title: PT-GDF10-2

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

data_processing:
Basecalls/demultiplexing performed using Illumina CASAVA 1.8.2
Aligned to mm10 using STAR2.4.0
Count read using HT-seq0.6.1 using mm10 RefSeq as reference
Normalization (TMM), and differential expression analysis using EdgeR
Genome_build: mm10

source_name: PT-GDF10: GDF10 siRNA adult animal stroke

growth_protocol: Adult C57BL/6 mouse grown under normal condition

extract_protocol:
RNA-Microprep kit (Zymo-Research)
Ovation RNA-seq System v2
69 bp paired-end RNA Sequencing

treatment_protocol: Mice were placed in a stereotactic apparatus with the skull exposed under anesthesia. A cold light source was used to produce a 2mm diameter focal stroke. Rose bengal was applied with 0.2ml per 25g mouse. After 5min, the brain was illuminated for 15min followed by suturing and allowed for recovering.

value: FACS sorted cortical neurons

tag: condition

value: stroke +GDF10 siRNA


title: PT-GDF10-1

status: Public on Oct 28 2017

type: SRA

city: Los Angeles

state: CA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue


title: HK-2 AGO2-PAR-CLIP CsA1

city: Boston

first: Christopher

middle: J

last: Benway

state: MA

address: 300 Longwood Ave, Enders 510

department: Nephrology

institute: Children's Hospital

data_processing:
Library strategy: PAR-CLIP
Base-calling and de-multiplexing were completed using CASAVA-1.8.2 software.
Reads were pre-processed by adapter clipping with the package 'cutadapt.' miRNA-seq reads were filtered by size (greater than 16 nt).
Alignment of miRNA reads to the hg19 reference genome was performed using Bowtie. Counts of reads mapping to mature miRNAs was obtained using HTSeq and GFF data obtained from miRBase (v 21). mRNA reads were aligned using TopHat and counted using HTSeq with a hg19 GTF reference based on UCSC gene exons obtained from Illumina iGenomes. DESeq2 was used to compute differential expression.
PAR-CLIP reads greater than 13 nt were aligned with Bowtie to the hg19 reference genome, allowing for 2 mismatches. AGO bound clusters of sequences were identified using the PIPE-CLIP bioinformatics pipeline. Crosslinking clutsters are defined as enriched clusters (p value < 0.05). containing reliable T>C crossliinking mutations (p value < 0.05)/
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq count matrices indicate the read counts aligned to mRNAs of miRNAs. DESeq2 output files indicate the calculated log2 fold change in expression and adjusted p-values. PAR-CLIP files contain, in BED format, the crosslinking sites determined by PIPE-CLIP analysis, including PeakScore and Annotation of the genes which are identified.

organism: Homo sapiens

source_name: human kidney proximal tubular cell line

growth_protocol: Human kidney proximal tubular epithelial cells (HK-2, ATCC) were grown in Keratinocyte-SFM supplemented with 5 ng/ml Epidermal Growth Factor 1-53 (EGF 1-53) and 0.05 mg/ml Bovine Pituitary Extract (BPE). Cells were maintained in 15 cm dishes until ~80% confluency.

extract_protocol:
Total RNAs were isolated from cells grown in 15 cm culture dishes using miRNeasy Kit (Qiagen) according to manufacturer's instructions. Small RNAs, including miRNAs, were isolated using the manufacturer's enrichment protocol. The larger RNA fraction (>200 nt) was enriched for mRNAs using NEBNext Poly(A)mRNA Magnetic Isolation Module (New England Biolabs). For PAR-CLIP, crosslinked cells were resuspended in NP40 lysis buffer and incubated on ice for 10 minutes. The lysates were cleared by centrifugation and syringe filter. RNAs in the cleared lysate were partially degraded by treatment with RNAse T1 for 15 minutes at 22°C followed by 5 minutes on ice. Immunoprecipitation of target Argonaute (AGO) protein was accomplished using antibody-bound Dynabeads Protein G magnetic particles (Thermo Fisher) for 2 hours in lysis buffer (lower salt concentration than IP buffer) at 4°C. The complete RNA isolation protocol was completed as described by Hafner et. al, 2010 (PMCID: PMC4180672).
mRNAs and miRNA libraries were constructed using NEBnext Multiplex Small RNA and mRNA Library Prep Sets for Illumina (New England Biolabs). PAR-CLIP cDNA libraries were constructed from recovered RNA by sequentially ligating a preadenylated 3'-adapter using T4 Rnl2(1-249)K227Q ligase (New England Biolabs) and an RNA 5'-adapter using T4 RNA ligase. Adapters are designed to be compatible with Illumina Small RNA library and sequencing protocols. After PCR amplification the libraries were size fractionated by agarose gel electrophoresis.

treatment_protocol: 24 hours prior to crosslinking, cells were treated with 5 ug/mL cyclosporine A (CsA, Sigma-Aldrich) or vehicle control (0.1% ethanol). ~16-18 hours prior to crosslinking, cells were treated with 100 uM 4-thiouridine (4-SU, Sigma-Aldrich). For UV crosslinking, attached cells were rinsed once with ice-cold PBS. PBS was removed completely and cells were irradiated on ice with 365 nm UV light (0.15 J/cm2) in a Stratalinker 2400 (Stratagene). Cells were scraped off in 1 ml PBS per plate and collected by centrifugation at 500 × g for 5 min. For mRNA-seq and miRNA-seq cells were treated with 5 ug/mL CsA or vehicle control (0.1% ethanol) for 48 hours.

tag: cell line

tag: crosslinker and crosslinked wavelength

tag: par-clip antibody

value: anti-AGO2 (Cell Signaling C34C6, #2897)


title: PT-GDF10-3


title: PostWL Subject 4

city: New York

first: Yupu

last: Liang

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description:
Human abdominal adipose tissue
Sample name: 04B

data_processing:
Aligning the input reads to reference genome using STAR
Count reads on exon level (-f exon) and gene level (default no -f) using featureCounts v1.5.0-p2
Genome_build: hg19
Supplementary_files_format_and_content: text file summarizing count information of gene presented after aligning samples to the reference genome, normalized by DESeq2

extract_protocol:
RNEasy Lipid Mini Kit
NY Genome Center

treatment_protocol: Diet-Induced Weight Loss

tag: subject id

tag: timepoint

value: PostWL

value: Subcutaneous adipose

tag: tissue source

value: Modified liposuction aspirate

tag: tissue preparation

value: Rinsed with saline, snap frozen

tag: Sex

value: female


title: PostWL Subject 9

description:
Human abdominal adipose tissue
Sample name: 09B


title: Toddler mutant 5 hpf

city: Salt Lake City

first: James

middle: A

last: Gagnon

state: UT

address: 1390 Presidents Circle, Crocker Science Center Receiving, Crocker Science Center Receiving

department: Biological Sciences

institute: University of Utah

data_processing:
Reads were aligned for each sample using TopHat v2.0.13 (Trapnell et al., 2009) with the following command “tophat -o <output directory> -p 16 --no-novel-juncs -G <gene table> <Bowtie2 genome index> <fastq reads>”
Transcript abundance and differential expression were determined using Cufflinks v2.2.1 (Trapnell et al., 2012) with the following command for each developmental stage “cuffdiff -p 16 -b <genome.fa -u -L <labels> -o <output directory> <gene table> <wild type aligned reads .bam file> <mutant aligned reads .bam file>”
Genome_build: zv9
Supplementary_files_format_and_content: tab delimited text files containing FPKMs

organism: Danio rerio

source_name: Whole embryos (n=50)

growth_protocol: Embryos were grown at 28.5C until point of collection

extract_protocol:
Total RNA was extracted using Trizol protocol
Libraries were constructed using Illumina TruSeq RNA Library Prep Kit v2

tag: developmental stage

value: 5 hpf

tag: genotype

value: Toddler mutant

value: Whole embryo


title: HK-2 miRNA Veh3

data_processing:
Base-calling and de-multiplexing were completed using CASAVA-1.8.2 software.
Reads were pre-processed by adapter clipping with the package 'cutadapt.' miRNA-seq reads were filtered by size (greater than 16 nt).
Alignment of miRNA reads to the hg19 reference genome was performed using Bowtie. Counts of reads mapping to mature miRNAs was obtained using HTSeq and GFF data obtained from miRBase (v 21). mRNA reads were aligned using TopHat and counted using HTSeq with a hg19 GTF reference based on UCSC gene exons obtained from Illumina iGenomes. DESeq2 was used to compute differential expression.
PAR-CLIP reads greater than 13 nt were aligned with Bowtie to the hg19 reference genome, allowing for 2 mismatches. AGO bound clusters of sequences were identified using the PIPE-CLIP bioinformatics pipeline. Crosslinking clutsters are defined as enriched clusters (p value < 0.05). containing reliable T>C crossliinking mutations (p value < 0.05)/
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq count matrices indicate the read counts aligned to mRNAs of miRNAs. DESeq2 output files indicate the calculated log2 fold change in expression and adjusted p-values. PAR-CLIP files contain, in BED format, the crosslinking sites determined by PIPE-CLIP analysis, including PeakScore and Annotation of the genes which are identified.


title: HK-2 miRNA Veh2


title: PostWL Subject 12

description:
Human abdominal adipose tissue
Sample name: 12B


title: 6-PT

source_name: PT: adult animal stroke

value: stroke


title: PostWL Subject 11

description:
Human abdominal adipose tissue
Sample name: 11B


title: PreWL Subject 10

description:
Human abdominal adipose tissue
Sample name: 10A

value: PreWL


title: HK-2 miRNA Veh4


title: HK-2 mRNA CsA4

molecule: polyA RNA


title: Toddler mutant 4 hpf

value: 4 hpf


title: PreWL Subject 8

description:
Human abdominal adipose tissue
Sample name: 08A


title: OA3

city: Middletown

first: Joseph

last: Coolon

state: CT

address: 52 Lawn Avenue Biology Department

department: Biology

institute: Wesleyan University

data_processing:
Raw sequencing reads were checked for quality using FASTQC (Andrews 2010) and overrepresented sequences were analyzed using NCBI BLAST (Altschul et al. 1990).
Reads were mapped to the D. sechellia genome using Bowtie2 with default parameters (Langmead & Salzberg 2012) and the current genome file available at the time analysis from ensembl: Drosophila_sechellia.GCA_000005215.1.dna.toplevel.fa (Yates et al. 2016).
Gene expression quantification and differential expression analysis was performed with Cuffdiff (Trapnell et al. 2010, 2013) using the previously mentioned genome file and current gene file available from ensembl: Drosophila_sechellia.GCA_000005215.1.34.gff3 (Yates et al. 2016).
In Cuffdiff, geometric normalization and length correction was used and bias correction was performed using the reference genome sequence. Data processing and visualization was performed in R (R Core Development Team 2010).
Genome_build: Drosophila_sechellia.GCA_000005215.1.dna.toplevel.fa
Supplementary_files_format_and_content: Cuffdiff output in tab delimited txt format.

organism: Drosophila sechellia

source_name: Whole fly

growth_protocol: Drosophila sechellia (14021-0428.25) flies were reared on cornmeal medium using a 16:8 light:dark cycle at 20 ̊C.

extract_protocol:
RNA was extracted from a homogenate of 10 whole adult flies using the Promega SV total RNA extraction system with modified protocol (Promega, Coolon et al. 2013). Three replicates were analyzed for each exposure environment (control or 0.7% OA).
A total of six RNA-seq samples were prepared by poly(A) selection.

