title: ChIPseq_U87EGFRvIII_shFOXG1_1_withFBS_H3K4me3.FL197

first: Feng

last: Liu

address: 197 Ruijin Er Lu

department: National Research Center for Translational Medicine (Shanghai)

institute: Ruijin Hospital, Shanghai Jiaotong University School of Medicine

description: cancer

data_processing:
ChIP-seq experiments were mapped to human genome build hg18 using Bowtie v0.12.5 (Langmead et al., 2009) with the following options: “-v 3 -m 1 --best –strata”. For a given locus, histone modification enrichment is quantified as E = log2 (ChIP RPKM / input RPKM), where RPKM is defined as the number of reads per kilobase of locus per million mapped reads, in either ChIP or input samples. To avoid division by zero, a pseudocount of 0.05 is added to both numerator and denominator. Given a set of differentially expressed genes, we created a set of bins +/-500kb from the transcription start sites of these genes. We also repeated this process to create 5000 random sets of bins corresponding to the same number of random genes. Given a set of enhancers, we assessed enrichment by overlapping with bins of differentially expressed genes and comparing with the overlap for random bin sets. Motif finding was performed using Homer v4.2 (Heinz et al., 2010).
Genome_build: hg18
Supplementary_files_format_and_content: bigwig

source_name: brain

growth_protocol: Cells were cultured at 37 celsius degree in 5% CO2, in Dulbecco’s Modified Eagle Media (DMEM, Cellgro) supplemented with 10%FBS (Hyclone) and 1% penicillin/streptomycin/glutamine (Invitrogen). Cells Frozen biopsy samples were from UCLA Brain Tumor Translational Resource.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as previously described (Heintzman et al., 2007). Briefly, 10-20 million of cultured cells and ~0.2 g of frozen tissue samples were cross-linked in 1% formaldehyde at room temperature for 10 and 25 minutes, respectively. Cross-linked samples were sonicated until chromatin fragments were of 200-600 bp in length. Chromatin immunoprecipitation was carried out using 3-5 µg of antibody and 200 µg of chromatin preparation in RIPA buffer at 4 degree overnight. After five washes in RIPA and one wash with 1xTE buffer, chromatins were eluted and reverse cross-linked at 65 oC overnight. DNA was purified after phenol extraction.
Libraries were prepared according to Illumina's instructions, using TruSeq DNA Sample Preparation Kits v2, Set A (Cat# FC-121-2001). 4-12 library preps were mixed for multiplexed single-read sequencing using Illumina Hi-seq 2000 (Illumina).

treatment_protocol: Serum-starved cells were obtained by culturing cells in DMEM for 24 hours. 10 uM of erlotinib is added to serum starved cells for 24 hr.

value: Gliobmastoma cell line


title: RNAseq_GBM_IDHmut-5661

status: Public on Sep 14 2015

type: SRA

city: Shanghai

country: China

description: cancer

library_source: transcriptomic

data_processing:
Paired-end RNA-seq experiments were mapped using Tophat v1.4.0(Trapnell et al., 2009) with the following parameters: “-g 1 --library-type=fr-firststrand”. For pairwise comparisons between two sets of samples, the number of sense exonic reads were quantified and input to edgeR (Robinson et al., 2010) to normalize and call differentially expressed genes at a p-value cutoff of 0.05.
Genome_build: hg18
Supplementary_files_format_and_content: bigwig

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cells were cultured at 37 celsius degree in 5% CO2, in Dulbecco’s Modified Eagle Media (DMEM, Cellgro) supplemented with 10%FBS (Hyclone) and 1% penicillin/streptomycin/glutamine (Invitrogen).

extract_protocol:
Total RNA was extracted from 1-2 million cells cultured in petri dish or 50-100 mg of tissue using the RNeasy mini kit (Qiagen). 5~10 µg of total RNA was used to prepare RNA-seq libraries according to Illumina protocol.
Libraries were prepared according to Illumina's instructions, using TruSeq DNA Sample Preparation Kits v2, Set A (Cat# FC-121-2001). 4-12 library preps were mixed for multiplexed single-read sequencing using Illumina Hi-seq 2000 (Illumina).

treatment_protocol: Serum-starved cells were obtained by culturing cells in DMEM for 24 hours.

tag: tissue

value: Gliobmastoma biopsy


title: Group4_shEset

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

description: Group4_LTR.txt, Group4_Genes.txt

data_processing:
The QC of the generated libraries was performed using FastQC. Reads were mapped to mm9 genome using STAR aligner software. Reads with more than 3 mismatches were filtered out. Tag Directories of the reads of each library were created using HOMER with the option -keepOne to ensure the inclusion of repeat sequences. Reads mapping to LTR sequences and reads mapping to exons were counted using analyzeRepeats.pl script of HOMER. The output files were then subjected to DESeq for differential analysis.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files that include FPKM values for all genes or LTR sequences in each Group.

organism: Mus musculus

source_name: E14 cells

growth_protocol: E14 mouse embryonic stem cells (mESCs) were cultured with mouse ESC medium (DMEM high glucose supplemented with 15% defined FBS (Hyclone), 2mM L-glutamine (Gibco), 1X PenStrep (Gibco), 100μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco) and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore)). All the EC and ESC cell lines used in this study were cultured on gelatin-coated tissue culture plates and all the cell lines were cultured at 37°C with 5% CO 2 .

extract_protocol:
Total RNA was extracted using the Trizol reagent (Invitrogen). Contaminating DNA was  removed by DNaseI (Ambion) treatment, and the RNA was further purified using the  QIAGEN RNeasy Kit.
The RNA-Seq libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit (Catalog #: RS-122-2101) as per manufacturer's instructions.

treatment_protocol: Lipofectamine 2000 (Invitrogen) was used for transfection of shRNA plasmids according to the manufacturer’s instructions. Puromycin was added to the culture medium 16 hours post-transfection and cells were harvested for experiments after 4 days of knockdown.

tag: genotype

value: Eset Knockdown


title: Control-for-Group 3

description: Group3_LTR.txt, Group3_Genes.txt

value: WT


title: Group2_shChaf1a_Rep2

description: Group2_LTR.txt, Group2_Genes.txt

value: Chaf1a Knockdown


title: Group2_shChaf1b_Rep2

description: Group2_LTR.txt, Group2_Genes.txt

value: Chaf1b Knockdown


title: Group2_shChaf1b_Rep1

description: Group2_LTR.txt, Group2_Genes.txt


title: Control-for-Group 2-Rep2

description: Group2_LTR.txt, Group2_Genes.txt


title: Group2_shChaf1a_Rep1

description: Group2_LTR.txt, Group2_Genes.txt


title: Control-for-Group 2-Rep1

description: Group2_LTR.txt, Group2_Genes.txt


title: Group1_shUbe2i_Rep2

description: Group1_LTR.txt, Group1_Genes.txt

value: Ube2i Knockdown


title: Group1_shUba2_Rep2

description: Group1_LTR.txt, Group1_Genes.txt

value: Uba2 Knockdown


title: Group1_shUbe2i_Rep1

description: Group1_LTR.txt, Group1_Genes.txt


title: Group1_shSumo2_Rep2

description: Group1_LTR.txt, Group1_Genes.txt

value: Sumo2 Knockdown


title: Group1_shTrim28

description: Group1_LTR.txt, Group1_Genes.txt

value: Trim28 Knockdown


title: Group1_shSumo2_Rep1

description: Group1_LTR.txt, Group1_Genes.txt


title: Group1_shSae1_Rep2

description: Group1_LTR.txt, Group1_Genes.txt

value: Sae1 Knockdown


title: Group1_shSenp6_Rep2

description: Group1_LTR.txt, Group1_Genes.txt

value: Senp6 Knockdown


title: Group1_shUba2_Rep1

description: Group1_LTR.txt, Group1_Genes.txt


title: Group1_shSenp6_Rep1

description: Group1_LTR.txt, Group1_Genes.txt


title: Group1_shSae1_Rep1

description: Group1_LTR.txt, Group1_Genes.txt


title: Control-for-Group 1-Rep2

description: Group1_LTR.txt, Group1_Genes.txt


title: Trim28

library_source: genomic

data_processing:
Fastq files were mapped to mm9 genome using STAR Aligner software with –AlignIntronMax parameter set to 1 to make the software compatible with ChIP-Seq libraries. Reads with more than 3 mismatches were filtered out. Mapped reads were visualized in the UCSC genome browser. Peaks were called using the findPeaks script of HOMER with the option –style factor.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files that include details about the significant peaks found in the ChIP-Seq libraries.

molecule: genomic DNA

growth_protocol: F9 mouse embryonic carcinoma cells (ECs) were cultured in Dulbecco’s modified Eagle medium high glucose medium (DMEM; Gibco), supplemented with 10% fetal bovine serum (FBS; Hyclone), 2mM L-glutamine (Gibco), 1 X PenStrep (Gibco). E14 and D3 mouse embryonic stem cells (mESCs) were cultured with mouse ESC medium (DMEM high glucose supplemented with 15% defined FBS (Hyclone), 2mM L-glutamine (Gibco), 1X PenStrep (Gibco), 100μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco) and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore)). All the EC and ESC cell lines used in this study were cultured on gelatin-coated tissue culture plates and all the cell lines were cultured at 37°C with 5% CO 2 .

extract_protocol:
10 million cells were cross-linked with 1% formaldehyde for 10 min at room temperature, with the formaldehyde then quenched by the addition of 200 mM glycine and cells then washed once with ice-cold PBS. Cell lysis was carried out with a buffer containing 10 mM Tris-Cl (pH 8), 100 mM NaCl, 10 mM EDTA, 0.25% Triton X-100 and protease inhibitor cocktail (Roche). Cells were then resuspended in 1% SDS lysis buffer containing 50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1% SDS, 2 mM EDTA, 1% Triton X-100, 0.1% NaDOC and protease inhibitor cocktail. The suspension was nutated for 15 mins at 4°C before spinning down to collect the chromatin pellet. The pellet was then washed twice with 0.1% SDS lysis buffer containing 50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 0.1% SDS, 2 mM EDTA, 1% Triton X-100, 0.1% NaDOC, 1 mM PMSF and protease inhibitor cocktail. Sonication was conducted using the Branson sonifier 250 on ice (11 cycles, power amplitude of 35%, 30s pulses on with 59.9 s pulses off). The chromatin solution was clarified by centrifugation at 20,000 g at 4°C for 45 mins and then pre-cleared with Dynabeads protein A (Life Technologies) for 2 hrs. The pre-cleared chromatin sample was incubated with 50 μl of Dynabeads protein A loaded with 5 μg antibody overnight. The beads were then washed three times with 0.1% SDS lysis buffer, once with 0.1% SDS lysis buffer/0.35 M NaCl, once with 10 mM Tris-Cl (pH 8), 1 mM  EDTA, 0.5% NP40, 0.25 LiCl, 0.5% NaDOC, and once with TE buffer (PH8.0). The immunoprecipitated material was eluted from the beads by heating for 45 min at 68°C in 50 mM Tris-Cl (pH 7.5), 10 mM EDTA, 1% SDS. To reverse the crosslinks, samples were incubated with 1.5 μg/ml Pronase at 42°C for 2 hr followed by 67°C for 6 hr. The samples were then extracted with phenol chloroform isoamyl alcohol followed by chloroform, ethanol precipitated in the presence of glycogen, and re-suspended in TE buffer.
The ChIP-Seq libraries were prepared using Illumina TruSeq ChIP Sample Prep Kit (Catalog #: IP-202-1012) as per manufacturer's instructions.

tag: chip antibody

value: rabbit anti-KAP-1 Affinity Purified,  1mg/ml, A300-274A,BETHYL


title: Input-For-Trim28


title: Sumo2

value: Anti-Sumo2+3 (abcam), Cat #:ab3742, Lot:GR54180-2


title: Control-for-Group 1-Rep1

description: Group1_LTR.txt, Group1_Genes.txt


title: Input-for-Sumo2


title: HA-Zfp809

value: HA-probe sc-7392 (Santa Cruz Biotechnology)

tag: treatment

value: Transient transfection of pCAG-HA-ZFP809 (isoform 2) into D3 ES cell line.


title: Group3_shAtf7ip

description: Group3_LTR.txt, Group3_Genes.txt

value: Atf7ip Knockdown


title: ChIPseq_U87EGFRvIII_shFOXG1_1_withFBS_H3K4me1.FL196

description: cancer

tag: cell line

value: Gliobmastoma cell line


title: HA-Chaf1a

source_name: F9 Cells

value: CRISPR and donor plasmids were co-transfected into F9 cells. The donor plasmid was cloned by combining  two homologous sequences of Chaf1a with 3HA in pCAG containing puromycin resistance.


