title: MCF7+EV_RNA_Seq

city: Bethesda

first: Elena

last: Pugacheva

state: MD

department: NIAID

institute: NIH

description: Processed data for this sample is included in the files RNA_Seq_MCF7+EV_VS_MCF7+BORIS_Clone1.txt.gz and RNA_Seq_MCF7+EV_VS_MCF7+BORIS_Clone2.txt.gz available on the sample pages for GSM1817676 and GSM1817677.

data_processing:
Sequences generated by the Illumina genome analyzer (36bp and 50bp reads) were aligned against either human (build hg19) or mouse (build mm9) genome using Bowtie program (http://bowtie-bio.sourceforge.net).  The alignment was performed with default parameters except the sequence tags that mapped to more than one location in the genome were excluded from the analysis using –m1 option.
Peaks were called using Model-based Analysis for ChIP-Seq (MACS) (http://liulab.dfci.harvard.edu/MACS) using default parameters. After MACS, we applied Peak Splitter algorithm (part of MACS) to call sub-peaks, summit of peaks and improve peak resolution.
For the Illumina RNA-seq library, fastq.gz files were mapped to UCSC Human reference (build hg19) using TopHat2 with the default parameter setting of 20 alignments per read and up to 2 mismatches per alignment.
For Ion Torrent RNA-seq sequencing, fastq.gz files were mapped to UCSC Human reference (build hg19) using two-step alignments. First, the reads were aligned with TopHat2. Second, the unmapped reads from the first step are then extracted and aligned with Bowtie2 with –local mode and --very-sensitive-local option.
For both Illumina and Ion Torrent RNA-seq, the resulting aligned reads (BAM files) were then analyzed with Cufflinks 2.0.0 to estimate the transcripts relative abundance using the UCSC reference annotated transcripts (build hg19). The expression of each transcript was quantified as the number of reads mapping to a transcript divided by the transcript length in kilobases and the total number of mapped reads in millions (FPKM).
Genome_build: hg19, mm9
Supplementary_files_format_and_content: Cuffdiff output.

source_name: Human breast cancer cell line

growth_protocol: K562, Delta47, Ovcar8, NHDF and MCF7 cell lines were grown in DMEM supplemented with 10% FCS and penicillin-streptomycin.

extract_protocol:
After overnight incubation with DiaMag magnetic beads (Diagenode, Inc.) and CTCF or BORIS monoclonal or polyclonal antibodies (characterized and described by PMID:15731119; PMID: 21659515; PMID:20231363), precipitated chromatin was then washed, decrosslinked, and digested with proteinase K. The resulting DNA was purified using phenol/chloroform/isoamyl alcohol. DNA concentration was assessed with Quant‐it PicoGreen dsDNA kit (Invitrogen) and 5–10 ng was used to generate sequencing libraries.
TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA). RNA-seq libraries were prepared using either Ion Total RNA-seq v2 kit or TruSeq Stranded RNA LT Kit (Illumina).

treatment_protocol: For ChIP-seq 100 million of asynchronously growing cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by quenching with 125 mM glycine for 10 min, washed twice with 1x PBS, and resuspended in ChIP lysis buffer (150 mM NaCl, 1% Triton X‐100, 0.1% SDS, 20 mM Tris–HCl pH8.0, 2 mM EDTA). Chromatin was sheared to an average length of 200–500 bp using a Bioruptor sonication.

tag: cell line

value: MCF7+EV (Empty Vector)


title: MCF7+BORIS_Clone1_RNA_Seq

status: Public on Jul 23 2015

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

value: MCF7+BORIS (Clone1, single-cell clone of MCF7 cell, stably expressing BORIS)


title: MCF7+BORIS_Clone2_RNA_Seq

value: MCF7+BORIS (Clone2, single-cell clone of MCF7 cell, stably expressing BORIS)


title: Input_NHDF_ChIP-seq

library_source: genomic

data_processing:
Sequences generated by the Illumina genome analyzer (36bp and 50bp reads) were aligned against either human (build hg19) or mouse (build mm9) genome using Bowtie program (http://bowtie-bio.sourceforge.net).  The alignment was performed with default parameters except the sequence tags that mapped to more than one location in the genome were excluded from the analysis using –m1 option.
Peaks were called using Model-based Analysis for ChIP-Seq (MACS) (http://liulab.dfci.harvard.edu/MACS) using default parameters. After MACS, we applied Peak Splitter algorithm (part of MACS) to call sub-peaks, summit of peaks and improve peak resolution.
For the Illumina RNA-seq library, fastq.gz files were mapped to UCSC Human reference (build hg19) using TopHat2 with the default parameter setting of 20 alignments per read and up to 2 mismatches per alignment.
For Ion Torrent RNA-seq sequencing, fastq.gz files were mapped to UCSC Human reference (build hg19) using two-step alignments. First, the reads were aligned with TopHat2. Second, the unmapped reads from the first step are then extracted and aligned with Bowtie2 with –local mode and --very-sensitive-local option.
For both Illumina and Ion Torrent RNA-seq, the resulting aligned reads (BAM files) were then analyzed with Cufflinks 2.0.0 to estimate the transcripts relative abundance using the UCSC reference annotated transcripts (build hg19). The expression of each transcript was quantified as the number of reads mapping to a transcript divided by the transcript length in kilobases and the total number of mapped reads in millions (FPKM).
Genome_build: hg19, mm9
Supplementary_files_format_and_content: Narrow peak (bed) and wig files were generated by MACS

molecule: genomic DNA

source_name: Human Normal Dermal Fibroblasts

value: NHDF

tag: chip antibody


title: BORIS_NHDF_ChIP-seq

value: custom mouse monoclonal BORIS (characterized in PMID:21659515)


title: Input_MCF7_ChIP-seq


title: MCF7+BORIS_Clone2_BORISAbs_ChIP-seq


title: MCF7+BORIS_Clone1_BORISAbs_ChIP-seq


title: MCF7+BORIS_Clone2_CTCFAbs_ChIP-seq

value: custom mouse monoclonal CTCF (characterized in PMID:15731119)


title: MyoD-1_ChIP-seq

city: Rehovot

first: kfir

middle: baruch

last: Umansky

state: Rehovot

address: POB 25

country: Israel

institute: Weizmann Institute

description: first IP experiement of MyoD

data_processing:
For Samples 1-4 and 13-16, basecalls were performed using CASAVA version 1.8.2. For Samples 5-12,  basecalls were performed using CASAVA version 1.7.0.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie with the following options: -a -m 1 --best --strata -v 1.
Peaks of enriched binding regions were detected by  merging  biological replicates of IP and NIS or IgG. Peaks were called using MACS1.4.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files containing peaks detected by MACS1.4.

organism: Mus musculus

source_name: Primary proliferating myoblasts

growth_protocol: We isolated SC from gastrocnemius muscles of 2-3 weeks old C57bl/6 WT mice. Cells were grown at 37°C, 5% CO2 on GHR MatrigelTM (BD Biosciences, USA) in proliferation medium (BIOAMF-2, Biological Industries, Israel), which was replaced daily. For MyoG ChIP-seq, PMs were differntiate for 24hr: cells were grown as above to 75-80% confluency and then induced to differentiate by serum starvation in differentiation media (DM): DMEM containing 4% horse serum (Gibco, UK) and 0.04U/mL human Insulin.  Each transcription factor experiment was performed in biological replicates.

extract_protocol:
Lysates were clarified from sonicated nuclei (sonicated to yield DNA fragments of ~300bp) and TF-DNA  complexes were isolated with  relevant antibody, washed and DNA was purified using Qiagen Minelute kit.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cell were fixed with formaldehyde and nuclear lysate were made

tag: strain

tag: tissue

value: muscle

tag: cell type

value: primary

tag: days in culture

value: Mouse anti MyoD (sc-32758, Santa Cruz Biotechnology)


title: CTCF_Ovcar8_ChIP-seq

source_name: Human ovarian cancer cell line


title: MCF7_CTCF_ChIP-seq


title: BORIS_Ovcar8_ChIP-seq


title: MCF7+BORIS_Clone1_CTCFABs_ChIP-seq


title: ChIP-Re_ChIP_Delta47_ChIP-seq

source_name: Human myeloma cell line

value: First, IP with custom mouse monoclonal BORIS Ab, next IP with  custom mouse monoclonal CTCF


title: ChIP-Re_ChIP_K562_ChIP-seq

source_name: Human chronic myelogenous leukemia; lymphoblastoid cells.


title: BORIS_K562_ChIP-seq

value: custom mouse monoclonal BORIS  (characterized in PMID:21659515)


title: BORIS_Delta47_ChIP-seq


title: Input_Ovcar8_ChIP-seq


title: CTCF_Delta47_ChIP-seq


title: Input_K562_ChIP-seq


title: MHV68 ∆HS infection rep1

city: Berkeley

first: Britt

last: Glaunsinger

state: California

address: 565 Li Ka Shing Center

department: Plant and Microbiology

institute: UC Berkeley

description: 4sU-labeled RNA

data_processing:
Read Quality and Adapter Trimming was done by Trim Galore
Alignment to either mouse genome (samples 1-6) or MHV68 viral genome (samples 3-6) using Tophat2
Gene Counts were assessed by htseq-count
Gene expression Normalization by DESeq2
Differential Expression between mock and WT, mock and ∆HS for cellular genes, and WT and ∆HS for viral genes determined by DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: txt(gene counts), xls(Differential Exp)

molecule: total RNA

source_name: NIH 3T3

growth_protocol: NIH 3T3 cells were grown in DMEM with 10% FBS and pen/strep

extract_protocol:
RNA was isolated by phenol-chloroform extraction. 4sU-labeled RNA was isolated by HPDP-biotin followed by streptavidin beads.
RNA was treated with RiboZero and an Illumina TruSeq library constructed

treatment_protocol: NIH 3T3 cells were infected with WT or ∆HS MHV68 for 24 hours. 500 uM 4sU was added to media for 30 minutes.

value: embryo

value: fibroblast


title: K562_BORISdepleted_RNA_Seq

value: mutant K562 (BORIS depleted)


title: MHV68 WT infection rep2

description: 4sU-labeled RNA


title: mock rep2

description: 4sU-labeled RNA


title: Input_Delta47_ChIP-seq


title: CTCF_K562_ChIP-seq


title: MHV68 ∆HS infection rep2

description: 4sU-labeled RNA


title: K562_RNA_Seq

description: Processed data for this sample is included in the file RNA_Seq_WT_K562_VS_BORIS_KO_Clone7.txt.gz available on the sample page for GSM1817680.


title: mock rep1

description: 4sU-labeled RNA


title: MHV68 WT infection rep1

description: 4sU-labeled RNA


title: mdx 2 (361)

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using tophat v2.0.10 with default parameters.
Reads per locus were quantified using the htseq-count software with the followng options: --stranded=no -t exon -m intersection-strict -q -i gene_id
The gtf file used for the quantification was prepared in-house based on the UCSC known genes.
Differential expression was calculated using DESeq2 version 1.6.3. The option "cooksCutoff=FALSE" was used when calculating the results.
Genome_build: mm9
Supplementary_files_format_and_content: DESeq2 results output. It contains raw htseq counts for each sample, DESeq2 normalized counts for each sample,  baseMean expression intensity, log2FoldChange, lfcSE, stat, pvalue and padj.

