title: WT90min_2

status: Public on Mar 20 2019

city: Beijing

first: Yifan

last: Zhou

address: No. 30 Shuangqing Road

department: School of Medicine

institute: Tsinghua University

data_processing:
The software for base calling is BaseCallV1.6.0.19379
We use internal software SOAPnuke to filter reads, followed as: (1) Remove reads with adaptors;(2) Remove reads in which unknown bases(N) are more than 10%; (3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 50% in a read).After filtering, the remaining reads are called "Clean Reads" and stored in FASTQ format.
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step. The software for base calling is HISAT2 v2.0.4, -p8--phred64--sensitive-I 1-X 10000.
We filter the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads.Then we assembled those clean reads into Unigenes, followed with Unigene functional annotation, SSR detection and calculate the Unigene expression levels and SNPs of each sample. Finally, we identify DEGs (differential expressed genes) between samples and do clustering analysis and functional annotations.
We mapped clean reads to reference using Bowtie2, and then calculate gene expression level with RSEM. RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. Then, we calculate pearson correlation between all samples using cor, perform hierarchical clustering between all samples using hclust, perform PCA analysis with all samples using princomp, and draw the diagrams with ggplot2 with fuctions of R. Software information: Bowtie2 : Version: v2.2.5 Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Genome_build: NCBI_GRCm38.p5
Supplementary_files_format_and_content: The processed data files include FPKM values for all the samples.

source_name: Splenocytes

extract_protocol:
The spleen was collected and smashed on ice. Total RNA samples were harvested using Trizol reagent. We use Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC: RNA concentration, RIN value,28S/18S and the fragment length distribution.
1. mRNA enrichment: Oligo dT Selection or rRNA depletion. 2. RNA fragment and reverse transcription: Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. 3. End repair, add A tailing and adaptor ligation:The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. 4. PCR amplification:The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer. 5. Denature and cyclization:Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6.Sequencing on BGISEQ- 500 platform.

treatment_protocol: The wilde type and GdX-/Y mice were injected with LPS (20 mg/kg body weight, i.p.), and the spleen was collected at 90 min or 6 hrs after injection.

tag: strain

tag: tissue

value: spleen

value: 8 weeks

tag: genotype

value: wild type


title: SCCOHT1_shCDK6_1

status: Public on Feb 04 2019

type: SRA

city: Montreal

first: Sidong

last: Huang

state: Quebec

address: 3655 promenade Sir-William-Osler

department: Biochemistry

country: Canada

institute: McGill University

library_source: transcriptomic

data_processing:
Sequencing reads were mapped to reference human genome sequence (hg19) downloaded from Illumina iGenomes using STAR57 (version 2.4.2. --quantMode)
The number of fragments was counted with HTSeq58 (version 0.6.1p1)  based on known gene from RefSeq database on UCSC Genome Browser.
Differentially expressed gene (DEG) analysis was performed using DESeq2 (v 1.16.1) bioconductor R package.
Genome_build: hg19
Supplementary_files_format_and_content: Comma seperated values including raw counts

molecule: total RNA

organism: Homo sapiens

source_name: SCCOHT Cell line

growth_protocol: BIN-67 and SCCOHT-1 cells were all cultured in RPMI with 7% fetal bovine serum (FBS), 1% penicillin/streptomycin and 2mM L-glutamine.

extract_protocol:
Total RNA from cell lines was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) by following the manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For CDK6 knockdown, cells were infected with control vector pLKO and two shRNAs targeting CDK6 for 8 hours followed by puromycin selection for 2 days before harvesting. For palbociclib treatment, cells were cultured in the presence of 0 or 100 nM palbociclib for 24 hours before harvesting.

tag: cell type

value: Cancer cells

tag: treatment

value: CDK6 Knockdown


title: SCCOHT1_pLKO

value: pLKO


title: WSB WT Female Rep6

status: Public on May 22 2019

city: Farmington

first: Asli

last: Uyar

state: CT

address: 10 Discovery Dr

department: Computational Sciences

country: USA

institute: The Jackson Laboratory

data_processing:
Sequenced reads were quality trimmed and filtered using Trimmomatic tool and reads passing the quality filtering were mapped to the mouse mm10 reference genome using ‘STAR’ aligner. Custom genomes were generated for CAST, PWK and WSB strains by incorporating REL-1505 variants into the reference genome.
HTSeq Python package was used to calculate raw read counts per transcript.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw read counts values for each Sample.

organism: Mus musculus

source_name: Whole brain

extract_protocol:
Left brain hemispheres (n=93) were snap frozen at harvest. RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher).
RNA libraries were prepared for sequencing using the KAPA mRNA HyperPrep Kit (KAPA Biosystems), according to the manufacturer’s instructions.

tag: strain/background

value: WSB

tag: genotype/variation

value: WT

tag: Sex

value: Female

tag: age

value: 8 months

value: Left brain hemisphere


title: Wild-type_7

status: Public on Jun 30 2019

city: Beaverton

first: Donald

middle: F.

last: Conrad

state: OR

address: 505 NW 185th Ave

department: Division of Genetics; Oregon National Primate Research Center

institute: Oregon Health & Science University

data_processing:
Base calls were performed with bcl2fastq.
Sequenced reads were tagged with molecular(UMI) and cell barcodes. Then reads with low quality scores were removed and the adaptor sequences were trimmed.
Reads were aligned to Mus_musculus.GRCm38.76 genome with STAR (v. 2.5.3a) with default configuration.
STAR aligned reads were merged with tagged SAM file to recover cell/molecular barcode information. Then the reads were annotated with exon and other annotation tags.
Digital gene expression matrix was extracted by counting the number of unique UMIs per gene within individual cell from exon-tagged bam files.
Additional step of bead synthesis error correction was performe by collapsing UMI counts when the first 11 bases of cell barcodes were the identical.
Genome_build: mm10
Supplementary_files_format_and_content: Digital Gene Expression(DGE) matrix of gene counts for each cell. Columns are cells and rows are genes.