title: HA-Control-For-Chaf1a


title: HA-Control-for Zfp809


title: ChIPseq_U87EGFRvIII_shSCR_withFBS_H3K4me3.FL189

description: cancer


title: ChIPseq_U87EGFRvIII_shSOX9_1_withFBS_H3K4me3.FL193

description: cancer


title: ChIPseq_U87EGFRvIII_shSOX9_1_withFBS_H3K4me1.FL192

description: cancer


title: ChIPseq_GBM_IDHmut5661_H3K4me3.FL168

description: cancer

value: Gliobmastoma biopsy


title: ChIPseq_U87EGFRvIII_withoutFBS_erlotinib_H3K4me3.FL164

description: cancer


title: ChIPseq_GBM_IDHmut5661_H3K4me1.FL167

description: cancer


title: ChIPseq_U87EGFRvIII_withoutFBS_erlotinib_H3K4me1.FL163

description: cancer


title: ChIPseq_GBM_2493_H3K4me3.FL153

description: cancer


title: ChIPseq_GBM_2483_H3K4me1.FL152

description: cancer


title: ChIPseq_GBM_2585_H3K4me1.FL155

description: cancer


title: ChIPseq_GBM_P69_H3K4me1.FL148

description: cancer


title: ChIPseq_GBM_R28_H3K4me1.FL133

description: cancer


title: ChIPseq_GBM_R28_H3K4me3.FL134

description: cancer


title: ChIPseq_GBM_P69_H3K4me3.FL142

description: cancer


title: ChIPseq_GBM_2585_H3K4me3.FL156

description: cancer


title: ChIPseq_GBM_B39_H3K4me3.FL130

description: cancer


title: RNAseq_U87_withoutFBS.RZY275

description: cancer


title: RNAseq_U87EGFRvIII_withFBS.RZY278

description: cancer


title: RNAseq_U87EGFRvIII_shSOX9_1_withoutFBS.FL183

description: cancer


title: RNAseq_U87EGFRvIII_shSOX9_1_withFBS.FL182

description: cancer


title: ChIPseq_U87EGFRvIII_shSCR_withFBS_H3K4me1.FL188

description: cancer


title: RNAseq_U87EGFRvIII_shFOXG1_1_withFBS.FL180

description: cancer


title: RNAseq_GBM_R28.RZY306

description: cancer


title: RNAseq_GBM_S08.RZY307

description: cancer


title: RNAseq_GBM_2493.RZY317

description: cancer


title: RNAseq_GBM_2585.RZY318

description: cancer


title: ChIPseq_U87_withoutFBS_input.FL79

description: cancer


title: ChIPseq_GBM_S08_H3K4me1.FL150

description: cancer


title: RNAseq_GBM_P69.RZY308

description: cancer


title: ChIPseq_U87_withoutFBS_H3K4me3.FL066

description: cancer


title: ChIPseq_U87_withFBS_H3K4me3.FL072

description: cancer


title: ChIPseq_GBM_S08_H3K4me3.FL138

description: cancer


title: ChIPseq_U87_withoutFBS_H3K4me1.FL122

description: cancer


title: ChIPseq_GBM_B39_H3K4me1.FL129

description: cancer


title: ChIPseq_U87_withFBS_H3K4me1.FL123

description: cancer


title: ChIPseq_U87EGFRvIII_withoutFBS_input.FL80

description: cancer


title: ChIPseq_U87_withoutFBS_H3K27ac.FL067

description: cancer


title: ChIPseq_U87_withFBS_H3K27ac.FL073

description: cancer


title: ChIPseq_U87_withFBS_input.FL77

description: cancer


title: ChIPseq_U87EGFRvIII_withoutFBS_H3K4me3.FL075

description: cancer


title: RNAseq_U87EGFRvIII_withoutFBS.RZY277

description: cancer


title: ChIPseq_U87EGFRvIII_withoutFBS_H3K4me1.FL124

description: cancer


title: RNAseq_U87_withFBS.RZY276

description: cancer


title: ChIPseq_U87EGFRvIII_withoutFBS_erlotinib_input.FL162

description: cancer


title: ChIPseq_U87EGFRvIII_withoutFBS_H3K27ac.FL076

description: cancer


title: ChIPseq_U87EGFRvIII_withoutFBS_erlotinib_H3K27ac.FL165

description: cancer


title: RNAseq_U87EGFRvIII_shFOXG1_1_withoutFBS.FL181

description: cancer


title: ChIPseq_U87EGFRvIII_withFBS_H3K4me3.FL069

description: cancer


title: ChIPseq_U87EGFRvIII_withFBS_input.FL78

description: cancer


title: ChIPseq_U87EGFRvIII_withFBS_H3K4me1.FL125

description: cancer


title: RNAseq_GBM_B39.RZY305

description: cancer


title: ChIPseq_U87EGFRvIII_withFBS_H3K27ac.FL070

description: cancer


title: ChIPseq_U87EGFRvIII_shSOX9_1_withFBS_H3K27ac.FL194

description: cancer


title: ChIPseq_U87EGFRvIII_shSOX9_2_withFBS_H3K27ac.FL227

description: cancer


title: ChIPseq_U87EGFRvIII_shSOX9_1_withFBS_input.FL191

description: cancer


title: ChIPseq_U87EGFRvIII_shSCR_withFBS_H3K27ac.FL225

description: cancer


title: ChIPseq_U87EGFRvIII_shSOX9_2_withFBS_input.FL226

description: cancer


title: ChIPseq_U87EGFRvIII_shFOXG1_2_withFBS_input.FL230

description: cancer


title: ChIPseq_U87EGFRvIII_shFOXG1_2_withFBS_H3K27ac.FL231

description: cancer


title: ChIPseq_U87EGFRvIII_shSCR_withFBS_input.FL224

description: cancer


title: ChIPseq_U87EGFRvIII_shFOXG1_1_withFBS_H3K27ac.FL229

description: cancer


title: ChIPseq_GBM_P69_input.FL140

description: cancer


title: ChIPseq_GBM_P69_H3K27ac.FL149

description: cancer


title: ChIPseq_GBM_S08_H3K27ac.FL151

description: cancer


title: ChIPseq_GBM_R28_H3K27ac.FL135

description: cancer


title: ChIPseq_GBM_IDHmut5661_input.FL166

description: cancer


title: ChIPseq_GBM_IDHmut5661_H3K27ac.FL169

description: cancer


title: ChIPseq_GBM_2585_input.FL147

description: cancer


title: ChIPseq_GBM_S08_input.FL136

description: cancer


title: ChIPseq_GBM_R28_input.FL132

description: cancer


title: 4Cseq_U87EGFRvIII_withFBS_SOX9_locus.GH306

description: cancer

data_processing:
Library strategy: 4C-seq
4C-Seq data were mapped using 4Cseqpipe (van de Werken et al., 2012) with the first cutter set as NlaIII (CATG) and the second cutter set as DpnII (GATC).
Genome_build: hg18
Supplementary_files_format_and_content: bigwig

extract_protocol:
4C was performed as previously described (van de Werken et.al., 2012), using NlaIII (CATG) as the first cutter and DpnII (GATC) as the second cutter.
Libraries were prepared according to Illumina's instructions, using TruSeq DNA Sample Preparation Kits v2, Set A (Cat# FC-121-2001). 4-12 library preps were mixed for multiplexed single-read sequencing using Illumina Hi-seq 2000 (Illumina).


title: ChIPseq_GBM_B39_input.FL128

description: cancer


title: 4Cseq_U87EGFRvIII_withFBS_FOXG1_locus.FL186

description: cancer


title: ChIPseq_Hippo_H3K4me3.AY1669

description: normal

value: hippocampus


title: ChIPseq_Hippo_H3K27ac.AY390

description: normal


title: ChIPseq_Hippo_Input.AY386

description: normal


title: ChIPseq_DLFC_H3K27ac.AY389

description: normal

value: dorsolateral prefrontal cortex


title: ChIPseq_U87EGFRvIII_shFOXG1_1_withFBS_input.FL228

description: cancer


title: ChIPseq_DLFC_Input.AY385

description: normal


title: ChIPseq_DLFC_H3K4me3.AY1668

description: normal


title: ex2_mm_d50_5

city: Santa Barbara

first: Kenneth

middle: S.

last: Kosik

state: California

address: UC Santa Barbara

department: NRI

country: USA

institute: UCSB

description: total RNA, rRNA depleted

data_processing:
RNA was sequenced on an Illumina HiSeq 2000, using stranded pairedend reads, with ~50 millions reads per sample.
Reads were mapped to the UCSC Human Reference Genome (hg19) using TopHat v2.0.10 (Kim et al., 2013). Reads mapping to genes were counted using htseq (v0.6.1) (Anders et al., 2015). Counts were upper quartile normalized using SVS (Golden Helix) for limited gene comparisons.
Genome_build: hg19
Supplementary_files_format_and_content: .txt file includes normalized counts of refSeq for each Sample

source_name: Neurons

growth_protocol: Neuronal differentiation was performed using an embryoid aggregate-based protocol. Briefly, iPSC colonies were removed from MEFs and cultured for 4 days in iPSC media, followed by 2 days in N2 neural induction media. Day 7 aggregates were plated onto matrigel-coated 6 well plates and maintained in N2 neural induction media, forming neuroepithelial structures. At day 17, neural rosettes were enzymatically isolated using STEMDiff Neural Rosette Selection Reagent (Stemcell Technologies). Rosettes were eight used directly for RNA isolation (for day 17 samples), or cultured in suspension for 7 days in N2/B27 neural induction media containing IGF-1 and cAMP. At day 24, neural aggregates were dissociated with Accutase in the presence of 10 uM ROCK-Inhibitor and plated for final differentiation on matrigel-coated 96 well plates in neural differentiation media containing IGF-1, cAMP, BDNF, and GDNF. Cells were maintained in culture until day 50, when RNA was harvested for neuronal samples.

extract_protocol:
Life Technologies PureLink RNA mini kit
Total RNA samples were converted into cDNA libraries using the TruSeq Stranded Total RNA-RiboZero Gold Sample Prep Kit (Illumina, #RS-122-2303), starting with 100 ng of total RNA.

tag: cell type

value: Human iPSC-derived neurons

value: DISC1 exon 2 mut/mut

tag: parental cell line

value: YZ1 hiPSC

tag: differentiation time

value: Embryoid body, day 50


title: ChIPseq_GBM_B39_H3K27ac.FL131

description: cancer


title: ex2_mm_d50_6

description: total RNA, rRNA depleted


title: ChIPseq_GBM_2585_H3K27ac.FL157

description: cancer


title: ex2_mm_d50_3

description: total RNA, rRNA depleted


title: ex2_mm_d50_4

description: total RNA, rRNA depleted


title: ex8_mm_d50_4

description: total RNA, rRNA depleted

value: DISC1 exon 8 mut/mut


title: ChIPseq_GBM_2493_H3K27ac.FL154

description: cancer


title: ChIPseq_GBM_2493_input.FL146

description: cancer


title: ex8_mm_d50_3

description: total RNA, rRNA depleted


title: ex8_wm_d50_5

description: total RNA, rRNA depleted

value: DISC1 exon 8 wt/mut


title: ex8_mm_d50_1

description: total RNA, rRNA depleted


title: ex8_mm_d50_2

description: total RNA, rRNA depleted


title: ex8_wm_d50_4

description: total RNA, rRNA depleted


title: ex8_wm_d50_6

description: total RNA, rRNA depleted


title: ex8_wm_d50_3

description: total RNA, rRNA depleted


title: ex8_wm_d50_2

description: total RNA, rRNA depleted


title: WT_d50_6

description: total RNA, rRNA depleted

value: wild-type


title: Foxd3_input

city: Koeln

first: Milos

last: Nikolic

state: Nordrhein-Westfalen

address: Robert Koch Str. 21

country: Germany

institute: Center for Molecular Medicine Cologne

description: Total genomic DNA (input from ChIPs)

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using ELAND software (Illumina Inc).
FH-Foxd3 bound regions were called using QuEST 2.4 with the following setting: KDE bandwith=30, ChIP seeding fold enrichment=30, ChIP extension fold enrichment=3, ChIP-to-background fold enrichment=3.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using QuEST 2.4; scores represent normalized enrichment fold calculated from ratio of ChIP and control scores

source_name: mouse embryonic stem cells

growth_protocol: FH-Foxd3 mESC line was established by transducing LF2 mESCs with FH-Foxd3 pTrip lentivirus followed by selection with neomycin. Fh-Foxd3 mESC  were grown under feeder-free conditions in Knockout-DMEM medium (KO-DMEM; Life Technologies) containing 15% FBS and LIF.

