title: 75_2_DCA_FFPE


title: 98_3.5_DCA_FFPE

status: Public on Aug 30 2016

type: SRA

city: RTP

first: Susan

last: Hester

state: NC

address: 109 TW Alexander Dr

country: USA

institute: US EPA

library_source: transcriptomic

data_processing:
After sequencing, basecall files were converted into FASTQ output files using Illumina CASAVA software and other tools developed at EA (available at https://github.com/ExpressionAnalysis/ ea-utils/). FASTQ data were demultiplexed, and sequencing adapters and other low quality bases were clipped to prepare reads for alignment using fastq-mcf --max-ns 4 --qual-mean 25 -H -p 5 -q 7 -l 25 -l 25
Filtered reads were mapped to mm10.fa using Star 2.4 with parameters --readFilesCommand zcat --chimSegmentMin 15 --chimJunctionOverhangMin 17 --chimScoreMin 1 --chimScoreDropMax 20 --chimScoreSeparation 10 --quantMode TranscriptomeSAM --outSAMattributes NH  --alignSJoverhangMin 8 --sjdbScore 3 --outSAMunmapped Within --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --sjdbOverhang 200
BAM files resulting from Star 2.4 were used as input for rsem-calculate-expression using default parameters.
Raw read counts were normalized across all samples using upper quartile normalization.
Genome_build: MM10
Supplementary_files_format_and_content: tab-delimited files with estimated counts for all genes and FPKM normalized counts for all genes

molecule: total RNA

organism: Mus musculus

source_name: formalin-fixed paraffin embedded left lateral and right media liver lobes

growth_protocol: Studies were conducted in 4 week-old male B6C3F1 mice maintained under standard housing conditions at the U.S. Environmental Protection Agency (US EPA) AAALAC-accredited animal facility (Research Triangle Park, NC). Animal care and procedures were conducted under protocols approved by the Institutional Animal Care and Use Committee of the USEPA.

extract_protocol:
For liquid nitrogen frozen (FROZ) liver samples, ~20 mg of liver tissue per sample was homogenized in RNAzol®RT , purified with the Qiagen RNeasy MinElute column protocol, evaluated for integrity using an Agilent 2100 Bioanalyzer, and quantitated using a Qubit fluorometer. For FFPE liver samples, four 10-μm sections were collected from each tissue block using a Leica RM 2155 microtome. FFPE sample were deparaffinized using Qiagen Deparaffinization Solution and RNA isolated and purified according to Qiagen AllPrep DNA/RNA FFPE Kit protocol. FFPE RNA quantitated as for FROZ samples.
Total RNA was converted into cDNA libraries using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold Library Prep Kit (#RS-122-2303, Illumina, San Diego, CA). Briefly, ribosomal RNA (rRNA) was removed from 100 ng of total RNA by hybridization to a biotinylated probe selective for rRNA species, followed by streptavidin bead binding, purification, and fragmentation by heat in the presence of divalent cations. Double-stranded cDNA was generated by removing the RNA template and synthesizing the second strand with dUTP in place of dTTP. A single ‘A’ base was added to the 3’ end to facilitate ligation of sequencing adapters, which contained a single ‘T’ base overhang. Adapter-ligated cDNA was amplified by polymerase chain reaction (PCR) to increase the amount of sequence-ready library. During this amplification the polymerase stalls when it encounters a ‘U’ base, rendering the second strand a poor template. The first strand thus serves as template for amplified sequence, preserving strand information. Final cDNA libraries were analyzed for size distribution and integrity using an Agilent Bioanalyzer (DNA 1000 kit #5067-1504), quantitated by qPCR (KAPA Library Quant Kit #KK4824, KAPA Biosystems, Wilmington, MA), and normalized to 2 nM in preparation for sequencing.Samples were sequenced at EA Genomics (Q2 Solutions, Durham, NC) using the Illumina HiSeq platform

treatment_protocol: DEHP (CAS No: 117-81-7; 99.5% purity, Chem Service) was administered in the feed for 7 days at dietary doses of 0, 1500, 3000, and 6000 ppm (as described in Lake et al. 2015). Dichloroacetic acid (CAS 79-43-6, Aldrich) was administered in the drinking water at doses of 0, 1.0, 2.0, and 3.5 g/L (as described in DeAngelo et al. 1991).

tag: tissue

value: liver

tag: sample preparation

value: formalin-fixed paraffin embedded

tag: strain

tag: age

value: 4 weeks

tag: Sex

value: male

tag: treatment

value: dichloroacetic acid (DCA)

tag: dose


title: 77_2_DCA_FFPE

value: 2 g/L


title: b-catenin-OE and Notch1-KO_sample3

city: Shanghai

first: Luo

last: Guo

address: 83# fenyang road, 9# building, room 613

country: China

institute: Fudan University

data_processing:
Preliminary processing of raw reads was performed using Casava 1.8 (Illumina).
Adapters and low-quality bases were trimmed using trimmomatic (version 0.23)
Trimmed reads for each sample were aligned to the Mus musculus UCSC mm10 genome using the TopHat version 2.0.10 software package (Bowtie 2 version 2.2.1 software).
Cufflinks software was used to generate assembled transcripts for each group, and the abundance was evaluated using read data.
These assemblies were used with the Cuffdiff tools from the Cufflinks 2.2.1 package to calculate the differential expression levels and to evaluate the statistical significance of the detected alterations.
Genome_build: mm10
Supplementary_files_format_and_content: microsoft excel file include FPKM values for all samples

extract_protocol:
The apical and middle turns of at least six cochleae from each group were pooled to isolate the total RNA using the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to the manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cochlear

value: postnatal 7


title: Notch1-KO_sample2

source_name: apical and middle turns of at least six cochleae


title: 74_2_DCA_FFPE


title: 54_1_DCA_FFPE

value: 1 g/L


title: Control_sample3


title: 50_1_DCA_FFPE


title: 52_1_DCA_FFPE


title: 49_1_DCA_FFPE


title: 7_0_Control_FFPE

value: 0 g/L


title: 6_0_Control_FFPE


title: 5_0_Control_FFPE


title: 73_2_DCA_FFPE


title: 102_3.5_DCA_FROZ

source_name: frozen liver (mixed lobes)

value: frozen


title: 53_1_DCA_FFPE


title: 3_0_Control_FFPE

source_name: formalin-fixed paraffin embedded left lateral and right medial liver lobes


title: 101_3.5_DCA_FROZ


title: 4_0_Control_FFPE


title: 98_3.5_DCA_FROZ


title: 76_2_DCA_FFPE


title: 78_2_DCA_FROZ


title: 99_3.5_DCA_FROZ


title: 76_2_DCA_FROZ


title: 75_2_DCA_FROZ


title: 97_3.5_DCA_FROZ


title: 77_2_DCA_FROZ


title: 53_1_DCA_FROZ


title: 54_1_DCA_FROZ


title: 73_2_DCA_FROZ


title: 51_1_DCA_FROZ


title: 52_1_DCA_FROZ


title: 74_2_DCA_FROZ


title: 8_0_Control_FROZ


title: 51_1_DCA_FFPE


title: 49_1_DCA_FROZ


title: 7_0_Control_FROZ


title: 6_0_Control_FROZ


title: 100_3.5_DCA_FROZ


title: 50_1_DCA_FROZ


title: 5_0_Control_FROZ


title: 4_0_Control_FROZ


title: 8C_DEHP_6_FFPE

source_name: formalin-fixed paraffin embedded left lateral, caudate, and right medial liver lobes

value: di(2-ethylhexyl)phthalate (DEHP)


title: 3_0_Control_FROZ


title: 64C_DEHP_6_FFPE


title: 44A_DEHP_6_FFPE


title: 71A_DEHP_3_FFPE


title: 29B_DEHP_6_FFPE


title: 9A_DEHP_3_FFPE


title: 67C_DEHP_3_FFPE


title: 35A_DEHP_3_FFPE


title: 72B_DEHP_1.5_FFPE


title: 60A_DEHP_1.5_FFPE


title: 40A_DEHP_1.5_FFPE


title: 45C_Control_0_FFPE

value: 0 ppm


title: 63A_Control_0_FFPE


title: 75A_Control_0_FFPE


title: 32A_Control_0_FFPE


title: 64C_DEHP4_6_FROZ


title: 8C_DEHP2_6_FROZ


title: 67C_DEHP2_3_FROZ


title: 44A_DEHP3_6_FROZ


title: 9A_DEHP1_3_FROZ


title: 72B_DEHP2_1.5_FROZ


title: 29B_DEHP1_6_FROZ


title: 71A_DEHP3_3_FROZ


title: 60A_DEHP1_1.5_FROZ


title: 75A_Control_0_FROZ


title: 40A_DEHP4_1.5_FROZ


title: 45C_Control_0_FROZ


title: 8_0_Control_FFPE


title: 63A_Control_0_FROZ


title: 32A_Control_0_FROZ


title: 3A_DEHP3_1.5_FROZ


title: 3A_DEHP_1.5_FFPE


title: MPP

city: New York

first: Catherine

last: Sawai

state: New York

address: 701 W. 168th Street - HHSC 9-906

institute: Columbia University Medical Center

data_processing:
Fastq files were aligned to mm10 genome and counts were generated using RNA Express (v. 1.0.0; STAR aligner and DeSeq2) application within the Illumina BaseSpace platform.
Genome_build: mm10
Supplementary_files_format_and_content: normalized_counts.txt: normalized counts of all samples as computed by DeSeq2, listed by Ensembl Gene ID.

source_name: Bone marrow

extract_protocol:
LSK CD48- CD150+ GFP+ and GFP- HSCs and LSK CD48+ CD150- MPPs were sorted by flow cytometry and pelleted. RNA was isolated by TRIzol reagent followed by the Arcturus PicoPure RNA Kit.
cDNA was prepared using the Clontech SMART-seq v4 Ultra Low Input RNA Kit, and library prep was prepared using the Clontech Low Input Library Prep Kit, both per manufacturer's instructions.

tag: population

value: MPP

tag: genotype


title: HSC_GFP-

value: HSC


title: F2-F_mRNA

city: Acton

first: Ian

middle: K

last: Greaves

state: act

address: clunies ross street

country: Australia

institute: csiro

description: Total RNA

data_processing:
*_sRNA.gz: Files were mapped using biokanga v2.95 with options with options -R5 -R500 -X.  Bed files include Chr, start, end, sRNA size
*_mRNA.csv:  Files were mapped to features using biokanga v2.95.  Files include RPKM along with Exon reads.  Exon reads were used for DESEQ analysis
*_mC.wig:  100bp mC levels for 100bp windows.  Methylation was mapped using bismark v0.13.0.
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: immature infloresence

growth_protocol: Arabidopsis thaliana accessions C24 and Landsberg erecta (Ler) were used as parental lines. Reciprocal C24 x Ler hybrids were generated by hand pollination. F2 self pollinated seeds were collected.  Seeds were sterilized and sown onto plates containing MS medium supplemented with 1% (w/v) sucrose and 0.6% agar. After 2 days at 4°C, the plates were transferred to a growth room with conditions of 22 °C/18 °C (day/night) and 16h light/8h dark cycle. At 18 days after sowing, the plants were transferred to soil and grown to the reproductive stage where immature infloresences were collected. Plants were grown under controlled light conditions (OSRAM L 36W/865 LumLux Daylight, 130 - 150μmol photons·m-2·s-1).