extract_protocol:
Whole testes were dissociated using two different methods, enzymatic and mechanical. Single-cell suspensions were either FACS sorted for enriching different germ cell subpopulations or directly paired to Drop-seq protocol to generate single-cell RNA sequencing libriaries.
Library preparations were perforemd with Drop-seq protocol (Macosko et al. Cell 2015)

tag: strain background

tag: gender

value: male

value: Wild-type

value: post natal 4 months

tag: tissue/cell type

value: Testis

tag: dissociation method

value: Mechanical


title: BIN67_100

value: 100 nM palbociclib


title: SCCOHT1_shCDK6_2


title: Wild-type_8

value: post natal 3 months 1 day


title: BIN67_shCDK6_2


title: BIN67_shCDK6_1


title: Plasma Sample 1 condition 2 rep3

status: Public on Jan 31 2019

city: San Francisco

first: Cassandra

middle: D

last: Belair

state: CA

address: 35 Medical Center Way

department: Urology

institute: UCSF

description:
3' adapter 0.85uM; 5' adapter 0.33uM unmodified
processed data file: CB02_completeSummary.txt
CB02_4N27_27N10_Mature_counts.txt
processed data file: CB02_Mature_counts_raw.txt

data_processing:
demultiplex: CutAdapt v1.11 --no-trim -e 0 -O 20
trim adapters: CutAdapt v1.11 -u 4 -m 17 -e 0 -O 20
align to custom genomes using bowtie v1.1.2 or bowtie2 v2.2.5 sequentially removing adapter/marker "contaminant" sequences, mature miRNA, other small RNAs, then finally to genomic sequences
bowtie2 --local -L 17 (contaminant genome)
bowtie -n 0 -l 18 --best (all other genomes)
all files in BCRB17 set were aligned using STAR
(all small RNA genomes) params='--genomeLoad NoSharedMemory --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMunmapped None  --outFilterMismatchNmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 1 --limitBAMsortRAM 4044427000'
(genomic) params2='--genomeLoad NoSharedMemory --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMunmapped None  --outFilterMismatchNmax 0.5 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 1 --limitBAMsortRAM 2544427000'
custom bash script to generate counts
custom bash or r scripts to collapse PCR duplicates using UMI
Genome_build: hg19 for human genome, small RNAs downloaded from RNACentral Database release5
Supplementary_files_format_and_content: delimited files containing either counts or sequences

source_name: plasma

extract_protocol:
Qiagen micro miRNeasy kit modified to use 1:7 plasma:Trizol or 1:3 plasma:Trizol LS
see manuscript for details

value: plasma

value: Male


title: human ACVR1 3

status: Public on Jan 25 2019

city: New York

first: Oren

middle: Josh

last: Becher

state: NY

address: 1468 Madison Avenue, A21-02

department: Pediatrics

institute: Mount Sinai

description: ACVR1 WT 3

data_processing:
Paired-end fastq files were clipped using fastq-mcf with the following parameters: --max-ns 4 --qual-mean 25 -H -p 5 -q 7 -l 25
Paired-end fastq files were imported into Galaxy [1] and aligned to the mm10 genome using RNA-STAR (Galaxy version 2.6.0b-1) with default parameters.
Aligned reads were counted using HTSeq-count with the Ensembl mm10 transcriptome GTF file as the feature file with the following parameters: stranded = no, mode = union, minimum alignment quality = 10, map nonunique or ambiguous reads = none.
[1] Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, Gruning B, Guerler A, Hillman-Jackson J, Von Kuster G, Rasche E, Soranzo N, Turaga N, Taylor J, Nekrutenko A, Goecks J. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 2016 Jul 8; 44(W1): W3-W10.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include HTSeq count values for each sample.

source_name: P3-P5 brainstem progenitors

growth_protocol: Brainstem progenitors from postnatal day 3-5 Nestin TVA pups were isolated and cultured in serum-free conditions with EGF and FGF2 as previously described.

extract_protocol:
Standard RNA isolation was performed by Expression Analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were infected with RCAS vectors expressing either ACVR1 WT alone, ACVR1 WT with H3.1K27M, R206H ACVR1 alone, or R206H ACVR1 with H3.1K27M.

value: Nestin TVA; p53 floxed

value: Brainstem progenitors

tag: vector expression

value: ACVR1 WT


title: human ACVR1 and H3.1K27M 3

description: ACVR1 WT K27M 3

value: ACVR1 WT and H3.1K27M


title: human ACVR1 R206H 1

description: R206H 1

value: ACVR1 R206H


title: human ACVR1 2

description: ACVR1 WT 2


title: Adult_Skin_Teff_2

status: Public on Dec 02 2018

first: Kelly

last: Remedios

address: 513 Parnassus Ave, HSW1201B

data_processing:
The primary sequencing output ( FASTQ) is produced by a combination of Illumina software (CASAVA v. 1.8.2) and EA developed tools. Low quality reads, bases, homopolymers and adapter sequences were removed with fastq-mcf (Expression Analysis)
Reads were then mapped to mm10 using the UCSC refFlat gene model
Reads were mapped using Tophat (v2.0.12) with Bowtie2 (2.1.0.0) and sorted with Samtools (0.1.19.0).
Reads were counted with HTSeq (0.6.1) using the settings union and stranded=no
Genome_build: mm10
Supplementary_files_format_and_content: comma separated value file contains raw counts for each sample

source_name: Skin

extract_protocol:
Sorted cells were pelleted flash frozen in liquid nitrogen. RNA was sent overnight on dry ice to Expression analysis, Quintiles to perform all subsequent processing and sequencing. RNA was isolated using by column purification.
RNA samples were converted into cDNA libraries using the Illumina SMARTer Ultra Low Input sample preparation kit.

value: Skin Teffs

value: 6 weeks

value: Skin

tag: characteristics


title: Adult_Skin_Treg_3

value: Skin Tregs


title: H_11_185

status: Public on Jan 04 2019

first: Zeguo

last: Sun

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

data_processing:
Illumina bcl2fastq version 2.19 were used for basecalling
Reads was aligned to hg38 by star 2.5.3a with default parameters
Read count was summarized with HTSeq 0.8.0
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

source_name: lung squamous cell carcinoma tumor samples

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels.  RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA).
RNA libraries were prepared according to instructions ofNEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA).

value: lung squamous cell carcinoma

tag: subgroup


title: LS-15045_S51_E1-50

status: Public on Dec 06 2018

city: Seattle

first: Allen

last: Institute

state: WA

address: 615 Westlake Ave N

institute: The Allen Institute for Brain Science

description:
nuclei_exon_counts.csv.gz
nuclei_exon_counts.csv.gz

data_processing:
50-base pair paired-end reads were aligned to GRCm38 (mm10) using a RefSeq annotation gff file retrieved from NCBI on 01/18/2016 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/). Sequence alignment was performed using STAR v2.5.3 (Dobin et al., 2013) in twopassMode. PCR duplicates were masked and removed using STAR option “bamRemoveDuplicates”. Only uniquely aligned reads were used for gene quantification. Gene counts were computed using the R GenomicAlignments package (Lawrence et al., 2013) sumarizeOverlaps function using “IntersectionNotEmpty”.
Reads that did not map to the genome were then aligned to synthetic constructs (i.e. ERCC) sequences and the E.coli genome (version ASM584v2). Quantification was performed using summerizeOverlaps from the R package GenomicAlignments [38].
Single nucleus quality control criteria: >500,000 genome-mapped reads, >75% reads aligned, and >50% unique reads. Single cell quality control criteria: >200,000 transcriptome mapped reads and >1000 genes detected (counts > 0).
Genome_build: mm10

source_name: Primary Visual Cortex (VISp)

growth_protocol: All procedures were approved by the Institutional Animal Care and Use Committee at the Allen Institute for Brain Science (Protocol no. 1511). Animals were provided food and water ad libitum and were maintained on a regular 12-h day/night cycle. Mice were housed at no more than 5 adults per cage, with various enrichment materials added, including nesting materials, gnawing materials, and plastic shelters. Nutritional and foraging enrichment was provided in the form of foods such as sunflower seeds and sucrose pellets. Mice were maintained on the C57BL/6J background.