extract_protocol:
Lysates were clarified from sonicated nuclei and FH-Foxd3-DNA complexes were isolated with antibodies against HA or Flag.
Lysates were clarified from sonicated nuclei and ChIP-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was size selected on agarose gel from 200-700 bp. Then isolated DNA was PCR amplified with Illumina primers for 18 cycles. 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: input


title: Foxd3_HA

description: ChIP against FH-Foxd3 using HA antibody

value: anti-HA (H3663, Sigma)


title: Foxd3_Flag

description: ChIP against FH-Foxd3 using Flag antibody

value: anti-Flag (F3165, Sigma)


title: WT_d50_4

description: total RNA, rRNA depleted


title: WT_d50_5

description: total RNA, rRNA depleted


title: ex8_wm_d50_1

description: total RNA, rRNA depleted


title: ex2_mm_d50_2

description: total RNA, rRNA depleted


title: WT_d50_3

description: total RNA, rRNA depleted


title: WT_d50_2

description: total RNA, rRNA depleted


title: ex2_mm_d50_1

description: total RNA, rRNA depleted


title: ex2_mm_d17_6

description: total RNA, rRNA depleted

source_name: Neural progenitor cells

value: Human iPSC-derived neural progenitor cells

value: Embryoid body, day 17


title: ex2_mm_d17_4

description: total RNA, rRNA depleted


title: ex2_mm_d17_5

description: total RNA, rRNA depleted


title: ex2_mm_d17_2

description: total RNA, rRNA depleted


title: ex8_mm_d17_5

description: total RNA, rRNA depleted


title: ex2_mm_d17_1

description: total RNA, rRNA depleted


title: ex8_mm_d17_3

description: total RNA, rRNA depleted


title: ex8_mm_d17_4

description: total RNA, rRNA depleted


title: ex8_wm_d17_6

description: total RNA, rRNA depleted


title: ex8_mm_d17_1

description: total RNA, rRNA depleted


title: ex8_mm_d17_2

description: total RNA, rRNA depleted


title: WT_d17_6

description: total RNA, rRNA depleted


title: WT_d17_3

description: total RNA, rRNA depleted


title: ex8_wm_d17_2

description: total RNA, rRNA depleted


title: WT_d17_5

description: total RNA, rRNA depleted


title: WT_d17_2

description: total RNA, rRNA depleted


title: WT_d17_1

description: total RNA, rRNA depleted


title: WT_d17_4

description: total RNA, rRNA depleted


title: 40_RIP_AGO4

status: Public on Sep 13 2015

city: Los Angeles

first: Steve

last: Jacobsen

state: CA

address: 4045 Terasaki Life Sciences Building

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: RIP

data_processing:
In general, qseq files received from the sequencing core were demultiplexed with an in-house Perl script and converted to fastq files for downstream analysis. For small RNA and PATH data, original reads were first trimmed using Cutadapt (v1.4), then mapped to the reference TAIR10 genome using Bowtie34 allowing only one unique hit (-m 1). We allowed zero mismatch for small RNA mapping (-v 0) and up to three mismatches for PATH mapping (-v 3). mRNA data were mapped using Tophat allowing two mismatches and only one unique hit.
Genome_build: TAIR10
Supplementary_files_format_and_content: ChIP-seq samples are associated with wig coverage files; For BS-seq processed data, the format is "position, strand, context(x=CG,y=CHG,z=CHH), methylated count, unmethylated count", RIP-seq samples and small RNA-seq samples are associated with files containing the sequence and raw read count.

organism: Arabidopsis thaliana

growth_protocol: The wild-type and mutant alleles in this study were in the background of Arabidopsis thaliana ecotype Columbia and have been previously described. Plants were grown in a growth chamber with 16 hour of light for five weeks. Immature inflorescence tissues including inflorescence meristem and early stages floral buds (up to stage 11/12) were collected.

extract_protocol:
Total RNA was first treated with RiboMinus™ Plant Kit for RNA-Seq (Invitrogen A10838-08) to remove rRNA, followed by size selection of RNA on a 15% UREA TBE Polyacrylamide gel (Invitrogen, EC6885BOX). Gels containing RNA with size between 15- to 27-nt were kept for small RNA library, while gels containing 28- to ~300-nt RNA were kept for PATH library. ChIP-seq was performed as described previously (Johnson et al., 2014). 5 ug Pol II antibodies (Abcam #ab817) were used for each ChIP. Libraries for Pol II ChIP-seq were generated using the Ovation Ultralow DR Multiplex System (NuGen #0330) and sequenced at a length of 50 bp. ChIP-seq data was visualized using ngsplot (Shen et al., 2014). AGO4-RIP was performed as previously described (Ji et al., 2011) with commercial AGO4 antibody (Agrisera #AS09 617). RNA isolated from RIP was used for library construction with Illumina TruSeq RNA Sample Preparation Kit (RS-122-2001) according to the standard manual. For BS-seq, DNA was isolated using the DNeasy Plant Mini Kit (Qiagen #69104) according to manufacturer instructions and quantified using the Qubit dsDNA High Sensitivity Kit (Life Technologies #Q32851). Libraries were constructed with 30ng DNA using the Ovation Ultralow Methyl-Seq Library Systems (NuGEN #0335). Bisulfite conversion was done using the EpiTect Bisulfite Kit (Qiagen # 59104). BS-seq Libraries were sequenced at a length of 50 bp.
After gel elution, library construction for both sRNA and PATH was done using the Illumina TruSeq Small RNA Sample Preparation Kit (RS-200-0012), except that at the final size selection step, PCR products were separated on a 6% TBE Polyacrylamide gel (Invitrogen, EC6265BOX) and selected for the range from 120- to ~1000-bp for PATH library. Gel-eluted PCR products with different TruSeq index sequences were pooled and sent for Illumina sequencing. The mRNA library was constructed using the Illumina TruSeq RNA Sample Preparation Kit (RS-122-2001) according to the standard manual. PATH libraries were sequenced using either paired-end mode with length of read1 being 120-bp and length of read2 being 30-bp (PE120+30), or single-end 100-bp (SE100); while sRNA and mRNA libraries were sequenced with single-end 50-bp (SE50). All sequencing was carried out on HiSeq2500 machines at the Broad Stem Cell Research Center (BSCRC) sequencing core at University of California, Los Angeles.

tag: ecotype

value: Columbia

value: immature inflorescence

tag: antibody

value: AGO4 antibodies (Agrisera #AS09 617)


title: WT_d50_1

description: total RNA, rRNA depleted


title: 39_sRNA_nrpb2_a

description: small RNA


title: 40_sRNA_nrpb2_b

description: small RNA


title: 38_sRNA_WT_b

description: small RNA

value: wildtype


title: 41_RIP_input

description: RIP


title: 37_sRNA_WT_a

description: small RNA


title: 36_BSseq_nrpb2_b

description: BS-seq


title: 35_BSseq_nrpb2_a

description: BS-seq


title: 34_BSseq_Wt_b

description: BS-seq


title: 33_BSseq_WT_a

description: BS-seq


title: ex2_mm_d17_3

description: total RNA, rRNA depleted


title: 31_Pol2ChIP_nrpd1

description: ChIP-seq

value: Pol II antibodies (Abcam #ab817)


title: 32_Pol2ChIP_dcl234

description: ChIP-seq


title: 30_Pol2ChIP_Col

description: ChIP-seq


title: ex8_wm_d17_1

description: total RNA, rRNA depleted


title: 27_sRNA_dcl3/4

description:
small RNA
library id: 27

data_processing:
In general, qseq files received from the sequencing core were demultiplexed with an in-house Perl script and converted to fastq files for downstream analysis. For small RNA and PATH data, original reads were first trimmed using Cutadapt (v1.4), then mapped to the reference TAIR10 genome using Bowtie34 allowing only one unique hit (-m 1). We allowed zero mismatch for small RNA mapping (-v 0) and up to three mismatches for PATH mapping (-v 3). mRNA data were mapped using Tophat allowing two mismatches and only one unique hit.
Genome_build: TAIR10
Supplementary_files_format_and_content: Five libraries (1, 2, 15, 16, 29) were analyzed in-depth for ~7000 loci. The raw read counts at these loci for these five libraries are contained in the file "P4RNA_siRNA_and_mRNA_abundance_at_Pol-IV_loci.xlsx" available on the series record.   The remaining libraries were analyzed at the level of "total abundance" at the same set of ~7000 loci. The number of "total abundance" for each library is listed in the in column H of the file "Summary_of_libraries.xlsx" which is also available on the series record.

extract_protocol:
not provided
Total RNA was first treated with RiboMinus™ Plant Kit for RNA-Seq (Invitrogen A10838-08) to remove rRNA, followed by size selection of RNA on a 15% UREA TBE Polyacrylamide gel (Invitrogen, EC6885BOX). Gels containing RNA with size between 15- to 27-nt were kept for small RNA library, while gels containing 28- to ~300-nt RNA were kept for PATH library. After gel elution, library construction for both sRNA and PATH was done using the Illumina TruSeq Small RNA Sample Preparation Kit (RS-200-0012), except that at the final size selection step, PCR products were separated on a 6% TBE Polyacrylamide gel (Invitrogen, EC6265BOX) and selected for the range from 120- to ~1000-bp for PATH library. Gel-eluted PCR products with different TruSeq index sequences were pooled and sent for Illumina sequencing. The mRNA library was constructed using the Illumina TruSeq RNA Sample Preparation Kit (RS-122-2001) according to the standard manual. PATH libraries were sequenced using either paired-end mode with length of read1 being 120-bp and length of read2 being 30-bp (PE120+30), or single-end 100-bp (SE100); while sRNA and mRNA libraries were sequenced with single-end 50-bp (SE50). All sequencing was carried out on HiSeq2500 machines at the Broad Stem Cell Research Center (BSCRC) sequencing core at University of California, Los Angeles.


title: 28_sRNA_dcl2/3/4_#2

description:
small RNA
library id: 28


title: 25_sRNA_dcl3

description:
small RNA
library id: 25


title: 24_sRNA_dcl2/4

description:
small RNA
library id: 24


title: 20_sRNA_rdr2

description:
small RNA
library id: 20


title: 18_sRNA_nrpd1

description:
small RNA
library id: 18


title: 21_sRNA_dcl3/nrpd1

description:
small RNA
library id: 21


title: 19_sRNA_nrp(d/e)2

description:
small RNA
library id: 19


title: 22_sRNA_dcl3/rdr2

description:
small RNA
library id: 22


title: 16_sRNA_dcl2/3/4_#1

description:
small RNA
library id: 16


title: 17_sRNA_Col_#2

description:
small RNA
library id: 17


title: 12_PATH_dcl2/3

description:
short RNA
library id: 12


title: 13_PATH_dcl3/4

description:
short RNA
library id: 13


title: 14_PATH_dcl2/3/4_#2

description:
short RNA
library id: 14


title: 15_sRNA_Col_#1

description:
small RNA
library id: 15


title: 9_PATH_Col_#3

description:
short RNA
library id: 9


title: 10_PATH_dcl2/4

description:
short RNA
library id: 10


title: 7_PATH_dcl3/nrpd1

description:
short RNA
library id: 7


title: 8_PATH_dcl3/rdr2

description:
short RNA
library id: 8


title: 6_PATH_rdr2

description:
short RNA
library id: 6


title: 5_PATH_nrp(d/e)2

description:
short RNA
library id: 5


title: 3_PATH_Col_#2

description:
short RNA
library id: 3


title: 1_PATH_Col_#1

description:
short RNA
library id: 1


title: 23_sRNA_Col_#3

description:
small RNA
library id: 23


title: 2_PATH_dcl2/3/4_#1

description:
short RNA
library id: 2


title: 26_sRNA_dcl2/3

description:
small RNA
library id: 26


title: EP_CAM48

status: Public on Sep 12 2015

city: San Antonio

first: Tim

middle: Hui-Ming

last: Huang

state: TX

address: 8403 Floyd Curl Drive

department: Molecular Medicin

institute: The University of Texas Health Science Center at San Antonio

data_processing:
Alignment: For each sample, reads in fastq file were aligned to human genome assembly hg18 using bowtie1.0.0  with no more than 1 mismatch in seed and no more than 20 multiple mappings for one read. Multiple mapped reads were then handled by LONUT, an algorithm developed originally to improve the detection of the enriched regions for ChIP-seq data.
Peak-calling: We used BELT for peak calling with the bin size of 300 bp and multiple enrichment thresholds including 0.9, 0.95 and 0.99. In briefly, we selected peaks called with enrichment threshold 0.95, as the estimated FDRs are less than 5% for all samples except EpCAM 12 hour, of which the FDR is 5.75%.
TSS-peak:TSS-bound peaks were identified by 1 bp overlap to TSS up/down 1kb region of human reference genes. Then, reads were binned by 100bp and the up/down 4kb region of TSS-bound peaks was retrieved for further examination of the difference between the two treatments at different hours.
Genome_build: hg18
Supplementary_files_format_and_content: BigWig files of aligned reads

source_name: RL95-2 cells

growth_protocol: Cells with different time points EGF treatment were fixed with 1% formaldehyde, and DNA cross-linked to protein complexes was sonicated to ~300-500 bp fragments.

