title: WT female E4.5, repeat 3 [Rlim KO]


title: WT male Trophoblast, repeat 5 [Rlim KO]

status: Public on Oct 11 2016

type: SRA

city: Worcester

first: Ingolf

last: Bach

state: MA

address: 364 Plantation St

department: Molecular, Cell and Cancer Biology

country: USA

institute: University of Massachusetts Medical School

library_source: transcriptomic

data_processing:
The bcl2fastq 2.16.0.10 software package was used to convert base call (BCL) files generated on the NextSeq system to fastq files
Sequenced reads were aligned to the mouse genome (mm10) using TopHat (version 2.0.12) with default setting except set parameter read-mismatches to 2
HTSeq (version 0.6.1p1) was used to count the features after the alignment
Bioconductor packages edgeR (version 3.10.0 ) and ChIPpeakAnno (version 3.2.0)  for transcriptome quantification, differential gene expression analysis and annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include the raw count values from HTSeq for each sample

molecule: total RNA

organism: Mus musculus

source_name: Whole embryo

extract_protocol:
Whole embryos were dissected at the indicated timepoints and the correct stage was verified under the binocular. Single embryos/trophoblast cells were placed in 10ul TCL Buffer (Qiagen) supplemented with 1% BME, and snap frozen.
RNA libraries were prepared for sequencing using standard Illumina protocols.  A total of 187 samples were distributed on two 96-well plates (plus 5 mock wells) and thawed at RT for 10 minutes prior to RNA purification using Ampure RNA beads (Beckmann-Coulter). RNA samples were re-suspended in solution containing 3’ RT primer and dNTPs. Reverse transcription was performed with SSII (Life Technologies), whose terminal transferase activity allows incorporation of a PCR binding site at the 3’ end of the cDNA using a template-switching oligonucleotide (custom synthesized from Exiqon) as a template. Subsequently, cDNA was amplified using 12 cycles of PCR, followed by tagmentation with Nextera kit (Illumina). Final libraries were amplified by 12 cycles of PCR and sequenced on a NextSeq 500.

tag: strain

tag: genotype

value: WT

tag: Stage

value: Trophoblast

tag: gender

value: male


title: WT female E4.5, repeat 2 [Rlim KO]

value: female


title: WT male E4.5, repeat 3 [Rlim KO]


title: WT female E4.5, repeat 1 [Rlim KO]


title: KO female E4, repeat 4 [Rlim KO]

value: Rlim KO


title: KO female E4, repeat 3 [Rlim KO]


title: WT male E4.5, repeat 2 [Rlim KO]


title: KO female E4, repeat 2 [Rlim KO]


title: KO female E4, repeat 1 [Rlim KO]


title: WT male E4.5, repeat 1 [Rlim KO]


title: KO male E4, repeat 4 [Rlim KO]


title: KO male E4, repeat 1 [Rlim KO]


title: KO male E4.5, repeat 1 [Rlim KO]


title: KO male E4, repeat 2 [Rlim KO]


title: KO male E4, repeat 3 [Rlim KO]


title: WT female E4, repeat 2 [Rlim KO]


title: WT female E4, repeat 3 [Rlim KO]


title: WT male E4, repeat 2 [Rlim KO]


title: KO female E3.5, repeat 1 [Rlim KO]


title: KO male E3.5, repeat 4 [Rlim KO]


title: WT male E4, repeat 1 [Rlim KO]


title: KO male E4, repeat 6 [Rlim KO]


title: WT female E4, repeat 1 [Rlim KO]


title: KO male E3.5, repeat 3 [Rlim KO]


title: KO male E3.5, repeat 2 [Rlim KO]


title: KO male E3.5, repeat 1 [Rlim KO]


title: KO female E3.5, repeat 5 [Rlim KO]


title: WT female E3.5, repeat 5 [Rlim KO]


title: WT female E3.5, repeat 4 [Rlim KO]


title: WT female E3.5, repeat 2 [Rlim KO]


title: WT female E4, repeat 4 [Rlim KO]


title: KO male E4.5, repeat 5 [Rlim KO]


title: KO male E4, repeat 5 [Rlim KO]


title: WT male E3.5, repeat 12 [Rlim KO]


title: WT female E3.5, repeat 1 [Rlim KO]


title: WT female E4, repeat 5 [Rlim KO]


title: KO male E3.5, repeat 5 [Rlim KO]


title: WT female E3.5, repeat 3 [Rlim KO]


title: KO female E3.5, repeat 3 [Rlim KO]


title: WT male E3.5, repeat 9 [Rlim KO]


title: WT male E3.5, repeat 10 [Rlim KO]


title: WT male E3.5, repeat 8 [Rlim KO]


title: WT male E3.5, repeat 11 [Rlim KO]


title: WT male E3.5, repeat 6 [Rlim KO]


title: WT male E3.5, repeat 3 [Rlim KO]


title: WT male E3.5, repeat 1 [Rlim KO]


title: WT male E3.5, repeat 5 [Rlim KO]


title: WT male E3.5, repeat 2 [Rlim KO]


title: KO female E3, repeat 3 [Rlim KO]


title: WT male E3.5, repeat 4 [Rlim KO]


title: KO female E3, repeat 5 [Rlim KO]


title: WT male E3.5, repeat 7 [Rlim KO]


title: KO female E3, repeat 1 [Rlim KO]


title: 30hRC_HVpSp_Input_Rep2

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

library_source: genomic

data_processing:
Illumina RTA software (v2.7.3) was used for basecalling and quality control.
Illumina BCL2 FASTQ (v2.16) was used to convert .bcl files into .fastq files and demultiplex the sequence data.
bowtie2 (version 2.2.9 for windows) was used to align the reads to the mm9 mouse genome using standard paramaters.
The obtained SAM files were processed using HOMER v4.8.3. HOMER tag directories were created using the ‘makeTagDirectory’ tool with the options -unique and -fragLength 150. The HOMER function ‘removeOutOfBoundsReads.pl’ was used to remove tags which overlapped the ends of the chromosome to prevent downstream processing problems. These tag directories were used to create bedgraphs using the ‘makeUCSCfile’ tool with the following options: -pseudo 1 -norm 1e8 -avg -log -fragLength 300 -inputFragLength 300. The –i option was used to indicate the input directory with which to compare its respective IP directory. Bedgraphs were subsequently converted into browser viewable bigwig (.bw) files using the ‘bedGraphToBigWig’ utility in UCSC hosted toolset (userApps.v333; http://hgdownload.soe.ucsc.edu/admin/exe/).
Genome_build: mm9
Supplementary_files_format_and_content: bigWig genome browser file

molecule: genomic DNA

source_name: ES cells. Ssea1+ fraction sorted after 30h of re-culture from the HV+S+ popultation.

growth_protocol: HV5.1 ES cells (Derived from E14 Tg2a ESCs - 129/Ola background - Canham et al., 2010) were cultured on 0.1% gelatin (Sigma G1890) coated Corning flasks in ESC medium (GMEM - Sigma G5154) supplemented with 10% fetal calf serum (FCS), 1x MEM non-essential amino acids (Life Technologies 11140-036), 0.1 μM 2-Mercaptoethanol (Sigma M6250), 2 mM L-Glutamine (Life Technologies 25030-024), 1 mM Sodium Pyruvate (Life Technologies 11360-039), and 1,000 U/ml of Lif. For passaging, 60-90% confluent culture flasks were washed in PBS, incubated for 2-3 mins at 37°C in attenuated trypsin (0.025% trypsin - (Invitrogen 15090-046), 1.27 mM EDTA and 1% Chicken serum (Sigma C5405) in PBS (Sigma D8537)), and tapped to release ESCs from the flasks. Attenuated trypsin was inactivated by adding nine volumes of ESC medium and this mixture was repeatedly pipetted to obtain a single cell suspension. ESCs were centrifuged, resuspended in ESC medium and replated onto gelatin coated flasks at a ratio of between 1:2 and 1:10, or at ~5 x 10^4 cells/cm^2. All centrifugation steps with live cells were performed at 330g for 3 min at room temperature (RT).

extract_protocol:
Approximately 0.5-2 x 10^6 FACS purified ESCs were centrifuged at 500 g for 3 min, washed twice with RT PBS and resuspended in 200 µl of culture media. Cells were fixed by the addition of an equal volume of culture media containing 2 % methanol free formaldehyde (Thermo Scientific Pierce PN28906; final concentration of 1 %) and incubated at RT for 10 min. Fixation was stopped by 5 min incubation with 125 mM glycine at room temperature. Cells were washed in PBS prior to short-term storage at -80 °C.   All of the following buffers were supplemented with the following just prior to use: 1 mM DTT and 1 x Protease inhibitors (Calbiochem - 539134-1SET). Cell pellets were resuspended in lysis buffer 1 (50 mM Tris-HCl pH 8.1, 10 mM EDTA and 20 % SDS) and incubated for 10 min at 4 °C. Lysates were diluted 1:10 in ChIP dilution buffer (0.1 % Triton X-100, 2mM EDTA, 150 mM NaCl, 20 mM and Tris-HCl pH 8.1) and sonicated with a single 30 s pulse using a soniprep 150 plus (MSE; set to 3.5) followed by a further 7 pulses using a chilled Bioruptor (Diagenode; 1 min cycles of 30 sec on / 30 sec off on ‘high’ setting at 4 °C). The sonicated extract was pre-cleared by centrifugation at 16,000 g for 10 min at 4 °C. The supernatant was transferred to a fresh tube and supplemented with BSA and triton X-100 to a final concentration of 25 mg/ml and 1 % respectively. 10 % of the IP volume of the chromatin was retained as an input reference. Anti-H3K27me3 antibody (Millipore 07-449) was pre-coupled to protein A Dynabeads (Life Technologies; 10001D) at a ratio of 1 µg antibody per 5 µl of dynabeads. Antibody-bound beads were added to the fragmented chromatin at 1 µg antibody per million cell equivalents and incubated for 10 h on a rotating wheel at 4 ºC. Bead-associated immune complexes were washed once with IP buffer, three times with wash buffer 1 (150 mM NaCl, 10 mM TrisHCl pH 8, 2 mM EDTA, 1% NP40 and 1 % sodium deoxycholate) and twice in 1x TE buffer (10mM Tris pH8 and 10mM EDTA). Each wash was performed at 4ºC on a rotating wheel for 10 min. Chromatin was released from the beads by incubation with elution buffer (0.1 M NaHCO3 and 1 % SDS) for 15 min at 37 ºC followed by the addition of RNaseA and Tris pH 6.8 (final concentration of 20 mg/ml and 100 mM respectively) and incubation at 65ºC for 2 hours followed by the addition of 50 µg of proteinase K and incubation at 65ºC for a further 4-6 h to degrade proteins and reverse the cross-links. Dynabeads were removed using a magnetic rack and the chromatin purified using PCR Purification columns (Qiagen) according to manufacturer’s instructions.
Libraries were prepared as previously described (Bowman et al., 2013 - PMID: 23837789) with the following modifications. No purification was performed between the A-tailing reaction and the ligation reactions; instead the ligation was supplemented with ligation reagents (400 U of T4 DNA ligase (NEB), 1 x buffer 2 (NEB), 7.5 % PEG-6000, 1 mM ATP and 13.3 nM of annealed Illumina adaptors (AU)) and incubated at 25 °C for 90 min. Size selection purifications following the ligation and amplification PCR steps were performed with 1x and 0.8 x reaction volumes of Agencourt AMPure XP beads (Beckman Coulter - A63880). Library amplification was performed using Illumina index primers and amplified with NEBNext High-Fidelity 2X PCR Master Mix (M0541S). 4 or 5 samples were multiplexed per single Illumina HiSeq 4000 lane. libraries were seqenced as 50bp single end reads on an Illumina HiSeq 4000.

treatment_protocol: For cell surface marker analysis by flow cytometry, 60-90% confluent ESC cultures were trypsinized and subsequently inactivated using nine volumes of FC buffer (10% FCS in PBS). After obtaining a single cell suspension, cells were centrifuged and resuspended in Ssea1 Mouse anti-Mouse IgM-kappa primary antibody (clone MC480; Developmental Studies Hybridoma Bank; 1:1500 in FC buffer) and incubated on ice for 15 mins. After two washes in ice cold FC buffer (10% FCS in PBS), cells were incubated in alexa647-conjugated Goat anti-Mouse secondary antibody (Molecular Probes A21238; 1:1000 in FC buffer) on ice for 15 mins, washed twice in FC buffer, and resuspended in 1 μg/ml DAPI in FC buffer to label dead cells. E14 ESCs labeled with secondary antibody and DAPI were used as negative controls. Forward and side scatter were used to filter out debris and cell clumps and DAPI staining was used to remove dead cells. Cells were run through a cell strainer (Corning 352235) prior to sorting on a BD FACSAriaIII. Sorted cells were collected at 4°C in 15 ml falcon tubes (Corning 352054) containing FC buffer. Different populations used in the same experiment were collected simultaneously and when multiple tubes of sorted cells were required, full tubes were stored on ice and pooled at the end of the sorting session. Sorted cells were checked for sufficient purity (>80% of cells detected as being in the original sorting gate) by running ~1000 cells through the sorter again.