treatment_protocol: 0~3 day old adult females were collected and exposed to either control food (Carolina Biological Supply Company ®), or food containing 0.7% OA (Sigma) for an exposure period of 24 hours

tag: strain

tag: age

value: 1-4 days

tag: diet

value: food containing 0.7 percent octanoic acid


title: Wild type 4 hpf

value: wild type


title: Wild type 6 hpf

value: 6 hpf


title: Control3

value: control food


title: WT-3

source_name: WT: adult animal control

value: FACS sorted cortical neurons

value: control


title: OA2


title: PreWL Subject 7

description:
Human abdominal adipose tissue
Sample name: 07A

value: Subcutaneous adipose


title: PreWL Subject 2

description:
Human abdominal adipose tissue
Sample name: 02A

value: Modified liposuction aspirate


title: HK-2 miRNA Veh1


title: HK-2 mRNA CsA2


title: WT-1


title: PostWL Subject 8

description:
Human abdominal adipose tissue
Sample name: 08B

value: PostWL

value: Rinsed with saline, snap frozen


title: 5-P4

source_name: P4 animal control


title: HK-2 mRNA CsA3


title: PostWL Subject 7

description:
Human abdominal adipose tissue
Sample name: 07B

value: female


title: Wild type 5 hpf

value: 5 hpf


title: WT-2


title: OA1


title: HK-2 mRNA Veh3


title: HK-2 mRNA Veh4


title: PostWL Subject 10

description:
Human abdominal adipose tissue
Sample name: 10B


title: 5-PT


title: HK-2 mRNA CsA1


title: Control2


title: 4-P4


title: 4-PT


title: 6-P4


title: PreWL Subject 1

description:
Human abdominal adipose tissue
Sample name: 01A


title: HK-2 mRNA Veh1


title: HK-2 mRNA Veh2


title: NB 1

status: Public on Oct 27 2017

city: Montreal

first: Nada

last: Jabado

state: Québec

address: 1001 Décarie Boulevard

department: Department of Pediatrics

country: Canada

institute: McGill University

data_processing:
Raw reads are trimmed for quality (phred33 >= 30) and length (n >= 30) using Trimmomatic (v. 0.32). Illumina adaptor sequences are clipped off using the palindromic mode.
Perform a sliding window trimming, cutting once the average quality within the window falls below 30. Cut 3 bases off the start of each read, if below quality 30. Cut 3 bases off the end of each read, if above quality 30. Cut the first 4 bases at the start of each read. Drop short reads (n <= 30).
Reads are aligned to the UCSC  hg19 genomes with STAR v2.3.0e using default settings, which removes multimapping reads. Feature annotation is provided by Ensembl ensGene.
Read counting is done with featureCounts v1.4.4. Unless stated otherwise, default settings are used. Read summarization is done at the gene symbol level. The minimum mapping quality score for a read to be counted is 3. Only primary alignments are counted. Reads rather than fragments are counted. Only reads mapping to exons are considered.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values containing raw read counts

source_name: matched normal brain control

extract_protocol:
Total RNA was extracted from human tumors using the AllPrepDNA/RNA/miRNA Universal Kit (Qiagen) according to instructions from the manufacturer.
Library preparation was performed with ribosomal RNA (rRNA) depletion methods according to instruction from the manufacturer (Epicentre) to achieve greater coverage of mRNA and other long non-coding transcripts. Paired-end sequencing was performed on the Illumina HiSeq 2000 platform.

tag: subject status

value: pediatric brain tumor patient

value: normal brain

tag: genotype/variation

value: H3.3WT; Low pdgfra


title: WT pHGG 1

source_name: pHGG that are wild-type for H3.3 and TP53

value: pediatric high-grade gliomas (pHGG)


title: K27M pHGG 1

source_name: pHGG with H3.3K27M and loss-of-function TP53 mutation

value: H3.3K27M; Tp53 mut; High Pdgfra


title: K27M pHGG 4


title: K27M pHGG 3


title: WT pHGG 2


title: WT pHGG 3


title: NB 3


title: ES_5hMeDIP_TKO_Dnmt3a1_rep1

city: Utrecht

first: Tuncay

last: Baubec

address: Padualaan 8

department: Department of Biology

country: Netherlands

institute: Utrecht University

description: enriched DNA

library_source: genomic

data_processing:
Library strategy: hMeDIP-Seq
Fastq reads were trimmed to 50bp length in order to remove adapter contaminations and low quality basecalls
Reads were aligned to mm9 mouse genome using Bowtie directly executed from the R package QuasR with standard alignment parameters allowing up to 2 missmatches and excluding multi-mappers
Coordinates of unique reads that map only once to the mouse genome were converted to GenomicRanges format for further analysis and to the WIG format for visualisation.
Genome_build: mm9
Supplementary_files_format_and_content: wig track format: read coverage per consecutive 100bp windows

molecule: genomic DNA

source_name: embryonic stem cell

growth_protocol: Wild type embryonic stem cells derived from mixed 129-C57Bl/6 background blastocysts, were cultivated on feeder cells or 0.2% gelatine coated dishes. ES cell growth medium consisted of DMEM (Invitrogen) supplemented with 15% foetal calf serum (Invitrogen), 1x non-essential amino acids (Invitrogen), 1mM L-glutamine, LIF and 0.001% beta-mercaptoethanol.

extract_protocol:
Genomic DNA was sonicated to 150-300 bp and RNAseA treated prior to end-repair and A-tailing using the NEB Ultra library kit and protocol. NEB adapters were ligated to the genomic DNA following the NEB Ultra protocol, and DNA was cleaned up using Ampure XP beads. Following cleanup, 5 ug adapter-ligated DNA was taken up in 500 ul TE and denatured for 10 min in boiling waterbath. 5-hmC was enriched using the Active Motif 5-hmC antibody (39769) following the MeDIP protocol from Mohn et al 2009, PMID:18987806.
After IP, library was PCR amplified with 15-18 cycles prior to sequencing.

tag: cell type

value: embryonic stem cells


title: ES_5hMeDIP_TKO_Dnmt3a2_rep2

description: enriched DNA


title: ES_5hMeDIP_Dnmt3aKO_rep2

description: enriched DNA


title: ES_5hMeDIP_TKO_Dnmt3a2_rep1

description: enriched DNA


title: WT pHGG 4

tag: tissue


title: K27M pHGG 5


title: NB 2


title: K27M pHGG 2


title: ES_bioDNMT3A1_rep1

description: enriched DNA

data_processing:
Reads were aligned to mm9 mouse genome using Bowtie directly executed from the R package QuasR with standard alignment parameters allowing up to 2 missmatches and excluding multi-mappers
Coordinates of unique reads that map only once to the mouse genome were converted to GenomicRanges format for further analysis and to the WIG format for visualisation.
Genome_build: mm9
Supplementary_files_format_and_content: wig track format: read coverage per consecutive 100bp windows

extract_protocol:
For cross-linking and chromatin extraction, cells were fixed for 10 minutes with 1% Formaldehyde at room temperature and incubated for 10 min on ice in presence of 1.2M Glycine. Cells were harvested and treated for 10 min with 10mM EDTA, 10mM TRIS, 0.5mM EGTA and 0.25% Triton X-100 and 10 min in 1mM EDTA, 10mM TRIS, 0.5mM EGTA and 200mM NaCl with subsequent lysis in 50mM HEPES, 1mM EDTA, 1% Triton X-100, 0.1% deoxycholate, 0.2% SDS and 300 mM NaCl for 2 hours on ice. Crosslinked chromatin was subjected to sonication in a Bioruptor Pico instrument (Diagenode) and diluted with equal volumes of 50mM HEPES, 1mM EDTA, 1% Triton X-100, 0.1% deoxycholate after successful sonication. ProteinA-dynabeads pre-cleared 150-250 µg chromatin were incubated with 40 µl blocked (1%CFSG, 100ng tRNA) Streptavidin-M280 magnetic beads over night at 4°C. Beads were washed with two rounds of 2% SDS, 1x high salt buffer, 1x LiCl Buffer and two rounds of TE. Beads were treated with RNaseA for 30 min at 37°C, Proteinase K for 3 hours at 50°C then de-crosslinked over night at 55°C. DNA was purified with Phenol-Chloroform extraction and EtOH precipitation.
ChIP-seq library using NEB ChIPlibrary protocol with index adapters.

value: wild type


title: ES_bioDNMT3A1_rep2

description: enriched DNA


title: ES_5hMeDIP_WT_rep2

description: enriched DNA


title: ES_bioN3B-DNMT3A

description: enriched DNA


title: K27M-AP-Tumor9_WES

description:
processed data file:
mm_WES_variants_raw_K27M-AP-Tumor9.vcf.gz
mm_WES_variants_union_K27M-AP-Tumor9.vcf.gz

data_processing:
Library strategy: DNA-seq
Raw reads are trimmed for quality (phred33 >= 30) and length (n >= 30) using Trimmomatic (v. 0.32). Illumina adaptor sequences are clipped off using the palindromic mode.
Perform a sliding window trimming, cutting once the average quality within the window falls below 30. Cut 3 bases off the start of each read, if below quality 30. Cut 3 bases off the end of each read, if above quality 30. Drop short reads (n <= 30).
The resulting reads were then aligned to the mm10 (GRCm38) reference genome using BWA-MEM v0.7.13
The split’N’Trim function of the Genome Analysis Toolkit (GATK) (v3.2-2) was used to split reads that have introns and reassign the mapping quality from 255 to 60. The IndelRealigner function of GATK was then used to realign indels. Duplicate reads were marked using the Picard toolset (v1.118). Variants are called using the mpileup function of samtools (v0.1.19) and using Annovar (February 2, 2016 version) over the mm10 refGene annotation.
Genome_build: mm10
Supplementary_files_format_and_content: vcf (raw variants) are provided on a sample-per-sample level. Files located in tar archive on series record.
Supplementary_files_format_and_content: vcf (raw variant calls on shared positions) contain the raw variant calls on positions harboring variants in any of the samples in this cohort. Files located in tar archive on series record.

source_name: Brain

extract_protocol:
Genomic DNA was extracted from cell pellets and frozen tumor tissue and the Agilent SureSelect Reagent Exome kit (Agilent) was used to prepare DNA libraries according to the manufacturer’s instructions.
Sequencing was performed on Illumina HiSeq 2000 using rapid-run mode with 100 bp paired-end reads.

value: H3.3K27M O/E; Trp53-/-; Atrx shRNA

value: brain

value: tumor cells

tag: tumor status

value: tumor


title: K27M-AP-Tumor8_WES

description:
processed data file:
mm_WES_variants_raw_K27M-AP-Tumor8.vcf.gz
mm_WES_variants_union_K27M-AP-Tumor8.vcf.gz


title: K27M-AP-Tumor6_WES

description:
processed data file:
mm_WES_variants_raw_K27M-AP-Tumor6.vcf.gz
mm_WES_variants_union_K27M-AP-Tumor6.vcf.gz


title: K27M-AP-Tumor7_WES

description:
processed data file:
mm_WES_variants_raw_K27M-AP-Tumor7.vcf.gz
mm_WES_variants_union_K27M-AP-Tumor7.vcf.gz


title: K27M-AP-Tumor5_WES

description:
processed data file:
mm_WES_variants_raw_K27M-AP-Tumor5.vcf.gz
mm_WES_variants_union_K27M-AP-Tumor5.vcf.gz


title: K27M-AP-Tumor4_WES

description:
processed data file:
mm_WES_variants_raw_K27M-AP-Tumor4.vcf.gz
mm_WES_variants_union_K27M-AP-Tumor4.vcf.gz


title: Control1

value: 1-4 days

value: control food


title: K27M-AP-Tumor2_WES

description:
processed data file:
mm_WES_variants_raw_K27M-AP-Tumor2.vcf.gz
mm_WES_variants_union_K27M-AP-Tumor2.vcf.gz


title: K27M-AP-Tumor3_WES

description:
processed data file:
mm_WES_variants_raw_K27M-AP-Tumor3.vcf.gz
mm_WES_variants_union_K27M-AP-Tumor3.vcf.gz


title: ES_5hMeDIP_TKO_Dnmt3a1_rep2

description: enriched DNA


title: K27M-AP T2

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_K27M-APP-2.vcf.gz

data_processing:
Raw reads are trimmed for quality (phred33 >= 30) and length (n >= 30) using Trimmomatic (v. 0.32). Illumina adaptor sequences are clipped off using the palindromic mode.
Perform a sliding window trimming, cutting once the average quality within the window falls below 30. Cut 3 bases off the start of each read, if below quality 30. Cut 3 bases off the end of each read, if above quality 30. Cut the first 4 bases at the start of each read. Drop short reads (n <= 30).
Reads are aligned to the UCSC mm10 genomes with STAR v2.3.0e using default settings, which removes multimapping reads. Feature annotation is provided by Ensembl ensGene.
Read counting is done with featureCounts v1.4.4. Unless stated otherwise, default settings are used. Read summarization is done at the gene symbol level. The minimum mapping quality score for a read to be counted is 3. Only primary alignments are counted. Reads rather than fragments are counted. Only reads mapping to exons are considered.
The split’N’Trim function of the Genome Analysis Toolkit (GATK) (v3.2-2) was used to split reads that have introns and reassign the mapping quality from 255 to 60. The IndelRealigner function of GATK was then used to realign indels. Duplicate reads were marked using the Picard toolset (v1.118). Variants are called using the mpileup function of samtools (v0.1.19) and using Annovar (February 2, 2016 version) over the mm10 refGene annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated values containing raw read counts. File name = mm_RNA-seq_raw_counts.txt.gz
Supplementary_files_format_and_content: vcf (raw variants) are provided on a sample-per-sample level. Files located in a tar archive = mm_RNA-seq_variants_raw.tar

extract_protocol:
Total RNA was extracted from cell pellets and mouse tumors using the AllPrepDNA/RNA/miRNA Universal Kit (Qiagen) according to instructions from the manufacturer.
Library preparation was performed with ribosomal RNA (rRNA) depletion methods according to instruction from the manufacturer (Epicentre) to achieve greater coverage of mRNA and other long non-coding transcripts. Paired-end sequencing was performed on the Illumina HiSeq 2500 platform.