extract_protocol:
Immunoprecipitation was carried out using antibodies against EpCAM and Lef-1 on SX-8G-Star Compact Automated System following the manufacturer’s instructions. Pull-down products were purified and checked for size distribution for quality control by 2100 Bioanalyzer.
Library construction and sequencing were performed in the Genome Sequencing Facility in University of Texas Health Science Center at San Antonio by HiSeq 2000 sequencing system under the guidelines.

value: EP CAM

tag: egf hr


title: LEF1_48


title: 29_mRNA-Col

description:
mRNA
library id: 29

data_processing:
In general, qseq files received from the sequencing core were demultiplexed with an in-house Perl script and converted to fastq files for downstream analysis. For small RNA and PATH data, original reads were first trimmed using Cutadapt (v1.4), then mapped to the reference TAIR10 genome using Bowtie34 allowing only one unique hit (-m 1). We allowed zero mismatch for small RNA mapping (-v 0) and up to two mismatches for PATH mapping (-v 2). mRNA data were mapped using Tophat35 allowing two mismatches and only one unique hit.
Genome_build: TAIR10
Supplementary_files_format_and_content: Five libraries (1, 2, 15, 16, 29) were analyzed in-depth for ~7000 loci. The raw read counts at these loci for these five libraries are contained in the file "P4RNA_siRNA_and_mRNA_abundance_at_Pol-IV_loci.xlsx" available on the series record.   The remaining libraries were analyzed at the level of "total abundance" at the same set of ~7000 loci. The number of "total abundance" for each library is listed in the in column H of the file "Summary_of_libraries.xlsx" which is also available on the series record.

growth_protocol: The mutant alleles of nrpd1-4, nrpe1-11, nrpde2 and dcl2-1/3-1/4-2 used in this study were in the background of Arabidopsis thaliana ecotype Columbia and have been previously described. Plants were grown in a growth chamber with 16 hour of light for five weeks. Immature inflorescence tissues including inflorescence meristem and early stages floral buds (up to stage 11/12) were collected.

extract_protocol: Total RNA was first treated with RiboMinus™ Plant Kit for RNA-Seq (Invitrogen A10838-08) to remove rRNA, followed by size selection of RNA on a 15% UREA TBE Polyacrylamide gel (Invitrogen, EC6885BOX). Gels containing RNA with size between 15- to 27-nt were kept for small RNA library, while gels containing 28- to ~300-nt RNA were kept for PATH library. After gel elution, library construction for both sRNA and PATH was done using the Illumina TruSeq Small RNA Sample Preparation Kit (RS-200-0012), except that at the final size selection step, PCR products were on separated on a 6% TBE Polyacrylamide gel (Invitrogen, EC6265BOX) and selected for the range from 120- to ~1000-bp for PATH library. Gel-eluted PCR products with different TruSeq index sequences were pooled and sent for Illumina sequencing. The mRNA library was constructed using the Illumina TruSeq RNA Sample Preparation Kit (RS-122-2001) according to the standard manual. PATH libraries were sequenced using paired-end mode with length of read1 being 120-bp and length of read2 being 30-bp (PE120+30); while sRNA and mRNA libraries were sequenced with single-end 50-bp (SE50). All sequencing was carried out on HiSeq2500 machines at the Broad Stem Cell Research Center (BSCRC) sequencing core at University of California, Los Angeles.


title: LEF1_24


title: LEF1_0


title: CAC rep 2

city: Baltimore

first: Rebecca

last: Beer

state: Maryland

address: 733 N Broadway Rm 460

department: Institute of Genetic Medicine

institute: Johns Hopkins University

description: processed data file: run2_samples21_genes_strict.txt

data_processing:
Reads were processed and mapped to Zv9/danRer7 using RSEM
EBseq was used to determine differential expression and significance values
Genome_build: Zv9/danRer7
Supplementary_files_format_and_content: tab-delimited text files using corrected and uncorrected foldchange values

organism: Danio rerio

extract_protocol:
Pancreas was dissected on ice and dissociated. CACs and non-CACs were sorted by FACS and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries.
Libraries were constructed using standard Illumina protocols

value: pancreas

tag: developmental stage

value: adult

tag: strain

value: AB

value: isolated centroacinar cells


title: non-CAC rep 2

value: isolated non-centroacinar cells


title: 11_PATH_dcl3

description:
short RNA
library id: 11


title: EP_CAM24


title: non-CAC rep 1

description: processed data file: origsample_genes_strict.txt


title: LEF1_12


title: EP_CAM12


title: CAC rep 1


title: EP_CAM0


title: 4_PATH_nrpd1

description:
short RNA
library id: 4


title: Dmel_infected_Symbiotic_Heterorhabditis_Bacteriophora_30h

first: Priti

last: Kumari

state: MD

address: 801 W Baltimore St

department: Institute For Genome Sciences

institute: University Of Maryland Baltimore School Of Medicine

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to D. melanogaster whole genome reference using TopHat v1.4.0
Reads Per Kilobase of gene per Million mapped reads (RPKM) were calculated for each sample.
Differential expression of genes were computed
Genome_build: D. melanogaster BDGP5; GCA_000001215.1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Drosophila melanogaster

growth_protocol:
Drosophila melanogaster: Oregon R adult flies were used for the transcriptomic analyses. Flies were reared on instant Drosophila diet (Formula 4-24 Drosophila medium) supplemented with yeast (Carolina Biological Supply), and maintained at 25°C and a 12:12-h light:dark photoperiodic cycle. Male and female adult flies aged 4–6 days old were used in infection assays with the nematodes and their bacteria                                                                                [PMID 22546901].
Heterorhabditis bacteriophora (Nematode): The entomopathogenic nematodes Heterorhabditis bacteriophora (strain TT01) were amplified in fourth instar larvae of the wax moth Galleria mellonella using the water trap technique. To confirm lack of Photorhabdus bacteria in Heterorhabditis nematodes (axenic), the worms were homogenized and the lysate was spread on selective media. Fresh IJ worms were collected and prepared through pelleting, washing and re-suspending in sterile distilled water. IJ nematodes carrying or lacking Photorhabdus bacteria were used 1-2 weeks after collection from the water traps. Heterorhabditis numbers were estimated by counting the average nematode density present in ten individual 50 μL drops of water using a stereo-microscope [PMID 22546901].
Photorhabdus luminescens (bacteria): The Gram-negative insect pathogenic bacteria Photorhabdus luminescens subsp. laumondii (strain TT01) were used for fly infections. Bacteria were cultured in Luria-Bertani broth (LB) and incubated for 18-24 h at 30°C. Bacterial cultures were centrifuged at 4°C, pelleted, washed in 1x sterile phosphate-buffered saline (PBS) and re-suspended in PBS. Bacterial density was measured using a NanoDropTM 2000c (Thermo Fisher Scientific) and a 10x serial dilution plating technique [PMID 22546901].

extract_protocol:
RNA was extracted from 40 adult flies infected with Heterorhabditis axenic nematodes, symbiotic nematodes, Photorhabdus bacteria only as well as from  uninfected controls. Samples were collected at 12 and 30 h post infection. Total RNA was extracted using the PrepEase RNA spin kit (Affymetrix) following the manufacturer’s instructions. Briefly, flies were homogenized using sterile plastic pestles and RNA was extracted using a silica-based column system including a DNAse treatment step for 15 min. Total RNA was re-suspended in 40 μL of sterile nuclease-free water. RNA concentration was measured using a Nanodrop. RNA integrity and quality were assessed using a Bioanalyser (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Infection Protocol: Nematode infections were carried out using nested 5 mL cups (Solo®) and filter papers (Whatman) that supported 10-15 adult flies per group. A 500-700 μL solution containing symbiotic or axenic Heterorhabditis nematodes was added to each container (100 IJ/fly). Treatments involving sterile water devoid of nematodes were used as negative controls. Infected and control flies were kept at 25°C. A PBS suspension (18.4 nL) containing Photorhabdus bacteria was injected into Drosophila adult flies at the lateral anterior side of the thorax through nano-injection (Nanoject II - Drummond Scientific). The number of Photorhabdus cells delivered into each fly was approximately 500-700 colony-forming units (CFUs). Control samples involved PBS injected flies and kept under the same conditions [PMID 22546901].

tag: drosophila (host) strain

value: OregonR

tag: drosophila (host) age

value: 4-6 days-old

tag: Sex

value: 1:1 ratio male/female

tag: sample collection time

value: 30 h post-infection

tag: # of flies used for extraction

tag: infected with

value: Heterorhabditis bacteriophora

tag: pathogen strain

tag: pathogen variation

value: carrying Photorhabdus (symbiotic)

tag: pathogen age/stage

value: 1-2 weeks old infective juveniles (IJs)

tag: infection dosage

value: 100 infective juveniles/fly


title: Dmel_infected_Symbiotic_Heterorhabditis_Bacteriophora_12h

value: 12 h post-infection


title: Dmel_infected_Photorhabdus_12h

source_name: whole flies_infected_Photorhabdus

value: Photorhabdus luminescens subsp laumondii

value: fresh overnight culture


title: Dmel_Uninfected_Control

source_name: whole flies_Uninfected_Control

value: 30 h post-PBS injection

value: none (uninfected control)


title: Dmel_infected_Phootrhabdus_30h

value: adult


title: Dmel_infected_Axenic_Heterorhabditis_Bacteriophora_30h

value: lacking Photorhabdus (axenic)


title: Dmel_infected_Axenic_Heterorhabditis_Bacteriophora_12h


title: Chrom3-160R-Rep2

status: Public on Sep 11 2015

city: Worcester

first: Fen-Biao

last: Gao

state: Massachusetts

address: 55 Lake Avenue North

department: Department of Neurology

institute: University of Massachusetts Medical School

data_processing:
We performed QC using trimmomatic removing PCR primers and low quality bases.
We aligned cleaned read were aligned to the mm10 genome using STAR and selected only for unqiuely mapping reads.
We determined raw reads counts using Bedtools.
Using DESeq, we determined differentially expressed genes.
Genome_build: BDGP6
Supplementary_files_format_and_content: tab delimited text files with raw reads counts per gene

source_name: Chrom3-160R_fly heads

growth_protocol: Flies were grown on standard medium at 25°C

extract_protocol:
RNA from liquid nitrogen frozen fly heads were extracted with Trizol
libraries were prepared according Zhang et al protocol (PMID: 23273270)
Strand Specific libraries prepared without poly(A) selection

tag: gender

value: male

tag: days after eclosion

tag: genotype/variation

value: expressing 160R from Chromosome 3

tag: tissue

value: Fly Heads


title: Chrom3-160R-Rep1


title: Chrom3-160R-Rep3


title: Chrom3-160R-Rep4


title: Chrom3-5R-Rep4

source_name: Chrom3-5R_fly heads

value: expressing 5R from Chromosome 3


title: Chrom3-5R-Rep3


title: Chrom3-5R-Rep1


title: Chrom3-5R-Rep2


title: Chrom2-160R-Rep3

source_name: Chrom2-160R_fly heads

value: expressing 160R from Chromosome 2


title: Chrom2-160R-Rep2


title: Chrom2-5R-Rep1

source_name: Chrom2-5R_fly heads

value: expressing 5R from Chromosome 2


title: Chrom2-5R-Rep3


title: Control

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

data_processing:
Reads were converted from Solexa Format with ShortRead( 1.26.0)
Adapter sequences were removed with ShortRead.
Mapping to miRBase 21 was performed with Bowtie (1.1.2)
Rsamtools (1.18.2) was used to convert and sort reads into binary format and subsequently to enumerate reads for each known miR.
Unmapped reads were tabulated and clustered into families of novel sequences.
Genome_build: NA
Supplementary_files_format_and_content: raw counts and normalized abundance estimates for both samples (Sup_Table_1.csv) and raw counts for unmapped_reads (Sup_Table_2.csv).