tag: cell type

value: mESC. HhexVenus Reporter line derived from E14Tg2a cells.

tag: purification antibody

value: None - Input material


title: 30hRC_HVnSp_Input_Rep2

source_name: ES cells. Ssea1+ fraction sorted after 30h of re-culture from the HV-S+ popultation.


title: 30hRC_HVpSp_H3K27me3_ChIP_Rep2

value: anti-H3K27me3 (07-449; Millipore)


title: 30hRC_HVpSp_Input_Rep1


title: KO female E3.5, repeat 2 [Rlim KO]


title: KO male E3, repeat 4 [Rlim KO]


title: KO male E3, repeat 3 [Rlim KO]


title: KO male E3, repeat 2 [Rlim KO]


title: 30hRC_HVpSp_H3K27me3_ChIP_Rep1


title: KO male E3, repeat 1 [Rlim KO]


title: KO female E3, repeat 4 [Rlim KO]


title: WT female E3, repeat 4 [Rlim KO]


title: 30hRC_HVnSp_H3K27me3_ChIP_Rep1


title: WT female E3, repeat 3 [Rlim KO]


title: HVpSn_H3K27me3_ChIP

source_name: ES cells. HV+S- FACs sorted population


title: KO female E3, repeat 2 [Rlim KO]


title: HVpSp_Input_Rep2

source_name: ES cells. HV+S+ FACs sorted population


title: HVnSp_Input_Rep2

source_name: ES cells. HV-S+ FACs sorted population


title: WT male E3, repeat 9 [Rlim KO]


title: 30hRC_HVnSp_Input_Rep1


title: WT male E3, repeat 8 [Rlim KO]


title: WT female E3, repeat 2 [Rlim KO]


title: WT male E3, repeat 7 [Rlim KO]


title: HVnSp_Input_Rep1


title: HVnSp_H3K27me3_ChIP_Rep2


title: WT male E3, repeat 4 [Rlim KO]


title: WT male E3, repeat 3 [Rlim KO]


title: 30hRC_HVnSp_H3K27me3_ChIP_Rep2


title: HVpSp_H3K27me3_ChIP_Rep1


title: HVnSp_H3K27me3_ChIP_Rep1


title: WT male E3, repeat 6 [Rlim KO]


title: WT male E3, repeat 5 [Rlim KO]


title: KO female E2.5, repeat 6 [Rlim KO]


title: KO female E2.5, repeat 5 [Rlim KO]


title: HVpSn_Input_Rep


title: KO female E2.5, repeat 4 [Rlim KO]


title: WT male E3, repeat 1 [Rlim KO]


title: HVpSp_Input_Rep1


title: KO female E2.5, repeat 3 [Rlim KO]


title: KO male E2.5, repeat 2 [Rlim KO]


title: KO female E2.5, repeat 1 [Rlim KO]


title: KO female E2.5, repeat 2 [Rlim KO]


title: HVpSp_H3K27me3_ChIP_Rep2


title: WT male E3, repeat 2 [Rlim KO]


title: KO male E2.5, repeat 1 [Rlim KO]


title: WT female E2.5, repeat 5 [Rlim KO]


title: WT female E2.5, repeat 4 [Rlim KO]


title: WT female E2.5, repeat 3 [Rlim KO]


title: WT female E2.5, repeat 2 [Rlim KO]


title: WT female E2.5, repeat 6 [Rlim KO]


title: WT female E2.5, repeat 1 [Rlim KO]


title: WT male E2.5, repeat 6 [Rlim KO]


title: WT male E2.5, repeat 5 [Rlim KO]


title: WT male E2.5, repeat 4 [Rlim KO]


title: WT male E2.5, repeat 1 [Rlim KO]


title: WT male E2.5, repeat 2 [Rlim KO]


title: KO female 8 cell, repeat 4 [Rlim KO]

value: 8 cell


title: WT male E2.5, repeat 3 [Rlim KO]


title: WT female E3, repeat 1 [Rlim KO]


title: SETDB1KO_rep2

city: Cambridge

first: Richard

last: Timms

address: Cambridge Biomedical Campus, Hills Road

department: CITIID, Department of Medicine

institute: University of Cambridge

data_processing:
Reads trimmed of adaptor sequences using Trim Galore
Aligned to the reference human genome using HISAT2
Uniquely mapping reads imported into SeqMonk and analysed using the RNA-seq quantiation pipeline and DEseq
Genome_build: GRCh37
Supplementary_files_format_and_content: Raw read counts for genes with DEseq FDR < 0.05

organism: Homo sapiens

source_name: HeLa cells

growth_protocol: RPMI 1640

extract_protocol:
miRNeasy kit (Qiagen) with on-column DNaseI digestion
Ribo-Zero Gold rRNA depletion (Epicentre) followed by TruSeq Stranded Total RNA Library Prep (Illumina)

tag: genotype/variation

value: SETDB1 KO

tag: cell line

value: HeLa


title: KO male 8 cell, repeat 4 [Rlim KO]


title: KO male 8 cell, repeat 6 [Rlim KO]


title: KO male 8 cell, repeat 5 [Rlim KO]


title: KO female 8 cell, repeat 1 [Rlim KO]


title: KO male 8 cell, repeat 3 [Rlim KO]


title: KO female 8 cell, repeat 3 [Rlim KO]


title: SETDB1KO_rep3


title: SETDB1KO_rep1


title: KO male 8 cell, repeat 2 [Rlim KO]


title: KO male 8 cell, repeat 1 [Rlim KO]


title: ATF7IPKO_rep2

value: ATF7IP KO


title: ATF7IPKO_rep3


title: WT female 8 cell, repeat 9 [Rlim KO]


title: Wild-type_rep2

value: Wild-type


title: WT female 8 cell, repeat 6 [Rlim KO]


title: Wild-type_rep1


title: ATF7IPKO_rep1


title: WT female 8 cell, repeat 8 [Rlim KO]


title: KO female 8 cell, repeat 2 [Rlim KO]


title: SETDB1 KO

data_processing:
Reads trimmed of adaptor sequences using Trim Galore
Aligned to the reference human genome using Bowtie2
Uniquely mapping reads imported into SeqMonk
H3K9me3 scores generated for a series of 1 kb windows across the genome, discounting windows with low H3K9me3 levels (<40 reads in wild-type cells)
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel spreadsheet listing H3K9me3 scores for 1 kb windows across the genome

extract_protocol:
Formaldehye-crosslinked chromatin was sheared by sonication to an average size of ~300bp and then immunoprecipitated with anti-H3K9me3 antibody ab8898 (Abcam)
NEBNext ChIP-seq Library Prep Kit (NEB)

tag: antibody

value: anti-H3K9me3, ab8898 (Abcam)


title: Wild-type_rep3


title: WT female 8 cell, repeat 3 [Rlim KO]


title: WT female 8 cell, repeat 7 [Rlim KO]


title: ATF7IP KO


title: HVpos_Ssea1pos_GROseq

description:
HVpos_GROseq
GRO-Seq

data_processing:
Basecalls performed using CASAVA version 1.9
Reads were aligned to the mm9 genome assembly using Bowtie2 version (2.1.0) with the following configurations -x -U -S.
Bowtie output SAM files were converted into sorted BAM files using the view (parameters -bSh) and sort functions in SAM tools (version 0.1.19).
processed data files format and content: wig (aka bedgraph) files were generated using the genomeCoverageBed function in bedTools (version 2.17.0) using parameters -ibam -g -bg. Replicate samples were combined into a single file by summing the read depths across each experiment at bp resolution. Scores represent raw read depth.
Genome_build: mm9

growth_protocol: E14 Tg2a ESCs (129/Ola background) and the derivative line HV5.1 (Canham et al., 2010) were cultured on 0.1% gelatin (Sigma G1890) coated Corning flasks in ESC medium (GMEM (Sigma G5154) supplemented with 10% foetal calf serum (FCS), 1x MEM non-essential amino acids (Life Technologies 11140-036), 0.1 μM 2-Mercaptoethanol (Sigma M6250), 2 mM L-Glutamine (Life Technologies 25030-024), 1 mM Sodium Pyruvate (Life Technologies 11360-039), and 1,000 U/ml of Lif. For passaging, 60-90% confluent culture flasks were washed in PBS, incubated for 2-3 mins at 37°C in attenuated trypsin (0.025% trypsin (Invitrogen 15090-046), 1.27 mM EDTA, and 1% Chicken serum (Sigma C5405) in PBS (Sigma D8537)), and tapped to release ESCs from the flasks. Attenuated trypsin was inactivated by adding nine volumes of ESC medium and this mixture was repeatedly pipetted to obtain a single cell suspension. ESCs were centrifuged, resuspended in ESC medium and replated onto gelatin coated flasks at a ratio of between 1:2 and 1:10, or at ~5 x 104 cells/cm2. All centrifugation steps with live cells were performed at 330g for 3 min at room temperature (RT).

extract_protocol:
All buffers were supplemented with RNasin Plus inhibitor to a final concentration of 80U/ml (Promega; N2611). Nuclei were prepared from FACS purified ESCs (3.5x10^6 per assay). ESCs were centrifuged at 500g for 3 mins, washed twice in ice-cold PBS and then resuspended in 200ml of NBA buffer (85mM NaCl, 5.5% Sucrose, 10 mM TrisHCl pH 7.5, 0.2 mM EDTA, 0.2 mM PMSF, 1 mM DTT, 1x Protease inhibitors (Calbiochem, 539134-1SET )). Cells were lysed by the addition of an equal volume of NBB buffer (NBA + 0.1% NP40; SigmaAldrich - I8896) followed by incubation on ice for 3 mins. Nuclei were recovered by centrifugation at 1000g and incubated in run-on reaction buffer (50 mM Tris-HCl pH 7.5, 10 mM MgCl2, 150 mM NaCl, 25% Glycerol, 0.5 mM ATP, 0.5 mM CTP, 0.5 mM GTP, 20mM BrUTP, 2 mM DTT and 1x Protease inhibitors (Calbiochem, 539134-1SET )) for 5 min at room temperature. In parallel un-sorted HV cells were incubated in run-on buffer with either BrUTP or UTP (required to control for background RNA signal in the immunoprecipitation). Stop buffer (20mM Tris pH7.5, 330mM NaCl, 12mM EDTA, 1.2% SDS and 40mgs/ml proteinase K) was added to 5x the reaction volume of each sample and incubated for 1 hr at 37°C. Each reaction was sonicated for a single 30 second pulse on high setting using a water bath sonicator at 4°C (Diagenode Bioruptor). RNAs were recovered by acid phenol extraction and isopropanol precipitation followed by DNA digestion (DNA-free kit, Ambion). Br-UTP-incorporated transcripts were immunoprecipitated using a monoclonal anti-BrdU antibody (Sigma B2531) and the isolated RNA reverse transcribed into single stranded DNA using SuperScript III Reverse Transcriptase followed by second strand synthesis using SuperScript Double-Stranded cDNA Synthesis Kit (Life Technologies; 18080044 and 11917-101 respectively).
GRO-seq libraries were prepared as previously described (Bowman et al., 2013; PMID 23837789) with the following modifications. No purification was performed between the A-tailing reaction and the ligation reactions; instead the ligation was supplemented with the ligation components:400 U of T4 DNA ligase (NEB), 1x buffer 2 (NEB), 7.5% PEG-6000, 1mM ATP and 13.3nM of annealed Illumina adaptors (PE or AU). Size selection purifications following the ligation and amplification PCR steps were performed with 1x and 0.8x reaction volumes of Agencourt AMPure XP beads (Beckman Coulter - A63880). Multiplexing was performed using multiplex primers 1-6 as described by Bowman et al (Bowman et al., 2013; PMID 23837789)

treatment_protocol: For cell surface marker analysis by flow cytometry, 60-90% confluent ESC cultures were trypsinized and subsequently inactivated using nine volumes of FC buffer (10% FCS in PBS). After obtaining a single cell suspension, cells were centrifuged and resuspended in Ssea1 Mouse anti-Mouse IgM-kappa primary antibody (clone MC480; Developmental Studies Hybridoma Bank; 1:1500 in FC buffer) and incubated on ice for 15 mins. After two washes in ice cold FC buffer (10% FCS in PBS), cells were incubated in alexa647-conjugated Goat anti-Mouse secondary antibody (Molecular Probes A21238; 1:1000 in FC buffer) on ice for 15 mins, washed twice in FC buffer, and resuspended in 1 μg/ml DAPI in FC buffer to label dead cells. E14 ESCs labelled with secondary antibody and DAPI were used as negative controls. Forward and side scatter were used to filter out debris and cell clumps and DAPI staining was used to remove dead cells. Cells were run through a cell strainer (Corning 352235) prior to sorting on a BD FACSAriaIII. Sorted cells were collected at 4°C in 15 ml falcon tubes (Corning 352054) containing FC buffer. Different populations used in the same experiment were collected simultaneously and when multiple tubes of sorted cells were required, full tubes were stored on ice and pooled at the end of the sorting session. Sorted cells were checked for sufficient purity (>80% of cells detected as being in the original sorting gate) by running ~1000 cells through the sorter again.