title: WT-AP 1

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_WT-AP-1.vcf.gz

value: H3.3WT O/E; Trp53-/-; Atrx shRNA

value: neural progenitor cells

value: preneoplastic


title: K27M-AP-Tumor10_WES

description:
processed data file:
mm_WES_variants_raw_K27M-AP-Tumor10.vcf.gz
mm_WES_variants_union_K27M-AP-Tumor10.vcf.gz


title: K27M-APP 2

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_K27M-APP-T3.vcf.gz

value: H3.3K27M O/E; Trp53-/-; Atrx shRNA; Pdgfra O/E


title: K27M-APP T1

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_K27M-APP-T4.vcf.gz


title: K27M-APP 1

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_K27M-APP-T2.vcf.gz


title: WT-AP 2

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_WT-AP-2.vcf.gz


title: K27M-P T1

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_K27M-P-T1.vcf.gz


title: K27M-AP-Tumor1_WES

description:
processed data file:
mm_WES_variants_raw_K27M-AP-Tumor1.vcf.gz
mm_WES_variants_union_K27M-AP-Tumor1.vcf.gz


title: K27M-AP 2

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_K27M-AP-2.vcf.gz


title: KL_5

city: Houston

first: Krithika

last: Lingappan

address: 6621 Fannin

institute: Baylor College of Medicine

description: Lung mRNA

data_processing:
Reads were mapped with TopHat 2.0. Only uniquely mapping reads were kept
The mapped reads were quantified with Cufflinks 2.0 and the GENCODE gene model.
Gene expression (FPKM) was quantile normalized using the R statistical system.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include quantile normalized FPKM values for each Sample

source_name: mouse lung

extract_protocol:
Lungs were harvested on PND7 or 21, flash frozen in liquid nitrogen, and RNA was extracted using the Zymo Direct-zol RNA kit followed by quality contro; of the extracted RNA samples
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

value: Female

tag: oxygen status

value: Room Air

tag: day


title: KL_9

description: Lung mRNA

value: Male


title: KL_3

description: Lung mRNA


title: KL_7

description: Lung mRNA


title: KL_8

description: Lung mRNA

value: Hyperoxia


title: EV-PDGFRA 2

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_EV-PDGFRA-2.vcf.gz

value: Pdgfra O/E


title: K27M-AP T1

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_K27M-APP-1.vcf.gz


title: K27M-AP 1

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_K27M-AP-1.vcf.gz


title: KL_33

description: Lung mRNA


title: K27M-APP T2

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_K27M-AP-T1.vcf.gz


title: KL_6

description: Lung mRNA


title: EV-PDGFRA 1

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_EV-PDGFRA-1.vcf.gz


title: hypothalamus_light_28_1

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 Gallus gallus genome (assembly Gallus_gallus-5.0) with reference annotation containing more than 25K genes listed in the Ensembl database.
Alignment and estimation of gene expression level were made using the RSEM package supported by Bowtie2 aligner.
Differentially expressed genes and their corresponding p-values were determined using the statistical methods DESeq2
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: raw.genes.csv.gz:  raw genes counts
Supplementary_files_format_and_content: res.pod.csv.gz: DESeq2 results for differential expressed gene analysis of cockerels hypothalamus in different point of life
Supplementary_files_format_and_content: res.prz.csv.gz: DESeq2 results for differential expressed gene analysis of cockerels pituitary in different point of life

organism: Gallus gallus

growth_protocol: The cockerels were reared in a deep-litter facility in experimental farm of the National Research Institute of Animal Production located in Aleksandrowice till 22 or 42 days of age, under the same, optimal, electronically controlled environmental conditions (temperature, lighting regime, air humidity) and were fed ad libitum with the same complete starter (1-21 days of age), grower (22-35 days of age) and finisher (36-42 days of age) diets containing 22, 20.5 and 20.5% crude protein and 2990, 3130 and 3130 kcal/kg metabolic energy.

extract_protocol:
RNA was isolated using PureLink® RNA Mini Kit (Ambion) 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).
A TruSeq RNA Sample Preparation Kit v2 (Illumina) was used to prepare cDNA libraries from 300 ng aliquots of the RNA samples according to the manufacturer’s protocol. The cDNA samples were ligated with indexed adaptors. 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: ROSS308 fast growing-chicken line

value: male

tag: shear force

value: light

value: hypothalamus

tag: replicant


title: KL_31

description: Lung mRNA


title: KL_28

description: Lung mRNA


title: hypothalamus_light_28_3

institute: National Research Institute of Animal Production


title: hypothalamus_light_28_4


title: hypothalamus_light_14_3


title: hypothalamus_light_28_2


title: KL_23

description: Lung mRNA


title: hypothalamus_light_14_2


title: KL_26

description: Lung mRNA


title: hypothalamus_light_14_1


title: KL_22

description: Lung mRNA


title: hypothalamus_light_14_4


title: KL_21

description: Lung mRNA


title: hypothalamus_heavy_28_4

value: heavy


title: hypothalamus_heavy_28_3


title: hypothalamus_heavy_28_2


title: hypothalamus_heavy_14_4


title: hypothalamus_heavy_14_2


title: KL_14

description: Lung mRNA


title: KL_17

description: Lung mRNA


title: KL_15

description: Lung mRNA


title: KL_13

description: Lung mRNA


title: KL_12

description: Lung mRNA


title: KL_11

description: Lung mRNA


title: hypophysis_light_28_2

value: hypophysis; pituitary gland


title: hypothalamus_heavy_14_3


title: hypothalamus_heavy_14_1


title: KL_27

description: Lung mRNA


title: KL_10

description: Lung mRNA


title: Mouse RNAseq Testis Male2 Adult

city: Lausanne

first: Diego

last: Cortez

address: Rue de Lausanne

country: Switzerland

institute: Univerity of Lausanne - CIG

data_processing:
RNA-seq reads were mapped to genomes using the GSNAP short read alignment program
Gene expression estimates of protein-coding genes (FPKM) were performed using Cufflinks (v2.2.1).
Genome_build: version 77 of Ensembl
Supplementary_files_format_and_content: Text file to be opened in R. The file contains the final expression values for all species used in this study.

source_name: Testis

extract_protocol:
QIAGEN RNeasy Kit
Illumina TruSeq Stranded mRNA Library protocol

value: Testis

tag: Stage

value: Adult


title: hypophysis_light_28_1

tag: Sex


title: hypophysis_light_28_4


title: KL_18

description: Lung mRNA


title: Mouse RNAseq Ovary Female2 Adult

description: Mouse_RNAseq_Ovary_Female2_Adult_1963sTS

source_name: Ovary

value: Ovary


title: Mouse RNAseq Liver Male1 Adult

source_name: Liver

value: Liver


title: Mouse RNAseq Liver Male2 Adult


title: hypothalamus_heavy_28_1


title: hypophysis_light_14_3


title: hypophysis_light_28_3


title: Mouse RNAseq Ovary Female1 Adult

description: Mouse_RNAseq_Ovary_Female1_Adult_1953sTS


title: Mouse RNAseq Liver Female2 Adult

description: Mouse_RNAseq_Liver_Female2_Adult_1962sTS


title: hypophysis_light_14_2


title: Mouse RNAseq Kidney Male2 Adult

source_name: Kidney

value: Kidney


title: hypophysis_light_14_1


title: Mouse RNAseq Kidney Female1 Adult

description: Mouse_RNAseq_Kidney_Female1_Adult_1951sTS


title: Mouse RNAseq Kidney Female2 Adult

description: Mouse_RNAseq_Kidney_Female2_Adult_2665sTS


title: hypophysis_heavy_28_3


title: Mouse RNAseq Liver Female1 Adult

description: Mouse_RNAseq_Liver_Female1_Adult_1952sTS


title: hypophysis_heavy_28_4


title: Mouse RNAseq Testis Male1 Adult


title: hypophysis_heavy_28_1


title: hypophysis_heavy_14_4


title: Mouse RNAseq Heart Male1 Adult

source_name: Heart

value: Heart


title: hypophysis_heavy_28_2


title: Mouse RNAseq Heart Male2 Adult


title: Mouse RNAseq Heart Female2 Adult

description: Mouse_RNAseq_Heart_Female2_Adult_2669sTS

value: Female


title: hypophysis_heavy_14_1


title: Mouse RNAseq Heart Female1 Adult

description: Mouse_RNAseq_Heart_Female1_Adult_1950sTS


title: Mouse RNAseq Brain Male2 Adult

value: Brain


title: hypophysis_light_14_4


title: Mouse RNAseq Brain Male1 Adult

value: Male


title: Opossum RNAseq Testis Male2 Adult

description: Opossum_RNAseq_Testis_Male2_Adult_3993sTS

organism: Monodelphis domestica


title: Mouse RNAseq Brain Female2 Adult

description: Mouse_RNAseq_Brain_Female2_Adult_1960sTS


title: Opossum RNAseq Testis Male1 Adult

description: Opossum_RNAseq_Testis_Male1_Adult_3956sTS


title: Opossum RNAseq Ovary Female2 Adult

description: Opossum_RNAseq_Ovary_Female2_Adult_3999sTS


title: Mouse RNAseq Brain Female1 Adult

description: Mouse_RNAseq_Brain_Female1_Adult_1948sTS


title: Opossum RNAseq Liver Male2 Adult

description: Opossum_RNAseq_Liver_Male2_Adult_3991sTS


title: Opossum RNAseq Liver Female2 Adult

description: Opossum_RNAseq_Liver_Female2_Adult_3997sTS


title: ES_input_rep1

description: input DNA

value: embryonic stem cells

value: wild type

tag: antibody

value: mixed 129-C57Bl/6


title: ES_input_rep2

description: input DNA

tag: genotype


title: Opossum RNAseq Kidney Male2 Adult

description: Opossum_RNAseq_Kidney_Male2_Adult_3992sTS


title: hypophysis_heavy_14_3

value: ROSS308 fast growing-chicken line

value: male


title: DnmtTKO+Dnmt3A1_WGBS

description: bisulphite converted genomic DNA

data_processing:
fastq files were split to 40bp length and individually aligned to the mouse mm9 genome using Bowtie directly executed from the R package QuasR with standard alignment parameters for bisulphite sequencing.
CG methylation scores were directly extracted as genomic ranges objects in R from aligned .bam files using the qMeth function in QuasR
Genome_build: mm9
Supplementary_files_format_and_content: tab-separated values: chr, CG_start, CG_end, tot_reads, meth_read, methylation_score

growth_protocol: Embryonic stem cells were cultivated on 0.2% gelatine coated dishes. ES cell growth medium consisted of DMEM (Invitrogen) supplemented with 15% foetal calf serum (Invitrogen), 1x non-essential amino acids (Invitrogen), 1mM L-glutamine, LIF and 0.001% beta-mercaptoethanol.

extract_protocol:
Genomic DNA extraction, followed by phenol/chloroform extraction and ethanol precipitation. RNaseA treatment was performed for 30 min at 37C
Prior library preparation unmethylated Lambda phage DNA and SssI-methylated T7 DNA were spiked-in to genomic DNA samples to control bisulphite conversion rates. For WGBS, 20ug of DNA was sonicated to ca 500bp using a Bioruptor Pico. Sonicated DNA were end-repaired and A-tailed using the NEB-Ultra Illumina library preparation kit (E7370). DNA fragments were ligated to methylated adapters (NEB E7535) following the NEB Ultra protocol. After adapter removal using Ampure XP beads (Beckman Coulter), DNA was converted using the Qiagen Epitect bisulphite conversion kit following the FFT sample protocol. After conversion library PCR amplification was performed with 10 cycles following NEB Ultra kit protocol, and cleaned up using Ampure XP beads.