extract_protocol:
Tissue samples were obtained from adult male and female transgenic mice carrying a Cre transgene and a Cre-reporter transgene. After euthanasia, the brain was rapidly dissected and mounted for coronal slice preparation on a Compresstome VF-300 vibrating microtome (Precisionary Instruments) and sectioned at  250 μm intervals.     For whole cell dissociation, 2 mg/ml of pronase in ACSF solution was added to dissected tissues and enzymatic digestion was carried out at room temperature. After digestion,The tissue was triturated and the cell suspension was incubated on ice in preparation for fluorescence-activated cell sorting (FACS). Live cells were sorted by excluding DAPI positive events and debris, and gating to include red fluorescent events (tdTomato-positive cells). Single cells were collected into strip tubes containing 11.5μl of collection buffer (SMART-Seq v4 lysis buffer), RNase Inhibitor, and ERCCs (External RNA Controls Consortium, MIX1 at a final dilution of 1x10-8) and tubes were then stored at -80°C.    For nuclei isolation, dissected tissues were placed into a homogenization buffer (10mM Tris pH 8.0, 250mM sucrose, 25mM KCl, 5mM MgCl2, 0.1% Triton-X 100, 0.5% RNase inhibitor, 1X protease inhibitor, and 0.1mM DTT). Tissues were placed into a 1ml dounce homogenizer and homogenized using 10 strokes of the loose dounce pestle followed by 10 strokes of the tight pestle to liberate nuclei . Mouse anti-NeuN antibody (EMD Millipore, MAB377, Clone A60) was added to the nuclei at a final dilution of 1:1000 and nuclei suspensions were incubated at 4°C for 30 minutes, followed by incubation in secondary antibody (goat anti-mouse IgG (H+L), Alexa Fluor 594 conjugated, ThermoFisher Scientific, 1:5000) for 30 minutes at 4°C and staining with DAPI. Single nuclei were captured by gating on DAPI-positive events, excluding debris and doublets, and then gating on Alexa Fluor 594 (NeuN) signal. Strip tubes containing FACS isolated single nuclei were then frozen at -80°C.
The SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech #634894) was used per the manufacturer’s instructions for reverse transcription of single cell RNA and subsequent cDNA synthesis. Mouse whole cells were subjected to 18 PCR cycles after the reverse transcription step, whereas mouse nuclei were subjected to 21 PCR cycles.     Sequencing libraries were prepared using NexteraXT (Illumina, FC-131-1096) with NexteraXT Index Kit V2 Set A (FC-131-2001). NexteraXT libraries were prepared at 0.5x volume, but otherwise followed the manufacturer’s instructions.

value: M

value: VISp

value: NeuN-positive

value: Pass

value: Glutamatergic

tag: molecule

value: Nuclei


title: RT112 APSCE Replicate2

status: Public on Feb 25 2019

city: Belfast

first: Rebecca

middle: Elizabeth

last: Steele

address: 97 Lisburn Road

department: CCRCB

country: United Kingdom

institute: Queen's University Belfast

data_processing:
RNA-Seq fastq reads were trimmed and aligned to Hg19 (GRCh37) using STAR.
Reads mapped to genes using HTSeq counts.
Differential expression analysis was performed on triplicate samples using DESeq2.
Genome_build: Hg19 (GRCh37)
Supplementary_files_format_and_content: counts

source_name: RT112 Cell line

extract_protocol:
Total RNA was extracted from cells using Ribozol™ RNA Extraction Reagent (Amresco) following manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard protocol by Otogenetics Corporation (Atlanta, USA)

value: Prostate


title: CAST APP/PS1 Female Rep2

value: CAST

value: Female

value: 8 months

value: Left brain hemisphere


title: TIC_HySp5 replicate 1

status: Public on Jan 18 2019

city: Geneva

first: Leonardo

last: Beccari

address: 30 Quai Ernest Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

library_source: genomic

data_processing:
Adapters and bad quality bases were removed with cutadapt (ref Martin et al 2011 version 1.8 options -m 15 -q 30 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC for ChIP and -a CTGTCTCTTATACACATCTGACGCTGCCGACGA for ChIPmentation).
Demultiplexed ChIP-seq reads from our sequenced samples were mapped onto the Human GRCh37 (hg19) genome assembly using bowtie2, version 2.2.6.2, implemented in Galaxy. Significantly enriched regions were identified using MACS2 (version 2.1.0.20151222.0 command line: macs2 callpeak -t input.bam --call-summits -B). Coverage files were normalized by the millions of mapped reads in each sample using a manually created R script. Normalized bedgraph files were converted to bigwig using the Wig/BedGraph-to-bigWig converter tool (version 1.1.1) implemented in the pubblic Galaxy server (https://usegalaxy.org/). The fastq files from the two biological replicates of each condition where merged and remapped in order to obtain the average coverage profile.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig of theChIPseq read coverage files, divided by the number of millions of mapped reads in each sample.

molecule: genomic DNA

source_name: HEK293 cells transfect with the hySp5 construct

growth_protocol: HEK293T cells, a kind gift from the laboratory of Ariel Ruiz i Altaba (University of Geneva Medical School), were maintained in DMEM High Glucose + 1mM Na pyruvate + 6mM L-glutamine + 10% fetal bovine serum.