source_name: P60 soleus whole muscle

extract_protocol:
RNA extraction was perfoemd using the 5PRIME PerfectPure tissue RNA extraction kit, according to the Kit's manual
RNA libraries were prepared for sequencing using standard Truseq Illumina protocols

tag: genotype

value: soleus


title: mdx/Runx1f/f 3 (374)

value: mdx/Runx1f/f 3 (374)


title: mdx/Runx1f/f 2 (363)

value: mdx/Runx1f/f 2 (363)


title: mdx 4 (375)


title: mdx 3 (373)


title: mdx/Runx1f/f 1 (359)

value: mdx/Runx1f/f 1 (359)


title: mdx 1 (358)


title: KO-rep3

city: Montreal

first: Gareth

last: Lim

state: Quebec

address: R08.482- 900 rue St Denis

country: Canada

institute: CRCHUM

description: Sample name: C2_2

data_processing:
Reads were aligned to the mouse genome using Tophat (v.2.0.11)
Differential gene expression was measured using Cufflinks (v.2.2.0)
Analyzed data are expressed in FPKM.
Genome_build: Ensembl mouse NCBIM37
Supplementary_files_format_and_content: [Lim_et al_14-3-3zKOWAT_Processed_data.xlsx] abundance measurement with replicates
Supplementary_files_format_and_content: [Lim_et al_14-3-3zKOWAT_Processed_data_Cuffdiff.xlsx] Output file from CuffDiff

source_name: WAT

growth_protocol: Mice were singly housed in microisolator cages and fed standard rodent chow ab libitum in a temperature-controlled environment with a 12:12 light:dark cycle. At 50 weeks of age, they were sacrificed and gonadal WAT was extracted and flash frozen

extract_protocol:
Frozen gonadal WAT was ground up with a mortal and pestle in liquid nitrogen, and RNA was extracted with the Qiagen Rneasy kit with the optional on-column Dnase treatment step.
Libraries were generated using Illumina's Truseq V2 library kit, and each sample was given a unique identifier prior to sequencing on an Illumina HiSeq 2500 (150 bpx2, 20 million paired-end reads)

tag: genotype/variation

value: 14-3-3zeta KO

tag: gender

value: Male

tag: developmental stage

value: adult

value: gonadal white adipose tissue


title: KO-rep1

description: Sample name: C2_0


title: KO-rep2

description: Sample name: C2_1


title: SAN_ChIP-seq_input DNA

city: Milan

first: Paola

last: Cattaneo

address: Via Fantoli 16/15

department: Institute of Genetic and Biomedical Research

country: Italy

institute: National Research Council of Italy

description: SAN_ChIP-seq_input DNA

data_processing:
Libraries were single-end sequenced on a Hi-Seq 2500 (Illumina) for 50 cycles  according to the manufacturer’s instructions.
Reads were aligned to the mouse mm9 genome assembly (NCBI Build 37) using Bowtie allowing up to two mismatches. Only tags that mapped uniquely to the genome were considered for further analysis.
Genomic binding peaks for transcription factor ISL1 were identified using the findPeaks command from HOMER ((http://homer.salk.edu/homer/)) with 8-fold enrichment over the input sample, 4-fold enrichment over local background, a minimal tag number of 16, and normalization to 10 million mapped reads per experiment
Peaks were annotated using the annotatePeaks command from HOMER ((http://homer.salk.edu/homer/)), assigning to gene targets based on the closest RefSeq defined TSS.
Genome_build: mm9
Supplementary_files_format_and_content: HOMER tab-delimited annPeak file

source_name: Sinoatrial node (SAN) cells

growth_protocol: SANs from  Hcn4-H2BGFP mice at postnatal day 1-day 3 were digested  with Collagenase II (1mg/ml)/Trypsin (0.1%) for ten minutes with periodical pipetting, and clear supernatants were collected. The digestion was repeated until SAN tissue was totally digested. The cell suspension was filtered through a 40um filter unit (Fisher). SAN cells were resuspended in 0.5ml DMEM medium and kept on ice and FACS-sorted for GFP signal.

extract_protocol:
SAN cells were first crosslinked in 2mM disuccinimidyl glutarate (Pierce) in PBS for 30 min, then subsequently in 1% formaldehyde (Sigma) in PBS for 10 min all at room temperature. The reactions were quenched by adding glycine (Sigma) to a final concentration of 125mM. The cells were immediately centrifuged (5 min, 700x g, 4°C) and washed twice with ice-cold PBS. Cells were resuspended in swelling buffer (10 mM HEPES/KOH pH7.9, 85 mM KCl, 1 mM EDTA, 0.5% IGEPAL CA-630 (Sigma), 1x protease inhibitor cocktail (Roche), 1 mM PMSF) for 5 min. Cell pellets were spun down and resuspended in 1ml RIPA buffer (10 mM Tris/HCl pH7.6, 1 mM EDTA, 1 mM EGTA, 0.1% SDS, 0.1% Na-Deoxycholate, 1% Triton X-100, 1x protease inhibitor cocktail (Roche), 1 mM PMSF). Chromatin was sheared to an average DNA size of 100-400 bp by administering 10 pulses of 30s duration at 12 W power output with 60s pause on wet ice using a Misonix 3000 sonicator. The lysate was cleared by centrifugation (5min, 16000 x g, 4°C). 1% of the supernatant was kept as ChIP input. Meanwhile Protein G Dynabeads were prepared with the ISL1 antibody (39.4D5, DSHB) by incubating Dynabeads Protein G and 5 μg specific antibody in 0.5% BSA/PBS for 1 hr at 4°C on rotator, then washed twice with 0.5% BSA/PBS and brought up to the original volume with 0.1% BSA/PBS. The protein-DNA complex of interest was immunoprecipitated by rotating the supernatant with 30μl Dynabeads Protein G-coated with specific antibody overnight at 4°C (Dynabeads from Invitrogen). Beads were washed with each buffer by rotating in 1 ml buffer at 4°C for 5 min: RIPA buffer (10 mM Tris/HCl pH7.6, 1 mM EDTA, 1 mM EGTA, 0.1% SDS, 0.1% Na-Deoxycholate, 1% Triton X-100, 1x protease inhibitor  cocktail (Roche), 1 mM PMSF), LiCl buffer (0.25 M LiCl, 1% NP40, 1% NaDOC), TE plus 0.2% Triton X-100 and TE plus 50mM NaCl. Immunoprecipitated chromatin was  eluted twice with 100 μl elution buffer each (TE, 2% SDS) into fresh tubes for 30 min and 10 min, respectively, eluates were pooled, the Na+ concentration was adjusted to 300 mM with 5 M NaCl and crosslinks were reversed overnight at 65°C in a hybridization oven. The samples were sequentially incubated at 37°C for 1hr each with 0.33 mg/ml RNase A and 0.5 mg/ml proteinase K. The DNA was isolated using the ChIP DNA Clean & Concentrator (Zymo Research) according to the manufacturer’s instructions.
Sequencing libraries were prepared from collected ISL1 ChIP and corresponding input DNA by blunting, A-tailing, adaptor ligation using NExtFlex barcoded adapters from Bioo Scientific. Libraries were PCR-amplified for 12-15 cycles, size selected for 225-375bp fragments by gel extraction and single-end sequenced on a Hi-Seq 2500 (Illumina) for 50 cycles.

tag: strain background

value: ICR

value: postnatal day1-day3

value: Sinoatrial node (SAN) cells


title: KO-rep5

description: Sample name: C2_4


title: WT-rep6

description: Sample name: C1_5

value: WT


title: SAN_ChIP-seq_ISL1

tag: chip antibody vendor

value: DSHB

tag: chip antibody cat. #


title: WT-rep4

description: Sample name: C1_3


title: WT-rep3

description: Sample name: C1_2


title: WT-rep1

description: Sample name: C1_0


title: WT-rep5

description: Sample name: C1_4


title: WT-rep2

description: Sample name: C1_1


title: H3K27ac-1_ChIP-seq

description: first IP experiement of H3K27ac (abcam, ab4729)

data_processing:
For all samples, basecalls were performed using CASAVA version 1.8.4.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie with the following options: -a -m 1 --best --strata -v 1.
Peaks of enriched binding regions were detected by  merging  for each biological replicate of Ipusing the same IgG as control. Peaks were called using MACS2.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files containing peaks detected by MACS2.

growth_protocol: We isolatedf SC from gastrocnemius muscles of 2-3 weeks old C57bl/6 WT or Runx1f/f mice. Cells were grown at 37°C, 5% CO2 on GHR MatrigelTM (BD Biosciences, USA) in proliferation medium (BIOAMF-2, Biological Industries, Israel), which was replaced daily.

extract_protocol:
Lysates were clarified from sonicated nuclei (sonicated to yield DNA fragments of ~300bp) and histone-DNA  complexes were isolated with  relevant antibody, washed and DNA was purified using Qiagen Minelute kit.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: primary

value: anti H3K27ac


title: IgG-1_ChIP-seq

description: IP experiement of mouse IgG (control)

value: mouse IgG (278-010, Ancell)


title: PM_ATAC-Seq

description: ATAC-seq of WT PM

data_processing:
Library strategy: ATAC (assay for transposase-accessible chromatin)
Basecalls were obtained using CASAVA version 1.8.4.
Illumina adaptors were removed using a custom python script, reads were treamed to 50 bp.
Reads were aligned to the mm9 genome assembly using Bowtie2 with default options, mitochondrial reads were removed from the analysis .
Replicated reads were removed using Picard tools, MarkDuplicates.
Reads with insert size smaller than 140 bases were selected for peak detectection, that was performed using the MACS2 callpeak function for broad peaks.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files containing peaks detected by MACS2.

extract_protocol: Libraries were prepared according to previous protocol (Buenrostro et al., 2013) using KAPA HiFi PCR kit (KAPA biosystems, # KK2601)

treatment_protocol: Cell were treated with transposase (Illumina #FC-121-1030)

value: No antibody


title: H3K27ac-2_ChIP-seq

description: second IP experiement of H3K27ac (abcam, ab4729)


title: H3K4me1-1_ChIP-seq

description: first IP experiement of H3K4me1 (Abcam, ab8895)

value: anti H3K4me1


title: H3K4me1-2_ChIP-seq

description: Second IP experiement of H3K4me1 (Abcam, ab8895)


title: mRS_Input_ChIP-seq

source_name: Mouse Round spermatids

value: mRS


title: C3-siCon-t=48-rep4

description: Sample 21

data_processing:
Reads were aligned to the mouse genome using Tophat (v.2.0.11)
Differential gene expression was measured using Cufflinks (v.2.2.0)
Analyzed data are expressed in FPKM.
Genome_build: MGSCv37 (Ensembl mouse NCBIM37)
Supplementary_files_format_and_content: Processed data file (.xls) reports FPKM data

growth_protocol: 3T3-L1 pre-adipocytes were grown in 25mM glucose DMEM, supplemented with 10% newborne calf serum.

extract_protocol:
Total RNA was extracted using the Qiagen Rneasy kit with the on-column Dnase treatment. Samples were stored at -80 C until use.
Libraries were generated using Illumina's Truseq V2 library kit, and each sample was given a unique identifier prior to sequencing on an Illumina HiSeq 2500 (150 bpx2, 20 million paired-end reads)

treatment_protocol: 3T3-L1 pre-adipocytes were seeded at 90,000 cells per well in a 12-well plate, followed by transfection with siRNA (control or against 14-3-3ζ). 24 hr after transfection, cells were induced to differentiate with of 172 nM insulin, 500 μM IBMX, and 500 nM dexamethasone in differentiation media containing 25 mM glucose DMEM and 10% fetal bovine serum.

value: 3T3-L1 pre-adipocyte cell line

tag: sirna type

value: siCon

tag: hours

tag: passage


title: C1-siCon-t=0-rep4

description: Sample 19


title: C2-siCon-t=241rep4

description: Sample 20


title: C4-sizeta-t=0-rep4

description: Sample 22


title: C6-sizeta-t=48-rep4

description: Sample 24


title: C6-sizeta-t=48-rep3

description: Sample 18


title: bKO [S05090]

city: Kisarazu

first: Osamu

last: Ohara

state: Chiba

address: 2-6-7 Kazusa-Kamatari

department: Technology Development

country: Japan

institute: Kazusa DNA Research Institute

data_processing:
Read alignment: TopHat v.2.0.13 with default settings
expression level: Cufflinks v.2.2.1 with default settings
Genome_build: mouse NCBI build 37.2

source_name: Pro-B cells

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen).
TruSeq RNA sample preparation kit v2

treatment_protocol: Pro-B cells (Lin-B220+IgM-CD43+CD25-CD19+) were FACS-sorted from six mice and pooled for each genotype.

value: Bone marrow


title: mRS_BORIS_ChIP-seq

value: custom rabbit polyclonal BORIS (characterized in PMID:20231363)


title: KO-rep4

description: Sample name: C2_3

value: 14-3-3zeta KO

value: Male

value: adult


title: bKO [S05088]


title: C5-sizeta-t=24-rep3

description: Sample 17


title: mRS_CTCF_ChIP-seq

value: custom mouse monoclonal CTCF (characterized in PMID:15731119)


title: Control [S05087]


title: C4-sizeta-t=0-rep3

description: Sample 16


title: C3-siCon-t=48-rep3

description: Sample 15


title: Control [S05086]


title: bKO [S05089]


title: Ribo-seq_203_ko, biological rep.2

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

data_processing:
Reads were aligned via Tophat. Alignments overlapping uniquely with CDS regions were then counted using HTSeq.
processed data files format and content: riboseq_counts_103114.txt; see README.txt for description of data

source_name: Primary Keratinocytes

growth_protocol: Primary Keratinocytes were isolated from neonatal mice using Dispase followed by Trypsin to obtain a single cell suspension. Keratinocytes were initially plated in E-Low Calcium media supplemented with .2mM Calcium Chloride. The following day the media was switched to E-low media with .05mM Calcium Chloride. Keratinocytes were initally plated in 10cm dishes.

