title: F3.5.2 200 micron 2D # 2

status: Public on Dec 05 2015

city: Buffalo

first: Michael

last: Buck

state: NY

address: 701 Ellicott St

department: Biochemistry

institute: SUNY at Buffalo

data_processing:
Raw sequencing reads were mapped to the Homo sapiens genome (hg19 build) using Tophat – version 2.0.7
count files generated with HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: space-delimited text files including variance stablized count values for each sample

source_name: Embryoid Body

growth_protocol: Generation of 200 or 500 micron uniform EBs was done by templating in custom microarrays of polydimethylsiloxane (PDMS) as previously described14

extract_protocol:
RNA was isolated with Ambion PureLink Mini RNA isolation kit
Total RNA was processed for sequencing using the TruSeq RNA Sample Preparation Kit (Illumina). Samples were four-plexed and 50bp single-end sequenced on an Illumina HiSeq2500.

treatment_protocol: Single cells we chemically dissociated 2D stem cell colonies using the Gentle Dissociation Agent (Stem Cell Technologies, Vancouver, Canada). Alternatively we generated small 2D clusters, by mechanical passaging for loading into microarrays.

tag: embryoid body size

tag: stem cell lines

tag: eb formation method


title: H3.3.1 200 micron 2D # 1

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens


title: ham_low_3

status: Public on Dec 06 2015

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

data_processing:
Basecalls performed using CASAVA version 1.8.2
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters and poly-A sequences
Reads shorter than 36 bp and reads with a quality lower thanthe default of 20 were removed from the dataset.
Cleaned sequences were aligned to the Sus scrofa genome (assembly Sscrofa10.2) with reference annotation containing more than 21K genes listed in the Ensembl database.
Alignment and estimation of gene expression level were made using the RSEM package supported by Bowtie 2 aligner.
Differentially expressed genes, gene isoforms and their corresponding p-values were determined using the statistical methods edgeR, baySeq and DESeq2
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: raw.genes.csv [raw genes counts]
Supplementary_files_format_and_content: raw.isoforms.csv [raw isoforms counts]
Supplementary_files_format_and_content: results.genes.xlsx [edgeR, baySeq and DESeq2 results for differential expression analysis (high vs low) for ham and loin across genes ]
Supplementary_files_format_and_content: results.isoforms.xlsx [edgeR, baySeq and DESeq2 results for differential expression analysis (high vs low) for ham and loin across isoforms]

organism: Sus scrofa

growth_protocol: The pigs were maintained at the Pig Test Station of the National Research Institute of Animal Production in Chorzelów under the same housing and feeding conditions according to SKURTCh procedure.

extract_protocol:
RNA was isolated using TRI Reagent (Applied Biosystems) according to the manufacturer’s protocol. Samples of muscles were homogenised with beads using a Bullet Blender 24 homogenizer (Next Advance). RNA was purified by a bead method (Agencourt RNAClean XP kit) and its quality and quantity was assessed by a Qubit Fluorometer (Invitrogen) and TapeStation 2200 system (RNA tapes, Agilent). Ribosomal RNA was removed from 5000 ng of total RNA using a Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat) (Epicentre). The absence of rRNA was verified on the TapeStation 2200.
A TruSeq RNA Sample Preparation Kit v2 (Illumina) was used to prepare cDNA libraries from 100 ng aliquots of the RNA-depleted samples according to the manufacturer’s protocol. The cDNA samples were ligated with indexed adaptors in the order shown in Table 2. Finally, the libraries were amplified in 15 cycles of PCR and their quantity was estimated using the Qubit 2.0 Fluorometer and 2200 TapeStation D1000 tapes. The final concentration of the cDNA libraries was normalised to 10 nM, after which they were pooled .
The libraries were diluted according to a cluster generation protocol and loaded into a v3 Illumina flowcell (16 samples per line with four technical replicates)

tag: breed

value: Polish Landrace

tag: age

value: 180 day-old

tag: Sex

value: female

tag: shear force

value: low

tag: tissue

value: semimembranosus muscle


title: H3.3.1 200 micron 2D # 2


title: fibre2B_11

institute: National Research Institute of Animal Production

data_processing:
Basecalls performed using CASAVA version 1.8.2
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters and poly-A sequences.
The raw reads were aligned to the Sus scrofa genome (assembly Sscrofa10.2) as a reference, while the whole procedure was followed by alignment parameters from ENCODE3's STAR-RSEM pipeline
The quality control metrics across aligned reads per sample were obtained using RNA-SeQC software
Differentially expressed genes, gene isoforms and their corresponding p-values were determined using the statistical methods edgeR, baySeq and DESeq2
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: raw.genes.csv: raw genes counts
Supplementary_files_format_and_content: raw.isoforms.csv: raw isoforms counts
Supplementary_files_format_and_content: results.genes.xlsx: edgeR, baySeq and DESeq2 results for differential expression analysis (fibre1 vs fibre2B) across genes
Supplementary_files_format_and_content: results.isoforms.xlsx: edgeR, baySeq and DESeq2 results for differential expression analysis (fibre1 vs fibre2B) across isoforms

source_name: longissimus lumborum muscle

extract_protocol:
The samples of longissimus lumborum muscle (taken from the some part of muscle as samples for histological analysis) was collected immediately after slaughter and stored at -20°C in RNAlater solution (Ambion Inc., Austin, USA). Total RNA was isolated using TRI Reagent (Ambion, Life Technologies) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 300 ng of total RNA for the construction of sequencing libraries.

value: 23 week

tag: type i fiber [%]

tag: type iib fiber [%]

tag: gender


title: F3.5.2 200 micron 2D # 1


title: H9 500 micron SC # 3

value: Single cell


title: H9 200 micron SC # 1


title: H9 500 micron SC # 1


title: H9 200 micron SC # 3


title: H9 500 micron 2D # 1


title: H9 200 micron 2D # 1


title: H9 200 micron 2D # 3


title: H9 500 micron 2D # 3


title: zfs1dd2_3

status: Public on Dec 04 2015

city: Durham

first: Melissa

last: Wells

state: NC

address: 111 TW Alexander Drive

department: LST

institute: NIEHS

description: RNA-seq from polyA+_RNA

data_processing:
Data were obtained using the Illumina Genome Analyzer CASAVA 1.8 Pipeline
ELAND was used to map mRNA-Seq reads to the whole genome reference assembly.
EpiCenter (Huang et al., 2011) was used to determine RPKM values and to identify differentially expressed genes between  groups
Supplementary_files_format_and_content: tab-delimited text file including RPKM values for each sample

organism: Candida albicans

source_name: Yeast

growth_protocol: Cultures were grown to mid-log phase in YPD at 30˚C

extract_protocol: Libraries were prepared according to Illumina's instructions

treatment_protocol: No treatment

tag: genotype/variation

value: zfs1 deletion


title: zfs1dd1_4

description: RNA-seq from polyA+_RNA


title: zfs1dd2_2

description: RNA-seq from polyA+_RNA


title: zfs1dd1_3

description: RNA-seq from polyA+_RNA


title: zfs1dd2_1

description: RNA-seq from polyA+_RNA


title: fibre2B_16


title: fibre1_5


title: zfs1dd1_1

description: RNA-seq from polyA+_RNA


title: zfs1dd1_2

description: RNA-seq from polyA+_RNA


title: CaWT_4

description: RNA-seq from polyA+_RNA

value: Wild Type


title: CaWT_3

description: RNA-seq from polyA+_RNA


title: ham_high_1

value: Pulawska

value: high


title: 5wk_tetoff_10289-3

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

data_processing:
Illumina Casava1.6 and Casava1.8 software was used for basecalling. All 50 nt reads use phred33 quality scores.
Sequence reads were mapped to the transcriptome, defined by annotation based on the UCSC mm10 genes.gtf but with mitochondrial RNAs and human-Mfn2 cDNA added, and associated bowtie2 index provided by Illumina iGenomes (incorporating the additional mitochondrial RNAs and human-Mfn2 cDNA), using tophat v2.0.10.
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the supplied gtf, based on UCSC mm10 genes.gtf but with mitochondrial RNAs and human-Mfn2 cDNA added.
htseq-count data allows each user maximum flexibility in performing sample (library) depth normalization and differential gene expression using software such as DESeq or edgeR.
Additionally, we used Cufflinks v2.1 to calculate FPKM for each gene entry in each library.  However, this was merely done for later graph display.  Actual calculations of differential gene expression used htseq-count data as input to DESeq.
Genome_build: mm10
Supplementary_files_format_and_content: single tab-delimited text files include htseq-count values for each gene, or FPKM values for each gene.

molecule: polyA RNA

organism: Mus musculus

source_name: 5wk_tetoff_heart_left ventricle

extract_protocol:
Hearts were removed and ventricular apexes were flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Polyadenylated RNA was isolated using oligo(dT) binding, followed by chemical fragmentation and preparation of non-strand-specific, single-end RNA-Seq libraries, as per Methods Mol Biol. 2015;1299:27-49, PMID 25836573.
non-strand-specific, single-end RNA-Seq

tag: strain background

value: FVB/N

value: tet-off control (tetoff)

value: 5 weeks

value: heart, left ventricle


title: CaWT_2

description: RNA-seq from polyA+_RNA


title: 5wk_tetoff_10289-1


title: 5wk_tetoff_10289-2


title: 5wk_ntg_15933-3_run-in-P1-batch

source_name: 5wk_ntg_heart_left ventricle

value: nontransgenic (ntg)


title: 5wk_ntg_15935-10_repeat-in-P1-batch


title: 5wk_ntg_15928-7_repeat-in-P1-batch


title: 5wk_ntg_15927-6_repeat-in-P1-batch


title: 5wk_ntg_15935-10


title: 5wk_ntg_15928-7


title: 5wk_ntg_10287-6


title: 5wk_Mfn2wt_15930-8

source_name: 5wk_Mfn2wt_heart_left ventricle

value: human-Mfn2-overexpressing (Mfn2wt)


title: 5wk_ntg_15927-6


title: 5wk_Mfn2wt_15931-9


title: 5wk_Mfn2AA_10289-8

source_name: 5wk_Mfn2AA_heart_left ventricle


title: 5wk_Mfn2AA_10287-8


title: P21_tetoff_10549-5

source_name: P21_tetoff_heart_left ventricle

value: P21 (3 weeks)


title: 5wk_Mfn2AA_10289-9


title: 5wk_Mfn2wt_15926-4


title: 5wk_Mfn2AA_10289-7


title: P21_tetoff_10549-2


title: P21_tetoff_10549-4


title: P21_tetoff_10534-3


title: P21_ntg_10547-2_repeat-in-P1-batch

source_name: P21_ntg_heart_left ventricle


title: P21_ntg_10583-1


title: P21_ntg_10547-7


title: CaWT_1

description: RNA-seq from polyA+_RNA


title: P21_ntg_10547-3


title: P21_ntg_10547-5_repeat-in-P1-batch


title: P21_ntg_10547-2


title: P21_Mfn2wt_10583-2

source_name: P21_Mfn2wt_heart_left ventricle


title: P21_Mfn2wt_10583-3


title: 5wk_Mfn2wt_15934-5


title: P21_Mfn2wt_10583-5


title: P21_ntg_10547-1


title: P21_Mfn2wt_10547-8


title: P21_Mfn2AA_10534-6

source_name: P21_Mfn2AA_heart_left ventricle


title: P21_Mfn2wt_10547-9


title: P21_Mfn2wt_10547-4


title: P21_Mfn2AA_10534-4


title: P21_Mfn2AA_10534-2


title: P21_Mfn2AA_10534-5


title: P21_tetoff_10549-3


title: P1_tetoff_10619-3

value: heart, whole


title: P1_tetoff_10619-2


title: P1_tetoff_10587-3


title: P21_ntg_10547-1_repeat-in-P1-batch


title: P21_ntg_10547-5


title: P1_tetoff_10587-1


title: P1_tetoff_10586-2


title: P1_ntg_10582-4


title: P1_ntg_10582-2


title: P1_ntg_10582-5


title: P1_ntg_10582-1


title: P21_Mfn2AA_10534-8


title: P1_ntg_10582-3


title: P1_Mfn2wt_10546-1


title: P21_Mfn2AA_10534-1


title: P1_Mfn2wt_10546-9


title: P1_Mfn2AA_10619-1


title: V1.5 MIN6 RNA rep3

city: Chapel Hill

first: Jeanette

last: Baran-Gale

address: 120 Mason Farm Rd.