tag: strain


title: Opossum RNAseq Kidney Male1 Adult

description: Opossum_RNAseq_Kidney_Male1_Adult_3954sTS


title: Opossum RNAseq Liver Female1 Adult

description: Opossum_RNAseq_Liver_Female1_Adult_3961sTS


title: Opossum RNAseq Kidney Female1 Adult

description: Opossum_RNAseq_Kidney_Female1_Adult_3960sTS


title: ES_5hMeDIP_Dnmt3aKO

description: enriched DNA


title: ES_5hMeDIP_DnmtTKO

description: enriched DNA

value: Dnmt-TKO


title: hypophysis_heavy_14_2

value: heavy


title: DnmtTKO_RRBS

description: bisulphite converted genomic DNA

data_processing:
RRBS: fastq files were pre processed with trim_galore using following parameters for RRBS --rrbs --non_directional -q 20 --length 20
processed fastq files were aligned to the mouse mm9 genome using Bowtie directly executed from the R package QuasR with standard alignment parameters for bisulphite sequencing.
CG methylation scores were directly extracted as genomic ranges objects in R from aligned .bam files using the qMeth function in QuasR
methylation scores obtained from 150 and 250bp libraries were pooled for further analysis
Genome_build: mm9
Supplementary_files_format_and_content: tab-separated values: chr, CG_start, CG_end, tot_reads, meth_read, methylation_score

extract_protocol:
Genomic DNA extraction, followed by phenol/chloroform extraction and ethanol precipitation. RNaseA treatment was performed for 30 min at 37C
Prior library preparation unmethylated Lambda phage DNA and SssI-methylated T7 DNA were spiked-in to genomic DNA samples to control bisulphite conversion rates. For RRBS, 20ug of DNA was digested for 18h with MspI and separated on 2% agarose gels. Digested DNA was excised at 150-250 and 250-350 bp. Digested DNA samples were end-repaired and A-tailed using the NEB-Ultra Illumina library preparation kit (E7370). DNA fragments were ligated to methylated adapters (NEB E7535) following the NEB Ultra protocol. After adapter removal using Ampure xp beads (Beckman Coulter), DNA was converted using the Qiagen Epitect bisulphite conversion kit following the FFT sample protocol. After conversion library PCR amplification was performed with 10 cycles following NEB Ultra kit protocol, and cleaned up using Ampure xp beads. Two libraries were generated each for 150-250bp and 250-350bp inserts.


title: Opossum RNAseq Heart Male1 Adult

description: Opossum_RNAseq_Heart_Male1_Adult_3953sTS


title: Opossum RNAseq Heart Male2 Adult

description: Opossum_RNAseq_Heart_Male2_Adult_3990sTS


title: WT_RRBS

description: bisulphite converted genomic DNA


title: ossified ligament tissues, biological rep4

city: Tianjin

first: Kun

last: Zhang

address: Qixiangtai Road NO.22

department: Department of Histology and Embryology

country: China

institute: Tianjin medical university

description:
rawcount.xls
normalized.xls

data_processing: Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

source_name: ligamentum flava tissues

growth_protocol: we collected the ossified and normal ligament flavums tissues from patients during surgery

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ossified ligament


title: Opossum RNAseq Heart Female2 Adult

description: Opossum_RNAseq_Heart_Female2_Adult_3996sTS


title: ES_5hMeDIP_WT

description: enriched DNA


title: Opossum RNAseq Heart Female1 Adult

description: Opossum_RNAseq_Heart_Female1_Adult_3959sTS


title: ossified ligament tissues, biological rep2

description:
rawcount.xls
normalized.xls


title: Opossum RNAseq Brain Male1 Adult

description: Opossum_RNAseq_Brain_Male1_Adult_3951sTS


title: Opossum RNAseq Brain Female1 Adult

description: Opossum_RNAseq_Brain_Female1_Adult_3957sTS


title: ossified ligament tissues, biological rep3

description:
rawcount.xls
normalized.xls


title: normal ligament tissues, biological rep4

description:
rawcount.xls
normalized.xls

value: normal ligament


title: normal ligament tissues, biological rep3

description:
rawcount.xls
normalized.xls


title: Opossum RNAseq Liver Male1 Adult

description: Opossum_RNAseq_Liver_Male1_Adult_3955sTS

value: Adult


title: normal ligament tissues, biological rep1

description:
rawcount.xls
normalized.xls


title: normal ligament tissues, biological rep2

description:
rawcount.xls
normalized.xls


title: Chicken RNAseq Testis Male2 Adult

description: Chicken_RNAseq_Testis_Male2_Adult_920sTS

value: Testis


title: Chicken RNAseq Testis Male1 Adult

description: Chicken_RNAseq_Testis_Male1_Adult_642sTS


title: 44-r94

city: Egham

first: Fabio

last: Manfredini

state: Surrey

address: Bourne Lab Room 4-17

country: United Kingdom

institute: Royal Holloway University of London

description:
SR_44
sampled 1 month after emerging from hibernation and showing fully developed ovaries with visible mature eggs
SR_44

data_processing:
Raw sequence data were pre-processed at BGI: this included removing adapters and filtering out low-quality sequences
Clean reads were checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) for quality control
Clean reads were aligned with TopHat for Illumina on the Galaxy web-based platform (https://usegalaxy.org/) to the latest version of the bumblebee genome including 10,673 contigs (Bter 1.1)
Mapped reads were converted into raw read counts with SAMtools idxstats
Read counts were analysed with R using the edgeR package from Bioconductor. Read counts were log2 transformed to correct for the skew to zero and large values. Only genes with at least 10 reads per sample were kept in the analysis (7,724 genes, 72% of the total)
Normalization was performed with Trimmed Mean of M-values (TMM), a method that is implemented in the edgeR Bioconductor package
We detected differential levels of gene expression using a modified Fisher’s exact test that takes into account both dispersion and multiple samples. Finally, raw P-values for each gene were corrected for multiple comparisons setting a false discovery rate (Benjamini-Hochberg) of 5%.
Genome_build: Bombus terrestris Bter 1.1 (https://www.hgsc.bcm.edu/arthropods/bumble-bee-genome-project; BCM-HGSC data <ftp://ftp.hgsc.bcm.edu/Bterrestris/Bter_1.1/>)
Supplementary_files_format_and_content: Excel spreadsheet file with three sheets: raw read counts, scaled read counts and normalized read counts for clustering
Supplementary_files_format_and_content: The public repository for the Contig  sequences that we used is ftp://ftp.hgsc.bcm.edu/Bterrestris/Bter_1.1/Contigs/

organism: Bombus terrestris

source_name: successfully reproductive_brain tissue

growth_protocol: Colonies of the bumble bee Bombus terrestris were purchased from Koppert BV (The Netherlands), housed under red light and at 24°C, and provided with sugar water ad libitum and fresh pollen every day. Males were removed from their mother colony once emerged and moved to wooden boxes in groups of no more than 40 individuals per box. Similarly, gynes (virgin sexual females) were removed from their colonies as soon as they emerged and moved to a wooden box. A maximum of 20 gynes were housed within each box and colonies were checked three times a day (early morning, mid-day and afternoon) for newly emerged gynes.

extract_protocol:
We isolated brain tissues from focal queens by placing frozen bee heads on dry ice and gently removing all external parts with a scalpel. To isolate RNA from brain tissue, we placed individual brains in a plastic tube with QIAzol Lysis reagent (Qiagen) and metal beads and disrupted brain tissues by means of a Tissue Lyser device (Qiagen). Finally, total RNA was isolated using RNeasy Plus Universal kit (Qiagen) and following manufacturer instructions. RNA quantities and quality were checked with a Nanodrop instrument first and then with an Agilent Bioanalyzer. Samples that satisfied concentration and quality requirement were processed for RNA sequencing.
Library construction was perfomred at BGI (Beijing Genomics Institute). Magnetic beads with Oligo (dT) were used to isolate mRNA. Mixed with the fragmentation buffer, the mRNA was fragmented into short fragments. Then cDNA was synthesized using the mRNA fragments as templates. Short fragments were purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments were connected with adapters. The suitable fragments were selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System were used in quantification and qualification of the sample library.
TruSeq mRNA sequencing (Illumina HiSeq 2000)

treatment_protocol: MATING. Gynes were provided with the opportunity to mate when they were 5 days old. For each group of 20 gynes, 40-60 males were released within a mating cage (size 50 x 50 x 60 cm) for a maximum of 30-40 minutes. Mating pairs were removed from the cage and placed in small plastic boxes (size 13 x 11 x 7 cm). Thereafter, mated queens were housed in new wooden boxes (size 24 x 15 x10 cm), provided with ad libitum food and sand for nesting for 3 days. After this period, a portion of these queens were snap-frozen in liquid nitrogen and allocated to the treatment group “Successfully Mated” (SM). To obtained the Failed Mated queen group (FM) instead, we sampled queens that were handled exactly the same as SM and were given the same opportunities but failed to mate. HIBERNATION. The remaining mated queens were hibernated for a period of 8 weeks. For this purpose, queens were placed in individual 50 ml Falcon tubes with a layer of damp sand at the bottom. Hibernating queens were maintained at 5° C in a climate chamber. After the 8-week period, queens were removed from the climate chamber and placed in wooden boxes equipped with sand, a pollen ball, fresh pollen daily and sugar water. They were kept in these conditions for 1 month after which time they were snap-frozen in liquid nitrogen, dissected under a microscope, and allocated to two different treatment groups according to the stage of ovary development. Queens showing fully developed ovaries with visible mature eggs were defined as “Successfully Reproductive” (SR), while queens showing undeveloped ovaries were defined as “Failed Reproductive” (FR).

tag: source

value: Commercial colony (Koppert BV)

tag: developmental stage

value: adult female

tag: estimated age

tag: caste

value: queen

tag: treatment

value: successfully reproductive

tag: colony of origin

value: brain tissue


title: 48-w19

description:
SR_48
sampled 1 month after emerging from hibernation and showing fully developed ovaries with visible mature eggs
SR_48

tag: tissue


title: 49-w57

description:
SR_49
sampled 1 month after emerging from hibernation and showing fully developed ovaries with visible mature eggs
SR_49


title: Chicken RNAseq Liver Male2 Adult

value: Liver

value: Male


title: Chicken RNAseq Ovary Female1 Adult

description: Chicken_RNAseq_Ovary_Female1_Adult_561sTS

value: Ovary

value: Female


title: Opossum RNAseq Kidney Female2 Adult

description: Opossum_RNAseq_Kidney_Female2_Adult_3998sTS

value: Kidney


title: Chicken RNAseq Liver Male1 Adult


title: Chicken RNAseq Ovary Female2 Adult

description: Chicken_RNAseq_Ovary_Female2_Adult_787sTSb


title: Dnmt3AKO_RRBS

description: bisulphite converted genomic DNA

tag: cell type

value: embryonic stem cells

value: mixed 129-C57Bl/6


title: ossified ligament tissues, biological rep1

description:
rawcount.xls
normalized.xls


title: 39-g79

description:
SR_39
sampled 1 month after emerging from hibernation and showing fully developed ovaries with visible mature eggs
SR_39


title: 38-b54

description:
FR_38
sampled 1 month after emerging from hibernation and showing undeveloped ovaries
FR_38

source_name: failed reproductive_brain tissue

value: failed reproductive


title: 40-r75

description:
SR_40
sampled 1 month after emerging from hibernation and showing fully developed ovaries with visible mature eggs
SR_40


title: Chicken RNAseq Liver Female2 Adult

description: Chicken_RNAseq_Liver_Female2_Adult_786sTS


title: Chicken RNAseq Liver Female1 Adult

description: Chicken_RNAseq_Liver_Female1_Adult_558sTS


title: Chicken RNAseq Kidney Male2 Adult

description: Chicken_RNAseq_Kidney_Male2_Adult_918sTS


title: 47-g96

description:
SR_47
sampled 1 month after emerging from hibernation and showing fully developed ovaries with visible mature eggs
SR_47


title: Chicken RNAseq Kidney Male1 Adult

description: Chicken_RNAseq_Kidney_Male1_Adult_555sTS


title: 36-y74

description:
FR_36
sampled 1 month after emerging from hibernation and showing undeveloped ovaries
FR_36