organism: Ambystoma mexicanum

source_name: Uninjured Tail

growth_protocol: All axolotls used in these experiments were bred at the Max Planck CBG (Dresden Germany) or the University of Minnesota in accordance with IACUAC protocol No.1411-32049A

extract_protocol:
Total RNA was extracted with Trizol (Life Technologies) according to the manufacturer’s protocol.
Isolation of the small RNA fraction, generation of libraries and subsequent deep sequencing was carried out by the Functional Genomics Library Construction Core at BC Cancer Agency Genome Sciences Centre, Canada

treatment_protocol: Control and blastema samples were generated by pooling tail tissue from 20 mature axolotls that had either never regenerated or 3 days post injury.

tag: cell type

value: Uninjured Tail


title: Chrom2-5R-Rep2


title: Chrom2-5R-Rep4


title: ILC2s

city: Cincinnati

first: Yui-Hsi

last: Wang

state: Oh

address: 3333 Burnet Ave

institute: CCHMC

description: RNA-Seq dUTP

data_processing:
RNA-Seq data analysis was performed using the BioWardrobe (PMID:26248465)
Briefly, reads were mapped to the mm10 genome and RefSeq-based transcriptome using RNA-STAR (v. 2.4.2a and assigned to the RefSeq genes  using the BioWardrobe algorithm.
STAR PARAMS:
--clip3pNbases 0      --seedSearchStartLmax 15   --alignSJDBoverhangMin 1
--outFilterMultimapNmax 1   --outFilterMismatchNmax 5   --clip5pNbases 0
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes RPKM values for each sample

molecule: polyA RNA

source_name: intestinal type-2 innate lymphiod cells

growth_protocol: 1. BMMCs were generated from bone marrow cells of naïve BALB/c mice after culturing with SCF (50ng/mL) plus IL-3 (10ng/mL) for 4 weeks. 2. MMC9s (beta7loc-Kit+ST2+FceR+) isolated from small intestine of mice developed food allergy. 3. MCPs (beta7hic-Kit+ST2+FceR+) isolated from small intestine of mice developed food allergy were cultured and expanded with SCF(50ng/mL) plus IL-3 (10ng/mL) for two weeks. 4. MMCs (c-Kit+ST-2+Fcer+) isolated from peritoneal of  mice  injected with zymogen, were cultured with SCF (50ng/mL) plus IL-3 (10ng/mL) and expanded for 2 weeks. 5. CD19+ B cells were isolated from mesenteric lymph nodes of mice developed food allergy. 6. CD8+ T cells were isolated from mesenteric lymph nodes of mice developed food allergy. 7. CD4+Th2 cells (CD4+IL-17-RB+ST2+) were isolated from small intestine of mice developed food allergy. 8. ILC2s (IL-17RB+c-Kit-ST2+ICOS+) were isolated from small intestine of mice developed food allergy. 9. Eosinophils (Siglec-F+CD11b+CCR3+)  were isolated from small intestine of mice developed food allergy.

extract_protocol:
RNA was extracted with Aurum™ Total RNA Mini Kit (Bio-Rad)
A modified dUTP method was used for preparation of RNA-Seq libraries[27]. Briefly, mRNA was purified from total RNA by Dynabeads® mRNA Purification Kit (Invitrogen) and reverse-transcribed with SuperScript® III (Invitrogen). The second strand was created by DNA Polymerase 1 (NEB) in the presence of RNase H and a dNTP mix containing dUTP instead dTTP. The cDNA was fragmented on a Covaris sonicator, and end repair and A-tailing were performed using the Quick Blunting kit and exo- Klenow fragment of DNA polymerase I, respectively (NEB). Illumina genomic adapters were ligated, and the sample was size-fractionated (~170–400 bp) on E-Gel EX 2% agarose (Invitrogen). After uracil-dna glycosylase (UDG) treatment (NEB) and a final PCR amplification step with Illumina primers (18 cycles), the cDNA libraries were size-fractionated (~175-400 bp) on a 2% agarose gel, quantified using a Qubit 2.0 fluorometer and dsDNA HS kit (Invitrogen), and sent to sequencing on a Illumina HiSeq 2500 sequencing system

value: intestinal type-2 innate lymphiod cells

tag: biowardrobe id


title: B cells

description: RNA-Seq dUTP

source_name: mesenteric lymph node B cells

value: mesenteric lymph node B cells


title: CD8 T cells

description: RNA-Seq dUTP

source_name: mesenteric lymph node CD8+ T cells

value: mesenteric lymph node CD8+ T cells


title: MMCs

description: RNA-Seq dUTP

source_name: peritoneal mast cells

value: peritoneal mast cells


title: MMC9s

description: RNA-Seq dUTP

source_name: intestinal IL-9-producing mast cells

value: intestinal IL-9-producing mast cells


title: Hdac3KO DP1_rep1

city: Nashville

first: Scott

last: Hiebert

state: TN

address: 2220 Pierce Ave

department: Biochemistry

institute: Vanderbilt University

description:
rRNA-depleted total RNA
DP1_WTvKO
KO_DP1vDP2

data_processing:
residual adapter trimmimg by Trimmomatic-0.32(usadellab.org)
Read alignment with TopHat (v.2.0.11)
Differential gene expression determined by Cuffdiff (v2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: gene.diff

source_name: sorted thymocytes

extract_protocol:
Total RNA was extracted with Trizol reagent and precipitated with isopropanol.
following ribosomal RNA depletion, RNA was used as input for Clontech SMARTer Stranded RNA-Seq kit

tag: strain


title: Hdac3KO DP2_rep2

description:
rRNA-depleted total RNA
DP2_WTvKO
KO_DP1vDP2


title: WT control DP1_rep2

description:
rRNA-depleted total RNA
DP1_WTvKO
WT_DP1vDP2

value: WT control


title: Hdac3KO DP2_rep1


title: WT control DP2_rep1

description:
rRNA-depleted total RNA
DP2_WTvKO
WT_DP1vDP2


title: Hdac3KO DP1_rep2


title: BMMCs

description: RNA-Seq dUTP

source_name: bone marrow-derived mast cells

value: bone marrow-derived mast cells


title: MCPs

description: RNA-Seq dUTP

source_name: intestinal mast cell progenitors

value: intestinal mast cell progenitors


title: BNa26_FPKM

city: Charlestown

first: Robert

last: Morris

address: 149 13th Street

institute: Mass. General Hospital Cancer Center

data_processing:
Illumina's HiSeq software used for basecalling
Sequenced libraries were mapped to the mouse genome (mm10) using TOPHAT (Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Trapnell C et al, Nature protocols 2012, 7, 562-578, doi:10.1038/nprot.2012.016). A RefSeq GTF file was used to annotate the mapped transcripts. FPKM matrixes and differentially regulated gene lists were generated using the Cufflinks-Cuffmerge-Cuffdiff pipeline (Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Trapnell C et al, Nature protocols 2012, 7, 562-578, doi:10.1038/nprot.2012.016).
Genome_build: mm10
Supplementary_files_format_and_content: Excel spreadsheet includes FPKM values for each Sample

source_name: adult lung tissue

extract_protocol:
Methods: RNA extraction: Ninety six hours following the last injection of tamoxifen mice were processed were sacrificed and dissected tissues flash frozen in liquid nitrogen for RNA extraction. RNA was extracted using the TRIzol-choloroform method and then DNase treated. RNA quality was validated using a bioanalyzer. Library construction and RNA-squencing was performed at the MGH NextGeneration Sequencing facility. Three mice were used per genotype, taking matched tissues from each mouse.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

tag: genotype

value: Rb1 knockout


title: BNa23_FPKM


title: Chrom2-160R-Rep4

value: male


title: WT control DP1_rep1


title: BNa25_FPKM


title: Chrom2-160R-Rep1


title: Blastema

source_name: 3 day post injury blastma

value: 3 day post injury blastma


title: BNa24_FPKM

value: Rb1 wild type


title: eosinophils

description: RNA-Seq dUTP

source_name: intestinal eosinophils

value: intestinal eosinophils


title: BNA15_FPKM

source_name: adult colon tissue

value: colon


title: BNa21_FPKM


title: CD4+TH2 cells

description: RNA-Seq dUTP

source_name: intestinal CD4+Th2 cells

value: intestinal CD4+Th2 cells


title: BNa22_FPKM


title: BNa12_FPKM


title: WT control DP2_rep2


title: BNa14_FPKM


title: BNa11_FPKM


title: DC4h-RNAseq

city: shang hai

first: Qian

last: Zhang

address: xiangyin road 800

institute: Second military medical university

data_processing:
Illumina Casava1.6 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads) as described in article: Mortazavi, A., B. A. Williams, et al. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 5(7): 621-8.
A strict algorithm was developed to identify differentially expressed genes refering to Audic, S. and J. M. Claverie (1997). The significance of digital gene expression profiles. Genome Res 7(10): 986-95.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: Mouse BMDC

growth_protocol: Mouse bone marrow cells were cultrued in  in RPMI-1640 medium with recombinant mouse GM-CSF (10ng/ml) and IL-4(1ng/ml) for 6 days

extract_protocol:
RNA was harvested using Trizol reagent，and isolated using an RNA isolation kit (QIAGEN).
The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.

treatment_protocol: sample 2 was treated with LPS(100ng/ml)for 4h in RPMI 1640 with recombinant mouse GM-CSF (10ng/ml) and IL-4(1ng/ml). And both samples were sorted by Moflo XDP(Dako Cytomation) based on surface marker CD86 and Iab.

value: bone marow derived dendritic cells

tag: cell subtype

value: immature DC stimulated by LPS for 4h


title: DC0h-RNAseq

value: immature DC


title: Sample 23 [S15]

city: Beijing

first: Zhixi

last: Tian

address: No.1 Building, No.1 West Beichen Road,Chaoyang District

data_processing:
Filter adaptors, length.Adaptor sequence see miRNA_adaptor.fa
Remove reads mapped noncoding rRNA,tRNA,snRNA and snoRNA in the Rfam database.
Map the reads to known miRNAs in miRBse version 20 using BWA.
Extract the unmapped reads and mapped to Glycine max genome v1.1.
Using MIREAP software to identify novel miRNAs.
Calculate the expression value TP5M.
Genome_build: Glycine max genome V1.1
Supplementary_files_format_and_content: total.sorted.expression.TP5M.fullinfo_processed.txt, including the MIRNA name, prime,mature sequence, chromosome, precursor start,precursor end, mature start, strand, old name, the the expression pattern of 23 samples. The number 1-23 corrsponds with the sample name number in each samples title. For esample, '1_TP5M' means the exprssion of Sample1 ,S8, got from 1thr-06-21-ste-4.fq.gz.

organism: Glycine max

source_name: 5 days after flowering at the stage of flowering

growth_protocol: Soybean (Glycine max cv. Williams 82) plants were grown in the Experimental Station of the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, in Beijing.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen).
Small RNA libraries were constructed as described previously (Lu et al.,2007). Briefly, small RNAs in the size range of 15-30 nucleotides(nt) were purified from 200 µg of total RNA by 15% denaturing polyacrylamide gel electrophoresis (PAGE) gels and ligated to an adapter. After first-strand synthesis and 16 cycles of PCR amplification, the final bands were PAGE gel purified and submitted for sequencing on a Hi-Seq 2000 analyzer.

treatment_protocol: No

tag: cultivar/line

value: cv. Williams 82

tag: developmental stage

value: flower


title: Sample 22 [S16]

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

source_name: flower at florescence stage on a different date

value: florescence stage on a different date


title: Sample 17 [S2]

source_name: root at the stage of germination

value: stage of germination

value: root


title: Sample 20 [S13]

source_name: bud before flowering at the stage of flowering

value: bud before flowering


title: Sample 15 [S17]

source_name: pod of one week at the beginning stage of seed development

value: pod


title: Sample 14 [S18]

source_name: pod of two weeks at the beginning stage of seed development


title: Sample 19 [S4]

source_name: new leaf at the stage of germination

value: new leaf


title: Sample 16 [S3]

source_name: stem at the stage of germination

value: stem


title: Sample 12 [S20]

source_name: developing seeds around 6 weeks

value: around 6 weeks

value: developing seeds


title: Sample 21 [S14]

source_name: florescence at the stage of flowering

value: stage of flowering

value: florescence


title: 15LL RNA-Seq

city: Boston

first: Ryan

last: McClure

address: 650 Albany St.