extract_protocol:
Total RNA for mRNA and sRNA libraries was isolated using the Direct-zol RNA miniprep kit (Zymo Research).  DNA was extracted using the Dneasy miniprep kit (Qiagen)
mRNA and sRNA Libraries were constructed by the Australian Genome Research Facility (AGRF). Methyl-seq libraries were constructed at CSIRO

treatment_protocol: Isolated DNA was converted twice with Epitect bisulfite kit (Qiagen)

value: immature infloresence

tag: sample type


title: F2-E_mRNA

description: Total RNA


title: F2-D_mRNA

description: Total RNA


title: F2-C_mRNA

description: Total RNA


title: F2-A_mRNA

description: Total RNA


title: F1-F_mRNA

description: Total RNA


title: 35A_DEHP4_3_FROZ


title: F1-A_mRNA

description: Total RNA


title: F1-B_mRNA

description: Total RNA


title: Ler-RepA_mRNA

description: Total RNA

value: parental line


title: F1-E_mRNA

description: Total RNA


title: Ler-RepB_mRNA

description: Total RNA


title: F1-C_mRNA

description: Total RNA


title: F1-D_mRNA

description: Total RNA


title: HSC_GFP+


title: F2-E_mC

description: Bisulphite converted DNA

library_source: genomic

molecule: genomic DNA


title: C24-RepA

description: Total RNA


title: F2-C_mC

description: Bisulphite converted DNA


title: F2-D_mC

description: Bisulphite converted DNA


title: F2-B_mC

description: Bisulphite converted DNA


title: F2-F_sRNA

description: small RNA


title: C24-RepB_mRNA

description: Total RNA


title: F2-B_mRNA

description: Total RNA


title: F2-E_sRNA

description: small RNA


title: F2-A_sRNA

description: small RNA


title: F2-C_sRNA

description: small RNA


title: F2-A_mC

description: Bisulphite converted DNA


title: F2-B_sRNA

description: small RNA


title: F1-E_sRNA

description: small RNA


title: F1-F_sRNA

description: small RNA


title: F1-C_sRNA

description: small RNA


title: F1-B_sRNA

description: small RNA


title: F1-A_sRNA

description: small RNA


title: Ler-RepB_sRNA

description: small RNA


title: F2-F_mC

description: Bisulphite converted DNA


title: C24-RepB_sRNA

description: small RNA


title: C24-RepA_sRNA

description: small RNA


title: F2-D_sRNA

description: small RNA


title: HCT116_J2_Combo

city: Grand Rapids

first: Peter

middle: A

last: Jones

state: MI

address: 333 Bostwick Ave

department: Center for Epigenetics

institute: Van Andel Research Institute

description:
double stranded RNA
20160114_JonesLabVAI_J2RNAseq_ERVcnt.xlsx

data_processing:
Count reads aligned to annotation from RepeatMasker
Genome_build: hg19
Supplementary_files_format_and_content: dsRNA measurement from J2 antibody pull down experiment in HCT116 cell line

organism: Homo sapiens

growth_protocol: HCT116 were maintained in McCoy’s 5A medium and cultured according to standard mammalian tissue culture protocols and sterile technique.

extract_protocol: The 5-Aza-CdR treated cells were lysed with lysis buffer (30 mM HEPES-KOH at pH 7.4, 20mM MgOAc, 5mM DTT, 150mM KOAc, 0.1% NP-40, protease inhibitors). RNase T1(single-strand-specific RNA endonuclease) was added into the lysis buffer. The cell lysates were used for dsRNA pull-down with 3Î¼g of J2 antibody (Scicons) on Dynabeads Protein G (Invitrogen) for 2 hours at 4Â°C. The beads were washed with wash buffer (30 mM HEPES-KOH at pH 7.4, 20mM MgOAc, 5mM DTT, 150mM KOAc, 0.1% NP-40, protease inhibitors). Digestions of single-stranded RNA were carried out by RNase T1 (Roche). Digestions of DNA were carried out by TURBO DNase (Thermo Fisher). dsRNA was purified and fragmented into âˆ¼200 bp by shearing (Covaris). cDNA library preparation. RNA-seq libraries were prepared by using the NEBNext Multiplex Small RNA Library Prep Set for Illumina.

treatment_protocol: HCT116 (3 x 10^5) cells were treated with 0.3 μM of 5-Aza-CdR (Sigma-Aldrich). After 24 hours, medium was replaced and maintained at Day 5.

tag: cell line

value: human colon carcinoma cell line HCT116

value: Combination

tag: antibody

value: J2 antibody


title: HCT116_J2_Aza


title: HCT116_Vc 2

data_processing:
alignment using TopHat2
assemble transcriptome using Cufflink
compute FPKM and differential gene expression using Cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: tsv containing FPKM and differential gene expression as output by cuffdiff

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with Zymo Direct-Zol RNA mini prep kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using KAPA Stranded RNA-Seq Kit with RiboErase (HMR) according to manufacturer's protocol and pooled according to strandard Illumina protocols
Total RNA sequencing with ribosomal RNA depleted

tag: cell type

value: human colon carcinoma cell line

value: Vitamin C


title: HCT116_Combo 2


title: HCT116_J2_PBS

value: PBS


title: msl2_mle_3

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

description: ChIP MSL2 MLE RNAi replicate 3

data_processing:
ChIP-seq reads were aligned to the dm6 genome assembly using bowtie version 1.1.1 parameter m=1
Aligned reads were extended to 200 bp fragments
Coverage vectors were generated by counting overlapping fragments at each genomic position
Genome_build: dm6
Supplementary_files_format_and_content: bedgraph files with coverage

organism: Drosophila melanogaster

source_name: S2 cell line

extract_protocol:
ChIP DNA; cells were crosslinked in growth medium using 1% formaldehyde for 60 minutes in icewater. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using a Covaris S220 (PIP 100 W, DF 20%, 200 CB for 30 min) to generate 180-bp chromatin fragments. Chromatin was precleared using a protein A/protein G-sepharose mixture for 1 hr at 4°C. 200 µl chromatin was incubated with appropriate amounts of antibodies in a total volume of 500 µl RIPA buffer at 4°C over night. After washing and crosslink revearsal, immunprecipitated nucleic acids were purified on GFX columns (GE Healthcare). Input DNA; cells were crosslinked in growth medium using 1% formaldehyde for 60 minutes in icewater. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using a Covaris S220 (PIP 100 W, DF 20%, 200 CB for 30 min) to generate 180-bp chromatin fragments. After crosslink revearsal, nucleic acids were purified on GFX columns (GE Healthcare).
The Diagenode MicroPlex library kit was used to prepare libraries from 1-2ng of either input or DIP DNA quantified using the Qubit® dsDNA HS Assay kit (Life Technologies Q32851)

treatment_protocol: 1×10e6 SL2 cells were incubated with 10 µg dsRNA for 1 hour in serum-free medium. After addition of serum-containing medium, cells were incubated for 7 days at 26°C before chromatin preparation

tag: chip antibody

value: MLE RNAi


title: F1-D_sRNA

description: small RNA


title: msl2_mle_2

description: ChIP MSL2 MLE RNAi replicate 2


title: msl2_mle_1

description: ChIP MSL2 MLE RNAi replicate 1


title: msl2_gst_2

description: ChIP MSL2 GST RNAi replicate 2

value: GST RNAi


title: msl2_gst_1

description: ChIP MSL2 GST RNAi replicate 1


title: HWT2_RNA-Seq

city: Chapel Hill

first: Taylor

last: Penke

address: 3344 Genome Sciences Building, 250 Bell Tower Drive

department: Genetics and Molecular Biology

institute: University of North Carolina Chapel Hill

description: RNA_cufflinks.diff, RNA_deseq2.txt

data_processing:
FAIRE and HP1a reads were aligned with Bowtie2 using default parameters.
FAIRE peaks were called using MACS2 with a shift size of 100bp and significance cutoff of 0.01. Peaks were called on individual replicates for each genotype and then combined into a merged peak set. HP1a ChIP data was examined at 1kb windows.
Bedtools was used to count the number of reads overlapping peaks or windows. For FAIRE data counts were normalized to sequencing depth (RPM). For HP1a ChIP data counts were divided by the number of uniquely mapped D. virilis reads multiplied by one million.
Statistical analysis was performed with edgeR for FAIRE data and ChIP data.
RNA reads were aligned with Tophat.
Transcriptome assembly was performed with Cufflinks and statistical analysis was performed with DESeq2.
Genome_build: melanogaster dm6, virilis dvir_r1.2
Supplementary_files_format_and_content: Processed files contain chromosome location of the peak, window, or transcript along with the log fold change of HWT and K9R genotypes and calculated p value from statistical program indicated above

source_name: imaginal wing disc

growth_protocol: All stocks were maintained on standard corn media. 50 ΔHisC, twi-GAL4/CyO females and 20 ΔHisC, UAS-2xEYFP/CyO ; HWT/HWT or K9R/K9R males were placed in a cage at 25C and allowed to lay eggs on a grape juice agar plate.~50 GFP positive larvae were moved to a corn media vial 48 hours after egg laying to separate ΔHisC, UAS-2xEYFP / ΔHisC, twi-GAL4 mutants from their siblings. Culture vials were cleared of wandering third instar larvae, and after 4-6 hours newly wandering larvae were selected.

extract_protocol:
40 imaginal wing discs per replicate were homogenized in Trizol and flash frozen in liquid nitrogen. RNA was chloroform extracted and isopropanol precipitated before column purification on Qiagen RNeasy purification with DNase digestion.
Total RNA TruSeq Stranded Ribo Zero Gold

tag: developmental stage

value: 3rd instar larvae

tag: genotype/variation

value: HWT


title: K9R2_RNA-Seq

description: RNA_cufflinks.diff, RNA_deseq2.txt


title: HWT3_RNA-Seq

description: RNA_cufflinks.diff, RNA_deseq2.txt


title: input_mle_2

description: ChIP input MLE RNAi replicate 2

value: none (input)


title: K9R3_RNA-Seq

description: RNA_cufflinks.diff, RNA_deseq2.txt


title: HWT1_RNA-Seq

description: RNA_cufflinks.diff, RNA_deseq2.txt


title: HWT_input_HP1a_ChIP-Seq

extract_protocol:
Nuclei were isolated from 50 whole larvae per replicate and fixed in 4% formaldehyde for 20 minutes. Chromatin was sonicated to 200-300bp fragments. 2.5% of Drosophila virilis chromatin from 3rd instar larvae was added as a spike-in. 10% of extract was set aside as an input. Pull down was performed with protein A/G magnetic beads preincubated with anti-HP1a PRB-291C (Covance).
ThruPlex DNA Seq Kit


title: Ler-RepA_sRNA

description: small RNA


title: HCT116_PBS 2


title: HWT2_HP1a_ChIP-Seq

value: anti-HP1a (Covance, PRB-291C, Lot #D14JF02175)


title: HWT1_HP1a_ChIP-Seq


title: input_mle_1

description: ChIP input MLE RNAi replicate 1


title: input_gst_2

description: ChIP input GST RNAi replicate 2


title: input_gst_1

description: ChIP input GST RNAi replicate 1


title: HCT116_Aza 2


title: input_gfp_3

description: ChIP input GFP RNAi replicate 1

value: GFP RNAi


title: K9R_input_HP1a_ChIP-Seq


title: K9R1_RNA-Seq

description: RNA_cufflinks.diff, RNA_deseq2.txt


title: msl2_sxl2_6d_2

description: ChIP MSL2 SXL RNAi construct 2 6d replicate 2

source_name: Kc cell line

extract_protocol:
ChIP DNA; 40 million cells were re-suspended in ice-cold homogenization buffer and fixed with 1% formaldehyde for 10 minutes at room temperature. After quenching with 125 mM glycine (final) the cells were collected and washed three-times with ice-cold RIPA buffer. Fixed nuclei were sonicated in RIPA buffer with a Covaris sonifier (PIP: 140, DF 20%, CB: 200) for 30 minutes. Chromatin was precleared using a protein A/protein G-sepharose mixture for 1 hr at 4°C. 200 µl chromatin was incubated with appropriate amounts of antibodies in a total volume of 500 µl RIPA buffer at 4°C over night. After washing and crosslink revearsal, immunprecipitated nucleic acids were purified on GFX columns (GE Healthcare). Input DNA; 40 million cells were re-suspended in ice-cold homogenization buffer and fixed with 1% formaldehyde for 10 minutes at room temperature. After quenching with 125 mM glycine (final) the cells were collected and washed three-times with ice-cold RIPA buffer. Fixed nuclei were sonicated in RIPA buffer with a Covaris sonifier (PIP: 140, DF 20%, CB: 200) for 30 minutes. After crosslink revearsal, nucleic acids were purified on GFX columns (GE Healthcare).
The Diagenode MicroPlex library kit was used to prepare libraries from 1-2ng of either input or DIP DNA quantified using the Qubit® dsDNA HS Assay kit (Life Technologies Q32851)

treatment_protocol: 1×10e6 SL2 cells were incubated with 10 µg dsRNA for 1 hour in serum-free medium followed by addtion of serum-containing medium. Every 3 days (3,6 and 9days) cells were split and either collected for ChIP experiments or treated again with SXL dsRNA

