title: 150

city: Birmingham, AL

first: Peter

last: Detloff

state: AL

address: 720 20th Street South

department: Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

data_processing:
Illumina bcl2fastq version 1.8.4 software was used creating the fastq files from the bcl files.
TopHat version 2.0.11 was used to align the raw RNA-Seq fastq reads to the mouse reference genome version 10 from the UCSC genome browser gateway using the short read aligner Bowtie version 2.1.0. TopHat was also used to analyse the mapping results to identify splice junctions between exons. See (i). Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009; 25:1105-11 and (ii). Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009; 10:R25. and (iii). Trapnell C, Roberts A, Goff L, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012; 7:562-78
Cufflinks version 2.1.1 used the aligned reads from TopHat to assemble transcripts, estimate their abundances and test for differential expression and regulation. Cuffmerge, which is part of Cufflinks, merged the assembled transcripts to a reference annotation and tracked Cufflinks transcripts across multiple experiments. Finally, Cuffdiff was used to identify significant changes in transcript expression, splicing and promoter use. Genes that met certain criteria (i.e. fold change ≥ ±2.0 and q-value < 0.05) were further analyzed using the IPA tool. See (i) Trapnell C, Roberts A, Goff L, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012; 7:562-78 and (ii). Trapnell C, Williams BA, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010; 28:511-5
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file from Cufflinks Cuffnorm that include FPKM values, normalized counts and gene symbol for each sample.

extract_protocol:
Dissected striatum from mouse brain flash frozen were homogenized in Trizol reagent and RNA was prepared according to manufacturers instructions.
Total RNA was subjected to two rounds of poly A+ selection and converted to cDNA. We used TruSeq library generation kits as per the manufacturer’s instructions (Illumina, San Diego, CA, USA). Library construction consisted of random fragmentation of the polyA mRNA, followed by cDNA production using random primers. The ends of the cDNA were repaired, A-tailed and adaptors ligated for indexing (up to twelve different barcodes per lane) during the sequencing runs. The cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for library quantitation (Kapa Biosystems, Woburn, MA) prior to cluster generation. Clusters were generated to yield approximately 725K-825K clusters/mm2. Cluster density and quality was determined during the run after the first base addition parameters were assessed. We ran paired end 2X50bp sequencing runs to align the cDNA sequences to the reference genome

value: striatum

tag: background strain

value: postnatal 21 weeks


title: WT

status: Public on Feb 01 2016

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: HDQ+/+

tag: tissue

value: brain

tag: tissue compartment

tag: genotype

value: HDQ+/+

tag: age


title: GRO-seq - mES - 12hr KD, 7SK ASO rep2

city: Stanford

first: Ryan

middle: Alexander

last: Flynn

state: CA

address: 380 Roth Way, Room 265

institute: Stanford University

description:
nascent RNA
processed data file: mm9_GRO-seq_12hr7SKASO_pos.bw, mm9_GRO-seq_12hr7SKASO_neg.bw

data_processing:
Library strategy: GRO-Seq
After demultiplexing, reads were stripped adaptors, mapped to a custon index of repetitive RNAs (PMID: 25411354), mapped to the mouse (mm9) genome using Bowtie2, and processed as previously described (PMID: 24843027)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files of merged biological replicates split for positive and negative strand reads of GRO-seq read density

growth_protocol: mESCs were grown on gelatin plates with serum and LIF.

extract_protocol:
Nuclei were isolated and run-on reactions performed as described previously (PMID: 24843027).
Run-on RNA (labeled with BrU) was isolated as previously described (PMID: 24843027) and deep sequencing libraries generated.

treatment_protocol: Cells were depleted of 7SK by nucleofecting antisense oligonucleotides for either 6 or 12 hours.

tag: cell type

value: ES cells

tag: cell line

tag: gender

value: male


title: Control33M_1

city: Tuxedo

first: Dana

last: Lauterstein

state: NY

address: 57 Old Forge Rd

department: Environmental Medicine

institute: New York University

description: Filtered Air Controls

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Samples with reads spanning multiple lanes were merged.
The sequencing reads were aligned to the mouse genome (UCSC build mm9) using the Bowtie aligner.
Likely PCR duplicates were removed with Samtools tool.
HTSeq was utilized to generate counts for each gene based on how many aligned reads overlap its exons.
Counts were normalized and tested for differential expression with the DESeq2 R package.
Genome_build: mm9
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.

source_name: Brain Tissue

extract_protocol:
Offspring (~1-mo-old) were sacrificed in accordance with IACUC protcol. At the time of sacrifice, brains were sectioned, snap frozen in liquid nitrogen, and stored at -80°C until RNA was extracted from the frontal cortex samples.
A standard protocol for RNA isolation using TRIzol Reagent (Invitrogen) was used, and the RNA samples were subsequently purified using a RNeasy Mini Kit (Qiagen, Valencia, CA, USA).
RNA was quantified using a NanoDrop ND-1000 fluorospectrometer (Thermo Scientific, Waltham, MA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Frontal Cortex

tag: strain

tag: Sex

value: Male


title: 315


title: 200


title: GRO-seq - mES - 12hr KD, 7SK ASO rep1


title: FRI;FLC cotyledons, day 6

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: library strategy: GMUCT 2.0

data_processing:
Adapter sequences were trimmed from raw sequence reads. Only trimmed reads were used in further processing
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: TAIR9

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: cotyledons

growth_protocol: Plants were sown in MetroMix 360 soil (Sun Gro Horticulture, Vancouver, British Columbia, Canada) in 12-well (for the shoot apex and primordia collections) or 96-well flats (for the fully-expanded leaf collections). Flats were elevated on supports above a water reservoir, with wicks made from strips of batting extending from each pot into the reservoir to ensure a constant moisture level.  Flats were kept at 4oC for five days, and then grown at 23oC under long day conditions (16 hr light :8 hr dark) at a light intensity of 100-125 umol m-2 s-1, provided by a one-to-one ratio of T8 Sylvania Octron 4100K Ecologic and GroLite WS fluorescent lamps (Interlectric). Flats were covered with a clear dome for the first 3-5 days to aid germination.  Plants were fertilized twice—at planting and at 20 days—with Peters 15-16-17.  Plant age was measured from the date flats were transferred to the growth chamber.

extract_protocol:
Samples were collected in tubes submerged in liquid nitrogen, so that the tissues were instantly flash frozen. RNA was extracted by Trizol (Life Technologies), followed by a chloroform phase separation according to the manufacturer's protocol. We then performed a second extraction using a 5:1 mix of acid phenol:chlorform, pH 4.5, and precipitated with 2 volumes of isopropanol.
GMUCT 2.0 libraries were made by a home assembled and modified version of Illumina's TruSeq small RNA sequencing kit protocol, as outlined in Willmann, Berkowitz, and Gregory (2014) Improved genome-wide mapping of uncapped and cleaved transcripts in eukaryotes—GMUCT 2.0. Methods 67:64-73.

tag: genetic background

value: Col-0 with FRI introgressed from Sf-2

value: FRI;FLC

tag: days after plants put in the growth chamber

tag: day length

value: 16 hours (long day conditions)


title: ExposednoNic_7M

description: Exposed to E-cigarettes with No Nicotine


title: ExposednoNic_2M


title: FRI;flc-3 shoot apices, day 11

description: library strategy: GMUCT 2.0

source_name: shoot apices plus leaf primordia ≤ 1 mm


title: Control31M_1

description: Filtered Air Controls


title: FRI;FLC fully-expanded leaf 11, day 33

description: library strategy: GMUCT 2.0

source_name: fully-expanded leaf 11 (rosette leaf)


title: FRI;flc-3 shoot apices, day 9

description: library strategy: GMUCT 2.0


title: FRI;FLC fully-expanded leaf 9, day 33

description: library strategy: GMUCT 2.0

source_name: fully-expanded leaf 9 (rosette leaf)


title: FRI;flc-3 fully-expanded leaves 1+2, day 14

description: library strategy: GMUCT 2.0

source_name: fully-expanded leaves 1+2 (rosette leaf)


title: FRI;flc-3 fully-expanded leaf 3, day 23

description: library strategy: GMUCT 2.0

source_name: fully-expanded leaf 3 (rosette leaf)


title: FRI;FLC shoot apices, day 11

description: library strategy: GMUCT 2.0


title: FRI;flc-3 fully-expanded leaf 11, day 32

description: library strategy: GMUCT 2.0

source_name: fully-expanded leaf 11 (cauline leaf)


title: FRI;flc-3 fully-expanded leaf 9, day 32

description: library strategy: GMUCT 2.0


title: TRP2-RNA

city: Chapel Hill

last: Miller

state: North Carolina

address: 6109B Neuroscience Research Building

institute: University of North Carolina - Chapel Hill

data_processing:
Reads were truncated to 50bp then filtered using TagDust and only reads with quality score greater than 20 for 90% of bases were retained. Reads were then aligned to the reference mouse genome (mm9) with GSNAP using a k-mer size of 15, indel penalty of 5, and allowing 1 mismatch. Reads aligning to blacklisted regions of the mouse genome were removed.
Transcript abundance was estimated by computing raw counts or RPKM using RefSeq gene models aggregated by gene symbol.
Genome_build: mm9
Supplementary_files_format_and_content: Expression matrix

source_name: astrocytes

growth_protocol: DMEM+10% FBS, 5% CO2

extract_protocol: Library sequencing was performed on a NextSeq500 system with a 75 cycle High Output kit (Illumina, San Digo, CA).

treatment_protocol: Total RNA was extracted from cell pellets (Qiagen RNAeasy kit, Germantown, MD), followed by library preparation using a Stranded mRNA-seq kit (KAPA Biosystems, Wilmington, MA) according to the manufacturer's instructions.

value: truncated SV40 T-antigen, KRas(G12D), Pten del/del

tag: passages


title: TRP1-RNA


title: AC2-RNA

value: Wild-type


title: AC1-RNA


title: ChIP-seq - mES - H3K36me3 - 12hr KD, 7SK ASO rep1

library_source: genomic

data_processing:
After demultiplexing, reads were stripped adaptors and mapped to the mouse (mm9) genome using Bowtie2 and visualized as bigWig files. Peaks were called using MACS2.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files of ChIP-seq read density

molecule: genomic DNA

source_name: Embryonic Stem Cells

growth_protocol: mES cells were grown on gelatin plates with serum and LIF.

extract_protocol:
Lysates were produced from soncated cell material and transcription factor associated DNA was enriched with specific antibodies.
Libraries were prepared according to NEBNext kit.

treatment_protocol: All cells were fixed with 1% formaldehyde for 10 minutes at room temperature.

tag: antibody

value: Abcam, Cat #ab9050


title: ChIP-seq - mES - H3K36me3 - 12hr KD, 7SK ASO rep2


title: ChIP-seq - mES - H3K36me3 - 12hr KD, Control ASO rep2


title: ChIP-seq - mES - H3K36me3 - 12hr KD, Control ASO rep1


title: ChIP-seq - mES - panH3 - 12hr KD, Control ASO rep2

value: Abcam, Cat #ab1791


title: ChIP-seq - mES - panH3 - 12hr KD, 7SK ASO rep1


title: TRP1-FAIRE

data_processing:
Reads were filtered such that their identical sequence could appear only up to five times, then were filtered using TagDust (Lassmann et al. 2009). Reads with quality score greater than 20 for 90% of bases were retained, and aligned to the reference mouse genome (mm9) with GSNAP (Wu and Nacu 2010) using a k-mer size of 15, indel penalty of 5, and allowing 1 mismatch. Reads aligning to more than four locations or overlapped blacklisted regions of the mouse genome were removed.
Peaks were identified for each sample using Fseq (Boyle et al. 2008).
Genome_build: mm9
Supplementary_files_format_and_content: bigWig of raw FAIRE-seq signal

extract_protocol:
FAIRE was performed as described previously (Simon 2012).
TruSeq libraries were constructed as per manufacturer's recommendations (NEB cat # E7370).


title: ChIP-seq - mES - panH3 - 12hr KD, 7SK ASO rep2


title: ChIP-seq - mES - panH3 - 12hr KD, Control ASO rep1


title: TR1-FAIRE

value: truncated SV40 T-antigen, KRas(G12D)


title: TR2-FAIRE


title: T2-FAIRE

value: truncated SV40 T-antigen


title: AC2-FAIRE


title: T1-FAIRE


title: icSHAPE - mES - Hexim1 coIP - NAI-N3 rep3

description: protein assocaited total RNA

data_processing:
After demultiplexing, reads were stripped adaptors (PMID: 25411354) and mapped to the mouse RN7SK RNA (Gene ID: 19817) using Bowtie2.
BAFcoIP samples have a 13nt barcode on the 5'end, Hexim1coIP samples have a 17nt barcode on the 5'end, each need to be trimmed before mapping to the 7SK snRNA sequence
icSHAPE reverse transcriptase (RT)  stops were isolated as the first nucleotide after the 5'end barcode. RT stops were used to calculated icSHAPE reactivity scores
Genome_build: mouse RN7SK (Gene ID: 19817)
Supplementary_files_format_and_content: excel file of 7SK icSHAPE reactivity scores at each nucleotide measured

growth_protocol: mES cells were grown on gelatin plates with serum and LIF, lysates made and BAF or Hexim1 complexes enriched with antibody conjugated beads (Arid1a, Santa Cruz, sc-32761; Hexim1, Abcam, ab25388)

extract_protocol:
Deep sequencing libraries were prepared using 3'end RNA ligation, cDNA synthesis with SuperScript III, cDNA circularization, and subsequent PCR amplification
icSHAPE (PMID: 25799993)

treatment_protocol: Enriched complexes were modifed with NAI-N3 as previously described (PMID: 25799993), reactions quenched and RNA isolated with TRIzol.


