/human_lincrnas/
Genome_build: hg19
Supplementary_files_format_and_content: Normalized WIGs and TXT file (for RPKM table).  In the wig files, the p and m in the names (e.g. 'p.wig' or 'm.wig') refer to the plus and minus strand respectively.

growth_protocol: K562 cells were grown in standard conditions (RPMI 10% FBS)

extract_protocol: Method for RNA: TRIzol. After polyA+ RNA isolation, libraries were prepared with the dUTP strand-specific protocol. After RT and second-strand synthesis, cDNA was end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with T4 ligase (Enzymatics). Fragments of 200±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530) after removal of the 2nd strand with heat-labile UDG (Roche).

treatment_protocol: K562 cells were treated for 48 hours either with 160 nM PMA or 100 uM hemin or DMSO alone as a control


title: K562.SCML2

data_processing:
Trimmed (3') sequences to 40 nts
Mapped to hg19 using bowtie -v2 -m1
Duplicates were removed with samtools rmdup
Wig coverage was calculated with IGVtools extending the reads to 200 nts
Wigs were normalized to 10,000,000 sequenced reads using a shell script
Genome_build: hg19
Supplementary_files_format_and_content: Normalized WIGs

extract_protocol: Method for DNA: isolation of nuclei, lysis and sonication, IP, cross link reversal, qiaquick PCR purification column. Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with LigaFast (Promega, city, state #M8225). Fragments of 300±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530).

treatment_protocol: Expression of the transgenes was induced by doxycycline treatment for 24 hours

value: SCML2 (in-house) batch# Rb1199-1004


title: K562.DMSO.input.PA


title: K562.hemin.SCML2.PA


title: K562.PMA.SCML2.PA


title: K562.input


title: 293Trex_N3-SCML2AdRBR.BMI1


title: K562.hemin.input.PA


title: 293Trex_N3-SCML2AdRBR.SCML2


title: 293Trex_N3-SCML2AdRBR.HA.b3


title: 293Trex_N3-SCML2A.SCML2


title: 293Trex_N3-SCML2AdRBR.HA

value: HA - Abcam ab9110 Lot#GR52735-1


title: 293Trex_N3-SCML2AdRBR.input


title: 293Trex_N3-SCML2A.input


title: 293Trex_N3.BMI1


title: 293Trex_N3.SCML2.b3


title: 293Trex_N3-SCML2A.input.b3


title: 293Trex_N3-SCML2A.HA


title: 293Trex_N3.HA


title: 293Trex_N3.SCML2


title: K562.BMI1


title: K562.DMSO.SCML2.PA


title: 293Trex_N3.input


title: UtE-iPS-7.EZH2

status: Public on Dec 25 2013

data_processing:
mapped to hg19 with BOWTIE -m4 -v2
1nt resolution bedgraphs were generated with the BEDtools bamToBed and genomeCoverageBed utilities after extending each read to 200
coverage was normalized to FP10M (fragments per 10 million reads sequenced)
bigWig files were generated with bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: FP10M-normalized bigWigs

source_name: hiPSC

growth_protocol: Human iPSCs were maintained on irradiated MEFs in 0222 medium (MED SHIROTORI CO., Ltd, Tokyo, Japan) supplemented with 10 ng/ml recombinant human basic fibroblast growth factor

extract_protocol:
Cells were lysed in ChIP buffer (50 mM Tris-HCl pH 7.9, 150 mM NaCl, 1% Triron X-100, 0.5% NP-40, 5 mM EDTA pH 8.0, 1 mM PMSF and protease inhibitor) and chromatin was sonicated to ~200 bp with a Diagenode Bioruptor
Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with LigaFast (Promega, city, state #M8225). Fragments of 300±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530).

tag: line name

tag: ip antibody

tag: antibody source

tag: antibody lot


title: UtE-iPS-6.input


title: UtE-iPS-7.H3K27me3

value: Millipore #07-449


title: UtE-iPS-6.JARID2


title: UtE-iPS-7.JARID2


title: UtE-iPS-6.H3K27me3


title: UtE-iPS-4.H3K27me3


title: UtE-iPS-6.EZH2


title: 293Trex_N3-SCML2A.BMI1

tag: cell line


title: UtE-iPS-4.JARID2


title: UtE-iPS-4.EZH2


title: UtE-iPS-11.input


title: UtE-iPS-11.JARID2


title: UtE-iPS-4.input


title: MRC5-iPS-25.input


title: UtE-iPS-11.H3K27me3


title: MRC5-iPS-25.JARID2


title: UtE-iPS-11.EZH2


title: MRC5-iPS-25.H3K27me3


title: Edom-iPS-2.JARID2.r2


title: Edom-iPS-2.JARID2.r1


title: Edom-iPS-2.input


title: UtE-iPS-7.input


title: AM-iPS-8.JARID2


title: Edom-iPS-2.H3K27me3.r1


title: AM-iPS-8.input


title: Edom-iPS-2.EZH2.r1


title: AM-iPS-6.JARID2


title: AM-iPS-6.input


title: AM-iPS-8.EZH2


title: MRC5-iPS-25.EZH2


title: AM-iPS-6.EZH2


title: MRC5-iPS-25_GFP.JARID2

treatment_protocol: cells were transduced with lentiviruses encoding either GFP or the MEG3 lncRNA