value: Kc

tag: RNAi

value: SXL construct 2

tag: days of treatment


title: msl2_sxl2_9d_2

description: ChIP MSL2 SXL RNAi construct 2 9d replicate 2


title: msl2_sxl2_6d_1

description: ChIP MSL2 SXL RNAi construct 2 6d replicate 1


title: input_mle_3

description: ChIP input MLE RNAi replicate 3


title: msl2_sxl2_9d_1

description: ChIP MSL2 SXL RNAi construct 2 9d replicate 1


title: msl2_sxl2_3d_1

description: ChIP MSL2 SXL RNAi construct 2 3d replicate 1


title: K9R2_HP1a_ChIP-Seq


title: K9R1_HP1a_ChIP-Seq


title: msl2_sxl2_3d_2

description: ChIP MSL2 SXL RNAi construct 2 3d replicate 2


title: msl2_sxl1_9d_2

description: ChIP MSL2 SXL RNAi construct 1 9d replicate 2

value: SXL construct 1


title: HWT2_FAIRE-Seq

extract_protocol:
3rd instar larvae were inverted and fixed in 4% paraformaldehyde for 10 minutes. Imaginal wing discs were dissected and stored at -20. 50 discs were pooled per replicate and disrupted in a bead beater. Extract was subsequently sonicated to 200-700bp. 10% of extract was set aside as input and the remainder was phenol chloroform extracted.
Tru-Seq DNA kit


title: HWT1_FAIRE-Seq


title: msl2_sxl1_6d_1

description: ChIP MSL2 SXL RNAi construct 1 6d replicate 1


title: msl2_sxl1_3d_2

description: ChIP MSL2 SXL RNAi construct 1 3d replicate 2


title: msl2_sxl1_9d_1

description: ChIP MSL2 SXL RNAi construct 1 9d replicate 1


title: msl2_gfp_3d_1

description: ChIP MSL2 GFP RNAi 3d replicate 1

value: GFP


title: msl2_sxl1_3d_1

description: ChIP MSL2 SXL RNAi construct 1 3d replicate 1


title: K9R2_FAIRE-Seq


title: input_sxl2_9d_2

description: ChIP input SXL RNAi construct 2 9d replicate 2


title: K9R3_FAIRE-Seq


title: K9R1_FAIRE-Seq


title: msl2_gfp_3d_2

description: ChIP MSL2 GFP RNAi 3d replicate 2


title: K9R3_HP1a_ChIP-Seq


title: input_sxl2_6d_2

description: ChIP input SXL RNAi construct 2 6d replicate 2


title: input_sxl2_9d_1

description: ChIP input SXL RNAi construct 2 9d replicate 1


title: input_sxl2_6d_1

description: ChIP input SXL RNAi construct 2 6d replicate 1


title: input_sxl2_3d_1

description: ChIP input SXL RNAi construct 2 3d replicate 1


title: input_sxl1_9d_2

description: ChIP input SXL RNAi construct 1 9d replicate 2


title: input_sxl1_9d_1

description: ChIP input SXL RNAi construct 1 9d replicate 1


title: input_sxl1_6d_2

description: ChIP input SXL RNAi construct 1 6d replicate 2


title: input_sxl1_3d_2

description: ChIP input SXL RNAi construct 1 3d replicate 2


title: msl2_sxl1_6d_2

description: ChIP MSL2 SXL RNAi construct 1 6d replicate 2


title: input_sxl1_3d_1

description: ChIP input SXL RNAi construct 1 3d replicate 1


title: input_gfp_3d_2

description: ChIP input GFP RNAi 3d replicate 2


title: input_sxl2_3d_2

description: ChIP input SXL RNAi construct 2 3d replicate 2


title: dipchip_msl2_526543_s2_1

description: DIP MSL2 R526A R543A S2 replicate 1

data_processing:
Library strategy: DIP-Seq
ChIP-seq reads were aligned to the dm6 genome assembly using bowtie version 1.1.1 parameter m=1
Aligned reads were extended to 200 bp fragments
Coverage vectors were generated by counting overlapping fragments at each genomic position
Genome_build: dm6
Supplementary_files_format_and_content: bedgraph files with coverage

source_name: S2 cell genomic DNA

extract_protocol:
Pellet from 60x106 S2 or Kc cells was resuspended in 1.2 ml of lysis buffer (10mM Tris pH8, 100mM NaCl, 25mM EDTA pH8, 0.5% SDS, 0.15mg/ml of proteinase K) and incubated at 56°C overnight. After addition of 3M sodium acetate, the nucleic acids were subjected to phenol-chloroform extraction and precipitated with equal volume of isopropanol at -20°C for 1 hour. Dried nucleic acids were then resuspended in TE buffer and sonicated with covaris (microTUBEs, Peak Incident Power 175W, Duty Factor 10%, Cycles per Burst 200, 430 seconds) to generate 200bp fragments. After RNAse digestion (0.1 mg/ml, 1h at 37°C), DNA was finally purified the GenElute kit from SIGMA. Synthetic DNA was produced using the Repli-g kit (QIAGEN) with 20ng of gDNA as starting material. Dip-seq experiments were performed as in Gosset at al. 2008 with few modifications. Briefly, 400ng of genomic DNA prepared as specified was incubated with 80 nM of MSL2-FLAG or mutated recombinant protein at 26°C for 30 minutes in 100ul of binding buffer (100mM KCl, 2mM MgCl2, 2mM Tris-HCl pH 7.5, 10% Glycerol, 10uM ZnCl2). For DIP experiments in presence of synthetic DNA, 10pM of the specified synthetic DNA was also added to the reaction. 10% of the reactions was taken as input material and subjected to deep sequencing. DNA-protein complexes were pulled-down using 15ul of FLAG beads slurry (M2, SIGMA) for 15 minutes at room temperature and washed twice with 100ul of binding buffer to eliminate unbound DNA. After proteinase K digestion (0.5mg/ml, 1h at 56°C), DNA was then purified with the GenElute kit from SIGMA and subjected to quantitative PCR and/or deep sequencing. The DIP experiments in presence of synthetic DNA were performed using the deltaRING construct.
The Diagenode MicroPlex library kit was used to prepare libraries from 1-2ng of either input or DIP DNA quantified using the Qubit® dsDNA HS Assay kit (Life Technologies Q32851)

tag: dip antibody

value: MSL2 R526A R543A

tag: mutation

value: R526A (MSL2.[(Arg526Ala, Arg543Ala)]


title: msl2_gfp_3

description: ChIP MSL2 GFP RNAi replicate 1


title: input_sxl1_6d_1

description: ChIP input SXL RNAi construct 1 6d replicate 1


title: dipchip_msl2_543_s2_1

description: DIP MSL2 R543A S2 replicate 1

value: MSL2 R543A

value: R543A (MSL2.Arg543Ala)


title: dipchip_msl2_wga_1

description: DIP MSL2 S2 replicate 3

source_name: amplified S2 cell genomic DNA


title: dipchip_msl2_s2_2

description: DIP MSL2 S2 replicate 2


title: input_gfp_3d_1

description: ChIP input GFP RNAi 3d replicate 1


title: dipchip_msl2_s2_1

description: DIP MSL2 S2 replicate 1


title: dipchip_input_wga_1

description: DIP input WGA


title: dipchip_input_s2_2

description: DIP input S2 replicate 2


title: dipchip_input_s2_3

description: DIP input S2 replicate 3


title: dipchip_input_kc_1

description: DIP input Kc replicate 1

source_name: Kc cell genomic DNA


title: dipchip_dRing_s2_1

description: DIP MSl2 dRing S2 replicate 1

value: MSL2 dRing

value: deletion RING domain (MSL2.Ala2_Val131del)


title: dipchip_dRing_s2_2

description: DIP MSL2 dRing S2 replicate 2


title: dipchip_dCXC_s2_2

description: DIP MSL2 dCXC S2 replicate 2

value: MSL2 dCXC

value: deletion CXC domain (MSL2.Pro523_Pro564)


title: dipchip_dRing_s2_3

description: DIP MSL2 dRing S2 replicate 3


title: dipchip_dPB_s2_1

description: DIP MSL2 dProBas S2 replicate 1

value: MSL2 dProBas

value: deletion Pro/Bas domain (MSL2.Gln650_Leu773)


title: dipchip_dCXC_s2_1

description: DIP MSL2 dCXC S2 replicate 1


title: jazQphyB_rep3

city: East Lansing

first: Gregg

last: Howe

address: 612 Wilson Rd

department: Plant Research Laboratory

institute: Michigan State University

data_processing:
Illumina Casava1.8.2 software used to convert and demultiplex basecall files to FASTQ.
Reads assessed for quality and filtered with Illumina quality control tools filters and FASTX toolkit (http://hannonlab.cshl.edu /fastx_toolkit/).
RSEM v1.2.11 (Li and Dewey, BMC Bioinformatics, 2011) used to map reads to the Arabidopsis genome using the Illumina iGenomes TAIR10 index with default parameters. Transcript abundances expressed as transcripts per million (TPM; reads per kilobase of model per million mapped reads normalized to transcript coverage).
Genome_build: TAIR10
Supplementary_files_format_and_content: expression data (jQpB_expression.txt) in tab-delimited matrix table for TPM (transcripts per million) values for all samples, as determined by RSEM
Supplementary_files_format_and_content: count data (jQpB_counts.txt) in tab-delimited matrix table for read counts for all samples, as determined by RSEM

source_name: whole plant

growth_protocol: Plant seedlings (Col-0 wildtype, jazQ, phyB-9, jazQ phyB-9) were grown on square Petri plates containing solid medium (half-strength Linsmaier and Skoog [2.365 g/L], 0.7% phytoblend agar, 0.8% sucrose). Plates were incubated vertically in a growth chamber maintained at 21 °C for 8 d after sowing in continuous light.

extract_protocol:
For each replicate sample, approximately 200 seedlings (whole plant, including roots) per genotype were pooled and immediately frozen in liquid nitrogen and stored at -80C until processing. Wildtype and mutant seedlings were grown on the same plate to minimize plate-to-plate variation. Three independent samples (biological replicates) were sequenced per genotype. Total RNA was isolated using a Qiagen RNeasy kit with Qiagen on-column DNase treatment to remove genomic DNA. RNA integrity was assessed with a 2100 Bioanalyzer (Agilent Bioanalyzer) and all samples had an integrity score of at least 7.0.
Barcoded sequencing libraries were prepared using the Illumina RNAseq kit according to the manufacturer's instructions. Normalized libraries were sequenced on the Ilumina HiSeq 2000 platform with multiplexing of six libraries per lane.

tag: ecotype

value: jazQ phyB-9

tag: age

value: 8 d

tag: replicate


title: phyB_rep3


title: phyB_rep2


title: phyB_rep1


title: dipchip_msl2_kc_1

description: DIP MSL2 Kc replicate 1


title: jazQ_rep3

value: jazQ


title: jazQ_rep2


title: WT.Treg_RNAseq.5

city: Nashville

first: Jeffrey

middle: C

last: Rathmell

state: Tennessee

address: 1161 21st Avenue South, A-5301 MCN

institute: Vanderbilt University Medical Center

description: Mouse Group 2; Wild Type Treg Cells

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.
RNA sequencing reads were mapped with the TopHat 2 aligner using the default parameters to the UCSC mm10 mouse reference genome.
Reads were examined for quality control and quantified using FeatureCounts.
Raw counts were normalized taking into account library sizes, filtering out genes with ~0 expression (remaining gene, n=13700), and applying the variance-stabilizing transformation using the DESeq2 software package.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts and normalized (varriance stabilized) text files as csv.

source_name: T-reg cells

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen).
Libraries were prepared with Illumina TruSeq Stranded mRNA sample kits using indexed adaptors (Illumina).
Pooled libraries were subjected to 75 bp paired-end sequencing according to the manufacturer’s protocol (Illumina HiSeq3000). Targeted sequencing depth was 30 million paired-end reads per sample.