title: icSHAPE - mES - Hexim1 coIP - NAI-N3 rep2

description: protein assocaited total RNA


title: AC1-FAIRE


title: icSHAPE - mES - Hexim1 coIP - NAI-N3 rep1

description: protein assocaited total RNA


title: icSHAPE - mES - Hexim1 coIP - DMSO rep2

description: protein assocaited total RNA


title: icSHAPE - mES - Hexim1 coIP - DMSO rep1

description: protein assocaited total RNA


title: icSHAPE - mES - Hexim1 coIP - DMSO rep3

description: protein assocaited total RNA


title: icSHAPE - mES - BAF coIP - NAI-N3 rep3

description: protein assocaited total RNA


title: Control5

description: Filtered Air Controls

value: Female


title: icSHAPE - mES - BAF coIP - NAI-N3 rep2

description: protein assocaited total RNA


title: icSHAPE - mES - BAF coIP - NAI-N3 rep1

description: protein assocaited total RNA


title: icSHAPE - mES - BAF coIP - DMSO rep3

description: protein assocaited total RNA


title: icSHAPE - mES - BAF coIP - DMSO rep2

description: protein assocaited total RNA


title: icSHAPE - mES - BAF coIP - DMSO rep1

description: protein assocaited total RNA


title: GRO-seq - mES - 12hr KD, Control ASO rep4

description: nascent RNA

data_processing:
After demultiplexing, reads were stripped adaptors, mapped to a custon index of repetitive RNAs (PMID: 25411354), mapped to the mouse (mm9) genome using Bowtie2, and processed as previously described (PMID: 24843027)
Replicates #1 and #2 have 13nt, 5'end barcodes, Replicates #3 and #4 have 17nt 5'end barcodes which need to be removed before mapping.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files of merged biological replicates split for positive and negative strand reads of GRO-seq read density

extract_protocol:
Nuclei were isolated and run-on reactions performed as described previously (PMID: 24843027).
Run-on RNA (labeled with BrU) was isolated as previously describd (PMID: 24843027) and deep sequencing libraries generated.

treatment_protocol: Cells were depleted of 7SK by nucleofecting antisense oligonucleotides for 12 hours.


title: TRP2-FAIRE


title: GRO-seq - mES - 12hr KD, Control ASO rep3

description: nascent RNA


title: GRO-seq - mES - 12hr KD, 7SK ASO rep3

description: nascent RNA


title: GRO-seq - mES - 12hr KD, 7SK ASO rep4

description: nascent RNA


title: ChIP-seq - mES - γ-H2AX - 12hr KD, Control ASO rep1

description:
Affinity purified genomic DNA
mm9_ChIP-seq_gH2AX_12hrControlASO.bw

value: Abcam, Cat# ab11174


title: ChIP-seq - mES - γ-H2AX - 12hr KD, 7SK ASO rep1

description:
Affinity purified genomic DNA
mm9_ChIP-seq_gH2AX_12hr7SKASO.bw


title: ChIP-seq - mES - γ-H2AX - 12hr KD, 7SK ASO rep2


title: TR3-FAIRE


title: ChIP-seq - mES - Input2 - 12hr KD, Control ASO rep2

description:
Affinity purified genomic DNA
mm9_ChIP-seq_Input2_gH2AX_12hrControlASO.bw

value: none (input)


title: ChIP-seq - mES - Input2 - 12hr KD, 7SK ASO rep2

description:
Affinity purified genomic DNA
mm9_ChIP-seq_Input2_gH2AX_12hr7SKASO.bw


title: ChIP-seq - mES - Input2 - 12hr KD, Control ASO rep1


title: ChIP-seq - mES - Input2 - 12hr KD, 7SK ASO rep1


title: ChIP-seq - mES - Pol II - JQ1 1hr, rep2

description:
Affinity purified genomic DNA
mm9_ChIP-seq_PolII_JQ1_1hr.bw

value: Santa Cruz, Cat# sc-899


title: ChIP-seq - mES - Input2 - DMSO 1hr

description:
Affinity purified genomic DNA
mm9_ChIP-seq_Input2_DMSO.bw

value: ES cells


title: ChIP-seq - mES - WT - Brd4, rep2

description:
Affinity purified genomic DNA
mm9_ChIP-seq_Brd4_rep1.bw

value: male

value: Bethyl, Cat #A301-985A


title: ChIP-seq - mES - Pol II - DMSO 1hr, rep2

description:
Affinity purified genomic DNA
mm9_ChIP-seq_PolII_DMSO_1hr.bw


title: ChIP-seq - mES - WT - Hexim1

description:
Affinity purified genomic DNA
processed data file: mm9_ChIP-seq_Hexim1_WT.bw

extract_protocol:
Lysates were produced from sonicated cell material and transcription factor associated DNA was enriched with specific antibodies.
Libraries were prepared according to NEBNext kit.

value: anti-Hexim1, Abcam, Cat# ab25388


title: ChIP-seq - mES - WT - Brd4, rep1


title: ChIP-seq - mES - WT - Ddx21

description:
Affinity purified genomic DNA
processed data file: mm9_ChIP-seq_Ddx21_WT.bw

value: anti-Ddx21, Novus Biologicals, Cat# NB100-1718


title: ChIP-seq - mES - Pol II - JQ1 1hr, rep1


title: ChIP-seq - mES - Baf155 - 12hr KD, 7SK ASO rep1

description:
Affinity purified genomic DNA
processed data file: mm9_ChIP-seq_Baf155_12hr7SKASO.bw

value: anti-Baf155, Gift from Crabtree Lab


title: ChIP-seq - mES - Baf155 - 12hr KD, 7SK ASO rep2


title: ChIP-seq - mES - Pol II - DMSO 1hr, rep1


title: ChIP-seq - mES - WT - Input

description:
Affinity purified genomic DNA
processed data file: mm9_ChIP-seq_Input_WT.bw


title: ChIP-seq - mES - Baf155 - 12hr KD, Control ASO rep1

description:
Affinity purified genomic DNA
processed data file: mm9_ChIP-seq_Baf155_12hrControlASO.bw


title: ChIP-seq - mES - Pou5f1 - 12hr KD, 7SK ASO rep1

description:
Affinity purified genomic DNA
processed data file: mm9_ChIP-seq_Pou5f1_12hr7SKASO.bw

value: anti-Pou5f1, Santa Cruz, Cat# sc-8629


title: ChIP-seq - mES - Pou5f1 - 12hr KD, 7SK ASO rep2


title: ChIP-seq - mES - γ-H2AX - 12hr KD, Control ASO rep2


title: ChIP-seq - mES - Input - 12hr KD, 7SK ASO rep2

description:
Affinity purified genomic DNA
processed data file: mm9_ChIP-seq_Input_12hrKD.bw


title: ChIP-seq - mES - Pou5f1 - 12hr KD, Control ASO rep2

description:
Affinity purified genomic DNA
processed data file: mm9_ChIP-seq_Pou5f1_12hrControlASO.bw


title: ChIP-seq - mES - Pou5f1 - 12hr KD, Control ASO rep1


title: ChIP-seq - mES - Input - 12hr KD, 7SK ASO rep1


title: ChIP-seq - mES - Input - 12hr KD, Control ASO rep1


title: ChIP-seq - mES - Input - 12hr KD, Control ASO rep2


title: ATAC-seq - mES - 12hr KD, Control ASO rep1

description:
DNA from open and chromatinized DNA
processed data file: mm9_ATAC-seq_12hrControlASO.bw

data_processing:
Library strategy: ATAC-seq
After demultiplexing, reads were stripped adaptors, mapped to the mouse genome (mm9) and processed as previously described (PMID: 24097267)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files of merged biological replicates of ATAC-seq experiments

extract_protocol:
Transposed DNA was isolated using MinElute Spin columns (Qiagen)
Paired-end libraries were generated as previously described (PMID: 24097267)

treatment_protocol: Cells were depleted of 7SK by nucleofecting antisense oligonucleotides for 12 hours and chromatin state was assayed by transposase


title: ATAC-seq - mES - 12hr KD, 7SK ASO rep1

description:
DNA from open and chromatinized DNA
processed data file: mm9_ATAC-seq_12hr7SKASO.bw


title: ATAC-seq - mES - 12hr KD, Control ASO rep2


title: ATAC-seq - mES - 12hr KD, 7SK ASO rep2


title: ChIP-seq - mES - Input2 - JQ1 1hr

description:
Affinity purified genomic DNA
mm9_ChIP-seq_Input2_JQ1.bw


title: MSC Frozen-Thawed donor 3

city: Rotterdam

first: Martin

last: Hoogduijn

address: 's-Gravendijkwal 230

country: Netherlands

institute: Erasmus MC

description:
FT3
human mRNA
MSC_Hoogduijn_allsamples_gene_counts.txt
toptags_FT_vs_C.txt

data_processing:
Basecalling: Illumina RTA 1.17.21.3
Demultiplexing: Illumina CASAVA 1.8.4
alignment: tophat_largeindex (tophat2 version 2.0.13)
regenerate input fastq from tophat alignment results (accepted_hits.bam and unmapped.bam) using picard-tools SamToFastq, with options "RC=true INCLUDE_NON_PRIMARY_ALIGNMENTS=false". This was done for sample 06, where the raw sequencer result fastq was inadvertedly lost.
ReadCounting: custom R script, based on IRanges package
Differential expression analysis: R and edgeR package, with model including terms for group and donor
Filtering for mouse-human cross alignment: custom R analysis on toptags result for I vs C comparison
Genome_build: hg19_mm10 combined genome consisting of all human and mouse chromosomes
Supplementary_files_format_and_content: MSC_Hoogduijn_allsamples_gene_counts.txt: tab separated text file, one gene per line, one column per sample
Supplementary_files_format_and_content: toptags*txt: tab separated text file, with toptags listing as produced by R/edgeR. 5 columns: logFC, logCPM, LR, Pvalue, FDR. Data lines have geneID as rowIDs. Header line has one column less than data lines, as is customary for R write.table()

organism: Homo sapiens

source_name: Mesenchymal stromal cells from abdominal adipose tissue

growth_protocol: MSC were isolated from adipose tissue and expanded to passage 3 in alpha minimal essential medium with 15% foetal calf serum and 1% p/s

extract_protocol:
mRNA was isolated by Trizol reagent
Illumina TruSeq RNA

tag: time of analysis

value: 1h after thawing

tag: localication

value: in vitro

tag: donor

value: female, 68y, healthy


title: MSC Continuous culture donor 3

description:
C3
human mRNA
MSC_Hoogduijn_allsamples_gene_counts.txt
toptags_FT_vs_C.txt
toptags_I_vs_C.txt

value: directly after trypsinisation


title: MSC Continuous culture donor 2

description:
C2
human mRNA
MSC_Hoogduijn_allsamples_gene_counts.txt
toptags_FT_vs_C.txt
toptags_I_vs_C.txt

value: female, 41y, healthy


title: MSC Injected donor 3

description:
I3
human mRNA mixed with mouse mRNA from the lung tissue
MSC_Hoogduijn_allsamples_gene_counts.txt
toptags_I_vs_C.txt

value: 2h after infusion of trypsinised MSC

value: in mouse lung


title: MSC Frozen-Thawed donor 1

description:
FT1
human mRNA
MSC_Hoogduijn_allsamples_gene_counts.txt
toptags_FT_vs_C.txt

value: male, 48y, healthy


title: MSC Injected donor 1

description:
I1
human mRNA mixed with mouse mRNA from the lung tissue
MSC_Hoogduijn_allsamples_gene_counts.txt
toptags_I_vs_C.txt


title: MSC Frozen-Thawed donor 2

description:
FT2
human mRNA
MSC_Hoogduijn_allsamples_gene_counts.txt
toptags_FT_vs_C.txt


title: MSC Continuous culture donor 1

description:
C1
human mRNA
MSC_Hoogduijn_allsamples_gene_counts.txt
toptags_FT_vs_C.txt
toptags_I_vs_C.txt


title: MSC Injected donor 2

description:
I2
human mRNA mixed with mouse mRNA from the lung tissue
MSC_Hoogduijn_allsamples_gene_counts.txt
toptags_I_vs_C.txt


title: Ctr_v1(c5)

first: Max

last: Costa

address: 57 Old Forge Road

institute: New York University School of Medicine

data_processing:
Basecalls performed using Illimuna bcl2fastq Conversion version 1.8.4
FastQC is used to do the quality control
RNA Seq reads were aligned to mm9 genome using Bowtie aligner version 0.12.9 with 2 mismatches allowed
Duplicated reads removed using samtools version 0.1.19
HTSeq version version 0.6.1p1 is used to find read counts
For differential expression analysis Deseq2/Bioconducter package is used, padj<0.1
Genome_build: hg19
Supplementary_files_format_and_content: Statistical analysis txt

source_name: BEAS2B bronchial epithelial cell

growth_protocol: The BEAS-2B immortalized human bronchial epithelial cell line was maintained in Dulbecco’s Modified Eagle Medium supplemented with 10% heat-inactivated fetal bovine serum and 1% of penicillin/streptomycin. The cells were routinely cultured at 37ºC with 5% CO2.

extract_protocol:
Total RNA was harvested using Trizol reagent.Tru-seq RNA Sample Preparation v2 Kit  was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BEAS-2B cells were transfected with of pcDNA3.1 vector or pcDNA3.1-SATB2 DNA using Lipofectamine® LTX Reagent with PLUS™ Reagent according to manufacturer’s protocol.