institute: University of North Carolina at Chapel Hill

data_processing:
Reads were first trimmed by cutAdapt (parameters -O 10 –e 0.1) to remove remnants of the 3’-adaptor sequence. Next the first 4 and last 4 bases were trimmed from the  NEXTflex reads to remove the degenerate adapter sequence.
Trimmed reads of size 14-41  nt. were next aligned, without mismatches allowed, to the mm9 genome using Bowtie(parameter set: -q -a -m 20 -n 0 -e 70 ).
All aligned reads separated by less than 65 nt. or less were merged.  These merged windows were then extended by 5 nt. on either end. All reads that could not be aligned without mismatches, or those that aligned without mismatches only to regions of the genome lacking transcriptional activity, were aligned (with mismatches allowed) to the extended windows using SHRiMP2.
Aligned reads are grouped by 5’-start position (5’-isomiRs) and are annotated with respect to the 5’-start position of the annotated (miRBase r19) miRNA at the same locus.
Genome_build: mm9
Supplementary_files_format_and_content: Collapsed aligned reads in BED format. The "Name" field is the type of alignment (Exact= no mismatches; 4A18 = 4 matches, an A mismatch then 18 matches). The "Score" field is the number of reads at this position with exactly this type of alignment.

source_name: Cell-line

growth_protocol: MIN6 cells were cultured in high glucose (25mM) DMEM supplemented with 10% heat-inactivated fetal bovine serum.

extract_protocol:
Libraries were constructe with either (1) Illumina V1.5 small RNA library prep kit, (2) Illumina TruSeq small RNA library prep kit, or (3) Bioo Scientific NEXTflexV2 small RNA libarary prep kit
Libraries were sequenced on the GAIIx or HiSeq

tag: cell line


title: V1.5 MIN6 RNA rep1


title: P1_Mfn2wt_10546-3


title: P1_Mfn2AA_10586-3


title: V1.5 MIN6 RNA rep2


title: TruSeq MIN6 RNA rep3


title: TruSeq MIN6 RNA rep2


title: P1_Mfn2wt_10546-6


title: TruSeq MIN6 RNA rep1


title: whOrg1_G9_hOrg33d_c1

status: Public on Dec 07 2015

city: Leipzig

first: Gray

last: Camp

address: Deutscher Pl. 6

department: Evolutionary Genetics

country: Germany

institute: Max Planck Institute for Evolutionary Anthropology

description:
Single cell G9 from human cerebral organoid experiment at 33d chip 1
whOrg1_G9_hOrg33d_c1

data_processing:
"freeIbis" was used as an efficient basecaller with calibrated quality scores for Illumina sequencers. (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.)
"leeHom" was used to trim adapters and merge Illumina sequencing reads. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.)
"deML" was used for robust demultiplexing of Illumina sequences using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.)
Reads were aligned against the human genome (build GRCh38.77 from ENSEMBLE) using TopHat v2.0.14. The genome was indexed using Bowtie v2.2.6
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks v2.2.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Master data frame including sample name, gene ID, and FPKM values for each single cell.

source_name: iPSC 409B2

growth_protocol: Cerebral organoids were generated using the same protocol as described Lancaster et al. Nature Protocols 2014, with the exception that mTESR1 (Stem Cell Technologies) was used during embryoid body formation.

extract_protocol:
Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions at a dilution of 1:40,000.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

treatment_protocol: Whole cerebral organoids and microdisseccted ventricles were dissociated in 2 ml of Accutase (StemPro) containing 0.2 U/µl Dnase I (Roche) for approximately 45 minutes. Dissociated cells were filtered through 40, 30, and 20 μm diameter strainers to create a single cell suspension.

tag: Stage

value: 33 days

value: Dissociated whole cerebral organoid


title: WT DNase-Seq low dose

city: Houston

first: Bokai

last: Zhu

state: Texas

address: One Baylor Plaza, M813

department: MCB

institute: Baylor College of Medicine

library_source: genomic

data_processing:
The sequences identified were mapped to the mouse genome (NCBI37/UCSC mm9) using BOWTIE function in Galaxy. Only the sequences uniquely mapped with no more than 2 mismatches were kept and used as valid reads. PCR duplicates were also removed.
Peak calling was carried out by MACS (version 1.4.2 20120305) in Galaxy/Cistrome (options --mfold 10, 30 --pvalue 1e-5), on each DNase-seq file.
To account for the different sequencing depths between samples, the signal files generated from MACS were normalized by Signal Extraction Scaling (SES) method (Meyer and Liu, 2014). The peak summits were used as the binding site centers, and the normalized signal files were used as the binding strength for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated by Galaxy/cistrome

molecule: genomic DNA

source_name: liver

extract_protocol:
Mouse liver samples were submerged in PBS and cut into small pieces. After spinning down, nuclei were extracted by resuspending cells in sucrose homogenization buffer (300 mM sucrose, 10 mM Tris-HCl, pH 7.4, 15 mM NaCl, 5 mM MgCl2, 0.1 Mm EGTA, 60 mM KCl, 0.2% IGEPAL CA-630, 0.5 mM DTT and 1x Protease inhibitor) for 5 minutes on ice. The nuclei were spun down at 500g for 5min at 4 °C with brakes off and washed with reaction buffer (1x RDD (Qiagen) with 2% glycerol) using pipettes tips with cut-off ends. Gentle mixing was applied to minimize the breakage of the genomic DNA. The final nuclei were digested with different units of DNase I  in 1x reaction buffer on ice for 1h in a cold room
DNaseI assays and library construction were carried out using the standard protocols developed by John Stamatoyannopoulos laboratory (John et al., 2013).

tag: strain

value: C57BL/6J/129 SV mixed background

value: Male

value: 10-20 weeks

tag: genotype

value: Wild-type


title: P1_ntg_10546-4


title: Obese_sRNA_rep10

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

description:
miRNA_counts.csv
piRNA_counts.csv
snRNA_counts.csv
tRF_counts.csv

data_processing:
Sequenced reads were trimmed for adaptor sequences using trimmomatic 0.30, then mapped to hg19 whole genome using bowtie v1.0.0 with parameters -n 1 -l 15 -S -a -m 1000 --best --strata --chunkmbs 256
ncRNAs with an expression less than 1 counts per million in half of the libraries were excluded, and differential expression was found using edgeR v. 3.6.0 using the exactTest function
Supplementary_files_format_and_content: csv files with the different features investigated, and how many reads in each sample map to those features.
Basecalls performed using CASAVA version 1.8.2
Genome_build: hg19

source_name: semen

extract_protocol:
Total RNA was isolated by the TRIzol® method (Life Technologies)
SncRNA sequencing libraries were prepared using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs), according to the manufacturer’s instructions. Molecules of 20-50 nucleotides were separated by acrylamide gel electrophoresis, extracted, and sequenced on a HiSeq Illumina instrument.

value: motile semen

tag: condition

value: obese

tag: patient


title: Obese_sRNA_rep9


title: P1_Mfn2AA_10586-7


title: Obese_sRNA_rep8


title: Obese_sRNA_rep7


title: input DNA, mESD-EpiSCs

city: Tokyo

first: Masato

last: Morikawa

address: 2-21-1 Kaga, Itabashi-ku

department: Advanced Comprehensive Research Organization

country: Japan

institute: Teikyo University

data_processing:
Reference files of the mouse genome mm9 (NCBI build 37, July 2007) and GTF annotation file were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html).
Low quality reads were eliminated using FASTX-Toolkit with the command "fastq_quality_filter -q 20 -p 100"
ChIP-seq data sets were aligned to the mm9 genome assembly using Bowtie (version 1.1.0) (Langmead et al., 2009) with the command "-S -a --best --strata -n 1 -m 1".
BAM files were sorted using Picard SortSam (http://picard.sourceforge.net/).
Smad1/5 binding regions were identified using MACS software (Model based analysis of ChIP-seq) (version 1.4.2) (Zhang et al., 2008) with a p-value threshold of 1e-5, which generated BED files and WIG files.
WIG to bigWig conversion was performed  using UCSC wigToBigWig.
To reduce the size of the bigWig files, regions with value less than 2 were removed using bwtool (Pohl and Beato, 2014) with the command "remove less 2".
Genome_build: mm9
Supplementary_files_format_and_content: BED and WIG files were generated using MACS (version 1.4.2).

source_name: mouse ESCs (E14)

growth_protocol: E14 cells were cultured at 37°C with 5% CO2 and were maintained on gelatin (Millipore)-coated dishes in Dulbecco's modified Eagle's medium (DMEM) (Gibco/Life Technologies), with 15% ES-qualified fetal bovine serum (FBS), 40 μM β-mercaptoethanol (both from Millipore), 2 mM L-Glutamine, 1xMEM nonessential amino acid, 100 U/ml penicillin and 100 μg/ml streptomycin (all from Gibco/Life Technologies), and 1000 U/ml LIF (Millipore). E14 cells were also maintained LIF+BMP-4 in basal media, such as ESGRO Complete Basal Medium (Millipore) and N2B27 medium, which consisted of one volume DMEM/F12 combined with one volume Neurobasal medium, supplemented with 0.5% N2 Supplement, 1% B27 Supplement, 50 μM β-mercaptoethanol, 2 μM L-Glutamate, 100 U/ml penicillin and 100 μg/ml streptomycin (all from Gibco/Life Technologies). Differentiation and maintenance of ESD-EpiSCs were essentially as described (Zhang et al., Development, 137, 2095-2105, 2010). ESD-EpiSCs were maintained on plates coated with FBS in N2B27 medium supplemented with 12 ng/ml FGF2 and 20 ng/ml Activin A. The cells were passaged every 2-3 days as clumps.

extract_protocol:
ChIP using anti-Smad1/5 antibody were performed essentially as described  (Koinuma et al, Mol Cell Biol, 29, 172-186, 2009). SMAD1/5-DNA complexes were isolated with antibody. Briefly, mESCs and mESD-EpiSCs were cultured in 100-mm plates and three to four plates (approximately 5x107 cells) were used for one immunoprecipitation. Cells were fixed with 1% formaldehyde for 10 min at RT with swirling. Cross-linking was stopped by addition of glycine to a final concentration of 125 mM and washed twice with ice-cold PBS. The cross-linked cells were harvested by scraping, pelleted, and resuspended in 1 ml of lysis buffer containing 50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 1% SDS, and protease inhibitor cocktail (P8340, Sigma-Aldrich). Chromatin was sonicated using a Bioruptor sonicator (Diagenode) for 5 min in a cycle of 30 sec ON and 30 sec OFF at ‘high’ power, in order to shear DNA with an average fragment size of 200-500 bp. Cell extract was diluted 10-fold in ChIP dilution buffer [20 mM Tris-HCl (pH 8.0), 2 mM EDTA, 1% Triton X-100, 150 mM NaCl, cOmplete EDTA-free protease inhibitor cocktail]. Anti-mouse IgG Dynabeads (Invitrogen Life Technologies) were preincubated with 10 µg of antibody at 4°C overnight. Chromatin was incubated with prepared beads at 4°C for more than 8 hr. The beads were then washed five times with RIPA buffer [50 mM HEPES-KOH (pH 7.0), 0.5 M LiCl, 1 mM EDTA, 0.7% deoxycholate, 1% NP-40] and once with TE buffer (pH 8.0). Immunoprecipitated samples were eluted and reverse cross-linked by incubation in elution buffer [50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 1% SDS] at 65°C overnight. Genomic DNA was then extracted with a QIAquick PCR purification kit (Qiagen).
The library was prepared using NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (New England Biolabs).

treatment_protocol: ESD-EpiSCs were treated with 10 ng/ml of BMP-4 for 1.5 h or 24 h.

tag: cell type

value: mouse ESD-EpiSCs

tag: protocol

tag: chip antibody


title: input DNA, mESCs

value: mouse ESCs (E14)


title: Smad1/5 ChIP-seq, mESD-EpiSCs, BMP4, 1.5h

value: anti-Smad1 (clone 913C1b, Bio Matrix Research, Japan)


title: RNA-seq, mESD-EpiSCs, BMP4, 24h

data_processing:
Reference files of the mouse genome mm9 (NCBI build 37, July 2007) and GTF annotation file were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html).
RNA-seq reads were aligned and gene expression levels in fragments per kilobase of exon per million fragments mapped (FPKM) were estimated using Tophat/Cufflinks (version 2.0.13 and 2.2.1, respectively) with the default parameter settings (Trapnell et al., 2012).
BAM files were sorted using Picard SortSam (http://picard.sourceforge.net/).
BAM to bigWig conversion was performed  using "samtools depth" combined with "UCSC wigToBigWig".
Genome_build: mm9
Supplementary_files_format_and_content: A tab-delimited text file includes FPKM values of genes for each Sample, which was generated by Cufflinks; bigWig files were generated by Tophat and wigToBigWig.

