title: C166: Tumor tissue


title: spleen_naiv_ko_8

status: Public on Mar 02 2016

type: SRA

city: Leipzig

first: Torsten

last: Schöneberg

address: Johannisallee 30

department: Institute of Biochemistry, Medical Faculty

country: Germany

institute: Leipzig University

library_source: transcriptomic

data_processing:
basecalling using freeIBIS
adapter were trimmed and reads were merged
reads were mapped using tophat 1.3.3 and bowtie 0.0.9v
aligned reads were filtered for quality (samtools view -q 255) and all reads mapping to the mitochondria genome were removed
readcounts were retrieved using intersectBED
differential expression analysis was performed using the Deseq package
Genome_build: mm9
Supplementary_files_format_and_content: readcounts are provided as space delimited text files for each sample

molecule: total RNA

organism: Mus musculus

source_name: Spleen

growth_protocol: Bone marrow was isolated from femurs and tibiae of 8–16 week old male WT or KO mice. 4x106 cells were plated and further cultivated for 10 days at 37°C in a humidified atmosphere containing 5% CO2 in a 3:2 mixture of RPMI 1640 supplemented with 10% heat-inactivated FBS, 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, 50 μM β-mercaptoethanol and a supernatant from a GM-CSF secreting X63 cell line.

extract_protocol:
Total RNA was extracted from DC cultures and spleen samples using the TRI REAGENT™ according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Dcs were harvested on day 10 and seeded (3x106 cells in 2.5 ml serum-free RPMI 1640) in 6-cm dishes. On day 11, Dcs were incubated with LPS for 8 h.

tag: cell type

value: Spleen

tag: strain

tag: age

value: 12 weeks

tag: genotype


title: spleen_naiv_ko_7


title: spleen_naiv_ko_6


title: 3pRR-R

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
STAR_2.4.0a paired-end mapping versus mm10.
FeatureCounts transcripts quantification (subread-1.4.6-p1-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M " options and Mus_musculus.GRCm38.77 Ensembl GTF annotation file.
Kallisto v0.42.3 transcripts quantification with Ensembl release 79 GTF file.
Genome_build: mm10
Supplementary_files_format_and_content: featurecounts_table.txt: raw counts from featureCounts (subread-1.4.6-p1-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M " options and Mus_musculus.GRCm38.77 Ensembl GTF annotation file. Kallisto_estcounts_table.txt: estimate counts produce with kallisto v0.42.3 with Ensembl release 79 GTF file. Kallisto_tpm_table.txt: transcript counts per million produce with kallisto v0.42.3 with Ensembl release 79 GTF file. BigWig files has been generated using samtools to discriminate expression strand for paired-end reads then genomeCoverageBed and bedGraphToBigWig from bedtools 2 suite.

source_name: lymphoid tissue

extract_protocol:
Total RNA was extracted using miRNeasy kit (Qiagen) from either freshly purified splenic B cells, obtained after gradient separation using Lympholyte Mammal (Cedarlane) followed by CD43 negative selection (Miltenyi Biotec), or from purified splenic B cells stimulated in vitro (106 cells m/L) for 48 hours in RMPI 1640 medium (Lonza) supplemented with 10% fetal calf serum (Lonza) and with 5µg/mL LPS (Cayla Invivogen), separated on a Lympholyte Mammal gradient. For each genotype (wt, 3’PALD/D, hs3b-4D/D, 3’RRD/D), RNA sample was prepared from a pool of equivalent numbers of purified B cells from 4 animals
1 µg of total RNA were depleted from ribosomal RNA, ligated, reverse transcribed and amplified (14 cycles) with the reagents from the truseq stranded total RNA kit (illumina). Libraries were quantified with the Bioanalyzer DNA 1000 Kit (Agilent). 4nM of libraries were then diluted and denatured according to the Illumina recommendations.  Paired-end 150-bp reads were sequenced on an Illumina Nextseq 500 sequencer.

value: Resting B cells from the spleen

tag: passages

value: Sorted (CD43 negative) primary cells

value: mixed background 129/C58BL/6

value: homozygous 3'RR KO animals, ref Vincent-Fabert C et al. Blood. 2010 Sep 16;116(11):1895-8. doi:10.1182/blood-2010-01-264689.


title: C152: Tumor tissue

city: Edmonton

first: Sambasivarao

last: Damaraju

state: Alberta

address: 11560 University Ave

department: Laboratory medicine and pathology

country: Canada

institute: University of Alberta

description: Genomic small RNA (size selected from total RNA)

data_processing:
Base calling and demultiplexing were done using CASAVA 1.8.2 with default settings
Trimming of adapters using cutadapt software (http://code.google.com/p/cutadapt/). Options were given to retain sequences longer than 17 nucleotides. Quality trimming was performed to retain only reads with a Sanger quality score cut-off of 30
Quality of the sequenced reads after adapter trimming was assessed using FASTQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Trimmed sequences were then aligned to the reference genome using Bowtie (31) and allowed a maximum of 2 mismatches. Human, hg19 genomic assembly (UCSC) downloaded from Illumina iGenome repository was used as a reference for mapping
.bam files were analyzed using Partek Genomics Suite 6.6
Data was normalized using Reads per Kilobase per Million (RPKM)
Genome_build: hg 19, miRBAse v 20 for annotating miRNAs
Supplementary_files_format_and_content: tab-delimited txt files containing RPKM normalized values of all miRNAs before batch correction for normal and tumor tissues