tag: transfection

value: pcDNA3.1 vector transfected


title: Ctr_v1(c4)

value: immortalized human bronchial epithelial cell


title: SATB2_1(S3)

value: pcDNA3.1-SATB2 transfected


title: SATB2_1(S7)


title: ChIP-seq - mES - Baf155 - 12hr KD, Control ASO rep2

value: ES cells

value: male


title: PC9_WT_VEH.rep1

city: Charlestown

first: Aaron

last: Hata

state: MA

address: 149 13th Street

department: Cancer Center

institute: Massachusetts General Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to HG19 Homo Sapiens genome using STAR
Counts Per Megabase of library size (CPM) were calculated using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: CPM.txt includes CPM values for each Sample

extract_protocol:
RNA extracted with Qiagen Rneasy Kit
RNA-Seq libraries were constructed from polyA-selected RNA using NEBNext Ultra Directional RNA library prep kit for Illumina (New England Biolabs).

treatment_protocol: Vehicle, 1mM gefitinib, 1mM WZ4002 for 24 hours

value: PC9 NSCLC cell line

tag: pc9 derivative

value: PC9 WZ4002-tolerant

tag: drug treatment

value: Vehicle


title: PC9_GT_VEH.rep2

value: PC9 gefitinib-tolerant


title: PC9_WT_WZ.rep1


title: PC9_WT_VEH.rep2


title: PC9_GT_GEF.rep2

value: Gefitinib


title: PC9_GT_VEH.rep1


title: PC9_GR3_VEH.rep1


title: PC9_GR3_WZ.rep1


title: PC9_GR3_VEH.rep2


title: PC9_GR2_WZ.rep2


title: PC9_GR3_WZ.rep2


title: PC9_GR2_VEH.rep2


title: PC9_GR2_WZ.rep1


title: PC9_GR2_VEH.rep1


title: PC9_WZ.rep1

value: Parental


title: PC9_WZ.rep2


title: PC9_GEF.rep2


title: PC9_VEH.rep2


title: PC9_GEF.rep1


title: PC9_VEH.rep1


title: A375 Rep 1

city: Boston

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to hg19 whole genome using Tophat 2.0.11 without novel splicing form calls
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts
Genome_build: hg19
Supplementary_files_format_and_content: excel files include RPKM values for each Sample

source_name: human melanoma cell line

growth_protocol: Human melanoma cell lines and adult human epidermal melanocytes (purchased from Life Technologies) were grown to near confluence.

extract_protocol:
Total RNA isolated using the standard Trizol protocol.
Illumina libraries were prepared using Ribo-Zero Magnetic Gold Kit (epicenter) and NEBNext Ultra RNA Library Prep Kit (NEB) and run on a Hiseq 2500

value: melanoma

value: long term culture


title: A375 Rep 2


title: RF9 - Hema-LP

source_name: normal human melanocytes

value: Hema-LP

value: normal human melanocytes


title: RF7 - UACC257


title: PC9_WT_WZ.rep2


title: RF6 - SKMEL30


title: RF2 - COLO679


title: PC9_GT_GEF.rep1


title: RF4 - SKMEL2


title: SKMEL2 input

description: ChIP'ed genomic DNA

data_processing:
ChIP-Seq aligned to hg19 with Bowtie with max mismatch 2bp
peaks were called using MACS 2.0 with the following setting: q-value 0.05
Genome_build: hg19
Supplementary_files_format_and_content: called peaked in narrowPeak bed file

source_name: human melanoma cell lines

growth_protocol: Human melanoma cells were grown to confluence in DMEM + 10% FCS, and ~ 1X108 cells were formaldehyde crosslinked and collected.

extract_protocol:
ChIP was performed using the methods of T. I. Lee, S. E. Johnstone, R. A. Young, Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc. 1, 729–748 (2006).
Libraries were prepared using the NEBNext Multiplex Oligos for Illumina kit (NEB) and run on an Illumina Hi-Seq2000.

tag: chip antibody


title: A375 H3K4Me1

description: ChIP'ed genomic DNA

tag: cell type

value: H3K4Me1 (ab8895) (Abcam)


title: LOX IMVI input

description: ChIP'ed genomic DNA

tag: cell line

value: LOX IMVI


title: Low_Pt1_anterior_medial

city: Dallas

first: Min

last: Ni

state: TX

address: 6000 Harry Hines Blvd

department: Children's Research Institute

institute: UT Southwestern Medical Center

data_processing:
Sequencing reads were aligned to human genome assembly hg19 by TopHat.
Transcripts were assembled and the abundance was estimated by Cufflinks.
The number of reads aligned to RefSeq annotated genes' exons were counted and further normalized to be of unit of FPKM ( number of fragments per kilo base of exon per million reads mapped) by Cuffnorm.
Genome_build: hg19
Supplementary_files_format_and_content: text file of gene read count values
Supplementary_files_format_and_content: text file of gene FPKM values

source_name: Lung tumor

extract_protocol:
Human tumor samples were hormogenized in Trizol and the total RNA was extracted using RNeasy Mini Kit (Qiagen) following the manufacturer's protocol.
1-3 ug of total RNA was processed for library generation using Ovation human FFPE RNA-Seq library systems (NuGen) following the manufacturer’s protocol.

tag: cancer type

value: Non-small cell lung cancer (NSCLC)

tag: perfusion group

value: low


title: Low_Pt7_anterior


title: Low_Pt6_anterior_medial


title: A375 input for H3K4Me1

description: ChIP'ed genomic DNA


title: Low_Pt7_posterior


title: COLO679 input

description: ChIP'ed genomic DNA


title: RF5 - SKMEL5


title: RF1 - CJM

value: CJM


title: UACC257 H3K27Ac

description: ChIP'ed genomic DNA

value: H3K27Ac (ab4729) (Abcam)


title: CJM input

description: ChIP'ed genomic DNA


title: UACC257 input

description: ChIP'ed genomic DNA


title: SKMEL30 input

description: ChIP'ed genomic DNA


title: Low_Pt6_anterior


title: High_Pt5_tumor

value: high


title: High_Pt4_tumor


title: High_Pt8_inferior


title: SKMEL30 H3K27Ac

description: ChIP'ed genomic DNA


title: COLO679 H3K27Ac

description: ChIP'ed genomic DNA


title: DMSO_B

first: avinash

last: waghray

address: 185 Cambridge Street, CPZN Room 4254A

department: Center for Regenerative Medicine

institute: Massachussets General Hospital

description: wildtype hESCs

data_processing:
RNASeq: Fastq files were mapped to the genome using Tophat: tophat -o -p 4
RNASeq: Output ".bam" files were process to get counts: cuffquant -o -p 4
RNASeq: Output ".cxb" files were processed to get differential gene expression values: cuffdiff -o -L
Genome_build: hg19
Supplementary_files_format_and_content: genes_fpkm.xlsx

source_name: hESCs

growth_protocol: H9 hESCs were cultured in mTeSR-1 media on Matrigel-coated plates

extract_protocol:
For mRNA-Seq sample preparation, the total RNA was isolated using Trizol reagent following the manufacturer’s instructions. Quality and quantity of total RNA was assayed using Nanodrop and Agilent Bioanalyzer.
For mRNA-seq, libraries were prepared using the TrueSeq protocol from Illumina. The concentration of the libraries was assayed using Agilent Bioanalyzer and sequenced  using 1*75bp on an NextSeq 500 platform

treatment_protocol: H9 human embryonic stem cells (hESCs) expressing pJAZ NLS-GFP-OsJAZ33 were treated cultured in mTeSR-1 media supplemented with 50 micromolar coronatine (Cor) or 0.1% DMSO for two days on Matrigel-coated plates. Cells were collected by trypsinization and RNA was prepared using TRIZOL (Ambion). Experiment was repeated twice (Replicate A and B)

value: embryonic stem cells

value: H9 hESCs expressing pJAZ NLS-GFP-OsJAZ33

tag: agent

value: DMSO


title: Cor_B

description: wildtype hESCs

value: coronatine


title: LOX IMVI H3K27Ac

description: ChIP'ed genomic DNA


title: Cor_A

description: wildtype hESCs


title: Low_Pt1_posterior_pleural


title: CJM H3K27Ac

description: ChIP'ed genomic DNA


title: DMSO_A

description: wildtype hESCs


title: AR_V7_2_miRNA

city: STRASBOURG

first: Félicie

last: COTTARD

address: 1 place de l'Hôpital

country: France

institute: INSERM U1113

data_processing:
RNA-seq reads were mapped onto the hg19 assembly of the human genome using Tophat v2.0.10 and the bowtie2 v2.1.0 aligner.
Quantification of gene expression was performed using HTSeq v0.5.4p3 using gene annotations from Ensemble release 75.
The normalization of read counts across libraries was performed with the method proposed by Anders and Huber.
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2, raw and normalized read count with statistical analysis.

source_name: LNCaP cell line

growth_protocol: LNCaP cells, clone FGC (ECACC) were cultured in RPMI-1640 media supplemented with 10% fetal bovine serum (FBS), 10 mM HEPES, 2 mM L-glutamine, 100 U/mL penicillin, 100 μg/mL streptomyci  and 1 mM pyruvate.

extract_protocol:
Total RNA was extracted using TriPure Reagent
The library of cDNA and the sequencing were performed by IGBMC Microarray and Sequencing platform (Illkirch, France) using the Hiseq2500 Technology.

treatment_protocol: 10 nM DHT for 72 hours

value: LNCaP

value: Prostate cancer cell line

tag: ar expression status

value: Transduction with lentiviral particles for expression of the AR-V7

tag: fluorescence

value: EGFP


title: AR_V7_1_miRNA


title: High_Pt8_superior


title: AR_WT_3_miRNA

value: Transduction with lentiviral particles for expression of the AR-WT


title: AR_WT_2_miRNA


title: Microbat cell line

city: Rockville

first: Reed

last: Shabman

state: MD

address: 9704 Medical Center Dr

department: Viral Genomics

institute: J. Craig Venter Institute

data_processing:
Sequence was generated using Illumina Genome Analyzer II and Bustard 1.9.5 was used for base calling
Sequence reads were trimmed of adaptor sequence and then mapped to each CDS of the Bat Gammaherpesvirus 8 genome (Genbank file KU220026) using the RNA-seq analysis tool in CLC Genomics Workbench version 8.5.
For RNA-seq analysis, default settings in CLC Genomics Workbench version 8.5 were used. Only reads mapping to the viral genome used in the analysis are provided and RPKM values provided for each CDS
Genome_build: Genbank file KU220026, PRJNA295864
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for the sample

organism:
Myotis velifer
Bat gammaherpesvirus 8

source_name: interscapular tumor_Myotis velifer incautus

growth_protocol: Dubeccos Modified Eagles Medium supplemented with 10% Fetal Bovine Serum

extract_protocol:
A confluent T75 flask of cells was trypsinized, pelleted, and lysed in Trizol.  Total RNA was extracted.
mRNA purification and standard Ilumina library construction was performed.

treatment_protocol: Cells were cultured for approximately 30 days prior to collection and RNA extraction

tag: tissue host

value: Bat tumor cell


title: AR-V7_2_mRNA


title: AR_WT_1_miRNA


title: AR-V7_3_mRNA


title: AR-WT_2_mRNA


title: AR-WT_1_mRNA


title: AR-V7_1_mRNA


title: AR-WT_3_mRNA


title: SKMEL2 H3K27Ac

description: ChIP'ed genomic DNA

value: melanoma

tag: passages

value: long term culture


title: GM12878 Rep2

city: La Jolla

first: Anthony

middle: D

last: Schmitt

state: California

address: 9500 GILMAN DR., BLDG. CMME RM 2071

department: Cellular and Molecular Medicine

institute: UC San Diego

description: library strategy: HiC

data_processing:
Basecalls performed using CASAVA version 1.4
Targeted HaploSeq reads were aligned as single ends to the hg19 genome assembly using BWA MEM with the following command - bwa mem -B 8 -M
Single ends from bwa were paired using inhouse scripts, followed by GATK pipeline to recaliberate based and realign Indels.
The final bam file from the above steps were used for haplotyping and genotyping. More specifically, genotype calls from parent-child trio data was used as input for HaploSeq based haplotyping.
Accuracy of haplotype calls from HaploSeq were compared with parent-child trio dataset to estimate accuracy.
Genome_build: hg19
Supplementary_files_format_and_content: VCF files were generated as targeted HaploSeq output

source_name: GM12878 Lymphoblastoid Cells

growth_protocol: Lymphoblastoid cell lines (LCLs) were generated by culturing adherent cells in RPMI medium (Gibco) supplemented with 15% FBS and 1% P/S.

extract_protocol:
In preparation for Hi-C assay, cells were pelleted and resuspsended in media supplemented with formaldehyde at a final concentration of 1% for chromatin crosslinking. Crosslinking was halted in ~200mM Glyceine, pelleted, washed with cold PBS, pelleted, snap frozen, and stored at -80 until experimentation.
Hi-C libraries were prepared using the published method (Lieberman-Aiden, Science, 2009). Briefly, cross-linked cell pellets were lysed and chromatin within intact nuclei were digested using HindIII. Digested ends were filled in using biotinylated dCTP and an E. coli DNA Pol I large fragment (Klenow polymerase). Blunt-ended DNA molecules were then proximally ligated using T4 DNA ligase. After chromatin cross-linking was reversed, ligated DNA was purified. Next, purified ligation products were treated with T4 DNA polymeras, dATPs and dGTPs to remove biotinylated dCTPs from unligated DNA molecules and column-purified. Then, ligation products were fragmented to ~400bp using a Covaris S2 instrument. Ends of fragmented molecules were then repaired using a combination of T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for eventual ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Yet after dA-tailing, DNA molecules were size selected on agarose gel from 200-600bp. After gel purification, biotinylated DNA molecules were pulled down using C1 streptavidin beads (Life Tech) and Illumina sequencing adapters were ligated using T4 DNA ligase. The bead-bound library was then PCR amplified using 14-15 cycles and purified using AMPure XP beads prior to target enrichment. For target enrichment, 500ng of Hi-C library was mixed with 500ng of RNA probes and incubated overnight at 65 degrees. The following day, captured DNA:RNA duplexes were bound to T1 streptavidin-coated beads (Life Tech), washed rigorously, and PCR amplified using 10-11 cycles. Final PCR amplicons were purified using AMPure XP beads and captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2500 following the manufacturer's protocols for 100 cycle, paired-end sequencing.