title: 37-b44

description:
FR_37
sampled 1 month after emerging from hibernation and showing undeveloped ovaries
FR_37


title: 33-g88

description:
FR_33
sampled 1 month after emerging from hibernation and showing undeveloped ovaries
FR_33


title: 32-b31

description:
FR_32
sampled 1 month after emerging from hibernation and showing undeveloped ovaries
FR_32


title: 45-y81

description:
SR_45
sampled 1 month after emerging from hibernation and showing fully developed ovaries with visible mature eggs
SR_45


title: 43-r84

description:
SR_43
sampled 1 month after emerging from hibernation and showing fully developed ovaries with visible mature eggs
SR_43


title: 28-g78

description:
FR_28
sampled 1 month after emerging from hibernation and showing undeveloped ovaries
FR_28


title: 31-r82

description:
FR_31
sampled 1 month after emerging from hibernation and showing undeveloped ovaries
FR_31


title: Chicken RNAseq Heart Male2 Adult

value: Heart


title: Chicken RNAseq Heart Male1 Adult


title: Chicken RNAseq Heart Female1 Adult

description: Chicken_RNAseq_Heart_Female1_Adult_560sTS


title: Chicken RNAseq Brain Male2 Adult

value: Brain


title: Chicken RNAseq Heart Female2 Adult

description: Chicken_RNAseq_Heart_Female2_Adult_785sTS

value: Adult


title: 23-g43

description:
SM_23
sampled 3 days after successful mating
SM_23

source_name: successfully mated_brain tissue

value: successfully mated


title: 27-b94

description:
FR_27
sampled 1 month after emerging from hibernation and showing undeveloped ovaries
FR_27

value: Commercial colony (Koppert BV)


title: 26-y49

description:
SM_26
sampled 3 days after successful mating
SM_26

value: adult female


title: Chicken RNAseq Brain Male1 Adult


title: 25-g73

description:
SM_25
sampled 3 days after successful mating
SM_25

value: queen


title: 22-y22

description:
SM_22
sampled 3 days after successful mating
SM_22


title: Chicken RNAseq Brain Female2 Adult

description: Chicken_RNAseq_Brain_Female2_Adult_783sTS


title: Genomic_capture_mES_Day0_1

city: Lincoln

first: Logan

middle: G

last: Engstrom

address: 27 Old Farm Rd

data_processing:
All raw DNA sequence data was aligned with BWA using settings bwa version 0.6.2 with the default settings and 8 threads.
Raw sequence data was processed as single-ended reads.
DNase-seq and DNase-capture reads were filtered so only reads with a mapping quality of 20 were retained
Coverage at a base was calculated using only the outermost coordinate of a read. DNase-seq and DNase-capture replicates were kept separate.
Genome_build: mm10
Supplementary_files_format_and_content: BED file with captured regions

source_name: Murine Embryonic Stem Cells

extract_protocol:
129P2/OlaHsd mouse embryonic stem cells were harvested at stage D0 of pancreatic differentiation and subjected to DNase I enzyme treatment followed by collection of 50-125 or 175-400 bp hypersensitive DNA. Illumina adapters were added according to standard Illumina protocols at the MIT BioMicroCenter.
The library construction was the same as in GSE53776

value: mESC


title: 19-r55

description:
SM_19
sampled 3 days after successful mating
SM_19

value: brain tissue


title: Genomic_capture_mES_Day0_2


title: 17-b92

description:
SM_17
sampled 3 days after successful mating
SM_17


title: Chicken RNAseq Kidney Female2 Adult

description: Chicken_RNAseq_Kidney_Female2_Adult_784sTS


title: 16-b86

description:
SM_16
sampled 3 days after successful mating
SM_16


title: DNase_capture_mES_Day0_2


title: DNase_capture_mES_Day0_1


title: 11-g47

description:
FM_11
exposed to males but failed to mate and handled/sampled in the same way as successfully mated
FM_11

source_name: failed mated_brain tissue

value: failed mated


title: Chicken RNAseq Kidney Female1 Adult

description: Chicken_RNAseq_Kidney_Female1_Adult_559sTS


title: 15-y90

description:
FM_15
exposed to males but failed to mate and handled/sampled in the same way as successfully mated
FM_15


title: 14-w90

description:
FM_14
exposed to males but failed to mate and handled/sampled in the same way as successfully mated
FM_14


title: KO B4 E16

city: St Lucia

first: Jens

last: Bunt

state: QLD

address: QBI Building 79

department: Queensland Brain Institute

country: Australia

institute: University of Queensland

description: RNA-seq of neocortex total RNA from E16 mice

data_processing:
CASAVA 1.8.2
TopHat 2.0.10
Cufflinks
TopHat 2.0.10
TRASE
CuffDiff 2.1.1
Genome_build: mm9
Supplementary_files_format_and_content: Regulation.xlsx: TSV output of CuffDiff comparing expression in KO samples with corresponding WT samples

source_name: Neocortex E16

growth_protocol: Nfia{tm1Rmg}(C57BL/6), and Nfia{tm1Rmg}(C57BL/6) mice were housed and handled in accordance with the Australian Code of Practice for the Care and Use of Animals for Scientific Purposes and with approval from the institutional Animal Ethics Committee. To generate timed-pregnant females, male and female mice were placed together overnight. The following day, E0, the females were checked for vaginal plugs.

extract_protocol:
Embryonic neocortical tissue was microdissected snap frozen on dry ice, and RNA was isolated using Trizol reagent.
RNA libraries were prepared for sequencing with Illumina TruSeq RNA Sample Prep Kit using standard Illumina protocols

value: E16 embryo

value: Neocortex

value: homozygous Nfib knockout


title: KO B3 E16


title: KO B2 E16


title: KO B1 E16


title: 10-y85

description:
FM_10
exposed to males but failed to mate and handled/sampled in the same way as successfully mated
FM_10


title: 6-b29

description:
FM_6
exposed to males but failed to mate and handled/sampled in the same way as successfully mated
FM_6


title: KO A4 E16

value: homozygous Nfia knockout


title: KO A3 E16


title: 5-w32

description:
FM_5
exposed to males but failed to mate and handled/sampled in the same way as successfully mated
FM_5


title: 4-r81

description:
FM_4
exposed to males but failed to mate and handled/sampled in the same way as successfully mated
FM_4


title: 21-w81

description:
SM_21
sampled 3 days after successful mating
SM_21


title: KO A2 E16


title: 2-b91

description:
FM_2
exposed to males but failed to mate and handled/sampled in the same way as successfully mated
FM_2


title: Platypus RNAseq Testis Male2 Adult

description: Platypus_RNAseq_Testis_Male2_Adult_1409sTS

organism: Ornithorhynchus anatinus

value: Testis

value: Male


title: WT B2 E16

value: wild type


title: KO A1 E16


title: Platypus RNAseq Testis Male1 Adult

description: Platypus_RNAseq_Testis_Male1_Adult_1403sTS


title: Platypus RNAseq Ovary Female2 Adult

description: Platypus_RNAseq_Ovary_Female2_Adult_748sTS

value: Ovary

value: Female


title: WT B1 E16


title: WT A1 E16


title: Platypus RNAseq Ovary Female1 Adult

description: Platypus_RNAseq_Ovary_Female1_Adult_746sTS

value: Adult


title: WT A2 E16


title: Platypus RNAseq Liver Male2 Adult

description: Platypus_RNAseq_Liver_Male2_Adult_1407sTS

value: Liver


title: K27M-APP-T-input

data_processing:
ChIP-seq reads were aligned to the mouse reference genome build mm10 (GRCm38) using bwa (v0.7.10-r789)
BigWig files were generated by converting bam to BigWig using bedtools (v2.17.0) and UCSC tools (20140212).  Read coverage was normalized according to coverage scaled according to total sample coverage and ChIP-Rx ratio (Orlando et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: BigWig: tracks for visualization of NGS data

extract_protocol:
Cells were fixed with 1% formaldehyde (Sigma). Fixed cell preparations were washed, pelleted and stored at -80°C. Sonication of lysed nuclei (lysed in a buffer containing 1% SDS) was performed on a BioRuptor UCD-300 for 60 cycles, 10s on 20s off, centrifuged every 15 cycles, chilled by 4°C water cooler. Samples were checked for sonication efficiency using the criteria of 150-500bp by gel electrophoresis. After the sonication, the chromatin was diluted to reduce SDS level to 0.1% and before the ChIP reaction 2% of sonicated drosophila S2 cell chromatin was spiked into the samples for quantification of total levels of histone mark after sequencing (see below).
The ChIP reaction was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. 25ul Protein A beads were washed and then incubated with 5ug of H3K27me3 antibody (Cell Signaling Technologies, #9733) and 2 million cells of sonicated cell lysate combined with protease inhibitors for 10 hr, followed by 20 min wash cycle with provided wash buffers. Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2µl RNase Cocktail at 65°C for 30 min followed by 2µl Proteinase K at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
Library preparation was carried out using Kapa HTP Illumina library preparation reagents. Briefly, 25ul of ChIP sample was incubated with 45ul end repair mix at 20°C for 30 min followed by Ampure XP bead purification. A tailing: bead bound sample was incubated with 50ul buffer enzyme mix for 30°C 30 min, followed by PEG/NaCl purification. Adaptor ligation: bead bound sample was incubated with 45ul buffer enzyme mix and 5ul of different TruSeq DNA adapters (Illumina) for each sample, for 20°C 15 min, followed by PEG/NaCl purification (twice). Library enrichment: 12 cycles of PCR amplification. Size selection was performed after PCR using a 0.6x/0.8x ratio of Ampure XP beads (double size selection) set to collect 250-450bp fragments.

value: H3.3K27M O/E; Trp53-/-; Atrx shRNA; Pdgfra O/E

value: brain

value: tumor cells

tag: tumor status

value: tumor

tag: chip antibody


title: Platypus RNAseq Liver Female2 Adult

description: Platypus_RNAseq_Liver_Female2_Adult_659sTS


title: Platypus RNAseq Liver Male1 Adult

description: Platypus_RNAseq_Liver_Male1_Adult_1401sTS


title: Platypus RNAseq Liver Female1 Adult

description: Platypus_RNAseq_Liver_Female1_Adult_486sTS


title: 9-y13

description:
FM_9
exposed to males but failed to mate and handled/sampled in the same way as successfully mated
FM_9

value: Commercial colony (Koppert BV)

value: adult female

value: queen

value: brain tissue


title: Platypus RNAseq Kidney Male2 Adult

description: Platypus_RNAseq_Kidney_Male2_Adult_1408sTS

value: Kidney


title: K27M-AP-T-H3K27me3

value: H3.3K27M O/E; Trp53-/-; Atrx shRNA

value: H3K27me3 (Cell Signaling Technologies, #9733)