organism: Homo sapiens

source_name: Breast

growth_protocol: Normal tissues were preserved as Fresh frozen tissues and tumor tissues were preserved as FFPE tissue blocks

extract_protocol:
Total RNA from FF tissues (normal) was isolated using TRIzol and Qiagen RNeasy kit according to manufacturer’s instructions. Total RNA from FFPE blocks was isolated using RecoverAll Total Nucleic Acid Isolation Kit (Life Technologies). RNA quality and quantity were analyzed with Bioanalyzer 2100 and RNA Nano Chips (Agilent Technologies).
Small RNAs were sequenced using TruSeq Small RNA Sequencing Kit (Illumina), TruSeq SR Cluster Kit v5-CS-GA (Illumina), and TruSeq SBS Kit v5-GA (Illumina) according to manufacturer’s instructions. All the samples were sequenced on Illumina Genome Analyzer IIx with 36 cycles single end protocol.

tag: tissue

value: Surgically resected tumor

tag: preservation type

value: Formalin fixed paraffin embedded (FFPE)

tag: tissue type

value: Invasive Ductal Carcinoma

tag: breast cancer subtype

value: Luminal A

tag: batch id

value: III


title: C140: Tumor tissue


title: C165: Tumor tissue


title: C135: Tumor tissue


title: spleen_naiv_ko_4


title: spleen_naiv_ko_5


title: C139: Tumor tissue


title: spleen_naiv_ko_2


title: C131: Tumor tissue

value: TNBC


title: C108: Tumor tissue

value: II


title: C1010: Tumor tissue

value: IV


title: spleen_naiv_ko_1


title: BM01-5: Tumor tissue


title: spleen_naiv_wt_9

value: wildtype


title: spleen_naiv_wt_10


title: BM01-29: Tumor tissue


title: spleen_naiv_wt_8


title: BM01-27: Tumor tissue


title: BM01-15: Tumor tissue


title: spleen_naiv_wt_6


title: spleen_naiv_wt_5


title: spleen_naiv_wt_7


title: spleen_naiv_ko_3


title: Scr

city: Durham

first: Jun

last: Wang

state: North Carolina

address: 308 Research Drive LSRC C231

department: Pharmacology and Cancer Biology

country: USA

institute: Duke University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg18 whole genome using tophat
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cuffdiff based on the protocol Cole Trapnell et al. Nature Biotechnology 31, 46-53 (2013)
Genome_build: hg18
Supplementary_files_format_and_content: diff files include RPKM values for each Sample

source_name: breast cancer cells

growth_protocol: 1833 cells were cultured in DMEM with 10% FBS

extract_protocol:
RNA was harvested using Qiagen Rneasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1833 cells were incubated 48 h with lentiviral medium containing Scr, or miAbl, or miArg or miAA microRNA in the presence of 8ug/mL Polybrene.

tag: cell line

tag: subtype

value: Triple negative

tag: metastasis

value: Bone metastasis

tag: knockdown

value: Scramble


title: miAbl

value: Abl


title: spleen_naiv_wt_4

value: Spleen

value: 12 weeks


title: miArg

value: Arg


title: MT5049_V02: Normal tissue

value: Reduction mammoplasty

value: Fresh frozen (FF)

value: Normal


title: MT5048_V02: Normal tissue


title: spleen_naiv_wt_3


title: spleen_naiv_wt_1


title: BM01-13: Tumor tissue

value: Surgically resected tumor

value: Formalin fixed paraffin embedded (FFPE)

value: Invasive Ductal Carcinoma


title: DGM-POU2AF1-Lenti-POU2AF1-repeat-3

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description:
Human tracheal basal cells were obtained from Lonza
DGM-POU2AF1-Lenti-POU2AF1-3

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Expression analysis was performed using Bowtie2 (v2.1.0.0, http://bowtie-bio.sourceforge.net), Tophat (v2.0.8, http://tophat.cbcb.umd.edu) and Cufflinks (v2..2.0, http://cufflinks.cbcb.umd.edu)
To correct for transcript length and depth of coverage raw paired-end sequenced reads were converted into fragments per kilobase of exon per million fragments sequenced (FPKM) resulting in the fpkm_tracking files.
Resultant fragments were aligned (mapped) to the reference genome build UCSC hg19 using Bowtie2
Non-aligned reads were segmented using Tophat and re-aligned to the genome, aligning reads that span introns and determining junction splice sites. Cufflinks assembled reads into transcripts and assembled reads merged using Cuffmerge; the reads generated from a transcript are directly proportional to the transcripts relative abundance. For the analysis, Tophat (which automatically runs Bowtie) was run for each read pair in a given lane
For each read pair, Tophat produced one file which contained all reads mapped to the human_g1k_v37 genome and RefSeq (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz) transcriptome
This process was carried out independently for each sample lane. Before running Cufflinks, Samtools (v0.1.19.0, http://samtools.sourceforge.net) was used to merge each sample's independent Tophat results into one file. This file contains all the aligned reads for each read pair. Finally Cufflinks was run on the merged Tophat output to produce a file with FPKM values for each sample
Genome_build: hg19
Supplementary_files_format_and_content: fpkm_tracking files are text files that include the RefSeq gene ID and location, the FPKM value, high and low confidence and status.