growth_protocol: E14 cells were cultured at 37°C with 5% CO2 and were maintained on gelatin (Millipore)-coated dishes in Dulbecco's modified Eagle's medium (DMEM) (Gibco/Life Technologies), with 15% ES-qualified fetal bovine serum (FBS), 40 μM β-mercaptoethanol (both from Millipore), 2 mM L-Glutamine, 1xMEM nonessential amino acid, 100 U/ml penicillin and 100 μg/ml streptomycin (all from Gibco/Life Technologies), and 1000 U/ml LIF (Millipore). E14 cells were also maintained LIF+BMP-4 in basal media, such as ESGRO Complete Basal Medium (Millipore) and N2B27 medium, which consisted of one volume DMEM/F12 combined with one volume Neurobasal medium, supplemented with 0.5% N2 Supplement, 1% B27 Supplement, 50 μM β-mercaptoethanol, 2 μM L-Glutamate, 100 U/ml penicillin and 100 μg/ml streptomycin (all from Gibco/Life Technologies). Differentiation and maintenance of ESD-EpiSCs were essentially as described (Zhang et al., 2010). ESD-EpiSCs were maintained on plates coated with FBS in N2B27 medium supplemented with 12 ng/ml FGF2 and 20 ng/ml Activin A. The cells were passaged every 2-3 days as clumps.

extract_protocol:
RNA was isolated using the RNeasy Kit (Qiagen).
Directional RNA-seq libraries were prepared according to a slightly modification of the protocol provided by Illumina. Briefly, 10 μg of total RNA were subjected to two rounds of oligo-dT purification using Dynabeads Oligo(dT)25 (Invitrogen/Life Technologies). The purified RNA was decapped with Tobacco Acid Pyrophosphatase (TAP) (Epicentre), followed by extraction with phenol:chloroform:isoamyl alcohol (PCIA) precipitation. 100 ng of poly(A)+ RNA were fragmented with 10x fragmentation buffer (Ambion/Life Technologies). Decapped and fragmented RNA was treated with Antarctic phosphatase (New England Biolabs) and T4 polynucleotide kinase (New England Biolabs). The modified RNA was cleaned up with an RNeasy MinElute kit (Qiagen). Libraries were constructed using the Illumina Small RNA sample preparation kit with the v1.5 sRNA 3'adaptor (Illumina).


title: Smad1/5 ChIP-seq, mESD-EpiSCs, BMP4, 24h


title: Smad1/5 ChIP-seq, mESCs, LIF+serum

value: LIF+serum


title: RNA-seq, mESD-EpiSCs


title: Smad1/5 ChIP-seq, mESCs, LIF+BMP-4

value: LIF+BMP-4 (10ng/ml)


title: RNA-seq, mESCs, LIF+serum


title: RNA-seq, mESD-EpiSCs, BMP4, 1.5h


title: Obese_sRNA_rep5


title: Obese_sRNA_rep3


title: Lean_sRNA_rep13

value: lean


title: Obese_sRNA_rep1


title: Lean_sRNA_rep12


title: Lean_sRNA_rep10


title: Obese_sRNA_rep2


title: Lean_sRNA_rep9


title: Obese_sRNA_rep6


title: Lean_sRNA_rep6


title: Lean_sRNA_rep7


title: RNA-seq, mESCs, LIF+BMP-4


title: Lean_sRNA_rep5


title: Lean_sRNA_rep4


title: Lean_sRNA_rep3


title: RRBS_rep6_1year

description:
CpGs_post_vs_1year.csv
CpGs_pre_vs_1year.csv
CpGs_pre_vs_post.csv

data_processing:
Files were prerpcessed with trim_galore v0.3.7 and the parameter --rrbs
Preprocessed reads were aligned to hg19 using bismark v0.12.5 and standard setting
Aligned reads were processed using methylit v0.9.2 using the settings suggested in the documentation, but keeping CpGs covered in all conditions in at least 3 individuals.
Supplementary_files_format_and_content: A csv file with CpGs interrogated, estimated change in methylation and annotation with nearest gene
Basecalls performed using CASAVA version 1.8.2
Genome_build: hg19

extract_protocol:
Genomic DNA was extracted with the Nucleon™ BACC Genomic DNA Extraction Kit (GE Healthcare, Life Sciences). The protocol was modified for processing of sperm, according to the manufacturer’s recommendations.
Reduced Representation Bisulfite Sequencing libraries were constructed as previously described (Boyle et al., 2012, Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling. Genome biology 13, R92). Briefly, 200 ng of genomic DNA was digested with 40 U of MspI enzymes (New England Biolabs) and ligated to TruSeq (Illumina) sequencing adaptors. Bisulfite conversion was conducted once with the EpiTecht bisulfite kit (Qiagen) in accordance with the manufacturer’s instructions, and the converted DNA was amplified by PCR and sequenced on a HiSeq Illumina instrument.

tag: surgery time period

value: 1 year post operation


title: Lean_sRNA_rep1


title: Lean_sRNA_rep2


title: RRBS_rep6_1week

value: 1 week post operation


title: RRBS_rep5_pre

value: Pre operation


title: RRBS_rep4_1year


title: RRBS_rep5_1week


title: Obese_sRNA_rep4


title: Lean_sRNA_rep11


title: Obese_RRBS_rep9

data_processing:
Files were prerpcessed with trim_galore v0.3.7 and the parameter --rrbs
Preprocessed reads were aligned to hg19 using bismark v0.12.5 and standard setting
Aligned reads were processed using methylit v0.9.2 using the settings suggested in the documentation, but keeping CpGs covered in at least 3 individuals in each group.
Supplementary_files_format_and_content: A csv file with CpGs interrogated, estimated change in methylation and annotation with nearest gene
Basecalls performed using CASAVA version 1.8.2
Genome_build: hg19

extract_protocol:
Genomic DA was extracted with the Nucleon™ BACC Genomic DNA Extraction Kit (GE Healthcare, Life Sciences). The protocol was modified for processing of sperm, according to the manufacturer’s recommendations.
Reduced Representation Bisulfite Sequencing libraries were constructed as previously described (Boyle et al., 2012, Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling. Genome biology 13, R92). Briefly, 200 ng of genomic DNA was digested with 40 U of MspI enzymes (New England Biolabs) and ligated to TruSeq (Illumina) sequencing adaptors. Bisulfite conversion was conducted once with the EpiTecht bisulfite kit (Qiagen) in accordance with the manufacturer’s instructions, and the converted DNA was amplified by PCR and sequenced on a HiSeq Illumina instrument.


title: Obese_RRBS_rep8


title: RRBS_rep4_1week


title: Obese_RRBS_rep7


title: RRBS_rep5_1year


title: Obese_RRBS_rep4


title: RRBS_rep3_1year


title: Obese_RRBS_rep5


title: Lean_sRNA_rep8


title: Obese_RRBS_rep3


title: RRBS_rep3_1week


title: Obese_RRBS_rep2


title: RRBS_rep3_pre


title: RRBS_rep2_1year


title: RRBS_rep6_pre


title: Lean_RRBS_rep9


title: RRBS_rep2_pre


title: Obese_RRBS_rep6


title: RRBS_rep2_1week


title: RRBS_rep1_1year


title: Lean_RRBS_rep6


title: Lean_RRBS_rep7


title: RRBS_rep1_1week


title: Lean_RRBS_rep3


title: RRBS_rep1_pre


title: P_D31M04B1

city: Baton Rouge

first: J. Michael

last: Salbaum

state: LA

address: 6400 Perkins Road

department: Regulation of Gene Expression

institute: Pennington Biomedical Research Center

description: SOLiD SAGE Kit with Barcoding Adaptor Module (#4452811) and SOLiD RNA Barcode Kit (#4427046)

data_processing:
conversion of SOLiD 5500 XSQ files to csfasta/qual files was performed using perl and bash shell scripts that were developed in-house. These scripts make use of Life Technologies XSQ conversion tools, version 1.5.
alignment of sequence tags back to a mouse reference genome was performed using a modified version of the Applied Biosystems SOLiD™ SAGE™ Analysis Software v1.10 that was developed in-house.
filtering non-unique tags, and establishing counts per RefSeq gene was performed using a modified version of the Applied Biosystems SOLiD™ SAGE™ Analysis Software v1.10 that was developed in-house.
Genome_build: The following version of RefSeg RNA was used for mapping sequence tags: Mouse (mm9): ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/RNA/rna.fa.gz
Supplementary_files_format_and_content: processed data files contain the counts per gene for 26608 mouse RefSeq genes

source_name: E8.5 embryo, neural tube protrusion

growth_protocol: Diabetic dams were mated, and the morning where presence of a vaginal plug was detected was designated as day 0.5 of gestation. Pregnant dams were single housed, and embryos were prepared at 8.5 days of gestation.

extract_protocol:
Total RNA was prepared using Trizol, RNA concentration was determined on a Qbit fluorometer, and 7-12ng RNA per sample was used for sequencing library construction.
Libraries were prepared using the Applied Biosystems SOLiDSAGE kit, according to AB's instructions for the SOLiD 4 System (except a 1:100 of Adaptor B dilution was used).

treatment_protocol: Cryosections of embryos at 8.5 days of gestation were used to prepare neural tube tissue by Laser microdissection. The anterior boundary of neural tube closure site 1 was determined and used as reference point to collect sections immediately anterior (open neural tube) of closure site 1. Teratogenic protrusions were microdissected from the open neural plate.

value: FVB

tag: morphology

value: separated protrusion

value: neural tube


title: RRBS_rep4_pre

tag: tissue


title: Lean_RRBS_rep5


title: oNTa09

source_name: E8.5 embryo, open neural tube at anterior boundary of closure 1

value: open neural tube


title: Lean_RRBS_rep2


title: P_D31M12D

value: attached protrusion


title: P_D37M10E


title: oNTa13


title: Lean_RRBS_rep1


title: oNTa14


title: Obese_MNase_rep8

description: consensusPeaks.bed

data_processing:
Sequenced reads were trimmed for adaptor sequences using trimmomatic 0.30, then reads were aligned to the hg19 genome assembly using Bowtie2 version 2.1.0 with the standard configurations.
Differential peak were analysed with DANPOS v. 2.1.3 with the parameters --edge 1 -x 1 --keep 1 --frsz 147 (no differences detected)
Individual peaks were called using macs2 version 2.0.10.20130915.1 with the following parameters, genome = human, broad peak calling on, and extension size of 147: -g hs --broad --nomodel --extsize 147
Differential peaks were detected using DiffBind v. 1.8.0 using the parameters: insertLength=147, score=DBA_SCORE_TMM_READS_EFFECTIVE, bRemoveDuplicates=TRUE, minOverlap=5 (no significant regions, FDR < 0.1)
Supplementary_files_format_and_content: xls files with peaks from the individual dataset, called by MACS2s. An bed file of consensus peaks (observed in at least 5 samples)
Basecalls performed using CASAVA version 1.8.2
Genome_build: hg19

extract_protocol:
Spermatozoa were lysed in 0.075% lysolecithan (Sigma) for 15 minutes on ice. After 2 rounds of Dithiothreitol treatment, chromatin was fragmented by Micrococcal Nuclease (100 units for 1 hr at 37˚C) (New England Biolabs) to obtain fragments of approximately 147 bp. The histone-bound DNA fragments were separated from the protamine-bound DNA by centrifugation. Histones were removed by Proteinase K (Qiagen) treatment and Phenol:Chloroform extraction.
DNA was ligated to TruSeq (Illumina) sequencing adapters using the standard Illumina protocol, and sequenced on a HiSeq Illumina platform.


title: Obese_RRBS_rep1


title: Obese_MNase_rep7

description: consensusPeaks.bed


title: Obese_MNase_rep6

description: consensusPeaks.bed


title: Obese_MNase_rep5

description: consensusPeaks.bed


title: Obese_MNase_rep4

description: consensusPeaks.bed


title: Lean_RRBS_rep4


title: Obese_MNase_rep2

description: consensusPeaks.bed


title: Obese_MNase_rep1

description: consensusPeaks.bed


title: Obese_MNase_rep3

description: consensusPeaks.bed


title: P_D31M04B2


title: Lean_MNase_rep8

description: consensusPeaks.bed


title: Lean_MNase_rep6

description: consensusPeaks.bed


title: oNTa10


title: Lean_MNase_rep4

description: consensusPeaks.bed


title: Lean_MNase_rep7

description: consensusPeaks.bed


title: Lean_MNase_rep9

description: consensusPeaks.bed


title: Lean_MNase_rep1

description: consensusPeaks.bed


title: Lean_MNase_rep2

description: consensusPeaks.bed


title: Lean_MNase_rep3

description: consensusPeaks.bed


title: delPHO23_rep3

city: Los Angeles

first: Zvi

last: Tamari

state: California

address: 5531 Boelter Hall

institute: UCLA

data_processing:
Illumina Casava1.8 software used for basecalling.
Adaptor and UMI barcodes were trimmed off and reads were aligned to the S288C_reference_sequence_R64-1-1_20110203 reference genome using Bowtie
Genome_build: S288C_reference_sequence_R64-1-1_20110203
Supplementary_files_format_and_content: Processed read count per gene per genotype. Each column represents a genotype and each row represents a gene. Data is averaged over three repeats. Reads were normalized by the mean expression level across all samples per gene. Samples containing fewer than 800000 total reads were not included in the analysis.