value: WildType

tag: mouse group

tag: strain


title: jazQphyB_rep2

tag: genotype


title: Col-0_rep3

value: wildtype


title: dipchip_input_s2_1

description: DIP input S2 replicate 1

value: none (input)


title: WT.Treg_RNAseq.4

description: Mouse Group 2; Wild Type Treg Cells


title: WT.Treg_RNAseq.2

description: Mouse Group 2; Wild Type Treg Cells


title: WT.Treg_RNAseq.3

description: Mouse Group 1; Wild Type Treg Cells


title: THP-1, CTCF ChIP-seq, 24 h EtOH replicate 4

city: Kuopio

first: Carsten

last: Carlberg

address: Yliopistonranta 1D

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description: Chromatin IP against VDR

data_processing:
Alignment to hg19 using Bowtie v1.0 with the following parameters: -n 1 – k 1 -m 1 -l 32 -t -q –best
Peak discovery using MACS2 with parameters: -m 5 50 –bw 150
Visualization as tdf in Integrative Genomics Viewer via conversion from sam to sorted bam (using samtools) and then to tdf (using igvtools)
Genome_build: hg19
Supplementary_files_format_and_content: TDF generated by IGVtools

source_name: human monocytic cell line THP-1

growth_protocol: THP-1 human monocytic leukemia cells were grown in RPMI 1640 supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and the cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
proteins were crosslinked with formaldehyde to DNA, then VDR-bound fragments were pulled down by chromatin immunoprecipitation
Standard protocol as suggested by the manufacturer for ChIP-seq libraries as utilized at the EMBL Gene Core in Heidelberg, Germany

treatment_protocol: cells were either treated with 100 nM of the natural VDR ligand 1,25-dihydroxyvitamin D3 (Sigma-Aldrich) or unstimulated

tag: treatment

value: EtOH

tag: treatment time

value: CTCF (Millipore 07-729)


title: Col-0_rep1


title: THP-1, CTCF ChIP-seq, 24 h 1,25(OH)2D3 replicate 4

description: Chromatin IP against VDR

tag: antibody


title: WT.Treg_RNAseq.1

description: Mouse Group 1; Wild Type Treg Cells


title: THP-1, CTCF ChIP-seq, 24 h 1,25(OH)2D3 replicate 3

description: Chromatin IP against VDR


title: T3

city: cheng du

first: Mao

last: Qing

department: neurosurgery

institute: west china hospital, Si chuan university

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 hg38 whole genome using Tophat and assembly transcripts using cufflinks.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: brian tissue

extract_protocol:
Glioma and surround brain tissue were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: brain tissue

tag: Sex

value: male


title: Glut1Tg.Treg_RNAseq1.4

description: Mouse Group 1; Glut 1 Treg Cells


title: THP-1, CTCF ChIP-seq, 24 h EtOH replicate 3

description: Chromatin IP against VDR


title: jazQ_rep1


title: T2


title: THP-1, CTCF ChIP-seq, 24 h EtOH replicate 2

description: Chromatin IP against VDR


title: jazQphyB_rep1


title: T1


title: Glut1Tg.Treg_RNAseq1.3

description: Mouse Group 1; Glut 1 Treg Cells


title: C3

source_name: glioblastoma

value: glioblastoma


title: Glut1Tg.Treg_RNAseq1.1

description: Mouse Group 2; Glut 1 Treg Cells


title: Glut1Tg.Treg_RNAseq1.2

description: Mouse Group 1; Glut 1 Treg Cells


title: Col-0_rep2


title: C1


title: lincAC006262.1_overexpression_rep2

city: Boston

first: David

middle: G

last: Hendrickson

address: 725 Parsons

institute: Harvard

description: Time 72 hoursafterlincAC006262.1 transduction rep2

data_processing:
Basecalls performed using CASAVA version 1.4
We aligned sequencing reads to human genome assembly hg19 using TopHat (Trapnell, Pachter, and Salzberg 2009) using the -M option
We estimated gene abundances per REPLICATE as well as depletion/ enrichment calls using the Cuffdiff 2
We made significance calls to date matched input samples per CONDITION using Cuffdiff 2 with the -u option
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample at gene and isoform level in addition to CuffDiff 2 generated p and q values with significance calls

molecule: polyA RNA

growth_protocol: MCF10A cells were cultured in Ham’s F12/DMEM (Cellgro) supplemented with 5% equine serum (Cellgro), 500ng/ml hydrocortisone (Sigma-Aldrich), 100ng/ml cholera toxin (List Biological Laboratories), 20ng/ml EGF (R&D Systems) and 10ug/ml insulin.

extract_protocol:
trizol RNA extraction
RNA whole transcriptome sequencing (RNA-seq) was carried out at 0 (1 replicate), 4 (2 replicates), 12 (1 replicate) and 36hrs (2 replicates) post tamoxifen treatment on polyA selected RNA using Illumina tru-seq library construction. RNA-seq was also carried out for the over-expression experiments in parental MCF10A cells that were untransduced (3 replicates), transduced with LINC00520 (2 replicates) or transduced with a control lincRNA AC006262.6 (2 replicates) on polyA selected RNA using Illumina tru-seq library construction harvested 72 hours post transduction.

tag: cell line

tag: cell type

value: breast cancer


title: linc00520_overexpression_rep2

description: Time 72 hoursafter linc00520 transduction rep2


title: linc00520_overexpression_rep1

description: Time 72 hoursafter linc00520 transduction rep1


title: Untransduced_control_rep3

description: Time 72 hours post mock transduction rep3


title: Untransduced_control_rep1

description: Time 72 hours post mock transduction rep1


title: T12

description: Time 12 hours post tamoxifen RNA-seq


title: THP-1, CTCF ChIP-seq, 24 h 1,25(OH)2D3 replicate 2

description: Chromatin IP against VDR


title: 611 rep3

first: Wei

last: Qi

address: Jinke Road

department: Biology

institute: China Novartis Institutes for BioMedical Research

description: C3H-10T1/2 preadipocytes were seeded in cell density 6E10^4, and were treated with 4uM CpdA 12h later. 48h later, we induced the confluent cells to differentiate to brown fat cells for 6 days together with the CpdA treatment.

data_processing:
Basecalls performed using Off-Line basecaller-1.9.4.
mRNA-Seq data processing: RNA-Seq reads of each sample were firstly mapped to the mm9 genome assembly using TopHat 2.0.12 with default parameters.
Read counts were obtained from TopHat-generated BAM files using SAMtools software.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RefSeq id and RPKM values for each Sample

growth_protocol: C3H-10T1/2 preadipocytes were cultured in DMEM/F12 plus 10% FBS

extract_protocol:
RNA was collected with TRIzol Reagent (Invitrogen).
Total RNA was processed using the Illumina TruSeq Stranded mRNA Sample Preparation Kit according to manufacturer’s protocol.

treatment_protocol: Brown adipocyte differentiation was induced by treating cells for 72 h in DMEM/F12 medium containing 10% FBS, 0.5 mM isobuylmethylxanthine, 125  μM indomethacin, 1 μM dexamethosone, 20 nM insulin, 1 nM T3 and 1 μM rosiglitazone (Alexis Biochemicals). After 72 h, cells were switched to medium containing 10% FBS, 20 nM insulin, 1 nM T3 and 1 μM rosiglitazone. The cells were treated with DMSO or 4 uM 611 (Cpd A) when they were seeded.

value: C3H-10T1/2 preadipocytes

tag: treated with

value: 4uM LSD1 inhibitor 611 (Cpd A)

tag: differentiation days

value: Induced to differentiate for 6 days


title: DMSO rep1

description: C3H-10T1/2 preadipocytes were seeded in cell density 6E10^4, and were treated with DMSO 12h later. 48h later, we induced the confluent cells to differentiate to brown fat cells for 6 days together with the DMSO treatment.

value: DMSO


title: 611 rep2


title: DMSO rep3


title: H3K4me2_Day0

description: ChIP-seq of H3K4me2 enrichment locations in C3H-10T1/2 preadipocytes

data_processing:
Basecalls performed using Off-Line basecaller-1.9.4.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.7
peaks were called using MACS 1.4.2 with the following setting: shift-size (73), p-value (0.00001)
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated by MACS, the score represents number of bp fall into the single base pair region.

source_name: Mesenchymal cell

growth_protocol: C3H-10T1/2 cells were cultured in DMEM/F12 plus 10% FBS.

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

tag: chip antibody

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #


title: 611 rep1


title: T36_rep1

description: Time 36 hours post tamoxifen RNA-seq


title: DMSO rep2


title: T0

description: Time zero RNA-seq


title: T4_rep1

description: Time 4 hours post tamoxifen RNA-seq rep1


title: Dam-comr-2

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

data_processing:
Sequenced reads were trimmed for adaptor sequence using cutadapt v1.7
The reads obtained were mapped to BDGP R6 Drosophila genome assembly using MOSAIK software with following parameters: -m all -mmp 0.1 -act 20 -a single
For further analysis, only the reads that started with GATC sequence were retained. The number of reads for each genomic fragment between the neighboring GATC sites (GATC fragments) was summed up.
The data were filtered for reproducibility: all GATC fragments were sorted according to the total read count in two biological samples. This list was binned into groups of 200 fragments having similar read counts. For each GATC fragment, a difference in read counts was calculated between the replicates. Those fragments that showed the difference above 2 standard deviations in the particular group were filtered out.
Genome_build: BDGP R6/dm6

source_name: adult testes

growth_protocol: The flies were kept at 23°C

extract_protocol:
25 adult testes were dissected in PBS.
DNA was isolated using phenol-chloroform method. 1ug of genomic DNA was digested by DpnI endonuclease. Digested DNA was ligated with double-stranded DNA adapters and then digested with DpnII endonuclease. Next, methylated fragments were selectively amplified using adapter-specific primer. Before the preparation of libraries for Illumina DamID-seq, the adapters used in DamID procedure were cut with DpnII enzyme. No further fragmentation was performed.

value: yw

value: testes

tag: developmental stage

value: 2 days old


title: lincAC006262.1_overexpression_rep1

description: Time 72 hoursafterlincAC006262.1 transduction rep1


title: C2


title: T4_rep2

description: Time 4 hours post tamoxifen RNA-seq rep2


title: LM-NSC008 p12 Diff

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

data_processing:
Reads per kilobase per million (RPKM) were calculated for RefSeq transcripts using an customized R script
Reads were aligned to the human genome (build hg19)
Differential expression analysis of RNA-seq data were performed using edgeR
Transcripts were defined as differentially expressed if they showed a fold-change value higher than 3 and p-value lower than 0.05
Genome_build: hg19
Supplementary_files_format_and_content: text file with RPKM values. For the header for each sample, please see 'description' field above.

source_name: Neural Stem Cells

growth_protocol: NSCs were cultured in serum-free medium (RHB-A) supplemented with basic fibroblast growth factor (bFGF), epidermal growth factor (EGF, 10), Gem21 NeuroPlex Serum-Free Supplement and penicillin-streptomycin

extract_protocol:
Human brain tissue (10-14 weeks of gestation) was dissociated using 0.1% collagenase and hyaluronidase solution and isolated NSCs were cultured
Illumina TruSeq RNA library preparation protocol

treatment_protocol: NSCs were transduced with retrovirus carriing L-MYC gene and stably expressed cells were isolated and further characterized

value: fetal brain derived neural stem cells

tag: passage number

value: p12 Diff

tag: gestional age of tissue

value: 14 weeks old fetal brain tissue


title: Dam-2

description: control sample


title: NSC008 p9

value: 13 weeks old fetal brain tissue


title: Dam-comr-1


title: NSC008 p2

value: 12 weeks old fetal brain tissue


title: Untransduced_control_rep2

description: Time 72 hours post mock transduction rep2


title: T36_rep2

description: Time 36 hours post tamoxifen RNA-seq


title: Mock early

city: Ames

first: Madan

last: Bhattacharyya

state: IA

address: G 303 Agronomy Hall

department: Agronomy

institute: Iowa State University

data_processing:
raw sequence reads were generated using Solexa GA pipeline 1.6
Adaptor sequences were trimmed off from the raw 75 bp sequence reads and reads were aligned to the F. virguliforme genome sequence (http://fvgbrowse.agron.iastate.edu/) using Bowtie program
generated SAM (Sequence Alignment/Map) output for each condition was used to extract mapped reads for corresponding genes using unix script command
Genome_build: genome sequence and gene IDs are available at http://fvgbrowse.agron.iastate.edu/gb2/gbrowse/fvirguli/
Supplementary_files_format_and_content: Text file with raw counts and RPKM values.

organism: Glycine max

source_name: 7 day old soybean root tissue 3 and 5 days post water incubation

growth_protocol: F. virguliforme Mont-1 isolate was maintained on Bilay agar plates [(0.1% KH2PO4 (w/v), 0.1% KNO3 (w/v), 0.05% MgSO4 (w/v), 0.05% KCl (w/v), 0.02% starch (w/v), 0.02% glucose (w/v), 0.02% sucrose (w/v) and 2% agar(w/v)] and sub-cultured on 1/3 PDA agar plates [0.04% potato starch (w/v), 0.2% glucose (w/v), 2% agar (w/v)]. Soybean [Glycine max (L.) Merrill] cultivar, ‘Williams 82’ highly susceptible to F. virguliforme, was sown in vermiculite under dark conditions at 22°C. The 7-day old seedlings were uprooted and used for root infection.