source_name: Lonza cells

growth_protocol: Lonza airway basal cells were cultured in 24 well plate and then infected with lenti-POU2AF1 or lenti-RFP. Uninfected basal cells were used as control.  After 72 hr infection samples were collected.

extract_protocol:
Total RNA from treated and untreated basal cells was extracted with TRIzol with subsequent RNA clean-up using the RNeasy MinElute RNA purification kit to remove residual DNA
The TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) was utilized as per protocol to generate cDNA that was then purified with QIA-quick PCR purification kit (Qiagen, Valencia, CA)
Samples were loaded onto an Illumina flowcell for paired-end 101 x 2 sequencing reactions using the Illumina HiSeq 2000, using a single flow cell with 4 samples multiplexed per lane of flow cell.

value: tracheal basal cells

tag: infection

value: infected with lenti-POU2AF1 virus


title: MT4974_V04: Normal tissue

value: III


title: repB_TP6

city: Heidelberg

first: Christophe

last: Chabbert

address: Meyerhofstrasse 1

institute: EMBL

description: 5' end capture

data_processing:
Library strategy: 5' cap sequencing
Illumina primers and molecular barcodes were trimmed using the HTSeq package in Python
Reads were aligned to the reference genome (v11) using GMAP (2012-03-23, allowing for the detection of new splicing junctions)
After filtering out multiple alignments, molecular barcodes were used to identify PCR duplicates
Reads were collapsed on their first based pair to be visualized in a bedgraph file
Genome_build: PlasmoDB-11.1_Pfalciparum3D7_Genome
Supplementary_files_format_and_content: Bedgraph format

organism: Plasmodium falciparum

source_name: schizont-stage parasite

growth_protocol: P. falciparum strain 3D7 was propagated under standard conditions in RPMI-1640 medium with L-glutamine, supplemented with 50 mg/l hypoxanthine, 25 mM HEPES, 0.25% sodium bicarbonate, 0.01 mg/ml gentamicin and 0.5% Albumax II (Invitrogen, Carlsbad, CA, USA)

extract_protocol:
Total RNA was isolated as previously reported (Kyes at al, 2000).
RNA samples were then treated with Terminator 5‘-Phosphate-Dependent Exonuclease. rRNA-depleted RNA was treated with of Calf Intestinal Alkaline Phosphatase (New England BioLabs). CIP-treated RNA was then incubated with Tobacco Acid Pyrophosphatase andincubated overnight with RNA adapters and T4 RNA ligase. RNA was chemically fragmented and reverse transcribed. cDNA second strand was synthesised using biotinylated primers. DNA libraries were constructed using the standard Illumina protocol and amplified with the KAPA HiFi HotStart ReadyMix.

treatment_protocol: Parasites were synchronized by two consecutive treatments with 5% sorbitol timed 12 hours apart for three or more successive generations and allowed to recover for another parasite asexual blood stage cycle before initiating time point samplings for two biological replicates.

tag: hours post-invasion

tag: rna type

value: capped mRNA


title: spleen_naiv_wt_2

tag: cell type

value: wildtype


title: MT1537: Normal tissue


title: BM01-34: Tumor tissue

value: Luminal A

value: IV


title: MT1491: Normal tissue


title: DGM-POU2AF1-Lenti-POU2AF1-repeat-2

description:
Human tracheal basal cells were obtained from Lonza
DGM-POU2AF1-Lenti-POU2AF1-2


title: DGM-POU2AF1-Lenti-POU2AF1-repeat-1

description:
Human tracheal basal cells were obtained from Lonza
DGM-POU2AF1-Lenti-POU2AF1-1


title: MT1451: Normal tissue


title: DGM-POU2AF1-Lenti-RFP-repeat-3

description:
Human tracheal basal cells were obtained from Lonza
DGM-POU2AF1-Lenti-RFP3

value: infected with lenti-RFP virus


title: MT1345: Normal tissue


title: repB_TP4

description: 5' end capture

source_name: trophozoite-stage parasite

tag: strain


title: repB_TP3

description: 5' end capture


title: repB_TP5

description: 5' end capture


title: miAA

value: Triple negative

value: Bone metastasis

value: Both Abl and Arg


title: DGM-POU2AF1-Lenti-RFP-repeat-2

description:
Human tracheal basal cells were obtained from Lonza
DGM-POU2AF1-Lenti-RFP2


title: repB_TP2

description: 5' end capture

source_name: ring-stage parasite


title: MT1299: Normal tissue

value: Reduction mammoplasty


title: MT1261: Normal tissue

value: Fresh frozen (FF)


title: MT1273: Normal tissue

value: Normal


title: DGM-POU2AF1-Lenti-RFP-repeat-1

description:
Human tracheal basal cells were obtained from Lonza
DGM-POU2AF1-Lenti-RFP1


title: DGM-POU2AF1-Uninfected-repeat-3

description:
Human tracheal basal cells were obtained from Lonza
DGM-POU2AF1-Uninfected3

value: uninfected without treatment


title: DGM-POU2AF1-Uninfected-repeat-2

description:
Human tracheal basal cells were obtained from Lonza
DGM-POU2AF1-Uninfected2