organism: Saccharomyces cerevisiae

source_name: cell population

growth_protocol: Cells were inoculated into YP-xylulose media with initial OD of 0.1

extract_protocol:
Log phase cells were harvested and frozen in liquid Nitrogen. Total RNA was extracted using a NucleoSpin® 96 RNA kit (Macherey-Nagel), substituting β-mercaptoethanol with DTT
RNA extracts were fragmented and polyadenylation was selected using PolydT beads. cDNA was prepared using Smartscribe and UMI-containing barcoded primers, and subjected to RNnase H treatment. A second adaptor was subsequently ligated.

tag: repetition

value: repetition 3


title: CB4_Input_RK063

city: New York

first: Riccardo

last: Dalla-Favera

address: 1130 St Nicholas Avenue

institute: Columbia University

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8.
Reads were aligned to the human genome (UCSC hg19) for human GC B cells using the Bowtie2 aligner v2.1.0, allowing up to two mismatches. Duplicate reads (i.e. reads of identical length mapping to exactly the same genomic locations) were removed with samtools v0.1.19 using the rmdup option.
Reads were normalized to total reads aligned (counts per million). Peak detection was done using ChIPseeqer v2.0, enforcing a minimum fold change of 2 between ChIP and input reads, a minimum peak width of 100 bp, and a minimum distance of 100 bp between peaks.
The threshold for statistical significance of peaks was set at 10^-5 for the FOXO1 samples and 10^-12 for the BCL6 samples.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files contain peak locations. Columns 1, 2, and 3 contain the chromosome, start, and end position of the peak respectively. The fourth column is the maximum peak height normalized per million mapped reads in each library.

source_name: germinal center B cells from tonsil tissues

growth_protocol: Germinal center B cells were isolated from human tonsil tissue by magnetic cell separation (CD77+), as described in Klein et al, Proc Natl Acad Sci U S A, 2003.

extract_protocol:
Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris). Nuclei were sonicated using the S220 Ultrasonicator (Covaris) in order to obtain chromatin fragments of 200-500bp. ChIP was performed using anti-BCL6 (N3, Santa Cruz) or the anti-FOXO1 (Abcam, ab39670) antibodies. ChIP DNA was isolated by the MinElute DNA isolation kit (Qiagen).
ChIP-seq libraries were constructed starting from 4ug of ChIP or Input DNA as reported in Blecher-Gonen et al., 2013, Nature protocol. Libraries were quantified using the KAPA SYBR FAST Universal qPCR Kit (KAPA Biosystems), normalized to 10nM, pooled and sequenced in an Illumina HiSeq 2500 instrument as single-end 100 bp reads, obtaining on average 25x10^6 reads/sample.

treatment_protocol: Purified GC B cells were cross-linked with 1% formaldehyde for 10 min at room temperature, quenched by the addition of glycine to a final concentration of 0.125 M, and frozen.

value: Germinal center B cells

tag: antibody

value: no antibody


title: CLIB215PHO23_rep3


title: CB5_Input_RK045


title: CB5_BCL6_RK050

value: anti-BCL6, N3 (Santa Cruz)


title: CB4_FOXO1_RK059

value: anti-FOXO1 (Abcam, ab39670)


title: CB4_BCL6_RK040


title: CLIB215RXT3_rep3


title: CB5_FOXO1_RK051


title: Lean_RRBS_rep10

value: motile semen


title: T73RXT3_rep3


title: delRXT3_rep3


title: CLIB215PHO23_rep2

value: repetition 2


title: NEXTFlex Mouse Liver RNA

source_name: Tissue: Liver

tag: Sex

value: female

value: liver


title: T73PHO23_rep2


title: TruSeq Mouse Liver RNA


title: NEXTFlex -MIN6 RNA rep6


title: delPHO23_rep2


title: Lean_RRBS_rep8

value: lean


title: Lean_MNase_rep5

description: consensusPeaks.bed


title: Rosa26-pi reporter mouse; MILI IP

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description:
MILI IP
RR254

data_processing:
Reads obtained from Rosa26-pi reporter mouse libraries were sorted into individual libraries based on the barcodes and the 3’ adapter sequences were clipped from the reads using cutadapt (DOI:http://dx.doi.org/10.14806/ej.17.1.200). Reads were then aligned to the specific reporter sequence using bowtie (Langmead et al., 2009) allowing no mismatches.
For the Exd1 libraires the barcodes were removed, and trimmed reads were mapped to the mouse genome mm9. The software used for processing the data (genomic coordinates etc) from the raw data files are in-house tools from Sachidanandam lab. They are described in a publication [PMID 18229681]
Genome_build: mm9 for Exd1 libraries, the reads from Rosa26-pi reporter mouse libraries were mapped to the reporter sequence.
Supplementary_files_format_and_content: Exd1 proccessed files contain mapping of the reads to mouse genome (mm9). The processed files for  Rosa26-pi reporter mouse libraries contain mapping of the reads to the specific reporter sequence knocked-in into the mouse genome .

source_name: Rosa26-pi reporter mouse_MILI IP

extract_protocol:
For preparation of small RNA libraries total RNA was isolated from the lysates or RNA was immunoprecipitated from the protein complexes with the indicated antibodies against PIWI protein and the RNAs were resolved by 15% urea-PAGE. Bands corresponding to piRNAs or the indicated size were excised from the gel and extracted with 400 µl of 0.4M NaCl solution at 25°C overnight.
Small RNA sequencing libraries  were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Cat No:E7300) according to manufacturer instructions. Libraries were sequenced on Illumina HiSeq platform (EMBL Heidelberg Gene core facility).

treatment_protocol: Exd1 null allele was made by an insertion of an in-frame triple stop codon cassette immediately downstream of the first codon in the exon 8. Rosa26-pi reporter mouse was made by insertion of reporter sequence into Rosa26 locus. The reporter sequence consists of the DsRed2 coding sequence, the 3′ UTR based on the LacZ backbone with binding sites for 35 MILI-bound piRNAs, flanking LoxP sites, SV40 polyA signal, FRT-flanked Keo reporter cassette (with its own polyA signal).

value: C57BL/6;129S4/SvJae mixed

tag: genotype/variation

value: Rosa26-pi reporter mouse

tag: developmental stage

value: testis

tag: ip antibody

value: MILI (mouse monoclonal); PMID 19465913

tag: molecule subtype

value: small RNA


title: Rosa26-pi reporter mouse; MIWI2

description:
MIWI2 IP
RR255

source_name: Rosa26-pi reporter mouse_MIWI2

tag: strain background

value: MIWI2 (rabbit polyclonal); PMID:24067652


title: T73RXT3_rep2

tag: strain

tag: genotype


title: CLIB215RXT3_rep2


title: Exd1 -/- ; total small RNA rep2

description:
total small RNA (~15-40 nt)
processed data file: Exd1_mappers.csv.gz
RR257

source_name: Exd1 -/-_total small RNA

value: total small RNA (~15-40 nt)


title: delRXT3_rep2


title: T73PHO23_rep3

value: repetition 3


title: CLIB215PHO23_rep1

value: repetition 1


title: Exd1 +/- ; total small RNA  rep1

description:
total small RNA (~15-40 nt)
processed data file: Exd1_mappers.csv.gz
RR258

source_name: Exd1 +/-_total small RNA


title: delPHO23_rep1


title: delRXT3_rep1


title: CLIB215RXT3_rep1


title: Exd1 +/- ; MIWI2 IP rep2

description:
MIWI2 IP
processed data file: Exd1_mappers.csv.gz
RR219

source_name: Exd1 +/-_MIWI2 IP


title: Exd1 -/- ; MIWI2 IP rep1

description:
MIWI2 IP
processed data file: Exd1_mappers.csv.gz
RR220

source_name: Exd1 -/-_MIWI2 IP


title: Exd1 +/- ; MIWI2 IP rep1

description:
MIWI2 IP
processed data file: Exd1_mappers.csv.gz
RR218


title: Exd1 -/- ; MILI IP rep2

description:
MILI IP
processed data file: Exd1_mappers.csv.gz
RR217

source_name: Exd1 -/-_MILI IP


title: T73RXT3_rep1


title: Exd1 -/- ; MIWI2 IP rep2

description:
MIWI2 IP
processed data file: Exd1_mappers.csv.gz
RR221


title: T73PHO23_rep1


title: Exd1 -/- ; MILI IP rep1

description:
MILI IP
processed data file: Exd1_mappers.csv.gz
RR216


title: Exd1 +/- ; MILI IP rep2

description:
MILI IP
processed data file: Exd1_mappers.csv.gz
RR215

source_name: Exd1 +/-_MILI IP


title: Exd1 +/- ; MILI IP rep1

description:
MILI IP
processed data file: Exd1_mappers.csv.gz
RR214


title: T6_S96I775E_4NQO_ChIP1

city: Morgantown

first: Xiaoqing

last: Rong-Mullins

state: West Virginia

address: 53 Campus Dr

institute: West Virginia University

description:
Rong_2015_SI_tableS3_chip1.xlsx
Rong_2015_SI_tableS4_chip2.xlsx

data_processing:
Base-calling was performed via Illumina CASAVA version 1.7
2.08-4.21 million read pairs were generated for each sample and mapped to the S288c genome using Bowtie v2.2.3 (Langmead and Salzberg. 2012) with preset --sensitive, resulting in alignment rates of 96.1-99.3%.
ChIP-enriched regions (peaks) were identified using CisGenome v2.0 (Ji et al. 2008) and MACS2 v2.1.0 (Zhang et al. 2008) with multiple parameter combinations to maximize the possibility of peak discovery.
ChIP-Seq peaks were confidence-ranked via a novel approach based on peak shape metrics.
Genome_build: sacCer3
Supplementary_files_format_and_content: Table S3 (Rong_2015_SI_tableS3_chip1.xlsx) describes all the peaks identified by CisGenome and MACS2, including the following tabs:  • CisGenome: positive peaks (enrichment in ChIP over input) identified by CisGenome  • MACS2_positive: positive peaks (enrichment in ChIP over input) identified by MACS2  • MACS2_negative: negative peaks (enrichment in input over ChIP) identified by MACS2.   Table S4 (Rong_2015_SI_tableS4_chip2.xlsx) describes the shape metrics of all the peak instances in all the consolidated peak regions in all the pileup dataset, including the following tabs:  • mC1_ct_wd_mi_posi_w200c10: positive peak instances, representing enrichment in ChIP over input  • mC1_ct_wd_mi_nega_w200c10: negative peak instances, representing enrichment in input over ChIP.

source_name: Saccharomyces cerevisiae strain S96 yrr1Δ

growth_protocol: Each of the three Myc-tagged isogenic strains with different alleles YRR1_S96, YRR1_YJM789, YRR1_S96-I775E, respectively, were grown as two replicated cultures in liquid YPD medium to mid-log phase. Each culture was diluted to early-log phase and divided into two subcultures. One subculture was incubated in liquid YPD medium with 0.25 µg/ml 4NQO and the other subculture without 4NQO. Both subcultures for each replicate were further grown for 2.5 h.