extract_protocol:
F. virguliforme infected soybean root samples were collected at 3, 5, 10 and 24 days post inoculation (dpi) from three independent experiments for sequencing transcripts. RNA samples of infected roots from three experiments, collected 3 and 5 dpi, were bulked and named as “early infection” whereas the pooled RNA sample isolated from the infected roots, collected 10 and 24 dpi, were termed as “late infection” time point for deep sequencing. Total RNAs were isolated from the germinating conidial spores, mycelia and infected root tissues using TRIzol Reagent (Invitrogen, Carlsbad, CA, U.S.A.). The quality of RNA samples was determined by running RNAs on a denaturing agarose gel.
Total RNAs, 10 µg each from early and late time points of F. virguliforme infected soybean root tissues, germinating conidial spores, and mycelia were used to purify poly (A)+ RNAs using oligo (dT) attached to the magnetic beads (Promega, Madison, WI).  Poly (A)+ RNAs were fragmented into short sequences in the presence of divalent cations at 94°C for 5 min. RNA samples were reverse transcribed using a cDNA synthesis kit from Illumina (Illumina, Inc. San Diego, CA, U.S.A.). RNA sample were sequenced in a single lane of the Illumina NGS platform GAII (Illumina, Inc. San Diego, CA, U.S.A.)

treatment_protocol: The roots of the Williams 82 seedlings were infected with F. virguliforme Mont-1 conidial spores (10^7 spores/mL) and incubated under dark conditions until harvesting of infected root tissues

tag: fusarium virguliforme strain

value: not infected

tag: soybean cultivar

value: Williams 82

value: root

tag: tissue age

value: 7 days


title: Mock late

source_name: 7 day old soybean root tissue 10 and 24 days post water incubation


title: HWT2_gDNA (FAIRE-seq input samples)

value: 3rd instar larvae

tag: genotype/variation

value: HWT


title: LM-NSC008 p12

value: 11 weeks old fetal brain tissue


title: Dam-1

description: control sample

tag: genotype

value: male


title: Late infection

organism:
Glycine max
Fusarium virguliforme Mont-1

source_name: 7 day old soybean root tissue infected by conidial spores (pooled RNA samples at 10 and 24 days post infection)

tag: tissue


title: LM-NSC008 p2

value: 10 weeks old fetal brain tissue


title: HCT116_Aza

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with Zymo Direct-Zol RNA mini prep kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared by the Genomic Services Laboratory (GSL) at HudsonAlpha Institute for Biotechnology using established protocols for directional RNA seq with ribosomal RNA reduction
Total RNA sequencing with ribosomal RNA depleted

value: human colon carcinoma cell line

tag: treatment


title: tut7-c2-30_S8

status: Public on Aug 29 2016

first: William

middle: F

last: Marzluff

address: 207 Fordham Hall

institute: The University of North Carolina at Chapel Hill

description: RNA

data_processing:
Reads were aligned to hg19 using Bowtie2 in --local mode
The AppEnD algorithm was used to identify 3' tails
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files containing 3' tails generated using AppEnD

source_name: HeLa Cells

growth_protocol: HeLa cells were plated at 2X10^5 cells per 10 cm dish and synchronized by double thymidine block. Cells were treated with HU for 15 minutes 3 hrs after release into S-phase and RNA prepared.

extract_protocol:
Total RNA was extracted with Trizol.
Libraries were prepared with Illumina sequences using two limited rounds of PCR after ligation of a custom linker to the 3' end of the RNA; cDNA was synthesized with a primer to the custom linker.

treatment_protocol: Cells were treated with hydroxyurea at 5 mM for 15 min[C].

tag: sirna

tag: hu timepoint

tag: cell line

value: HeLa


title: Early infection

source_name: 7 day old soybean root tissue infected by conidial spores (pooled RNA samples at 3 and 5 days post infection)


title: tut3-c2-30_S4

description: RNA


title: K9R2_gDNA (FAIRE-seq input samples)

source_name: imaginal wing disc


title: K9R3_gDNA (FAIRE-seq input samples)


title: HCT116_PBS

tag: cell type

value: PBS


title: HWT1_gDNA (FAIRE-seq input samples)


title: tut7-c2-0_S5

description: RNA


title: HCT116_Vc

value: Vitamin C


title: tut3-c2-0_S3

description: RNA


title: situt7-0_S1

description: RNA


title: si7-hEXO-30_S5

description: RNA


title: situt7-30_S2

description: RNA


title: siTUT4-7-30_S1

description: RNA


title: HCT116_Combo

value: Combination


title: siTUT4-7-0_S8

description: RNA


title: si7-hEXO-0_S4

description: RNA


title: C2-7h-30_S3

description: RNA

value: Control


title: C2-7h-0_S2

description: RNA


title: c2-74-30_S7

description: RNA


title: c2-74-0_S6

description: RNA


title: situt3-30b_S1

description: RNA


title: C2-HU-45_S7

description: RNA


title: siHEXO-HU-45_S5

description: RNA

value: hEXO


title: siHEXO-HU-0_S4

description: RNA


title: C2-HU-0_S6

description: RNA


title: siTUT3-0_S5

description: RNA


title: siTUT4-30_S3

description: RNA


title: 3control-30_S10

description: RNA


title: siTUT4-0_S2

description: RNA


title: 3control-0_S9

description: RNA


title: siTUT7-HU-30_S3

description: RNA


title: siTUT4-NK-30_S6

description: RNA


title: siTUT4-mix-30_S8

description: RNA


title: siTUT4-mix-0_S7

description: RNA


title: C2-HU-0_S2

description: RNA


title: C2-HU-30_S4

description: RNA


title: MNTI DNA

city: Oxford

first: Bass

last: Hassan

state: Oxfordshire

address: South Parks Road

department: Sir William Dunn School of Pathology, Oxford Molecular Pathology Institute

country: United Kingdom

institute: University of Oxford

description: Tumor DNA subject to somatic variants.

data_processing:
Library strategy: exome-seq
RNA-Seq: TopHat 2.0.13 and Bowtie2 2.2.5 were used to align paired-end reads to the human reference genome (hg19).
RNA-Seq: Cufflinks 2.2.1 was used to generate normalized abundance measurements as fragments per kilobase per million mapped reads (FPKM).
RNA-Seq: CummeRbund 2.6.1 was used for statistical analysis of differential expression of transcripts in the MNTI relative to a dataset from human neural crest cells (GEO acession: GSE28875)
RNA-Seq: FusionCatcher 0.99.4c was used to identify putative fusion genes from RNA-Seq data.
Whole-exome sequencing: BWA 0.6.2 was used to align reads to the human reference genome (hg19). Local realignment around potential indels was done with GATK 1.6 and duplicate reads were marked using Picard 1.89. Base quality scores were recalibrated using GATK's covariance recalibration.
Whole-exome sequencing: SNP variants were called using VarScan2 and Indel variants were called using GATK SomaticIndelDetector. SNP novelty was determined against dbSNP release 135. Deleterious SNPs were identified using the Variant Effect Predictor, release 77 (Ensembl).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing FPKM values for the abundance of each transcript in the MNTI
Supplementary_files_format_and_content: Text files containing output from FusionCatcher listing putative fusion genes in the MNTI
Supplementary_files_format_and_content: Variant call files of Single Nucleotide Polymorphisms (SNPs) and Indels detected in the MNTI and germline DNA

source_name: MNTI excised from fibula

growth_protocol: Not applicable

extract_protocol:
RNA was extracted from tumor using an RNeasy Fibrous Tissue kit (Qiagen).
Genomic DNA was extracted from tumor using a DNeasy Blood & Tissue kit (Qiagen).
Genomic DNA from blood was obtained from the Children’s Cancer and Leukaemia Group Tissue Bank, Newcastle, UK.
RNA libraries were prepared for sequencing using standard Illumina protocols
For whole-exome sequencing, targets were captured using SureSelect (Agilent). Samples were prepared and enriched according to the manufacturer's instructions. The concentration of each library was determined using a QPCR NGS Library Quantification Kit (G4880A, Agilent).

treatment_protocol: Tumor was flash frozen in liquid nitrogen.

value: Fibula tumor

tag: age

value: 2 months

tag: gender

value: Female

value: Tumor


title: CCLG14-464

description: Germline DNA providing genetic background.

source_name: Blood

value: Blood

value: Wild-type


title: patient2_normal fibroblasts from unaffected skin

city: Turku

first: Johanna

last: Ivaska

address: Tykistökatu 6

institute: University of Turku

data_processing:
The base calling was done using bcl2fastq (v1.8.4)
Read alignment was done using TopHat (v2.0.10) to hg19 human genome reference
Genewise read counts were calculated using HTSeq (v0.5.4p3)
Genome_build: hg19
Supplementary_files_format_and_content: files are tab delimited text filse containing the genewise read counts for each sample

growth_protocol: cells grown in vitro in full serum containing medium

extract_protocol:
RNA was isolated using NucleoSpin kit (Macherey-Nagel).
Library preparation was done according to Illumina TruSeq® RNA Sample Preparation v2 Guide

treatment_protocol: collected from 10 cm cell culture dishes, lysed in RLT lysis buffer (Qiagen)

tag: subject status

value: Head and neck squamous cell carcinoma (HNSCC) patient

tag: patient id

value: patient 2

value: normal fibroblasts (NF) from unaffected skin


title: 4control-30_S5

description: RNA


title: patient1_cancer associated fibroblasts

value: patient 1

value: cancer associated fibroblasts (CAF)


title: 4contrcontol-0_S4

description: RNA

value: HeLa


title: patient1_normal fibroblasts from unaffected skin


title: patient3_normal fibroblasts from unaffected skin

value: patient 3


title: patient2_cancer associated fibroblasts


title: siTUT7-HU-0_S1

description: RNA


title: Thermus at MARS5 24 hours, biological rep 3

city: Washington

first: Baochuan

last: Lin

state: DC

address: 4555 Overlook Avenue, S. W.

department: Center for Bio/Molecular Science & Engineering

institute: US Naval Research Laboratory

description: RNAseq data from Thermus scotoductus SA-01 cultured at cultured at MARS 5 microwave digestor for 24 hours

data_processing:
Illumina Casava1.7 software used for basecalling.
Read quality trimming trimmomatic .33 using parameters “HEADCROP:8 LEADING:20 SLIDINGWINDOW:5:20 MINLEN:50”
mapped reads to T. scotoductus SA-01, CP001962.1 and plasmid CP001963.1 using Bowtie2 parameter "–very-sensitive"
htseq-count used to count reads that mapped to T. scotoductus SA-01, CP001962.1 and plasmid CP001963.1 gene features
Supplementary_files_format_and_content: comma separated text file containing the raw read counts of all samples

organism: Thermus scotoductus SA-01

growth_protocol: Frozen 200 µl stocks of T. scotoductus were cultured aerobically in 10 mL of Castenholz-TYE medium at 65°C to an OD600nm of 1.0 (approx. 24 hr.).  A 1% inoculation of this culture was added to Teflon vessels (MARS5 accessory) containing 60 mL of Castenholz-TYE medium pre-warmed to 65°C.  Triplicate biological experiments were performed in parallel by placing these vessels either into a convective incubator or a MARS 5 microwave digestor (2.45 GHz, 300W) with an internal IR probe to maintain the temperature at 65 ± 1°C throughout the experiment.  Three aliquots of 3 mL were removed at 8, 14, and 24 hours after inoculation  from each vessel.