title: MT1253: Normal tissue


title: repA_TP6

description: 5' end capture


title: DGM-POU2AF1-Uninfected-repeat-1

description:
Human tracheal basal cells were obtained from Lonza
DGM-POU2AF1-Uninfected1


title: repA_TP2

description: 5' end capture


title: dc_LPS_ko_4

source_name: Dendritic Cells

value: Bone marrow derived dendritic cells

tag: age

value: 8-16 weeks


title: repA_TP3

description: 5' end capture


title: repA_TP1

description: 5' end capture


title: dc_LPS_ko_3

tag: genotype


title: dc_LPS_wt_3


title: dc_LPS_ko_2


title: dc_LPS_wt_2


title: dc_LPS_wt_1


title: dc_naiv_ko_4


title: dc_naiv_ko_3


title: dc_naiv_ko_2


title: dc_naiv_wt_4


title: dc_naiv_wt_1


title: RNAseq-T-ALL_5

city: Montreal

first: Daniel

last: Sinnett

state: Quebec

address: 3175 Cote-Sainte-Catherine

institute: CHU Sainte-Justine

data_processing:
AB SOLID data:  Primary alignment with Lifescope software version 2.1
ILLUMINA data: Primary alignment with STAR
Mark duplicate with PICARD version 1.107
SplitNCigar with GATK version 3.2-2
Read counts using HTSeq version 0.6.1p1 with Ensembl GRCH37 version 75
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: Tumoral biospecimen

extract_protocol:
see Baccichet A, Qualman SK, Sinnett D. Allelic loss in childhood acute lymphoblastic leukemia. Leuk Res. 1997;21(9):817-23.
Total RNA was extracted from bone marrow samples at diagnosis for patients 432, 437, 547, 693, 716, 743, 744, 748, 791 and 849 using the mirVana Isolation kit (Ambion) according to the manufacturer’s protocol. The Allprep DNA/RNA Mini kit (Qiagen) was used for relapse samples in patients 791 and 879. For patient 744, mature RNA was also purified using the Ambion's MicroPoly(A)Purist kit (Small Scale mRNA Purification Kit P/N AM1919). Following a DNAse I treatment, total or mature RNA samples were quantified by NanoDrop ND1000 (Thermo-Fisher Scientific) and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent). Ribosomal ribonucleic acid (rRNA) were depleted using the Invitrogen RiboMinus Eukaryote kit (Life Technologies). cDNA libraries were prepared using the SOLiD Total RNA-seq kit (diagnosis samples) and the Illumina TruSeq Stranded Total RNA kit (relapse samples) based on manufacturer’s protocol and sequenced on the Life Technologies SOLiD 5500 System or the Illumina HiSeq 2500 System.

value: Bone marrow

tag: age diagnosis (month)

tag: patient id


title: dc_naiv_wt_2


title: repB_TP1

description: 5' end capture


title: BCPAP-Prx_Dox

city: Los Angeles

first: Young-Kwon

last: Hong

state: CA

address: 1450 Biggy St. NRT6501

institute: University of Southern California

data_processing:
Raw data files in FASTQ format was analyzed with Illumina BaseSpace
TopHat algorithm was used to align the raw reads to human hg19 genome assembly
Cufflinks was used to quantify the aligned reads and to analyze differentially expressed genes
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited gene.fpkm_tracking files include FPKM values generated by the Cufflinks algorithm

source_name: Dox-treated sample

growth_protocol: The cells were grown in standad culture media (DMEM containing 10% Fetal Bovine Serum and antibiotics)

extract_protocol:
Cells were collected directly into Trizol lysis buffer (Sigma-Aldrich) and total RNA was immediately extracted following the manufacturer’s protocol. Total RNAs were dissolved in H2O and quantified on a NanoDrop 2000 spectrophotometer (NanoDrop Products, Wilmington, DE, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Doxycyclin (0.5 µg/ml) or PBS was treated for 48 hours

value: BCPAP

value: Thyroid cancer


title: BCPAP-Prx_PBS

source_name: PBS-treated control


title: BCPAP-Ctr_Dox


title: repA_TP5

description: 5' end capture

value: capped mRNA


title: repA_TP4

description: 5' end capture


title: FT4_RNA-Seq

status: Public on Mar 01 2016

city: Shenyang

first: Shengnan

last: Huang

address: 120 Dongling Road Shenhe District Shenyang P.R. China

country: China

institute: Shenyang Agricultural University

data_processing:
Illumina HiSeq™ 2000 used for base calling
All raw reads were filtered by removing reads with adaptors and low-quality reads. Clean reads were mapped to the reference database for the B. rapa genome (Version 1.5, http://brassicadb.org/brad/) using SOAPaligner/SOAP2 (Li et al., 2009).
Gene expression levels were calculated using the RPKM (Reads Per kb per Million reads) method (Mortazavi et al., 2008) in six libraries
The DESeq software was applied to analyze DEGs based on the RPKM-derived baseMean for each gene between samples (Anders and Huber, 2010). To identify DEGs, the False Discovery Rate (FDR ≤ 0.001) method was used to determine the threshold of P-value in multiple tests (Benjamini and Hochberg, 1995).
Genome_build: Version 1.5, http://brassicadb.org/brad/
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values,length,coverage... for each gene

organism: Brassica rapa subsp. oleifera

source_name: the third true leaves

extract_protocol:
The third true leaves of Chinese cabbage were sampled, total RNA was extracted using Trizol reagent
cDNA libraries were prepared for sequencing using standard Illumina protocols