extract_protocol:
Ribosome protected RNA fragments were isolated as described in the Artseq Ribosome Profiling kit guidelines (EpiCentre)
Artseq Ribosome Profiling Kit guidelines (EpiCentre)

treatment_protocol: Cultures were treated with Cycloheximide (50mg/ml) in E-low media for 1 min at 37 degrees C, then washed with PBS containing cycloheximide, then harvested in Mammalian Polysome buffer containing cycloheximide.

value: Primary Keratinocytes

tag: passages


title: Ribo-seq_203_ko, biological rep.1


title: C5-sizeta-t=24-rep4

description: Sample 23

tag: cell line


title: C2-siCon-t=241rep3

description: Sample 14


title: Control [S05085]


title: HRas_miR-203_ko, biological rep.2

data_processing:
Reads were aligned with Bowie followed by Tophat. Reads from all 3Seq libraries were combined for peak calling using Macs. Peaks were then filtered to exclude likely internal priming events and annotated to transcripts. Read alignments for each library were then counted within each peak.
processed data files format and content: 3seq_peaks_filtered_alllibrariescounts.txt; 3seq_cleavagesites_filtered_alllibraries.bed; see README.txt for description of data

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) according to the manufacturers instructions
3seq library preparation was performed as described in Wang L, Dowell RD, Yi R. Genome-wide maps of polyadenylation reveal dynamic mRNA 3'-end formation in mammalian cell lineages. RNA 2013 Mar;19(3):413-25.

treatment_protocol: Control (pbabe-vector) or HRasg12V (pbabe-hRasG12V) retroviral vectors were used to infect the keratinocytes 3 days after plating. 2 days following infection, cultures were treated with 2ug/ml puromycin and selected for 2 more days. Cultures were then expanded and harvested


title: C1-siCon-t=0-rep3

description: Sample 13


title: HRas_miR-203_ko, biological rep.1


title: WT_2-2

city: Singapore

first: Lina

last: Yao

address: 5 Science Drive 2

department: Department of Microbiology and Immunology

country: Singapore

institute: National University of Singapore

description:
Sample 6
RNA was collectd on day 12

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low-quality sequence in Partek Flow, then mapped to the in-house Dunaliella tertiolecta transcriptome database by Bag2D program.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Dt_v1, Dt_v10 (the FASTA and annotation files on Serie record)
Supplementary_files_format_and_content:
Additional file 1.xls: processed data for sample 1,2
Additional file 4.xls: processed data for sample 3-6

organism: Dunaliella tertiolecta

source_name: Wild type_day12

growth_protocol: Dunaliella tertiolecta strain UTEX LB-999 was obtained from the UTEX Culture Collection of Algae (University of Texas at Austin, TX). D. tertiolecta cells were grown in flasks in sterile ATCC-1174 DA liquid medium (American Type Culture Collection at Manassas, Virginia) containing 0.5M NaCl incubated on a rotary shaker at 25°C, under 12 h light/12 h dark with light intensity of 30 μmol photons•m-2•s-1.

extract_protocol:
Total RNA of D9, WT was extracted on day 8 and day 12 from D. tertiolecta cells using an RNeasy® Plant Mini Kit (Qiagen, Valencia, CA, USA), according to manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: UTEX LB-999

value: Wild type

tag: culture day

value: day 12


title: HRas_miR-203_wt, biological rep.2

tag: strain


title: D9_2-2

description:
Sample 4
RNA was collectd on day 12

source_name: D9 mutant_day12

value: D9 mutant


title: Control [S00143]

data_processing:
Read alignment: TopHat v.1.4.0 with default settings
expression level: Cufflinks v.1.3.2 with default settings
Genome_build: mouse NCBI build 37.2
Supplementary_files_format_and_content: cuffdif_out: differential gene detection
Supplementary_files_format_and_content: genes.fpkm: abundance measurements

tag: tissue


title: bKO [S00144]


title: WT_2-1

description:
Sample 5
RNA was collectd on day 12


title: HRas_miR-203_wt, biological rep.1

tag: cell type


title: C3-siCon-t=48-rep2

description: Sample 9


title: C4-sizeta-t=0-rep2

description: Sample 10


title: Ribo-seq_203_wt, biological rep.2


title: C1-siCon-t=0-rep2

description: Sample 7


title: D9_2-1

description:
Sample 3
RNA was collectd on day 12


title: C2-siCon-t=241rep2

description: Sample 8


title: vector_miR-203_ko, biological rep.1

value: Primary Keratinocytes plated without feeder layer


title: D9_1

description:
Sample 1
RNA was collectd on day 8

source_name: D9 mutant_day8

value: day 8


title: vector_miR-203_ko, biological rep.2


title: vector_miR-203_wt, biological rep.2


title: Ribo-seq_203_wt, biological rep.1


title: C6-sizeta-t=48-rep1

description: Sample 6


title: vector_miR-203_wt, biological rep.1


title: C5-sizeta-t=24-rep1

description: Sample 5


title: C6-sizeta-t=48-rep2

description: Sample 12


title: small_rna_seq_miR-203_ko_epi

data_processing:
Reads were aligned to a mouse mature miRNA database (miRbase) using blast. miRNA alignments were then counted for each miRNA using custom python scripts (min. alignment =18nt)
processed data files format and content: miRNA_counts_203wt_ko.txt; see README.txt for description of data

source_name: Total Epidermis

growth_protocol: Animals were housed in a specific pathogen free barrier facility

extract_protocol:
Total epidermal RNAs were isolated by treating skin with Dispase enzyme for 1 hr at 37 degrees C and physcially removing the epidermis from the dermis. The RNA was then extracted using Trizol (Invitrogen) according to the manufacturers instructions
small-RNA-seq was performed by utilizing high efficiency 5' and 3' RNA adaptor ligation followed cDNA and PCR amplification as described in Zhang Z, Lee JE, Riemondy K, Anderson EM et al. High-efficiency RNA cloning enables accurate quantification of miRNA expression by deep sequencing. Genome Biol 2013;14(10):R109

value: Skin

tag: age


title: small_rna_seq_miR-203_wt_epi


title: C4-sizeta-t=0-rep1

description: Sample 4


title: C5-sizeta-t=24-rep2

description: Sample 11


title: small_rna_seq_hras, biological rep.1

data_processing:
Reads were aligned to a mouse mature miRNA database (miRbase) using blast. miRNA alignments were then counted for each miRNA using custom python scripts (min. alignment =18nt)
processed data files format and content: miRNA_counts_vector_ras.txt; see README.txt for description of data

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) according to the manufacturers instructions
small-RNA-seq was performed by utilizing high efficiency 5' and 3' RNA adaptor ligation followed cDNA and PCR amplification as described in Zhang Z, Lee JE, Riemondy K, Anderson EM et al. High-efficiency RNA cloning enables accurate quantification of miRNA expression by deep sequencing. Genome Biol 2013;14(10):R109


title: C2-siCon-t=241rep1

description: Sample 2


title: IgG_c-Jun-1_ChIP-seq

description: first IP experiement of Rabbit IgG

value: muscle

value: primary

tag: days in culture

tag: chip antibody

value: Rabbit IgG (in house purified)


title: C1-siCon-t=0-rep1

description: Sample 1

value: 3T3-L1 pre-adipocyte cell line

value: siCon


title: small_rna_seq_vector, biological rep.1


title: small_rna_seq_vector, biological rep.2


title: c-Jun-2_ChIP-seq

description: second IP experiement of c-Jun

value: Rabbit anti c-Jun (sc-1694, Santa Cruz Biotechnology)


title: small_rna_seq_hras, biological rep.2


title: WT_1

description:
Sample 2
RNA was collectd on day 8

source_name: Wild type_day8

tag: genotype/variation


title: Ago2-HITS-CLIP, biological rep.3

data_processing:
Reads were first aligned to a mouse mature miRNA database (miRbase) using Blast. Unaligned reads were then aligned to the mouse genome using Novoalign. Overlapping alignments were then clusted to identify HITS-CLIP peaks. Peaks were then annotated to the genome and miRNA seeds were searched to predict targets for individual miRNAs.
processed data files format and content: all_3utr_hitsclip_clusters.bed; miR203_3utr_hitsclip_clusters.bed:see README.txt for description of data

growth_protocol: Primary Keratinocytes were isolated from neonatal mice using Dispase followed by Trypsin to obtain a single cell suspension. Keratinocytes were initially plated in E-Low Calcium media supplemented with .2mM Calcium Chloride. The following day the media was switched to E-low media with .05mM Calcium Chloride. Keratinocytes were initally plated in 10cm dishes, then expanded to 15cm dishes prior to harvesting

extract_protocol:
Keratinocytes were lysed in Lysis Buffer (50mM Tris pH 7.4 100mM NaCl 1mM MgCl2 1% NP-40 .5% Na-Deoxycholate .1% SDS). Ago2-RNA crosslinked material was recovered using IP, and purified via Novex PAGE followed by transfer to nitrocellulose and extraction with Phenol-Chloroform
Ago2-Hits-Clip libraries were prepared using methods described in Wang, Zhen, James Tollervey, Michael Briese, Daniel Turner, and Jernej Ule. (2009) CLIP: Construction of cDNA Libraries for High-Throughput Sequencing from RNAs Cross-Linked to Proteins in Vivo. Methods 48, no. 3 (July 2009): 287–93.

treatment_protocol: Cultures were irradiated twice with 200mJ/cm2 UVC prior to harvesting in Lysis Buffer (50mM Tris pH 7.4 100mM NaCl 1mM MgCl2 1% NP-40 .5% Na-Deoxycholate .1% SDS)

tag: clip-antibody

value: mAb against mouse Ago2 clone 2D4 (Wako)


title: IgG_c-Jun-2_ChIP-seq

description: second IP experiement of Rabbit IgG


title: c-Jun-1_ChIP-seq

description: first IP experiement of c-Jun


title: H3K4me1_EID_R1

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description: chromatin IP against H3K4me1

data_processing:
Alignment: Sequence reads were obtained and mapped to Drosophila melanogaster (dm3, April 2006) genome using GEM (PubMed ID: 23103880). All reads mapping with two or fewer mismatches were retained. PeakSeq (http://www.gersteinlab.org/proj/PeakSeq/) was used to create the signal maps as wig files.
Peak-calling: Peak detection was performed with the PeakSeq program (http://www.gersteinlab.org/proj/PeakSeq/). The final peak files are provided in BED format.
Genome_build: dm3
Supplementary_files_format_and_content: WIG file represents genome wide ChIP profile
Supplementary_files_format_and_content: BED file represents signal enriched regions

organism: Drosophila melanogaster

source_name: Eye imaginal discs, chromatin IP against H3K4me1

growth_protocol: Flies were grown on standard media at 25ºC

extract_protocol:
Chromatin from Drosophila third instar larvae wing/eye discs was immunoprecipitated with 2 ug of antibody using standard protocols.
Libraries were prepared according to Illumina instructions.

tag: genotype

value: wt

tag: genetic background

value: Canton S

value: eye imaginal discs

tag: developmental stage

value: third instar larvae

value: anti-H3K4me1 (Diagenode, catalog number CS-037-100)


title: H3K27ac_WID_R1

description: chromatin IP against H3K27ac

source_name: Wing imaginal discs, chromatin IP against H3K27ac

value: wing imaginal discs

value: anti-H3K27ac (Abcam , catalog number ab4729)


title: H3K9ac_EYE_ChIPSeq

description: Chromatin IP against H3K9ac

data_processing:
Alignment: Sequence reads were obtained and mapped to Drosophila melanogaster (dm3, April 2006) genomes using GEM (PubMed ID: 23103880). All reads mapping with two or fewer mismatches were retained. PeakSeq (http://www.gersteinlab.org/proj/PeakSeq/) was used to create the signal maps as wig files.
Genome_build: dm3
Supplementary_files_format_and_content: WIG, genome wide ChIP profile

source_name: Eye imaginal discs

extract_protocol:
Chromatin from Drosophila third instar larvae wing/eye discs was immunoprecipitated with 2 ug of antibody using standard protocols.
Libraries were prepared according to Illumina instructions

tag: strain background

value: wild type

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: Ago2-HITS-CLIP, biological rep.1

treatment_protocol: Cultures were irradiated twice with 200mJ/cm2 UVC prior to harvesting in

value: Primary Keratinocytes plated without feeder layer

tag: passages


title: H3K27me3_EYE_ChIPSeq

description: Chromatin IP against H3K27me3

value: Upstate/Millipore


title: H3K27ac_EID_R1

description: chromatin IP against H3K27ac

source_name: Eye imaginal discs, chromatin IP against H3K27ac


title: H3K4me1_WID_R1

description: chromatin IP against H3K4me1

source_name: Wing imaginal discs, chromatin IP against H3K4me1


title: H3K9ac_WING_ChIPSeq

description: Chromatin IP against H3K9ac

source_name: Wing imaginal discs


title: WING_RNASeq

description: RNA-seq of wing discs

data_processing:
Alignment: Sequence reads were obtained and mapped to Drosophila melanogaster (dm3, April 2006) genomes using GEM (PubMed ID: 23103880). All reads mapping with two or fewer mismatches were retained. PeakSeq (http://www.gersteinlab.org/proj/PeakSeq/) was used to create the signal maps as wig files.
Genome_build: dm3
Supplementary_files_format_and_content: (WIG, genome wide profile)

extract_protocol: RNA was extracted from 50 wing imaginal discs or 100 eye-antennal imaginal dics with a Zymo RNA MicroPrep extraction kit following the instructions of the manufacturer. DNase treatment was performed for 20 minutes at 37ºC and RNA was purified with RNA Clean & Concentrator Kit, of Zymo Research. Libraries were prepared according to Illumina instructions.