value: Lymphoblastoid Cell Line (LCL)


title: PC9_EZH2inh_H3K4me3_Dmspike

status: Public on Jan 31 2016

city: South San Francisco

first: Suchit

last: Jhunjhunwala

address: 1 DNA Way, MS-444A

institute: Genentech

data_processing:
50-nucleotide sequence reads were aligned to the hg19 genome using the BWA algorithm with default settings. Only reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches and mapped uniquely to the genome, were used in subsequent analyses.
The aligned read files were sorted and duplicates removed using sort and rmdup functions from samtools version 0.1.18 (Li et al., 2009).
WIG files were generated using IGVTools (version 2.2.2) count function with a window size of 25 nucleotides, an extension of 100 beyond the 50-nucleotide read length, and genome hg19 (Robinson et al., 2011; Thorvaldsdottir et al., 2013). The WIG files were scaled assuming an effective genome length of 2.79B base pairs, so that the mean signal would be 1.0.
Genome_build: hg19

source_name: NSCLC

growth_protocol: PC9 cells were cultured at 37 °C with 5% CO2 in RPMI-1640 (Invitrogen) supplemented with 10% FBS (HyClone) and antibiotics (Invitrogen). Drosophila Schneider (S2) cells were cultured at 28 °C without CO2 in Schneider’s medium (04-351Q, Lonza) containing 1% FBS. OSS Drosophila cells cultured as described (Niki et al. 2006)

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reactions were set up using precleared chromatin and antibodies and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on HiSeq 2500 (50 nt reads, single end).

treatment_protocol: Cells were treated with 1 μM EZH2 inhibitor GSK126 in the same media with 5% FBS for 5 days

value: H3K4me3 (CST 9751 Lot 7)

tag: treatment

tag: timepoint

value: 5 days


title: PC9_control_H3K4me3_Dmspike

data_processing:
50-nucleotide sequence reads were aligned to the hg19 genome using the BWA algorithm with default settings. Only reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches and mapped uniquely to the genome, were used in subsequent analyses.
The aligned read files were sorted and duplicates removed using sort and rmdup functions from samtools version 0.1.18 (Li et al., 2009).
WIG files were generated using IGVTools (version 2.2.2) count function with a window size of 25 nucleotides, an extension of 100 beyond the 50-nucleotide read length, and genome hg19 (Robinson et al., 2011; Thorvaldsdottir et al., 2013). The WIG files were scaled assuming an effective genome length of 2.79B base pairs, so that the mean signal would be 1.0.
The stdnorm and dmnorm files for this Sample were identical even though the data were normalized by two different methods.
Genome_build: hg19


title: PC9_EZH2inh_H3K27me3_Dmspike

value: H3K27me3 (CST 9733BF Lot 10)


title: PC9_control_H3K27me3_Dmspike


title: PC9_control_H3K4me3


title: PC9_EZH2inh_H3K27me3


title: PC9_control_H3K27me3


title: AR_V7_3_miRNA


title: DA53 ESCs

city: Beijing

first: Xiaolong

last: Cui

address: No.1 Beichen West Road

department: State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

description: processed data in Bulk_RNAseq.txt

data_processing:
Illumina Casava1.8 software was used for basecalling.
Quality of sequencing reads were assessed using FastQC (version 0.10.1).
Low quality bases were trimmed with a cutoff of Phred quality score 20 using Fastq Quality Trimmer program in FASTX-Toolkit (version 0.0.13).
High quality reads were mapped to the reference genome (version mm10 and rn5) using TopHat (version 2.0.10).
Cufflinks (version 2.1.1) was used to charaterize the transcriptomes based on the RefSeq reference annotation.
Genome_build: mm10, rn5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Rattus norvegicus

source_name: embryonic stem cell line DA53

extract_protocol:
Total RNAs were isolated using Trizol reagent.
Total RNAs were prepared for illumina mRNA-Seq libraries using the TruSeq RNA Sample Prep Kit according to the manufacture's instruction.

value: G0/G1 stage embryonic stem cell


title: RF3 - LOXIMVI

value: LOXIMVI


title: GM12878 Rep1

description: library strategy: HiC


title: ED94_8908_MALE_rep3

city: Bethesda

first: Brian

last: Oliver

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

data_processing:
Basecalls performed using CASAVA version 1.8.2.
RNA-Seq reads were aligned to the Drosophila genome assembly (Berkley Drosophila Genome Project Release 5, obtained from FlyBase. http://www.flybase.org) using TopHat 2.0.10 (Trapnell et al., 2009. Bioinformatics) with -g 1 and -G parameters. As a gene model for the -G parameter, we used an annotation file from FlyBase (5.57) where we removed genes from uncertain physical locations (e.g., chrU and chrUextra).
From the alignment result, abundance of transcripts were measured as read counts using HTseq (Anders et al., 2014. Bioinformatics) with default options (-m union -t exon).
From the alignment result, Fragments per Kilobase per Million mapped reads (FPKM) values were calculated using Cufflinks (Trapnell et al., 2010. Nature Biotechnology). We used -G, -b, and -u parameters in running Cufflinks.
genome build: Release 5
Supplementary_files_format_and_content: Tab-delimited text files that are generated from HTseq and Cufflink. Each contains read counts and FPKM values, respectively, at gene level.

organism: Drosophila melanogaster

source_name: whole animal

growth_protocol: Drosophila melanogaster were raised at 25 oC on the standard yeast/cornmeal medium (Fly Facility, University of Cambridge, UK) for w1118 isogenic flies, and on the standard fly agar (Bloomington Drosophila Stock Center, Indiana University, IN) for w1118/OregonR hybrid flies. Virgin w1118 or ModENCODE OregonR females were crossed to DrosDel strain males and the non-balancer flies were collected and aged for 3-5 days.

extract_protocol:
For the hybrid background flies, single, day 3-5 adult male or female flies were partially crushed, stored in 100ul of RNAlater (Life Technologies, Grand Island, NY), and frozen at - 80oC for long-term storage until RNA preparation. RNA was isolated from each genotype in biological triplicates. We used Mini-BeadBeater 96 (Biospec Products, Bartlesville, OK) for the homogenization of flies. Approximately 100ul of 1mm glass beads (Biospec Products, Bartlesville, OK) were added to the flies in RNAlater in 1ml Axygen 96 well plate (Corning, Union City, CA). We processed plates 3 x 1min with a 2min rest on ice between each homogenization. We added 600ul of RLT buffer (Qiagen, Valencia, CA) to each well to dilute the RNAlater solution. Total RNA was isolated with RNeasy 96 kits (Qiagen, Valencia, CA) according to manufacturer’s handbook (Protocol for Isolation of Total RNA from Animal Cells using spin technology, Cat#19504). The amount of total RNA extract was measured using Quant-iT RiboGreen (Life Technologies, Grand Island, NY).
We mixed 400ng of total RNA in 50ul of nuclease-free water with 50ul of 2:5 dilution of Dynabeads Oligo(dT)25 (Life Technologies, Grand Island, NY) that we pre-rinsed and diluted with Binding Buffer (20mM Tris-HCl pH7.5, 1.0M LiCl, 2mM EDTA). We heated the mixture to 65oC for 5min in a thermocycler, and cooled down on ice for 1min. After 15min of incubation at room temperature, we collected the beads with a magnetic stand, and rinsed with 200ul Washing Buffer (10mM Tris-HCl pH7.5, 0.15M LiCl, 1mM EDTA) for 1min at 1,000 rpm (Thermomixer, Eppendorf, Hauppauge, NY). We collected the beads again with a magnetic stand, and eluted with 50ul of 10mM Tris-HCl pH7.5 at 80oC for 2min. We rebound the eluate to the beads by incubating with 50ul Binding buffer, and rinsed with 200ul Washing Buffer as above. We eluted and fragmented the poly A+ RNA with 16ul of Fragmentation Buffer that contained 1:4 dilution of 5X First Strand Buffer from Protoscript II (New England BioLabs, Ipswich, MA), 500ng of random primers (Life Technologies, Grand Island, NY), and 20pg of ERCC spike-ins Pool 78A or 78B (Zook et al., 2012. PLOS One) at 9 oC for 6min. The beads were removed using a magnetic stand, we reverse transcribed with10units of SuperRase-in (Life Technologies, Grand Island, NY), 100units of Protoscript II reverse transcriptase, 5mM DTT, and 625 uM dNTPs (Enzymatics, Beverly, MA.). We used a thermocycler set at 25oC for 10min; 42oC for 50min; 70oC for 15min. We cleaned-up the DNA-RNA hybrids with 1.9 volumes of MagNA beads (Rohland and Reich, 2012. Genome Research), and mixed with 0.85 volumes of ethanol and we bound DNA-RNA hybrid to the beads at room temperature for 15min. We collected beads on a magnetic stand and rinsed with 200ul of 80% ethanol twice. After air-drying for 5min, we eluted the beads with 16ul of Elution Buffer. For the second strand synthesis, we added 2.5 units of RNase H (Enzymatics, Beverly, MA.) and 10 units of DNA polymerase I in 1X Blue Buffer (Enzymatics, Beverly, MA.), 10mM DTT, 0.5mM each dATP, dCTP, and dGTP (Enzymatics, Beverly, MA.) and 1mM dUTP (ThermoFisher Scientific, Waltham, MA. 1 mM final) and incubated for 5 hours at 16oC. We cleaned-up DNA products MagNA beads and eluted as above but we used bound beads for the next purification steps. Purified double-stranded DNA was subjected to end-repair with NEBNext End Repair Module (New England BioLabs) as per manufacturer’s protocol for 20ul samples. We replenished beads with 1.9 volume of XP buffer (Wang et al., PLOS One. 2011) and cleaned up as above. For adapter ligation, we performed adenylation on blunt-ended DNA by adding 2.5 units of Klenow 3’-5’ exo (Enzymatics, Beverly, MA.) and incubation at 37oC for 30min in 1X Blue Buffer. We again used 1.9 volume of XP buffer to clean up as above. We eluted DNA with 10ul of Elution buffer, and added 1ul of one of 24 differently barcoded adapters from the TruSeq v2 kit (Illumina, San Diego, CA) for 24ul ligation reactions with T4 DNA ligase (Rapid) (Enzymatics, Beverly, MA.) for 20min at 20oC. We stopped the ligation by adding ⅓ volume of 0.03M EDTA, and cleaned up with 24ul of XP buffer as above. After eluting with 30ul Elution buffer, we cleaned up again with 1 volume of XP buffer add brought samples to a 12ul final volume. We digested dUTP incorporated strands of DNA with 5 units of Uracil DNA Glycosylase (New England BioLabs) for 30min at 37oC. Then we amplified with 1.5ul of P5 and P7 primers (Integrated DNA Technology, Coralville, Iowa) with KAPA HiFi HotStart DNA polymerase (KAPA Biosystems, Wilmington, MA) in 30ul reactions. We used the following PCR parameters: 98oC for 45 sec, 14 X 98 oC for 15sec; 60oC for 30sec; 72 oC for 30 sec, followed by 72oC for 5min. We cleaned up amplified DNA with MagNA beads. Libraries were quantified with Quant-iT PicoGreen (Life Technologies), and pooled to be sequenced in Illumina HiSeq 2000 (Illumina, San Diego, CA).

treatment_protocol: S2R+ cells were bathed with ~500 bp double strand RNA for knockdown. The dsRNA treatments followed the DRSC protocol (http://www.flyrnai.org/DRSC-PRR.html). Length of incubation was 1 day.

tag: developemntal stage

value: adult

tag: Sex

value: MALE

tag: drosdel id

tag: bloomington stock center id

tag: genetic background


title: ED94_8908_MALE_rep2


title: ED94_8908_MALE_rep1


title: ED929_9193_MALE_rep3


title: ED929_9193_MALE_rep2


title: ED94_8908_FEMALE_rep3

value: FEMALE


title: ED94_8908_FEMALE_rep1


title: ED929_9193_FEMALE_rep3


title: ED929_9193_MALE_rep1


title: ED94_8908_FEMALE_rep2


title: PC9_EZH2inh_H3K4me3

tag: chip antibody


title: ED929_9193_FEMALE_rep1


title: ED87_8677_FEMALE_rep3


title: ED87_8677_MALE_rep1


title: ED929_9193_FEMALE_rep2


title: ED87_8677_FEMALE_rep2


title: ED87_8677_FEMALE_rep1


title: ED8186_25164_MALE_rep1


title: ED8186_25164_MALE_rep2


title: ED8186_25164_MALE_rep3


title: ED8186_25164_FEMALE_rep3


title: ED8186_25164_FEMALE_rep2


title: ED8186_25164_FEMALE_rep1


title: ED8185_24111_MALE_rep2


title: ED8185_24111_MALE_rep3


title: DA25 ESCs

description: processed data in Bulk_RNAseq.txt

source_name: embryonic stem cell line DA25

tag: cell type


title: ED8185_24111_MALE_rep1


title: ED8185_24111_FEMALE_rep3


title: ED8185_24111_FEMALE_rep2


title: Rvb1 WT replicate 2

status: Public on Feb 02 2016

city: Kansas City

first: Gaye

middle: L

last: Hattem

state: Missouri

address: 1000 E. 50th Street

department: Proteomics

institute: Stowers Institute

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and mapped to SacCer3 whole genome using tophat version 2.0.3
Read counts for each gene were calculated with Rsubread 1.16.1, normalized counts were obtained using DESeq2 1.6.3
FPKM values were calculated with DESeq2 1.6.3
Genome_build: SacCer3

organism: Saccharomyces cerevisiae

source_name: yeast cells tagged with Rvb1

growth_protocol: 5 ml yeast cells were grown to an OD600 of 1.2 to 1.5 in YPD media by shaking at 30 °C, harvested and used for isolation of total RNA.