tag: common name

value: Chinese cabbage

tag: tissue

value: the third true leaves

tag: developmental stage

value: the day 15 to day 24 after the appearance of the third true leaves

value: wild type


title: FT2_RNA-Seq


title: DRM5_RNA-Seq

value: developmentally retarded mutant (drm)


title: DRM4_RNA-Seq


title: bulk_HepG2_gDNA

city: Beijing

first: Yu

last: Hou

state: Beijing

address: No.5 Yiheyuan Street

department: School of life sciences

institute: Peking University

description: bulk genome DNA seq

library_source: genomic

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Adapter sequence and low-quality sequences were trimmed.
For RNA seq data, TopHat (version 2.0.10) were used for sequence alignment to mouse mm9 genome. Gene expression level (FPKM) were calculated using Cufflinks (version 2.1.1).
For RRBS data, Bismark were used for sequence alignment to mouse mm9 genome, and metlevel of each CpG site were calculated manually.
For gDNA seq data, bwa were used for sequence alignment to the mouse (mm9) genome, and the depth for each 10M window were calculated by summing the sequencing depth of all the positions in each window.
Genome_build: mm9

molecule: genomic DNA

source_name: HepG2 cell line

growth_protocol: The HepG2 cell line were cultured in RPMI 1640 with 10% FBS, and digested with trypsin before single cell picking.

extract_protocol:
The RNA and DNA of each single cell were separated and extracted by Trio-seq.
For RNA seq and genome DNA seq data, we constructed the sequencing libraries using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #7370L). RRBS libraries were constructed using RRBS protocol as described in 2013 (Guo et al. 2013)

treatment_protocol: HepG2 cells were digested with trypsin before single cell picking.

tag: gender

value: Male

value: hepatocellular carcinoma


title: bulk_HepG2_RNA

description: bulk RNA seq

tag: cell line


title: scRNA-seq_HepG2_2

description: single cell RNA seq


title: bulk_HepG2_RRBS

description: bulk RRBS


title: DRM2_RNA-Seq


title: scTrio_HepG2_6_RRBS

description: single cell RRBS


title: scRRBS_HepG2_2

description: single cell RRBS


title: scTrio_HepG2_6_RNA

description: single cell RNA seq


title: scRRBS_HepG2_1

description: single cell RRBS


title: scTrio_HepG2_5_RNA

description: single cell RNA seq


title: scTrio_HepG2_3_RRBS

description: single cell RRBS


title: scTrio_HepG2_5_RRBS

description: single cell RRBS


title: scTrio_HepG2_4_RNA

description: single cell RNA seq


title: scTrio_HepG2_3_RNA

description: single cell RNA seq


title: scTrio_HepG2_1_RRBS

description: single cell RRBS


title: scTrio_HepG2_1_RNA

description: single cell RNA seq


title: scTrio_HepG2_2_RNA

description: single cell RNA seq


title: BCPAP-Ctr_PBS


title: FT5_RNA-Seq


title: scTrio_HepG2_2_RRBS

description: single cell RRBS


title: PreB_iPS_p3_3 Hi-C

city: Utrecht

first: Elzo

last: de Wit

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: TruSeq libraries prepared from 3C template

data_processing:
Library strategy: HiC
Forward and reverse (R1,R2) sequencing files are seperately aligned to the mouse genome (mm9) using bwa mem. Duplicates are removed and mapped pairs are filtered using the hicup_filter from the HiCUP package. Pairs that fall within 1kb of each other are removed from the sample as they likely represent non-cut genomic DNA fragments.
Genome_build: mm9
Supplementary_files_format_and_content: Hi-C summary files contain the genomic position and strand of the two pairs of a Hi-C ligation

source_name: PreB iPS p3 3

growth_protocol:
ESCs and iPSCs were cultured on Mitomycin-C treated MEFs in KO-DMEM (Invitrogen) supplemented with 1% nonessential amino acids (Invitrogen), 0.1 mM β-mercaptoethanol (Invitrogen), 1,000 U/ml LIF (Millipore) and 15% fetal bovine serum (FBS, Invitrogen) (ESC medium). Naïve ESCs were cultured in serum-free N2B27 medium on gelatin-coated dishes. N2B27 medium (500ml) was generated by inclusion of the following: 240ml DMEM/F12 (Invitrogen), 240ml Neurobasal (Invitrogen), 5ml N2 supplement (Invitrogen), 10ml B27 supplement (Invitrogen), 1,000 U/ml LIF (Millipore), 1% nonessential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Invitrogen), and the small molecules PD0325901 (Stemgent, 1μM) and CHIR (Stemgent, 3μM). CD19 + pre-B cells and Mac1 + macrophages were isolated from bone marrow with monoclonal antibodies to CD19 and Mac-1 (BD Pharmingen) respectively, using MACS sorting (Miltenyi Biotech). B cells were grown in RPMI medium with 10% FBS and 10ng/ml IL-7 (Peprotech); macrophages in DMEM with 10% FBS and 10ng/ml each of CSF1 and IL-3 (Peprotech). MEFs were established from day 13.5 mouseembryos and cultured in DMEM containing 10% FBS. NSC were isolated and cultured aspreviously described (Di Stefano et al., 2009). All media were supplemented with L-glutamineand penicillin/streptomycin (GIBCO).
Reprogramming experiments with B cells were performed as previously described (Di Stefano et al., 2014); with MEFs, macrophages and NSCs were conducted by plating 100.000 cells/well on gelatinized plates seeded with irradiated MEFs, using ESC medium supplemented with 2 μg/ml of doxycycline. For the isolation of iPSC lines, doxycycline was washed out after 15 days of reprogramming and colonies with ESC-like morphology were picked at 20 days before further passaging. iPSC lines were expanded for an additional 9 days (3 passages) to obtain P3 iPS cell lines or for 20 passages to obtain P20 iPS cell lines.