title: EYE_RNASeq

description: RNA-seq of eye discs


title: C3-siCon-t=48-rep1

description: Sample 3

tag: cell line

tag: sirna type

tag: hours

tag: passage


title: NIS-1_ChIP-seq

description: first IP experiement of NIS

data_processing:
For Samples 1-4 and 13-16, basecalls were performed using CASAVA version 1.8.2. For Samples 5-12,  basecalls were performed using CASAVA version 1.7.0.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie with the following options: -a -m 1 --best --strata -v 1.
Peaks of enriched binding regions were detected by  merging  biological replicates of IP and NIS or IgG. Peaks were called using MACS1.4.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files containing peaks detected by MACS1.4.

source_name: Primary proliferating myoblasts

extract_protocol:
Lysates were clarified from sonicated nuclei (sonicated to yield DNA fragments of ~300bp) and TF-DNA  complexes were isolated with  relevant antibody, washed and DNA was purified using Qiagen Minelute kit.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: strain

tag: tissue

value: muscle

tag: cell type

value: primary

value: Rabbit non immune serum


title: H3K4me3_EYE_ChIPSeq

description: Chromatin IP against H3K4me3

extract_protocol: Chromatin from Drosophila third instar larvae wing/eye discs was immunoprecipitated with 2 ug of antibody using standard protocols. Libraries were prepared according to Illumina instructions.

tag: chip antibody

value: anti-H3K4me3 (Millipore-Upstate/07-473)


title: H3K36me3_EYE_ChIPSeq

description: Chromatin IP against H3K36me3

value: anti-H3K36me3 antibody (Abcam/ab9050)


title: Ago2-HITS-CLIP, biological rep.4

value: mAb against mouse Ago2 clone 2D4 (Wako)


title: Runx1-2_ChIP-seq

description: second IP experiement of Runx1

tag: days in culture

value: Runx1 (in house)


title: H3_EYE_ChIPSeq

description: Chromatin IP against H3

value: wt

value: Canton S

value: anti-H3 antibody (Abcam/ab1791)


title: Runx1-1_ChIP-seq

description: first IP experiement of Runx1


title: H3_WING_ChIPSeq

description: Chromatin IP against H3

value: third instar larvae


title: COLD - 6-cDNA_S25_L001_R1_001

status: Public on Jul 22 2015

city: Pretoria

first: Habibu

last: Aliyu

state: Gauteng

address: Lynnwood

department: Genetics

country: South Africa

institute: Centre for Microbial Ecology and Genomics

data_processing:
CLC Genomics Workbench 7.5 was used to map the reads against the genome of Nesterenkonia sp. AN1
“Empirical analysis of DEG” (EDGE) tool implemented in CLC Genomics Workbench 7.5 was used to identify differentially expressed transcripts.
Genome_build: NestAN1.1
Supplementary_files_format_and_content: OPTM vs. COLD.xls

organism: Nesterenkonia sp. AN1

source_name: Nesterenkonia sp. AN1 grown at 5 ºC

extract_protocol:
Total RNA was extracted using Direct-zol™ RNA Mini Prep kits (Zymo Research Corp, USA) as per the manufacturer’s instructions.
Total RNA was depleted of ribosomal RNA using Ribo-ZeroTM rRNA removal kit (Epicentre, USA), the Illumina paired - end library constructed according to the manufacturer’s instructions.

tag: protocol

value: grown at 5 C


title: HM1 Heat shock

city: Stanford

first: Gretchen

middle: Marie

last: Ehrenkaufer

state: CA

address: Grant S-143, 300 Pasteur Dr.

department: Microbiology and Immunology

institute: Stanford Uninversity

description: small RNA

data_processing:
Basecalling was performed using Illumina Sequencing Data Analysis software
Adaptor sequences were removed from each read
Duplicate sequences were removed
Unique reads were filtered by removing all reads that mapped to invadens  tRNA, rDNA, LINES and SINES
Filtered reads were mapped to the E. histolytica genome using bowtie with the parameters: -v 0 --all
Genome_build: E. histoyiitca HM-1:IMSS  version 1.3 (http://amoebadb.org)
Supplementary_files_format_and_content: counts

organism: Entamoeba histolytica

source_name: E. histolytica trophozoites

growth_protocol: E. histolytica trohozoites were grown in TYI at 37°C

extract_protocol:
At each time point, parasites were harvested by chilling on ice, spun down, and washed 1x in cold PBS. RNA was isolated using Trizol (Invitrogen) following the manufacturer's protocol.
We used the NEBNext multiplex small RNA library prep set for Illumina (NEB#E7300S) and followed the manufacturer’s protocol with the following modifications: total RNA (25-50 µg) was first fractioned for the size 15-30nt RNA using 12% polyacrylamide urea gel. The size-selected RNA was then treated with tobacco acid pyrophosphatase [TAP] to convert 5’ poly-P to 5’ single-P (Epicentre). The RNA sample was then fed into the pipeline as described in the manufacturer's protocol. Once the cDNA was made, the barcode primers were incorporated into each sample using PCR with kit’s provided barcoded primer; typically we used 8-12 PCR cycles to get a clear final PCR product band. The final PCR product was quantified using Nanodrop, and samples were pooled and shipped to the collaborator for Illumina sequencing. The platform MiSeq (Illumina) was used, the number
Sequencing of E. histolytica small RNAs during stress response

treatment_protocol: For  oxidative stress, parasites were treated with 1mM  H2O2 for 1hr. For  heat-shock  parasites were palce at 42°C for 1hr. Using one flask T25 culture, 18 tubes (16ml) cultures were set up, and grown for 2 days at 37°C. On the day of treatment, 18 tubes were divided into three groups (6 tubes each). One group used as untreated control, one group for H2O2 treatment, one group for 42°C treatment.

tag: isolation method

value: RNA isolated by Trizol

tag: treatment

value: 42°C for one hour


title: Ago2-HITS-CLIP, biological rep.2

tag: clip-antibody


title: COLD - 5-cDNA_S24_L001_R1_001


title: HM1 Basal growth

description: small RNA


title: OPTM - 4-cDNA_S23_L001_R1_001

source_name: Nesterenkonia sp. AN1 grown at 21 ºC

value: grown at 21 C


title: NIS-2_ChIP-seq

description: second IP experiement of NIS


title: OPTM - 3-cDNA_S22_L001_R1_001


title: DBANaive3

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

data_processing:
RNAseq reads were aligned to the mm10 genome assembly using STAR 2.3.0 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Standard mouse housing

extract_protocol:
Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sciatic nerve crush vs sham injured

value: DBA

value: Naive

value: dorsal root ganglion


title: DBANaive4


title: DBAAx5d4


title: DBAAx5d3


title: DBANaive1


title: DBAAx5d2


title: CASTNaive3

value: CAST


title: CASTNaive1


title: CASTAx5d3


title: CASTNaive2


title: CASTNaive4


title: CASTAx5d1


title: HM1 Oxidative stress

description: small RNA

value: 1mM Hydrogen peroxide  for 1hr


title: C57Naive4


title: CASTAx5d2


title: CASTAx5d4


title: C57Naive3


title: C57Naive1


title: C57Ax5d3


title: C57Ax5d2


title: C57Ax5d1


title: C57Ax5d4


title: DBANaive2


title: WT_cyc14E_sl13

first: Peter

middle: Acuña

last: Combs

address: Gilbert Rm 309, 371 Serra Mall

department: Biology

institute: Stanford University

data_processing:
base calling: CASAVA_v1.8.0
mapping: STAR v2.3.0.1
quantification: cufflinks v2.2.1 (--multi-read-correct --frag-bias-correct --GTF --mask-file)
quantification: kallisto v0.42 (-l 400 --plaintext)
quality masking: Low-quality samples were masked with "---" using MakeSummaryTable.py, in order to indicate that there was a slice at that position, but it did not pass one or more quality metrics (--strip-low-reads 500000 --strip-on-unique --strip-as-nan --strip-low-map-rate). Available online at https://github.com/petercombs/EisenLab-Code/blob/master/MakeSummaryTable.py
Genome_build: FlyBase r6.03
Supplementary_files_format_and_content: tab-separated values of FPKMs (cufflinks) or TPM (kallisto)

source_name: Slice of Canton-S embryo

growth_protocol: 25C incubator. 2 hour lay, age to appropriate stage in incubator.

extract_protocol:
TruSeq
TRIzol

treatment_protocol: Methanol fixation of tissues

value: Embryo

tag: carrier species

value: S. cerevisiae

tag: Stage

value: cycle 14E


title: WT_cyc14E_sl11

value: T. delbruckii


title: WT_cyc14E_sl10


title: DBAAx5d1


title: WT_cyc14E_sl08


title: WT_cyc14E_sl07


title: WT_cyc14E_sl09


title: WT_cyc14E_sl04


title: WT_cyc14E_sl06


title: WT_cyc14D_sl14

value: cycle 14D


title: WT_cyc14E_sl12


title: WT_cyc14E_sl01


title: WT_cyc14E_sl05


title: WT_cyc14D_sl11


title: WT_cyc14D_sl10


title: WT_cyc14D_sl13


title: WT_cyc14D_sl09


title: WT_cyc14D_sl07


title: WT_cyc14E_sl03


title: WT_cyc14E_sl02


title: C57Naive2


title: WT_cyc14D_sl03


title: WT_cyc14D_sl04


title: WT_cyc14D_sl02


title: WT_cyc14D_sl01


title: WT_cyc14D_sl06


title: WT_cyc14D_sl12


title: WT_cyc14C_sl10

value: cycle 14C


title: WT_cyc14C_sl08


title: WT_cyc14C_sl07


title: WT_cyc14C_sl09


title: WT_cyc14C_sl06


title: WT_cyc14C_sl04


title: WT_cyc14C_sl05


title: WT_cyc14C_sl03


title: WT_cyc14C_sl01


title: WT_cyc14C_sl02


title: WT_cyc14B_sl09

value: cycle 14B


title: WT_cyc14B_sl13


title: WT_cyc14B_sl10


title: WT_cyc14D_sl05


title: WT_cyc14B_sl07


title: WT_cyc14B_sl05


title: WT_cyc14B_sl12


title: WT_cyc14B_sl08


title: WT_cyc14B_sl03


title: WT_cyc14B_sl01


title: WT_cyc14B_sl04


title: WT_cyc14A_sl08

value: cycle 14A


title: WT_cyc14A_sl10


title: WT_cyc14A_sl09


title: WT_cyc14B_sl02


title: WT_cyc14A_sl11


title: WT_cyc14A_sl07


title: WT_cyc14A_sl06


title: WT_cyc14A_sl05


title: WT_cyc14A_sl04


title: WT_cyc14A_sl03


title: WT_cyc14A_sl01


title: WT_cyc14A_sl02


title: WT_cyc14B_sl11


title: WT_cyc14B_sl06


title: WT_cyc13_sl10

value: cycle 13


title: WT_cyc13_sl08


title: WT_cyc13_sl09


title: WT_cyc13_sl06


title: WT_cyc13_sl05


title: WT_cyc13_sl07


title: WT_cyc13_sl04


title: WT_cyc13_sl03


title: WT_cyc11_sl13

value: cycle 11


title: WT_cyc11_sl14


title: WT_cyc13_sl02


title: WT_cyc11_sl12


title: WT_cyc11_sl08


title: WT_cyc11_sl10


title: WT_cyc11_sl11


title: WT_cyc11_sl07


title: WT_cyc11_sl06


title: WT_cyc11_sl09


title: WT_cyc11_sl05


title: WT_cyc11_sl03


title: WT_cyc11_sl04


title: WT_cyc13_sl11


title: WT_cyc11_sl01


title: zld_cyc14D_sl12

source_name: Slice of zelda- germline clone


title: zld_cyc14D_sl11


title: zld_cyc14D_sl10


title: R90WW_P10_C

status: Public on Jul 27 2015

city: St. Louis

first: Philip

last: Ruzycki

state: MO

department: Ophthalmology and Visual Sciences

institute: Washington University in St. Louis

data_processing:
Reads mapped to NCBI37/mm9 using Tophat (Version 2.0.5) with automatic parameters
Reads assigned to UCSC annotated genes using Htseq (Version 0.6.1p1)
Expression of mutants was compared to age matched WT control using EdgeR (Version 3.6.8). Genes that passed the filter criteria of CPM >5 in all replicates in one comparison groups were included in the comparison
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Data file includes HTSeq determined CPM values for each gene in all genotypes.  Also includes EdgeR calculated FC and FDR values for each gene.