value: mESCs. HexVenus Reporter line derived from E14Tg2a cells.

value: anti-BrdU antibody (Sigma B2531)


title: Wild-type


title: WT female 8 cell, repeat 1 [Rlim KO]


title: T14: uRCC with wildtype NF2

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The output data (FASTQ files) are mapped to the target genome using the rnaStar aligner [Dobin2012] that maps reads genomically and resolves reads across splice junctions.  We use the 2 pass mapping method outlined in [Engström2013] in which the reads are mapped twice. The first mapping pass uses a list of known annotated junctions from Ensemble. Novel junctions found in the first pass are then added to the known junctions and a second mapping pass is done.
After mapping we compute the expression count matrix from the mapped reads using HTSeq (www-huber.embl.de/users/anders/HTSeq) and one of several possible gene model databases.
The raw count matrix generated by HTSeq are then be processed using the R/Bioconductor package DESeq (www-huber.embl.de/users/anders/DESeq) which is used to both normalize the full dataset and analyze differential expression between sample groups.
Program versions: htseq/HTSeq-0.5.3, picard/picard-tools-1.124, R/R-3.2.0, star/STAR-STAR_2.5.0a, samtools/samtools-0.1.19
Genome_build: UCSC HG19

source_name: tumor tissue

extract_protocol:
Total RNA was purified from tumor tissues using mirVana™ miRNA Isolation Kit (Ambion) according to the manufacturer's instruction for total RNA isolation.
RNA samples are used for Hi-Seq library construction with the TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer’s instructions.

tag: tissue

value: Renal cell carcinoma

tag: histology

value: unclassified


title: HVpos_Ssea1pos_Input

data_processing:
Basecalls performed using CASAVA version 1.9
Reads were aligned to the mm9 genome assembly using Bowtie2 version (2.1.0) with the following configurations -x -U -S.
Bowtie output SAM files were converted into sorted BAM files using the view (parameters -bSh) and sort functions in SAM tools (version 0.1.19). Duplicated reads were removed using the rmdup function (parameters: -s).
processed data files format and content: wig (aka bedgraph) files were generated using the genomeCoverageBed function in bedTools (version 2.17.0) using parameters -ibam -g -bg. Replicate samples were combined into a single file by summing the read depths across each experiment at bp resolution.  Scores represent raw read depth.
Genome_build: mm9

extract_protocol:
Approximately 1 x 10^6 FACS purified ESCs were centrifuged at 500g for 3 mins, washed twice in ice-cold PBS and were resuspended in 200ml of NBA buffer (85mM NaCl, 5.5% Sucrose, 10 mM TrisHCl pH 7.5, 0.2 mM EDTA, 0.2 mM PMSF, 1 mM DTT, 1x Protease inhibitors (Calbiochem, 539134-1SET )). Cells were lysed by the addition of an equal volume of NBB buffer (NBA + 0.1% NP40; SigmaAldrich - I8896) followed by incubation on ice for 3 mins. Nuclei were pelleted at 1000g for 3 mins at 4ºC, then washed with NBR buffer (85 mM NaCl, 5.5% Sucrose, 10 mM TrisHCl pH 7.5, 3 mM MgCl2, 1.5 mM CaCl2, 0.2 mM PMSF and 1 mM DTT) and pelleted at 2000g for 3 mins at 4ºC. Nuclei were resuspended in NBR supplemented with RNaseA (to 20mg/ml) at a concentration of 16.7x10^6 nuclei per ml and incubated at 20 ºC for 5 mins. Chromatin was then fragmented for 10 mins at 20 ºC with the addition of 0.133 U/μl micrococcal nuclease (Boehringer units; SigmaAldrich - N3755-500UN; titrated to give predominantly mono-nucleosomes). Micrococcal Digestion was stopped with the addition of an equal volume of STOP buffer (215 mM NaCl, 10 mM TrisHCl pH 8, 20 mM EDTA, 5.5 %, Sucrose, 2 % TritonX 100, 0.2 mM PMSF, 1 mM DTT, 2X Protease Inhibitors). Digested nuclei were left on ice overnight to release soluble, fragmented chromatin. Chromatin was then centrifuged at 12,000g for 10 mins at 4ºC and the soluble chromatin (supernatant) transferred to a fresh tube. 20% of the released chromatin was retained as an input reference.
ChIP libraries were prepared as previously described (Clouaire et al., 2012; PMID 22855832) with the following modifications. The end repair step was removed and the A-tailing reaction (reaction 2) was supplemented with 10 U of Polynucleotide Kinase (NEB) and 1mM ATP. Following heat inactivation, the samples were supplemented with ligation reagents (400 U of T4 DNA ligase (NEB), 1x buffer 2 (NEB), 7.5% PEG-6000, 1mM ATP and 13.3nM of annealed Illumina adaptors (PE or AU)) and incubated at 16°C overnight. Ligated DNA was purified using MinElute PCR columns (Qiagen) and eluted in 2x10 μl water. Purified libraries were amplified as previously described (Clouaire et al., 2012) and DNA fragments corresponding to mono- to tri-nucleosomes excised from an agarose gel and purified using the QIAEX II gel extraction kit according to manufacturer’s instructions (Qiagen).

value: non-immunoprecipitated input material


title: HVneg_Ssea1pos_Input

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to the mm9 genome assembly using Bowtie2 version (2.1.0) with the following configurations -x -U -S.
Bowtie output SAM files were converted into sorted BAM files using the view (parameters -bSh) and sort functions in SAM tools (version 0.1.19). Duplicated reads were removed using the rmdup function (parameters: -s).
processed data files format and content: wig (aka bedgraph) files were generated using the genomeCoverageBed function in bedTools (version 2.17.0) using parameters -ibam -g -bg. Replicate samples were combined into a single file by summing the read depths across each experiment at bp resolution.  Scores represent raw read depth.
Genome_build: mm9


title: HVpos_Ssea1pos_H3K27me3_ChIP

data_processing:
Basecalls performed using CASAVA version 1.9
Reads were aligned to the mm9 genome assembly using Bowtie2 version (2.1.0) with the following configurations -x -U -S.
Bowtie output SAM files were converted into sorted BAM files using the view (parameters -bSh) and sort functions in SAMtools (version 0.1.19).
processed data files format and content: wig (aka bedgraph) files were generated using the genomeCoverageBed function in bedTools (version 2.17.0) using parameters -ibam -g -bg.  Scores represent raw read depth.
Genome_build: mm9

extract_protocol:
Approximately 1 x 10^6 FACS purified ESCs were centrifuged at 500g for 3 mins, washed twice in ice-cold PBS and were resuspended in 200ml of NBA buffer (85mM NaCl, 5.5% Sucrose, 10 mM TrisHCl pH 7.5, 0.2 mM EDTA, 0.2 mM PMSF, 1 mM DTT, 1x Protease inhibitors (Calbiochem, 539134-1SET )). Cells were lysed by the addition of an equal volume of NBB buffer (NBA + 0.1% NP40; SigmaAldrich - I8896) followed by incubation on ice for 3 mins. Nuclei were pelleted at 1000g for 3 mins at 4ºC, then washed with NBR buffer (85 mM NaCl, 5.5% Sucrose, 10 mM TrisHCl pH 7.5, 3 mM MgCl2, 1.5 mM CaCl2, 0.2 mM PMSF and 1 mM DTT) and pelleted at 2000g for 3 mins at 4ºC. Nuclei were resuspended in NBR supplemented with RNaseA (to 20mg/ml) at a concentration of 16.7x10^6 nuclei per ml and incubated at 20 ºC for 5 mins. Chromatin was then fragmented for 10 mins at 20 ºC with the addition of 0.133 U/μl micrococcal nuclease (Boehringer units; SigmaAldrich - N3755-500UN; titrated to give predominantly mono-nucleosomes). Micrococcal Digestion was stopped with the addition of an equal volume of STOP buffer (215 mM NaCl, 10 mM TrisHCl pH 8, 20 mM EDTA, 5.5 %, Sucrose, 2 % TritonX 100, 0.2 mM PMSF, 1 mM DTT, 2X Protease Inhibitors). Digested nuclei were left on ice overnight to release soluble, fragmented chromatin. Chromatin was then centrifuged at 12,000g for 10 mins at 4ºC and the soluble chromatin (supernatant) transferred to a fresh tube. 20% of the released chromatin was retained as an input reference and the remainder incubated for 3 hours at 4ºC on a rotating wheel with anti-H3K27me3 (07-449; Millipore) antibody pre-coupled to protein A dynabeads (Life Technologies; 10002D; 1mgs of antibody bound to 10ml of dynabeads slurry per immunoprecipitation). Immune complexes bound to beads were washed three times with wash buffer 1 (150 mM NaCl, 10 mM TrisHCl pH 8, 2 mM EDTA, 1% NP40 and 1 % sodium deoxycholate) and twice in 1x TE buffer (10mM Tris pH8 and 10mM EDTA) at 4ºC on a rotating wheel for 10 mins. Chromatin was released from the beads by incubation with elution buffer (0.1 M NaHCO3 and 1 % SDS) for 15 mins at 37 ºC followed by the addition of proteinase K and Tris pH6.8 (final concentration of 100ug/ml and 100mM respectively) and incubation at 55ºC overnight. Dynabeads were removed using a magnetic rack and the chromatin purified using MinElute PCR Purification columns (Qiagen) according to manufacturer’s instructions.
ChIP libraries were prepared as previously described (Clouaire et al., 2012; PMID 22855832) with the following modifications. The end repair step was removed and the A-tailing reaction (reaction 2) was supplemented with 10 U of Polynucleotide Kinase (NEB) and 1mM ATP. Following heat inactivation, the samples were supplemented with ligation reagents (400 U of T4 DNA ligase (NEB), 1x buffer 2 (NEB), 7.5% PEG-6000, 1mM ATP and 13.3nM of annealed Illumina adaptors (PE or AU)) and incubated at 16°C overnight. Ligated DNA was purified using MinElute PCR columns (Qiagen) and eluted in 2x10 μl water. Purified libraries were amplified as previously described (Clouaire et al., 2012) and DNA fragments corresponding to mono- to tri-nucleosomes excised from an agarose gel and purified using the QIAEX II gel extraction kit according to manufacturer’s instructions (Qiagen).