title: K27M-APP-T-H3K27me3


title: Platypus RNAseq Kidney Male1 Adult

description: Platypus_RNAseq_Kidney_Male1_Adult_1402sTS

value: Male


title: Platypus RNAseq Kidney Female2 Adult

description: Platypus_RNAseq_Kidney_Female2_Adult_658sTS


title: K27M-P-T-input


title: K27M-P-T-H3K27me3


title: K27M-APP-input

value: neural progenitor cells

value: preneoplastic


title: Platypus RNAseq Heart Male2 Adult

description: Platypus_RNAseq_Heart_Male2_Adult_1406sTS

value: Heart


title: Platypus RNAseq Kidney Female1 Adult

description: Platypus_RNAseq_Kidney_Female1_Adult_482sTS

value: Adult

value: Female


title: WT-APP-input

value: H3.3WT O/E; Trp53-/-; Atrx shRNA; Pdgfra O/E


title: K27M-APP-H3K27me3

value: H3.3K27M O/E; Trp53-/-; Atrx shRNA;Pdgfra O/E

value: brain


title: WT-APP-H3K27me3


title: Platypus RNAseq Heart Male1 Adult

description: Platypus_RNAseq_Heart_Male1_Adult_1400sTS


title: Platypus RNAseq Heart Female2 Adult

description: Platypus_RNAseq_Heart_Female2_Adult_657sTS


title: Platypus RNAseq Brain Male2 Adult

description: Platypus_RNAseq_Brain_Male2_Adult_1404sTS

value: Brain


title: K27M-AP-input


title: EV-APP-H3K27me3

value: Trp53-/-; Atrx shRNA; Pdgfra O/E


title: EV-APP-input


title: Platypus RNAseq Brain Male1 Adult

description: Platypus_RNAseq_Brain_Male1_Adult_739sTS


title: Platypus RNAseq Heart Female1 Adult

description: Platypus_RNAseq_Heart_Female1_Adult_501sTS


title: Platypus RNAseq Brain Female2 Adult

description: Platypus_RNAseq_Brain_Female2_Adult_655sTS


title: K27M-AP-H3K27me3


title: K27M-AP-T-input

value: tumor cells

value: tumor


title: WT-AP 5

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_WT-AP-5.vcf.gz

value: H3.3WT O/E; Trp53-/-; Atrx shRNA


title: Platypus RNAseq Brain Female1 Adult

description: Platypus_RNAseq_Brain_Female1_Adult_487sTS


title: Anolis RNAseq Testis Male4 Adult

description: Anolis_RNAseq_Testis_Male4_Adult_1282sTS

organism: Anolis carolinensis

value: Testis


title: WT-AP 3

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_WT-AP-3.vcf.gz


title: WT-AP-H3K27me3


title: EV-AP-H3K27me3

extract_protocol:
Cells were fixed with 1% formaldehyde (Sigma). Fixed cell preparations were washed, pelleted and stored at -80°C. Sonication of lysed nuclei (lysed in a buffer containing 1% SDS) was performed on a BioRuptor UCD-300 for 60 cycles, 10s on 20s off, centrifuged every 15 cycles, chilled by 4°C water cooler. Samples were checked for sonication efficiency using the criteria of 150-500bp by gel electrophoresis. After the sonication, the chromatin was diluted to reduce SDS level to 0.1% and before the ChIP reaction 2% of sonicated drosophila S2 cell chromatin was spiked into the samples for quantification of total levels of histone mark after sequencing (see below).
The ChIP reaction was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. 25ul Protein A beads were washed and then incubated with 5ug of H3K27me3 antibody (Cell Signaling Technologies, #9733) and 2 million cells of sonicated cell lysate combined with protease inhibitors for 10 hr, followed by 20 min wash cycle with provided wash buffers. Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2µl RNase Cocktail at 65°C for 30 min followed by 2µl Proteinase K at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers' protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
Library preparation was carried out using Kapa HTP Illumina library preparation reagents. Briefly, 25µl of ChIP sample was incubated with 45µl end repair mix at 20°C for 30 min followed by Ampure XP bead purification. A tailing: bead bound sample was incubated with 50µl buffer enzyme mix for 30°C 30 min, followed by PEG/NaCl purification. Adaptor ligation: bead bound sample was incubated with 45µl buffer enzyme mix and 5µl of different TruSeq DNA adapters (Illumina) for each sample, for 20°C 15 min, followed by PEG/NaCl purification (twice). Library enrichment: 12 cycles of PCR amplification. Size selection was performed after PCR using a 0.6x/0.8x ratio of Ampure XP beads (double size selection) set to collect 250-450bp fragments.

value: Trp53-/-; Atrx shRNA


title: K27M-APP T4

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_K27M-AP-T4.vcf.gz

value: H3.3K27M O/E; Trp53-/-; Atrx shRNA; Pdgfra O/E


title: Pog_Exp_smallRNA

city: Santa Cruz

first: Todd

middle: M.

last: Lowe

address: 1156 High Street

institute: University of California Santa Cruz

description: processed files of the small RNA reads (bigwig files) are separated into two files based on if they are on the plus or minus strand

data_processing:
Barcodes, linkers, and adapters are removed using in-house script.
Processed reads were mapped to the appropriate genome using BLAT requiring a minimum of 90% identity (-minIdentity), a maximal gap of 3 (-maxIntron) and a minimum score (matches minus mismatches) of 16 (-minScore) using alignment parameters for this size range (-tileSize=8 -stepSize=4). Reads that mapped equally well to multiple positions in the genome were excluded.
PSL file processed to determined paired reads (Illumina data only)
PSL files are converted into BED format
BED files are converted to bedgraph files using genomeCoverageBed
bedgraph files are converted to bigWig format using bedGraphToBigWig
Genome_build: Pyrobaculum aerophilum IM2, Pyrobaculum arsenaticum DSM 13514, Pyrobaculum calidifontis JCM 11548, Pyrobaculum islandicum DSM 4184, Pyrobaculum oguniense TE7
Supplementary_files_format_and_content: Processed files are in bigwig format and can be visualized by uploading them into the UCSC Microbial Genome Browser.  Files contain best mapped reads to the respective genomes.

organism: Pyrobaculum oguniense

source_name: cell culture

growth_protocol: Cells were grown as described in (1) Bernick et. al. 2012. Diversity of Antisense and Other Non-Coding RNAs in Archaea Revealed by Comparative Small RNA Sequencing in Four Pyrobaculum Species. Frontiers in Microbiology. 3 (July): 231 and (2) Bernick et al. 2012. Complete genome sequence of Pyrobaculum oguniense. Standards in Genomic Sciences. 6(3):336-345

extract_protocol:
Small RNA was size selected from total RNA. Total RNA was extracted from exponential or stationary cultures; 100µg of each preparation was loaded onto a 15% polyacrylamide gel, and size selected in the range 16–70 nt. The gel was post-stained with SYBR Gold and the tRNA band was used as the upper exclusion point. The lower exclusion point was set at 75% of the region between xylene cyanol (XC) and bromophenol blue (BP) loading dye bands (Ambion protocol). Samples were eluted, EtOH precipitated.
For 454 library prep, to the size selected RNA, a 3' linker (5'-adenylated, 3' ddC) was added as described by Lau et al., 2001. Science; IDTDNA, Linker 1). A second gel purification was performed as above, excising the gel fragment above the XC dye band to remove excess 3' linker. The recovered linked RNAs were reverse transcribed (RT) using Superscript III (Invitrogen)with a DNA primer complementary to Linker 1. Following RT, Exonuclease I (EXO1,Thermo) was added to the RT reaction mixture, and incubated for 30 min to remove excess primer. We utilized standard alkaline lysis treatment with NaOH-EDTA at 80˚C for 15 min to remove any residual RNA, as well as to inactivate the reverse transcriptase and the EXO1 ssDNA nuclease. Neutralization and small fragment removal was performed with water-saturated G50 columns (Ambion NucAway). The recovered single stranded cDNA was dried to near completion using a Servo SpeedVac, followed by a second 5'-adenylated linker addition (IDTDNA – Linker 2) to the cDNA using T4 RNA ligase. (Ambion). A 2µL volume of this reaction was amplified by PCR (20µL reaction, 16 cycles). This was followed by a second amplification (20µL reaction, 16 cycles) using 2µL from the first amplification as template using Roche 454-specific hybrid adapters based on the method described by Hannon (http://genoseq.ucla.edu/images/a/a9/SmallRNA.pdf). A four-base barcode was included in the 5' hybrid primer. The final reaction was cleaned using the Zymo clean kit following the manufacturer’s protocol.  For Illumina library prep, The native 3' end of the RNA is tagged by ligating a 5'-preadenylated, 3'-end-blocked linker (L1) with T4 RNA ligase. The linker-ligated RNA is reverse transcribed and a 5'-preadenylated, 3'-end-blocked linker (L2) is ligated to the 3’-end of the cDNA. The cDNA library was PCR amplified and Illumina adapters attached.

tag: growth phase

value: Exponential

tag: rna size

value: small RNA


title: Pog_Stat_smallRNA

value: Stationary


title: Anolis RNAseq Testis Male1 Adult

description: Anolis_RNAseq_Testis_Male1_Adult_1695sTS

tag: Stage

value: Male


title: Anolis RNAseq Testis Male2 Adult

description: Anolis_RNAseq_Testis_Male2_Adult_1712sTS

value: Adult

tag: Sex


title: K27M-APP T3

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_K27M-AP-T2.vcf.gz


title: Anolis RNAseq Ovary Female3 Adult

description: Anolis_RNAseq_Ovary_Female3_Adult_1288sTS

value: Ovary

value: Female


title: K27M-AP T4

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_K27M-APP-T1.vcf.gz

value: H3.3K27M O/E; Trp53-/-; Atrx shRNA


title: Xenopus RNAseq Testis Male2 Adult

description: Xenopus_RNAseq_Testis_Male2_Adult_1056sTSb

organism: Xenopus tropicalis


title: Xenopus RNAseq Testis Male1 Adult

description: Xenopus_RNAseq_Testis_Male1_Adult_955sTS


title: WT-AP-input

value: brain

value: neural progenitor cells

value: preneoplastic


title: K27M-AP 4

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_K27M-AP-4.vcf.gz


title: K27M-AP 3

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_K27M-AP-3.vcf.gz


title: Anolis RNAseq Ovary Female2 Adult

description: Anolis_RNAseq_Ovary_Female2_Adult_1707sTS


title: EV ctl 5

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_EV-ctl-5.vcf.gz

value: wild type


title: Anolis RNAseq Liver Male3 Adult

value: Liver


title: Anolis RNAseq Liver Male1 Adult


title: Anolis RNAseq Liver Male2 Adult


title: EV-PDGFRA 3

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_EV-PDGFRA-3.vcf.gz

value: Pdgfra O/E


title: Xenopus RNAseq Ovary Female2 Adult

description: Xenopus_RNAseq_Ovary_Female2_Adult_1090sTSb


title: Xenopus RNAseq Ovary Female1 Adult

description: Xenopus_RNAseq_Ovary_Female1_Adult_960sTS


title: EV ctl 4

description:
mm_RNA-seq_raw_counts.txt.gz
mm_RNA-seq_variants_raw_EV-ctl-4.vcf.gz


title: EV-AP-input


title: Xenopus RNAseq Liver Male2 Adult

description: Xenopus_RNAseq_Liver_Male2_Adult_1053sTS


title: Anolis RNAseq Liver Female3 Adult

description: Anolis_RNAseq_Liver_Female3_Adult_1266sTS


title: Xenopus RNAseq Liver Male1 Adult


title: sh4

city: Tokyo

first: Motoharu

last: Awazawa

address: 1-21-1 Toyama, Shinjuku

country: Japan

institute: National Institute for Global Health and Medicine

data_processing:
Illumina Casava software used for basecalling
RNAseq reads were aligned mus_musculus
Fragments Per Kilobase of exon per Million mapped fragments (FPKM) were calculated using a Cufflinks
Genome_build: genome build mm10
Supplementary_files_format_and_content: excel file with FPKM values.

source_name: Soleus muscle

extract_protocol:
Soleus muscles were removed, snap frozen in liquid nitrogen, and totalRNA was harvested using miRVana miRNA Isolation Kit (Ambion, Life Technologies). Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
After poly-A selection (using poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperature. The RNA fragments underwent reverse transcription using random primers. This is followed by second strand cDNA synthesis with DNA Polymerase I and RNase H. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and, using 10 µl template, amplified (14 PCR cycles) to create the final cDNA libraries.

treatment_protocol: db/db mice were injected with AAV encoding shRNA targeting mouse Eda or the control scrambled shRNA sequence the titer of 2-3x10e10 particles/body.

value: Soleus muscle

tag: age

value: 11 weeks

tag: aav/knockdown

value: shEda


title: Anolis RNAseq Liver Female2 Adult

description: Anolis_RNAseq_Liver_Female2_Adult_1705sTS


title: Scr4

tag: genotype

value: scrambled


title: Xenopus RNAseq Liver Female2 Adult

description: Xenopus_RNAseq_Liver_Female2_Adult_1048sTS


title: Anolis RNAseq Ovary Female1 Adult

description: Anolis_RNAseq_Ovary_Female1_Adult_1700sTS


title: sh3


title: M127012016_WB_H4K16ac

data_processing:
Basecalls performed using CASAVA version 1.8.
ChIP-Seq reads were aligned to the AnoCar2.0 genome assembly using BWA v0.7.15 with default parameters.
PCR duplicates and reads mapping to multiple genome positions were filtered out from the alignments.
In order to allow comparisons between different samples and across genomic features, the data were: i) normalized by library size; ii) all samples were input normalized by dividing the read counts of ChIPed samples by the read counts in the corresponding input over a window size of 50bp; these analyses were performed using the deepTools (v2.4.0).
Genome_build: AnoCar2.0
Supplementary_files_format_and_content: BigWig files were produced using deepTools v2.4.0.

source_name: Brain, Male, H4K16ac ChIP

extract_protocol:
The DNA was purified using QIAquick PCR Purification columns (Qiagen) according to manufacturer’s instructions.
5 ng of input and ChIPed DNA were used to prepare sequencing libraries using NEBNext Ultra II Library Prep kit as described by the manufacturer (New England Biolab, E7645S).