extract_protocol:
Standard protocols were followed to extract total RNA from yeast cells using the yeast RNA purification kit (Epicenter, Madison, WI) followed by enrichment of poly(A)+ RNA by oligo(dT) selection.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: wild type

tag: strain


title: ED87_8677_MALE_rep3


title: ED87_8677_MALE_rep2


title: ED8142_24135_MALE_rep3


title: ED8142_24135_MALE_rep2


title: ED8142_24135_MALE_rep1


title: ED8142_24135_FEMALE_rep3


title: ED800_9192_MALE_rep1


title: ED793_9061_MALE_rep2


title: ED80_9191_FEMALE_rep1


title: ED800_9192_MALE_rep2


title: ED793_9061_MALE_rep3


title: ED800_9192_MALE_rep3


title: ED800_9192_FEMALE_rep1


title: ED80_9191_MALE_rep2


title: ED793_9061_MALE_rep1


title: ED800_9192_FEMALE_rep3


title: ED793_9061_FEMALE_rep3


title: ED7853_24124_MALE_rep2


title: ED8185_24111_FEMALE_rep1


title: ED8142_24135_FEMALE_rep2


title: ED80_9191_MALE_rep3


title: ED80_9191_FEMALE_rep3


title: ED8142_24135_FEMALE_rep1


title: ED793_9061_FEMALE_rep1


title: ED80_9191_FEMALE_rep2


title: ED7853_24124_FEMALE_rep1


title: ED800_9192_FEMALE_rep2


title: ED7853_24124_FEMALE_rep2


title: ED793_9061_FEMALE_rep2


title: ED7853_24124_FEMALE_rep3


title: ED80_9191_MALE_rep1


title: ED7853_24124_MALE_rep1


title: ED784_7421_MALE_rep3


title: ED784_7421_MALE_rep1


title: ED784_7421_MALE_rep2


title: ED7853_24124_MALE_rep3


title: ED784_7421_FEMALE_rep2


title: ED784_7421_FEMALE_rep3


title: ED778_7420_MALE_rep3


title: ED779_24110_FEMALE_rep1


title: ED779_24110_MALE_rep1


title: ED779_24110_FEMALE_rep2


title: ED778_7420_FEMALE_rep1


title: ED778_7420_MALE_rep2


title: ED777_7419_MALE_rep3


title: ED779_24110_MALE_rep2


title: ED777_7419_MALE_rep1


title: ED778_7420_FEMALE_rep3


title: ED778_7420_FEMALE_rep2


title: ED777_7419_FEMALE_rep3


title: ED776_7418_MALE_rep3


title: ED776_7418_FEMALE_rep3


title: ED776_7418_MALE_rep2


title: ED776_7418_MALE_rep1


title: ED776_7418_FEMALE_rep2


title: ED779_24110_MALE_rep3


title: ED784_7421_FEMALE_rep1


title: ED776_7418_FEMALE_rep1


title: ED7762_24119_MALE_rep2


title: ED7762_24119_MALE_rep1


title: ED778_7420_MALE_rep1


title: ED779_24110_FEMALE_rep3


title: ED777_7419_MALE_rep2


title: ED777_7419_FEMALE_rep2


title: ED777_7419_FEMALE_rep1


title: ED7762_24119_FEMALE_rep3


title: ED7762_24119_FEMALE_rep2


title: ED775_8907_MALE_rep3


title: ED775_8907_MALE_rep2


title: ED775_8907_MALE_rep1


title: ED775_8907_FEMALE_rep3


title: ED775_8907_FEMALE_rep2


title: ED774_7417_MALE_rep3


title: ED775_8907_FEMALE_rep1


title: ED774_7417_MALE_rep2


title: ED774_7417_MALE_rep1


title: ED774_7417_FEMALE_rep1


title: ED774_7417_FEMALE_rep2


title: ED773_7416_MALE_rep3


title: ED7762_24119_MALE_rep3


title: ED773_7416_MALE_rep1


title: ED773_7416_FEMALE_rep3


title: ED773_7416_FEMALE_rep1


title: ED773_7416_FEMALE_rep2


title: ED773_7416_MALE_rep2


title: ED761_24109_MALE_rep3


title: ED761_24109_MALE_rep2


title: ED774_7417_FEMALE_rep3


title: ED761_24109_MALE_rep1


title: ED761_24109_FEMALE_rep3


title: ED761_24109_FEMALE_rep1


title: ED761_24109_FEMALE_rep2


title: ED7762_24119_FEMALE_rep1


title: ED746_8043_MALE_rep3


title: ED746_8043_FEMALE_rep3


title: ED746_8043_MALE_rep2


title: ED746_8043_MALE_rep1


title: ED729_24134_MALE_rep3


title: ED729_24134_MALE_rep1


title: ED746_8043_FEMALE_rep2


title: ED746_8043_FEMALE_rep1


title: ED729_24134_FEMALE_rep2


title: ED729_24134_FEMALE_rep3


title: ED700_8042_MALE_rep2


title: ED700_8042_MALE_rep3


title: ED700_8042_MALE_rep1


title: ED700_8042_FEMALE_rep3


title: ED700_8042_FEMALE_rep2


title: ED700_8042_FEMALE_rep1


title: ED7007_8936_MALE_rep3


title: ED7007_8936_MALE_rep2


title: ED7007_8936_FEMALE_rep1


title: ED7007_8936_FEMALE_rep2


title: ED7007_8936_MALE_rep1


title: ED7007_8936_FEMALE_rep3


title: ED695_8041_MALE_rep2


title: ED695_8041_MALE_rep3


title: ED695_8041_MALE_rep1


title: ED729_24134_MALE_rep2


title: ED695_8041_FEMALE_rep1


title: ED690_24133_MALE_rep3


title: ED695_8041_FEMALE_rep2


title: ED695_8041_FEMALE_rep3


title: ED729_24134_FEMALE_rep1


title: ED690_24133_MALE_rep1


title: ED632_26659_MALE_rep3


title: ED690_24133_MALE_rep2


title: ED632_26659_MALE_rep1


title: ED632_26659_MALE_rep2


title: ED632_26659_FEMALE_rep2


title: ED632_26659_FEMALE_rep3


title: ED49_9190_FEMALE_rep1


title: ED49_9190_FEMALE_rep3


title: ED49_9190_FEMALE_rep2


title: ED489_24127_MALE_rep1


title: ED489_24127_FEMALE_rep2


title: ED489_24127_FEMALE_rep3


title: ED489_24127_FEMALE_rep1


title: ED479_9189_MALE_rep1


title: ED479_9189_MALE_rep3


title: ED479_9189_MALE_rep2


title: ED475_9273_MALE_rep2


title: ED475_9273_MALE_rep3


title: ED479_9189_FEMALE_rep2


title: ED479_9189_FEMALE_rep1


title: ED475_9273_MALE_rep1


title: ED475_9273_FEMALE_rep3


title: ED4651_8904_MALE_rep3


title: ED475_9273_FEMALE_rep1


title: ED4651_8904_MALE_rep1


title: ED475_9273_FEMALE_rep2


title: ED4651_8904_MALE_rep2


title: ED632_26659_FEMALE_rep1


title: ED4559_24121_MALE_rep1


title: ED4559_24121_MALE_rep2


title: ED4651_8904_FEMALE_rep2


title: ED4651_8904_FEMALE_rep3


title: ED479_9189_FEMALE_rep3


title: ED4651_8904_FEMALE_rep1


title: ED4559_24121_FEMALE_rep3


title: ED4559_24121_FEMALE_rep2


title: ED4559_24121_FEMALE_rep1


title: ED441_24652_MALE_rep1


title: ED441_24652_MALE_rep3


title: ED441_24652_MALE_rep2


title: ED441_24652_FEMALE_rep2


title: ED40_9188_MALE_rep2


title: ED441_24652_FEMALE_rep1


title: ED40_9188_MALE_rep3


title: ED40_9188_FEMALE_rep3


title: ED40_9188_MALE_rep1


title: ED40_9188_FEMALE_rep1


title: ED385_9341_MALE_rep2


title: ED385_9341_MALE_rep3


title: ED40_9188_FEMALE_rep2


title: ED385_9341_FEMALE_rep3


title: ED4559_24121_MALE_rep3


title: ED385_9341_MALE_rep1


title: ED385_9341_FEMALE_rep2


title: ED384_9297_MALE_rep3


title: ED384_9297_MALE_rep1


title: ED384_9297_MALE_rep2


title: ED385_9341_FEMALE_rep1


title: ED441_24652_FEMALE_rep3


title: ED369_8903_MALE_rep2


title: ED369_8903_MALE_rep3


title: ED384_9297_FEMALE_rep1


title: ED384_9297_FEMALE_rep3


title: ED384_9297_FEMALE_rep2


title: ED369_8903_MALE_rep1


title: ED369_8903_FEMALE_rep3


title: ED369_8903_FEMALE_rep1


title: ED354_9187_MALE_rep3


title: ED354_9187_MALE_rep2


title: ED354_9187_MALE_rep1


title: ED354_9187_FEMALE_rep1


title: ED353_9186_MALE_rep3


title: ED354_9187_FEMALE_rep3


title: ED354_9187_FEMALE_rep2


title: ED353_9186_MALE_rep2


title: ED353_9186_MALE_rep1


title: ED353_9186_FEMALE_rep2


title: ED353_9186_FEMALE_rep1


title: ED353_9186_FEMALE_rep3


title: ED347_9272_MALE_rep2


title: ED347_9272_MALE_rep3


title: ED347_9272_MALE_rep1


title: ED343_9185_MALE_rep2


title: ED343_9185_FEMALE_rep3


title: ED343_9185_MALE_rep3


title: ED343_9185_FEMALE_rep1


title: ED343_9185_FEMALE_rep2


title: ED369_8903_FEMALE_rep2


title: ED206_8038_MALE_rep3


title: ED334_9343_MALE_rep2


title: ED206_8038_MALE_rep2


title: ED206_8038_FEMALE_rep3


title: ED334_9343_MALE_rep1


title: ED206_8038_FEMALE_rep2


title: ED206_8038_FEMALE_rep1


title: ED19_8901_MALE_rep3


title: ED19_8901_MALE_rep1


title: ED19_8901_FEMALE_rep3


title: ED1473_9266_MALE_rep3


title: ED19_8901_FEMALE_rep1


title: ED19_8901_MALE_rep2


title: ED19_8901_FEMALE_rep2


title: ED1473_9266_MALE_rep2


title: ED1473_9266_FEMALE_rep2


title: ED1473_9266_FEMALE_rep3


title: ED1473_9266_MALE_rep1


title: ED343_9185_MALE_rep1


title: ED1473_9266_FEMALE_rep1


title: ED1466_9340_MALE_rep3


title: ED334_9343_MALE_rep3


title: ED206_8038_MALE_rep1


title: ED1466_9340_MALE_rep1


title: ED1466_9340_FEMALE_rep2


title: ED1466_9340_MALE_rep2


title: ED1466_9340_FEMALE_rep3


title: ED1466_9340_FEMALE_rep1


title: ED1454_9357_FEMALE_rep2


title: ED1454_9357_MALE_rep2


title: ED1454_9357_FEMALE_rep3


title: ED1454_9357_MALE_rep1


title: ED1454_9357_MALE_rep3


title: ED1378_9682_MALE_rep3


title: ED1378_9682_MALE_rep2


title: ED1454_9357_FEMALE_rep1


title: ED1378_9682_MALE_rep1


title: ED1378_9682_FEMALE_rep3


title: ED1378_9682_FEMALE_rep1


title: ED1378_9682_FEMALE_rep2


title: ED136_9176_MALE_rep1


title: ED136_9176_FEMALE_rep2


title: ED136_9176_FEMALE_rep1


title: ED136_9176_FEMALE_rep3


title: ED134_8900_MALE_rep3


title: ED134_8900_MALE_rep2


title: ED134_8900_FEMALE_rep2


title: ED134_8900_FEMALE_rep3


title: ED134_8900_MALE_rep1


title: ED1317_9175_MALE_rep3


title: ED134_8900_FEMALE_rep1


title: ED1317_9175_MALE_rep2


title: ED1317_9175_MALE_rep1


title: ED1317_9175_FEMALE_rep3


title: ED1315_9269_MALE_rep1


title: ED1317_9175_FEMALE_rep1


title: ED1315_9269_MALE_rep2


title: ED1315_9269_FEMALE_rep3


title: ED1315_9269_FEMALE_rep2


title: ED1315_9269_FEMALE_rep1


title: ED136_9176_MALE_rep2


title: ED1305_9222_MALE_rep3


title: ED136_9176_MALE_rep3


title: ED1305_9222_MALE_rep2


title: ED1317_9175_FEMALE_rep2


title: ED1305_9222_MALE_rep1


title: ED1305_9222_FEMALE_rep1


title: ED1303_8679_MALE_rep3


title: ED1305_9222_FEMALE_rep2


title: ED1303_8679_FEMALE_rep2


title: ED1303_8679_FEMALE_rep1


title: ED1272_24116_MALE_rep3


title: ED1272_24116_MALE_rep2


title: ED1315_9269_MALE_rep3


title: ED1303_8679_FEMALE_rep3


title: ED1303_8679_MALE_rep1


title: ED1272_24116_FEMALE_rep2


title: ED1272_24116_FEMALE_rep1


title: ED12527_24129_MALE_rep2


title: ED1272_24116_FEMALE_rep3


title: ED12527_24129_MALE_rep3


title: ED1272_24116_MALE_rep1


title: ED12527_24129_FEMALE_rep3


title: ED12527_24129_MALE_rep1


title: ED125_24120_MALE_rep2


title: ED125_24120_MALE_rep3


title: ED1305_9222_FEMALE_rep3


title: ED125_24120_MALE_rep1


title: ED125_24120_FEMALE_rep1


title: ED125_24120_FEMALE_rep3


title: ED123_8943_MALE_rep3


title: ED12527_24129_FEMALE_rep2


title: ED125_24120_FEMALE_rep2


title: ED1303_8679_MALE_rep2


title: ED123_8943_FEMALE_rep2


title: ED1231_9174_FEMALE_rep3


title: ED123_8943_FEMALE_rep1


title: ED1231_9174_FEMALE_rep2


title: ED12527_24129_FEMALE_rep1


title: ED1226_9288_MALE_rep1


title: ED1226_9288_FEMALE_rep3


title: ED1226_9288_FEMALE_rep2


title: ED1203_8935_MALE_rep1


title: ED1203_8935_FEMALE_rep3


title: ED1226_9288_MALE_rep2


title: ED123_8943_MALE_rep2


title: ED1226_9288_FEMALE_rep1


title: ED1202_24466_MALE_rep3


title: ED1203_8935_FEMALE_rep2


title: ED1202_24466_MALE_rep2


title: ED1203_8935_MALE_rep2


title: ED1231_9174_FEMALE_rep1


title: ED1203_8935_FEMALE_rep1


title: ED1202_24466_FEMALE_rep2


title: ED123_8943_MALE_rep1


title: ED1226_9288_MALE_rep3


title: ED1203_8935_MALE_rep3


title: ED1202_24466_MALE_rep1


title: ED123_8943_FEMALE_rep3


title: ED1202_24466_FEMALE_rep1


title: ED1200_9173_MALE_rep2