source_name: Whole Retina

extract_protocol:
Four retinas (2Male, 2Female) were collected and pooled to represent each biological replicate. Retinas were processed for RNA using the PerfectPure RNA tissue kit (5Prime).  Quality was assessed using the Agilent Bioanalyzer, and samples with minimum 8.0 RIN score submitted for library preparation.
mRNA was extracted using the DynaI mRNA Direct Kit (Life Technologies), mRNA was then fragmented and reverse transcribed to double stranded cDNA using andom primers before the additon of Illumina adaptors.  rRNA was depleted using Ribo-Zero (Epicentre).

tag: age

tag: genotype/variation

value: retina


title: zld_cyc14D_sl08


title: zld_cyc14D_sl06


title: WT_cyc13_sl01


title: zld_cyc14D_sl07


title: zld_cyc14D_sl04


title: zld_cyc14D_sl05


title: zld_cyc14D_sl02


title: zld_cyc14D_sl03


title: zld_cyc14B_sl07


title: zld_cyc14D_sl01


title: zld_cyc14B_sl05


title: zld_cyc14B_sl06


title: zld_cyc14B_sl08


title: WT_cyc11_sl02


title: zld_cyc14B_sl04


title: zld_cyc14B_sl01


title: zld_cyc14B_sl02


title: zld_cyc14D_sl09


title: 30 ' following memory retrieval rep2

city: Spokane

first: Lucia

last: Peixoto

state: WA

address: PO Box 1495

department: College of Medicine

institute: Washington State University, Spokane

description: processed data column: RT5

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to mm9 whole genome using GSNAP with parameters -m 7 -N 1, only unique and concrodent reads were kept for subsequent analysis
Gene counts were obtained with HTSeq 0.6.1 using ENSEMBL65 genome annotation
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text file containing raw read counts per gene (rows) for all samples (columns)

source_name: Hippocampus

growth_protocol: C57BL/6J adult male mice (2 months of age) were obtained from Jackson Laboratories and housed individually for a week on a 12 hr. /12 hr. light/dark schedule with lights on at 7 am (Zeitgeber time (ZT) 0). Food and water were available ad libitum throughout the experiment.

extract_protocol:
RNA extraction was performed using Qiagen RNAeasy Microarray Tissue kit. All RNA extractions were performed the same day within a week of tissue collection.
2µg of RNA was used for library preparation using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) with Poly A selection according to the manufacturer’s instructions. Completed libraries were size-selected (200-400 bp) on an agarose gel to remove any high basepair fragments, quantified by qPCR (KAPA Biosystems, Boston, MA), and submitted to the Penn Genome Frontiers Institute (PGFI) sequencing core at UPENN for sequencing. 3 libraries were multiplexed per lane (one biological replicate of each 3 conditions) and sequenced on an Illumina HiSeq 2000 using Type 3 chemistry, resulting in an average of 64 million 100 bp pair-end reads per sample.

treatment_protocol: Each animal was handled daily for 3 days prior to contextual fear conditioning (FC). Handling consisted of manipulation of the animals for 1-2 minutes per mouse in the same room as the experimental setting without exposure to the context. The conditioning protocol entailed a single 2-second, 1.5-mA foot shock, terminating at 2.5 minutes after placement of the mouse in the chamber, starting at 10 am (ZT3) daily. Tissue was collected at 30 minutes after FC (FC) as well as 30 minutes after testing for retrieval of the memory (RT). Testing was performed at 24 hours after training over a 5-minute interval, which is sufficient to induce reconsolidation [27, 28]. The average freezing was 55 +/- 10%. Tissue was immersed in RNAlater (Qiagen) and immediately frozen. Animals that were handled but not trained were dissected at the same time of day (CC).

tag: developmental stage

value: 2 months old

tag: genotype

value: WT male


title: 30 ' following memory retrieval rep3

description: processed data column: RT6


title: 30 ' following memory retrieval rep5

description: processed data column: RT8


title: 30 ' following memory retrieval rep4

description: processed data column: RT7


title: zld_cyc14A_sl05


title: zld_cyc14A_sl04


title: 30 ' following contextual fear conditioning rep4

description: processed data column: FC7


title: 30 ' following contextual fear conditioning rep5

description: processed data column: FC8


title: 30 ' following memory retrieval rep1

description: processed data column: RT3


title: 30 ' following contextual fear conditioning rep3

description: processed data column: FC6


title: zld_cyc14A_sl02


title: zld_cyc14A_sl01


title: zld_cyc13_rep3_sl07


title: control rep5

description: processed data column: CC8


title: zld_cyc13_rep3_sl06


title: 30 ' following contextual fear conditioning rep2

description: processed data column: FC5


title: zld_cyc14A_sl03


title: 30 ' following contextual fear conditioning rep1

description: processed data column: FC3


title: zld_cyc13_rep3_sl05


title: zld_cyc13_rep3_sl04


title: zld_cyc14B_sl03


title: control rep2

description: processed data column: CC5


title: zld_cyc14A_sl06


title: zld_cyc13_rep3_sl03


title: zld_cyc13_rep3_sl02


title: zld_cyc13_rep3_sl01


title: zld_cyc13_rep2_sl05


title: zld_cyc13_rep2_sl06


title: zld_cyc13_rep2_sl04


title: zld_cyc13_rep2_sl03


title: control rep4

description: processed data column: CC7


title: zld_cyc13_rep2_sl02


title: control rep3

description: processed data column: CC6


title: zld_cyc13_rep2_sl01


title: zld_cyc13_rep1_sl07


title: zld_cyc14D_sl13


title: IR1, in vivo

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

data_processing:
alignment: TopHat v1.4.1 using default settings
expression levels: Cufflinks v1.3.0 and cuffdiff using default settings
GSEA anlalysis with GeneSigDB v4
Genome_build: hg19 (Ucsc)
Supplementary_files_format_and_content: text file with FPKM values

source_name: IRp HSC, in vivo

growth_protocol: C57Bl/6 mice were used for all samples. For "in vivo" samples BM was harvested and sorted for Lineage-negative, cKit+, Sca1+ (LSK) cells, then processed immediately for RNA-seq LSK from 3 mice were pooled for each "in vivo" sample. For in vitro samples: 200 LSK  were cultured with mSCF, hFlt3L, hIL-11, and hIL-6  for 6 days. LSK were then resorted and processed for RNA-seq. One mouse was used for each in vitro sample.

extract_protocol:
Total RNA was extracted with the miRNeasy Kit (Qiagen) according to manufacturer's instructions.
RNA libraries were prepared for sequencing using TruSEQ RNA Sample Prep v2 using standard Illumina protocols.

treatment_protocol: To generate IRp mice, C57Bl/6 mice were sublethally irradiated with 2.5Gy Cs-137 and allowed to homeostatically restore for a minimum of 9 weeks. Mice were then used for "in vivo" or "in vitro" LSK RNA-seq

tag: condition

value: IR exposed


title: CTRLDL3, in vitro

source_name: IRp BM cells + DL1, in vitro

value: normal + DL1


title: CTRL1, in vivo

source_name: IRp BM cells, in vivo

value: normal


title: IRDL1, in vitro

source_name: IRp HSC + DL1, in vitro

value: IR exposed + DL1


title: IRDL3, in vitro


title: zld_cyc13_rep1_sl08

value: Embryo


title: IR3, in vivo


title: IRDL2, in vitro


title: zld_cyc13_rep1_sl06

value: S. cerevisiae


title: IR2, in vivo


title: CTRL2, in vivo


title: CTRLDL1, in vitro


title: CTRL3, in vivo


title: IR3, in vitro

source_name: IRp HSC, in vitro


title: zld_cyc13_rep1_sl04


title: CTRLDL2, in vitro


title: zld_cyc13_rep1_sl03


title: control rep1

description: processed data column: CC3


title: zld_cyc13_rep1_sl02


title: zld_cyc13_rep1_sl05


title: IR2, in vitro


title: IR1, in vitro


title: CTRL3, in vitro

source_name: IRp BM cells, in vitro


title: zld_cyc11_sl07


title: zld_cyc13_rep1_sl01


title: zld_cyc11_sl06


title: CTRL1, in vitro


title: zld_cyc11_sl04


title: zld_cyc11_sl05


title: zld_cyc11_sl01


title: VYS_input_DNA

city: Vienna

first: Quanah

middle: J

last: Hudson

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
RNAseq reads were aligned with GSNAP version 2012-12-12 alowing novel splicing events detection; ChIPseq reads were alined using GSNAP version 2012-12-12; WGBS reads were alined using GSNAP version 2012-12-12
read counts were summarized using RPKM_count.py from the RSeQC version 2.3.3 or using bedtools and further processed using custom scripts in R
peaks were called using MACS version 1.4.2 with the default settings
Whole genome bisulfite-seq metylation calling was done using bissnp pipeline
Genome_build: mm10

source_name: VYS

extract_protocol:
material from native ChIP was Phenol:Chloroform extracted
TruSeq protocol

value: visceral yolk sac

tag: genetic background

value: FVB


title: zld_cyc11_sl03


title: WT_cyc14D_sl08

value: cycle 14D


title: liver FxC WGBSseq

source_name: liver

extract_protocol:
DNA was harvested with TriReagent using standard manufacturer protocol
TruSeq protocol

value: liver

value: FVBxCast


title: zld_cyc11_sl02


title: VYS_H3K4me3_ChIPSeq

data_processing:
processed data file format and content: bed (ChIPseq peaks called by MACS)
RNAseq reads were aligned with GSNAP version 2012-12-12 alowing novel splicing events detection; ChIPseq reads were alined using GSNAP version 2012-12-12; WGBS reads were alined using GSNAP version 2012-12-12
read counts were summarized using RPKM_count.py from the RSeQC version 2.3.3 or using bedtools and further processed using custom scripts in R
peaks were called using MACS version 1.4.2 with the default settings
Whole genome bisulfite-seq metylation calling was done using bissnp pipeline
Genome_build: mm10


title: VYS endoderm CxF WGBSseq

source_name: VYS endoderm

value: visceral yolk sac endoderm

value: CastxFVB


title: cystic EBs CxF WGBSseq

source_name: cystic EBs

value: cystic EBs

value: 15 day differentiation

tag: es cell clone

value: CF clone C2


title: liver CxF WGBSseq

tag: tissue


title: hb_cyc14D_rep2_sl22

source_name: Slice of RNAi-mediated hunchback depleted embryo

extract_protocol:
SMARTseq2
TRIzol


title: hb_cyc14D_rep2_sl24


title: hb_cyc14D_rep2_sl21


title: cystic EBs FxC WGBSseq

value: FC clone A2


title: hb_cyc14D_rep2_sl20


title: hb_cyc14D_rep2_sl23


title: VYS endoderm FxC WGBSseq


title: cystic EBs d15 brB RNAseq

data_processing:
processed data file format and content: *.F.bw are bigWig file for + strand mm10. *.R.bw are bigWig file for - strand mm10.
3 additional supplementary file on Series record: refSeqTranscriptsCountTable.txt (table of reads counts summarized over refSeq transcripts), refseqTranscriptsRPKMsTable.txt (table of RPKMs summarized over refSeq transcripts), and repeatMaskerIntergenicCountTable.txt (table of reads counts summarized over intergenic repeats (annotation from repeatmasker.org)).
RNAseq reads were aligned with GSNAP version 2012-12-12 alowing novel splicing events detection; ChIPseq reads were alined using GSNAP version 2012-12-12; WGBS reads were alined using GSNAP version 2012-12-12
read counts were summarized using RPKM_count.py from the RSeQC version 2.3.3 or using bedtools and further processed using custom scripts in R
peaks were called using MACS version 1.4.2 with the default settings
Whole genome bisulfite-seq metylation calling was done using bissnp pipeline
Genome_build: mm10

extract_protocol:
RNA was harvested with TriReagent using standard manufacturer protocol
(Sultan et al., 2012)

value: Bl6/129 Jennifer Nichols


title: cystic EBs d10 brA RNAseq

extract_protocol:
RNA was harvested with TriReagent using standard manufacturer protocol
ScriptSeq v1 protocol