extract_protocol:
24 hours after transfection, cells were collected by scraping, washed twice in pre-warmed culture medium and fixed in 1% FA solution (Sigma) for 15 minutes. The fixative was quenched by adding Glycine (125 mM) and incubation for 3 minutes. The cells were washed once in ice-cold PBS and re-suspended in 5 mL chromatin prep buffer (Active Motif), containing 0.1mM PMSF and 0.1% protease inhibitor cocktail (PIC). To release the nuclei the sample was transferred into a pre-cooled 15 mL glas Douncer and dounced with 30 strokes. After 10 minutes incubation on ice and centrifugation at 1250 g for 5 minutes at 4°C, the nuclei were re-suspended in 500 uL sonication buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1 mM PMSF, 1% PIC). Following another 10 minutes incubation on ice, the chromatin was sonicated with a Bioblock Scientific VibraCell 75042 sonicator (Amplitude: 25%, Time: 12 minutes, 30 seconds on, 30 seconds off, 24 cycles). Note: The sonication conditions were optimized to have a fragmentation size of around 250 bp. Then 100 uL of the sonicated chromatin was added to 900 uL ChIP dilution buffer (0.1% NP-40, 0.02 M HEPES pH 7.3, 1 mM EDTA pH 8.0, 0.15 M NaCl, 1 mM PMSF, 1% PIC) and incubated with 4 ug anti-HA antibody (NB600-363, Novus Biologicals) over night at 4°C on a rotator. Next, the sample was loaded on a ChIP-IT ProteinG Agarose Column (Active Motif) and incubated for 3 hours at 4°C on a rotator. The column was washed 6 times with 1 mL buffer AM1 (Active Motif) and the DNA eluted with 180 uL of pre-warmed buffer AM4 (Active Motif). The sample was decrosslinked by adding 30 uL 10x TE buffer, 18 uL 5 M NaCl, 57 uL H2O and incubated for 5 hours at 65°C. 5 uL of RNAse A (10 ug/uL) was added and the sample incubated at 37°C for 30 minutes before adding 10 uL of Proteinase K (10 ug/uL), and further incubation for 2 hours at 55°C. The DNA was purified with the MiniElute PCR purification kit (Qiagen). For preparing the Input DNA, 5 uL sonicated chromatin was added to 5 uL 5M NaCL in 40 uL H2O, and incubated for 15 minutes at 95°C. Next the sample was incubated at 37°C for 5 minutes with 2.5 uL of RNAse A (10 ug/ul), 2.5 uL PK (10 ug/uL) was then added, and the incubation continued at 55°C for 30 minutes. 10 uL were taken for purification (MiniElute PCR purification kit from Qiagen).
5-10 ng of purified DNA were used to make libraries according to the manufacturer’s protocol (Illumina). The material was sequenced with 50 bp single-end reads on the Illumine HiSeq according to the manufacturer’s specifications.

treatment_protocol: HEK293T cells were seeded into a 10 cm dish (920 000 cells) and transfected  18-19 hours later with X-tremeGENETM HP DNA transfection reagent (Roche).  Plasmids used were: HySp5-420, ZfSp5-377, HySp5-ΔDBD-337, ZfSp5-ΔDBD-289, 3666 ng

tag: transfected with

value: hySp5 construct

tag: cell line

tag: time

value: 24h post- transfection

tag: antibody


title: scTrioSeq2Met_CRC15_MO3_574

status: Public on Nov 29 2018

first: Yu

last: Hou

state: Beijing

address: No.5 Yiheyuan Street

department: School of life sciences

country: China

institute: Peking University

description: single cell DNA methylome seq

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
The raw sequencing reads were trimmed to remove sequencing adapters, amplification primers, and low-quality bases in read ends.
For the data from scRNA-seq performed according to Tang protocol (Tang et al., 2009), trimmed clean reads were aligned to human reference genome (hg19) using STAR (v2.5.0) 2-pass mapping steps. For the data from scRNA-seq performed according to the multiplexed scRNA-seq method, the analyses were done as the previous paper (Dong et al., 2018).
For bisulfite sequencing data, trimmed clean reads were mapped to human reference genome (hg19) using Bismark (v0.7.6)
Genome_build: hg19
Supplementary_files_format_and_content: The FPKM.txt files include the FPKM values of RefSeq genes. The TPM.txt files include the TPM values of RefSeq genes. The SingleC files include the DNA methylation level of each singleC sites.

source_name: CRC

growth_protocol: The HEp-2 (ATCC CCL-23) cell line were cultured in RPMI 1640 with 10% FBS, and digested with trypsin before single cell picking.

extract_protocol:
The single viable cells were individually picked into 200-uL tubes containing lysis buffer. For scTrio-seq2, we used magnetic beads (Invitrogen, cat. #65011) to separate the nucleus and RNA of one single cell. We added 0.2 ?L magnetic beads to each single-cell lysis buffer. Then the single cells were lysed and vortexed for 1 min to release RNA. The lysis products were then centrifuged at 1,000 × g for 5 min at 4°C, and placed on the magnetic rack for 5 min. The magnetic beads can aggregate on the surface of the nucleus to maintain the nucleus in the pellet, while the RNA was released in the supernatants. The supernatants containing RNA were transferred to a new tube for transcriptome sequencing. The remaining beads containing a single nucleus were re-suspended with lysis buffer of scBS-seq for DNA methylation sequencing
For single-cell whole-genome bisulfite sequencing, the scBS-seq libraries were constructed according to the published protocol as described in 2017 (Clark et al., 2017). For CRC01 and CRC02, the transcriptome sequencing libraries were constructed according to Tang protocol (Tang et al., 2009); for the remaining patients, the transcriptome sequencing libraries were constructed according to a multiplexed scRNA-seq method, in which the poly T primers were combined with barcodes and unique molecule identifiers (UMIs) (Dong et al., 2018).

treatment_protocol: Informed consent was obtained from all patients preoperatively. Multi-regional sampling tissues were collected. For each tumor, 3-6 regions, including both surface and center areas, were sampled. Except for the MP of CRC01 which was sampled after six cycles of chemotherapy, other tumors were all sampled before treatment. Patient-derived tumors and adjacent normal tissue were collected and processed immediately after surgical resection. The dissected tissues were then mechanically dissociated and enzymatically digested to single-cell suspension using collagenase type II (Invitrogen, cat. #17101015) and collagenase type IV (Invitrogen, cat. #17104019). For 5 patients (CRC11, CRC12, CRC13, CRC14, and CRC15), leukocytes were depleted by magnetic-activated cell sorting (MACS) (CD45 Microbeads, Miltenyi Biotec, cat. #130-045-801) or fluorescence-activated cell sorting (FACS) (BV421 Mouse Anti-Human CD45, BD Horizon, cat. #563879).