title: WT male 8 cell, repeat 5 [Rlim KO]

value: WT

value: male


title: T04: uRCC with wildtype NF2


title: WT female 8 cell, repeat 2 [Rlim KO]

value: female


title: WT male 8 cell, repeat 4 [Rlim KO]


title: T15: uRCC with NF2-loss


title: T13: uRCC with wildtype NF2


title: HVneg_Ssea1pos_GROseq

description:
HVneg_GROseq
GRO-Seq

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to the mm9 genome assembly using Bowtie2 version (2.1.0) with the following configurations -x -U -S.
Bowtie output SAM files were converted into sorted BAM files using the view (parameters -bSh) and sort functions in SAM tools (version 0.1.19).
processed data files format and content: wig (aka bedgraph) files were generated using the genomeCoverageBed function in bedTools (version 2.17.0) using parameters -ibam -g -bg. Replicate samples were combined into a single file by summing the read depths across each experiment at bp resolution. Scores represent raw read depth.
Genome_build: mm9


title: WT female 8 cell, repeat 5 [Rlim KO]


title: C2_8w

city: Yokohama

first: Kosuke

last: Miyauchi

state: Kanagawa

address: 1-7-22 Suehiro-sho

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

data_processing:
Read alignment: TopHat2 v2.0.8 with default settings
expression level: Cufflinks v2.1.1 with default settings
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

source_name: Skin

extract_protocol:
Skin were removed, treated with RNALater, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Skin

tag: age

value: 8 weeks


title: C2_5w

value: 5 weeks


title: WT male 8 cell, repeat 3 [Rlim KO]

value: 8 cell


title: WT male 8 cell, repeat 2 [Rlim KO]


title: T02: uRCC with NF2-loss


title: HVneg_Ssea1pos_H3K27me3_ChIP

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to the mm9 genome assembly using Bowtie2 version (2.1.0) with the following configurations -x -U -S.
Bowtie output SAM files were converted into sorted BAM files using the view (parameters -bSh) and sort functions in SAMtools (version 0.1.19).
processed data files format and content: wig (aka bedgraph) files were generated using the genomeCoverageBed function in bedTools (version 2.17.0) using parameters -ibam -g -bg.  Scores represent raw read depth.
Genome_build: mm9

value: anti-H3K27me3 (07-449; Millipore)


title: WT female 8 cell, repeat 4 [Rlim KO]


title: T05: uRCC with NF2-loss


title: C2_10w

value: 10 weeks


title: C2_3w

value: 3 weeks


title: C1_10w


title: KO female 4 cell, repeat 3 [Rlim KO]

value: Rlim KO

value: 4 cell


title: WT male 8 cell, repeat 1 [Rlim KO]


title: KO female 4 cell, repeat 2 [Rlim KO]


title: KT_UT

city: Salt Lake City

first: Christopher

middle: A

last: Reilly

state: UT

address: 30 S 2000 E, Room 201 Skaggs Hall

department: Pharmacology and Toxicology

institute: University of Utah

data_processing:
Reference fasta files were generated by combining hg38 chromosome sequences with splice junction sequences generated by USeq (v8.8.8) MakeTranscriptome. Ensembl (build 84) transcript models were used.
Reads were aligned with Novoalign (v2.08.01) allowing up to 50 alignments per read.
USeq SamTranscrimptomeParser was used to select the best alignment and convert coordinates of reads aligning to splices to genomic space.
Per gene read counts were generated with USeq DefinedRegionDifferentialSeq.  Gene models were created by collapsing transcripts, maximizing exons.
DESeq2 (v1.10.1) was used to determine differentially expressed genes using default settings.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited file containing log2 Fold Changes, FDR and raw counts for all tested genes

source_name: NHBE

growth_protocol: all NHBE cells were grown in BEGM (Lonza) and sub cultured before reaching confluence using trypLE.  Cells were used from passage 4-6. No plate coat was used.

extract_protocol:
Cell culture medium was removed and cells were snap frozen.  RNA was extracted using Rneasy kit (qiagen) with on column Dnase I digestion.
Intact poly(A) RNA was purified from total RNA samples (100-500 ng) with oligo(dT) magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Preparation Kit (RS-122-2101, RS-122-2102).  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 10 nM and equal volumes were pooled in preparation for Illumina sequence analysis.

value: Normal Human Bronchial Epithelial Cells (NHBE)

value: TRPV1 I585I/V (HET)

tag: passage

value: between 4 and 6


title: C1_5w


title: 9853_UT


title: 14359_UT

value: TRPV1 WT


title: H2_10w

value: Stat3f/f K5cre


title: KO female 4 cell, repeat 1 [Rlim KO]


title: KO male 4 cell, repeat 4 [Rlim KO]


title: C1_3w


title: H1_10w


title: D2_10w


title: SSM_FLI_Shiva9_1

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

data_processing:
Illumina bcl2fastq v1.8.4 software used for extraction of FASTQ files
FASTQ files were mapped using Tophat (v2.0.6) vs. the H. sapiens genome GRCh37 obtained from Ensembl
Mapped reads were counted HTSeq Python framework.
RPKM values were computed using R programming language.
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel file includes raw counts and RPKM values of each sample

source_name: total RNA extracted from HFF cells

growth_protocol: Cells were cultured as recommended by ATCC in Dulbeccos modified Eagles low glucose medium (DMEM) with L-glutamine (PAA Laboratories, Pasching, Austria), supplemented with 10% fetal bovine serum (FBS) (PAA Laboratories). Cells were grown under normal air conditions in a 9.5% CO2 atmosphere at 37oC. For sub-culturing, the remaining medium was discarded and cells were washed in 1 x PBS (pH 7.4) (PAA Laboratories) and detached using trypsin/EDTA (PAA Laboratories). Primary fibroblasts were sub-cultured in a 1:4 (= 2 population doublings (PDs)) or 1:2 (= 1 PD) ratio. For stock purposes, cryo-conservation of the cell strains at various PDs were undertaken in cryo-conserving medium (DMEM + 10% FBS + 5% DMSO). Cells were immediately frozen at -80ºC and stored for two to three days. Afterwards, cells were transferred to liquid nitrogen for long time storage. Re-freezing and re-thawing was not performed to avoid premature senescence [Honda et al., 2001]. One vial of each of the two fibroblast cell strains (MRC-5 and HFF) were obtained and maintained in culture from an early PD. After obtaining enough stock on confluent growth of the fibroblasts in 75 cm2 flasks, cells were sub-cultured into three separate 75 cm2 flasks (“triplicates”) and were passaged until they were senescent in culture.

extract_protocol:
Total RNA was isolated using Qiazol (Qiagen, Hilden, Germany) according to the manufacturer’s protocol, with modifications. In brief, the fibroblasts were pelleted in 2 ml safe-lock tubes (Eppendorf, Hamburg, Germany). 1 ml cooled Qiazol and one 5 mm stainless steel bead (Qiagen) were added. Homogenization was performed using a TissueLyzer II (Qiagen) at 20 Hz for 1 min. After incubation for 5 min at RT, 200 ml chloroform was added. The tube was shaken for 15 sec and incubated for 3 min at RT. Phase separation was achieved by centrifugation at 12,000 x g for 20 min at 4oC. The aqueous phase was transferred into a fresh cup and 10 mg of glycogen (Invitrogen, Darmstadt, Germany), 0.16 volume NaOAc (2 M, pH 4.0) and 1.1 volume isopropanol were added, mixed and incubated for 10 min at RT. The RNA was precipitated by centrifugation with 12,000 x g at 4oC for 20 min. The supernatant was removed and the pellet was washed with 80% ethanol twice and air dried for 10 min. The RNA was re-suspended in 20 l DEPC-treated water by pipetting up and down, followed by incubation at 65oC for 5 min. The RNA was quantified with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80oC until use.
Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit v2 following the manufacturer’s instruction.

treatment_protocol: Cellular senescence was induced by γ-irradiation. Human fibroblast strains were irradiated by ionizing radiation in a Gamma cell GC40 (MDS Nordion, Ottawa, Canada) using the radioactive isotope 137Cs as source. Exposure time was determined by correcting the irradiation dose of 1.23 Gy/min with the decay factor time equating to roughly 62 sec/Gy. Young PD fibroblast strains (MRC-5 at PD 32, HFF at PD 16) were seeded 48 hrs before radiation exposure. Once cells were 70% confluent, they were subjected to different doses of -irradiation (0, 2, 15, 20 Gy) at room temperature (RT) and subsequently cultured at 37°C.

tag: population doublings

tag: agent

value: irradiation 20GY

value: HFF


title: KO male 4 cell, repeat 1 [Rlim KO]

value: male


title: SSM_FLI_Shiva9_2


title: WT female 4 cell, repeat 3 [Rlim KO]

value: WT

value: female


title: H2_8w

value: Skin

value: 8 weeks


title: D1_10w


title: C1_8w


title: SSM_FLI_Shiva10_3

source_name: total RNA extracted from MRC-5 cells


title: SSM_FLI_Shiva10_2


title: SSM_FLI_Shiva10_1


title: WT female 4 cell, repeat 2 [Rlim KO]


title: WT male 4 cell, repeat 6 [Rlim KO]


title: H1_8w


title: D2_8w


title: WT male 4 cell, repeat 5 [Rlim KO]


title: D1_8w


title: Phil_UT


title: T06: uRCC with NF2-loss

value: Renal cell carcinoma

value: unclassified


title: H2_5w

value: 5 weeks


title: KO male 4 cell, repeat 3 [Rlim KO]

value: Rlim KO


title: SSM_FLI_Shiva9_3


title: KO male 4 cell, repeat 2 [Rlim KO]

value: 4 cell


title: WT male 4 cell, repeat 4 [Rlim KO]


title: WT male 4 cell, repeat 2 [Rlim KO]


title: H1_5w


title: D2_5w


title: D1_5w


title: WT male 4 cell, repeat 3 [Rlim KO]


title: WT male 4 cell, repeat 1 [Rlim KO]


title: WT female 4 cell, repeat 1 [Rlim KO]


title: thermal stress at 37 °C

city: Guangzhou

first: Jun

last: Li

state: Guangdong

address: xingangxilu 164hao

department: South China Sea Institute of Oceanology

country: China

institute: Chinese Academy of Sciences

description: Hong Kong Oysters usually inhabit the estuarine or intertidal zone, which always experience dramatic changes in salinity, oxygen and temperature. 10 oysters were taken out randomly and mixed together from thermal-stressed treatment for the RNA isolation.

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to reference using SOAPaligner/soap2
The removal of poor quality sequences and trimming of adaptor sequences from the raw sequence data was carried out using cutadapt (v1.8.1)
Supplementary_files_format_and_content: RPKM

molecule: polyA RNA

organism: Magallana hongkongensis

source_name: Crassostrea hongkongensis

growth_protocol: C. hongkongensis were  acclimated with aerated sand-filtered seawater in the laboratory for 2 weeks prior to the experiment. The oysters were fed twice daily with Tetraselmis suecica and Isochrysis galbana.

extract_protocol: Gill were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Oysters were placed in pre-warmed (37 °C) seawater and shocked for 1 h and then returned to ambient seawater (23 °C).

value: gill

tag: developmental stage

value: adult

tag: Sex

value: not determined

tag: geographic location

value: China:Guangdong Province, Zhanjiang

tag: description

value: 10 oysters gill were taken out randomly and mixed together from thermal-stressed treatment for the RNA isolation.

tag: collection date

tag: cultivar

value: wild

tag: latitude and longtitude

tag: environment material

tag: environment biome

tag: environment feature

tag: temperature

tag: estimated size

value: 10 cm± 0.8cm

tag: propagation

value: missing

tag: ploidy

value: diploid

tag: isolation and growth condition


title: HMGB2 CHIP-seq in senescent cells

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
Chip-seq files were aligned using bowtie version 0.12.9 to human genome hg19
Peak calling was done with homer (v1.0) software comparing Senescent vs Growing cells with options -style histone and -style factor
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains significant peaks in bed format
peaks_SvsGR_broad.bed.txt:  for -style histone option
peaks_SvsGR_narrow.bed.txt:  for -style factor option

source_name: IMR90 cell line

growth_protocol: IMR90 human fibroblasts were cultured according to the ATCC in low oxygen (2%)

extract_protocol:
10 ng of ChIP DNAs were extracted from growing (control) and RAS-infected senescent IMR90 cells
ChIP-seq libraries were prepared from 10 ng of ChIP DNAs with NEBNExt Ultra DNA Library Prep Kit for Illumina (New England Biosciences, Ipswich, MA)

treatment_protocol: ChIP in growing (control) and RAS-infected senescent IMR90 cells was performed at day 2 using rabbit anti-HMGB2 (Abcam, Cambridge, MA)

tag: cell line

tag: cell type

value: human fibroblasts

tag: cell condition

value: RAS-induced senescent cells

tag: chip antibody

value: rabbit anti-HMGB2

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat.#

tag: chip antibody lot #


title: H1_2w

tag: strain

tag: tissue

value: Skin

tag: age

value: 2 weeks

tag: genotype

value: Stat3f/f K5cre


title: D1_2w


title: D2_2w


title: OTP90_2

city: evry

first: remi

last: bounon

state: essonne

address: 2 avenue Gaston Crémieux

department: BAP

country: France

institute: INRA

data_processing:
default parameters to Torrent Suite Software version 4.0
Mapping with Bowties2 on messager RNA TAIR 10 reference (parameters : no MultiHit, local reads mapping, TAIR 10 refrence with one gene model)
Genome_build: Arabidopsis thaliana TAIR 10
Supplementary_files_format_and_content: our processed data files contain 3 comment lines corresponding to the time of processing, the number of reads parsed and the number of reads mapped. An example is shown below: #sam2pkm :2014-02-14 11:16:22.632693 # total read parsed : 34170794 # total read mapped : 28674853. Then the column headers #id    len    nb_single : "id" corresponds to the locus identifier (Arabidopsis Genome Initiative code); "len" corresponds to the length of the gene model in nt;"nb_single" corresponds to the number of reads mapped on the gene model