value: 10 day differentiation

value: A9 Anton Wutz


title: hb_cyc14D_rep2_sl19


title: cystic EBs d10 brB RNAseq


title: liver F brB RNAseq


title: hb_cyc14D_rep2_sl17


title: CTRL2, in vitro

value: normal

tag: strain


title: hb_cyc14D_rep2_sl16

value: Embryo


title: hb_cyc14D_rep2_sl15


title: liver F brA RNAseq


title: hb_cyc14D_rep2_sl18


title: VYS mesoderm F brB RNAseq

source_name: VYS mesoderm

value: visceral yolk sac mesoderm


title: hb_cyc14D_rep2_sl13


title: hb_cyc14D_rep2_sl08


title: hb_cyc14D_rep2_sl14


title: cystic EBs d15 brA RNAseq


title: hb_cyc14D_rep2_sl10


title: hb_cyc14D_rep2_sl11


title: VYS endoderm F brB RNAseq


title: hb_cyc14D_rep2_sl05


title: VYS mesoderm F brA RNAseq


title: VYS endoderm F RNAseq

data_processing:
processed data file format and content: bigWig file for mm10. no strand information.
3 additional supplementary file on Series record: refSeqTranscriptsCountTable.txt (table of reads counts summarized over refSeq transcripts), refseqTranscriptsRPKMsTable.txt (table of RPKMs summarized over refSeq transcripts), and repeatMaskerIntergenicCountTable.txt (table of reads counts summarized over intergenic repeats (annotation from repeatmasker.org)).
RNAseq reads were aligned with GSNAP version 2012-12-12 alowing novel splicing events detection; ChIPseq reads were alined using GSNAP version 2012-12-12; WGBS reads were alined using GSNAP version 2012-12-12
read counts were summarized using RPKM_count.py from the RSeQC version 2.3.3 or using bedtools and further processed using custom scripts in R
peaks were called using MACS version 1.4.2 with the default settings
Whole genome bisulfite-seq metylation calling was done using bissnp pipeline
Genome_build: mm10

extract_protocol:
RNA was harvested with TriReagent using standard manufacturer protocol
(Huang et al., 2011)


title: rosettes_dm_peg_H3T3ph_rep1

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

description: Treated with 30% Polyethylene glycol (PEG 6,000) for 5 hours to induce drought stress

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the Arabidopsis thaliana genome assembly (TAIR10) using bowtie version 0.12.8 with default parameters.
Tag density files where generated using the resulting SAM files from above step, and an in-house perl script.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited tag density.txt file: chromosome, start, end, count. Locations one-based.

organism: Arabidopsis thaliana

source_name: rosette leaves

growth_protocol: Columbia-0 and double mutant at3g03940/at518190 knockdown plants were grown in 12 hr light for 3 weeks in pots with soil covered with miracloth to prevent soil contamination of leaf tissues.

extract_protocol:
Watered or water deficit treated vegetative tissues were fixed in 1% formaldehyde for 10 min after vacuum infiltration of the tissues in phosphate buffered saline (PBS) with 0.007% silwet. Fixation was stopped by quenching with 125 mM glycine. Next, the tissue was rinsed twice in ice cold water, blotted dry and flash frozen in liquid nitrogen. Chromatin was isolated and resuspended in 300 ml nuclei lysis buffer and sonicated for four 15 sec pulses using a Branson sonifier 450 at an output between 10 – 15%. 100 ml of sheared chromatin was diluted in 900 ml ChIP dilution buffer and precleared, using 5 ml of protein A Dynabeads (Invitrogen, Carlsbad, CA). Protein A beads were removed on a magnet, and the precleared chromatin was incubated overnight at 4 °C with antibodies against either mono-methylated H3K4 (10 mL, Abcam ab8895), dimethylated H3K4 (6 mL, Upstate 07-212), or trimethylated H3K4 (6 mL, Abcam ab8580). Next the antibody/chromatin complex was precipitated by incubating the mix with 40 ml protein A beads for 1 hour followed by collection of the beads on a magnet. The beads were washed and chromatin eluted and de-crosslinked using procedures. DNA was recovered by phenol/chloroform extraction and ethanol precipitation in the presence of Novagen pellet paint (CN Bioscience) and resuspended in 30 mL of TE buffer.
Purified DNA was end modified, ligated to amplification primers, amplified, and sequenced according to the manufacturer’s protocols (Illumina, San Diego, CA).

treatment_protocol: Control was kept in normal watered state, for other samples (peg) drought stress was induced by treatment with 30% Polyethylene glycol (PEG 6,000) for 5 hours.

value: rosette leaves

value: 21 days

tag: chip antibody

value: double mutant at3g03940/at518190 -/-


title: VYS endoderm F brA RNAseq

value: FVB


title: rosettes_dm_peg_H3T3ph_rep2


title: hb_cyc14D_rep2_sl07

value: cycle 14D


title: hb_cyc14D_rep2_sl09


title: hb_cyc14D_rep2_sl12


title: hb_cyc14D_rep2_sl06


title: rosettes_dm_watered_H3T3ph_rep1

description: Watered condition


title: hb_cyc14D_rep2_sl04


title: rosettes_dm_peg_H3K4me3_rep2


title: rosettes_dm_watered_H3T3ph_rep2

description: Watered condition


title: rosettes_dm_peg_H3K4me3_rep1


title: hb_cyc14D_rep2_sl03


title: hb_cyc14D_rep2_sl01


title: rosettes_dm_watered_H3K4me3_rep2

description: Watered condition


title: hb_cyc14D_rep1_sl21


title: rosettes_dm_peg_H3K4me1_rep2


title: rosettes_dm_peg_H3K4me1_rep1


title: hb_cyc14D_rep1_sl20


title: hb_cyc14D_rep1_sl19


title: rosettes_dm_watered_H3K4me1_rep1

description: Watered condition


title: rosettes_dm_watered_H3K4me1_rep2

description: Watered condition


title: rosettes_dm_peg_H3_rep1


title: hb_cyc14D_rep1_sl18


title: rosettes_dm_watered_H3_rep1

description: Watered condition


title: hb_cyc14D_rep1_sl17


title: hb_cyc14D_rep2_sl02


title: rosettes_wildtype_peg_H3T3ph_rep2


title: rosettes_wildtype_peg_H3K4me3_rep3


title: hb_cyc14D_rep1_sl13


title: hb_cyc14D_rep1_sl10


title: rosettes_wildtype_peg_H3T3ph_rep4


title: hb_cyc14D_rep1_sl11


title: hb_cyc14D_rep1_sl15


title: hb_cyc14D_rep1_sl16


title: hb_cyc14D_rep1_sl12


title: rosettes_wildtype_peg_H3T3ph_rep1


title: rosettes_wildtype_peg_H3K4me3_rep2


title: rosettes_wildtype_peg_H3T3ph_rep3


title: rosettes_dm_watered_H3K4me3_rep1

description: Watered condition


title: rosettes_wildtype_peg_H3K4me3_rep1


title: hb_cyc14D_rep1_sl09


title: rosettes_wildtype_peg_H3K4me1_rep4


title: hb_cyc14D_rep1_sl06


title: rosettes_wildtype_peg_H3T3ph_rep5


title: hb_cyc14D_rep1_sl14


title: hb_cyc14D_rep1_sl05


title: rosettes_wildtype_peg_H3K4me1_rep3


title: hb_cyc14D_rep1_sl04


title: rosettes_wildtype_peg_H3K4me1_rep2


title: rosettes_wildtype_peg_H3K4me1_rep1


title: hb_cyc14D_rep1_sl03


title: hb_cyc14D_rep1_sl02


title: rosettes_wildtype_peg_H3_rep3


title: rosettes_wildtype_peg_H3_rep4


title: hb_cyc14D_rep1_sl01


title: hb_cyc13_rep1_sl24

value: cycle 13


title: hb_cyc13_rep1_sl21


title: hb_cyc13_rep1_sl20


title: hb_cyc14D_rep1_sl08


title: hb_cyc13_rep1_sl19


title: rosettes_wildtype_watered_H3T3ph_rep2

description: Watered condition


title: rosettes_wildtype_watered_H3T3ph_rep1

description: Watered condition


title: hb_cyc13_rep1_sl22


title: rosettes_wildtype_peg_H3_rep2


title: hb_cyc14D_rep1_sl07


title: rosettes_wildtype_watered_H3T3ph_rep3

description: Watered condition


title: rosettes_wildtype_watered_H3K4me3_rep3

description: Watered condition


title: hb_cyc13_rep1_sl18


title: rosettes_wildtype_watered_H3K4me3_rep2

description: Watered condition


title: hb_cyc13_rep1_sl17


title: rosettes_wildtype_watered_H3K4me1_rep3

description: Watered condition


title: hb_cyc13_rep1_sl16


title: rosettes_wildtype_watered_H3K4me3_rep1

description: Watered condition


title: hb_cyc13_rep1_sl14


title: hb_cyc13_rep1_sl23


title: rosettes_wildtype_peg_H3_rep1


title: hb_cyc13_rep1_sl13


title: rosettes_wildtype_watered_H3K4me1_rep2

description: Watered condition


title: rosettes_wildtype_watered_H3_rep3

description: Watered condition


title: rosettes_wildtype_watered_H3T3ph_rep4

description: Watered condition


title: hb_cyc13_rep1_sl12


title: hb_cyc13_rep1_sl10


title: rosettes_wildtype_watered_H3_rep2

description: Watered condition


title: rosettes_wildtype_watered_H3_rep1

description: Watered condition


title: hb_cyc13_rep1_sl09


title: hb_cyc13_rep1_sl11


title: hb_cyc13_rep1_sl05


title: TM_rep1

city: Durham

first: Gregory

last: Crawford

state: NC

address: 101 Science Drive

department: Center for Genomic and Computational Biology

institute: Duke University

data_processing:
Single-end basecalls were done by using Illumina CASAVA 1.3 software.
First 20 bp of Dnase-seq raw reads were mapped to hg19 with BWA, with 2 mismatches allowed, to generate bam files, then bam files were converted to bed file by bedtools. After removing PCR artifacts bigWig files were created by using fseq (PMID: 18784119).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig format (hg19)

source_name: postmortem donor tissue

growth_protocol: Lens capsules were collected from discarded tissue during routine cataract surgery (patients did not have any evidence of XFS). They were placed in cell culture media supplemented with 10% DMSO, snap frozen, and stored at -80 until use. Human trabecular meshwork and Schlemm's canal cells were isolated from postmortem donor tissue using previously described methods (Stamer et al., Current Eye Research, 1995; Stamer et al., IOVS, 1998). Donors did not have any evidence of XFS. The cells were maintained in DMEM media supplemented with 10% FBS until reaching confluence. At this point, cells were grown in media supplemented with 1% FBS for one week to allow differentiation.

extract_protocol:
Cells were Lysed and nuclei were digested according to the publication PMID: 20150147.
Libraries were prepared according to the publication PMID: 20150147.