tag: disease

value: Carcinoma


title: scTrioSeq2Met_CRC15_MO2_624

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC15_ML6_225

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC15_ML6_226

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC15_MO1_557

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC15_ML5_248

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC15_ML5_231

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC15_MO1_572

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC15_ML4_209

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC15_ML3_208

description: single cell DNA methylome seq


title: det1-1_D_rep1_IP

status: Public on Aug 31 2018

city: Paris

first: Fredy

last: BARNECHE

address: Rue d'Ulm

department: IBENS

country: France

institute: CNRS

description: ChIP DNA

data_processing:
Illumina CASAVA 1.8 software used for basecalling and demultiplexing.
Read mapping and peak calling: Spike-in ChIP-seq data were mapped using STAR with the following configurations STAR --alignIntronMax 1 --alignEndsType EndToEnd against a genome that combines the Arabidopsis thaliana (TAIR10) and Drosophila melanogaster (dm6) genomes. To calculate the reference scaling factors, the reads mapping to Drosophila genome were first normalized according to the number of input reads and then used to obtain the normalization factor in each sample. H2BUb enriched regions were obtained using MACS2 with the following configurations MACS2 callpeak -f BAM --keep-dup 1 -g 1e+8.
ChIP-seq data visualization: The values in the bedgraph pilup files obtained with MACS2 were first scaled with the spike-in normalization factors. The values obtained for replicates were averaged and converted to bigwig files for gene track visualization.
H2BUb ChIP-seq peaks annotation: The peaks obtained from each two replicates with MACS2 and having a FDR below 0.01 were intersected using bedtools utility intersect. Peaks exhibiting intersection regions beyond 10% of input peak lengths were kept. Finally, the resulting peaks were merged (bedtools merge) and annotated with gene (corresponding to -250 pb from TSS to TES) and TEs regions (Transposable Elements) extracted from TAIR10.
H2Bub differential enrichment analysis: The peaks having an FDR below 0.01 were merged and annotated with gene and TEs regions (Transposable Elements) extracted from TAIR10. Only peaks that had intersection regions greater than 150 bp were kept for further analysis. The number of ChIP-seq reads mapping into each peak coordinates was calculated using bedtools utility multicov and grouped by gene-ID or TE-ID using bedtools utility groupby. These counts were used to run H2BUb differential enrichment analysis using DESeq2. The counts were scaled by the spike-in normalisation factors before running differential analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: *.bw: bigWig files containing Chr, start position, end position and spike-in normalized counts.

organism: Arabidopsis thaliana

source_name: 5-day-old seedlings

growth_protocol: Arabidopsis used in this study were in the Columbia-0 (Col) ecotype. The det1-1 Arabidopsis lines have previously been described (Chory et al., 1989).

extract_protocol:
Chromatin extraction and immunoprecipitation were carried out as in Bourbousse et al., 2012. Chromatin was extracted from Arabidopsis seedlings and S2 Drosophila cells. 100μg of Arabidopsis chromatin was mixed with 3μg of Drosophila chromatin and immunoprecipitation was performed with an anti-H2Bub antibody (MM-0029-P, Medimabs).
The resulting DNA then was used for library preparation with Illumina ChIP-Seq TruSeq kit. The ChIP libraries were sequenced in SE50 mode on a NextSeq High machine.

treatment_protocol: Light (L): Seedlings were grown under a 16h/8h (23/19°C) light/dark photoperiod (100 μmol.m−2.s−1); Dark (D): Seedlings were grown under a 16h/8h (23/19°C) in constant darkness.

tag: ecotype/background

value: 5 days

tag: tissue

value: seedling

tag: treatment

value: Dark

tag: chip antibody

value: anti-H2Bub (MM-0029-P, Medimabs)


title: det1-1_L_rep2_IP

description: ChIP DNA

tag: genotype/variation

tag: age

value: Light


title: scTrioSeq2Met_CRC15_ML5_230

description: single cell DNA methylome seq


title: det1-1_L_rep1_IP

description: ChIP DNA


title: WT_D_rep1_IP

description: ChIP DNA

value: wild-type


title: WT_D_rep2_IP

description: ChIP DNA


title: det1-1_D_rep2_IP

description: ChIP DNA


title: IgM-MGUS1_C01

status: Public on Nov 17 2018

city: Rochester

first: Jie

state: MN

address: 200 First Street SW

institute: Mayo Clinic

data_processing:
Basecalls performed using Illumina bcl2fastq2 versions bcl2fastq-1.8.4 (before therapy) and 2.17.1.14 after therapy)
Sequence reads were aligned to the hg19 genome assembly using TopHat2
Raw and normalized gene counts (RPKM) are generated by Featuregenecounts
Raw gene counts are converted to TPM
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

molecule: polyA RNA

source_name: plasma cells from perpheral blood

extract_protocol: Bone marrow aspirates were collected from 15 patients after informed consent and subjected to ACK lysis and mononuclear cell isolation. Plasma cells were separated by positive selection using CD138 coated magnetic beads (MACS; Miltenyi Biotec, CA) in a RoboSep system (STEMCELL Technology, Canada). CD138 positive cells were examined using Vi-CELL XR (Beckman Coulter, CA) to determine cell number, viability and average size. A microfluidic mRNA-Seq chip (Fluidigm, CA) was used for capturing cells from each sample at a concentration of 500 cells/μl and run in the Fluidigm C1 system to  generate double stranded cDNA using SMARTer Ultra Low RNA kit for Illumina (Takara, CA).  All samples were assessed for cell capture in a C1 chip by direct observation under a microscope and for cDNA quality using Fragment Analyzer (HS Large Fragment kit, Advanced Analytical Technologies, IA).

tag: tumor stage

value: IgM-MGUS

tag: patient


title: det1-1_D_rep1_input

description: Input DNA


title: WT_L_rep1_IP

description: ChIP DNA


title: det1-1_D_rep2_input

description: Input DNA


title: det1-1_L_rep2_input

description: Input DNA


title: det1-1_L_rep1_input

description: Input DNA


title: WT_D_rep2_input

description: Input DNA


title: WT_D_rep1_input

description: Input DNA


title: WT_L_rep2_input

description: Input DNA


title: det1-1ubp22_L_rep2

description: mRNA

data_processing:
Illumina CASAVA 1.8 software used for basecalling and demultiplexing.
Read Filtering and Mapping: RNA sequencing data were aligned to TAIR10 reference genome using STAR with the following configurations --outFilterMismatchNmax 2 --outFilterMultimapNmax 1000 --alignIntronMin 20 --alignIntronMax 6000.
RNA-seq Analysis: Raw read counts and RPKMs for genes were based on TAIR10 gene models. Expression levels of individual genes were obtained using HTSeq tool and for each gene the RPKM (Reads Per Kilobase Million) was calculated. Differential expression analysis was performed using DESeq2.
Genome_build: TAIR10
Supplementary_files_format_and_content: *.tsv: Tab-separated text files are output files from DESeq2.

growth_protocol: Arabidopsis used in this study were in the Columbia-0 (Col) ecotype and grown for 5 days on MS medium 0.9% agar without sugar. The det1-1 Arabidopsis lines have previously been described (Chory et al., 1989). The ubp22-1 mutant corresponds to the line GABI_263H06. The double mutant det1-1ubp22-1 was generated by crossing.

extract_protocol:
Total RNAs from ~12 seedlings were extracted using the Quick-RNA MiniPrep kit (Zymo). 1µg of RNA was used for library preparation.
The resulting cDNA then was used for library preparation with Illumina TruSeq stranded RNA library preparation (polyA-enrichment). The RNA libraries were sequenced in SE50 mode on a NextSeq 500 machine.