institute: Boston University

data_processing:
The 50-base short read sequences produced by the 5500XL SOLiD  sequencer were mapped in color space using SOLiD LifeScope software version 2.5 using the default parameters
Resulting BAM files were then examined with Rockhopper (McClure et al. 2013 Nucleic Acids Research) to determine RPKM levels of genes
Genome_build: Synechococcus 7002 NC_010474, NC_010475, NC_010476, NC_010477, NC_010478, NC_010479 and NC_010480
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Picosynechococcus sp. PCC 7002

source_name: Synechococcus 7002, grown with 140 µE m-2 s-1

growth_protocol: Synechococcus 7002 was routinely grown in modified A+ media (Stevens and Porter 1980) containing 17 mM NH4

extract_protocol:
RNA was extracted using Trizol following by DNAseI treatment using Qiagen RNAseay mini column
Template cDNA was prepared using the Applied Biosystems SOLiD® Total RNA-Seq Kit (Life Technologies, Carlsbad, CA) according to manufacturer's protocol. Sequencing was carried using the SOLiDTM 5500XL protocol (Life Technologies).

treatment_protocol: Synechococcus sp. PCC 7002 was grown in a turbidostat and subjected to carbon, light or nitrogen limitations or a high light/high O2 adapted strain was subjected to high or normal oxygen levels

tag: light wavelength 630 nm/680 nm ratio

value: Light limitation


title: Sample 13 [S19]

source_name: pod of three weeks at the beginning stage of seed development


title: BNa13_FPKM

value: colon

value: Rb1 knockout


title: Sample 18 [S1]

source_name: cotyledon at the stage of germination

value: cotyledon


title: BNa16_FPKM


title: 3NL RNA-Seq

source_name: Synechococcus 7002, grown with 0.9 mM NH4Cl

value: Nitrogen limitation


title: Sample 11 [S21]

source_name: developing seeds around 8 weeks

value: cv. Williams 82

value: around 8 weeks


title: Sample 9 [S22]

source_name: developing seeds around 10 weeks

value: around 10 weeks


title: 7CL RNA-Seq

source_name: Synechococcus 7002, grown with 7.7 mM NaHCO3

value: Carbon limitation


title: 11LL RNA-Seq


title: 18NL RNA-Seq


title: 14CL RNA-Seq


title: Sample 10 [S23]

source_name: senescence leaf

value: senescence leaf


title: ASB7 RNA-Seq

source_name: Synechococcus 7002, high light/high O2 adapted EH1 - 7.1% dissolved O2

value: Adapted strain, 7.1% dissolved O2


title: Sample 8 [S11]

source_name: flower bud at the stage of flower bud differentiation

value: stage of flower bud differentiation

value: flower bud


title: Sample 7 [S12]

source_name: leaf bud at the stage of flower bud differentiation

value: leaf bud


title: ASB6 RNA-Seq

source_name: Synechococcus 7002, high light/high O2 adapted EH1 - 16.5% dissolved O2

value: Adapted strain, 16.5% dissolved O2


title: Sample 6 [S9]

source_name: new leaf at the stage of flower bud differentiation

value: new leaf


title: Sample 5 [S10]

source_name: old leaf at the stage of flower bud differentiation

value: old leaf


title: Sample 4 [S7]

source_name: old cotyledon at the trefoil stage

value: trefoil stage

value: old cotyledon


title: Sample 1 [S8]

source_name: stem at the trefoil stage

value: stem


title: Sample 3 [S5]

source_name: new leaf at the trefoil stage


title: Sample 2 [S6]

source_name: old leaf at the trefoil stage


title: ZUMA-0018

status: Public on Sep 10 2015

city: Badalona

first: Miguel

middle: A.

last: Peinado

address: Can Ruti Campus

country: Spain

institute: IGTP

description: NSUMA technique to assess the methylation status of Alu repeats

data_processing:
Pre-processing. Reads sequences were obtained from the Illumina instruments  qseq format and were pre-processed in different steps in order to remove misleading reads and improve the mapping accuracy. Bases at the 3’ end of the reads with low quality (PHRED score <= 2) were end clipped. The adapters sequence used in the PCR amplification were also removed using iterative searches of 5’ to 3’ fragments. Ambiguous bases (Ns) at both ends of the read were also removed. Finally, reads shorter than 10 bp or with more than 30% of ambiguous bases were filtered out from the analysis.
Mapping. Once trimmed and cleaned, reads were mapped to the human reference genome (build GRCh37/hg19) with Bowtie 0.12.7 using the following parameters: -S –p 8 –v 2 –phred64-quals –best –l 28 –k 2. The value of option v is the number of mismatches allowed.
Post-processing. Once mapped, ambiguous reads (those that are mapped in several genome locations) were disambiguated when the number of mismatches allowed the assignment of a unique position in the human genome with a higher probability, otherwise they were rejected. Reads mapped in unknown chromosome were annotated as chrUn (scaffolds and contigs which could not be placed on chromosomes) and excluded from further analyses. The unambiguous reads (including uniquely mapped reads) were selected for further analysis. The information was stored using the standard SAM/BAM format.
Counting of reads in regions of interest (NSUMA universe) was performed using coverageBed of the bedtools suite 2.16.2
Genome_build: hg19
Supplementary_files_format_and_content: Normalized number of reads by NSUMA amplicon for each sample.
Supplementary_files_format_and_content: ZUMA-xxxx_coverage.txt The file contains describes the amplicon location and its coverage according to the NSUMA technique in the sample. Consists in a BED6+ file depicting the (chromosome, start, end, amplicon_type, amplicon_numeric_identifier and strand) of the amplicon; plus four coverage columns, namely (number of reads in the amplion, number of bases of the amplicon covered with at lesat one read, the length of the amplicon, the fraction of bases of the amplicon that had non-zero coverage).

organism: Gorilla gorilla

source_name: Blood

extract_protocol:
The method is based in the AUMA technique (Rodríguez, 2008; doi: 10.1093/nar/gkm1105), although important modifications were introduced to expand significantly the genomic coverage and to introduce internal controls that allow normalization and control of some technical biases. Briefly, one microgram of DNA was digested for 16 h at 25C with the methylation-sensitive restriction endonuclease SmaI  (Roche Diagnostics GmH, Mannheim, Germany) leaving blunt ends (CCC/GGG), followed by a second digestion with the methylation-insensitive restriction enzyme MseI (T/TAA)  (16h at 37C, Roche Diagnostics GmH, Mannheim, Germany) that leaves sticky ends. Adapters blunt-SmaI (ADPT-S1 GATAGTATGCCCGGGTGA plus the 5’ phosphorylated ADPT-S2 TCACCCGGGCATAC) and sticky-MseI (ADPT-M1 CTGAGGCTGGATCCCTG plus the 5’ phosphorylated ADPT-M2 TACAGGGATCCAGCCTCAG) were prepared by incubating the two oligonucleotides for 2 min at 65ºC and then cooling to room temperature for 30-60 min. Digested DNA and 2nmol of blunt and sticky adapters were ligated overnight at 16C using T4 DNA ligase (New England Biolabs, Beverly, MA). The product was purified using the Illustra GFX Purification kit (GE Healthcare, Buckinghamshire, UK) and eluted in 200 ul of bidistilled water. The ligation product consists of three types of molecules according to the flanking sites SmaI-SmaI, SmaI-MseI and MseI-MseI. Only the products containing SmaI adapters represent unmethylated fragments (Figure 1A). Next, a PCR (95ºC 2 min; 95ºC 30 sec, 60ºC 1 min, 72ºC 1min for 30 cycles; 72ºC 5min) was performed using two primers, one that anneals the MseI adapter (ADPT-M1A CTGAGGCTGGATCCCTGTAA) and another one homologous to the SmaI adapter plus TT at the 3’ end (ADPT-S1TT GATAGTATGCCCGGGTGAGGGTT) to enrich in Alu sequences. The final product appeared as a smear when run in an agarose gel and most of the amplicons ranged from 50 bp to 1000 bp.
The NSUMA PCR product was sheared by sonication with a Bioruptor (Diagenode) to a size of 100-300 bp. DNA fragments were blunt end repaired with T4 DNA polymerase and Klenow fragment (NEB) and purified with a QIAquick PCR purification kit (Qiagen). Thereafter, 3’-adenylation was performed by incubation with dATP and the Klenow (3´→5´ exo-) fragment of DNA polymerase I (NEB). DNA was purified using MinElute spin columns (Qiagen) and ligated to double-stranded adapters (GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG/ACACTCTTTCCCTACACGACGCTCTTCCGATCT) using rapid T4 DNA ligase (NEB). The sample was purified again using a MinElute spin column and run on a 2% agarose gel, and fragments in the size range of interest, 150 bp plus 65 bp of adapters, were excised with a sterile single-use scalpel and recovered from the gel by QIAquick gel extraction. Then, adapter-ligated fragments were enriched, and adapters were extended, by selectively amplifying with an 18-cycle PCR reaction using Phusion DNA polymerase (Finnzymes), and primers 1.1 (5’ P- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and 2.0 (5’ P-CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT) (library size of approximately 150 plus 92 bp of adapters). Finally, the quality of libraries was confirmed on the Agilent Technologies 2100 Bioanalyzer and by cloning into a blunt TOPO vector. Six colonies were sequenced by conventional Sanger method to verify correct adapter ligation and sequence match. Libraries were quantified by TaqMan Universal PCR No AmpErase kit (Applied Biosystems-Roche). DNA was loaded into a single read (SR) flow cell for cluster generation using a SR-cluster generation kit v4 (Illumina). During this process, DNA molecules were immobilized on the surface of the flow cell, amplified in situ to create same-sequence containing clusters, and following surface blocking and DNA denaturation, binding of sequencing primer was performed. The flow cell was then mounted on a Genome Analyzer II instrument for sequencing, and 35-50 sequencing cycles were carried out using v4 SBS kits. Each flow cell ran on the Genome Analyzer IIx contained a PhiX control lane (loaded at a concentration of 4pM) that was used to monitor run quality.

value: Blood


title: D250

city: Waurn Ponds

first: christophe

last: lefevre

state: vic

address: pigdons road

department: School of medicine

country: Australia

institute: Deakin University

description: tammar milk collected at phase3 lactation day250

data_processing:
Base calling
Barcode deconvolution and stripping
Alignment to mature miRNA database (miRBase)
Alignment of remaining reads to miRNA precursor database (miRBase)
Read abundance counting and normalization to library read size
Genome_build: Genome_build: miRBase 19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count from mirAligner

organism: Notamacropus eugenii

source_name: tammar phase3 Milk

extract_protocol:
the milk samples were thawed on ice and centrifuged at 5000xg to isolate the fat and cells. Skim milk was centrifuged at 17,000Xg for 20 min to isolate any remaining cells and fat. miRNAs were isolated from skim milk by using commercially available miRNA isolation Kit (mirVana™ miRNA Isolation Kit, Ambion) and the isolation was performed as instructed in the manufacturer’s manual. The miRNA was eluted with 100µl of elution solution provided in the kit.
BGI small RNA-seq (40 nucleotide cut-off)

value: Milk

tag: day


title: D120

description: tammar milk collected at phase 2B lactation day120

source_name: tammar phase2B Milk


title: D120serum

description: blood serum sample collected at phase2B lactation day120

source_name: Serum

value: blood serum


title: D175

description: tammar milk collected at phase 2B lactation day175

source_name: tammar phase2BMilk


title: D35

description: tammar milk collected at phase 2A lactation day35

source_name: tammar phase2A Milk


title: ZUMA-0020


title: D75

description: tammar milk collected at phase 2A lactation day75


title: NIH3T3_RNA-seq_C3

city: Ipswich

first: Guoqiang

address: 240 County Road

institute: New England Biolabs Inc

description: processed data file: RNA-seq_log2fdc.txt

data_processing:
For RRBS, adaptor and low quality sequences (Phred score < 20) were trimmed from RRBS reads using the trim_galore package (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with the parameter of --RRBS --paired. Reads were mapped to the mouse reference genome mm10 using Bismark with Bowtie2. CpG methylation was extracted from uniquely mapped reads using Bismark methylation extractor with the parameter of -p --no_overlap. Differential methylation analysis was carried out using the methylKit package, where logistic regression test was implemented on single CpG sites or genomic region sliding windows (window size 5 kb, step size 5 kb). The p-value of differential methylation test was corrected to q-values using the sliding linear model method. CpG sites or genomic regions with q-values < 0.01 were considered significantly differentially methylated.
For RNA-seq, sequencing reads were mapped to mm10 using TopHat2 (-r 60 --library-type fr-firststrand) with a known transcriptome file supplied (UCSC May 23, 2014). The number of reads mapped to each known gene were counted using htseq-count tools (-t exon -s reverse -i gene_id) and analyzed with DESeq2, where a negative binomial generalized linear model test is implemented on raw counts. The p-value of differential expression was corrected using Benjamini-Hochberg adjustment method and adjusted p-value was obtained. Genes with adj p-value < 0.01 were considered significantly differentially expressed. Sample distance was calculated using Euclidean distance on the rlog-transformed counts. Heatmap were generated using the Z-scored-transformed rlog values of significantly changed genes. Gene ontology analysis was carried out using the AmiGO 2 tools. Multiple comparisons were corrected using Bonferroni correction.
Genome_build: mm10
Supplementary_files_format_and_content: RRBS_CpG_methylation_call.txt: tab-delimited text file including the coordinates of CpG sites (1-based), strand, pvalue, qvalue and meth.diff
Supplementary_files_format_and_content: RNA-seq_log2fdc.txt: gene symbol, baseMean, log2FoldChange, lfcSE, stat, pvalue and padj of each gene

source_name: NIH3T3_RNA-seq_control clone

growth_protocol: NIH3T3 stable clones were cultured in DMEM media supplemented with 10% of Fetal Bovine Serum.