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit followed the manufacturer’s protocol with the following modification.  180 µL of lysozyme (15 mg/mL) re-suspended in TE Buffer (30 mM Tris-HCl, 1 mM EDTA, pH 8) plus 20 µL Proteinase K (Qiagen) was added to each cell pellet and samples incubated with agitation (125 rpm) for 25 min at room temperature.  The optional on-column DNase digestion was extended to 1 hr.
Ribosomal RNA were depleted from RNA samples using Ribo-Zero rRNA Removal Kit for Bacteria (Illumina, San Diego, CA) according to manufacture recommend protocol prior to RNA library preparation.  RNA library preparation was carried out using NEBNext® Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs, Inc., Ipswich, MA) according to manufacture recommend protocol.

tag: growth

value: stationary phase

tag: sample type

value: elongated morphologies


title: Thermus at MARS5 24 hours, biological rep 1


title: siTUT4-NK-0_S5

description: RNA


title: Thermus at oven 24 hours, biological rep 3

description: RNAseq data from Thermus scotoductus SA-01 cultured at convective incubator for 24 hours

value: no elongation


title: Thermus at MARS5 14 hours, biological rep 3

description: RNAseq data from Thermus scotoductus SA-01 cultured at cultured at MARS 5 microwave digestor for 14 hours

value: log phase


title: Thermus at oven 24 hours, biological rep 1


title: Thermus at MARS5 14 hours, biological rep 2


title: Thermus at MARS5 24 hours, biological rep 2


title: Thermus at oven 14 hours, biological rep 2

description: RNAseq data from Thermus scotoductus SA-01 cultured at convective incubator for 14 hours


title: Thermus at MARS5 14 hours, biological rep 1


title: Thermus at oven 24 hours, biological rep 2


title: MNTI RNA

data_processing:
RNA-Seq: TopHat 2.0.13 and Bowtie2 2.2.5 were used to align paired-end reads to the human reference genome (hg19).
RNA-Seq: Cufflinks 2.2.1 was used to generate normalized abundance measurements as fragments per kilobase per million mapped reads (FPKM).
RNA-Seq: CummeRbund 2.6.1 was used for statistical analysis of differential expression of transcripts in the MNTI relative to a dataset from human neural crest cells (GEO acession: GSE28875)
RNA-Seq: FusionCatcher 0.99.4c was used to identify putative fusion genes from RNA-Seq data.
Whole-exome sequencing: BWA 0.6.2 was used to align reads to the human reference genome (hg19). Local realignment around potential indels was done with GATK 1.6 and duplicate reads were marked using Picard 1.89. Base quality scores were recalibrated using GATK's covariance recalibration.
Whole-exome sequencing: SNP variants were called using VarScan2 and Indel variants were called using GATK SomaticIndelDetector. SNP novelty was determined against dbSNP release 135. Deleterious SNPs were identified using the Variant Effect Predictor, release 77 (Ensembl).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing FPKM values for the abundance of each transcript in the MNTI
Supplementary_files_format_and_content: Text files containing output from FusionCatcher listing putative fusion genes in the MNTI
Supplementary_files_format_and_content: Variant call files of Single Nucleotide Polymorphisms (SNPs) and Indels detected in the MNTI and germline DNA

value: Fibula tumor


title: Thermus at MARS5 8 hours, biological rep 3

description: RNAseq data from Thermus scotoductus SA-01 cultured at cultured at MARS 5 microwave digestor for 8 hours


title: Thermus at oven 14 hours, biological rep 1


title: Thermus at oven 8 hours, biological rep 2

description: RNAseq data from Thermus scotoductus SA-01 cultured at convective incubator for 8 hours


title: Thermus at oven 14 hours, biological rep 3


title: patient3_cancer associated fibroblasts


title: Thermus at oven 8 hours, biological rep 1


title: Thermus at MARS5 8 hours, biological rep 1


title: LateG1-dox_rep3

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

country: France

institute: Institut Pasteur

description:
exonic_counts
intronic_counts

data_processing:
basecalls performed using CASAVA 1.8
reads were aligned with Bowtie
ChIP-Seq: peaks were identified with MACS, filtered with DESEQ2 (FDR<0,2), quantitated with SeqMonk
RNA-Seq: counts were calculated using the iRNAseq pipeline as previously described (PMID:25564527)
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited files
Supplementary_files_format_and_content: Esrrb_peaks - annotated peak coordinates with RPKM values in all replicates
Supplementary_files_format_and_content: exonic_counts - exonic raw counts in all replicates
Supplementary_files_format_and_content: intronic_counts - intronic raw counts in all replicates

source_name: embryonic stem cells

growth_protocol: ES cells were cultured on plastic coated with 0.1% gelatine (SIGMA, cat. G1890-100G). The cells were passaged every 2-3 days using trypsin and replated at a 1:10 ratio. Cells were cultured either in conventional ES cell media consisting of DMEM +GlutaMax-I (Gibco, cat. 31966-021) supplemented with 10% FCS (Gibco 10270-098), 0.1% 2-mercaptoethanol (Gibco, cat. 31350-010), 1x MEM non-essential amino acids (Gibco, cat. 1140- 035), and 100 ng/ml recombinant LIF (MILTENYI BIOTEC, cat. 130-099-895).

extract_protocol: Illumina TruSeq Stranded mRNA sample preparation kit

value: EKOiE-Ccna-Gfp

tag: strain

tag: cell-cycle phase

value: late G1

value: 24h DOX withdrawal


title: G2-dox_rep3

description:
exonic_counts
intronic_counts


title: G2+dox_rep1

description:
exonic_counts
intronic_counts

value: DOX


title: G2+dox_rep2

description:
exonic_counts
intronic_counts


title: G2-dox_rep2

description:
exonic_counts
intronic_counts


title: LateG1+dox_rep2

description:
exonic_counts
intronic_counts


title: G2+dox_rep3

description:
exonic_counts
intronic_counts


title: G2-dox_rep1

description:
exonic_counts
intronic_counts


title: EarlyG1-dox_rep3

description:
exonic_counts
intronic_counts

value: early G1


title: LateG1+dox_rep1

description:
exonic_counts
intronic_counts


title: LateG1-dox_rep2

description:
exonic_counts
intronic_counts


title: LateG1+dox_rep3

description:
exonic_counts
intronic_counts


title: Rabbit_IgG_ChIPSeq

city: Bethesda

first: Brian

middle: Andrew

last: Lewis

state: MD

address: 9000 Rockville Pike

department: metabolism Branch

institute: National Cancer Institute-NIH

data_processing:
RTA 2.4.6 Illumina instrument run time analysis software
Bcl2fastq 2.17 Barcode demultiplexed allowing 1 mismatch
Trimmomatic 0.30 with options SE -threads 16 -phred33 ILLUMINACLIP:  adapters.fa:2:36:10 LEADING:10 TRAILING:10  MAXINFO:50:0.97 MINLEN:20
Bowtie2 2.1.0 with options –p 8 –x bowtie2_ref/genome_prefix –U read1.fastq  –S result.sam
macs 2.1.0 with default options except -B for the signal tracks
Genome_build: hg19

source_name: B cell

extract_protocol:
Approximately 30 to 50 million cells were cross-linked in 1% formaldehyde for 5 mins and quenched with 1 M Tris pH 8.0. Cells were washed twice with cold PBS and placed in 1 ml Low Salt Buffer (150 mM NaCl, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.5% NP-40, 1% Triton X-100) with complete protease inhibitor mixture (Roche Applied Science). Cells were sonicated for 15 mins (20 sec. on, 40 sec. off) with a Sonicator Ultrasonic Processor XL (Misonix Incorporated). Lysate was spun down at 13200 rpm for 20 mins and immunoprecipitation performed with 10 µg 8WG16 (Covance, MMS-126R), normal mouse IgG (Santa Cruz, sc-2025), normal rabbit IgG (Santa Cruz, sc-2027), SPT5 (Santa Cruz sc-28878), TRIM28/TIF1b (Abcam ab622553), OGA/NCOAT (Santa Cruz sc-376429), or O-GlcNAc (RL2; Santa Cruz sc-59624) overnight at 4°C. 50 µl protein G beads (Roche), pre-blocked with 0.5% BSA, and were incubated with the lysate for 3 hrs at 4°C. Beads were washed for 5 mins 4 times with RIPA Buffer (10 mM Tris, pH 7.6; 150 mM NaCl; 1 mM EDTA; 1% Triton X-100; 0.1% Sodium deoxycholate; 0.1% SDS) and once with Rinse Buffer (10 mM Tris, pH 7.6; 50 mM NaCl; 1 mM EDTA). The cross-link is reversed in 100 µl Elution Buffer 1 (10 mM Tris, pH 7.6; 1 mM EDTA; 1% SDS) for 10 min at 65°C. 150 µl Elution Buffer 2 (10 mM Tris, pH 7.6; 1 mM EDTA; 0.67% SDS) is added and treated with RNase A (Roche Applied Science) for 30 min at 37°C, and then with Proteinase K (Roche Applied Science) overnight at 65°C. DNA is recovered using a MinElute PCR Purification Kit (QIAGEN). DNA was quantified by Qubit dsDNA High Sensitivity Quantification. Libraries were constructed with 25 ng DNA using the KAPA Hyper Prep Kit (KAPA Biosystems) with NEXTflex DNA Barcodes (BIOO Scientific).
Libraries were constructed with 25 ng DNA using the KAPA Hyper Prep Kit (KAPA Biosystems) with NEXTflex DNA Barcodes (BIOO Scientific).

value: BJAB B-cell line

value: Cell line derived from Burkitt's lymphoma

tag: passage

value: Multiple

tag: chip antibody

value: rabbit IgG

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody catalog #

tag: chip antibody lot #


title: EarlyG1-dox_rep2

description:
exonic_counts
intronic_counts

tag: treatment


title: Thermus at MARS5 8 hours, biological rep 2


title: EarlyG1+dox_rep2

description:
exonic_counts
intronic_counts


title: Mouse_IgG_ChIPSeq

value: mouse IgG


title: EarlyG1-dox_rep1

description:
exonic_counts
intronic_counts


title: EarlyG1+dox_rep3

description:
exonic_counts
intronic_counts


title: EarlyG1+dox_rep1

description:
exonic_counts
intronic_counts


title: TRIM28_ChIPSeq

value: Abcam


title: Mitosis_ctl1

extract_protocol: Diagenode MicroPlex kit

value: EKOiE

value: mitosis

value: 48h DOX withdrawal


title: SPT5_ChIPSeq


title: OGA_ChIPSeq

value: NCOAT


title: OGlcNAc_ChIPSeq


title: Mitosis_ctl2


title: PolII_ChIPSeq

value: Covance

value: Not Available


title: Mitosis_rep4


title: LateG1-dox_rep1

description:
exonic_counts
intronic_counts

value: EKOiE-Ccna-Gfp

value: late G1


title: TC_YB_10

city: New York

first: Takatoshi

last: Chinen

state: NY

address: 417 East 68th Street

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Raw reads were trimmed using Trimmomatic v0.32 with standard settings to remove low-quality reads and adaptor contamination.
The trimmed reads were then aligned to the mouse genome (Ensembl assembly GRCm38) using TopHat2 v2.0.11 implementing Bowtie2 v2.2.2 with default settings.
Read alignments were sorted with SAMtools v0.1.19 before being counted to genomic features using HTSeq v0.6.1p1. The overall read alignment rate across all samples was 74.5%.
Differential gene expression was analyzed using DESeq2 1.6.3 in R version 3.1.047.
Genome_build: GRCm38

source_name: Splenic T naïve cells

extract_protocol:
Sorted cells were lysed with TRIzol and stored at -80 degree. Total RNA was extracted according to the manufacturer’s manual (Life Technologies).
cDNA libraries were generated after SMART amplification (Clontech).  Samples were individually indexed and libraries were prepaired following Illumina TruSeq paired-end library preparation protocols.

tag: genotype

value: Male

value: CD4+Foxp3-CD62LhiCD44lo cells


title: TC_YB_9


title: Mitosis_rep1

tag: cell line

value: DOX


title: TC_YB_7

tag: cell type


title: Mitosis_rep2


title: Interphase_ctl2

value: asynchronous


title: TC_YB_6

source_name: Splenic Treg cells

value: CD4+Foxp3+GITRhiCD25hi cells


title: Mitosis_rep3


title: TC_YB_11


title: A1552ΔqstR-TntfoX induced (1631+ara), replicate 3

city: Lausanne

first: Melanie

last: Blokesch

address: Station 19 / EPFL-SV-UPBLO

department: School of Life Sciences

country: Switzerland

institute: Swiss Federal Institute of Technology Lausanne (EPFL)

description: Bacterial in vitro culture.

data_processing:
Data processing was done by Microsynth (Balgach, Switzerland).
Reads were mapped onto the reference genome using the TopHat and Bowtie 2 software.
Reads were counted using HTSeq.
The counted transcripts were normalized and subjected to statistical analysis through the DESeq2 software package.
Genome_build: Reference genome (NC_002505.1, NC_002506.1)
Supplementary_files_format_and_content: Tab-delimited text file includes locus tags and DESeq2 normalized counts (sense and antisense combined).

organism: Vibrio cholerae

source_name: A1552ΔqstR-TntfoX induced

growth_protocol: V. cholerae strains were grown in 6 x 2.5 ml LB medium without or with 0.02% arabinose at 30C until an optical density at 600 nm (OD600) of 1.5-1.8 was reached. At this time, the bacteria were harvested by centrifugation at 4C.

extract_protocol:
RNA was isolated using standard RNA isolation kits. The RNA was cleaned up after DNase treatment using an RNA clean-up procedure (GenElute Mammalian Total RNA miniprep kit; Sigma). Ribodepletion was performed using a Ribo-Zero Magnetic kit (Epicentre) for Gram-negative bacteria.
RNA libraries were prepared with a TruSeq Stranded mRNA sample prep kit (Illumina).