extract_protocol:
Genomic DNA associated with pMyc-Yrr1 protein was immuno-precipitated using anti-Myc antibody. The ChIP and input DNA was prepared for sequencing using Illumina TruSeq DNA Library Prep Kit.
Libraries were prepared for sequencing on Illumina HiSeq using standard Illumina protocols

tag: yrr1 allele transformed

tag: growth medium

value: YPD + 4NQO

value: anti-Myc


title: T6_S96I775E_4NQO_ChIP2


title: Other Cells 2

city: Kyoto

first: Noriko

last: Funayama

state: Kyoto

address: Kitashirakawa-Oiwake, Sakyo-ku

department: Biophysics

institute: Kyoto University

data_processing:
For de novo transcriptome assembly : Oases software with default parameters produced 133,045 transcripts grouped into 39,484 loci with an average length of 1,216 nucleotides (not shown). Visual inspection of this assembly revealed that many predicted isoforms were in fact transcripts differing by only a few substitutions or gaps. Therefore, we decided to select a single transcript for each locus based on criteria of size and fold-coverage, using the publicly available Oases-to-csv python script (https://code.google.com/p/oases-to-csv/downloads/list). Then we kept only the orfs over 270 nucleotides long using Transdecoder (http://transdecoder.sourceforge.net/), and ended up with 17,419 transcripts with an average length of 1,152 nt (provided in File S1). This is of the same order of magnitude as the transcriptome of the close species Ephydatia muelleri, recently released on the Compagen platform (http://www.compagen.org/), containing 21,804 transcripts over 270 nt long with an average length of 1,242 nt.
Gene expression levels were calculated using RSEM-1.2.4 (55): reads from each duplicate were mapped on the 17,419 reference transcripts using default Bowtie parameters (parameter bowtie-m 200, seed length of 25 nt). Resulting expected counts were analysed using EdgeR 3.0.0 (56) (which assumes that read counts have a negative binomial distribution): duplicate reproducibility was first confirmed by principal component analysis (Fig. S1); reads counts were TMM normalised; the common dispersion was calculated for each condition
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Ephydatia fluviatilis

source_name: FACS sorted mix of differentiated cells

growth_protocol: Gemmules were isolated and juvenile sponges were cultivated from them in M-medium

extract_protocol:
RNeasy Micro kit (Qiagen, Hilden, Germany), following the instructions of the manufacturer. DNase digestion was performed. For each replicate, 10 ng of total RNA were used as the starting material
SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech Takara Bio Inc., Mountain View, USA).

treatment_protocol: for de novo transcriptome sequencing, 450 μg of total RNA was extracted from sponges at different stages using an IsogenLS kit (Nippon Gene Co., Ltd). For RNA-seq on cell fractions, Choanocytes were labelled following a protocol slightly modified from (20): stage 5 sponges (7 days old) were incubated in 2 μg.ml-1 Hoechst 33342 (in M-medium) for 30 minutes. During the last 8 minutes of this incubation, sponges were fed FluoSpheres (carboxylate-modified microspheres, 0.2 μm in size, yellow-green fluorescent (505/515 nm) (Molecular Probes, Eugene, OR, USA)), at a concentration of 1μl ml-1 in M-medium. Then the sponges were washed 3 times for 5 minutes each with M-medium. Archeocytes were labelled as follows: sponges were cultivated in M-medium with 2 μg μl-1 Rhodamine 123 in the dark until they reached stage 1-2. Rho 123 is a fluorescent dye that accumulates in the mitochondria due to their transmembrane potential (53), and we found that it was also incorporated into the abundant vitelline platelets present in the archeocyte cytoplasm (probably because the vitelline platelets contain mitochondria (54)). Then sponges were washed 3 times for 1 hour each in normal M-medium and incubated in 2 μg ml-1 Hoechst 33342 (in M-medium) for 30 minutes and washed 3 times for 5 minutes each in M-medium. Cells belonging to the “other cells” fraction were collected from stage 1-2 sponges labelled with Rho123 and Hoechst 33342, and fed FluoSpheres as described above. Gemmules used in these experiments were isolated from the same mother sponge. Before FACS sorting, sponges were rinsed with Ca2+, Mg2+-free medium (CMFM: Na2SiO3, 22.48 g l-1; NaHCO3, 13.34 g l-1; KCl, 0.37 g l-1) twice and scraped and pipetted to dissociate cells in 2 ml of CMFM. Dissociated cells were filtered using a 35-μm nylon mesh (cell-strainer cap tube, Beckton-Dickinson Falcon, Franklin Lakes, NJ, USA) to remove spicules, and then maintained on ice. Dissociated cells were stained with 2 μg ml-1 propidium iodide (PI, Dojindo, Kumamoto, Japan) on ice for 5 min and immediately subjected to cell sorting using a BD FACS Aria 2 (BD Bioscience, San-Jose CA, USA). We empirically determined thresholds to collect Hoechst-positive, PI-negative viable cells. Archeocytes were isolated as large cells displaying Rho123 fluorescence (40,000 cells collected per biological replicate), choanocytes as small cells displaying FluoSphere fluorescence (100,000 cells collected per biological replicate), and “other cells” as cells having no fluorescence and SSC/FSC values not overlapping with those of choanocytes or archeocytes (100,000 cells collected per biological replicate). The cell collection device was maintained at 4°C throughout the procedure. The collected samples were centrifuged at 13,000 rpm, 4°C, 10 minutes, and the supernatant was removed. Samples were frozen at -80°C.

value: wild type

value: whole juvenile sponges

tag: cell type

value: Other Cells


title: T6_S96I775E_4NQO_Input


title: T5_S96I775E_YPD_ChIP2

value: YPD


title: Other Cells 1


title: Exd1 -/- ; total small RNA  rep1

description:
total small RNA (~15-40 nt)
processed data file: Exd1_mappers.csv.gz
RR256


title: Archeocyte 2

source_name: FACS sorted archeocytes

value: Archeocyte


title: T6_S96I775E_4NQO_ChIP3


title: Archeocyte 1


title: T4_S96_4NQO_ChIP3


title: Choanocyte 2

source_name: FACS sorted choanocytes

value: Choanocyte


title: T5_S96I775E_YPD_ChIP3


title: T5_S96I775E_YPD_Input


title: T4_S96_4NQO_Input


title: Choanocyte 1


title: T4_S96_4NQO_ChIP2


title: T3_S96_YPD_ChIP2


title: T3_S96_YPD_ChIP1


title: T2_YJM789_4NQO_ChIP2


title: T3_S96_YPD_Input


title: T2_YJM789_4NQO_ChIP1


title: T3_S96_YPD_ChIP3


title: T2_YJM789_4NQO_Input


title: T1_YJM789_YPD_Input


title: T2_YJM789_4NQO_ChIP3


title: T1_YJM789_YPD_ChIP2


title: T1_YJM789_YPD_ChIP3


title: T1_YJM789_YPD_ChIP1


title: Reference transcriptome

source_name: whole juvenile sponges


title: T5_S96I775E_YPD_ChIP1


title: Naked Mole Rat Adult Liver 3

status: Public on Dec 03 2015

city: Bronx

first: Sheila

last: MacRae

address: 1301 Morris Park Ave, Rm 468

department: Genetics

institute: Albert Einstein College of Medicine

data_processing:
Basecalling and demultiplexing run by CASAVA_1.8.4
Adapter/index trimming performed by trim_galore 0.3.7
genomic alignment performed using STAR 2.3.1
HTSeq 0.6.1 generated tables of reads per gene
Genome_build: hg19,HetGla2,mm10
Supplementary_files_format_and_content: Table of sequenced RNA fragments per gene feature per sample

organism: Heterocephalus glaber

source_name: liver

extract_protocol:
Harvested livers were preserved in RNAlater (ThermoFisher Scientific)
Total RNA quality was checked on an Agilent 2100 Bioanalyzer; only samples with a RNA Integrity Number greater than 8.5 were used for subsequent analysis. Total RNA was treated with DNaseI, column purified using the miRNeasy Mini Kit (Qiagen), and depleted of ribosomal RNA with Ribo-Zero Magnetic Gold Kit (Epicentre), followed by ethanol precipitation. Depleted RNA was converted to cDNA using SuperScript III First-Strand Synthesis Kit (Invitrogen) with 80 ng random hexamers and 50 μM oligo dT and subsequently ethanol precipitated. Single-stranded cDNA was converted to dsDNA by DNA polymerase I while incorporating dU/VTPs (10 mM). Samples were fragmented in 1 × TE to 200–300 bp using Covaris. After fragmentation, samples were purified using the MinElute PCR purification kit (Qiagen). Fragmented samples underwent standard end-repair, dA-tailing and adapter ligation using Illumina TruSeq adapters for multiplexing. Adapter-ligated cDNA was treated with uracil-DNA glycosylase followed by enrichment PCR using Q5 polymerase (New England Biolabs) for 18 cycles. Libraries were size selected for 150–600 bp on a 2% low-melt ultra low-range agarose gel stained with SYBR Gold (Invitrogen) to eliminate adaptor dimers.

value: liver

tag: age

value: 1 year


title: Naked Mole Rat Adult Liver 2


title: Naked Mole Rat Adult Liver 1


title: SF370_EL_39°C

city: Oklahoma City

first: William

middle: Michael

last: McShan

state: OK

address: 1110 N. Stonewall Ave.

department: Pharmaceutical Sciences

institute: University of Oklahoma Health Sciences Center

data_processing:
Genesifter  software was used for base-calling and alignment.
BWA Reseq PE (Targeted, GATKv3) pipeline was used to align with S. pyogenes M1 GAS reference genome. Pairwise analyses were done using Genesifter software and gene lists were exported as tab delimited files.
Pairwise settings were as follows: normalize to mapped reads, statistical analysis using t-test, differential genes originally shown if 1.5fold or more, narrowed to 3 fold min for final analysis, data correct using Benjamini Hochberg method.
Genome_build: ASM678v2

organism: Streptococcus pyogenes

source_name: Whole bacterial cell

growth_protocol: Incubator with 5% CO2

extract_protocol:
PlyC lysin followed by Trizol reagent (Life Technologies)
RNA libraries were prepared for sequencing using standard Illumina protocols with TruSeq V2 chemistry and methods.

treatment_protocol: Cells stored in RNA-Later until RNA extraction

tag: growth stage

value: Early logarithmic

tag: temperature

value: 39degree C

value: Todd Hewitt Broth


title: CEM1∆4_LL_39°C

value: Late logarithmic


title: SF370_LL_39°C


title: CEM1∆4_EL_39°C


title: SF370_LL_37°C

value: 37degree C


title: T4_S96_4NQO_ChIP1


title: CEM1∆4_EL_37°C


title: SF370_EL_37°C


title: Carp_3_G

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

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

data_processing:
Sequencing data were processed with illumina2bam-tools v. 1.12
BAM files were converted to fastq format using SamToFastq.jar (picard-tools v1.100) with the INCLUDE_NON_PF_READS parameter set to FALSE
All reads were trimmed for adapter sequences and low-quality sequences using trimgalore v0.3.3 with the following command: trim_galore -q 20 --phred33 -a "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" --stringency 1 -e 0.1 --length 16 --output_dir $output_dir $input_fastq.
Reference-free processing (creation of the deduced genomes and processing) was performed using the RefFreeDMA software/pipeline (http://RefFreeDMA.computational-epigenetics.org)
Bisulfite alignment of the RRBS reads to the deduced genomes and to the reference genomes was performed using BSMAP v2.74 with the following command line: bsmap -a $input_fastq -d $ref_genome_fasta -o $output_bam -D C-CGG -w 100 -v 0.08 -r 1 -p 4 -n 0 -S 1 -f 5 –u.
DNA methylation calling was performed using the biseqMethCalling.py software (Bock, 2010)
Genome_build: hg19, bosTau6, GCA_000951615.1, human_deduced_genome.fa, bovine_deduced_genome.fa, carp_deduced_genome.fa
Supplementary_files_format_and_content: Tab-delimited text files include CpG methylation calls for each sample. Files ending with "_ded" were produced using the deduced genomes (human_deduced_genome.fa, bovine_deduced_genome.fa, carp_deduced_genome.fa) as reference. Files ending with "_ref" were produced using the published reference genomes (hg19, bosTau6, GCA_000951615.1) as reference.

organism: Cyprinus carpio

source_name: peripheral blood

extract_protocol:
The Allprep DNA/RNA Mini kit (Qiagen) was used for DNA isolation. Cells were lysed in 600 µl Buffer RLT Plus supplemented with 1% β-Mercaptoethanol and vortexed thoroughly for at least five minutes. The procedure of isolating DNA and RNA was performed according to protocol. DNA was stored at -20˚C.
For RRBS, 100 ng of genomic DNA was digested for 12 hours at 37°C with 20 units of MspI (New England Biolabs, R0106L) in 30 μl of 1x NEB buffer 2. To retain even the smallest fragments and to minimize the loss of material, end preparation and adaptor ligation were performed in a single-tube setup. End fill-in and A-tailing were performed by addition of Klenow Fragment 3’ > 5’ exo- (New England Biolabs, M0212L) and dNTP mix (10 mM dATP, 1 mM dCTP, 1 mM dGTP). After ligation to methylated Illumina TruSeq LT v2 adaptors using Quick Ligase (New England Biolabs, M2200L), the libraries were size selected by performing a 0.75x clean-up with AMPure XP beads (Beckman Coulter, A63881). The libraries were pooled in combinations of six based on qPCR data and subjected to bisulfite conversion using the EZ DNA Methylation Direct Kit (Zymo Research, D5020) with the following changes to the manufacturer’s protocol: conversion reagent was used at 0.9x concentration, incubation performed for 20 cycles of 1 min at 95°C, 10 min at 60°C and the desulphonation time was extended to 30 min. These changes increase the number of CpG dinucleotides covered, by reducing double-strand break formation in larger library fragments. Bisulfite-converted libraries were enriched using PfuTurbo Cx Hotstart DNA Polymerase (Agilent, 600412). The minimum number of enrichment cycles was estimated based on a qPCR experiment. After a 2x AMPure XP clean-up, quality control was performed by a Qubit dsDNA HS (Life Technologies, Q32854) and Experion DNA 1k assay (BioRad, 700-7107). The RRBS libraries were sequenced on the Illumina HiSeq 2000 platform in 50 bp single read mode.