extract_protocol:
Cells are cross linked using 2% formaldehyde for 10min at room temperature in PBS 10%FCS, nuclei are isolated, after which chromatin is digested with DpnII subsequently ligated. After reversal of the cross links the DNA is purified (3C template).
The 3C template is fragmented and TruSeq libraries are prepared according to the vendor protocol.

treatment_protocol: cells are cross linked using 2% formaldehyde for 10minutes at room temperature in 10%FCS/PBS

value: PreB iPS p3


title: scRNA-seq_HepG2_1

description: single cell RNA seq


title: PreB_iPS_p3_2 Hi-C

source_name: PreB iPS p3 2


title: PreB_iPS_p20_3 Hi-C

source_name: PreB iPS p20 3

value: PreB iPS p20


title: PreB_iPS_p3_1 Hi-C

source_name: PreB iPS p3 1


title: PreB_1 Hi-C

source_name: PreB 1

value: PreB


title: NSC_iPS_p3_3 Hi-C

source_name: NSC iPS p3 3

value: NSC iPS p3


title: PreB_iPS_p20_1 Hi-C

source_name: PreB iPS p20 1


title: PreB_iPS_p20_2 Hi-C

source_name: PreB iPS p20 2


title: PreB_2 Hi-C

source_name: PreB 2


title: NSC_iPS_p3_1 Hi-C

source_name: NSC iPS p3 1


title: NSC_iPS_p20_3 Hi-C

source_name: NSC iPS p20 3

value: NSC iPS p20


title: NSC_iPS_p20_2 Hi-C

source_name: NSC iPS p20 2


title: NSC_iPS_p3_2 Hi-C

source_name: NSC iPS p3 2


title: scTrio_HepG2_4_RRBS

description: single cell RRBS


title: NSC_iPS_p20_1 Hi-C

source_name: NSC iPS p20 1


title: MEF_iPS_p3_3 Hi-C

source_name: MEF iPS p3 3

value: MEF iPS p3


title: NSC_1 Hi-C

source_name: NSC 1

value: NSC


title: MEF_iPS_p20_3 Hi-C

source_name: MEF iPS p20 3

value: MEF iPS p20


title: MEF_iPS_p3_1 Hi-C

source_name: MEF iPS p3 1


title: MEF_iPS_p20_1 Hi-C

source_name: MEF iPS p20 1


title: MEF_iPS_p20_2 Hi-C

source_name: MEF iPS p20 2


title: MEF_3 Hi-C

source_name: MEF 3

value: MEF


title: macrophages_iPS_p3_3 Hi-C

source_name: macrophages iPS p3 3

value: macrophages iPS p3


title: MEF_2 Hi-C

source_name: MEF 2


title: macrophages_iPS_p20_3 Hi-C

source_name: macrophages iPS p20 3

value: macrophages iPS p20


title: macrophages_iPS_p3_1 Hi-C

source_name: macrophages iPS p3 1


title: macrophages_iPS_p3_2 Hi-C

source_name: macrophages iPS p3 2


title: MEF_1 Hi-C

source_name: MEF 1


title: macrophages_iPS_p20_2 Hi-C

source_name: macrophages iPS p20 2


title: macrophages_2 Hi-C

source_name: macrophages 2

value: macrophages


title: WCE_p20

description: DNA

data_processing:
Fastq files were aligned to the mouse genome (mm9) using bwa aln.
Peak calling was performed using MACS2 (callpeak), with --extsize 180 and -g mm.
Genome_build: mm9
Supplementary_files_format_and_content: narrowPeak

extract_protocol: ChIP experiments were performed as described previously (van Oevelen et al., 2008) using an antibody against H3K27ac (ab4729, Abcam) and CTCF (Millipore, 07-729). DNA libraries were prepared using Illumina's reagents and instructions.

value: p20 iPS whole cell extract


title: macrophages_1 Hi-C

source_name: macrophages 1


title: E14_ESC_1 Hi-C

source_name: E14 ESC 1

value: E14 ESC


title: H3K27ac_ChIP_preB_p20

description: ChIP

value: preB derived p20 iPS


title: macrophages_iPS_p20_1 Hi-C

source_name: macrophages iPS p20 1


title: H3K27ac_ChIP_preB_p3

description: ChIP

value: preB derived p3 iPS


title: H3K27ac_ChIP_MEF_p20

description: ChIP

value: MEF derived p20 iPS


title: H3K27ac_ChIP_NSC_p20

description: ChIP

value: NSC derived p20 iPS


title: H3K27ac_ChIP_MEF_p3

description: ChIP

value: MEF derived p3 iPS


title: H3K27ac_ChIP_macrophage_p20

description: ChIP

value: macrophage derived p20 iPS


title: H3K27ac_ChIP_macrophage_p3

description: ChIP

value: macrophage derived p3 iPS


title: MEF_iPS_p3_2 Hi-C

source_name: MEF iPS p3 2


title: H3K27ac_ChIP_NSC_p3

description: ChIP

value: NSC derived p3 iPS


title: 1x Chimera

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

description: processed data in file mm9_myf5_2_gene.counts.csv

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were aligned to MM9 genome using tophat 2.0.8
Read counts for the genes are collected by Bioconductor Biostrings and IRanges packages.
The annoated gene are collected from Gencode.
Genome_build: mm9
Supplementary_files_format_and_content: gene.counts.csv.gz contains the read counts for each gene in all samples.