organism: Arabidopsis thaliana

extract_protocol:
extraction_ARN_Trizol
RNA libraries were prepared for sequencing using standard LifeTechnologies protocols for Ion Torrent Proton (4476286_Ion Total RNA-Seq Kit v2_UG_RevE.pdf)
RNA Seq in Stranded Single End, sizing 230bp, ribo RNA dépletion (Ribominus_EukaryotePlantProbeSpecificity _2_.pdf)

treatment_protocol: no treatment

tag: ecotype/genotype

tag: organ

value: aerial

tag: developmental stage


title: col0_2


title: col0_1


title: LARCs 14d, biological rep1

status: Public on Oct 10 2016

city: Singapore

first: Thomas

last: Dick

address: Centre for Translational Medicine, Block MD6, 15-01, 14 Medical Drive

department: Microbiology

country: Singapore

institute: National University of Singapore

data_processing:
Illumina Casava1.7 software was used for basecalling
RNA sequencing reads were mapped to the M. smegmatis mc2155 reference genome (NCBI accession: NC_008596) using BWA (v0.5.9) with default parameters
Sequencing reads mapping to predicted open reading frames were quantified using HTSeq based on the NCBI RefSeq annotation
Differential expression analyses were performed in R (version 2.15.1) using the Bioconductor package, edgeR
Genome_build: NC_008596.1
Supplementary_files_format_and_content: Raw counts: generated from edgeR containing raw counts of sequencing reads for genes for all samples
Supplementary_files_format_and_content: Normalised counts: generated from edge R containing normalized counts based on 3 biological replicates for all samples
Supplementary_files_format_and_content: Differential expression analyses: generated from edgeR containing log2 fold change of genes compared with time 0

organism: Mycolicibacterium smegmatis MC2 155

source_name: Mycobacterium smegmatis culture shock-starved for 14d

growth_protocol: Log-phase culture of Mycobacterium smegmatis were routinely generated by growing at 37°C with agitation in Middlebrook 7H9 broth supplemented with 0.5% bovine albumin, 0.2% glucose, 0.085% NaCl, 0.5% glycerol, 0.0003% catalase and 0.05% Tween80 until it reaches an optical density at 600nm of 0.5.

extract_protocol:
Cultures were harvested by centrifugation (2000 × g, 10 min, 25°C). The pellet was resuspended in 1 ml of Trizol (Invitrogen). Bacterial cultures in Trizol were then disrupted by bead beating (FastPrep Instrument and BLUE Kit tubes (BIO 101); two cycles of 30 s at maximum speed with cooling on ice between cycles). The samples were centrifuged for 1 min at 4°C/13,000 rpm and the supernatant was transferred to a new tube containing 200 µl chloroform, mixed and incubated at RT for 5 min. After centrifugation at 4°C/13,000 rpm for 10 min, RNA was extracted from the aqueous phase with isopropanol according the supplier’s manual followed by a treatment with DNase I, Amplification Grade (Invitrogen) treatment with subsequent ammonium acetate / isopropanol precipitation.The Gram-Positive Bacteria Ribo-Zero (Epicentre) rRNA Magnetic Removal Kit was used to remove bacterial rRNA from total RNA preparations.
RNA-seq libraries were prepared according to the TruSeq RNA Sample Preparation v2 Guide (Illumina) without fragmentation and without size selection.

treatment_protocol: For nutrient-starvation experiments, log-phase cultures were harvested by centrifugation (2000 × g, 10 min, 25°C). After washing three times with PBS-0.025% Tween80 (mild starvation) or PBS-0.025% Tyloxapol (shock starvation), the cultures were diluted to a final OD600 of 0.10–0.15. A volume of 50 ml of this suspension was transferred into a 1 liter roller bottle (Corning) and starved for up to 14 days with rolling at 2 rpm at 37°C. Samples were collected at 1h, 3h, 24h and 14d after the first contact with starvation media.

tag: starvation condition

value: shock starvation

tag: media

value: PBS

tag: timepoint


title: LARCs 14d, biological rep3


title: LARCs 24h, biological rep2

source_name: Mycobacterium smegmatis culture shock-starved for 24h


title: LARCs 24h, biological rep3


title: LARCs 3h, biological rep3

source_name: Mycobacterium smegmatis culture shock-starved for 3h


title: LARCs 24h, biological rep1


title: OTP90_1


title: LARCs 1h, biological rep3

source_name: Mycobacterium smegmatis culture shock-starved for 1h


title: LARCs 3h, biological rep1


title: LARCs 3h, biological rep2


title: HMGB2 CHIP-seq in growing cells

tag: cell line

value: growing cells


title: LARCs 0h, biological rep3

source_name: Mycobacterium smegmatis log-phase culture

value: log-phase


title: LARCs 0h, biological rep2


title: LARCs 0h, biological rep1


title: SMRCs 14d, biological rep2

source_name: Mycobacterium smegmatis culture mild-starved for 14d

value: mild starvation


title: SMRCs 14d, biological rep3


title: control group at ambient seawater  (23 °C)

description: Hong Kong Oysters usually inhabit the estuarine or intertidal zone, which always experience dramatic changes in salinity, oxygen and temperature.

treatment_protocol: The control group was always kept in ambient seawater (23 °C).

value: gill

value: adult

tag: Sex

value: not determined

tag: collection date

tag: cultivar

value: wild

tag: geographic location

value: China:Guangdong Province, Zhanjiang

tag: latitude and longtitude

tag: environment material

tag: environment biome

tag: environment feature

tag: temperature

tag: estimated size

tag: propagation

tag: ploidy

tag: isolation and growth condition


title: LARCs 14d, biological rep2

tag: starvation condition


title: SMRCs 14d, biological rep1

tag: media


title: SMRCs 24h, biological rep3

source_name: Mycobacterium smegmatis culture mild-starved for 24h

tag: timepoint


title: H2_2w

tag: strain

tag: tissue

tag: age

tag: genotype


title: SMRCs 3h, biological rep2

source_name: Mycobacterium smegmatis culture mild-starved for 3h


title: SMRCs 3h, biological rep3


title: SMRCs 24h, biological rep1


title: LARCs 1h, biological rep1


title: LARCs 1h, biological rep2


title: SMRCs 1h, biological rep3

source_name: Mycobacterium smegmatis culture mild-starved for 1h


title: SMRCs 3h, biological rep1


title: SMRCs 0h, biological rep3


title: SMRCs 0h, biological rep2


title: SMRCs 1h, biological rep1


title: SMRCs 0h, biological rep1


title: C2AT_R2

city: Urbana

first: Zaida

last: Luthey-Schulten

state: IL

address: 600 South Mathews Avenue

department: Chemistry

institute: University of Illinois at Urbana-Champaign

description:
TMA
DifferentiallyExpressedGenes.MultiFactor.xlsx

data_processing:
Reads were mapped to the reference genome NC_003552 with Rockhopper v2.0.2 using default parameters.
Ribosomal reads were subtracted from subsequent analysis.
Differentially expression analysis was performed on all datasets that did not have dwell time to allow degradation (8 MeOH, 5 TMA, and 3 acetate total) using: 1) edgeR v3.8.5, 2) PoissonSeq v1.1.2, and 3) DESeq3 v1.6.3; all with default parameters and normalization techniques. A multifactor design was used in each method taking the first factor as the growth substrate and the second factor as the library preparation kit (ScriptSeq™ or TruSeq™). Differentially expressed genes with p ≤ 0.01 were considered differentially expressed and can be found in the file “DifferentiallyExpressedGenes.MultiFactor.xlsx”.
Half-lives were computed for datasets that that include degradation of RNA.  Expression profiles were normalized to RPKMs.  Then subsequent profiles were normalized so that the gene superoxide dismutase B (sodB) gene had a half-life of 120 minutes.  Half-lives were computed for all other genes based on this normalization, and those with uncertainty in the fit greater than 50% the fit value and positive half-life were kept.  Results can be found in the file “HalfLives.xlsx”.
Genome_build: NC_003552
Supplementary_files_format_and_content: DifferentiallyExpressedGenes.MultiFactor.xlsx; Excel File; Contains a list of differentially expressed genes between the three growth substrates as predicted by DESeq2, edgeR and PoissonSeq.
Supplementary_files_format_and_content: HalfLives.xlsx; Excel File; Contains all the half-lives computed for growth in acetate, methanol and trimethylamine.
Supplementary_files_format_and_content: ReadCounts.xlsx; Excel File; Contains mapped read counts from all RNAseq datasets before further processing or removal of rRNA reads.  Contains worksheets for raw read count, RPKM normalized read count and quartile normalized read counts.

organism: Methanosarcina acetivorans

growth_protocol: Cells were adapted for at least 30 generations in the substrate of interest, before performing the RNA extraction.

extract_protocol:
Total RNA was isolated from mid exponential phase cultures using TRIzol (Invitrogen, Carslbad, CA) and the ZR Fungal/Bacterial RNA MiniPrep kit (Zymo Research, Irvine, CA). The 16S- and 23S-rRNA were subtracted using sample-specific biotin-labeled 16S and 23S RNA probes.
Fifty nanograms of rRNA-depleted messenger RNA were converted to indexed RNAseq libraries with the ScriptSeq™ v2 or TruSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies, Madison, WI). The libraries were pooled in equimolar concentration and quantitated by qPCR with the Library Quantification kit Illumina compatible (Kapa Biosystems, Woburn, MA). The pooled libraries were sequenced for 101 cycles plus 7 cycles for the index read on a HiSeq2000 using TruSeq SBS version 3 reagents. The fastq files were generated and demultiplexed with Casava 1.8.2 (Illumina, San Diego, CA).

tag: growth media

value: High salt media with 50 mM trimethylamine


title: LK75

description: HalfLives.xlsx

tag: biological replicate

tag: time point

value: 240 min after halting transcription with actinomycin D


title: LK42

description: HalfLives.xlsx

value: 120 min after halting transcription with actinomycin D


title: C2AM1

description:
MeOH
DifferentiallyExpressedGenes.MultiFactor.xlsx

value: High salt media with 125 mM methanol


title: C2AT_R1


title: LK40

description: HalfLives.xlsx

value: 30 min after halting transcription with actinomycin D


title: LK37

description:
HalfLives.xlsx
DifferentiallyExpressedGenes.MultiFactor.xlsx

value: 0 min after halting transcription with actinomycin D


title: LK39

description: HalfLives.xlsx

value: 20 min after halting transcription with actinomycin D


title: LK41

description: HalfLives.xlsx

value: 60 min after halting transcription with actinomycin D


title: LK35

description: HalfLives.xlsx


title: LK33

description: HalfLives.xlsx


title: LK32

description: HalfLives.xlsx


title: LK34

description: HalfLives.xlsx


title: SMRCs 24h, biological rep2


title: LK31


title: C2AM3


title: SMRCs 1h, biological rep2


title: LK30

description: HalfLives.xlsx


title: LK29

description: HalfLives.xlsx


title: LK28

description: HalfLives.xlsx


title: LK26

description: HalfLives.xlsx


title: LK27

description: HalfLives.xlsx


title: LK60

description: HalfLives.xlsx

value: High salt media with 120 mM acetate


title: LK36

description: HalfLives.xlsx


title: LK25


title: LK59

description: HalfLives.xlsx


title: LK55


title: LK58

description: HalfLives.xlsx


title: LK53

description: HalfLives.xlsx


title: LK51

description: HalfLives.xlsx


title: LK50

description: HalfLives.xlsx


title: LK57

description: HalfLives.xlsx


title: LK47

description: HalfLives.xlsx


title: LK46

description: HalfLives.xlsx


title: LK48

description: HalfLives.xlsx


title: LK49


title: LK43


title: LK44

description: HalfLives.xlsx


title: LK23

description: HalfLives.xlsx


title: LK21

description: HalfLives.xlsx


title: LK18

description: HalfLives.xlsx

value: 5 min after halting transcription with actinomycin D


title: LK52

description: HalfLives.xlsx


title: LK22

description: HalfLives.xlsx


title: LK56

description: HalfLives.xlsx


title: LK20

description: HalfLives.xlsx


title: LK19

description: HalfLives.xlsx

value: 10 min after halting transcription with actinomycin D


title: LK15

description: HalfLives.xlsx


title: LK14

description: HalfLives.xlsx


title: LK13

description: HalfLives.xlsx


title: LK54

description: HalfLives.xlsx


title: LK17


title: LK11

description: HalfLives.xlsx


title: LK12

description: HalfLives.xlsx


title: LK9


title: LK10

description: HalfLives.xlsx


title: LK6

description: HalfLives.xlsx


title: LK5

description: HalfLives.xlsx


title: LK45

description: HalfLives.xlsx


title: LK4

description: HalfLives.xlsx


title: LK3

description: HalfLives.xlsx


title: LK2

description: HalfLives.xlsx


title: Trim25-KO_brain_d5_PbA_3

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

description: rRNA depleted total RNA

data_processing:
The quality of sequence reads was confirmed using FastQC tool (Babraham Bioinformatics).
Reads were mapped to the mouse UCSC mm9 reference assembly using TopHat v2.0.9 in conjunction with Bowtie 1.0.0 algorithm (Langmead et al., 2009; Trapnell et al., 2009; Kim et al., 2013)
Gene expression was quantified by counting the number of uniquely mapped reads with featureCounts using default parameters (Liao et al., 2014).
Normalization and differential gene expression analysis was conducted independently for PbA and EAE datasets using the edgeR Bioconductor package (Robinson and Oshlack, 2010).
We retained genes that had a minimum expression level of 5 counts per million reads (CPM) in at least 3 samples for PbA, and at least 2 out of 4 for EAE datasets. Genes with differential expression in Usp15L749R were considered significant if fold change ≥ |1.5| and adjusted p value < 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each sample.