treatment_protocol: Leukocytes were isolated from whole blood by removing the erythrocytes through hypotonic lysis. Specifically, 5 ml of whole blood was incubated with 9 ml ddH2O for one minute. The lysis was stopped by adding 1 ml of 10x phosphate buffered saline (PBS) to the sample. Leukocytes were pelleted by centrifuging for five minutes at 550g. If the pellet was still red, a second round of lysis was initiated by resuspending the pellet in 1 ml 1x PBS. Subsequently, 4.5 ml of ddH2O was added and after 30 seconds the lysis reaction was stopped by adding 0.5 ml 10x PBS. Leukocytes were pelleted by centrifuging for three minutes at 550g. Finally, the pellet was washed in 1 ml 1x PBS and then resuspended in 500-800 µl RPMI-1640 medium supplemented with 10% fetal calf serum (FCS). The cell suspension was then filtered into a FACS tube, and cell populations were sorted by FACS based on their forward and side scatter properties. Sorting was performed on a BD FACS Aria 1 with a 70 µm nozzle, which allowed for a maximum sorting speed of 30,000 events per second. For each population, between 500,000 and three million cells were obtained. Giemsa stained cytospins were produced for each sorted cell population, and the purity was assessed at 100x magnification.

value: granulocyte

value: M


title: Carp_2_M

value: monocyte


title: Carp_4_E

value: erythrocyte

value: F


title: Carp_4_MG

value: granMono


title: Carp_2_MG


title: Carp_4_L

value: lymphocyte


title: Carp_3_L


title: Carp_3_M


title: Carp_4_M


title: Carp_3_E


title: Carp_2_G


title: Carp_2_E


title: Carp_4_G


title: CEM1∆4_LL_37°C


title: Carp_2_L


title: Carp_1_MG


title: Carp_1_L


title: JM46.5

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

description: Processed data file: counts_RPKMs.txt

data_processing:
Sequence information was extracted in FastQ format using Illumina's Casava software v1.8.4.
Reads were mapped using Tophat (v2.0.6) to the N. furzeri genome (tophat2 -p 24 -o OUTPUT --no-coverage-search -g 1 GENOME INPUT.FASTQ).
Uniquely mapped reads were counted for each gene_id using featureCounts v1.4.3-p1 (featureCounts -T 8 -a ANNOTATION.GTF -s 0 -t exon -g gene_id -o COUNTS.CSV INPUT.SAM).
Counts were normalized to RPKM values as described in Mortazavi et al. (2008) using the length of the regarding transcript as reported by featureCounts.
Genome_build: genome v20150522 and annotation v20140422 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (http://nfingb.fli-leibniz.de/)
Supplementary_files_format_and_content: counts_RPKMs.txt: Tab-delimited text file includes raw counts and RPKM values of all genes for each sample.

organism: Nothobranchius furzeri

source_name: total RNA extracted from skin

extract_protocol:
Extraction was done as described in Baumgart et al. 2012 (PMID: 22487494).
For library preparation, an amount of around 2.5 μg of total RNA per sample was processed using Illumina's TruSeq RNA Sample Prep Kit v2 following the manufacturer's instruction.

tag: strain/background

tag: tissue

value: skin

value: 39 weeks

tag: FISH id


title: JM6.1

description: Processed data file: counts_RPKMs.txt

source_name: total RNA extracted from brain

value: brain


title: JM8.5

description: Processed data file: counts_RPKMs.txt


title: Carp_1_M

tag: Sex


title: JM8.1

description: Processed data file: counts_RPKMs.txt


title: JM6.5

description: Processed data file: counts_RPKMs.txt


title: JM46.1

description: Processed data file: counts_RPKMs.txt


title: JM41.5

description: Processed data file: counts_RPKMs.txt


title: JG5_5

data_processing:
*******************
File: GSE69122_Nfurzeri_GRZ_BrainLiverSkin_NormalAgeing_12weeks_counts_RPKM.xls
Illumina Casava v1.8.2 software used for extraction of FASTQ files
FASTQ files were mapped using Bowtie versus a transcriptome catalogue of N. furzeri containing 19,812 transcripts
Uniquely mapped reads for each transcript were counted using R Statistical Language and Bioconductor.
The read counts were normalized with respect to the size of the individual genes and to the total amount of mappable reads obtained in the sequencing process, resulting in RPKM-values (Mortazavi et al. 2008) for each gene.
The transcripts were annotated additionally using Ensembl gene identifiers from D. rerio, while 13,561 shared a best bi-directional BLAST hit between both species.
genome build: Transcriptome sequence published by Petzold et al. 2013 [PMID: 23496936]
processed data files format and content: Excel file including raw counts and RPKM values for each sample
*******************
File: GSE69122_count_RPKMs_genome.xls
Illumina Casava v1.8.2 software used for extraction of FASTQ files
FASTQ files were mapped using Tophat (v2.0.6) to the N.furzeri genome.
Uniquely mapped reads were counted for each gene_id using featureCounts v1.4.3-p1 (featureCounts -T 8 -a $GTF -s 0 -t exon -g gene_id -o featureCounts_gene.txt $SAMFILE)
RPKM values were computed using exon lengths provided by featureCounts as described in Mortazavi et al. 2008.
genome build: genome v20150522 and annotation v20140422 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (http://nfingb.fli-leibniz.de/)
processed data files format and content: Excel file includes raw counts and RPKM values
*******************

source_name: skin

extract_protocol:
The organs of the fishes were dissected and transferred into 2 ml tubes with 1 ml cooled QIAzol (Qiagen, Hilden, Germany) and one 5 mm stainless steel bead (Qiagen) was added. Homogenization was performed using a TissueLyzer II (Qiagen) at 30 Hz for 3x 1 min. After incubation for 5 min at room temperature 200 µl chloroform was added. The tube was shaken for 15 s and incubated for 3 min at room temperature. Phase separation was achieved by centrifugation at 12,000x g for 20 min at 4°C. The aqueous phase was transferred into a fresh cup and 10 µg of Glycogen (Invitrogen, Darmstadt, Germany), 0.16x volume NaAc (2 M; pH 4.0) and 1.1x volume isopropanol were added, mixed thoroughly and incubated for 10 min at room temperature. The RNA was precipitated by a centrifugation step with 12,000 x g at 4°C 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 resuspended in 20 µl DEPC-treated water by pipetting up and down, followed by incubation at 65°C for 5 min. The RNA was quantified with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80°C until use.
Sequencing procedure was done using Illumina methodology [Bentley et al, 2008]. Around 2.5 µg of total RNA was used for library preparation (Illumina, TruSeq™ RNA Sample Prep Kit v2) using the manufacturer’s description.

value: 12 weeks

value: GRZ


title: Carp_1_E


title: Carp_3_MG


title: JG7_5


title: JG13_5


title: JM41.1

description: Processed data file: counts_RPKMs.txt


title: JM38.1

description: Processed data file: counts_RPKMs.txt


title: JG6_5


title: fin LS35 20weeks longitudinal group3 batch2

data_processing:
FASTQ files were extracted using Illumina CASAVA v1.8.0 (Sample 1-50), CASAVA v1.8.2 (Sample 51-95) or bcl2fastq v1.8.4 (Sample 96-185) software.
FASTQ files were mapped using Tophat (v2.0.6) vs. the N. furzeri genome.
Uniquely mapped reads were counted for each gene_id using featureCounts v1.4.3-p1 (featureCounts -T 8 -a $GTF -s 0 -t exon -g gene_id -o featureCounts_gene.txt $SAMFILE) .
RPKM values were computed using exon lengths provided by featureCounts and the sum of all mapped reads per sample according to Mortazavi et al. (2008).
Genome build: Genome v20150522 and annotation v20140422 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (http://nfingb.fli-leibniz.de/). In addition, 18 mitochondrial genes were included.
Supplementary_files_format_and_content: Text files including raw counts and RPKM values of each sample.

source_name: total RNA extracted from fin clipping

growth_protocol: Animal maintenance was performed as described by Terzebasi et al., 2008 and 2009.

extract_protocol:
For library preparation an amount of around 1 μg of total RNA per sample was processed using Illumina’s TruSeqTM RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer’s instruction.
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol/chloroform extraction method. Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80 °C until use.

value: tailfin

value: 20 weeks

tag: age at death

value: 71.9 weeks

tag: treatment


title: JG15_3

value: liver


title: JG14_3


title: JM38.5

description: Processed data file: counts_RPKMs.txt


title: JG13_3


title: JG11_3


title: fin LS34 20weeks longitudinal group3 batch2

value: 63.4 weeks


title: JG14_1

source_name: brain


title: JM12.5

description: Processed data file: counts_RPKMs.txt


title: JM24.1

description: Processed data file: counts_RPKMs.txt


title: JG14_5


title: Carp_1_G

value: granulocyte


title: JG10_1


title: fin LS32 20weeks longitudinal group3 batch2

value: 59.3 weeks


title: JG13_1


title: JG11_1


title: fin LS33 10weeks longitudinal group3 batch2

value: 10 weeks

value: 66.3 weeks


title: fin LS31 20weeks longitudinal group3 batch2

value: 58.7 weeks


title: fin LS35 10weeks longitudinal group3 batch2


title: fin LS34 10weeks longitudinal group3 batch2


title: fin LS32 10weeks longitudinal group3 batch2


title: JG15_1


title: JG10_3


title: liver MR30 27weeks rotenone

source_name: total RNA extracted from liver

extract_protocol:
For library preparation an amount of around 2.5 μg of total RNA per sample was processed using Illumina’s TruSeqTM RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer’s instruction.
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol/chloroform extraction method. Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80 °C until use.

treatment_protocol: Rotenone dissolved in DMSO or equal amounts of pure DMSO was added to final concentrations of 15 pM. Treatment started when the fish reached the age of 5 weeks (young group) or 23 weeks (old group). For cleaning purpose and renewal 30% water was changed twice per week and fresh Rotenone and DMSO was added to the tanks. After 4 weeks 5 animals of each treatment group were sacrificed and RNA was extracted from brain, liver and skin tissues.