treatment_protocol: The harvested bacteria were washed in pre-chilled PBS buffer, lysed through resuspension in Tri reagent, and stored at -80C until their processing.

tag: strain/background

value: A1552 delta-qstR-TntfoX (#1631)

tag: genotype/variation

value: A1552 delta-qstR with TntfoX transposon

tag: medium supplement

value: 0.02% arabinose


title: TC_YB_8

tag: gender


title: TC_YB_12


title: Interphase_ctl1


title: Interphase_rep4


title: A1552ΔqstR-TntfoX induced (1631+ara), replicate 2

description: Bacterial in vitro culture.


title: TC_YB_5


title: TC_YB_4


title: A1552ΔhapR-TntfoX induced (2644+ara), replicate 3

description: Bacterial in vitro culture.

source_name: A1552ΔhapR-TntfoX induced

value: A1552 delta-hapR-TntfoX (#2644)

value: A1552 delta-hapR with TntfoX transposon


title: A1552ΔqstR-TntfoX induced (1631+ara), replicate 1

description: Bacterial in vitro culture.


title: Th2_2

city: New Haven

first: Edward

middle: Isaac

last: Herman

state: Connecticut

address: 300 Cedar St, 541D TAC, PO Box 208031

department: School of Medicine

institute: Yale University

data_processing:
Bustard was used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat version 2.0.6 and Bowtie version 1.3.0 with default options
Differential expression computed with Cufflinks version 2.0.2 and default options
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: Th2 cells

extract_protocol:
Spleens were removed at 8 days post-infection with Nippostrongylus brasiliensis. Cells were sorted based on CD4+CD44+ CXCR5 and PD-1 expression and presence of reporter molecules (Tfh21 are CXCR5+PD-1+IL-21+IL-4-, Tfh21+4 are CXCR5+PD-1+IL-21+IL-4+, Tfh4 are CXCR5+PD-1+IL-21-IL-4+, Th2 are CXCR5-PD-1-IL-21-IL-4+, ). RNA was isolated using Qiazol reagent and miRNeasy kit. Sample preparation and Illumina HiSeq 2000 sequencing was conducted at the Yale Center for Genomic Analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: infected with

value: IL-21/IL-4 dual reporter

tag: day harvested

value: 8 days post-infection

tag: tissue

value: spleen

tag: sorted fraction

tag: replicate


title: WT_4

first: Andrew

last: Cox

state: MA

address: 77 Avenue Louis Pasteur

department: Brigham and Women's Hospital

institute: Harvard Medical School

data_processing:
Alignment: STAR (v2.3.0e_r291)
Read counting: htseq-count (v0.6.0, parameters –t exon)
Genome_build: zv9
Supplementary_files_format_and_content: raw counts mapped to Ensembl transcriptome

organism: Danio rerio

source_name: larvae

extract_protocol:
WT and seph mutant larvae were isolated at 5 dpf, and RNA was extracted with TRIzol (Life Technologies) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: WT


title: Interphase_rep2

tag: strain

tag: cell-cycle phase


title: Th2_1


title: Tfh4_2

source_name: IL-4 expressing follicular helper T (Tfh) cells


title: A1552-TntfoX induced (1626+ara), replicate 3

description: Bacterial in vitro culture.

source_name: A1552-TntfoX induced

value: A1552 (WT) with TntfoX transposon


title: TC_YB_3


title: A1552ΔhapR-TntfoX induced (2644+ara), replicate 2

description: Bacterial in vitro culture.


title: A1552-TntfoX induced (1626+ara), replicate 1

description: Bacterial in vitro culture.


title: Interphase_rep1

value: EKOiE


title: TC_YB_2


title: TC_YB_1


title: WT_3


title: A1552ΔhapR-TntfoX induced (2644+ara), replicate 1

description: Bacterial in vitro culture.


title: A1552-TntfoX induced (1626+ara), replicate 2

description: Bacterial in vitro culture.


title: WT_1


title: WT_2


title: Interphase_rep3


title: Tfh4_1


title: Tfh21_2

source_name: IL-21-expressing follicular helper T (Tfh) cells


title: Tfh21_4_1

source_name: IL-21 and IL-4-expressing follicular helper T (Tfh) cells


title: SepH_2

value: SepH mutant


title: SepH_4


title: SepH_1


title: SepH_3


title: Tfh21_4_2


title: A1552-TntfoX uninduced (1626-ara), replicate 2

description: Bacterial in vitro culture.

source_name: A1552-TntfoX uninduced

value: no arabinose


title: A1552-TntfoX uninduced (1626-ara), replicate 1

description: Bacterial in vitro culture.


title: A1552-TntfoX uninduced (1626-ara), replicate 3

description: Bacterial in vitro culture.


title: 1772116-090_H11

status: Public on Aug 28 2016

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Read processing was performed as described (Islam et al., Nat Methods (2014) 11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA sythesis. We rejected cells that had less than 2000 mRNA molecules,  more than 26,000 mRNA molecules (putative doublets) as well as cells that formed a separate cluster with no specific gene expression (putative damaged or dead cells). Genes that were detected at less than 4 molecules in the whole datasets were eliminated.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited table of total number of detected mRNA molecules from each gene in each cell identified by the "Title" field in Samples list.

source_name: thoracic ganglion

growth_protocol: R26R-Tomato (Jackson Laboratory) mice were crossed to the Wnt1-Cre (PS Danelian et at., Current biology (1998) 8:1323-1326) to allow delineation of sympathetic ganglia against surronding tissue. Animals were kept in cages in groups, with food and water ad libitum, under 12-h light-dark cycle conditions.

extract_protocol:
Sympathetic ganglia (SG) were collected in freshly oxygenated artificial cerebral spinal fluid (ASCF) kept on ice. SG were transferred into a 3cm plastic  dish  containing  2.7mL of 37°C digestion solution (500μL TrypLE™  Express (Life  Technologies), 2000μL Papain solution (Worthington Biochemical, 25U/ml), 100 μL DNAseI (Worthington  Biochemical, 1  mM) and 100 μL Collagenase/Dispase (Roche) 20 mg/ml). SGs were mechanically triturated  every 30 min  using glass  pasteur pipettes. After 1h incubation at 37°C, 100 μL fresh Collagenase/Dispase (20mg/mL) solution was added and SGs  were ripped open by using fine forceps. The solution was filtered using a 40μm cell strainer (FALCON) and collected in a 15 ml plastic tube. The digestion solution was diluted in 3ml ACSF and centrifuged at 100xg for 4 min at 4°C. The supernatant was removed and the pellet resuspended in 0.5 mL ASCF and 0.5 mL Neurobasal-A medium (Gibco). The cell suspension was transferred onto 80μl of Optiprep Density Solution (Sigma), 460 μL of ACSF and 460 μL Neurobasal media with supplements, and centrifuged at 100xg for 10min at 4°C and the solution concentrated to 100 μL by removing the supernatant. 10μL DNaseI was added to avoid cell clustering.  Cell density wasa djusted to 400-500 cells/μL.
The Fluidigm C1 Autoprep System microfluidic chip (medium size) was used to capture cells (Zeisel et al., Science (2015) 6;347(6226):1138-42). Cells at the capture sites were visually inspected and only single healthy cells were selected for library preparation. Cell barcoding and fragmentation were performed in a single step using Tn5 DNA transposase as described previously (ibid.) but using a different Binding and Blocking buffer (10mM Tris, 250mM NalCl, 5mM EDTA, 0.5% SDS).