extract_protocol:
Genomic DNA were extracted using Easy-DNA™ gDNA Purification Kit (Life Technologies). Total RNA were extracted using TRIZol reagent.
For RRBS, 1 μg of genomic DNA from stable clones overexpressing 14-3-3ε or control vector was digested by MspI, end-repaired and dA-tailed according to manufacturer’s conditions (New England Biolabs). Methylated NEB Illumina loop adaptor was ligated to digested DNA (E7370S, New England Biolabs). Ligation product was size-selected for 150 to 400 bp fragments on 2% agarose gels and bisulfite converted using the EZ DNA Methylation Kit (Zymo Research). Libraries were enriched by PCR using EpiMark Hot Start Taq DNA Polymerase (New England Biolabs). For RNA-seq, libraries were constructed using the NEBNext® Ultra™ Directional RNA Library Prep Kit (New England Biolabs) per the manufacturer’s instructions. Average insert size of libraries was 200 bp.

treatment_protocol: 14-3-3ε was cloned into p3xFLAG-CMV-10 vector (Sigma-Aldrich). NIH3T3 stable cell line overexpressing 14-3-3ε was generated by selecting the cells transfected with 14-3-3ε constructs in 800 μg/mL of G418. After a week in culture single colonies were picked up and verified by western blotting using anti-FLAG antibody.

tag: cell line

value: Mouse embryonic fibroblast cell line

tag: clone id

value: Control clone 3

value: control


title: NIH3T3_RNA-seq_EP10

value: 14-3-3-epsilon clone 10

value: overexressing the 14-3-3-epsilon homologue


title: NIH3T3_RNA-seq_EP12

value: 14-3-3-epsilon clone 12


title: D175serum

description: blood serum sample collected at phase2B lactation day175


title: ZUMA-0019


title: NIH3T3_RNA-seq_C2

value: Control clone 2


title: MC1-ZE7 cells (Em-) Msp I

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description:
pZscan4c-Emerald (Em-) Msp I
library strategy: HELP tag sequencing

data_processing:
HELP pipeline is described in Suzuki et al. Genome Biol 2010 (PMID: 20359321).
To quantify DNA methylation in Em+ and Em- sorted cells we used data from HELP tagging method at genome locations within 1 kb from centers of each H3K27ac peak. DNA methylation was inferred from angle <50, where angle was estimated as: 100*atan(x/y)/(pi/2) 5. Peaks of H3K27ac, where <3 tags were obtained with HpaII restriction enzyme, were not used in the analysis. Decreased in DNA methylation at H3K27ac peaks was inferred from the increase of >=1.5 fold in the number of tags obtained with HpaII restriction enzyme. Peaks were sorted by the decreasing logratio of H3K27ac in Em+/Em- cells, and then the proportion of peaks with DNA methylation or decreased DNA methylation in Em+ vs. Em- cells was estimated in a sliding window of 300 peaks.
Presence of chromatin modifications and cofactors was evaluated using ChIP-seq data.  The number of ChIP-seq tags was then counted in each H3K27ac peak  for Em+ and Em- cells. If the width of a peak was <1 kb, then ChIP-seq tags was then counted in a 1 kb intervals centered at the peak. If tag counts were >2 fold more abundant than in control, then the histone modification or cofactor was considered present. DNA methylation (>50%) was assessed using genome-wide bisulfite sequencing data9. Lamin B1 binding and abundance of H3K9me2 histone modifications was inferred from positive log-ratio of signal intensity in tiling array experiments10,11 for oligos aligned to each H3K27ac peak. Probes within 1 kb centered at H3K27ac peak were averaged. The proportion of H3K27ac peaks with histone modifications or cofactors was estimated separately in H3K27ac peaks that had increased acetylation (>3 fold) in Em+ cells compared to Em- cells, and in other H3K27ac peaks. Statistical significance was evaluated using a hypergeometric distribution as a null-hypothesis. A portion of these data (DNA methylation, lamin B1 binding, and H3K9me2 histone marks) was used to generate. Peaks were sorted by decreasing logratio of H3K27ac between Em+ and Em- cells, and then the proportion of peaks with >50% DNA methylation or average logratio for lamin B1 binding and H3K9me2 histone marks was estimated in a sliding window of 300 peaks.
Genome_build: mm9
Supplementary_files_format_and_content: *hcount.txt file contents:
Supplementary_files_format_and_content: (1) MspI site ID
Supplementary_files_format_and_content: (2) Chromosome
Supplementary_files_format_and_content: (3) MspI site position
Supplementary_files_format_and_content: (4) Number of forward reads
Supplementary_files_format_and_content: (5) Number of reverse reads
Supplementary_files_format_and_content: (6) Total number of reads

growth_protocol: MC1-ZE7 ES cells were cultured on gelatin-coated feeder-free plates in complete ES medium, DMEM (Gibco), 15% FBS (Atlanta Biologicals), 1000 U/ml leukemia inhibitory factor (LIF) (ESGRO, Chemicon), 1 mM sodium pyruvate, 0.1 mM non-essential amino acids (NEAA), 2 mM GlutaMAX, 0.1 mM beta-mercaptoethanol, and penicillin/streptomycin (50 U/50 µg/ml). Medium was changed daily and cells were split every 2 to 3 days routinely.

extract_protocol:
Genomic DNA was extracted from individual cell populations separately. Cells were lysed in sodium dodecyl sulfate (SDS)-containing DNA extraction buffer (100 mM Tris-HCl, pH 8.0, 200 mM NaCl, 50 mM EDTA) and treated with proteinase K for 3 h at 55°C. The residual RNA was digested by incubation in the presence of RNase A for 1 h in 37°C. Lysates were subjected to three rounds of phenol–chloroform–isoamylalcohol (PCI; Invitrogen) extraction and the genomic DNA was precipitated by ethanol, washed with 70% ethanol, dried, and then dissolved in TE (10 mM Tris-HCl, pH 8.0, 1mM EDTA). The quality of purified genomic DNA was checked by gel and Nanodrop (260/280=1.7-1.9, 260/230>2).
The HELP tagging assay was performed on purified genomic DNAs. The protocol was modified for NEBNext Multiplex Oligos for Illumina (NEB) from the original protocol (http://wasp.einstein.yu.edu/index.php/Protocol:HELP_tagging). Briefly, genomic DNA was digested by HpaII or MspI, the former only cutting at CCGG sequences where the central CG dinucleotide is unmethylated. AS and AE adapters were prepared by annealing two oligo DNAs separately. The first Illumina AE adapter was ligated to the compatible cohesive end created, juxtaposing an EcoP15I site beside the HpaII/MspI digestion site and allowing EcoP15I to digest within the flanking genomic DNA sequence. An A-overhang was created, allowing the ligation of the second Illumina AS adapter. This created both AE-insert-AS products and AS-insert-AS molecules. By performing a T7 polymerase-mediated in vitro transcription from a promoter sequence located on the AE adapter, we selectively enriched for the AE-insert-AS product as single-strand RNA. After cDNA synthesis by specific primers, PCR amplification was performed corresponding primer set. The quantification was performed by KAPA quantification kit.

treatment_protocol: The ES cells were FACS-sorted according to the fluorescent intensity of Emerald and centrifuged to collect. The cells were snap-frozen and stored in -80 C.

value: FACS sorted Emerald- ES cells

value: MC1 (129S6/SvEvTac)

tag: passages


title: tet-Zscan4 ES cells (Dox+; Zscan4-)

description: 5mC Zscan4-

data_processing:
Sequence tags for meDIP experiment were counted in 23946 peak regions identified previously for the H3K27ac chromatin modification. If the peak was shorter than 1 Kb, then the peak region was expanded to 1 Kb to get more sequence tags and enhance the statistical power of analysis. The number of sequence tags was then normalized by the total number of tags.
Genome_build: mm9
Supplementary_files_format_and_content: text

source_name: tet-Zscan4c ES cells

growth_protocol: tet-Zscan4c ES cells were cultured on gelatin-coated feeder-free plates in complete ES medium, DMEM (Gibco), 15% FBS (Atlanta Biologicals), 1000 U/ml leukemia inhibitory factor (LIF) (ESGRO, Chemicon), 1 mM sodium pyruvate, 0.1 mM non-essential amino acids (NEAA), 2 mM GlutaMAX, 0.1 mM beta-mercaptoethanol, and penicillin/streptomycin (50 U/50 µg/ml). Medium was changed daily and cells were split every 2 to 3 days routinely.

extract_protocol:
The genomic DNA isolated from tet-Zscan4c cells (Dox+/Dox-) were randomly sheared by sonication to generate DNA fragments between 300 and 1000 bp. The sonicated DNA (4 μg) was diluted in 450 μl TE, denatured for 10 minutes in boiled water and immediately cooled on ice for 10 minutes. The DNA was incubated with 10 μl of 5mC antibody in 51 μl of 10x IP buffer (100 mM Na-Phosphate pH 7.0, 1.4 M NaCl, 0.5 % Triton X-100) for 2 h at 4°C with shaking. 40 μl of Dynabeads was added to the sample and incubated for 2 hours at 4°C with shaking. The beads were washed with 700 μl of IP buffer for 10 minutes at RT three times, collected with a magnetic rack. After treatment with proteinase K, 5mC-antibody-enriched DNA was extracted and purified.
Library preparation was performed using ChIP-seq sample preparation kit (Illumina). Sequencing analysis was performed on the Illumina Genome Analyzer II according to the manufacturer’s instructions.

treatment_protocol: Zscan4-Flag was repressed in the complete ES medium supplemented with 1.5 µg/ml of Dox, but induced in the absence of Dox.

value: tet-Zscan4 Dox+ ES cells

tag: chip antibody

value: 5mC (Eurogentec #BI-MECY-1000)


title: MC1-ZE7 cells (Em+ high fraction) H3K9me2

description: H3K9me2 Em+

data_processing:
The sequence tags for H3K9me2 ChIP-seq were counted within 10 Kb regions (in 200 bp increments) centered at each of the 23946 peak regions identified previously for the H3K27ac chromatin modification (See GSE51679 under the SuperSeries). The number of sequence tags was then normalized by the total number of tags (i.e., it was divided by the total number of tags in each experiment and multiplied by the average total number of tags in all experiments). The data matrix is used in ploting the heat map in the associated paper.
Genome_build: mm9
Supplementary_files_format_and_content: text

source_name: MC1-ZE7 ES cells

extract_protocol:
FACS sorted MC1-ZE7 cells were cross-linked with 1% formaldehyde for 10 min at room temperature. The reaction was stopped by 125 mM glycin. The cells were washed with PBS and stored at –80°C prior to use. The cells were lysed in Lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS) containing proteinase inhibitor cocktail (Roche). Sonication was coducted with the Misonix sonicator XL to generate DNA fragments of approximately 150-450 bp. The sonicated lysates were diluted in ChIP dilution buffer (20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100) containing proteinase inhibitor cocktail and incubated overnight at 4°C with 30 µl of protein G magnetic beads (Invitrogen) that had been preincubated for 3 h with 3 µg of antibodies. The precipitants were washed three times with RIPA buffer (10 mM Tris-HCl, pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate) and once with 10 mM Tris-HCl, pH 8.0, 5 mM EDTA, 10 mM NaCl. Bound chromatin was eluted from the beads at 70°C, 1,300 r.p.m in Elution buffer (20 mM Tris-HCl, pH 7.5, 5 mM EDTA, 50 mM NaCl, 1% SDS), followed by crosslink reversal at 70°C for 6 h. After treatment with RNase A and proteinase K, DNA was purified by a phenol-chloroform-isoamylalcohol extraction and isopropanol precipitation.
Library preparation was performed using ChIP-seq sample preparation kit (Illumina) with several modifications as follows. A 1:30 dilution of the Adaptor Oligo Mix was used in the ligation step. A range of fragment size (200-300 bp) was selected by separation on a 2% low melting temperature agarose gel (Lonza). DNA purification in each reaction was carried out using AMPure XP beads (Beckman). In the experiment of second replication, PCR amplification were coducted prior to size selection and a range of fragment size (200-500 bp) was selected. Sequencing analysis was performed on the Illumina Genome Analyzer II according to the manufacturer’s instructions.