value: Brain

tag: marker


title: Scr3


title: Anolis RNAseq Kidney Male3 Adult

description: Anolis_RNAseq_Kidney_Male3_Adult_1270sTS

value: Kidney


title: Xenopus RNAseq Liver Female1 Adult

description: Xenopus_RNAseq_Liver_Female1_Adult_958sTS


title: Xenopus RNAseq Kidney Male1 Adult

description: Xenopus_RNAseq_Kidney_Male1_Adult_954sTS

value: Male


title: Anolis RNAseq Kidney Male2 Adult

description: Anolis_RNAseq_Kidney_Male2_Adult_1711sTS

value: Adult


title: sh2


title: Scr2


title: Xenopus RNAseq Kidney Female2 Adult

description: Xenopus_RNAseq_Kidney_Female2_Adult_1049sTS


title: sh1


title: Xenopus RNAseq Kidney Female1 Adult

description: Xenopus_RNAseq_Kidney_Female1_Adult_959sTS


title: Anolis RNAseq Kidney Female2 Adult

description: Anolis_RNAseq_Kidney_Female2_Adult_1706sTS


title: Anolis RNAseq Kidney Female1 Adult

description: Anolis_RNAseq_Kidney_Female1_Adult_1699sTS


title: Xenopus RNAseq Heart Male1 Adult

value: Heart


title: Xenopus RNAseq Heart Female2 Adult

description: Xenopus_RNAseq_Heart_Female2_Adult_1047sTS

value: Female


title: Anolis RNAseq Heart Male2 Adult


title: F127012016_Lv2_H4K16ac

source_name: Liver, Female, H4K16ac ChIP

tag: developmental stage


title: D48hrs-1

city: Chongqing

first: Xuejiao

last: Liu

state: Chongqing

address: Tiansheng

institute: Southwest university

data_processing:
Samples were sequenced on Ion proton platform, the original image data is transferred into sequence data via base calling and saved as BAM file
Duplication sequences, adaptor sequences and low-quality reads were removed from the raw data, then the clean reads were mapped to Tetranychus urticae whole genome using TMAP with an maxium mismatch of 2 bases [The file with the name of Tetranychus_urticae.main_genome_200909.scaffolds.fasta.gz and with the date of  Sep 29 2009 03:46:56 PM in https://bioinformatics.psb.ugent.be/gdb/tetranychus/ represents the Tetranychus urticae genome used for read alignment.]
Genes expression level are quantified by a software package: Sailfish. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated and used for downstream differentially expression analysis
Genome_build: Tetranychus urticae genome (database web link: http://bioinformatics.psb.ugent.be/orcae/overview/Tetur)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Tetranychus cinnabarinus

source_name: adult tissue

growth_protocol: T. cinnabarinus was reared on cowpea seedlings (Vigna unguiculata) in an artificial climate chamber at 26±1°C, 60-80% relative humidity, with a 14/10 h light/dark photoperiod.

extract_protocol:
At 24 h post treatment and 48 h post treatment, all the alive mites from each treatment were collected and frozen immediately in liquid nitrogen. Total RNA of each sample was extracted using the RNeasy® plus Micro Kit (Tiangen, Beijing, China) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: scopoletin (LC50)

tag: time

tag: strain

value: susceptible strain

value: 2-day old adult mite


title: D48hrs-2

tag: treatment


title: Xenopus RNAseq Kidney Male2 Adult

description: Xenopus_RNAseq_Kidney_Male2_Adult_1054sTS


title: Anolis RNAseq Liver Female1 Adult

description: Anolis_RNAseq_Liver_Female1_Adult_1698sTS


title: Xenopus RNAseq Heart Female1 Adult

description: Xenopus_RNAseq_Heart_Female1_Adult_957sTS


title: Xenopus RNAseq Brain Male2 Adult

description: Xenopus_RNAseq_Brain_Male2_Adult_1051sTS

source_name: Brain


title: D24hrs-2


title: Anolis RNAseq Heart Female3 Adult

description: Anolis_RNAseq_Heart_Female3_Adult_1269sTS


title: D24hrs-1


title: Anolis RNAseq Heart Male1 Adult


title: Anolis RNAseq Kidney Male1 Adult

description: Anolis_RNAseq_Kidney_Male1_Adult_1694sTS


title: Day14-ZIKV-Rep3

first: Kayvan

last: Etebari

address: Building No 8

department: School of Biological Sciences

institute: The University of Queensland

data_processing:
The CLC Genomics Workbench version 10.1.1 was used for bioinformatics analysis in this study. RNA-Seq analysis has been done by mapping next-generation sequencing reads, distributing and counting the reads across genes and transcripts.
All libraries were trimmed from any vector, sequencing primers and adapter sequence remaining.  Low quality reads (quality score below 0.05) and reads with more than 2 ambiguous nucleotides were discarded. Clean reads were subjected to RNAseq analysis toolbox for mapping reads to the reference genome with mismatch, insertion and deletion cost of 2, 3 and 3 respectively. Mapping was performed with stringent criteria and allowed a length fraction of 0.8 in mapping parameter, which encounter at least 80% of nucleotides in a read must be aligned to the reference genome. The minimum similarity between the aligned region of the read and the reference sequence was set at 80%.
The relative expression levels were output as RPKM (Reads Per Kilobase of exon model per Million mapped reads) values, which take into account the relative size of the transcripts and only uses the mapped-read datasets (i.e. excludes the non-mapped reads) to determine relative transcript abundance. To explore genes with differential expression profile between two samples, CLC genomic workbench uses multi-factorial statistics based on a negative binomial Generalized Linear Model (GLM). Each gene is modeled by a separate GLM and this approach allows us to fit curves to expression values without assuming that the error on the values is normally distributed. TMM (Trimmed mean of M values) normalization method was applied on all data set to calculate effective libraries sizes, which are then used as part of the per-sample normalization
The Wald Test was also used to compare each sample against its control group to test whether a given coefficient is non-zero. We considered genes with more than 2 fold change and false discovery rate (FDR) less than 0.05 as statistically significant modulated genes.
Genome_build: The latest assembly of Aedes aegypti genome (GCF_000004015.4) was used as reference

organism: Aedes aegypti

growth_protocol: Two-three day old female Aedes aegypti (Galveston strain) mosquitoes were infected with ZIKV (Mex 1-7 strain) at 2 x 105 focus forming units (FFU)/ml) in a sheep blood meal (Colorado Serum Company). At 2, 7 and 14 days post-infection (dpi) RNA was extracted from whole mosquitoes using the mirVana RNA extraction kit (Life Technologies) following the protocol for extraction of total RNA.

extract_protocol: Total RNA (1.0ug) was poly A+ selected and fragmented using divalent cations and heat (940 C, 8 min). The NEBNext Ultra II RNA library kit (New England Biolabs) was used for RNA-Seq library construction. Fragmented poly A+ RNA samples were converted to cDNA by random primed synthesis using ProtoScript II reverse transcriptase (New England Biolabs). After second strand synthesis, the double-stranded DNAs were treated with T4 DNA polymerase, 5’ phosphorylated and then an adenine residue was added to the 3’ ends of the DNA. Adapters were then ligated to the ends of these target template DNAs.  After ligation, the template DNAs were amplified (5-9 cycles) using primers specific to each of the non-complimentary sequences in the adapters. This created a library of DNA templates that have non-homologous 5’ and 3’ ends.  A qPCR analysis was performed to determine the template concentration of each library. Reference standards cloned from a HeLa S3 RNA-Seq library were used in the qPCR analysis. Cluster formation was performed using 15.5-17 billion templates per lane using the Illumina cBot v3 system.  Sequencing by synthesis, paired end 50 base reads, was performed on an Illumina HiSeq 1500 using a protocol recommended by the manufacturer.

treatment_protocol: Viral infection in mosquitoes was confirmed by Taqman qPCR on ABI StepOnePlus machine (Applied Biosystems) using a ZIKV-specific primer. Primer and probe sequences are listed in Table S4. RNA from ZIKV positive samples was pooled (N=5) for times points 7 and 14. Limited ZIKV positive samples were detected at day 2, likely due to the virus titer being at the limits of detection for qPCR. For this time point, at least 1 qPCR positive individual was included in each pool. For all time point, three independent pools were used to create libraries for infected and uninfected samples. Control mosquitoes were fed with blood devoid of ZIKV and collected at the same time points and processed in the same way as infected ones.

tag: infection

value: ZIKV Infected

value: Galveston

value: Whole body


title: Day14-ZIKV-Rep2

tag: tissue


title: Xenopus RNAseq Heart Male2 Adult

description: Xenopus_RNAseq_Heart_Male2_Adult_1052sTS


title: CK48hrs-2

value: solvent control


title: Anolis RNAseq Kidney Female3 Adult

description: Anolis_RNAseq_Kidney_Female3_Adult_1267sTS


title: Day14-Mock-Rep3

value: Control


title: Anolis RNAseq Heart Female2 Adult

description: Anolis_RNAseq_Heart_Female2_Adult_1704sTS


title: Day14-ZIKV-Rep1


title: Scr1

value: Soleus muscle

value: 11 weeks


title: Anolis RNAseq Heart Female1 Adult

description: Anolis_RNAseq_Heart_Female1_Adult_1697sTS


title: Anolis RNAseq Heart Male3 Adult


title: CK24hrs-2


title: Day14-Mock-Rep2


title: Anolis RNAseq Brain Male3 Adult


title: Day14-Mock-Rep1


title: Anolis RNAseq Brain Male2 Adult


title: CK24hrs-1


title: Day7-ZIKV-Rep3


title: Anolis RNAseq Brain Male1 Adult


title: Human RNAseq Testis Male2 Adult

source_name: Testis

value: Testis


title: Xenopus RNAseq Brain Male1 Adult

value: Brain


title: Human RNAseq Testis Male1 Adult


title: ANOF2060716

data_processing:
Library strategy: DNA-Seq
Basecalls performed using CASAVA version 1.8.
DNA-Seq reads were aligned to the AnoCar2.0 genome assembly using bowtie v2.2.8 with default parameters.
PCR duplicates and reads mapping to multiple genome positions were filered out from the alignments.
RNA-Seq reads were aligned to the AnoCar2.0 genome assembly using HISATv2.0.4
Genome_build: AnoCar2.0
Supplementary_files_format_and_content: VCF files were produced using bcftools v1.3.1

source_name: Liver

extract_protocol:
The DNA was purified using Qiaquick PCR Purification columns (Qiagen) according to manufacturer’s instructions.
SMARTer Ultra Low Input RNA kit

value: liver


title: Anolis RNAseq Brain Female3 Adult

description: Anolis_RNAseq_Brain_Female3_Adult_1268sTS


title: Xenopus RNAseq Brain Female2 Adult

description: Xenopus_RNAseq_Brain_Female2_Adult_1046sTS


title: Anolis RNAseq Brain Female2 Adult

description: Anolis_RNAseq_Brain_Female2_Adult_1703sTS


title: Human RNAseq Liver Female1 Adult

value: Liver


title: Human RNAseq Liver Male1 Adult

value: Adult

value: Male


title: Anolis RNAseq Brain Female1 Adult

description: Anolis_RNAseq_Brain_Female1_Adult_1696sTS

value: Female


title: Human RNAseq Kidney Male2 Adult

source_name: Kidney

value: Kidney


title: CK48hrs-1

value: susceptible strain


title: Xenopus RNAseq Brain Female1 Adult

description: Xenopus_RNAseq_Brain_Female1_Adult_956sTS


title: Pis_Exp_smallRNA

description: processed files of the small RNA reads (bigwig files) are separated into two files based on if they are on the plus or minus strand