source_name: mouse M&M MEFs transduced with 1x lenti-Chimera

growth_protocol: M&M MEFs were grown in DMEM containing 10% FBS

extract_protocol:
Total RNA was harvested from lentivirally transduced M&M MEFs that were  differentiated as described in treatment protocol.
RNA libraries were prepared using oligo-dT selection and sequenced on the Illumina HiSeq 2500 cording to the manufacturer's instructions.

treatment_protocol: M&M MEF cells were infected in DMEM media containing polybrene at a final concentration of 8 µg /ml. After 24 hours, media was replaced with fresh Differentiation media (DMEM w/o serum, insulin, transferin, and heat inactivated horse serum), and after 20 hours the cells were harvested.

value: mouse embryonic fibroblasts

tag: genotype/variation


title: 1x MyoD_B

source_name: mouse M&M MEFs transduced with 1x lenti-MyoD (second batch of lenti-virus, balanced against the Chimera)


title: 1x GFP

description: processed data in file mm9_myf5_gene.counts.csv

source_name: mouse M&M MEFs transduced with 1x lenti-GFP


title: 2x MyoD

source_name: mouse M&M MEFs transduced with 2x lenti-MyoD


title: 1x MyoD_A

source_name: mouse M&M MEFs transduced with 1x lenti-MyoD


title: 2x Myf5

source_name: mouse M&M MEFs transduced with 2x lenti-Myf5


title: 1x Myf5

source_name: mouse M&M MEFs transduced with 1x lenti-Myf5


title: NV

source_name: Untransduced M&M MEFs


title: GFP-60

source_name: mouse M&M MEFs transduced with lenti-GFP, MOI=60


title: GFP-120

source_name: mouse M&M MEFs transduced with lenti-GFP, MOI=120


title: GFP-30

source_name: mouse M&M MEFs transduced with lenti-GFP, MOI=30


title: WCE_p3

description: DNA

value: p3 iPS whole cell extract


title: H4Ac_Myf5_input

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were aligned to human genome hg19 using BWA (0.7.5)
Peaks were called using in-house peak calling algorithm
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq peaks in csv format

source_name: ChIP-Seq with no antibody in mouse M&M MEF cells transduced with Myf5

extract_protocol:
Native ChIP for histone acetylation was performed by combining the nuclei isolation protocol from Gerber et al, 1997 and the MNase digestion and chromatin extraction method from Cao et al, 2010. Briefly: nuclei were harvested from 10 million cells by lysis in RSB+0.1% NP-40 for 10 min. Nuclei were rinsed with RSB and resuspended in 250 μl douncing buffer containing 15 U of MNase, and then incubated at 37°C for 18 min. The reaction was stopped by adding EDTA to 10 mM and moving the nuclei to ice. 1 ml of hypotonic lysis buffer with protease inhibitors was added to each sample. 50 μl of 0.25 M NaButyrate was added to each sample and the samples were rotated at 4°C for 1 hour. Insoluble material was removed by centrifugation (3800 xg for 5 min, 4°C). 100 μl of the supernatant (soluble chromatin) was removed and reserved for input DNA.
No antibody was added to 1 ml of soluble chromatin and rotated overnight at 4°C. Nucleosome-antibody complexes were isolated with protein A:G agarose beads in the same manner as the xChIPs. ChIP samples were validated by qPCR and prepared for sequencing per the Nugen Ovation Ultralow library system with direct read barcodes.

treatment_protocol: M&M MEF cells were infected in DMEM + 10% FBS media containing polybrene at a final concentration of 8 µg /ml. After 12 hours, media was replaced with fresh DMEM +10% FBS, and after 24 hours (from infection) the cells were transitioned to Differentiation media (DMEM containing insulin and transferin). Cells were harvested after 20 hours in Differentiation media. Negative controls for MyoD and Myf5 ChIPs were cells infected with lenti-GFP.