source_name: Brain

extract_protocol:
Brains from perfused PbA-infected mice (at day 3 and 5) and from spinal cords of mice undergoing EAE (at day 7) were harvested and frozen in liquid nitrogen. Total RNA was isolated using Trizol-chloroform (Life Technologies), followed by DNase-digestion and purification on RNeasy columns (Qiagen). RNA integrity was assessed on a Bioanalyzer RNA pico chip.
RNA-seq libraries were prepared following rRNA depletion and using Illumina TruSeq Stranded Total RNA Library preparation kit. The RNA-seq libraries were sequenced on an Illumina HiSeq 2500 sequencer in paired-end 50bp configuration.

treatment_protocol: Seven to eight week old mice were infected intravenously with 106 parasitized red blood cells (pRBCs).

tag: strain/background

tag: genotype/variation

value: Trim25 KO

value: Brain

tag: treatment

value: Plasmodium berghei ANKA infection (day 5)


title: Trim25-KO_brain_d5_PbA_2

description: rRNA depleted total RNA


title: B6_brain_d5_PbA_3b

description: rRNA depleted total RNA

value: wild-type


title: Trim25-KO_brain_d5_PbA_1

description: rRNA depleted total RNA


title: B6_brain_d5_PbA_2b

description: rRNA depleted total RNA


title: B6_brain_d5_PbA_1b

description: rRNA depleted total RNA


title: USP15L749R_brain_d3_PbA_2

description: rRNA depleted total RNA

value: Plasmodium berghei ANKA infection (day 3)


title: USP15L749R_brain_d3_PbA_1

description: rRNA depleted total RNA


title: USP15L749R_brain_d3_PbA_3

description: rRNA depleted total RNA


title: B6_brain_d3_PbA_1

description: rRNA depleted total RNA


title: B6_brain_d3_PbA_3

description: rRNA depleted total RNA


title: Z.fish 13hpf input

city: Chicago

first: Guan-Zheng

last: Luo

address: 929 E 57th St

institute: UChicago

data_processing:
Single-ended 50bp reads are mapped by Bowtie 1.0 to Z.fish genome (danRer10) with parameter -M 1  --best –strata.
Peaks are called by MACS2.0 by comparing IP reads with input reads.
Peaks called by MACS2.0 with qvalue < 0.01 are selected as significant peaks.
Genome_build: danRer10
Supplementary_files_format_and_content: bed files are generated by MACS2.0. The genomic loci and scores of peaks are included.

organism: Danio rerio

source_name: 13 hours post fertilization Z.fish embryo

growth_protocol: Zebrafish (Danio rerio) embryos were derived from the Tubingen zebrafish lines. Embryos were incubated in Holtfreter’s solution at 28.5ºC.

extract_protocol:
Phenol/chloroform extraction and DNA precipitation with 1/10 volume of 5 M NaCl and 1 volume of isopropanol were performed. The obtained DNA pellet was dissolved with 3dH2O.
NEBNext® DNA Library Prep Master Mix Set for Illumina® E6040L was used to construct Illumina compatible DNA library.

value: Tubingen

tag: antibody

tag: Stage

value: 13 hours post fertilization embryo


title: B6_brain_d3_PbA_2

description: rRNA depleted total RNA


title: Z.fish 11hpf input

source_name: 11 hours post fertilization Z.fish embryo

value: 11 hours post fertilization embryo


title: Z.fish 12hpf input

source_name: 12 hours post fertilization Z.fish embryo

value: 12 hours post fertilization embryo


title: Z.fish 64C input (Ab antibody)

source_name: Z.fish embryo of 64 cell stage

value: m6A (Abcam, ab151230, lot 4c)

value: 64-cell stage embryo


title: USP15L749R_spinalcord_d7_EAE_19

description:
rRNA depleted total RNA.
USP15-19_EAE
Processed data file: EAE_samples_cpm_counts.txt

data_processing:
The quality of sequence reads was confirmed using FastQC tool (Babraham Bioinformatics).
Reads were mapped to the mouse UCSC mm9 reference assembly using TopHat v2.0.9 in conjunction with Bowtie 1.0.0 algorithm (Langmead et al., 2009; Trapnell et al., 2009; Kim et al., 2013).
Gene expression was quantified by counting the number of uniquely mapped reads with featureCounts using default parameters (Liao et al., 2014).
Normalization and differential gene expression analysis was conducted independently for PbA and EAE datasets using the edgeR Bioconductor package (Robinson and Oshlack, 2010).
We retained genes that had a minimum expression level of 5 counts per million reads (CPM) in at least 3 of the 9 samples for PbA, and at least 2 out of 4 for EAE datasets. Genes with differential expression in Usp15L749R were considered significant if fold change ≥ |1.5| and adjusted p value < 0.05.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each sample.

source_name: Spinal cord, USP15(L749R), EAE (day 7)

extract_protocol:
Brains from perfused PbA-infected mice (at day 5) and from spinal cords of mice undergoing EAE (at day 7) were harvested and frozen in liquid nitrogen. Total RNA was isolated using Trizol-chloroform (Life Technologies), followed by DNase-digestion and purification on RNeasy columns (Qiagen). RNA integrity was assessed on a Bioanalyzer RNA pico chip.
RNA-seq libraries were prepared following rRNA depletion and using Illumina TruSeq Stranded Total RNA Library preparation kit. The RNA-seq libraries were sequenced on an Illumina HiSeq 2500 sequencer in paired-end 50bp configuration.

treatment_protocol: 8- to 12-week-old female mice were treated with myelin oligodendrocyte glycoprotein (MOG; peptide sequence 35-55) emulsified in Complete Freund Adjuvent (CFA) (50 μg/mouse, s.c., at day 0) and pertussis toxin (PTX; 300 ng/mouse, i.p., at days 0 and 2).

tag: gender

value: Female

value: Spinal cord

value: experimental autoimmune encephalomyelitis (EAE) (day 7)


title: Z.fish 64C input


title: Z.fish 64C 6mA-IP-seq


title: B6_spinalcord_d7_EAE_8

description:
rRNA depleted total RNA.
B6-8_EAE
Processed data file: EAE_samples_cpm_counts.txt

source_name: Spinal cord, wild-type, EAE (day 7)


title: Z.fish 13hpf 6mA-IP-seq Rep2


title: LK1

value: High salt media with 125 mM methanol

value: 0 min after halting transcription with actinomycin D


title: Z.fish 12hpf 6mA-IP-seq Rep2


title: Z.fish 11hpf 6mA-IP-seq Rep2


title: B6_spinalcord_d7_EAE_7

description:
rRNA depleted total RNA.
B6-7_EAE
Processed data file: EAE_samples_cpm_counts.txt


title: USP15L749R_spinalcord_d7_EAE_21

description:
rRNA depleted total RNA.
USP15-21_EAE
Processed data file: EAE_samples_cpm_counts.txt


title: USP15L749R_brain_d5_PbA_3

description:
rRNA depleted total RNA.
USP15-3_d5_PbA
Processed data file: PbA_samples_cpm_counts.txt

source_name: Brain, USP15(L749R), PbA infection (day 5)

treatment_protocol: Seven- to eight-week-old mice were infected intravenously with 10^6 parasitized red blood cells (pRBCs).

value: Plasmodium berghei ANKA (PbA) infection (day 5)


title: Z.fish 13hpf 6mA-IP-seq Rep1


title: Z.fish 12hpf 6mA-IP-seq Rep1


title: LK7

description: HalfLives.xlsx

value: 10 min after halting transcription with actinomycin D


title: USP15L749R_brain_d5_PbA_2

description:
rRNA depleted total RNA.
USP15-2_d5_PbA
Processed data file: PbA_samples_cpm_counts.txt

value: Brain


title: USP15L749R_brain_d5_PbA_1

description:
rRNA depleted total RNA.
USP15-1_d5_PbA
Processed data file: PbA_samples_cpm_counts.txt


title: B6_brain_d5_PbA_3

description:
rRNA depleted total RNA.
B6-3_d5_PbA
Processed data file: PbA_samples_cpm_counts.txt

source_name: Brain, wild-type, PbA infection (day 5)


title: B6_brain_d5_PbA_2

description:
rRNA depleted total RNA.
B6-2_d5_PbA
Processed data file: PbA_samples_cpm_counts.txt


title: B6_brain_NI_4

description:
rRNA depleted total RNA.
B6-4_NI
Processed data file: PbA_samples_cpm_counts.txt

source_name: Brain, wild-type, no treatment

treatment_protocol: Uninfected control.


title: B6_brain_d5_PbA_1

description:
rRNA depleted total RNA.
B6-1_d5_PbA
Processed data file: PbA_samples_cpm_counts.txt


title: B6_brain_NI_2

description:
rRNA depleted total RNA.
B6-2_NI
Processed data file: PbA_samples_cpm_counts.txt


title: aspen rep3

city: Marseille

first: Marie-Noëlle

last: Rosso

address: 163 avenue de Luminy

department: Biodiversity and Biotechnology of Fungi - BBF

institute: INRAE - Aix Marseille University

description: Liquid cultures of P. coccineus CIRM-BRFM 310 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.( g.l-1), 1 mm Wiley-milled aspen (15 g.l-1 )

data_processing:
Raw fastq file reads were filtered and trimmed using the JGI QC pipeline.
QCed reads from each library were aligned to the reference genome Pycnoporus coccineus BRFM 310 v1.0, available via Mycocosm JGI portal, using TopHat2 (Galaxy Tool Version 0.7-INRA MIGALE bioinformatics platform) with only unique mapping allowed.
Read counts were determined by HTSeq  (Galaxy Tool Version 0.3.2-INRA MIGALE bioinformatics platform)
Read counts were normalized using ddsNorm from the DESeq Bioconductor package (version 1.5)
Genome_build: Pycnoporus coccineus BRFM 310 v1.0, available via Mycocosm JGI portal
Supplementary_files_format_and_content: Excel files include HTSeq raw read count values for each sample; txt files include DESeq normalized read count values for each sample

organism: Trametes coccinea

source_name: mycelium

extract_protocol:
Total RNA was extracted from 100 mg tissue ground with FastPrep Lysis Matrix A (MP Biomedicals) in 1 ml TRIZOL (Ambion). Nucleic acids were precipitated with isopropanol, resuspended in water and treated with RNase-Free DNase I (QIAGEN). Total RNA was precipitated with LiCl and resuspended in DEPC-treated water. RNA quantity and quality were determined using the Experion RNA StdSens kit (QIAGEN).
Double stranded cDNAs were synthesized from Poly A RNA and fragmented (200-300bp) before construction of the sequencing libraries (Kapa Library Amplification Kit ; Kapa Biosystems).
Illumina HighSeq-2500 JGI platform generating paired end reads of 150bp each.

treatment_protocol: Mycelium and remaining solid substrate were immediately frozen in liquid nitrogen and stored at -80°C before RNA extraction.

value: CIRM-BRFM 310

tag: substrate

value: aspen

tag: day

value: day 3


title: aspen rep2


title: aspen rep1


title: WT_ACC_R3

city: Potsdam

first: Isabel

last: Bäurle

address: Karl-Liebknecht-Str. 24-25

department: Institut für Biochemie und Biologie

institute: Universität Potsdam

data_processing:
Read adapters were removed using Trimmomatic version 0.32 (Bolger et al., 2014).
Reads were mapped against the Arabidopsis thaliana TAIR10 reference using bwa mem version 0.7.12-r1044 (Li, 2013).
Mapping files were further transformed into sorted bam files and indexed using samtools version 1.2 (Li et al., 2009). Duplicate reads were removed using samtools rmdup. Coverage files in bedGraph format were computed using bedtools genomecov (v2.25.0).
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: Coverage files in bedGraph format.