value: GFP


title: AM-iPS-6.H3K27me3


title: MRC5-iPS-25_MEG3.JARID2

value: MEG3 lncRNA


title: MRC5-iPS-25_MEG3.EZH2


title: MRC5-iPS-25_MEG3.input

value: input


title: Edom-iPS-2.H3K27me3.r2


title: MRC5-iPS-25_GFP.input


title: E14.JARID2.NT.190k.b1

description: crosslinked RNA

data_processing:
Library strategy: PAR-CLIP-Seq
3' adapter (TTGATATAAATAGTGCCCATGGATC) trimmed with fastx_clipper
mapped to the mm9 genome using BOWTIE allowing for up to two mismatches and removing optical/PCR duplicates
putative RNA-binding sites identified with PARalyzer software (Corcoran et al., 2011) requiring at least two T->C conversions per RCS
Genome_build: mm9
Supplementary_files_format_and_content: BED files containing all unfiltered RCSs

growth_protocol: E14 cells were grown in standard ESC conditions including 15% ESC certified serum

extract_protocol:
Whole cell extracts were obtained by incubating the cells for 10 min at 37C in an appropriate volume of CLIP buffer (20 mM HEPES pH 7.4, 5 mM EDTA, 150 mM NaCl, 2% lauryldimethylbetaine) supplemented with protease inhibitors, 20 U/ml Turbo DNase (Life technologies), and 200 U/ml murine RNase inhibitor (New England Biolabs).
After clearing the lysate by centrifugation, immunoprecipitations were carried out in the same CLIP buffer for 1 hour at 4C, after which, when required, the extracts were treated with various concentration of RNAse A + T1 cocktail (Ambion) for 5’ at 37C. Immunocomplexes were recovered by adding protein G-coupled dynabeads (Life technologies) for 45 min at 4C. Contaminating DNA was removed by treating the beads with Turbo DNase (2U in 20 μl). Crosslinked RNA was labeled by successive incubation with 5U Antarctic phosphatase (New England Biolabs) and 5U T4 PNK (New England Biolabs) in presence of 10 μCi [γ-32P] ATP (PerkinElmer, MA). Labeled material was resolved on 8% bis-tris gels, transferred to nitrocellulose membranes and exposed to autoradiography films for 1–24 hours.
100 pmol of a 3’-blocked DNA adapter were ligated to the RNA after dephosphorylation and before 5’ labeling by incubating the beads with T4 RNA ligase 1 (New England Biolabs) for 1 hour at 25C. After autoradiography, bands of interest were excised and the RNA eluted from the membrane by treating with proteinase K for 30’ at 37C and then proteinase K in presence of 3.5M urea for 30’ at 55C. Custom designed 5’ RNA adapters were ligated, the products size-selected on polyacrylamide or agarose gels.

treatment_protocol: cells were pulsed with either 100 µM 4-SU for 16h (JARID2 PAR-CLIP) or 500 µM 4-SU for 2h (EZH2 PAR-CLIP)

tag: cell type

value: E14 embyonic stem cells

tag: excised band size

tag: limited rnase treatment

value: no


title: MRC5-iPS-25_GFP.EZH2

value: in-house


title: E14.JARID2.NT.115k.b1

description: crosslinked RNA


title: E14.JARID2.RNAse.190k.b1

description: crosslinked RNA

value: yes


title: Edom-iPS-2.EZH2.r2


title: E14.JARID2.RNAse.115k.b1

description: crosslinked RNA


title: E14.HA-EZH2.HA.b1

status: Public on Oct 19 2013

description:
Sample name: 130725_SK_sample9
crosslinked RNA

data_processing:
Library strategy: PAR-CLIP-seq
3' adapter (TTGATATAAATAGTGCCCATGGATC) trimmed with fastx_clipper
collapsed with fast fastx_collapser
mapped to the mm9 genome using BOWTIE -v2 -m40 --best --strata
putative RNA-binding sites identified with PARalyzer software (Corcoran et al., 2011) requiring at least two T->C conversions per RCS (RNA contact site)
Genome_build: mm9
Supplementary_files_format_and_content: BED file containing all unfiltered RCSs