organism: Pyrobaculum islandicum

value: Exponential

value: small RNA


title: Day7-Mock-Rep3

value: Galveston


title: Day7-ZIKV-Rep2

value: ZIKV Infected

value: Whole body


title: Day7-ZIKV-Rep1


title: Day7-Mock-Rep2

value: Control


title: Day7-Mock-Rep1


title: Day2-ZIKV-Rep3


title: Human RNAseq Kidney Male1 Adult


title: C74


title: Human RNAseq Kidney Female1 Adult

description: Human_RNAseq_Kidney_Female1_Adult_873sTS


title: Pca_Stat_smallRNA

organism: Pyrobaculum calidifontis

value: Stationary


title: Day2-ZIKV-Rep2


title: Pca_Exp_smallRNA


title: C42


title: Day2-ZIKV-Rep1


title: C31


title: Par_Stat_smallRNA

organism: Pyrobaculum arsenaticum


title: Human RNAseq Heart Male1 Adult

source_name: Heart

value: Heart


title: Par_Exp_smallRNA


title: Human RNAseq Heart Female1 Adult


title: Human RNAseq Heart Male2 Adult


title: Pae_Stat_smallRNA

organism: Pyrobaculum aerophilum


title: Pis_Stat_smallRNA


title: C14


title: Day2-Mock-Rep3


title: Human RNAseq Brain Male1 Adult


title: Day2-Mock-Rep1


title: Pae_Exp_smallRNA


title: C17


title: C05


title: Human RNAseq Brain Female1 Adult

description: Human_RNAseq_Brain_Female1_Adult_2134sTS


title: iPSCs_2

status: Public on Oct 26 2017

first: Bruno

last: Di Stefano

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

description: iPS cells derived from MEF replicate 2

data_processing:
ATAC-seq reads were aligned to the mm10 genome assembly using BWA-MEM with default parameter
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated using deeptools

organism: Mus musculus

source_name: iPS cells derived from MEF

growth_protocol: Mouse embryonic fibroblasts (MEFs) were derived from E13.5 embryos. The head, limbs, spinal cord, gonads, and internal organs were removed and the remaining tissue was minced in 200 μl of Trypsin-EDTA. Following a 5 minutes incubation at 37°C, the Trypsin-EDTA was quenched in 10 ml of MEF growth media (500 ml DMEM,  10% fetal bovine serum, 1X non-essential amino acids, 1X Glutamax, 55 μM beta-mercaptoethanol) and cultured at 37°C at 4% oxygen. iPSCs were cultured on mitomycin C treated MEF feeder cells in KO-DMEM (Invitrogen) supplemented withL-glutamine, penicillin/streptomycin, nonessential amino acids, β-mercaptoethanol, 1,000 U/ml LIF (ESC medium) and 15% fetal bovine serum (FBS, Invitrogen).reprogrammable MEFs were seeded at a density of 15,000 cells per well of a 12 well plate coated with 0.2% gelatin (Sigma). For cell reprogramming experiments, OSKM inducible MEF were cul;tured in induction media contained ES culture media (500 ml KO-DMEM (Life Technologies) 15% fetal bovine serum (Hyclone), 1X non-essential amino acids (Life Technologies), 1X Glutamax (Life Technologies), 1000 U/ml leukemia inhibitory factor, 55 μM beta-mercaptoethanol (Sigma)) supplemented with 50 μg/ml ascorbic acid (Sigma) and 2 μg/ml doxycycline hyclate (Sigma).

extract_protocol:
60.000 cells were washed once with 100µl PBS and resuspended in 50µl lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.2% IGEPAL CA-630)
The suspension of nuclei was then centrifuged for 10min at 500g at 4°C, followed by the addition of 50µl transposition reaction mix (25µl TD buffer, 2.5µl Tn5 Transposase and 22.5µl Nuclease Free H2O) and incubation at 37°C for 30min. DNA was isolated using MinElute Kit (Qiagen). Libraries were amplified by PCR (13 cycles). After the PCR reaction, the library was selected for fragments between 100 and 1000bp with AmpureXP beads (Beckman Coulter). Libraries were purified with Qiaquick PCR (Qiagen) and integrity checked on a Bioanalyzer before sequencing.

treatment_protocol: Cells were trypsinized

tag: strain background

value: B6/129 hybrid

tag: cell type

value: iPS cells derived from MEF


title: isk_1

city: Cologne

first: Ismene

last: Karakasilioti

state: NRW

address: Gleueler str. 50

country: Germany

institute: Max Planck Institute for Metabolism Research

data_processing:
Illumina Casava software used for basecalling
RNAseq reads were aligned mus_musculus
Fragments Per Kilobase of exon per Million mapped fragments (FPKM) were calculated using a Cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: text file with FPKM

source_name: npy neurons 1

extract_protocol:
Total RNA was extracted according to manufacturer's instructions (PicoPure RNA isolation kit, ThermoFisher Scientific, USA) and all samples were DNAse-treated (ThermoFisher Scientific, USA).
Due to low amount of input material, pre-amplification using the Ovation¨ RNASeq System V2 was performed. Total RNA was used for first strand cDNA synthesis, using both poly(T) and random primers, followed by second strand synthesis and isothermal strand-displacement amplification. For library preparation, the Illumina Nextera¨ XT DNA sample preparation protocol (Part # 15031942 Rev. C) was used, with 1 ng cDNA input. After validation (Agilent 2200 TapeStation) and quantification (Invitrogen Qubit System) all 5 transcriptome libraries were pooled.

treatment_protocol: The brain area corresponding to the hypothalamus was micro-dissected under a brightfield stereoscope. Each sample contained hypothalami from 4 mice (males and females) and tissue samples were processed in ice-cold HBSS buffer, until enzymatic treatment. Samples were centrifuged to remove HBSS and were subsequently incubated for 15 minutes in pre-incubation buffer, at 37 C. Enzyme mix was added and each sample was manually dissociated by gentle pipetting, throughout a total duration of 35 minutes and according to manufacturer's instructions (Neural tissue dissociation kit, Miltenyi biotech, Germany). Subsequently, samples were centrifuged at 500 xg, 10 minutes, 4 C and the cell pellet was re-suspended in cold 1x PBS, containing 5% fetal calf serum.

value: C57/BL6 N

value: hypothalamic brain sections

value: Npy-promoter driven GFP+ neurons

value: young adults - 6 weeks


title: isk_5

source_name: pomc neurons 2

value: Pomc-promoter driven GFP+ neurons


title: isk_4

source_name: pomc neurons 1


title: isk_3

source_name: npy neurons 3


title: siNudt21 day6_2

description: siNudt21transfected MEF induced with OSKM for 6 days replicate 2

value: E13.5 embryo

value: Mouse Embryonic fibroblasts (MEFs)

tag: transfected with

tag: induced with

value: OSKM for 6 days

tag: time points


title: isk_2

source_name: npy neurons 2


title: iPSCs_1

description: iPS cells derived from MEF replicate 1


title: siCtrl day6_1

description: siCTRL transfected MEF induced with OSKM for 6 days replicate 1

value: siCtrl


title: siNudt21 day3_2

description: siNudt21transfected MEF induced with OSKM for 3 days replicate 2

value: OSKM for 3 days

value: day 3


title: siNudt21 day3_1

description: siNudt21 transfected MEF induced with OSKM for 3 days replicate 1


title: Day2-Mock-Rep2

value: Galveston

value: Whole body

value: Adult


title: MEF_2

description: Mouse Embryonic fibroblasts

source_name: Mouse Embryonic fibroblasts


title: siCtrl day3_2

description: siCTRL transfected MEF induced with OSKM for 3 days replicate 2


title: MEF_1

description: Mouse Embryonic fibroblasts


title: MEF induced to express OKSM for 9 days and selected for SSEA-  [PAS-seq]

city: Irvine

first: Elmira

last: Forouzmand

address: B228 Medical Science I

department: Department of Microbiology and Molecular Genetics

institute: University of California Irvine

data_processing:
Reads with a string of As (at least 15) were trimmed and kept. These reads were mapped to mouse genome (mm9), using TopHat v2.1.0 with the setting -g 1.
Alignmnet with the possibility of internal priming were removed if a read had 6 or more consecutive As or more than 7 As in the 10 nucleotide downstream of polyA site.
Bigwig files were generated from the remaing reads, using deepTools 2.4
From the remaing reads those with their 3' end in the interval of -40nt to +40nt of potential polyA sites were used to generate the count table.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include read counts for polyA sites for each Sample

source_name: MEF

growth_protocol: MEFs were derived from mice carrying an inducible, polycistronic OKSM cassette in the 3’ UTR of Col1a1, the M2-rtTA transactivator at the Rosa26 locus, and an EGFP reporter construct under control of Pou5f1 regulatory elements. MEFs cells were grown in MEF growth media (500 ml DMEM (Life Technologies) 10% fetal bovine serum (Hyclone), 1X non-essential amino acids (Life Technologies), 1X Glutamax (Life Technologies), 55 μM beta-mercaptoethanol (Sigma)) and cultured at 37°C at 4% oxygen.

extract_protocol:
RNA isolation was performed using the miRNeasy mini kit (Qiagen). RNA was eluted from the columns using RNase-free water and quantified using a Nanodrop ND-1000.
Total RNA was extracted with Trizol as per manual (Life technologies), 10 μg total RNA was fragmented with fragmentation reagent (Ambion) at 70 oC for 10 minutes followed by precipitation with ethanol. After centrifugation, RNA was dissolved and Reverse transcription was performed with PASSEQ7-2 RT oligo : [phos]NNNNAGATCGGAAGAGCGTCGTGTTCGGATCCATTAGGATCCGAGACGTGTGCTCTTCCGATCTTTTTTTTTTTTTTTTTTTT[V-Q] and Superscript III. cDNA was recovered by ethanol precipitation and centrifugation. 120-200 nucleotides of cDNA was gel-purified and eluted from 8% Urea-PAGE. Recovered cDNA was circularized with CircligaseTM II (Epicentre) at 60 oC overnight. Buffer E (Promega) was added in cDNA and heated at 95 oC for 2 minutes, and then cool to 37 oC slowly. Circularized cDNA was linearized by adding BamH I (Promega). cDNA was centrifugated after ethanol precipitation. PCR was carried out with primers PE1.0 and PE2.0 contaning index. Around 200 bp of PCR products was gel-purified and submitted for sequencing (single read 100 nucleotides).

treatment_protocol: To induce expression of the pluripotency factors, reprogrammable MEFs were seeded at a density of 15,000 cells per well of a 12 well plate coated with 0.2% gelatin (Sigma). Induction media contained ES culture media (500 ml KO-DMEM (Life Technologies) 15% fetal bovine serum (Hyclone), 1X non-essential amino acids (Life Technologies), 1X Glutamax (Life Technologies), 1000 U/ml leukemia inhibitory factor, 55 μM beta-mercaptoethanol (Sigma)) supplemented with 50 μg/ml ascorbic acid (Sigma) and 2 μg/ml doxycycline hyclate (Sigma). Unless otherwise indicated, reprogrammable MEFs were induced for 10 days, followed by 4 days of doxycycline withdrawal to ensure transgene independence.


title: MEF induced to express OKSM for 9 days and selected for SSEA+  [PAS-seq]


title: MEF induced to express OKSM for 6 days and selected for SSEA+  [PAS-seq]


title: MEF induced to express OKSM for 6 days and selected for SSEA-  [PAS-seq]


title: Control MEF cells_replicate 2  [PAS-seq]

value: control


title: iPSC cells_replicate 1  [PAS-seq]

source_name: iPSC


title: iPSC cells_replicate 2  [PAS-seq]


title: siNudt21 day6_1

description: siNudt21 transfected MEF induced with OSKM for 6 days replicate 1

value: B6/129 hybrid


title: MEF cells treated with luciferase siRNA and induced to express OKSM for 6 days_replicate 2  [PAS-seq]


title: Untransfected MEF cells induced to express OKSM for 6 days _replicate 2  [PAS-seq]

value: induced to express OKSM for 6 days


title: MEF cells treated with luciferase siRNA and induced to express OKSM for 6 days _replicate 1  [PAS-seq]


title: Control MEF cells_replicate 1  [PAS-seq]


title: MEF cells treated with Nudt21 siRNA and induced to express OKSM for 6 days _replicate 2  [PAS-seq]


title: siCtrl day6_2

description: siCTRL transfected MEF induced with OSKM for 6 days replicate 2


title: Untransfected MEF cells induced to express OKSM for 3 days _D3_replicate 2  [PAS-seq]

value: induced to express OKSM for 3 days


title: MEF cells treated with Nudt21 siRNA and induced to express OKSM for 3 days _D3_replicate 1 [PAS-seq]


title: MEF cells treated with Nudt21 siRNA and induced to express OKSM for 6 days _replicate 1  [PAS-seq]


title: Untransfected MEF cells induced to express OKSM for 3 days _D3_replicate 1 [PAS-seq]


title: MEF cells treated with luciferase siRNA and induced to express OKSM for 3 days _D3_replicate 2  [PAS-seq]