growth_protocol: Arabidopsis thaliana Col-0 and 35S::FRG1-YFP seedlings were grown on GM medium (1 % (w/v) glucose) under a 16 h/ 8 h light/dark cycle at 23°C/21°C. Seeds were stratified for 5 d at 4°C in darkness.

extract_protocol:
ChIP was performed as described (Lämke et al., 2016) using GFP isolation kit (Miltenyi Biotec, cat. # 130-091-125, batch # 5140613098).
Library preparation and 100 bp single-end sequencing on a Illumina HiSeq 2500 machine were performed by ATLAS Biolabs (Berlin, Germany). Data were delivered as de-multiplexed fastq files.

treatment_protocol: 5 d-old seedlings of both genotyes were treated with an acclimatizing HS (ACC) of 37°C for 60 min, 23°C for 90 min and 44°C for 45 min starting eight hours after light onset, or left untreated (NHS). After HS, plants were returned to normal growth conditions and harvested 28 h later.

tag: ecotype background

tag: developmental stage

value: 6 day old seedling

value: WT

tag: treated with

value: acclimatizing (ACC) heat stress

value: Seedling


title: WT_NHS_R1

value: none (untreated; NHS)

tag: tissue


title: Z.fish 11hpf 6mA-IP-seq Rep1

tag: strain

value: Tubingen

value: 11 hours post fertilization embryo


title: pine rep1

description: Liquid cultures of P. coccineus CIRM-BRFM 310 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), ground and sifted pine wood fragments < 2 mm (15 g.l-1)

value: pine


title: WT_NHS_R2


title: WT_ACC_R1


title: pine rep3


title: WT_NHS_R3


title: pine rep2


title: WT_ACC_R2


title: 35S::FRG1-YFP_NHS_R3


title: 35S::FRG1-YFP_NHS_R2


title: maltose rep2

description: Liquid cultures of P. coccineus CIRM-BRFM 310 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (20 g.l-1)

value: maltose


title: 35S::FRG1-YFP_NHS_R1


title: maltose rep3


title: 35S::FRG1-YFP_ACC_R3


title: maltose rep1


title: 35S::FRG1-YFP_ACC_R2


title: B6_brain_NI_3

description:
rRNA depleted total RNA.
B6-3_NI
Processed data file: PbA_samples_cpm_counts.txt

value: wild-type


title: sRNA_LW3_b

city: Wuhan

first: Yao

state: Hubei

address: No.1, Shizishan Street, Hongshan District

department: College of Animal Sciences and Technology

institute: Huazhong Agricultural University

description: TPMs for sRNA samples.txt

data_processing:
The Solexa pipeline (i.e., the software delivered with the Illumina Genome Analyzer) used for base-calling.
After filtering the low quality reads, all clean reads were aligned to the pig reference genome (ftp://ftp.ncbi.nlm.nih.gov/genomes/Sus_scrofa/) by Tophat with 2 nt fault tolerance.
Clean reads were obtained after removing low-quality reads and maintaining reads with lengths 14 nt and above. The sequencing length varied because of the different sequencing batches. Two lengths, 40 and 80 nt, were detected in the SE reads, with an index sequence of 7 nt. A database for balance with random bases of 3 nt was built to cut off the low-quality bases. Therefore, the obtained effective lengths of the longest bases were 28 and 69 nt. To detect the distribution, clean reads were mapped to the whole pig genome by using Tophat. Rfam(Burge et al., 2013) was used to identify sequence tags originating from repeats. Unique sequences were aligned with miRBase (V20.0)(Kozomara & Griffiths-Jones, 2011) to identify known porcine miRNAs (including mature and precursor miRNA). To determine new possible unknown miRNAs, samples were predicted by miRDeep2(Friedlander et al., 2008). Candidate piRNAs were classified from sequences of 24–32 nt, which did not originate from known sRNAs, imperfectly mapped to the genome or transcriptome and aligned with piRNA database(Sai Lakshmi & Agrawal, 2008). The expression profile of sRNA was normalized in transcripts per million (TPM). Correlation and DE analyses of sRNA were similar to those of mRNAs. Target prediction and functional annotation of DE miRNAs were performed with Miranda(Betel, Koppal, Agius, Sander, & Leslie, 2010) and DAVID.
Processed data files format and content: TPMs for sRNA samples
Genome_build: Sscrofa 10.2

organism: Sus scrofa

growth_protocol: 20 days and 200 days boars

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) in accordance with the manufacturer’s instructions.
Total RNA was treated with RQ1 DNase (Promega, Madison, Wisconsin, USA) to remove DNA. For each sample, 10 μg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen, Carlsbad, California, USA) before use for directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95 °C, followed by end repair and 5′ adaptor ligation. Reverse transcription was performed with the RT primers harboring the 3’ adaptor sequence and randomized hexamers. The cDNAs were purified and amplified. The PCR products corresponding to 200–500 bp were purified, quantified and then stored at –80 °C until used for sequencing. Total RNA (3 μg) was used for sRNA cDNA library preparation with the Balancer NGS Library Preparation Kit for sRNA (GnomeGen, San Diego, CA, USA) in accordance with the manufacture's instructions. In brief, RNAs were sequentially ligated to 3′- and 5′-end adaptors, reverse transcribed to cDNA and then amplified by PCR. Whole libraries were applied to 10% native PAGE gel electrophoresis; bands corresponding to mRNA insertion were cut and eluted. After ethanol precipitation and washing, the purified sRNA libraries were quantified with a Qubit Fluorometer (Invitrogen, Carlsbad, California, USA) before cluster generation and 36 nt single-end sequencing analysis using the Illumina GAIIx (Illumina, San Diego, CA, USA) in accordance with the manufacturer’s instructions.

tag: breed

value: Large White

tag: age

value: 20 days

value: sexual immaturity

value: testis


title: sRNA_LW3_a

description: TPMs for sRNA samples.txt

value: 200 days

value: sexual maturity


title: sRNA_LW2_b

description: TPMs for sRNA samples.txt


title: sRNA_LW1_b

description: TPMs for sRNA samples.txt


title: 35S::FRG1-YFP_ACC_R1


title: sRNA_LC2_b

description: TPMs for sRNA samples.txt

value: Lu Chuan


title: sRNA_LC3_b

description: TPMs for sRNA samples.txt


title: sRNA_LW1_a

description: TPMs for sRNA samples.txt


title: 96 hpf Nfe2 KO Water rep 3

city: Hamilton

first: Andrew

middle: G.

last: McArthur

state: Ontario

address: 1280 Main Street West

department: Biochemistry & Biomedical Sciences

institute: McMaster University

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), water controls. RNA sampled at 96 hours post-fertilization (hpf). Replicate 3

data_processing:
Raw RNA-Sequencing (RNA-Seq) reads were obtained from HudsonAlpha as 50bp paired-end reads in FASTQ format with approximately 25 million reads per sample. Reads were analyzed for various quality control parameters including: per base sequence quality, per sequence GC content, sequence length distribution and sequence duplication levels and Kmer content using the FastQC tool (Version 0.11.4).
Reads were then aligned to the Ensembl GRCz10 zebrafish reference genome using Tophat2 (Version 2.0.14), which functions based on Bowtie2 alignment software (Version 2.2.5) using a mean inner distance of 300 bp, a maximum intron length of 380,000bp and all other parameters set to default values.
Read counts for each gene were then obtained for the aligned reads using the Htseq-counts tool (Version 0.6.1). The Tophat accepted hits BAM file was analyzed against the Ensembl GTF zebrafish gene annotation reference, with pre-sorting by name through Samtools Sort (Samtools version 0.1.19) within the Htseq-count software. Raw counts data obtained from Htseq-counts were normalized using DESeq2 (Version 1.10.1) in R (version 3.2.3, 64bit platform) using size factors obtained from the total dataset and virtual reference sample based on the data.
Genome_build: GRCz10
Supplementary_files_format_and_content: EXCEL DeSeq2 normalized counts

growth_protocol: Adults were held in 2:1 female to male groups at a density of ≤ 5 fish/l in aerated, filtered, and re-circulated system water (28.5 °C) and fertilized eggs were obtained from multiple group breedings. Wildtype animals were on the AB background (Zebrafish International Resource Center, Eugene, OR). Fish husbandry protocols were approved by the Bates College Institutional Animal Care and Use Committee (Animal Welfare Assurance Number Number A3320-01) and the University of Michigan Institutional Animal Care and Use Committee (Animal Welfare Assurance Number Number A3114-01). To create a germline nfe2 knockout, a pair of vectors containing TAL effector nucleases (TALENs) targeting exon 3 of nfe2 were generated using the REAL (Restriction Enzyme And Ligation) assembly method. Component plasmids were obtained from Addgene (www.addgene.org/talengineering/talenkit/). Briefly, target sites were selected and TALENs designed using Zifit (http://zifit.partners.org/ZiFiT/), followed by assembly. mRNA was synthesized from the vectors and injected into single cell zebrafish embryos on an AB/TL hybrid background (Shavit et al, in preparation).  The TALEN target sequences are: 5'- TCACCCACCTCTTATGAG-3' and 5'- CATGACTACACGTGGTCA-3'.  A subsequent founder deletion of eight base pairs (GCACATGA) was found via sequencing in exon three starting at nucleotide position 468 from the translational start site; this deletion resulted in a frame shift, causing a change in protein sequence starting at amino acid 111 (M→ D) and the introduction of a premature stop codon 13 amino acids later.  The frameshift was introduced 161 amino acids prior to the Cap'n'collar (CNC) family basic leucine zipper domain that is responsible for DNA binding.

extract_protocol:
Total RNA was isolated from pooled animals using the Aurum Total RNA Mini Kit (BioRad, Hercules, California, USA) following the manufacturer’s protocol. At HudsonAlpha Institute for Biotechnology (Huntsville, AL, USA), the quality of the RNA was checked using Caliper Instrumentation (PerkinElmer, Waltham, MA, USA) and RiboGreen reagents (Invitrogen, Carlsbad, CA, USA).
Directional mRNA libraries with poly(A) selection were made using New England Biolabs (Ipswich, MA, USA) reagents:  NEBNext Poly (A) mRNA Isolation Magnetic Module, NEBNext First Strand Synthesis Module, NEBNext Second Strand Synthesis Module (with dUTP), NEBNext End Repair Module, NEBNext dA Tailing Module, and the NEBNext Quick Ligation Module.  Quality analysis of the libraries was carried out using PicoGreen (Thermo Fisher, Waltham, MA, USA) and Caliper instrumentation (PerkinElmer, Waltham, MA, USA). 50 base pair (bp), paired end, libraries were sequenced using the Illumina HiSeq v4 platform at HudsonAlpha Institute for Biotechnology (Huntsville, AL, USA).

treatment_protocol: Waterborne exposures to either diquat or tBOOH were carried out at three different developmental stages: 2 hours post fertilization (hpf), 48hpf, and 96hpf in 3 pools of 30 embryos per condition. Animals were exposed to no treatment, 20µM diquat or 1mM tBOOH for a 4-hour dosing period in glass scintillation vials in a 20mL volume of 0.3x Danieau’s. For phenotypic analysis, animals were moved to 0.3x Danieau’s for 48 hours post-exposure (hpe) and imaged with a Leica M165 FC stereoscope and DFC310FX camera. For RNA-Seq experiments, animals were moved to 0.3x Danieau’s for 4 hpe before being flash frozen using liquid nitrogen and stored at -80°C.