extract_protocol:
Whole cell extracts were obtained by incubating the cells for 10 min at 37C in an appropriate volume of CLIP buffer (20 mM HEPES pH 7.4, 5 mM EDTA, 150 mM NaCl, 2% lauryldimethylbetaine) supplemented with protease inhibitors, 20 U/ml Turbo DNase (Life technologies), and 200 U/ml murine RNase inhibitor (New England Biolabs).
[Immunoprecipitation and size selection protocol] After clearing the lysate by centrifugation, tandem affinity purification was performed, first with streptacting macropreps (3h, 4C), then elution with 2 mM biotin and finally an overnight IP with HA antibodies. The extracts were treated with various concentration of RNAse A + T1 cocktail (Ambion) for 5’ at 37C. Immunocomplexes were recovered by adding protein G-coupled dynabeads (Life technologies) for 45 min at 4C. Contaminating DNA was removed by treating the beads with Turbo DNase (2U in 20 μl). Crosslinked RNA was labeled by successive incubation with 5U Antarctic phosphatase (New England Biolabs) and 5U T4 PNK (New England Biolabs) in presence of 10 μCi [γ-32P] ATP (PerkinElmer, MA). Labeled material was resolved on 8% bis-tris gels, transferred to nitrocellulose membranes and exposed to autoradiography films for 4 hours.
100 pmol of a 3’-blocked DNA adapter were ligated to the RNA after dephosphorylation and before 5’ labeling by incubating the beads with T4 RNA ligase 1 (New England Biolabs) for 1 hour at 25C. After autoradiography, bands of interest were excised and the RNA eluted from the membrane by treating with proteinase K for 30’ at 37C and then proteinase K in presence of 3.5M urea for 30’ at 55C. Custom designed 5’ RNA adapters were ligated, the products size-selected on polyacrylamide gels.

treatment_protocol: cells were pulsed with either 100 µM 4-SU for 500 µM 4-SU for 2h (EZH2 PAR-CLIP) and irradiated with 400 mJ/cm2 of UVB (312 nm)

tag: background strain

tag: tag

value: HA

value: Abcam, cat# ab9110


title: E14.HA-EZH2.HA.b2

description:
Sample name: 130725_SK_sample10
crosslinked RNA


title: E14.HA-EZH2.HA.b3

description:
Sample name: 130725_SK_sample11
crosslinked RNA


title: E14.HA-EZH2.HA.b4

description:
Sample name: 130725_SK_sample12
crosslinked RNA


title: E14.PA.b2

description:
Sample name: 130725_SK_sample14
internal reference: e14_EZH2-dRBR.EtOH.TOT.PA.120622.gz
processed data file: E14.RPKM.ENS67.txt
strand-specific RNA-seq

data_processing:
reads were trimmed to 30 nts
mapped to mm9 with BOWTIE -m40 -v2 --best
reads were assigned to gene model in ENSEMBL v67 using the R package DEG-seq
Genome_build: mm9
Supplementary_files_format_and_content: Table of raw RNA-seq counts and normalized RPKM values for all genes models in ENSEMBL v67. The table is linked as a supplementary file on the Series record.

extract_protocol:
Cells were lysed in TRIzol and RNA extracted with standard procedures. PolyA selection was performed with two rounds of purification on oligodT(25) magnetic beads.
RNA was fragmented by boiling in presence of divalent cations. RT was performed with random hexamers and dUTP was incorporated in the 2nd strand to retain strand information. Libraries were prepared according to manufacturer's instructions (Illumina). cDNA was end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with LigaFast (Promega, #M8225). Fragments of 300±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530) after treatment with UDG to remove the second strand.

tag: clone name

tag: cellular compartment

value: whole cell


title: E14.SUZ12.b1

description:
Sample name: 130725_SK_sample7
internal reference: E14.SUZ12.b1.gz

value: Cell signaling, cat# 3737


title: E14.SUZ12.b2

description:
Sample name: 130725_SK_sample8
internal reference: E14.SUZ12.b2.gz


title: E14.PA.b1

description:
Sample name: 130725_SK_sample13
internal reference: e14_EZH2-WT.EtOH.TOT.PA.120622.gz
processed data file: E14.RPKM.ENS67.txt
strand-specific RNA-seq


title: E14.input

description:
Sample name: 130725_SK_sample6
internal reference: E14.input.gz


title: AM-iPS-8.H3K27me3


title: E14.H3K27me3.b2

description:
Sample name: 130725_SK_sample4
internal reference: E14.H3K27me3.b2.gz


title: E14.H3K27me3.b3

description:
Sample name: 130725_SK_sample5
internal reference: E14_HA-EZH2.dox.H3K27me3.gz


title: E14.EZH2.b1

description:
Sample name: 130725_SK_sample1
internal reference: E14.EZH2.120816.gz


title: E14.H3K27me3.b1

description:
Sample name: 130725_SK_sample3
internal reference: E14.H3K27me3.b1.gz


title: E14.EZH2.b2

description:
Sample name: 130725_SK_sample2
internal reference: E14_N3-EZH2.EtOH.EZH2.120816.gz