value: sympathetic neuronal cells

tag: Sex

value: M

tag: age

tag: celltype identifier


title: 1772116-090_H02


title: 1772116-090_F03


title: 1772116-090_F07


title: Tfh21_1


title: 1772116-090_E04

value: Unclassified


title: 1772116-090_C01


title: 1772116-090_C06


title: 1772116-090_C04


title: 1772116-090_A09


title: 1772116-090_B09


title: 1772116-090_A05


title: 1772116-080_H03

value: F


title: 1772116-082_D01


title: 1772116-084_G07


title: 1772116-080_D04


title: 1772116-090_A01


title: 1772116-090_A03


title: 1772116-082_E02


title: 1772116-080_G12


title: 1772116-080_F06


title: 1772116-090_E06


title: 1772116-067_H11


title: 1772116-090_D11


title: 1772116-067_G02


title: 1772116-067_F12


title: 1772116-067_D06


title: 1772116-067_C04


title: 1772116-067_B02


title: 1772116-090_C12


title: 1772116-066_G09


title: 1772116-066_C02


title: 1772116-066_A03


title: 1772116-066_E05


title: 1772116-059_H01


title: 1772116-055_H07


title: 1772116-055_H04


title: 1772116-055_H03


title: 1772116-055_H02


title: 1772116-055_G10


title: 1772116-055_E03


title: 1772116-055_E12


title: 1772116-055_C09


title: 1772116-055_D10


title: 1772116-055_C01


title: 1772116-055_C12


title: 1772116-055_D04


title: 1772116-054_H11


title: 1772116-055_A03


title: 1772116-055_B07


title: 1772116-054_H07


title: 1772116-066_A08


title: 1772116-059_C10


title: 1772116-055_H01


title: 1772116-054_H02


title: 1772116-055_F11


title: 1772116-054_G03


title: 1772116-054_F12


title: 1772116-051_F07


title: 1772116-054_D06


title: 1772116-055_A07


title: 1772116-051_G09


title: 1772116-051_E08


title: 1772116-051_F03


title: 1772116-051_G03


title: 1772116-051_D05


title: 1772116-051_C02


title: 1772116-051_B08


title: 1772116-050_G10


title: 1772116-051_A03


title: 1772116-054_G04


title: 1772116-051_B02


title: 1772116-051_A05


title: 1772116-051_C06


title: 1772116-051_A02


title: 1772116-050_F10


title: 1772116-054_C09


title: 1772116-050_H05


title: 1772116-050_F05


title: 1772116-050_B02


title: 1772116-050_D05


title: 1772116-050_F04


title: 1772116-050_C12


title: 1772116-050_A02


title: 1772116-050_B06


title: 1772116-049_F08


title: 1772116-050_A07


title: 1772116-050_A09


title: 1772116-049_G09


title: 1772116-049_E02


title: 1772116-054_B07


title: 1772116-049_A09


title: 1772116-049_C10


title: 1772116-048_H07


title: 1772116-048_D07


title: 1772116-048_E01


title: 1772116-046_F03

value: Glutamatergic


title: 1772116-046_G10


title: 1772116-048_A04


title: 1772116-046_D06


title: 1772116-046_D02


title: 1772116-045_G12


title: 1772116-045_F02


title: 1772116-046_F11


title: 1772116-045_F06


title: 1772116-045_E08


title: 1772116-045_C10


title: 1772116-045_E02


title: 1772116-049_D10


title: 1772116-045_A09


title: 1772116-045_B05


title: 1772116-045_C12


title: 1772116-043_H09


title: 1772116-045_B12


title: 1772116-045_D12


title: 1772116-045_A05


title: 1772116-048_E06


title: 1772116-043_H02


title: 1772116-043_H06


title: 1772116-043_H08


title: 1772116-043_F12


title: 1772116-043_C10


title: 1772116-043_E02


title: 1772116-043_D12


title: 1772116-043_B09


title: 1772116-043_C05


title: 1772116-043_C04


title: 1772116-043_A10


title: 1772116-043_B04


title: 1772116-043_A06


title: 1772116-043_A05


title: 1772116-043_A02


title: 1772116-043_A03


title: 1772099-317_A12


title: 1772099-312_G04


title: 1772116-043_F10


title: 1772099-312_G07


title: 1772099-312_D06


title: 1772099-312_A09


title: 1772099-312_B08


title: 1772099-228_H08


title: 1772116-043_E07


title: 1772099-228_H04


title: 1772099-228_G06


title: 1772099-228_H02


title: 1772099-228_G04


title: 1772099-228_G09


title: 1772099-228_F11


title: 1772099-228_H07


title: 1772099-228_F07


title: 1772099-228_F03


title: 1772099-228_E08


title: 1772099-228_E07


title: 1772099-228_F01


title: 1772099-228_G11


title: 1772099-228_D10


title: 1772099-228_D08


title: 1772099-228_G05


title: 1772099-228_E04


title: 1772099-228_D05


title: 1772099-228_D06


title: 1772099-228_D07


title: 1772099-228_D09


title: 1772099-228_D02


title: 1772099-228_E06


title: 1772099-228_G02


title: 1772099-228_C10


title: 1772099-228_D01


title: 1772099-228_C09


title: 1772099-228_D03


title: 1772099-228_F10


title: 1772099-228_B10


title: 1772099-228_B11


title: 1772099-228_G03


title: 1772099-228_C03


title: 1772099-228_B09


title: 1772099-228_B07


title: 1772099-228_E09


title: 1772099-228_B05


title: 1772099-228_B01


title: 1772099-228_A08


title: 1772099-226_H11


title: 1772099-226_H05


title: 1772099-226_H08


title: 1772099-226_G11


title: 1772099-226_H04


title: 1772099-226_G02


title: 1772099-226_F11


title: 1772099-226_G10


title: 1772099-226_F04


title: 1772099-226_E10


title: 1772099-226_F03


title: 1772099-226_E08


title: 1772099-226_F02


title: 1772099-226_E02


title: 1772099-226_D04


title: 1772099-226_D06


title: 1772099-226_D03


title: 1772099-226_C08


title: 1772099-228_B03


title: 1772099-226_D02


title: 1772099-226_C09


title: 1772099-226_B10


title: 1772099-226_G06


title: 1772099-226_C01


title: 1772099-228_A10


title: 1772099-226_B06


title: 1772099-226_A12


title: 1772099-226_A11


title: 1772099-226_B02


title: 1772099-226_D11


title: 1772099-226_A06


title: 1772099-225_H11


title: 1772099-225_H07


title: 1772099-226_H07


title: 1772099-225_H03


title: 1772099-226_A09


title: 1772099-225_H02


title: 1772099-225_F10


title: 1772099-226_B07


title: 1772099-226_A01


title: 1772099-225_E08


title: 1772099-225_F01


title: 1772099-225_G07


title: 1772099-225_D10


title: 1772099-225_D12


title: 1772099-225_D03


title: 1772099-225_B11


title: 1772099-226_B05


title: 1772099-226_A02


title: 1772099-225_B06


title: 1772099-225_E07


title: 1772099-225_E05


title: 1772099-225_E04


title: 1772099-225_A12


title: 1772099-225_A07


title: 1772099-225_A09


title: 1772099-225_C02


title: 1772099-225_A02


title: 1772099-221_F05


title: 1772099-221_E06


title: 1772099-221_F12


title: 1772099-221_H05


title: 1772099-221_G10


title: 1772099-221_E05


title: 1772099-221_E04


title: 1772099-221_D06


title: 1772099-221_C08


title: 1772099-221_D01


title: 1772099-221_C09


title: 1772099-221_C06


title: 1772099-221_B12


title: 1772099-221_C04


title: 1772099-221_B05


title: 1772099-225_B09


title: 1772099-221_B07


title: 1772099-221_A12


title: 1772099-221_B10


title: 1772099-221_B04


title: 1772099-221_A09


title: 1772099-221_A07


title: 1772099-220_H08


title: 1772099-220_H09


title: 1772099-220_H05


title: 1772099-220_H02


title: 1772099-220_H03


title: 1772099-220_G09


title: 1772099-220_E12


title: 1772099-220_E11


title: 1772099-220_H01


title: 1772099-220_F05


title: 1772099-220_D11


title: 1772099-220_F10


title: 1772099-220_E08


title: 1772099-220_D07


title: G.30/4-5/2/In

city: Poznan

first: Elzbieta

last: Kaja

address: Umultowska 89

department: Bioinformatics

country: Poland

institute: Adam Mickiewicz University in Poznan

data_processing:
adapter removal, miRNA prediction and annotation was performed with ShortStack 1.2.4
Genome_build: Malus x domestica v1.0
Supplementary_files_format_and_content: tab-delimited text file with the following fields: mature novel miRNA sequence and expression values in eighteen small RNA deep-sequencing libraries ( in raw reads)

organism: Malus domestica

source_name: Actively-growing leaf tissue

growth_protocol: Plant material was purchased from Cameron Nursery (Eltopia, Washington).  ‘Crimson Gala’ scions were bench-grafted onto two distinct rootstocks: Malling 27 EMLA (M.27) and Geneva 30 (G.30). The trees were bench-grafted by the nursery, by splicing a two-bud, dormant shoot and planted at Rock Springs, PA in March 2005.  Actively-growing shoots were collected in May 2012. Three biological replicates of Gala/G.30 and Gala/M.27 scion-rootstock combinations were used in further analysis (6 separate apple trees).

extract_protocol:
Leaf samples were ground with a mortar and pestle and chilled with liquid nitrogen. The frozen powder was mixed with extraction buffer (2% cetyltrimethylammonium bromide, 2% polyvinylpyrolidone, 100 mMTris pH 8.0, 25 mMethylenediaminetetraacetic acid, 2 M NaCl, 0.5 g L-1 (w/v) spermidine, 2% ß-mercaptoethanol) and total RNA was isolated using 0.8 M LiCl and isopropanol (Sigma).  Total RNA concentration and purity were determined using NanoDrop (Thermo Fischer Scientific). Total RNA quality was determined withBioAnalyzer (Agilent). The RNA samples had high and consistent RNA integrity values.
18 apple libraries were prepared with TruSeq Small RNA Sample Preparation Kit (Illumina) according to the manufacturers protocol. 50 nt single-end sequencing on a HiSeq2500 (Illumina) in rapid run mode was performed in the Genomics Core Facility of the Pennsylvania State Univeristy at University Park, PA. Adapter sequences were removed with Short Stack v.1.2.4 Redundant and nonredundant reads in each library were counted and RPM (reads per million) values were calculated

treatment_protocol: Apple shoots were cut in the field and placed directly in water. Inoculation was performed in the laboratory according to Norelli et al. (Norelli et al., 2009). The top five leaves of all the shoots that were treated with bacteria were transversely bisected with scissors immersed in a suspension of 1 X 109 CFU of Erwinia amylovora strain HKN06P1 ml-1 50 mM phosphate buffer pH6.5. Control samples were treated in a similar way but with no bacteria in the buffer. The shoots were collocated in water with fertilizer, covered with a plastic bag to maintain the humidity and stored at 180C. They were receiving 14 hours of light and 10 hours of darkness. 2 and 72 hours post inoculation (hpi), the inoculated or just cut leaves were collocated in aluminum foil, submerged in liquid nitrogen and stored at -80 until RNA isolation.

tag: rootstock

tag: tag

value: leaf


title: G.30/4-5/2/C


title: G.30/1-4/2/In


title: 1772099-221_A01

tag: cell type


title: 1772099-221_A04


title: 1772099-220_C12


title: 1772099-220_B04


title: G.30/1-13/2/In


title: 1772099-220_B12


title: G.30/1-13/2/C


title: G.30/1-4/2/C


title: 1772099-220_A11


title: 1772099-220_B03


title: M.27/1-8/In


title: 1772099-220_A09


title: M.27/5-5/In


title: 1772099-220_A04


title: G.30/1-4/In


title: 1772099-220_A03


title: M.27/1-8/C


title: 1772099-220_A01


title: G.30/1-13/In


title: 1772099-104_H08


title: G.30/4-5/In


title: 1772099-220_D02


title: 1772099-104_H03


title: M.27/1-12/C


title: M.27/5-5/C


title: 1772099-104_H02


title: G.30/1-4/C


title: M.27/1-12/In


title: 1772099-104_F12


title: G.30/4-5/C


title: G.30/1-13/C


title: 1772099-104_F08


title: 1772099-104_G08


title: Ad/NICD LPS Replicate8

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 901 W State St

institute: Purdue University

description:
Biological replicate 8 of 8. Ad/NICD Liposarcoma
Ad/NICD LPS14

data_processing:
Paired-end reads from lanes L004 and L005 were concatenated and processed using Trimmomatic for quality (Phred <20) from both 5' and 3' ends. After trimming, reads of 30 nt or less were removed.  Trimming generated some unpaired reads.
Both paired and unpaired reads were aligned against the mouse GRCm38 genome assembly using iGenomes genome fasta file and iGenomes Bowtie2 small index files using TopHat 2.1.0
TopHat 2.1.0; command_line; -a 20 -m 1 -I 100000 -g 9 -N 3 --read-gap-length 1 --read-edit-dist 4 --read-realign-edit-dist 0; Data_input paired and unpaired fastq for each sample; Data_output accepted_hits.bam for each sample.
cufflinks 2.2.1; command_line; -G GRCm38_iGenome.gtf -b GRCm38_iGenome/genome.fa -u -N -F 0.05; Data_input accepted_hits.bam for each sample; Data_output annotation gtf files for each sample.
cuffmerge 2.2.1; command_line;  -g GRCm38_iGenome.gtf -s GRCm38_iGenome/genome.fa; Data_input path/sample.gtf; Data_output merged.gtf
cuffquant 2.2.1; command_line; -u -b GRCm38_iGenome/genome.fa -max-bundle-frags 10000000; Data_input merged.gtf, accepted_hits.bam for each sample; Data_output abundances.cxb for each sample.
cuffdiff 2.2.1; command_line; -u  -c 12 -FDR 0.05 -b GRCm38_iGenome/genome.fa --max-bundle-frags 10000000 -L Tumor,IngWAT --compatible-hits-norm; Data_input merged.gtf abundances.cxb files grouped by treatment Data_output 23 data and summary files, two are provided
Genome_build: GRCm38; ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/Ensembl/GRCm38/Mus_musculus_Ensembl_GRCm38.tar.gz
Supplementary_files_format_and_content: genes_FPKM_table.txt.gz; This file contains the cuffdiff genes.read_group_tracking FPKM data reformated from long to wide format.  The FPKM values for each sample are in columns. Rows contain FPKM data by gene_names and locus
Supplementary_files_format_and_content: gene_exp.dif.gzf; This file contains the statistical comparisons between tumor (liposarcoma) and WAT groups generated by cuffdiff 2.2.1.

source_name: Liposarcoma

extract_protocol:
WAT and LPS were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
Total RNA was depleted of rRNA using the Illumina Ribo-Zero Gold kit. Libraries were made from the depleted RNA using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

value: liposarcoma

value: 10-month old


title: 1772099-104_F03


title: Ad/NICD LPS Replicate7

description:
Biological replicate 7 of 8. Ad/NICD Liposarcoma
Ad/NICD LPS13

value: 11-month old


title: Ad/NICD LPS Replicate5

description:
Biological replicate 5 of 8. Ad/NICD Liposarcoma
Ad/NICD LPS07


title: Ad/NICD LPS Replicate6

description:
Biological replicate 6 of 8. Ad/NICD Liposarcoma
Ad/NICD LPS12

value: 9-month old


title: Ad/NICD LPS Replicate4

description:
Biological replicate 4 of 8. Ad/NICD Liposarcoma
Ad/NICD LPS06

value: 12-month old


title: Ad/NICD LPS Replicate3

description:
Biological replicate 3 of 8. Ad/NICD Liposarcoma
Ad/NICD LPS05


title: Ad/NICD LPS Replicate2

description:
Biological replicate 2 of 8. Ad/NICD Liposarcoma
Ad/NICD LPS04


title: Ad/NICD WAT Replicate4

description:
Biological replicate 4 of 4. Ad/NICD White adipose tissue
Ad/NICD WAT10

source_name: White adipose tissue

value: white adipose

value: Three-week old


title: Ad/NICD LPS Replicate1

description:
Biological replicate 1 of 8. Ad/NICD Liposarcoma
Ad/NICD LPS03


title: SSC Rnase R-treated rep2

city: Beijing

first: Chunsheng

last: Han

state: Beijing

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

data_processing:
RNA-seq reads generated from 4 types of SPCs were aligned to the mouse genome (UCSC mm9) with Tophat-2.0.6.
Mapped reads were subsequently assembled into transcripts guided by reference annotation (mm9, USCS gene annotation) with Cufflink-2.0.2.
Differential gene and expression analysis was conducted by using cuffdiff.
RNA-seq reads generated from SSCs (with and without RNase R treatment ) were aligned to the mouse genome (UCSC mm9) with BWA-MEM.
circRNAs were identified using the CIRI program.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: bigWig files were generated using bam2wig; The bigWig format is for display of dense, continuous data that will be displayed in the Genome Browser as a graph

source_name: SSC Rnase R-treated

growth_protocol: Mouse spermatogonial stem cells(SSCs) were cultured by following a protocol described in one of our previous study (PMID: 25356638).

extract_protocol:
RNA extraction followed standard protocol using Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Spermatogenic cells were freshly isolated by using the STAPUT method and cultured spermatogonial stem cells were harvested directly without special treatment.

value: F1 pups of DBA/2 and C57BL6

value: male

tag: development stage

value: 5 dpp

tag: tissue/cell type

value: spermatogonial stem cells (SSCs)


title: SSC rep1

source_name: SSC


title: SSC rep2