value: embryo

tag: genotype

value: Nfe2 knock-out


title: 96 hpf Nfe2 KO Water rep 2

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), water controls. RNA sampled at 96 hours post-fertilization (hpf). Replicate 2


title: sRNA_LC1_b

description: TPMs for sRNA samples.txt


title: sRNA_LC2_a

description: TPMs for sRNA samples.txt


title: sRNA_LC3_a

description: TPMs for sRNA samples.txt


title: sRNA_LC1_a

description: TPMs for sRNA samples.txt


title: 96 hpf Nfe2 KO tBOOH rep 3

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), exposed to 1 mM tBOOH. RNA sampled at 96 hours post-fertilization (hpf). Replicate 3


title: 96 hpf Nfe2 KO tBOOH rep 2

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), exposed to 1 mM tBOOH. RNA sampled at 96 hours post-fertilization (hpf). Replicate 2


title: 96 hpf Nfe2 KO tBOOH rep 1

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), exposed to 1 mM tBOOH. RNA sampled at 96 hours post-fertilization (hpf). Replicate 1


title: mRNA_LW3_a

description: RPKMs for mRNA samples.txt

data_processing:
The Solexa pipeline (i.e., the software delivered with the Illumina Genome Analyzer) used for base-calling.
After filtering the low quality reads, all clean reads were aligned to the pig reference genome (ftp://ftp.ncbi.nlm.nih.gov/genomes/Sus_scrofa/) by Tophat with 2 nt fault tolerance.
Raw sequence reads were processed into clean reads as follows: the two N-containing reads and the sequence adaptor were removed; low-quality reads were cut off, and the remaining reads with lengths 16 nt and above were considered clean. The single-ended read length was 80 nt; the index sequence was 7 nt. A database for balance with random bases of 3 nt was built to intercept the back of low-quality bases and obtained the effective length of up to 69 nt. All clean reads were aligned to the pig reference genome (ftp://ftp.ncbi.nlm.nih.gov/genomes/Sus_scrofa/) by Tophat with 2 nt fault tolerance. In the transcriptome data, vast majority of uniquely mapped reads (single-position alignment) originated from the mature mRNAs. The abovementioned mapping results showed that the majority of the polyA RNAs in this project were mature mRNAs or ncRNAs. The multi-position alignment (multiple mapped) reads were rRNA and tRNA-based. To ensure the credibility of the analysis results, uniquely mapped reads were used for subsequent statistical analysis. The expression profile of mRNAs was reflected by the reads per kilobase of exon model per million mapped reads (RPKMs), which were calculated using the formula published by Mortazavi(Mortazavi, Williams, McCue, Schaeffer, & Wold, 2008). Correlation analysis of gene expression levels between samples and cluster analysis of samples were performed to detect the degree of homogeneity in the samples. The edgeR (Robinson, McCarthy, & Smyth, 2010) software package was applied to detect DEGs. Genes with P ≤ 0.01 and |log2 Ratio| ≥ 1 were considered as DEGs. The functions of the DEGs were determined through the GO term and KEGG pathway annotation with the DAVID gene annotation tool (Huang da, Sherman, & Lempicki, 2009). Only GO-BP terms or KEGG pathways with P < 0.05 were considered significant.
Processed data files format and content: RPKMs for mRNA samples
Genome_build: Sscrofa 10.2


title: mRNA_LW1_b

description: RPKMs for mRNA samples.txt


title: 96 hpf Nfe2 KO Diquat rep 3

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), exposed to 20 μM Diquat. RNA sampled at 96 hours post-fertilization (hpf). Replicate 3


title: 96 hpf Nfe2 KO Diquat rep 2

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), exposed to 20 μM Diquat. RNA sampled at 96 hours post-fertilization (hpf). Replicate 2


title: mRNA_LC2_b

description: RPKMs for mRNA samples.txt


title: mRNA_LW1_a

description: RPKMs for mRNA samples.txt


title: 96 hpf AB Water rep 3

description: 30 pooled zebrafish wildtype embryos (AB background), water controls. RNA sampled at 96 hours post-fertilization (hpf). Replicate 3

value: wildtype


title: 96 hpf AB Water rep 1

description: 30 pooled zebrafish wildtype embryos (AB background), water controls. RNA sampled at 96 hours post-fertilization (hpf). Replicate 1


title: mRNA_LW2_b

description: RPKMs for mRNA samples.txt


title: mRNA_LC3_b

description: RPKMs for mRNA samples.txt


title: 96 hpf AB Water rep 2

description: 30 pooled zebrafish wildtype embryos (AB background), water controls. RNA sampled at 96 hours post-fertilization (hpf). Replicate 2


title: 96 hpf Nfe2 KO Diquat rep 1

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), exposed to 20 μM Diquat. RNA sampled at 96 hours post-fertilization (hpf). Replicate 1


title: sRNA_LW2_a

description: TPMs for sRNA samples.txt


title: mRNA_LC1_b

description: RPKMs for mRNA samples.txt


title: 96 hpf AB tBOOH rep 3

description: 30 pooled zebrafish wildtype embryos (AB background), exposed to 1 mM tBOOH. RNA sampled at 96 hours post-fertilization (hpf). Replicate 3


title: 96 hpf AB tBOOH rep 2

description: 30 pooled zebrafish wildtype embryos (AB background), exposed to 1 mM tBOOH. RNA sampled at 96 hours post-fertilization (hpf). Replicate 2


title: mRNA_LC3_a

description: RPKMs for mRNA samples.txt


title: 96 hpf Nfe2 KO Water rep 1

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), water controls. RNA sampled at 96 hours post-fertilization (hpf). Replicate 1


title: mRNA_LW3_b

description: RPKMs for mRNA samples.txt


title: 96 hpf AB tBOOH rep 1

description: 30 pooled zebrafish wildtype embryos (AB background), exposed to 1 mM tBOOH. RNA sampled at 96 hours post-fertilization (hpf). Replicate 1


title: mRNA_LC2_a

description: RPKMs for mRNA samples.txt


title: mRNA_LW2_a

description: RPKMs for mRNA samples.txt


title: 96 hpf AB Diquat rep 1

description: 30 pooled zebrafish wildtype embryos (AB background), exposed to 20 μM Diquat. RNA sampled at 96 hours post-fertilization (hpf). Replicate 1


title: mRNA_LC1_a

description: RPKMs for mRNA samples.txt


title: 96 hpf AB Diquat rep 2

description: 30 pooled zebrafish wildtype embryos (AB background), exposed to 20 μM Diquat. RNA sampled at 96 hours post-fertilization (hpf). Replicate 2


title: 96 hpf AB Diquat rep 3

description: 30 pooled zebrafish wildtype embryos (AB background), exposed to 20 μM Diquat. RNA sampled at 96 hours post-fertilization (hpf). Replicate 3


title: 48 hpf Nfe2 KO Water rep 3

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), water controls. RNA sampled at 48 hours post-fertilization (hpf). Replicate 3


title: 48 hpf Nfe2 KO Diquat rep 2

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), exposed to 20 μM Diquat. RNA sampled at 48 hours post-fertilization (hpf). Replicate 2


title: 48 hpf Nfe2 KO Diquat rep 1

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), exposed to 20 μM Diquat. RNA sampled at 48 hours post-fertilization (hpf). Replicate 1


title: 48 hpf Nfe2 KO tBOOH rep 3

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), exposed to 1 mM tBOOH. RNA sampled at 48 hours post-fertilization (hpf). Replicate 3


title: 48 hpf Nfe2 KO Water rep 2

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), water controls. RNA sampled at 48 hours post-fertilization (hpf). Replicate 2


title: 48 hpf Nfe2 KO Diquat rep 3

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), exposed to 20 μM Diquat. RNA sampled at 48 hours post-fertilization (hpf). Replicate 3


title: 48 hpf Nfe2 KO tBOOH rep 1

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), exposed to 1 mM tBOOH. RNA sampled at 48 hours post-fertilization (hpf). Replicate 1


title: 48 hpf AB Water rep 2

description: 30 pooled zebrafish wildtype embryos (AB background), water controls. RNA sampled at 48 hours post-fertilization (hpf). Replicate 2


title: 48 hpf AB Diquat rep 3

description: 30 pooled zebrafish wildtype embryos (AB background), exposed to 20 μM Diquat. RNA sampled at 48 hours post-fertilization (hpf). Replicate 3


title: 48 hpf Nfe2 KO Water rep 1

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), water controls. RNA sampled at 48 hours post-fertilization (hpf). Replicate 1


title: 48 hpf AB Water rep 3

description: 30 pooled zebrafish wildtype embryos (AB background), water controls. RNA sampled at 48 hours post-fertilization (hpf). Replicate 3


title: 48 hpf AB Diquat rep 2

description: 30 pooled zebrafish wildtype embryos (AB background), exposed to 20 μM Diquat. RNA sampled at 48 hours post-fertilization (hpf). Replicate 2


title: 48 hpf AB tBOOH rep 3

description: 30 pooled zebrafish wildtype embryos (AB background), exposed to 1 mM tBOOH. RNA sampled at 48 hours post-fertilization (hpf). Replicate 3


title: 2 hpf Nfe2 KO Water rep 1

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), water controls. RNA sampled at 2 hours post-fertilization (hpf). Replicate 1


title: 48 hpf AB Diquat rep 1

description: 30 pooled zebrafish wildtype embryos (AB background), exposed to 20 μM Diquat. RNA sampled at 48 hours post-fertilization (hpf). Replicate 1


title: 2 hpf Nfe2 KO tBOOH rep 3

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), exposed to 1 mM tBOOH. RNA sampled at 2 hours post-fertilization (hpf). Replicate 3


title: 48 hpf AB Water rep 1

description: 30 pooled zebrafish wildtype embryos (AB background), water controls. RNA sampled at 48 hours post-fertilization (hpf). Replicate 1


title: 2 hpf Nfe2 KO Water rep 2

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), water controls. RNA sampled at 2 hours post-fertilization (hpf). Replicate 2


title: 2 hpf Nfe2 KO Water rep 3

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), water controls. RNA sampled at 2 hours post-fertilization (hpf). Replicate 3


title: 2 hpf Nfe2 KO tBOOH rep 1

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), exposed to 1 mM tBOOH. RNA sampled at 2 hours post-fertilization (hpf). Replicate 1


title: 2 hpf Nfe2 KO tBOOH rep 2

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), exposed to 1 mM tBOOH. RNA sampled at 2 hours post-fertilization (hpf). Replicate 2


title: 2 hpf Nfe2 KO Diquat rep 2

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), exposed to 20 μM Diquat. RNA sampled at 2 hours post-fertilization (hpf). Replicate 2


title: 2 hpf Nfe2 KO Diquat rep 3

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), exposed to 20 μM Diquat. RNA sampled at 2 hours post-fertilization (hpf). Replicate 3


title: 2 hpf Nfe2 KO Diquat rep 1

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), exposed to 20 μM Diquat. RNA sampled at 2 hours post-fertilization (hpf). Replicate 1


title: 48 hpf AB tBOOH rep 2

description: 30 pooled zebrafish wildtype embryos (AB background), exposed to 1 mM tBOOH. RNA sampled at 48 hours post-fertilization (hpf). Replicate 2


title: BS-seq_H9_hPGCLC_d12_2

first: Felix

last: Krueger

address: Granta Park

institute: Altos Labs

data_processing:
Library strategy: PBAT
PBAT: Raw sequence reads from PBAT libraries were trimmed to remove poor quality reads and adapter contamination using Trim Galore (v0.4.1, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The remaining sequences were mapped using Bismark (v0.14.4) (Krueger and Andrews, 2011) with the following set of parameters to the mouse reference genome GRCm38 or the human reference genome GRCh37 in paired-end mode: --pbat to be able to count overlapping parts of the reads only once while writing out unmapped singleton reads; in a second step remaining singleton reads were aligned in single-end mode for Read 1: --pbat; or single-end mode for Read 2: defaults. Reads were then deduplicated and CpG methylation calls were extracted from the deduplicated mapping output ignoring the first 6bp of each read to reduce the methylation bias typically observed in PBAT libraries using the Bismark methylation extractor (v0.14.4) with the following parameters: a) paired-end mode: --ignore 6 --ignore_r2 6; b) single-end mode: --ignore 6.
genome build: GRCh37
processed data files format and content: Bismark CpG coverage report files are from paired-end mapping only, are tab-delimited and use 1-based genomic coordinates for every covered cytosine position in the experiment and are in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

extract_protocol:
PBAT: For small sample amounts (PGCLC samples) post-bisulfite adaptor tagging (PBAT) libraries were prepared directly from cell lysates following recently described protocols (Miura et al., 2012; Smallwood et al., 2014). PBAT libraries were prepared by bisulfite converting Proteinase K digested cell lysates using the EZ DNA Methylation-Direct Kit (Zymo). After cleanup, 1st strand synthesis was performed using 6N-forward oligos at 37°C for 90 minutes. Subsequently, samples were treated with Exonuclease I for 1 hour at 37°C, and DNA was purified using AMPure XP beads (Agencourt). Samples were eluted in 2nd strand synthesis mix with 6N-reverse oligos and incubated at 37°C for 90 minutes. DNA was purified and amplified with KAPA HiFi HotStart DNA Polymerase (KAPA Biosystems). All amplified libraries were purified and assessed for quality and quantity using High-Sensitivity DNA chips on the Agilent Bioanalyzer. High-throughput sequencing of all libraries was carried out with a 125 bp paired-end protocol on a HiSeq 2000 instrument (Illumina).
Genomic DNA and total RNA were isolated from the samples using the Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions.

tag: background strain/cell line

tag: cell type

value: PGC-like cells (PGCLCs)

value: Wild-type


title: 2 hpf AB Water rep 3

description: 30 pooled zebrafish wildtype embryos (AB background), water controls. RNA sampled at 2 hours post-fertilization (hpf). Replicate 3


title: BS-seq_H9_hPGCLC_d12_1