treatment_protocol: The ES cells were FACS-sorted according to the fluorescent intensity of Emerald.

value: FACS sorted Emerald+ ES cells

value: H3K9me2 (Abcam ab1220)


title: tet-Zscan4 ES cells (Dox-; Zscan4+)

description: 5mC Zscan4+

value: tet-Zscan4 Dox- ES cells


title: MC1-ZE7 cells (Em+ high fraction) Msp I

description:
pZscan4c-Emerald (Em+High) Msp I
library strategy: HELP tag sequencing


title: MC1-ZE7 cells (Em-) Hpa II

description:
pZscan4c-Emerald (Em-) Hpa II
library strategy: HELP tag sequencing


title: MC1-ZE7 cells (Em+ high fraction) H3K27ac rep1

description: H3K27ac Zscan4+ rep1

data_processing:
ChIP-seq reads were aligned to the mouse genome (mm9) using Bowtie with maximum 2 mismatches allowed and maximum number of matches in the genome <=10 (so that duplicated regions in the genome, such as Zscan4 gene cluster, are still covered by ChIP-seq reads). Redundant reads (that start from the same nucleotide) were removed. To compare genome-wide histone H3K27 acetylation we counted the number of tags per each 1 Kb interval in each replication of Zscna4+ and Zscan4- cells. Intervals that had <15 total reads in all were combined with neighboring genome intervals. Then, we used ANOVA with error variance adjustment (maximum of actual error variance and average error variance for genome segments with a similar number of total reads) using the algorithm of NIA Array Analysis6. The difference was considered statistically significant based on FDR <0.05, to account for multiple comparison tests. Genome regions with differential histone acetylation were associated with the genes based on the distance <100 Kb from the transcription start site (TSS). Genes located at distances >5 fold the minimal distance were not analyzed.
To identify peaks of H3K27ac we used HOMER findPeaks (http://biowhat.ucsd.edu/homer/ngs/index.html); peaks identified using "factor" and "histone" modes were combined for each ChIP-seq sample. Peaks wider than 2 Kb were not analyzed because they did not accurately predict genome locations. To select reproducible peaks, we selected for analysis only those peks that overlapped in both ChIP-seq replications either in Zscan4+ or Zscan4- cells. Peaks identified in Zscan4+ or Zscan4- cells were combined if they overlapped or were separated by <500 bp. Then ChIP-seq reads were counted in each peak, normalized by the total number of mapped non-redundatn sequence reads. The logratio of Em+/Em- was estimated for each peak, and then was used to sort the peaks.
Genome_build: mm9
Supplementary_files_format_and_content: peak files

value: H3K27ac (Active Motif #39133)


title: MC1-ZE7 cells (Em+ high fraction) H3K27ac rep2

description: H3K27ac Zscan4+ rep2


title: MC1-ZE7 cells (Em+ high fraction) Hpa II

description:
pZscan4c-Emerald (Em+High) Hpa II
library strategy: HELP tag sequencing


title: MC1-ZE7 cells (Em-) H3K9me2

description: H3K9me2 Em-


title: 30_After

city: Montreal

first: Mahmoud

last: Aarabi

state: Quebec

address: 1001 Boulevard Décarie

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
Full details can be found in Aarabi et al. (Hum. Mol. Genet. 2015). Briefly, eight samples of sperm DNA libraries were multiplexed for paired end sequencing in one lane of a HiSeq 2000 sequencer (Illumina) followed by initial data processing and alignment of reads by the software pipeline bsmap version 2.6. Analysis was based on 100 bp step-wise tiling windows, ≥2 CpG per tile as well as ≥10× CpG coverage of each tile per sample.
Genome_build: GRCh37
Supplementary_files_format_and_content: csv files include coordinates and normalized methylation values of differentially methylated tiles after folic acid supplementation with >2 CpGs and >10x sequencing coverage

source_name: Sperm

extract_protocol:
Sperm DNA was extracted using the QIAamp DNA Mini kit (QIAGEN, Mississauga, ON, Canada) according to the manufacturer’s protocols with minor modifications.
Full details can be found in Aarabi et al. (Hum. Mol. Genet. 2015). Briefly, ~500 ng of genomic DNA was digested with MspI, size selected, end-repaired, 3'-terminal A extended and ligated to Illumina adapters containing methylated cytosines, bilsufite converted using the EpiTect Bisulfite Kit (QIAGEN), PCR amplified with 20-25 cycles and sequenced.

tag: time point

value: After folic acid supplementation


title: 29_After


title: 30_Before

value: Before folic acid supplementation


title: MC1-ZE7 cells (Em-) H3K27ac rep2

description: H3K27ac Zscan4- rep2


title: 29_Before


title: 26_After


title: 25_After


title: 27_After


title: 27_Before


title: 28_After


title: 23_After


title: 23_Before


title: 26_Before


title: 22_After


title: 24_Before


title: 28_Before


title: 20_Before


title: 20_After


title: 22_Before


title: 19_After


title: 19_Before


title: 25_Before


title: 21_After


title: 24_After


title: 18_Before


title: 17_After


title: MC1-ZE7 cells (Em-) H3K27ac rep1

description: H3K27ac Zscan4- rep1


title: 18_After


title: 21_Before


title: 17_Before


title: 16_After


title: 15_After


title: 14_After


title: 15_Before


title: 14_Before


title: 13_After


title: 13_Before


title: 12_Before


title: 11_Before


title: 10_After


title: 5_After


title: 12_After


title: 10_Before


title: 6_Before


title: 5_Before


title: 7_After


title: 6_After


title: 4_Before


title: 3_After


title: 11_After


title: 2_Before


title: 1_After


title: 3_Before


title: MC1-ZE7 cells (Em-) rep2

description: Whole RNA-seq Em+

data_processing:
Paired-end RNA-seq reads were aligned to mouse genome mm10 using Bowtie-2. We used reads with quality score MAPQ >=6, maximum 2 mismatches, and maximum distance of 700 pb between 3' and 5' reads. Intersection of sequence reads with genes was evaluated using genomic coordinates of exons downloaded from the UCSC database (files refGene.txt, knownGene.txt, ensGene.txt, and wgEncodeGencodeCompVM2.txt). Finally we estimated FPKM based on gene length and total number of reads in each sample.
Genome_build: mm10
Supplementary_files_format_and_content: text,fpkm

extract_protocol:
Total RNA was extracted using Trizol solution (Roche) from individual cell populations separately. The extraction followed the manufacture’s instruction. Briefly, 200 ul chroloform was mixed with 1ml Trizol containing 3x10^6 cells, centrifuged and its aqueous phase was precipitated by isopropanol alcohol. The RNA pellet was washed by 70% ethanol and resolved in nuclease free water. The quality of total RNA was checked by Nanodrop (260/280=1.9-2.1, 260/230>2) and BioAnalyzer 2000 (RIN>7).
500 ng total RNA was used to remove rRNA, mtrRNA using TruSeq Stranded Total RNA with Ribo-Zero Gold Sample Prep Kit (Illumina). The cDNA was fragmented with alkaline-denatured fragmentation with 2min at 94 C, which produced the fragments with size 130-290 bp. The library was quantified by KAPA quantification kit and sequenced by HiSeq 2500.

treatment_protocol: The ES cells were FACS-sorted according to the fluorescent intensity of Emerald and centrifuged to collect. The cells were resolved in Trizol and stored in -80 C.


title: 16_Before


title: 1_Before


title: MC1-ZE7 cells (Em-) rep1

description: Whole RNA-seq Em+


title: MC1-ZE7 cells (Em+ high fraction) rep1

description: Whole RNA-seq Em-


title: NIH3T3_RRBS_EP12

description: processed data file: RRBS_CpG_methylation_call.txt

source_name: NIH3T3_RRBS_14-3-3ε-overexressing clone

value: Mouse embryonic fibroblast cell line


title: 7_Before


title: NIH3T3_RRBS_C2

source_name: NIH3T3_RRBS_control clone


title: ZUMA-0027

value: Blood


title: NIH3T3_RRBS_EP10


title: ZUMA-0026


title: 4_After


title: 2_After


title: MC1-ZE7 cells (Em+ high fraction) rep2

description: Whole RNA-seq Em-


title: HCC.high7

city: Yokohama

first: Kosuke

last: Hashimoto

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

country: Japan

institute: RIKEN

data_processing:
Basecalls performed using CASAVA version 1.8
Artificial sequences and ribosomal RNAs were identified and removed using TagDust and RNAdust.
Reads were aligned to the genome using BWA v0.5.9.
Transcription start sites (CAGE peaks) were identified using Paraclu.
Genome_build: hg19/GRCh37 for human and mm9/NCBI37 for mouse
Supplementary_files_format_and_content: Tab-delimited text files in the bed-like format including FDR, fold change, expression values (tpm) for 105 human samples

source_name: Mdr2-KO liver

extract_protocol:
Total RNA of tissues were extracted using mirVana kit (Ambion) and the quality of the RNA samples was assessed using Agilent RNA 6000 nano kit.
Total RNA was used to synthesize cDNA with random primers. Full-length cDNAs were biotinylated and captured by streptavidin-coated magnetic beads. The cDNAs were released from cap-trapped RNAs, ligated to 5' linkers including barcode sequences, and digested with EcoP15I. The detailed protocol is described in Ref [PMID:22362160]

value: Liver

tag: etiology/histology

tag: gender

value: male


title: FlagChIP_Rif1-Flag_taz1∆

city: Tokyo

first: Yutaka

last: Kanoh

address: 2-1-6 Kamikitazawa, Setagaya-ku

department: Genome Medicine

institute: Tokyo Metropolitan Institute of Medical Science

description:
taz1∆
Rif1ChIP_taz1delta.bedgraph

data_processing:
All fastq files were aligned to S.pombe reference genomic ASM294v2 from Pombase by Bowtie1.0.0 with defalt setting.
The generated SAM files by Bowtie were converted to BAM and sorted by Samtools.
Peaks were called with Model-based analysis of ChIP-seq (MACS2.0.10) using following parameters; macs2 callpeak -t ChIP.sam -c Input.sam -f SAM -g 1.4e107 -n result_file -B -q 0.01 --nomodel
The generated treat_pileup.bedgraph files were loaded on Integrated Genome Browser.
Genome_build: ASM294v2
Supplementary_files_format_and_content: bedgraph

organism: Schizosaccharomyces pombe

growth_protocol: The stains were grown until mid log phase in YES medium at 30ºC. Cells containing nda3-KM311 mutation were arrested at M-phase at 20ºC for 5 hr. Cells were released into sequential cell cycle at 30ºC.

extract_protocol:
The cell wall was disrupted by zirconia beads and multi-beads shocker (Yasui Kikai Co.). Lysates were prepared by sonication and clarified by centrifugation. Protein and DNA complexes were immuno-precipitated by antibody conjugated with Protein G Dynabeads.
BrdU-incorporated genomic DNA was purified by Qiagen Genomic-tip and genomic buffer set. Purified genomic DNA was sheared by sonication. The fragmented DNA was heat-denatured and BrdU-substituted DNA was immuno-precipitated by Anti-BrdU antibody conjugated with anti-IgG1a-dynabeads.
ChIP, BrdUIP, and Input DNA was sheared to around 150bp by S220 Focused-ultrasonicators (COVARIS, INC.). The fragmented DNA were end-repaired, ligated to sequencing adapters and amplified according to the protocol of NEBNext® ChIP-Seq Library Prep Master Mix Set and NEBNext Multiplex Oligos for Illumina (New England Biolabs) to prepare library. The size and concentration of libraries were checked by Bioanalyzer 2000 and real-time PCR using KAPA Library Quantification Kits, respectively.

treatment_protocol:
Cells during G1 phase were fixed with 1% Formaldehyde at 20min after release.
Cells were arrested at early S-phase in 25mM HU at 60min after release from M-phase arrest and then the early replicated regions were labeled with 200µg/ml BrdU.

tag: genotype/variation

tag: epitope-tag

tag: antibody

value: ANTI-FLAG M2 Monoclonal Antibody(Sigma), Subclass; IgG1, Clone; M2, Cat No.; F1804