title: det1-1ubp22_L_rep1

description: mRNA


title: WT_L_rep1_input

description: Input DNA


title: det1-1_L_rep1

description: mRNA


title: WT_L_rep2_IP

description: ChIP DNA


title: det1-1_L_rep2

description: mRNA


title: ubp22_L_rep2

description: mRNA


title: ubp22_L_rep1

description: mRNA


title: WT_D_rep2

description: mRNA


title: det1-1_D_rep2

description: mRNA


title: WT_L_rep2

description: mRNA


title: WT_D_rep1

description: mRNA


title: M2-2

status: Public on Jun 15 2018

city: Hefei

first: Hengsheng

last: Wang

address: Changjiang Rode 130

institute: Anhui Agriculture University

data_processing:
The raw sequencing reads from all the runs were first trimmed for lo- quality regions and adapter  sequences. Reads containing N (indicating uncertain base information) greater than 10% were removed, and low quality reads were removed. Clean reads (~90% of the total read count) were mapped to the maize genome (B73_RefGen_v4 annotation build, http://plants.ensembl.org/Zea_mays/Info/Index) and a recent internal maize transcriptome using Tophat 2 with default parameters (Pertea 2010). The DESeq Bioconductor package (Version: 1.28.0) was used to normalize the mapped reads. Data quality analysis was evaluated by visualizing the results of principal component analysis (PCA).
The mapped sequence reads for all of the identified genes were used for differential expression analysis by the DESeq method. Using Cufflinks 2.2.1 and Cuffdiff, gene expression levels were calculated as reads per kilobase of transcript sequence per million base pairs sequenced (FPKM) (Trapnell et al. 2016). Based on statistical analyses, genes with a P-value < 0.05 and an absolute value |log2 ratio ≥ 1| were considered to be significant differentially expressed genes (DEGs). GO enrichment analysis was conducted using Blast2GO (https://www.blast2go.com/) with FDR < 0.05. Based on their expression patterns, the DEGs were clustered by the Genesis K-means method
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.

organism: Zea mays

source_name: Stem from big flare period of middle hybrid

growth_protocol: Three different maize hybrids, with extremely distinct plant height, which were further classified into low (L), middle (M) and high (H) group, were selected for RNA sequencing at three key developmental stages, namely, jointing stage (I), big flare period (II) and tasseling stage (III).

extract_protocol:
1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.  1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR. Sequencing was performed using 12pM hybridization to a 2x100 paired end flow cell.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Eighteen samples from the low, middle and high hybrid at three development stages were used for RNA sequencing.

value: Stem

tag: developmental stage

value: big flare period

tag: hybrid/phenotype

value: middle (M, Dan 598xCML444)


title: L2-2

source_name: Stem from big flare period of low hybrid

value: low (L, Dan 598xFAPW)


title: WT_L_rep1

description: mRNA


title: M3-2

source_name: Stem from tasseling stage of middle hybrid

value: tasseling stage


title: L1-2

source_name: Stem from jointing stage of low hybrid

value: jointing stage


title: 20EM-2

status: Public on Aug 11 2017

city: hefei

first: xing

middle: yong

last: chen

state: anhui

address: 130 West Changjiang Road

department: School Of Animal Science And Technology

institute: Anhui Agricultural University

data_processing:
The small RNA sequence reads were pre-processed using FASTXToolkit (fastx_toolkit-0.0.13.2; http://hannonlab.cshl.edu/fastx_toolkit/commandline.html), excluding low-quality reads (ambiguous N, quality < 10 nt, and length <18 nt) as well as 3′ adapter, 5′adapter and poly(A) sequences.
Further annotation analyses were performed using the commercial software CLC Genomic Workbench 5.5.
Briefly, the resulting clean reads were aligned against various databases, including ncRNA, piRNA, and Rfam, allowing a maximum mismatch of 2 nt to remove noncoding RNA, such as rRNA, tRNA, snRNA, and snoRNA.The remaining sequences were analyzed by BLAST Gallus gallus search against Sanger miRBase (version 21.0).
Reads that did not match any database above were marked as non-annotation. Non-annotated sequences were searched against the Gallus gallus genome using the miRCat program included in the sRNAToolkit (http://srna-workbench.cmp.uea.ac.uk/tools/analysis-tools/mircat/). Using default settings, 100 nucleotides of genomic sequence flanking each side of the sequences were extracted for RNA secondary structure prediction using RNAfold [1]. Only with tipical stem-loop hairpins and the free energy lower than -20 kcal/mol could be considered to be potential novel miRNAs.
Normalize the expression of miRNA in eighteen libraries to get the expression of transcript per million (TPM). Normalization formula: Normalized expression = Actual miRNA count/Total count of clean reads×1000000.
Genome_build: Gallus gallus
Supplementary_files_format_and_content: miRNA reads count

organism: Anas platyrhynchos

source_name: 20EM rep2

extract_protocol:
Total RNA was extracted from the tissue using a mirVana miRNA Isolation Kit (Ambion, USA). The purified RNA yield was determined by the absorbance at 260 nm with an ND-2000 NanoDrop spectrophotometer (Thermo Fisher, USA), and RNA quality was evaluated with a BioAnalyzer 2100 system (Agilent Technologies, USA).
RNA smaller than 200 base pairs (bp) was enriched with the mirVana miRNA isolation kit (Ambion). The RNA was then precipitated with ethanol and dissolved in water. Small RNAs had linkers ligated to them and bar-coded cDNAs were prepared using a TruSeq Small RNA Sample Prep Kit (Illumina, USA) following the manufacturer’s instructions.

value: 20 embryonic day

value: skin

tag: breed

value: Pekin Duck


title: 20EM-3

source_name: 20EM rep3


title: det1-1_D_rep1

description: mRNA


title: 10WK-2

source_name: 10WK rep2

value: 10 week of age


title: 0dpc_1

status: Public on Jul 03 2018

city: Delhi

first: Beena

last: Pillai

address: Mathura Road

country: India

institute: IGIB

data_processing:
The quality of RNA sequencing reads were checked using FastQC followed by adapter trimming by Trimmomatic (default parameters) .
The data was then de novo assembled using Trinity package (Grabherr et al., 2011). to align reads to the reference. To get a common reference, all the samples were assembled together in a single assembly using Trinity.
The assemblies were annotated using Trinotate pipeline (https://trinotate.github.io/).
Denovo RNA seq differential expression analysis was done using reference made by Trinity and Tuxedo pipeline.
Genome_build: To get a common reference, all the samples were assembled together in a single assembly using Trinity and annotated by Trinotate.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Eisenia fetida

source_name: Three segments around the 60th segment (from anterior)

growth_protocol: Eisenia fetida earthworms were procured from farmers engaged in vermicomposting and then maintained in a culture in the laboratory at around 22oC with moderate humidity.