title: ED1200_9173_MALE_rep3


title: ED1200_9173_MALE_rep1


title: ED1200_9173_FEMALE_rep1


title: ED1200_9173_FEMALE_rep2


title: ED1196_24115_MALE_rep3


title: ED1196_24115_FEMALE_rep3


title: ED1196_24115_MALE_rep2


title: ED1202_24466_FEMALE_rep3


title: ED1161_24114_MALE_rep2


title: ED1161_24114_MALE_rep3


title: ED1196_24115_FEMALE_rep1


title: ED1161_24114_FEMALE_rep1


title: ED1196_24115_MALE_rep1


title: ED1161_24114_FEMALE_rep2


title: ED1196_24115_FEMALE_rep2


title: ED1109_8945_MALE_rep3


title: ED1109_8945_MALE_rep2


title: ED1200_9173_FEMALE_rep3


title: ED1109_8945_FEMALE_rep3


title: ED1161_24114_FEMALE_rep3


title: ED1109_8945_MALE_rep1


title: ED1161_24114_MALE_rep1


title: ED108_24629_MALE_rep3


title: ED1109_8945_FEMALE_rep2


title: ED1102_24113_FEMALE_rep1


title: ED1102_24113_FEMALE_rep2


title: ED108_24629_MALE_rep2


title: ED108_24629_MALE_rep1


title: ED108_24629_FEMALE_rep3


title: ED1109_8945_FEMALE_rep1


title: ED108_24629_FEMALE_rep2


title: ED108_24629_FEMALE_rep1


title: ED1054_24112_FEMALE_rep2


title: ED1054_24112_FEMALE_rep3


title: ED105_24118_MALE_rep2


title: ED105_24118_FEMALE_rep3


title: ED1054_24112_FEMALE_rep1


title: ED105_24118_MALE_rep1


title: ED105_24118_FEMALE_rep2


title: ED105_24118_FEMALE_rep1


title: ED1050_8946_MALE_rep1


title: ED1004_25163_MALE_rep3


title: ED1004_25163_MALE_rep1


title: ED1050_8946_FEMALE_rep3


title: ED1004_25163_MALE_rep2


title: ED1004_25163_FEMALE_rep1


title: ED1054_24112_MALE_rep3


title: ED1054_24112_MALE_rep1


title: ED1004_25163_FEMALE_rep2


title: ED1050_8946_MALE_rep2


title: S3 active Chemotype 3 with DMSO and oleic acid 4hrs rep 3

description:
dme_3111043
active_#3_4.3
dme_C7

data_processing:
We mapped reads that passed Chastity (score > 0.6) base-calling filtering (Illumina CASAVA pipeline 1.8.2). Reads were mapped to the Drosophila melanogaster reference genome including ERCC spike-in controls sequences using Tophat 2 (v2.0.10) with parameters -g 1 --library-type fr-firststrand -G Dmel.FB5.57.ERCC.gtf (Trapnell et al., 2009).
Genome reference (Dmel.FB5.57.ERCC.fa ) and gene model (Dmel.FB5.57.ERCC.gtf) used for the analysis correspond to BDGP Release5 and FlyBase Release Dmel.FB5.57. We deleted chrU, chrUextra, from original .fasta and .gff files and add ERCC sequences and  ERCC annotation. We used perl script to convert .gff to .gtf file and make it compatible with Tophat 2 and other downstream software
To include all annotated genes and RNA species in the downstream analysis and HTSeq read counts we changed the feature type (third column in gff/gtf file formats) for miRNA genes from “miRNA” to “exon”, because it was the only one RNA species without exon annotation.
We used bowtie (v.2-2.1.0) implemented in Tophat 2 to make Bowtie indexes for genome. We used samtools (v0.1.19) (Li et al., 2009) to make indexes for chromosomes and to sort, merge alignments, and for reads statistics. Mapped reads at the gene-level were counted by HT-Seq (0.5.4p1) (Anders et al., 2014) with parameter --stranded=reverse -i gene_id -t exon and the same annotation used in mapping.
We calculated and normalized gene expression levels for each replicate using Cufflinks (2.1.1) (Roberts et al., 2011) with output FPKM value for each gene. Statistics to determine differentially expressed genes between samples was done using Cuffdiff (2.1.1.) (Trapnell et al., 2013).
Genome_build: Drosophila melanogaster Release 5
Supplementary_files_format_and_content: gene_dme_fpkm_cufflinks.4.txt file contains matrix with FPKM value for 36 samples. Column names in the file correspong to sample names in the Samples table, row names - correspond to FlyBase gene_ID.
Supplementary_files_format_and_content: dme_HTSeq_raw_read_counts.4.txt file contains matrix with raw read counts for 36 samples. Column names in the file correspong to sample names in the Samples table, row names - correspond to FlyBase gene_ID.
Supplementary_files_format_and_content: Supplementary.TableX1(gene_dme_fpkm_cuffdiff).xlsx contains matrix with a summary of one of the output file from CuffDiff with FPKM values for each gene for each sample, have README sheet.
Supplementary_files_format_and_content: Supplementary.TableX2(gene_dme_diff_cuffdiff).xlsx contains matrix with a summary of one of the output file from CuffDiff indicating significance of difference of  gene expression between two samples, have README sheet.

source_name: cell line

growth_protocol: 2 x 106 Drosophila S3 cells (obtained from the Drosophila Genomics Resources Center) per 6-well were seeded in 2mL of Scheider's medium supplemented with 10% heat-inactivated serum and penicillin/streptomycin and grown over night

extract_protocol:
The plates were removed from the -80°C freezer, and RNA was extracted with the RNeasy Mini Kit (Qiagen, West Sussex, UK) according to the manufacturer's instructions. In brief, the cells were resuspended in 600µL of the RLT buffer provided with the kit. The RLT buffer was supplemented with 40µL of a 1M DTT solution per mL of RLT buffer. Otherwise, the standard protocol was followed and RNA was eluted by 2 times 30µL. Purified total RNA was stored at -80°C until further use. Dynabeads Oligo (dT)25 (Life Technologies, Carlsbad, CA) were used to purify mRNA according to manufacturer instructions, except that we used 200ng of total RNA adjusted the volume to 50µl with dH2O, added 10µl of the washed Dynabeads in a 50µl binding buffer slurry, heated the samples at 65°C for 5min and immediately chilled on ice.
To prepare RNA-Seq stranded libraries we modified an existing protocol (Wang et al., 2011). All steps were done using 96-well PCR plates (USA Scientific, Ocala, Fl). We incubated all reactions in a Tetrad PTC-225 Termal Cycler (MJ Research, Waltham, MA). To clean up enzymatic reactions and size select library fragments at any of several steps below, we used 0.1% w/v carboxyl-modified Sera-Mag Magnetic Speed-beads (MagNA beads, Thermo Fisher Scientific, Waltham, MA) in XP buffer [20% PEG 8000, 2.5 M NaCl, (Sigma Aldrich, St. Louis, MO)] following protocol (Rohland and Reich, 2012), except that we incubated samples with beads for 10 min and used 80% ethanol for washing. For cleaning without size-selection we used 1.6X MagNA beads in XP buffer (except where noted) and for selecting fragments > 200bp - 1X MagNA beads in XP buffer. Unless noted, we left the beads in the sample after each step. We used Alpaqua 96R Ring Magnet Plates (Alpaqua, Beverly, MA) for magnetic bead separation. We measured RNA quantity with Quant-iTª RiboGreen and DNA with Quant-iTª PicoGreen (Invitrogen, Carlsbad, CA) in 384-well plates, PS, Fluotrac 600, black (Greiner Bio-One Inc, Longwood, Fl) using a Gemini EM Fluorescence Microplate Reader (Molecular Devices, Sunnyvale, CA) according to manufacturer instructions. We used Agilent Bioanalyzer RNA chips and High Sensitivity DNA chips on the 2100 Bioanalyzer system (Agilent, Santa Clara, CA) according to manufacturer instructions and visually inspected electrophoregrams for sharp peaks for simple pass/fail calls based on signs of obvious degradation and to check for library size and adapter dimer contamination.
We fragmented mRNA bound to Dynabeads at 94°C for 8min in 16µl of 1.25X first strand MMuLV RT buffer (New England Biolabs, Beverly, MA), with 100ng random primers (Invitrogen, Carlsbad, CA), and 10pg ERCC spike-in controls (Jiang et al., 2011) from pools 78A and 78B (Zook et al., 2012) obtained from Marc Salit (NIST, National Institute of Standards and Technology, Gaithersberg MD). We chilled the samples immediately on ice for 2min and eluted from the beads. We transferred 15µl of the eluate to fresh 96-well PCR plate. We added 5µl of the first strand synthesis mixture [0.3mM dNTPs, 5mM DTT, and 10U M-MuLV RT (New England Biolabs, Beverly, MA), and 0.5U SuperRase-In (Life Technologies, Carlsbad, CA)] to the fragmented RNA in the fragmentation buffer and performed a reverse transcription reaction. We bound RNA/cDNA hybrid with 32µl MagNA bead XP buffer slurry, washed, and eluted samples in 16µl of dH2O. We then performed a second strand synthesis with dUTP by adding 5µl of 1X NEB buffer2 (New England Biolabs, Beverly, MA), with 1mM each of dATP, dCTP, dGTP and 2mM dUTP (Thermo Fisher Scientific, Waltham, MA), 10U DNA PolI, 2.5U RNAseH, and 2.5mM DTT (New England Biolabs, Beverly , MA) and incubated at 16°C for 5 hours. We rebound, washed, and eluted as above. We repaired ends by adding 4µl of NEBNext End Repair Module (New England Biolabs, Beverly, MA) to the eluate following manufacturer instruction. We then rebound samples to MagNA beads, washed, and eluted as above. Next we performed dA-tailing by adding 4µl of 1X Blue Buffer, with 1U Klenow 3’-5’ exo- (Enzymatics, Beverly, MA) and 1mM dATP, to the eluate and incubated at 37°C for 30min. We then rebound samples to MagNA beads and washed as above, eluted with 21µl dH2O, and transferred 10µl of cDNA without beads to each of two fresh plates. One plate was used in the following and one plate was frozen as a back-up. We ligated RNA Adapter Indexes AR001-AR016, AR018-AR023, AR025, and AR027 (Illumina, San Diego, CA) to dsDNA by adding 1µl of an adapter to each 10µl sample and 13µl of 1X Rapid Ligation Buffer with 30U T4 DNA Ligase (Enzymatics, Beverly, MA), and incubated at 25°C for 10min. We stopped reactions with a final concentration of 0.01M EDTA. We added 25µl MagNA beads XP buffer slurry (final PEG = 13.6%), bound cDNA to the beads, washed and eluted in 30µl of dH2O as above. We size-selected libraries by adding 1X XP buffer (30µl), washed, eluted samples with 24µl dH2O, and transferred 23µl of cDNA without beads to fresh plate. 11.5µl of the eluate was transferred to another plate and used in the next step; the remaining samples were frozen as a back-up. We mixed dsDNA product with 2.5U (0.5µl) of Uracil DNA Glycosylase (New England Biolabs, Beverly, MA) and 3µl of PCR Primer Cocktail (Illumina, San Diego, CA) and incubated at 37°C for 30min to digest the second strand DNA. We added 15µl 2X KAPA HiFi HotStart ReadyMix (Kapa Biosystems, Woburn, MA) directly to the UDG digested DNA mixture and performed a PCR amplification with the following programmed cycle: 95°C for 2min, followed by 12 cycles of 98°C for 20sec, 65°C for 30sec, and 72°C for 30sec; then 72°C for 5min. We purified product by adding 30µl MagNa beads XP buffer slurry, eluted in 30µl dH2O and transferred 29µl of cDNA library without beads to a fresh plate as described above. To assay plate-level failure, we took 11 samples from each 96-well plate and examined electropherograms for the strong signal in the 300-350 bp library target size and weak signal in the 100-150bp range (primer dimer products).