value: 27 weeks

value: 15pM rotenone


title: skin MR30 27weeks rotenone

value: skin


title: fin LS33 20weeks longitudinal group3 batch2


title: brain MR30 27weeks rotenone


title: skin MR29 27weeks rotenone


title: fin LS39 20weeks longitudinal group2 batch2

value: 48.9 weeks


title: fin LS40 20weeks longitudinal group2 batch2

value: 49.4 weeks


title: fin LS38 20weeks longitudinal group2 batch2

value: 46.9 weeks


title: liver MR29 27weeks rotenone


title: fin LS31 10weeks longitudinal group3 batch2


title: skin MR28 27weeks rotenone


title: brain MR29 27weeks rotenone

value: brain


title: fin LS36 20weeks longitudinal group2 batch2

value: tailfin

value: 45.1 weeks


title: brain MR28 27weeks rotenone


title: fin LS40 10weeks longitudinal group2 batch2


title: fin LS37 20weeks longitudinal group2 batch2

value: 20 weeks

value: 45.4 weeks


title: fin LS39 10weeks longitudinal group2 batch2


title: liver MR28 27weeks rotenone

value: liver


title: skin MR27 27weeks rotenone


title: fin LS38 10weeks longitudinal group2 batch2


title: liver MR27 27weeks rotenone


title: fin LS37 10weeks longitudinal group2 batch2


title: fin LS36 10weeks longitudinal group2 batch2


title: brain MR27 27weeks rotenone


title: fin LS45 20weeks longitudinal group1 batch2

value: 35.0 weeks


title: liver MR26 27weeks rotenone


title: fin LS43 20weeks longitudinal group1 batch2

value: 33.9 weeks


title: fin LS44 20weeks longitudinal group1 batch2

value: 34.1 weeks


title: brain MR26 27weeks rotenone


title: skin MC9 27weeks DMSO

value: DMSO


title: fin LS42 20weeks longitudinal group1 batch2

value: 30.6 weeks


title: fin LS41 20weeks longitudinal group1 batch2


title: brain MC9 27weeks DMSO

value: 27 weeks


title: liver MC9 27weeks DMSO


title: fin LS44 10weeks longitudinal group1 batch2

value: 10 weeks


title: fin LS45 10weeks longitudinal group1 batch2


title: brain MC8 27weeks DMSO


title: skin MC8 27weeks DMSO

value: skin


title: liver MC8 27weeks DMSO


title: fin LS43 10weeks longitudinal group1 batch2


title: fin LS42 10weeks longitudinal group1 batch2


title: skin MC7 27weeks DMSO


title: fin LS28 20weeks longitudinal group3 batch1

value: 66.1 weeks


title: fin LS29 20weeks longitudinal group3 batch1

value: 69.9 weeks


title: skin MC6 27weeks DMSO


title: fin LS30 20weeks longitudinal group3 batch1

value: 70.4 weeks


title: brain MC7 27weeks DMSO

value: brain


title: fin LS24 20weeks longitudinal group3 batch1

value: tailfin

value: 59.1 weeks


title: fin LS23 20weeks longitudinal group3 batch1

value: 20 weeks

value: 58 weeks


title: brain MC10 27weeks DMSO


title: skin MC10 27weeks DMSO


title: fin LS21 20weeks longitudinal group3 batch1

value: 57.3 weeks


title: liver MC5 9weeks DMSO

value: liver

value: 9 weeks


title: liver MC10 27weeks DMSO


title: brain MC6 27weeks DMSO


title: liver MC6 27weeks DMSO


title: skin MR26 27weeks rotenone

value: 15pM rotenone


title: fin LS25 20weeks longitudinal group3 batch1

value: 61.9 weeks


title: fin LS26 20weeks longitudinal group3 batch1

value: 61.6 weeks


title: skin MC5 9weeks DMSO

value: DMSO


title: skin MC4 9weeks DMSO


title: fin LS22 20weeks longitudinal group3 batch1

value: 58.7 weeks


title: brain MC5 9weeks DMSO


title: fin LS27 20weeks longitudinal group3 batch1

value: 63.4 weeks


title: fin LS41 10weeks longitudinal group1 batch2

value: 10 weeks

value: 30.6 weeks


title: NORAD-KO

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 5323 Harry Hines Boulevard

department: Molecular Biology

institute: UT Southwestern Medical Center Dallas

description: PAR-CLIP RNA

data_processing:
QC using NGS-QC-Toolkit (default setting).
Adapters were trimmed using Cutadapt (v.1.2.1) (default setting).
High quality reads (phred score ≥20) longer than 15 nt were first aligned to repeat masked NORAD and then to the repeat masked human transcriptome (Ensembl GRCh37.75) using Bowtie (v.1.0.0) allowing at most 1 mismatch.
Read clustering and sorting were done using bedtools. Clusters with at least 5 reads were kept.
T to C mutations were identified using PIPE-CLIP (CLIP clusters were defined by 5 or more reads and at least 1 T to C mutation).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including genomic location, cluster reads, T to C mutations and gene name

growth_protocol: HCT116 cells and isogenic NORAD−/− cells were grown to ~80% confluence.

extract_protocol:
4-thiouridine-labeled cells were washed with cold PBS and crosslinked using 365 nm UV with 150 mJ/cm2 total energy in a Spectrolinker XL-1500 (Spectroline).  A total of ~720 million cells (36 150 mm dishes) per CLIP condition were collected and resuspended in NP-40 lysis buffer (50 mM HEPES-KOH, pH 7.5, 150 mM KCl, 2mM EDTA-NaOH, pH 8.0, 1 mM NaF, 0.5% NP-40 substitute, 0.5 mM DTT, and Complete EDTA-free protease inhibitor cocktail).  After centrifugation, the soluble fraction was filtered through a 5 mm syringe filter and incubated with 1 U/m RNase T1 at 22ºC for 15 min.  100 mg PUM2 antibody (K-14, sc-31535, Santa Cruz) was conjugated to Protein G magnetic beads and incubated with RNase-treated lysate at 4ºC for 4 hours.  Bead-bound PUM2 RNP complexes were washed with IP wash buffer (50 mM HEPES-KOH, pH 7.5, 300 mM KCl, 0.05% NP-40 substitute, 0.5 mM DTT and Complete EDTA-free protease inhibitor cocktail) followed by an additional RNase T1 treatment (1 U/mL at 22ºC for 15 min).  Beads were further washed with high-salt wash buffer (50 mM HEPES-KOH, pH 7.5, 500 mM KCl, 0.05% NP-40 substitute, 0.5 mM DTT and Complete EDTA-free protease inhibitor cocktail) and the 5'  ends of PUM2 bound RNAs were labeled with 32P using calf intestinal alkaline phosphatase followed by T4 PNK and [gamma-32P]-ATP.  100 mM unlabeled ATP was added after radiolabeling to ensure all RNA species were 5'  phosphorylated.  Labeled RNP complexes were eluted from beads by boiling in 1X SDS-PAGE loading buffer (62.5 mM Tris HCl pH 6.8, 1.5% SDS, 8.3% Glycerol, 0.005% Bromophenol blue) and resolved on an SDS-PAGE gel.  After autoradiography, bands corresponding to the PUM2 RNP size (~120 kDa) were excised and electro-eluted using D-tube dialyzer tubes (Milipore) in MOPS-SDS running buffer.  Eluted samples were then digested with 1.2 mg/mL Proteinase K (Sigma) at 55ºC for 30 min.  RNA was isolated using phenol/chloroform extraction followed by ethanol precipitation.
Sequencing libraries were constructed using the TruSeq Small RNA Library Preparation Kit (Illumina).  Sequencing was performed on a NextSeq 500 (Illumina).

treatment_protocol: 4-thiouridine (Sigma) was added to the media at final concentration of 100 mM for 18 hours.

tag: cell line

value: Colorectal cancer cell line

value: NORAD-/-


title: liver MC7 27weeks DMSO

value: 27 weeks


title: fin LS18 20weeks longitudinal group2 batch1

value: tailfin

value: 50 weeks


title: WT

description: PAR-CLIP RNA

value: wild-type


title: skin MC3 9weeks DMSO

value: skin


title: fin LS17 20weeks longitudinal group2 batch1

value: 20 weeks

value: 49.7 weeks


title: brain MC4 9weeks DMSO

value: brain

value: 9 weeks


title: prr9-1 CCR2::LUC Input

city: East Lansing

first: Tiffany

middle: L

last: Liu

state: Michigan

address: 3260 Molecular Plant Sciences Building

department: Plant Biology

institute: Michigan State University

description: Anti-HA antibody used to immunoprecipitate HA-tagged PRR9

data_processing:
Quality filtering using Fastx Toolkit fastq_quality_trimmer with -t 20 -l 30
Alignment to Arabidopsis genome using Bowtie with -m 1
Binding site identification using MACS2 with –broad
Binding sites were associated with the nearest transcriptional start site using ChIPpeakAnno
Genome_build: TAIR10
Supplementary_files_format_and_content: bed format for MACS2 broad_peaks and summits, text files for annotated binding sites

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Plants were grown in cycling 12 h light/12 h dark for two weeks.

extract_protocol:
See Liu et al., “Direct regulation of abiotic responses by the Arabidopsis circadian clock component PRR7” (2013) for ChIP-seq extract protocol
Illumina compatible libraries were prepared using the Rubicon Genomics ThruPLEX-FD Prep Kit for multiplexing.

treatment_protocol: Plants were collected at ZT4.

value: whole seedlings

tag: collection time

value: Two weeks

tag: growth

value: Cycling 12 h light/12 h dark


title: prr9-1 CCR2::LUC Immunoprecipitated


title: fin LS20 20weeks longitudinal group2 batch1

value: 50.3 weeks


title: liver MC3 9weeks DMSO

value: liver

value: DMSO


title: prr9-1 PRR9::HA-PRR9 CCR2::LUC #109 Immunoprecipitated


title: fin LS16 20weeks longitudinal group2 batch1

value: 49.9 weeks


title: prr9-1 PRR9::HA-PRR9 CCR2::LUC #109 Input


title: liver MC4 9weeks DMSO


title: fin LS15 20weeks longitudinal group2 batch1

value: 49 weeks


title: fin LS19 20weeks longitudinal group2 batch1


title: liver MC2 9weeks DMSO


title: fin LS14 20weeks longitudinal group2 batch1

value: 48 weeks


title: fin LS10 20weeks longitudinal group1 batch1

value: tailfin

value: 36.4 weeks


title: liver MC1 9weeks DMSO


title: brain MC2 9weeks DMSO


title: fin LS13 20weeks longitudinal group2 batch1

value: 48.7 weeks


title: skin MC2 9weeks DMSO

value: skin


title: fin LS11 20weeks longitudinal group2 batch1

value: 20 weeks

value: 46.9 weeks


title: skin MC1 9weeks DMSO


title: fin LS12 20weeks longitudinal group2 batch1

value: 47.9 weeks


title: brain MC1 9weeks DMSO

value: brain

value: 9 weeks


title: PUM2-OE CLONE2 rep2

description: processed data file: PUM2edgeR.txt

data_processing:
QC using NGS-QC-Toolkit.
High quality reads (phred score ≥20) were aligned to hg19 using Tophat2 (v.2.0.10) with library type setting ‘fr-firststranded’ and other parameters set to default.
Read count per gene was generated using HTSeq-count.
Differential gene expression was determined using edgeR (v.1.10.1).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including gene symbol, logFoldChange, p-values, FPKM and gene name from EdgeR.

growth_protocol: 500,000 cells were plated in 6-well plates and grown in 10% serum-containing media.

extract_protocol:
Cell lysates were obtained by adding RLT solution (Qiagen) to monolayer cells and RNA was isolated using RNeasy columns followed by DNase I digestion. 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-seq libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat Sample Preparation kit (Illumina) and sequenced using the 100 bp paired-end protocol on an Illumina HiSeq 2000.

treatment_protocol: Exponentially growing cells were harvested 36 hours after plating.