extract_protocol:
The regenerated tissue and the tissue adjacent to it, termed control, were collected separately. RNA was isolated using the Trizol method. Briefly, the tissues were frozen in liquid nitrogen, homogenized using a mortar and pestle in the presence of 1ml Trizol reagent and transferred to a microfuge tube. Phase separation was done by adding 200uL chloroform and centrifugation at 10,000g. The aqueous phase was collected and equal volume of isopropanol was added to precipitate RNA. Pellet was collected by centrifugation at 10,000g, followed by repeated 70% ethanol washes. The RNA was then air dried and dissolved in nuclease-free water
Approximately, 1ug of RNA was taken per sample and RNA sequencing libraries were made using TruSeq v2 Library Prep Kit as per manufacturer's protocol. Briefly, the RNA was polyA selected using OligodT magnetic beads followed by shearing into 200-500bp fragments. This sheared RNA was then used to generate cDNA. The cDNA was end-repaired to blunt ends . These blunt ends were then A-tailed i.e. a "A" overhang was added so as to ligate the adapters in the next step. The adapter ligated cDNA was then amplified by PCR and purified by AMPure XP beads. This library was then quality checked and sequenced on Illumina HiSeq 2500. For small RNA sequencing, total RNA was isolated from bodywall and sequenced on the illumina platform. ~800ng of Total RNA was used as the starting material. Briefly, 3’ adaptors were ligated to the   specific 3’OH group of microRNAs followed by 5’ adaptor ligation. The ligated products were  reverse transcribed with Superscript III Reverse transcriptase by priming with Reverse   transcriptase primers. The cDNA was enriched and barcoded by PCR (15 cycles) and   cleaned using Polyacrylamide gel. The library was size selected in the range of 140 – 160 bp   followed by overnight gel elution and salt precipitation using Glycogen, 3M Sodium Acetate and absolute ethanol. The precipitate was re-suspended in Nuclease free water. The prepared library was quantified using Qubit Fluorometer, and validated for quality on High Sensitivity Bioanalyzer Chip (Agilent).

treatment_protocol: Earthworms were cut transversely at approximately two thirds of the body length (60 +/- 6 segments) and allowed to regenerate for 15, 20 or 30 days . At 15, 20 and 30 days post cut (dpc), the regenerated tissue (15R,20R and 30R) and the adjacent tissue (15C, 20C and 30C) were collected.  Samples from non-regenerating worms were collected from the 60th+3segments (control) on day0. One set of samples (sample 22-24) are segments 60-posterior end collected on day0.

tag: number of worms

value: pooled from 50 worms

tag: type of tissue

value: Tissue collected immediately after cutting for regeneration experiment.


title: PGC-1α null sample 1

status: Public on Jun 27 2017

type: RNA

city: Birmingham

first: Rita

middle: M

last: Cowell

state: AL

address: 2000 9th Avenue South

department: Neuroscience

institute: Southern Research

description:
8129677053_E
Replicate 1

hyb_protocol: Stained with strepavidin-Cy3 for visualization

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was analyzed in GenomeStudio. Gene lists were created in Gene Spring and analyzed with Ingenuity Pathway Analysis. WEB-based Gene SeT AnaLysis Toolkit was used to determine transcription factor sequence enrichment for downregulated genes and for gene ontology

label: Biotin

source_name: mouse brain striatum

label_protocol: cDNA was generated then converted to cRNA and biotin labels were added

growth_protocol: housed two to five in a cage at 26 +/- 2°C room temperature with food and water ad libitum

extract_protocol: Tissue was flash frozen at -80°C until use when they were incubated in RNALater-ICE then isolated with Trizol. RNA concentration and purity was determined with a NanoDrop 2000

treatment_protocol: aged to P30

tag: strain

value: PGC-1α null

value: striatum

tag: cell type

value: medium spiny neurons

tag: background strain


title: PGC-1α null sample 3

description:
8129677053_G
Replicate 3


title: PGC-1α wild type sample 1

description:
8129677053_A
Replicate 1

value: PGC-1α wild type


title: PGC-1α wild type sample 4

description:
8129677053_D
Replicate 4


title: PGC-1α null sample 2

description:
8129677053_F
Replicate 2


title: PGC-1α wild type sample 2

description:
8129677053_B
Replicate 2


title: PGC-1α wild type sample 3

description:
8129677053_C
Replicate 3


title: SHSY5Y PGC-1a/GFP Adenovirus 3

status: Public on Jun 23 2017

description:
Replicate 3
F

data_processing: Data was analyzed in GenomeStudio. Genes that were upregulated were compared with Allen Brain Atlas's Neuroblast feature against neuron specific genes.

source_name: SHSY5Y Cell Culture

growth_protocol: Grown in standard media at 37°C under standard conditions to confluency

extract_protocol: RNA was isolated with Trizol and purified with RNease MinElute Cleanup kit. RNA was adjusted to 200 ng/ul.

treatment_protocol: infected with adenovirus for 48 hours

tag: virus


title: SHSY5Y GFP Adenovirus 2

description:
Replicate 2
B

value: GFP


title: SHSY5Y PGC-1a/GFP Adenovirus 1

description:
Replicate 1
D


title: SHSY5Y GFP Adenovirus 1

description:
Replicate 1
A


title: Tiirats4

status: Public on Aug 01 2016

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

data_processing:
Color-space base calling
Mapping, alignment with Lifescope
Lifescope transcriptome workflow
Genome_build: hg19

source_name: blood

growth_protocol: blood sample

extract_protocol:
Tempus blood kit
RNA was amplified with Ovation RNA-Seq System V2 Kit (NuGen, Emeryville, CA, USA) and the output double stranded DNA was used to prepare SOLiD 5500 W System DNA fragment library according to manufacturer’s protocols (Thermo Fisher Scientific Inc, Waltham, MA, USA). The barcoding primers in library preparation and fragment sequencing chemistry was applied (75 bp in forward directions). In case of 12 samples per flowchip lane approximately 33 million mappable reads were expected per one sample, which would be enough for successful whole transcriptome expression pattern analysis.
fragment

treatment_protocol: case-control design

tag: hypotrophy

value: case

tag: Sex

value: M

tag: relation

value: son


title: SHSY5Y PGC-1a/GFP Adenovirus 2

description:
Replicate 2
E


title: PGC-1α null sample 4

description:
8129677053_H
Replicate 4

tag: tissue


title: SHSY5Y GFP Adenovirus 3

description:
Replicate 3
C


title: PAH044 9611518137_R02C02

status: Public on May 01 2016

type: genomic

city: Brisbane

first: Katia

last: Nones

state: QLD

address: 300 Herston Road

institute: QIMR Berghofer MEdical Research Institute

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol, iScan

data_processing: Methylation data was background subtracted in GenomeStudio and normalized by beta-mixture quantile (BMIQ) normalization to adjust for the type II bias. Normalization was done using the waterRmelon Bioconductor R package (Pidsley R, CC YW, Volta M, Lunnon K, Mill J, Schalkwyk LC. A data-driven approach to preprocessing Illumina 450K methylation array data. BMC genomics. 2013;14:293)

label: Cy3 and Cy5

source_name: Tumour

label_protocol: standard Illumina protocol

extract_protocol: Most DNA extractions were performed via the phenol-chloroform-isoamyl alcohol method [Maniatis T, Fritsch E, Sambrook J. Molecular cloning: A laboratory manual] a small set of 22 tumors/matched normal DNA was extracted AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA).