treatment_protocol: On day 2 of the experiment, the medium was replaced by Schneider's medium supplemented with 5% heat-inactivated serum, penicillin/streptomycin and the respective medium additions such as 0.1% DMSO, 200µM oleic acid and 1µM of the given small molecule as well as combinations of the different additives (see sample overview). After four hours, the medium was removed and the cells were washed twice with PBS and in the end the plate was frozen @ -80°C until RNA extraction.

tag: cell line

tag: compound

tag: dmso

tag: oleic acid

tag: incubation time


title: S3 inactive Chemotype 3 with DMSO and oleic acid 4hrs rep 2

description:
dme_3011042
inactive_#3_4.2
dme_E7


title: S3 active Chemotype 3 with DMSO and oleic acid 4hrs rep 2

description:
dme_3111042
active_#3_4.2
dme_B7


title: S3 inactive Chemotype 3 with DMSO and oleic acid 4hrs rep 3

description:
dme_3011043
inactive_#3_4.3
dme_F7


title: S3 inactive Chemotype 3 with DMSO and oleic acid 4hrs rep 1

description:
dme_3011041
inactive_#3_4.1
dme_D7


title: ED1054_24112_MALE_rep2


title: ED105_24118_MALE_rep3


title: S3 inactive Chemotype 2 with DMSO and oleic acid 4hrs rep 3

description:
dme_2011043
inactive_#2_4.3
dme_H6


title: ED1050_8946_MALE_rep3


title: ED1050_8946_FEMALE_rep1


title: ED1050_8946_FEMALE_rep2


title: S3 active Chemotype 2 with DMSO and oleic acid 4hrs rep 2

description:
dme_2111042
active_#2_4.2
dme_D6


title: S3 active Chemotype 2 with DMSO and oleic acid 4hrs rep 1

description:
dme_2111041
active_#2_4.1
dme_C6


title: S3 inactive Chemotype 2 with DMSO and oleic acid 4hrs rep 2

description:
dme_2011042
inactive_#2_4.2
dme_G6


title: S3 active Chemotype 2 with DMSO and oleic acid 4hrs rep 3

description:
dme_2111043
active_#2_4.3
dme_E6


title: S3 inactive Chemotype 1 with DMSO and oleic acid 4hrs rep 1

description:
dme_1011041
inactive_#1_4.1
dme_H5


title: S3 inactive Chemotype 1 with DMSO and oleic acid 4hrs rep 3

description:
dme_1011043
inactive_#1_4.3
dme_B6


title: S3 inactive Chemotype 2 with DMSO and oleic acid 4hrs rep 1

description:
dme_2011041
inactive_#2_4.1
dme_F6


title: ED1004_25163_FEMALE_rep3


title: S3 active Chemotype 1 with DMSO and oleic acid 4hrs rep 3

description:
dme_1111043
active_#1_4.3
dme_G5


title: S3 active Chemotype 1 with DMSO and oleic acid 4hrs rep 2

description:
dme_1111042
active_#1_4.2
dme_F5


title: S3 DMSO and oleic acid 4hrs rep 1

description:
dme_0011041
vehicle_OA_4.1
dme_G4


title: S3 DMSO and oleic acid 4hrs rep 2

description:
dme_0011042
vehicle_OA_4.2
dme_H4


title: S3 DMSO and oleic acid 4hrs rep 3

description:
dme_0011043
vehicle_OA_4.3
dme_A5


title: S3 active Chemotype 1 with DMSO and oleic acid 4hrs rep 1

description:
dme_1111041
active_#1_4.1
dme_E5


title: S3 oleic acid 4hrs rep 6

description:
dme_0001046
OA_4.6
dme_D2


title: S3 oleic acid 4hrs rep 5

description:
dme_0001045
OA_4.5
dme_C2


title: S3 DMSO 4hrs rep 3

description:
dme_0010043
vehicle_noOA_4.3
dme_C4


title: S3 DMSO 4hrs rep 2

description:
dme_0010042
vehicle_noOA_4.2
dme_B4


title: S3 DMSO 4hrs rep 1

description:
dme_0010041
vehicle_noOA_4.1
dme_A4


title: S3 oleic acid 4hrs rep 1

description:
dme_0001041
OA_4.1
dme_G1


title: S3 oleic acid 4hrs rep 3

description:
dme_0001043
OA_4.3
dme_A2


title: S3 inactive Chemotype 1 with DMSO and oleic acid 4hrs rep 2

description:
dme_1011042
inactive_#1_4.2
dme_A6


title: S3 none 4hrs rep 6

description:
dme_0000046
noOA_4.6
dme_F1


title: S3 oleic acid 4hrs rep 2

description:
dme_0001042
OA_4.2
dme_H1


title: S3 oleic acid 4hrs rep 4

description:
dme_0001044
OA_4.4
dme_B2


title: S3 none 4hrs rep 5

description:
dme_0000045
noOA_4.5
dme_E1


title: S3 none 4hrs rep 3

description:
dme_0000043
noOA_4.3
dme_C1


title: Df(2L)ED441/+_male_rep2

data_processing:
Basecalls performed using CASAVA version 1.8.2.
RNA-Seq reads were aligned to the Drosophila genome assembly (Berkley Drosophila Genome Project Release 5, obtained from FlyBase. http://www.flybase.org) using TopHat 2.0.10 (Trapnell et al., 2009. Bioinformatics) with -g 1 and -G parameters. As a gene model for the -G parameter, we used an annotation file from FlyBase (5.57) where we removed genes from uncertain physical locations (e.g., chrU and chrUextra).
From the alignment result, abundance of transcripts were measured as read counts using HTseq (Anders et al., 2014. Bioinformatics) with default options (-m union -t exon).
From the alignment result, Fragments per Kilobase per Million mapped reads (FPKM) values were calculated using Cufflinks (Trapnell et al., 2010. Nature Biotechnology). We used -G, -b, and -u parameters in running Cufflinks.
Genome_build: Release 5
Supplementary_files_format_and_content: Tab-delimited text files that are generated from HTseq and Cufflink. Each contains read counts and FPKM values, respectively, at gene level.

source_name: Whole animal

growth_protocol: The Drosophila deletion stocks were generated by DrosDel (http://www.drosdel.org.uk) as described in (Ryder et al., 2007). Flies were maintained at 25oC on standard yeast/cornmeal medium (Fly Facility, University of Cambridge, UK). We crossed males from DrosDel lines to w1118 virgin females to generate hemizygotes without balancer chromosomes. The w1118 line we used is the parental line for the DroDel project, so all flies are isogenic other than for the deleted region they carry. We prepared duplicates of 15-25 sexed Df/+ progeny (mean 21.65, standard deviation 7.4) 5 days post eclosion for RNA extraction.

extract_protocol:
Flies were homogenized in 500 μl of RNAlater solution (Life Technologies, Grand Island, NY, USA) for 90 seconds in 96 deep well plates with 3 mm tungsten carbide beads (Qiagen, West Sussex, UK) using a Qiagen Tissue Lyser II (Qiagen, West Sussex, UK). Extraction of total RNA was performed using the RNeasy 96 kit (Qiagen, Valencia, CA, USA) based on the manufacturer's guide (Protocol for Isolation of Total RNA from animal cells using QIAvac96 vacuum manifold, Cat#19504). We made a minor modification to dilute the RNAlater solution, so instead of mixing 150 μl of RLT buffer (Qiagen, Cat#79216) and 150 μl of 70% ethanol, we mixed 150 μl of RLT buffer, 120 μl of 100% ethanol, and 30 μl of lysate in RNAlater and applied this to the extraction columns.
Libraries were prepared using Illumina's (San Diego, CA, USA) TruSeq RNA sample preparation kit v2 - set A and B (Cat # RS-122-200). RNA amount was quantified using RiboGreen kits (Life Technology, Grand Island, NY, USA). 100 ng of RNA was used as input to follow the 1/2 scaled protocol from the original manufacturer's High Sample Protocol (Illumina, Part# 15026495 Rev. C). We added 10 pg (353 samples) or 500 pg (43 samples) of external RNAs as spike-in during the 8 minute RNA fragmentation step. The constructed libraries were sequenced with a HiSeq 2000 (Illumina, San Diego, CA, USA).

tag: tissue

value: Whole animal

tag: gender

value: male


title: S3 none 4hrs rep 1

description:
dme_0000041
noOA_4.1
dme_A1


title: S3 none 4hrs rep 4

description:
dme_0000044
noOA_4.4
dme_D1


title: S3 none 4hrs rep 2

description:
dme_0000042
noOA_4.2
dme_B1


title: Df(2L)ED441/+_male_rep1


title: Df(2L)ED441/+_female_rep2

value: female


title: Df(2L)ED108/+_male_rep1


title: Df(2L)ED108/+_female_rep2


title: Df(2L)ED108/+_female_rep1


title: Df(2L)ED50001/+_male_rep2


title: Df(2L)ED50001/+_male_rep1


title: Df(2L)ED1202/+_male_rep2


title: Df(2L)ED50001/+_female_rep2


title: Df(2L)ED1202/+_male_rep1


title: Df(2L)ED1202/+_female_rep2


title: Df(2L)ED50001/+_female_rep1


title: Df(2L)ED1202/+_female_rep1


title: Df(2L)ED8142/+_male_rep2


title: Df(2L)ED8142/+_male_rep1


title: Df(2L)ED8142/+_female_rep2


title: Df(2L)ED729/+_male_rep2


title: Df(2L)ED729/+_female_rep1


title: Df(2L)ED729/+_female_rep2


title: Df(2L)ED8142/+_female_rep1


title: Df(2L)ED729/+_male_rep1


title: Df(2L)ED690/+_male_rep2


title: Df(2L)ED108/+_male_rep2


title: Df(2L)ED690/+_male_rep1


title: Df(2L)ED629/+_male_rep1


title: Df(2L)ED690/+_female_rep1


title: Df(2L)ED441/+_female_rep1


title: Df(2L)ED629/+_male_rep2


title: Df(2L)ED690/+_female_rep2


title: Df(2L)ED629/+_female_rep2


title: Df(2L)ED578/+_male_rep2


title: Df(2L)ED578/+_male_rep1


title: Df(2L)ED578/+_female_rep1


title: Df(2L)ED548/+_male_rep2


title: Df(2L)ED578/+_female_rep2


title: Df(2L)ED548/+_male_rep1


title: Df(2L)ED548/+_female_rep1


title: Df(2L)ED12527/+_male_rep1


title: Df(2L)ED548/+_female_rep2


title: Df(2L)ED12527/+_female_rep2


title: input_mDNA_new3

city: Los Angeles

first: Andrew

middle: P

last: McMahon

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

data_processing:
Base call by bcl2fastq v. 2.17
Fastq files were aligned using Novoalign. Human data was aligned to hg19, and mouse data was aligned to mm9.
ChIP-Seq peaks were called using QuEST (Valouev et al., 2008).
peak files were generated by extracting the chromosome numbers coordinates and QuEST enrichment score from QuEST.out files
wig profiles were generated using QuEST
Genome_build: hg19/mm9
Supplementary_files_format_and_content: wiggle files represents ChIP-Seq tags; peak files

source_name: mouse embryonic kidney

extract_protocol:
Cortex of human embryonic kidneys were micro-dissected and fixed in crosslinking buffer containing 1% PFA for 30 min, then homogenized, followed by chromatin extraction and sonication. Sonicated chromatin was then immuno-precipitated with the indicated antibodies. The precipitated DNA was subsequently collected with Qiagen PCR product purification kit. Mouse embryonic kidneys were processed in a similar way.
Libraries were constructed using ThruPLEX-FD Prep Kit (Rubicon Genomics), and subsequently sequenced by Illumina HiSeq 2000.