tag: cell type

value: trabecular meshwork cells


title: Lens_rep1

source_name: Lens capsules

value: Lens capsules cells


title: SC_rep1

value: Schlemm's canal cells


title: hb_cyc13_rep1_sl06


title: hb_cyc13_rep1_sl04


title: hb_cyc13_rep1_sl15


title: hb_cyc13_rep1_sl03


title: hb_cyc13_rep1_sl02


title: rosettes_wildtype_watered_H3K4me1_rep1

description: Watered condition


title: G20_cyc14D_rep2_sl19

source_name: Slice of 2.4X bicoid overexpression embryo


title: hb_cyc13_rep1_sl01


title: G20_cyc14D_rep2_sl20


title: G20_cyc14D_rep2_sl18


title: G20_cyc14D_rep2_sl17


title: rosettes_wildtype_watered_H3_rep4

description: Watered condition


title: G20_cyc14D_rep2_sl14


title: G20_cyc14D_rep2_sl16


title: G20_cyc14D_rep2_sl15


title: hb_cyc13_rep1_sl08


title: G20_cyc14D_rep2_sl12


title: G20_cyc14D_rep2_sl10


title: hb_cyc13_rep1_sl07


title: G20_cyc14D_rep2_sl07


title: G20_cyc14D_rep2_sl11


title: G20_cyc14D_rep2_sl09


title: G20_cyc14D_rep2_sl06


title: G20_cyc14D_rep2_sl05


title: G20_cyc14D_rep2_sl08


title: G20_cyc14D_rep2_sl04


title: G20_cyc14D_rep2_sl03


title: G20_cyc14D_rep1_sl19


title: G20_cyc14D_rep2_sl01


title: G20_cyc14D_rep2_sl02


title: G20_cyc14D_rep1_sl17


title: G20_cyc14D_rep1_sl20


title: G20_cyc14D_rep1_sl18


title: G20_cyc14D_rep2_sl13


title: G20_cyc14D_rep1_sl14


title: G20_cyc14D_rep1_sl16


title: G20_cyc14D_rep1_sl12


title: G20_cyc14D_rep1_sl11


title: G20_cyc14D_rep1_sl15


title: G20_cyc14D_rep1_sl07


title: G20_cyc14D_rep1_sl09


title: G20_cyc14D_rep1_sl06


title: G20_cyc14D_rep1_sl08


title: G20_cyc14D_rep1_sl10


title: G20_cyc14D_rep1_sl05


title: G20_cyc14D_rep1_sl04


title: G20_cyc14D_rep1_sl03


title: G20_cyc14D_rep1_sl02


title: G20_cyc14D_rep1_sl01


title: G20_cyc13_rep2_sl22


title: G20_cyc13_rep2_sl21


title: G20_cyc13_rep2_sl20


title: G20_cyc13_rep2_sl19


title: G20_cyc13_rep2_sl18


title: G20_cyc13_rep2_sl16


title: G20_cyc13_rep2_sl17


title: G20_cyc13_rep2_sl15


title: G20_cyc13_rep2_sl12


title: G20_cyc13_rep2_sl14


title: G20_cyc13_rep2_sl13


title: G20_cyc13_rep2_sl11


title: G20_cyc14D_rep1_sl13


title: G20_cyc13_rep2_sl10


title: G20_cyc13_rep2_sl08


title: G20_cyc13_rep2_sl06


title: G20_cyc13_rep2_sl07


title: G20_cyc13_rep2_sl09


title: G20_cyc13_rep2_sl05


title: G20_cyc13_rep2_sl04


title: G20_cyc13_rep2_sl03


title: G20_cyc13_rep2_sl02


title: G20_cyc13_rep2_sl01


title: G20_cyc13_rep1_sl26


title: G20_cyc13_rep1_sl25


title: G20_cyc13_rep1_sl24


title: G20_cyc13_rep1_sl22


title: G20_cyc13_rep1_sl21


title: G20_cyc13_rep1_sl19


title: G20_cyc13_rep1_sl18


title: G20_cyc13_rep1_sl16


title: G20_cyc13_rep1_sl15


title: G20_cyc13_rep1_sl17


title: G20_cyc13_rep1_sl14


title: G20_cyc13_rep1_sl12


title: G20_cyc13_rep1_sl13


title: G20_cyc13_rep1_sl08


title: G20_cyc13_rep1_sl09


title: G20_cyc13_rep1_sl07


title: G20_cyc13_rep1_sl05


title: G20_cyc13_rep1_sl02


title: G20_cyc13_rep1_sl06


title: G20_cyc13_rep1_sl03


title: G20_cyc13_rep1_sl01


title: bcd_cyc14D_rep2_sl23

source_name: Slice of RNAi-mediated bicoid depleted embryo


title: 2011G2

city: Beijing

first: Qiu-hong

last: Pan

address: Tsinghua East Road No.17,Haidian district

department: College of Food Science and Nutritional Engineering

country: China

institute: China Agriculture University

data_processing:
The original image data was transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.
The dirty raw reads including reads with adaptors, reads in which unknown bases are more than 10% and low quality reads (the percentage of the low quality bases of
Clean reads were mapped to reference sequences using CLC software. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level was calculated by using RPKM method (Reads Per kb per Million reads). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Vitis vinifera NCBI RefSeq mRNAs
Supplementary_files_format_and_content: Results include the coverage of each gene, RPKM values, toatal number of reads that aligned to gene, and the description of gene for each sample

organism: Vitis vinifera

source_name: grape berry

growth_protocol: The vines used for grape sampling were cultivated in 2001 (in gaotai region) and 2006 (in changli rigion), respectively. The grapevines in both regions were planted from cutting stems and trained on a vertical shoot positioning (VSP), arranged in north-south oriented rows spaced 2.0 m apart, with a distance of approximately 1.0 m between two plants in each row. The management of the vineyards was in accordance with the local wine grape production technical rules.

extract_protocol:
Approximately 50 berries were randomly selected from a 1000-berry biological replicate for RNA extraction. Total RNAs for RNA-seq analysis and real-time polymerase chain reaction (PCR) experiments were extracted from frozen deseeded berries using a plant RNA isolation kit (Sigma RT-250, St. Louis, MO, USA), and further incubated with DNase I (Promega, USA) according to the manufacturer’s instructions. RNA integrity and quality were assessed by analysis with the Aglient 2100 Bioanalyzer.
The Gene Expression Sample Prep Kit (IlluminaInc; San Diego, CA, USA) was used for sequence tag preparation according to the manufacturer's protocol.

tag: cultivar

value: Muscat Blanc a Petits Grains

tag: origin

value: Gaotai region of Gansu province


title: 2011G3


title: 2011G4


title: bcd_cyc14D_rep2_sl22


title: G20_cyc13_rep1_sl23


title: bcd_cyc14D_rep2_sl21


title: G20_cyc13_rep1_sl20


title: 2011C4

value: Changli region of Hebei province


title: 2011C3


title: G20_cyc13_rep1_sl10


title: bcd_cyc14D_rep2_sl20


title: G20_cyc13_rep1_sl11


title: 2011C2


title: 2011C1


title: bcd_cyc14D_rep2_sl17


title: 2010G4


title: bcd_cyc14D_rep2_sl16


title: 2010G3


title: bcd_cyc14D_rep2_sl18


title: G20_cyc13_rep1_sl04


title: bcd_cyc14D_rep2_sl15


title: 2011G1


title: bcd_cyc14D_rep2_sl13


title: 2010G2


title: 2010G1


title: bcd_cyc14D_rep2_sl14


title: 2010C4


title: 2010C3


title: 2010C1


title: bcd_cyc14D_rep2_sl12


title: bcd_cyc14D_rep2_sl09


title: 2010C2


title: bcd_cyc14D_rep2_sl10


title: bcd_cyc14D_rep2_sl11


title: bcd_cyc14D_rep2_sl08


title: bcd_cyc14D_rep2_sl07


title: bcd_cyc14D_rep2_sl19


title: bcd_cyc14D_rep2_sl06


title: bcd_cyc14D_rep2_sl05


title: bcd_cyc14D_rep2_sl03


title: bcd_cyc14D_rep2_sl04


title: bcd_cyc14D_rep2_sl01


title: bcd_cyc14D_rep2_sl02


title: bcd_cyc14D_rep1_sl22


title: bcd_cyc14D_rep1_sl20


title: bcd_cyc14D_rep1_sl19


title: bcd_cyc14D_rep1_sl18


title: bcd_cyc14D_rep1_sl16


title: bcd_cyc14D_rep1_sl15


title: bcd_cyc14D_rep1_sl12


title: bcd_cyc14D_rep1_sl14


title: bcd_cyc14D_rep1_sl11


title: bcd_cyc14D_rep1_sl13


title: bcd_cyc14D_rep1_sl10


title: bcd_cyc14D_rep1_sl09


title: bcd_cyc14D_rep1_sl08


title: bcd_cyc14D_rep1_sl06


title: bcd_cyc14D_rep1_sl05


title: bcd_cyc14D_rep1_sl07


title: bcd_cyc14D_rep1_sl04


title: 14d_CT3

city: Dallas

first: Galvin

last: Swift

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: U TX Southwestern Medical Center

data_processing:
Illumina HiSeq Control Software version 2.0.10.0 used for basecalling
Sequences were mapped to mm9 mouse genome using TopHat v2.0.4 (by use of Bowtie v0.12.7.0) with parameters --no-novel-juncs --segment -length 25 --segment-mismatches 3
Sequences per gene were counted using Samtools ( v0.1.18.0) /HTSeq (v0.6.0)
Counts-per-million (CPM) were calculated using TMM normalization according to Robinson et al., Bioinformatics, 2010. Data set was filtered for minimal expression by "keep <- rowSums(cpm(d)) >= 3"
Genome_build: mm9
Supplementary_files_format_and_content: Normalized counts-per-million (CPM) for each sample in tab-delimited text file

source_name: pancreas

extract_protocol:
RNA preparation:  pancreas was homogenized in 4 M Guanidine Thiocyanate, 0.1 M Tris HCl pH 7.5, 1% 2-mercaptoethanol with a Tekmar Tissuemizer.  RNA was isolated from an aliquot of the homogenate by addition of N-Lauroylsarcosine sodium salt to 0.5%, Potassium Acetate pH 5.5 to 0.1 M, and Acetic Acid to 0.08 M, followed by addition of 0.75 volume ethanol while vortexing.  RNA was allowed to precipitate from the solution at -20 C for at least 1 hour, collected by centrifugation at 12,000 g for 5', and the RNA pellet resuspended in Trizol (equal volume to starting homogenate).  Subsequent steps were as per manufacturer's protocol (Life Technologies).
RNA libraries were prepared for sequencing using standard Illumina True-seq protocols

treatment_protocol: Tamoxifen treatment: On day 0, 1, 2, mice received 0.25 mg tamoxifen/g mouse at 50 mg/ml in corn oil by gavage.  Mice were sacrificed on day 14.

tag: gender

value: F

tag: age at sacrifice

value: 4 mo

value: pancreas

tag: mouse id


title: 14d_cKO1

value: 5 mo


title: High gain, low intake [20113025]

city: Clay Center

first: Amanda

middle: K

last: Lindholm-Perrry

address: State Spur 18D

department: NEMRU

institute: USMARC

data_processing:
Sequences were mapped to the reference Bos taurus genome UMD 3.1 using tophat (version 2.08b)
align reads across splice junctions between exons annotated by Ensembl (version 3.1.70)
The resulting alignments were combined to create clusters of reads (or patches), which represented non-redundant genomic regions in the reference genome sequence.  Cluster boundaries were created by taking all samples into account during the cluster generation to define the left-most and right-most end coordinates of each cluster.  Only uniquely mapped reads were taken into consideration.
Clusters created in this manner underwent linear normalization by multiplying each sample’s locus coverage by the total reads of the lowest read-count sample divided by the respective sample's total reads.  This normalized expression data was the basis for the expression comparison.
The comparative expression approach stepped through each cluster and compared every possible pairing of samples and generated a log2 (A/B), where A and B were the two normalized average coverage of each sample, A and B. Pairwise P-values were determined among the samples using Welch's t-test for unequal variance.  The resulting comparative expressions were visualized in ActiveSite (Cofactor Genomics).
Genome_build: UMD3.1 Genome Assembly

organism: Bos taurus

source_name: High gain_low intake

growth_protocol: Steers had ad libitum access to a ration consisting of: 57.35% dry-rolled corn, 30% wet distillers grains soluble, 8% alfalfa hay, 4.25% steakmaker (Land O'Lakes Feed LLC, Gray Summit, MO, USA), and 0.4% urea.

extract_protocol:
Papillae were clipped from the rumen wall and immediately frozen in liquid nitrogen. 50-100mg of tissue were homogenized in TriZol reagent. Manufacturers protocol was followed.
oligo-dt beads were used to select poly-adenylated RNA to be sheared to appropriate size for the synthesis of cDNA.  The resulting double stranded cDNA was end-repaired and A-tailed in preparation for adaptor ligation.  Adaptors were indexed and ligated to the cDNA, which was then size selected on a 2% SizeSelect™ E-Gel (Invitrogen, Carlsbad, CA, USA).  The size selected cDNA was amplified via polymerase chain reaction.  Library quality was assessed by measuring nanomolar concentration and the fragment size in base pairs.  All 16 samples were sequenced at 1×50 basepairs per sequence read.

treatment_protocol: No specific treatment. Animals were chosen for this study based on the cartesian quadrant that they were allocated to based on their gain and dry matter intake.