value: Tumour


title: PAH001 7539308063_R06C01


title: PAH017 7539308045_R03C02


title: PAH008 7539308063_R05C02


title: SOG007 7539308117_R03C01


title: PAH009 7539308063_R06C02


title: PAH023 7507875012_R01C02


title: SOG067 3999876157_R05C01


title: SOG115 3999876157_R05C02


title: PAH013 7539308045_R04C02


title: SOG070 3999876157_R06C01


title: PAH034 7539308080_R02C02


title: SOG027 3999876086_R06C02


title: SOG032 3999876021_R05C02


title: PAH040 3999876164_R03C02


title: PAH041 7539308080_R06C02


title: SOG132 3999876164_R01C01


title: PAH014 7507875012_R03C02


title: PAH031 7507875012_R05C01


title: PAH015 7507875012_R04C02


title: PAH025 7507875012_R02C01


title: SOG089 3999876020_R06C01


title: SOG138 3999876164_R04C01


title: SOG082 3999876020_R02C01


title: SOG100 3999876157_R01C02


title: SOG087 3999876020_R05C01


title: SOG064 3999876157_R04C01


title: Low Risk_560-138790

status: Public on Nov 23 2015

city: Durham

first: Deborah

middle: A

last: Lewis

state: NC

address: 201 Trent Dr

institute: Duke University Medical Center

hyb_protocol: Standard Illumina hybridization protocol

data_processing: A comprehensive quality control process was performed on all arrays using the lumi package (version 2.6.0) in Bioconductor in the R environment  (version 2.14.0) for statistical computing.  Quality of the raw data was assessed using the percent of probes present, MA plots, boxplots of the expression distribution, and heatmaps to visualize the correlation between samples.  Samples in which the percent of probes present was 15% or less were excluded. The lumi package was used to make background corrections, log-transform expression values, and carry out quantile normalization.

label: biotin

source_name: Low Risk_whole blood

label_protocol: RNA was amplified and the cRNA was biotinylated using the Ambion Illumina TotalPrep RNA Amplification Kit (Life Technologies, Carlsbad, CA).

extract_protocol: Total RNA was isolated from whole blood drawn into PAXgene tubes using the PAXgene Blood RNA kit (PreAnalytiX; Qiagen GmbH-USA).  The quality and quantity of the RNA was confirmed using the Nanodrop 1000 Spectrophotomer (Thermo Fisher Scientific, Wilmington, DE) and by RT PCR.

tag: phenotype/group

value: Low Risk

value: whole blood


title: SOG036 3999876086_R02C01


title: Low Risk_560-138509


title: SOG039 3999876086_R03C01


title: Low Risk_560-138472


title: SOG028 3999876021_R01C02


title: Low Risk_560-138466


title: Low Risk_560-138506


title: SOG091 3999876020_R01C02


title: Low Risk_285-02605


title: Low Risk_560-841


title: Low Risk_560-138445


title: Low Risk_560-133382


title: SOG081 3999876020_R01C01


title: SOG065 3999875096_R06C01


title: Low Risk_560-138510


title: SOG078 3999875096_R06C02


title: Low Risk_285-00668


title: Low Risk_285-02568


title: Low Risk_560-138517


title: Low Risk_560-138450


title: Low Risk_560-133441


title: Low Risk_262-00772


title: Low Risk_560-138448


title: Low Risk_054-00604


title: Low Risk_262-00782


title: Low Risk_560-133424


title: Low Risk_054-00611


title: Low Risk_560-129959


title: Low Risk_560-138452


title: Low Risk_262-00716


title: Low Risk_054-00587


title: Low Risk_262-00706


title: Low Risk_262-00709


title: Low Risk_054-00599


title: Low Risk_560-133379


title: Low Risk_054-00431


title: Low Risk_054-00549


title: Low Risk_054-00099


title: High Risk_560-139568

source_name: High Risk_whole blood

value: High Risk


title: High Risk_560-139599


title: High Risk_560-138848


title: High Risk_560-138446


title: High Risk_560-138791


title: High Risk_560-139524


title: High Risk_560-138830


title: High Risk_560-138823


title: High Risk_560-129115


title: High Risk_560-138762


title: High Risk_560-127537


title: High Risk_285-02625


title: Low Risk_560-133364


title: High Risk_560-133426


title: High Risk_560-105670


title: High Risk_285-02598


title: High Risk_560-102342


title: High Risk_285-02313


title: High Risk_285-02610


title: High Risk_285-02110


title: High Risk_285-02584


title: High Risk_285-02421


title: High Risk_285-01413


title: High Risk_285-02627


title: High Risk_560-107614


title: High Risk_560-102389


title: Low Risk_262-00787


title: High Risk_560-127543


title: High Risk_285-01396


title: High Risk_285-02299


title: High Risk_285-00711


title: High Risk_285-00693


title: High Risk_285-00330


title: High Risk_285-00132


title: High Risk_285-01781


title: High Risk_285-00316


title: High Risk_285-01304


title: High Risk_054-00575


title: High Risk_262-00778


title: High Risk_285-00119


title: High Risk_262-00743


title: Healthy Control_560-138792

source_name: Healthy Control_whole blood

value: Healthy Control


title: Healthy Control_560-138787


title: High Risk_285-00677


title: Healthy Control_560-138475


title: Healthy Control_560-138783


title: Healthy Control_560-138469


title: Healthy Control_560-138521


title: Healthy Control_560-138807


title: Healthy Control_262-015


title: Healthy Control_560-138784


title: Healthy Control_560-138747


title: Healthy Control_560-138478


title: Healthy Control_262-006


title: Healthy Control_262-011


title: Healthy Control_262-013


title: Healthy Control_262-012


title: Healthy Control_560-138547


title: Healthy Control_262-004


title: Healthy Control_560-130171


title: Healthy Control_262-003


title: Healthy Control_262-002


title: Healthy Control_262-009


title: Healthy Control_262-005


title: Healthy Control_054-004


title: Healthy Control_054-001


title: Medulloblastoma #447

status: Public on Sep 02 2008

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

hyb_protocol: 10 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol.

data_processing: Expression data (.cel files) were normalized with the MAS5 algorithm (target signal = 100) using GCOS software (Affymetrix). Data from the duplicate arraying experiments were averaged and further analyzed.

source_name: tumor

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 μg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer's protocol.

tag: Gender

value: F

tag: Histology

value: Classic

tag: Metastatic stage


title: Medulloblastoma #338

value: Desmoplastic


title: Medulloblastoma #316


title: Medulloblastoma #318


title: Medulloblastoma #335


title: Medulloblastoma #315


title: Medulloblastoma #446


title: Medulloblastoma #332


title: Medulloblastoma #339


title: Medulloblastoma #325


title: Medulloblastoma #440


title: Medulloblastoma #313


title: Medulloblastoma #312


title: Medulloblastoma #334


title: Medulloblastoma #337


title: Medulloblastoma #311


title: Healthy Control_560-138810