tag: developmental stage

value: 16.5 days

value: Swiss Webster


title: input_mDNA_new1


title: input_mDNA_new2


title: mSix2_hu_ChIP-Seq_3

value: SIX2 antibody (MyBiosource, MBS610128)


title: Df(2L)ED12527/+_female_rep1


title: Df(2L)ED501/+_male_rep2


title: Df(2L)ED501/+_male_rep1


title: mSix2_hu_ChIP-Seq_1


title: Df(2L)ED629/+_female_rep1


title: mSix2_hu_ChIP-Seq_2


title: Df(2L)ED501/+_female_rep1


title: Df(2L)ED501/+_female_rep2


title: mSix2_ms_ChIP-Seq_1

value: Six2 antibody (Proteintech,11562-1-AP)


title: mSix2_ms_ChIP-Seq_3


title: Df(2L)ED489/+_male_rep1


title: Df(2L)ED489/+_female_rep2


title: Df(2L)ED489/+_male_rep2


title: Df(2L)ED7853/+_female_rep2


title: Df(2L)ED7853/+_male_rep2


title: Df(2L)ED12527/+_male_rep2


title: Df(2L)ED247/+_female_rep2


title: Df(2L)ED247/+_male_rep1


title: Df(2L)ED247/+_female_rep1


title: Df(2L)ED243/+_male_rep2


title: Df(2L)ED243/+_male_rep1


title: albumen 1

city: Heverlee

first: Els

last: Willems

state: Antwerp

address: Kasteelpark Arenberg 30 box 2456

department: Biosystems

country: Belgium

institute: KU Leuven

data_processing:
Sequencing of all samples was carried out in 1 lane of 1 flow cell on the HiSeq2000 (Illumina), using single end chemistry with read lengths of 50 base pairs.
The quality of the reads was verified using the FASTQC software (Illumina) with all the reads having passed the Phred score (≥ 28).
Reads were mapped to the chicken genome (Galgal4.71) using TopHat (v2.0.8b)
Quality filtering was performed with SAMtools (0.1.19-44428cd) removing all reads from the alignment that are non-primary mappings or have a mapping quality ≤ 20
Per sample, the transcripts were identified from the mapping with Cufflinks v2.1.1
With the Cuffmerge tool, all per-sample transcript lists were merged together with the reference annotation into one file.
With Cuffcompare, the identified transcripts were matched with known transcripts and genes, based on overlapping coordinates on the reference genome.
The number of reads in the alignments that overlap with the gene features were counted using HTSeq-count (0.5.4p3). The reads that could  be attibuted to more than one gene (ambiguous, about 1.3 million per sample) or could not be attributed to any gene (no feature, about 1.1 million per sample) were not counted.
Genes that had less than 1 counts-per-million were considered ‘absent’ and therefore removed from the dataset
Per sample, GC-content was corrected using full quantile normalization on bins of GC-content with the EDASeq package from Bioconductor for within-sample normalisation.
Between-sample normalization was carried out to correct for library size and RNA composition, as it is known that these are sources of large variation, using full quantile normalization with the EDASeq package from Bioconductor
The statistical modelling assumed the design of the experiment as log (Count) = β1 x control + β2 x sham + β3 albumen-deprived. For each gene, the coefficiënts β were estimated with the EdgeR package (3.2.3) of Bioconductor, by fitting a negative binomial generalized linear model (GLM). The following comparisons were tested: control vs albumen-deprived, sham vs albumen-deprived and sham vs.control.
Genome_build: Galgal4.71

organism: Gallus gallus

source_name: Liver cells

growth_protocol: Fertilized Isa Brown layer-type eggs (Vepymo, Poppel, Belgium) were randomly divided over the three treatments (control, sham and albumen-deprived). The eggs were incubated with the blunt end up in a forced-draft incubator (PAS Reform, the Netherlands) at a dry bulb temperature of 37.6°C and a wet bulb temperature of 29.0°C and were turned every hour over 90°. After hatch, only the female chicks were reared in floor pens with wood shavings as litter until 55 weeks of age. All floor pens were located in one environmentally controlled room. Room temperature was initially set at 34°C and was gradually decreased until 20°C at 5 weeks of age. This temperature was maintained until 55 weeks of age. A 23 h light cycle was initially provided and gradually decreased to 10 h at 6 weeks. At 14 weeks, the light cycle was gradually prolonged to 15 h at 19 weeks to stimulate sexual maturation. The hens received soy-wheat-corn based diets ad libitum formulated according to the developmental requirements based on the Isa Brown Management Guide (Research Diet Services, Wijk bij Duurstede, the Netherlands). At 55 weeks of age, the laying hens were killed and 8 liver samples per group were randomly collected and snap frozen in liquid nitrogen before storage at -80°C. Frozen liver tissue was homogenized by grinding into powder in liquid nitrogen before use.

extract_protocol:
Total RNA was extracted using 750 µl of TRIzol (Invitrogen, Paisley, UK) added to approximately 50 mg of crushed liver sample taken at 55 weeks of age (n = 8 per group), and incubated for 5 min at room temperature. 300 µl of chloroform (Sigma Aldrich, St. Louis, MO, USA) was added to create a phase separation. After a short vortex step, the samples were centrifuged at 14,000 rpm for 15 min at 4°C. The aqueous phase was transferred to fresh tubes, mixed with 375 µl ice-cold isopropanol (Prolabo, VWR, West Chester, PA, USA) and incubated for 10 min at room temperature. After centrifugation (14,000 rpm, 10 min, 4°C), the supernatant was discarded and the remaining RNA pellet was washed with 750 µl ice-cold 70% ethanol (Prolabo). After a final centrifugation step (7,500 rpm, 5 min, 4°C), the supernatant was carefully removed and the remaining RNA pellet was dissolved in 1: 1000 DEPC-treated water (Fluka). The RNA concentration and quality (260/280 ratio) was measured using UV-spectroscopy (Implen, Westburg, Leusden, The Netherlands). In addition, the integrity of RNA samples was verified on the BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA).
Samples (n = 3 per group, 2 µg RNA) were prepared by TruSeq library preparation (RS122, Illumina, San Diego, CA, USA) to generate single end unstranded sequencing libraries, according to the manufacturer’s recommendations.

treatment_protocol: Preliminary experiments were conducted to determine the optimal timing, amount and method for albumen removal. After one day of incubation, albumen removal was established in the albumen-deprived group. Eggs were first disinfected with 70% ethanol and iso-Betadine (Meda Manufacturing, Merignac, France). After drilling a hole near the sharp end of the egg, using an electric drill (Dremel, Robert Bosch Tool Corporation, Mount Prospect, Illinois), 3 ml of albumen was removed using a 18 G needle (Neolus, Terumo, Tokyo, Japan) and 5 ml syringe (Terumo, Tokyo, Japan). Caution was taken to insert the needle as shallow as possible to minimize disturbance in the egg. The removed albumen was replaced by about the same volume of sterile saline using a 21 G needle (Neolus, Terumo, Tokyo, Japan) and 5 ml syringe (Terumo, Tokyo, Japan). Finally, the hole was sealed using a drop of paraffin. The sham group was mock-treated, similar to the albumen-deprived group, except for the actual albumen removal and saline injection. A third group received no treatment (control group).

value: Adult hen (55 weeks of age)

value: Isa Brown laying hen

tag: sample coding

tag: barcode

value: ATCACG


title: sham 2

value: ACAGTG


title: sham 3

value: GATCAG


title: albumen 2

value: CGATGT


title: albumen 3

value: ACTTGA


title: Df(2L)ED489/+_female_rep1


title: control 3

value: CAGATC


title: control 2

value: GCCAAT


title: mSix2_ms_ChIP-Seq_2


title: control 1

value: TTAGGC


title: Df(2L)ED243/+_female_rep1

value: Whole animal


title: sham 1

value: TGACCA


title: Tfh_IgG

first: Huiping

last: Lu

address: Tsinghua university

institute: Tsinghua university

description: control sample for Tfh_Bcl6

data_processing:
Basecalls performed using CASAVA version 1.8.2.
ChIP-seq reads were aligned to the mm9 genome using bowtie.
peaks were called using SICER version 1.1.
Genome_build: mm9
Supplementary_files_format_and_content: wig file generated using SICER version 1.1

source_name: in vivo-generated T follicular helper (Tfh) cells from Bcl6-RFP reporter mice

extract_protocol:
Bcl6-DNA complex was isolated by anti-Bcl6 antibody (SC858 (N-3), Santa Cruz)
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Prep Kit.

value: IgG


title: Df(2L)ED243/+_female_rep2

value: female


title: Df(2L)ED4559/+_male_rep1

value: male


title: Df(2L)ED4559/+_female_rep2


title: Tfh_Bcl6


title: nonTfh_Bcl6

description: control sample for Tfh_Bcl6

source_name: in vivo-generated non-T follicular helper (nonTfh) cells from Bcl6-RFP reporter mice


title: Df(2L)ED7853/+_female_rep1


title: Df(2L)ED125/+_male_rep2


title: Df(2L)ED4559/+_female_rep1


title: Df(2L)ED125/+_male_rep1


title: Df(2L)ED7762/+_male_rep2


title: Df(2L)ED125/+_female_rep2


title: Df(2L)ED125/+_female_rep1


title: Df(2L)ED7762/+_female_rep1


title: Df(2L)ED7762/+_female_rep2


title: Df(2L)ED105/+_male_rep1


title: Df(2L)ED105/+_female_rep2


title: Df(2L)ED105/+_male_rep2


title: Df(2L)ED1272/+_male_rep2


title: Df(2L)ED105/+_female_rep1


title: Df(2L)ED1272/+_male_rep1


title: Df(2L)ED1196/+_female_rep1


title: Df(2L)ED1196/+_male_rep2


title: Df(2L)ED1196/+_female_rep2


title: Df(2L)ED1196/+_male_rep1


title: Df(2L)ED1161/+_female_rep2


title: Df(2L)ED1161/+_male_rep2


title: Df(2L)ED1272/+_female_rep2


title: Df(2L)ED1102/+_male_rep2


title: Df(2L)ED1102/+_male_rep1


title: Df(2L)ED1161/+_female_rep1


title: Df(2L)ED1102/+_female_rep2


title: Df(2L)ED7762/+_male_rep1


title: Df(2L)ED1054/+_female_rep2


title: Df(2L)ED1054/+_male_rep1


title: Df(2L)ED1054/+_male_rep2


title: Df(2L)ED1054/+_female_rep1


title: Df(2L)ED8185/+_female_rep2


title: Df(2L)ED1272/+_female_rep1


title: Df(2L)ED1161/+_male_rep1


title: Df(2L)ED8185/+_male_rep2


title: Df(2L)ED779/+_male_rep1


title: Df(2L)ED779/+_female_rep2


title: Df(2L)ED8185/+_male_rep1


title: Df(2L)ED8185/+_female_rep1


title: Df(2L)ED761/+_male_rep2


title: Df(2L)ED779/+_male_rep2


title: Df(2L)ED761/+_female_rep2


title: Df(2L)ED779/+_female_rep1


title: Df(2L)ED1378/+_male_rep2


title: Df(2L)ED761/+_female_rep1


title: Df(2L)ED761/+_male_rep1


title: Df(2L)ED1378/+_male_rep1


title: Df(2L)ED7853/+_male_rep1


title: S3 active Chemotype 3 with DMSO and oleic acid 4hrs rep 1

description:
dme_3111041
active_#3_4.1
dme_A7


title: Df(2L)ED1378/+_female_rep2


title: Df(2L)ED1454/+_male_rep2


title: Df(2L)ED1378/+_female_rep1


title: Df(2L)ED1102/+_female_rep1


title: Df(2L)ED1454/+_male_rep1


title: Df(2L)ED1454/+_female_rep2


title: Df(2L)ED5878/+_male_rep2


title: Df(2L)ED1454/+_female_rep1


title: Df(2L)ED5878/+_female_rep2


title: Df(2L)ED5878/+_female_rep1


title: Df(2L)ED334/+_male_rep1


title: Df(2L)ED334/+_male_rep2


title: Df(2L)ED680/+_female_rep1


title: Df(2L)ED680/+_male_rep1


title: Df(2L)ED334/+_female_rep2


title: Df(2L)ED680/+_female_rep2


title: Df(2L)ED680/+_male_rep2


title: Df(2L)ED385/+_male_rep1


title: Df(2L)ED385/+_male_rep2


title: Df(2L)ED1466/+_male_rep1


title: Df(2L)ED1466/+_female_rep2


title: Df(2L)ED334/+_female_rep1


title: Df(2L)ED1466/+_male_rep2


title: Df(2L)ED385/+_female_rep2


title: Df(2L)ED385/+_female_rep1


title: Df(2L)ED611/+_male_rep2


title: Df(2L)ED1466/+_female_rep1


title: Df(2L)ED611/+_male_rep1


title: Df(2L)ED5878/+_male_rep1


title: Df(2L)ED611/+_female_rep2


title: Df(2L)ED384/+_male_rep2


title: Df(2L)ED611/+_female_rep1


title: Df(2L)ED384/+_male_rep1


title: Df(2L)ED384/+_female_rep2


title: Df(2L)ED384/+_female_rep1


title: Df(2L)ED1226/+_male_rep1


title: Df(2L)ED1226/+_male_rep2


title: Df(2L)ED1226/+_female_rep1


title: Df(2L)ED499/+_male_rep2


title: Df(2L)ED499/+_male_rep1


title: Df(2L)ED347/+_male_rep2


title: Df(2L)ED475/+_male_rep1


title: Df(2L)ED499/+_female_rep1


title: Df(2L)ED475/+_female_rep1


title: Df(2L)ED347/+_female_rep1


title: Df(2L)ED347/+_male_rep1


title: Df(2L)ED475/+_female_rep2


title: Df(2L)ED250/+_male_rep2


title: Df(2L)ED250/+_female_rep2


title: Df(2L)ED1315/+_male_rep1


title: Df(2L)ED347/+_female_rep2


title: Df(2L)ED1315/+_male_rep2


title: Df(2L)ED279/+_male_rep2


title: Df(2L)ED1315/+_female_rep2


title: Df(2L)ED279/+_male_rep1


title: Df(2L)ED250/+_female_rep1


title: Df(2L)ED279/+_female_rep2


title: Df(2L)ED279/+_female_rep1


title: Df(2L)ED250/+_male_rep1


title: Df(2L)ED1226/+_female_rep2


title: Df(2L)ED1473/+_male_rep2


title: Df(2L)ED1473/+_male_rep1


title: Df(2L)ED475/+_male_rep2


title: Df(2L)ED499/+_female_rep2


title: Df(2L)ED1473/+_female_rep2


title: Df(2L)ED1305/+_male_rep2