value: Colorectal cancer cell line

value: PUM2 overexpression


title: PUM2-OE CLONE2 rep1

description: processed data file: PUM2edgeR.txt


title: fin LS9 20weeks longitudinal group1 batch1

value: 35 weeks


title: fin LS8 20weeks longitudinal group1 batch1

value: 33.9 weeks


title: skin JM24 39weeks normal aging

value: 39 weeks


title: fin LS7 20weeks longitudinal group1 batch1

value: 33.7 weeks


title: skin JM18 39weeks normal aging


title: PUM1-OE CLONE2 rep1

description: processed data file: PUM1edgeR.txt

value: PUM1 overexpression


title: fin LS6 20weeks longitudinal group1 batch1

value: 32 weeks


title: brain MC3 9weeks DMSO

value: DMSO


title: PUM1-OE CLONE1 rep2

description: processed data file: PUM1edgeR.txt


title: skin JM15 39weeks normal aging


title: PUM1-OE CLONE2 rep2

description: processed data file: PUM1edgeR.txt


title: PUM1-OE CLONE1 rep1

description: processed data file: PUM1edgeR.txt


title: GFP rep3

description: processed data file: PUM1edgeR.txt

value: GFP


title: GFP rep2

description: processed data file: PUM1edgeR.txt


title: skin JM13 39weeks normal aging


title: fin LS5 20weeks longitudinal group1 batch1

value: tailfin

value: 32.4 weeks


title: fin LS4 20weeks longitudinal group1 batch1

value: 20 weeks

value: 31.6 weeks


title: PUM2-OE CLONE1 rep2

description: processed data file: PUM2edgeR.txt


title: NORAD-KO CLONE3

description: processed data file: NORADedgeR.txt

value: NORAD-/-


title: skin JM74 27weeks normal aging

value: skin

value: 27 weeks


title: PUM2-OE CLONE1 rep1

description: processed data file: PUM2edgeR.txt

value: Colorectal cancer cell line


title: fin LS3 20weeks longitudinal group1 batch1

value: 29.1 weeks


title: NORAD-KO CLONE2

description: processed data file: NORADedgeR.txt


title: skin JM83 27weeks normal aging


title: skin JM72 27weeks normal aging


title: skin JM62 27weeks normal aging


title: fin LS1 20weeks longitudinal group1 batch1

value: 32.6 weeks


title: WT rep2

description: processed data file: NORADedgeR.txt

value: wild-type


title: WT rep3

description: processed data file: NORADedgeR.txt


title: fin LS29 10weeks longitudinal group3 batch1

value: 10 weeks

value: 69.9 weeks


title: skin JM55 27weeks normal aging


title: WT rep1

description: processed data file: NORADedgeR.txt


title: fin LS28 10weeks longitudinal group3 batch1

value: 66.1 weeks


title: GFP rep1

description: processed data file: PUM1edgeR.txt


title: fin LS27 10weeks longitudinal group3 batch1

value: 63.4 weeks


title: skin JM88 20weeks normal aging


title: fin LS26 10weeks longitudinal group3 batch1

value: 61.6 weeks


title: skin JM1 39weeks normal aging

value: 39 weeks


title: skin JM87 20weeks normal aging


title: fin LS2 20weeks longitudinal group1 batch1

value: tailfin

value: 28.7 weeks


title: NORAD-KO CLONE1

description: processed data file: NORADedgeR.txt


title: fin LS25 10weeks longitudinal group3 batch1

value: 61.9 weeks


title: skin JM79 20weeks normal aging

value: 20 weeks


title: fin LS24 10weeks longitudinal group3 batch1

value: 59.1 weeks


title: fin LS23 10weeks longitudinal group3 batch1

value: 58 weeks


title: skin JM84 20weeks normal aging

value: skin


title: fin LS22 10weeks longitudinal group3 batch1

value: 58.7 weeks


title: fin LS21 10weeks longitudinal group3 batch1

value: 57.3 weeks


title: fin LS20 10weeks longitudinal group2 batch1

value: 50.3 weeks


title: skin JM116 12weeks normal aging

value: 12 weeks


title: skin JM109 12weeks normal aging


title: fin LS19 10weeks longitudinal group2 batch1

value: 10 weeks


title: skin JM104 12weeks normal aging


title: fin LS30 10weeks longitudinal group3 batch1

value: 70.4 weeks


title: skin JM95 5weeks normal aging

value: 5 weeks


title: fin LS17 10weeks longitudinal group2 batch1

value: 49.7 weeks


title: skin JM112 12weeks normal aging


title: fin LS18 10weeks longitudinal group2 batch1

value: 50 weeks


title: skin JM91 20weeks normal aging


title: fin LS16 10weeks longitudinal group2 batch1

value: 49.9 weeks


title: bone marrow_RNAseq_3

first: Jalal

middle: Ahmed

last: Khan

state: New York

address: 1301 Morris Park Ave

department: 1Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research

institute: Icahn School of Medicine

data_processing:
The paired-end RNA-seq reads were aligned to the mm9 build of the mouse genome and Ensembl gene annotation was performed with Genomic Short-read Nucleotide Alignment Program (GSNAP)
Assignment of reads to genes was performed by the HTSeq-count component of the HTSeq python library; Assignments were made using known transcripts in the Ensembl General Feature Format annotation file using the union strategy and alignments with a quality score lower than 10 were excluded. 37,996 mRNA transcripts were identified from 126,895,716 read pairs.
The R package DESeq (9) was used to identify differentially expressed genes. Gene expression was normalized with the estimated dispersion with the “pooled-CR” method and “maximum” sharing mode.
Genes with extreme expression value were removed from further analysis. Statistically significant differentially expressed genes were determined with negative binomial test
Genome_build: mm9
Supplementary_files_format_and_content: Excel spreasheet, normalized transcript abundance

source_name: bone marrow_RNAseq

extract_protocol:
cDNA libraries were derived from sorted cells using the SMARTer® Ultra™ Low Input RNA for Illumina® Sequencing – HV
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: adult bone marrow

value: Primary cells - FACS sorted


title: bone marrow_RNAseq_2


title: skin JM103 5weeks normal aging


title: Bov_4_M

organism: Bos taurus

value: monocyte

value: F


title: skin JM102 5weeks normal aging


title: fetal liver_RNAseq_2

source_name: fetal liver_RNAseq

value: fetal liver


title: fetal liver_RNAseq_1


title: skin JM110 12weeks normal aging


title: skin JM100 5weeks normal aging


title: Bov_4_L

value: lymphocyte


title: fin LS14 10weeks longitudinal group2 batch1

value: tailfin

value: 48 weeks


title: Bov_4_G

value: granulocyte


title: fin LS13 10weeks longitudinal group2 batch1

value: 48.7 weeks


title: liver JM18 39weeks normal aging

value: liver

value: 39 weeks


title: Bov_3_M


title: BJ RASG12V + CRISPR sgRNA p21enhancer_Tiling_Hit38

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

data_processing:
Sequenced reads were aligned to the human genome (hg19) using TopHat2 and gene expression counts were calculated using HTseq based on Ensembl’s human gene annotations. Expression levels were normalized using quantile normalization.
Genome_build: hg19

source_name: hTERT-immortalized BJ cells

growth_protocol: BJ/hT/HRASG12V cells were cultured in DMEM medium (Gibco), supplemented with 10% FCS (Hyclone), and 1% penicillin/streptomycin (Gibco).

extract_protocol:
RNA-seq samples were processed with TruSeq RNA library prep kit v2 (Illumina)
RNA-seq libraries were prepared according to Illumina's instructions

treatment_protocol: Cells were treated with 100nM tamoxifen (4-Hydroxytamoxifen, Sigma) to induce HRASG12V expression

value: hTERT-immortalized BJ cells

tag: ras activation

value: Yes

tag: genetic manipulation

value: CRISPR sgRNA p21enhancer_Tiling_Hit38


title: liver JM15 39weeks normal aging


title: BJ RASG12V + CRISPR sgRNA p21enhancer_Tiling_Hit147

value: CRISPR sgRNA p21enhancer_Tiling_Hit147


title: Bov_3_L


title: BJ RASG12V + CRISPR sgRNA p21enhancer_Tiling_Hit4

value: CRISPR sgRNA p21enhancer_Tiling_Hit4


title: fin LS11 10weeks longitudinal group2 batch1

value: 10 weeks

value: 46.9 weeks


title: liver JM13 39weeks normal aging


title: BJ RASG12V +  CRISPR sgRNA for Enhancer3507_Hit3

value: CRISPR sgRNA for Enhancer3507_Hit3


title: fin LS10 10weeks longitudinal group1 batch1

value: 36.4 weeks


title: liver JM12 39weeks normal aging


title: skin JM94 5weeks normal aging

value: skin

value: 5 weeks


title: Bov_3_G

value: F


title: fin LS15 10weeks longitudinal group2 batch1

value: tailfin

value: 49 weeks


title: Bov_2_M

value: monocyte

value: M


title: liver JM1 39weeks normal aging

value: liver

value: 39 weeks


title: fin LS8 10weeks longitudinal group1 batch1

value: 33.9 weeks


title: Bov_2_L

value: lymphocyte


title: BJ RASG12V +  CRISPR sgRNA for Enhancer3507_Hit2

value: hTERT-immortalized BJ cells

value: Yes

value: CRISPR sgRNA for Enhancer3507_Hit2


title: fin LS9 10weeks longitudinal group1 batch1

value: 10 weeks

value: 35 weeks


title: BJ RASG12V +  CRISPR sgRNA for Enhancer3507_Hit1

value: CRISPR sgRNA for Enhancer3507_Hit1


title: liver JM83 27weeks normal aging

value: 27 weeks


title: liver JM74 27weeks normal aging


title: fin LS7 10weeks longitudinal group1 batch1

value: 33.7 weeks


title: fin LS6 10weeks longitudinal group1 batch1

value: 32 weeks


title: Bov_2_G

value: granulocyte


title: Bov_1_M


title: fin LS12 10weeks longitudinal group2 batch1

value: tailfin

value: 47.9 weeks


title: BJ RASG12V + p53 targeting using shRNA

value: p53 silencing using shRNA


title: BJ RASG12V + p53 targeting using CRISPR

value: p53 targeting using CRISPR-Cas9


title: fin LS4 10weeks longitudinal group1 batch1

value: 31.6 weeks


title: liver JM72 27weeks normal aging

value: liver


title: Bov_1_L

value: lymphocyte

value: M


title: fin LS5 10weeks longitudinal group1 batch1

value: 32.4 weeks


title: Bov_1_G


title: liver JM61 27weeks normal aging


title: liver JM85 20weeks normal aging

value: 20 weeks


title: Mouse Adult Liver 3

description:
MM3
SRX871395

value: 28 months


title: fin LS3 10weeks longitudinal group1 batch1

value: 10 weeks

value: 29.1 weeks


title: BJ control

value: hTERT-immortalized BJ cells

value: No


title: Mouse Adult Liver 2

description:
MM2
SRX871370


title: Human Adult Liver 3

value: Adult (unknown)


title: Mouse Adult Liver 1

description:
MM1
SRX871336


title: liver JM84 20weeks normal aging


title: Human Adult Liver 2


title: fin LS1 10weeks longitudinal group1 batch1

value: 32.6 weeks


title: fin LS2 10weeks longitudinal group1 batch1

value: tailfin

value: 28.7 weeks


title: liver JM82 20weeks normal aging


title: liver JM79 20weeks normal aging


title: Human Adult Liver 1


title: liver JM69 27weeks normal aging

value: 27 weeks


title: CAB3

city: Genève

first: Ozren

last: Stojanovic

address: 1, rue Michèl-Servet

department: Faculté de Médecine, Dept. PHYM

description: whole tissue

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
The reads were mapped using TopHat v.2 to the UCSC mm10 genome release.
The gene features were counted with HTSeq v0.5.3p9 (htseq-count). Normalization and differential expression analysis was performed with the statistical analysis R/Bioconductor package edgeR v. 3.4.2
Genome_build: mm10
Supplementary_files_format_and_content: excel file, edgeR normalized counts

source_name: 6 C + antibiotics 30 days

extract_protocol:
RNA extracted by Trizol (Invitrogen) according to manufacturer's instructions
The libraries were prepared with 300 ng of total RNA as starting material and processed with the Illumina Truseq mRNA stranded kit according to the manufacturer instruction.

treatment_protocol: Mice were kept 30 days at room temperature or at 6C, 2 per cage, under SPF conditions, with or without administration of antibiotic coctail in drinking water. Fasted 5h before sacrifice.

value: jejunum


title: CAB2

description: whole tissue


title: CAB1

description: whole tissue


title: liver JM75 20weeks normal aging


title: day31 Cold6 cecum

data_processing:
Library strategy: 16S rRNA gene V4-region miSeq
Using QIIME and custom scripts, sequences were quality filtered and demultiplexed using exact matches to the supplied DNA barcodes.
Resulting sequences were then searched against the Greengenes reference database of 16S rRNA gene sequences, clustered at 97% by uclust (closedreference OTU picking).
The longest sequence from each Operation Taxonomic Unit (OTU) thus formed was then used as the OTU representative sequence, and assigned taxonomic classification via mothur's bayesian classifier, trained against the Greengenes database clustered at 98%.
Taxa are filtered to those present in at least one of the samples (Filter-1), or to taxa significantly increased in their abundance in one category compared to the alternate categories (Filter-5). For Filter-5, ANOVA (analysis of variance) was employed to calculate p-values. Additionally, q-values were calculated using the Benjamini-Hochberg procedure to correct p-values, controlling for false discovery rates.
Supplementary_files_format_and_content: processed_counts.xlsx containes abundance of each OUT in every sample with taxonomical classification.

organism: mouse gut metagenome

source_name: cecum

extract_protocol:
Bacterial DNA content was extracted using QIAamp Fast DNA stool Mini Kit (Qiagen). 40 DNA isolates from mice feces and 9 biospecimens of mice cecal content were received in Second Genome’s service laboratory on March 28 and April 2, 2014. The samples arrived intact, frozen and according to specification, and were immediately stored at -20°C. The biospecimen’s DNA are isolated using the MoBio PowerMag DNA isolation kit as per vendor’s protocol. The combined DNA samples ranged in concentration of 25-159.8 ng/μl. All samples were quantified via the Qubit® Quant-iT dsDNA Broad-Range Kit (Invitrogen, Life Technologies, Grand Island, NY) to ensure that they met minimum concentration and mass of DNA. The sample set met specifications.
To enrich the sample for bacterial 16S V4 rDNA region, DNA was amplified utilizing fusion primers designed against the surrounding conserved regions which are tailed with sequences to incorporate Illumina (San Diego, CA) flow cell adapters and indexing barcodes. Each sample was PCR amplified with two differently bar coded V4 fusion primers. 49 samples met the post-PCR quantification minimum and were advanced for pooling and sequencing.

treatment_protocol: 31 day on 6 C (Cold) or room temperature (RT)

value: cecum of C57BL6/J mouse

tag: collection day

value: cold


title: BJ RASG12V

tag: cell type

value: Yes


title: RAB3

description: whole tissue

source_name: room temp + antibiotics 30 days


title: liver JM115 12weeks normal aging

value: liver

tag: age

value: 12 weeks


title: BJ RASG12V + control CRISPR sgRNA

value: control CRISPR-Cas9 sgRNA