tag: breed

value: Crossbred

tag: gender type

value: male; steer

tag: feed gain and intake group

value: High gain_low intake

value: rumen papillae


title: bcd_cyc14D_rep1_sl02

value: Embryo

tag: carrier species

tag: Stage


title: bcd_cyc14D_rep1_sl21

value: cycle 14D


title: bcd_cyc14D_rep1_sl03


title: 14d_cKO2

tag: genotype

value: M


title: 14d_CT2


title: 14d_cKO3


title: bcd_cyc14D_rep1_sl17


title: 14d_CT1


title: bcd_cyc13_rep2_sl21

value: cycle 13


title: Low gain, low intake [20113071]

source_name: Low gain_low intake

tag: age

value: Low gain_low intake


title: bcd_cyc13_rep2_sl19


title: High gain, low intake [20113029]


title: Low gain, low intake [20113092]


title: bcd_cyc13_rep2_sl18


title: Low gain, high intake [20113247]

source_name: Low gain_high intake

value: Low gain_high intake


title: Low gain, low intake [20113158]


title: High gain, high intake [20113212]

source_name: High gain_high intake

value: High gain_high intake


title: bcd_cyc13_rep2_sl17


title: bcd_cyc13_rep2_sl15


title: bcd_cyc13_rep2_sl14


title: bcd_cyc13_rep2_sl16


title: bcd_cyc13_rep2_sl13


title: High gain, low intake [20113417]


title: bcd_cyc13_rep2_sl12


title: Low gain, low intake [20113426]


title: bcd_cyc13_rep2_sl11


title: Low gain, high intake [20113446]


title: High gain, high intake [20113533]


title: bcd_cyc13_rep2_sl10


title: bcd_cyc14D_rep1_sl01


title: High gain, high intake [20113456]


title: bcd_cyc13_rep2_sl08


title: bcd_cyc13_rep2_sl20


title: Low gain, high intake [20113536]


title: bcd_cyc13_rep2_sl09


title: bcd_cyc13_rep2_sl07


title: Low gain, high intake [20113541]


title: Hepatocellular Carcinoma [P11_PVTT]

city: Shanghai

first: Hong

last: Zhang

address: Ming Dao Building  138 Yi Xue Yuan Road

department: Institute for Biomedical Sciences

institute: Fudan University

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat2.0.9
The aligned read files processed by TopHat were then processed by Cufflinks2.1.1, which uses the normalized RNA-seq fragment counts to measure the relative abundances of the transcripts. The unit of measurement is Fragments Per Kilobase of exon per Million fragmentsmapped (FPKM).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: Hepatocellular Carcinoma

extract_protocol:
Total RNA was extracted from ANT,HCC and PVTT tissues with TRIzol according to the manufacturer's protocol (Invitrogen).
We used Illumina standard kit according to the TruSeq RNA Sample Prep Guide (Illumina).

value: Portal vein tumor thrombus

value: HCC

tag: tumor stage

value: III


title: bcd_cyc13_rep2_sl06

tag: tissue


title: bcd_cyc13_rep2_sl05


title: High gain, low intake [20113063]


title: Hepatocellular Carcinoma [P10_PVTT]


title: High gain, high intake [20113400]


title: bcd_cyc13_rep2_sl04


title: E. invadens 72h cyst ~27nt small RNA

description: small RNA

data_processing:
Basecalling was performed using Illumina Sequencing Data Analysis software
Adaptor sequences were removed from each read
Duplicate sequences were removed
Unique reads were filtered by removing all reads that mapped to invadens  tRNA, rDNA, LINES and SINES
Filtered reads were mapped to the E. invadens genome using bowtie with the parameters: -v 0 --all
Genome_build: E. invadens IP-1 version 1.3 (http://amoebadb.org)
Supplementary_files_format_and_content: counts

organism: Entamoeba invadens

source_name: E. invadens IP-1 cysts

growth_protocol: E. invadens was grown in standard axenic culture conditions (LYI @ 25°C)

extract_protocol:
At each time point, parasites were harvested by chilling on ice, spun down, and washed 1x in cold PBS.  All samples were lysed using a French press at 400psi. Following lysis, RNA was isolated using Trizol (Invitrogen) following the manufacturer's protocol.
We used the NEBNext multiplex small RNA library prep set for Illumina (NEB#E7300S) and followed the manufacturer’s protocol with the following modifications: total RNA (25-50 µg) was first fractioned for the size 15-30nt RNA using 12% polyacrylamide urea gel. The size-selected RNA was then treated with tobacco acid pyrophosphatase [TAP] to convert 5’ poly-P to 5’ single-P (Epicentre). The RNA sample was then fed into the pipeline as described in the manufacturer's protocol. Once the cDNA was made, the barcode primers were incorporated into each sample using PCR with kit’s provided barcoded primer; typically we used 8-12 PCR cycles to get a clear final PCR product band. The final PCR product was quantified using Nanodrop, and samples were pooled and shipped to the collaborator for Illumina sequencing. The platform MiSeq (Illumina) was used, the number
Sequncing of small  RNAs during development

treatment_protocol: Encystation was induced by incubation in 47% low glucose media (LG); Excystation was induced by incubation in LG + 1% glucose 1mg/ml bile and 40mM sodium barcarbonate

tag: isolation method

value: Pre-treatment with 0.1% sarkosyl for 30 min, Lysis by French Press; RNA isolated using Trizol (Invitrogen)

tag: strain


title: E. invadens 24h cyst ~27nt small RNA

description: small RNA

value: Lysis by French Press; RNA isolated using Trizol (Invitrogen)


title: bcd_cyc13_rep2_sl03


title: bcd_cyc13_rep2_sl02


title: Hepatocellular Carcinoma [P9_PVTT]

tag: cell type


title: bcd_cyc13_rep2_sl01


title: E. invadens trophozoite ~27nt small RNA

description: small RNA

source_name: E. invadens IP-1 trophozoites


title: bcd_cyc13_rep1_sl18


title: bcd_cyc13_rep1_sl17


title: bcd_cyc13_rep1_sl16


title: Hepatocellular Carcinoma [P8_PVTT]


title: Hepatocellular Carcinoma [P7_PVTT]


title: bcd_cyc13_rep1_sl15


title: bcd_cyc13_rep1_sl12


title: bcd_cyc13_rep1_sl14


title: bcd_cyc13_rep1_sl10


title: bcd_cyc13_rep1_sl13


title: bcd_cyc13_rep1_sl07


title: E. invadens 8h excyst ~27nt small RNA

description: small RNA

source_name: E. invadens IP-1 excysting


title: bcd_cyc13_rep1_sl05


title: Hepatocellular Carcinoma [P5_PVTT]


title: bcd_cyc13_rep1_sl09


title: Hepatocellular Carcinoma [P4_PVTT]


title: bcd_cyc13_rep1_sl08


title: bcd_cyc13_rep1_sl06


title: bcd_cyc13_rep1_sl04


title: Hepatocellular Carcinoma [P3_PVTT]


title: bcd_cyc13_rep1_sl02


title: bcd_cyc13_rep1_sl03


title: Hepatocellular Carcinoma [P2_PVTT]


title: bcd_cyc13_rep1_sl11


title: bcd_cyc13_rep1_sl01


title: NIGHT1

city: Arcachon

first: Anthony

last: Bertucci

address: Place du Dr Peyneau

country: France

institute: University of Bordeaux

data_processing:
Data were mapped to the Acropora millepora transcriptome using Burrows-Wheeler Aligner. combinedcounts.txt supplementary file lists contig names and counts for each sample.
Genome_build: PRJNA74409
Supplementary_files_format_and_content: tab-delimited text file including count values for each sample

organism: Acropora millepora

source_name: Branch tips

extract_protocol:
Total RNA was extracted from the samples using Trizol Reagent (Invitrogen) and dissolved in RNAse free water. RNA quantity and quality were assessed using a NanoDrop ND-1000 spectrometer and denaturing gel electrophoresis. Before being shipped on dry ice to the Macrogen sequencing facilities in Seoul, South Korea, each RNA sample was precipitated in ethanol and sodium-acetate (2x and 0.1x sample volume respectively), and stored at -80°C.
In accordance with Macrogen procedure and Illumina Hiseq 2000 requirements

value: whole polyps

tag: developmental stage

value: adult

tag: sampling time

value: midnight


title: NIGHT2


title: MethylCap-seq_48hpf

city: Darlinghurst

first: Ozren

last: Bogdanovic

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

description: kit: Diagenode (#AF-100-0048)

data_processing:
Library strategy: MethylCap-seq
Basecalls performed using CASAVA version 1.8.2
Reads were aligned to the danRer7 genome using bowtie2 (version 2.2.1.) with default settings
Duplicate reads were removed using samtools rmdup (-s option)
Peaks were called using macs2 (https://github.com/taoliu/MACS/)
Genome_build: danRer7
Supplementary_files_format_and_content: ChIP-seq: BED, peak file (macs2 "broadPeak")
Supplementary_files_format_and_content: MethylCap-seq: BED, peak file (macs2 "narrowPeak")

organism: Danio rerio

source_name: zebrafish embryo

extract_protocol:
Samples were prepared as described in (Bogdanovic et al; 2013, Methods)
Libraries were prepared as described in (Bogdanovic et al; 2013, Methods)

value: whole embryo

value: mixture of AB and Tubingen strains


title: DAY3

value: midday


title: MethylCap-seq_dome

description: kit: Diagenode (#AF-100-0048)

value: dome


title: Hepatocellular Carcinoma [P6_PVTT]


title: MethylCap-seq_24hpf

description: kit: Diagenode (#AF-100-0048)


title: DAY2


title: Hepatocellular Carcinoma [P1_PVTT]


title: NIGHT3


title: DAY1


title: H3K27me3_ChIP-seq_48hpf

description: antibody: Millipore (#07-449, LOT: JBC1852356)

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were aligned to the danRer7 genome using bowtie2 (version 2.2.1.) with default settings
Duplicate reads were removed using samtools rmdup (-s option)
Peaks were called using macs2 (https://github.com/taoliu/MACS/)
Genome_build: danRer7
Supplementary_files_format_and_content: ChIP-seq: BED, peak file (macs2 "broadPeak")
Supplementary_files_format_and_content: MethylCap-seq: BED, peak file (macs2 "narrowPeak")


title: H3K27me3_ChIP-seq_dome


title: SW480/pRTR-p53-VSV +DOX RNA-Seq

status: Public on Jul 21 2015

city: Munich

first: Sabine

last: Huenten

address: Thalkirchner Strasse 36

country: Germany

data_processing:
Reads of both samples were processed separatley in a three step procedure using the short read alignment program bowtie (version 0.12.7). First, reads were aligned to pre-rRNA sequences (18S,5.8S,28S and spacer regions). Second, unaligned reads were aligned to ENSEMBL (version 60) transcripts. Finally, the remaining unaligned reads were aligned to the human genome assembly hg19.
Bowtie alignments were performed with a seed region of 60nt, allowing up to 3 mismatches in the seed and 10 mismatches in the whole read. Reads, that could be aligned equally well to more than one position were discarded.
Gene expression values were calculated via the RPKM (reads per kilobase of gene per million mapped reads) measure.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM file including rpkm values.

source_name: Colorectal cancer cells

growth_protocol: SW480 cells and their derivatives were cultured in DMEM grwoth medium containig 10% FBS at 37°C and 5%CO2.

extract_protocol:
Total RNA was isolated using the High Pure RNA Isolation Kit, Roche.
RNA libraries were prepared for sequencing using standard Illumina protocols according to standard procedures of GATC, Konstanz.

treatment_protocol: SW480 cells were treated with DOX (100 ng/ml) for 48 hours to induce ectopic expression of p53.

tag: vector

tag: treatment

value: 48 hours doxycyclin

tag: cell line


title: SW480/pRTR-p53-VSV +DOX ChIP-Seq

data_processing:
ChIP-Seq reads were aligned to the hg19 genome assembly using the short read alignment program bowtie (version 0.12.7)
Bowtie was called with the following parameters: -q -n 3 -l 60 --best --strata -k 5 -e 1000 --suppress 5,6,7
Reads aligned equally well to more than one position were discarded, as well as alignments with more than 10 mismatches
Peak-calling was performed using MACS (version 1.4.2). All optional parameters were set to default.
Genome_build: hg19
Supplementary_files_format_and_content: Peaks called by MACS are provided in BED (0-based) and XLS (1-based) file format

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols according to standard procedures of GATC, Konstanz.

treatment_protocol: Before cross-linking SW480 cells were treated with DOX (100 ng/ml) for 16 hours to induce ectopic expression of p53.

tag: chip antibody

value: VSV (V4888, Sigma)

value: 16 hours doxycyclin

tag: stably transfected vector


title: SW480/pRTR +DOX RNA-Seq

value: pRTR


title: MOLP8_KD_1

city: Boston

first: Salomon

last: Manier

state: Massachusetts

address: 77 Ave Louis Pasteur

department: Medical Oncology

institute: DFCI

data_processing:
We used Bcbio_nextgen (https://github.com/chapmanb/bcbio-nextgen/) to process the RNA-seq data
Cutadapt was used to trim adapters
Trimmed reads were aligned to Human reference genome (GRCh37) with tophat2
Read counts for each gene was calculated by HT-seq
Genome_build: GRCh37
Supplementary_files_format_and_content: RPKM files

source_name: Multiple Myeloma cell line

growth_protocol: Cells were grown in RPMI 10% FBS containg

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (QIAGEN).
NEBNext RNA library prep kit

treatment_protocol: Puromycin 1ug/mL for selection

tag: condition

value: LIN28B KO cells


title: MOLP8_CT_3

value: Scrambled control cells


title: MOLP8_CT_2


title: MOLP8_CT_1


title: SW480/pRTR +DOX ChIP-Seq