title: GFP-15

source_name: mouse M&M MEFs transduced with lenti-GFP, MOI=15


title: H4Ac_GFP_inut

source_name: ChIP-Seq with no antibody in mouse M&M MEF cells transduced with GFP


title: H4Ac_MyoD_input

source_name: ChIP-Seq with no antibody in mouse M&M MEF cells transduced with MyoD


title: H4Ac_Myf5

source_name: ChIP-Seq with H4Ac antibody 39925 in mouse M&M MEF cells transduced with Myf5

extract_protocol:
Native ChIP for histone acetylation was performed by combining the nuclei isolation protocol from Gerber et al, 1997 and the MNase digestion and chromatin extraction method from Cao et al, 2010. Briefly: nuclei were harvested from 10 million cells by lysis in RSB+0.1% NP-40 for 10 min. Nuclei were rinsed with RSB and resuspended in 250 μl douncing buffer containing 15 U of MNase, and then incubated at 37°C for 18 min. The reaction was stopped by adding EDTA to 10 mM and moving the nuclei to ice. 1 ml of hypotonic lysis buffer with protease inhibitors was added to each sample. 50 μl of 0.25 M NaButyrate was added to each sample and the samples were rotated at 4°C for 1 hour. Insoluble material was removed by centrifugation (3800 xg for 5 min, 4°C). 100 μl of the supernatant (soluble chromatin) was removed and reserved for input DNA.
20 μl of antibody was added to 1 ml of soluble chromatin and rotated overnight at 4°C. Nucleosome-antibody complexes were isolated with protein A:G agarose beads in the same manner as the xChIPs. ChIP samples were validated by qPCR and prepared for sequencing per the Nugen Ovation Ultralow library system with direct read barcodes.


title: Myf5_ChIP_Rep1_Rep2

source_name: ChIP-Seq with Myf5 antibody Sc-302x (lot CO612) in mouse M&M MEF cells transduced with Myf5

extract_protocol:
Cells were fixed in 1% formaldehyde for 11 minutes, quenched with glycine, lysed, and then sonicated to generate final DNA fragments of ~150–600 bp.
The soluble chromatin was diluted 1:10 and pre-cleared with a 1:1 Protein A:G slurry for 2 hours at 4oC. Chromatin was mixed with antibody overnight at 4oC, then Protein A:G beads for 2 hours. Beads were washed and de-crosslinked overnight for ~16 hours in 1%SDS, 0.1M NaHCO3 and 70 ug Proteinase K.


title: H4Ac_MyoD

source_name: ChIP-Seq with H4Ac antibody 39925 in mouse M&M MEF cells transduced with MyoD


title: Mock_MyoD_ChIP

source_name: ChIP-Seq with MyoD antibody 6975 in mouse M&M MEF cells transduced with GFP


title: bulk_mESC_gDNA

description: bulk genome DNA seq

source_name: mouse embryonic stem cell

treatment_protocol: mES cells were digested with trypsin before single cell picking.

value: Male

tag: passage


title: Mock_Myf5_ChIP

source_name: ChIP-Seq with Myf5 antibody Sc-302x (lot CO612) in mouse M&M MEF cells transduced with GFP


title: H4Ac_GFP

source_name: ChIP-Seq with H4Ac antibody 39925 in mouse M&M MEF cells transduced with GFP


title: scRRBS_mESC_1

description: single cell RRBS


title: MyoD_ChIP_Rep1_Rep2

source_name: ChIP-Seq with MyoD antibody 6975 in mouse M&M MEF cells transduced with MyoD


title: bulk_mESC_RRBS

description: bulk RRBS


title: scRRBS_mESC_2

description: single cell RRBS


title: scRNA-seq_mESC_2

description: single cell RNA seq


title: scTrio_mESC_6_RRBS

description: single cell RRBS


title: scTrio_mESC_6_RNA

description: single cell RNA seq


title: scTrio_mESC_5_RRBS

description: single cell RRBS


title: scTrio_mESC_5_RNA

description: single cell RNA seq


title: scTrio_mESC_4_RRBS

description: single cell RRBS


title: bulk_mESC_RNA

description: bulk RNA seq


title: scRNA-seq_mESC_1

description: single cell RNA seq


title: scTrio_mESC_3_RRBS

description: single cell RRBS


title: scTrio_mESC_4_RNA

description: single cell RNA seq


title: scTrio_mESC_2_RRBS

description: single cell RRBS


title: LasR_mutant_sample2

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

institute: Technische Universität Braunschweig

description: PA14 LasR deletion mutant

data_processing:
RNA-seq reads were mapped to the PA14 genome using the Stampy aligner with default settings.
Differential expression was estimated using the R library edgeR excluding rRNA/tRNA genes and making use of the biological replicates for each condition
Genome_build: gi|116048575|ref|NC_008463.1|
Supplementary_files_format_and_content: The processed files in CSV format include Genes, log2FC, uncorrected P-value and corrected P-value (Padj). The P-values are presented in the Phred-scale (-10*log10(actual P-value))

organism: Pseudomonas aeruginosa

source_name: LasR_mutant_planktonic culture

growth_protocol: The Harvard Medical School PA14 transposon mutants [PMID:16477005] were grown in LB medium at 37°C and 180 r.p.m. until OD600=2.0.

extract_protocol:
Using Rneasy kit (Qiagen) plus Qiashredder columns.
Customized protocol (Dötsch et al., PloS ONE, 2012). Bacterial rRNA was depleted using MICROBExpress kit with the Pseudomonas module (Ambion) and fragmented by sonication using Covaris Adaptive Acoustics device (Covaris). Upon ligation of barcoded adapters, reverse transcription with SuperScript II kit (Invitrogen) followed. Amplification was done by PCR using Illumina platform compatible primers. Established cDNA library was normalized by double strand specific nuclease treatment (Evrogen) according DSN Normalization Sample Preparation Guide from Illumina.

treatment_protocol: Cells from 3 pooled cultures were harvested by addition of the same volume of RNA-protect buffer (Qiagen) and centrifugation.

tag: strain background

value: LasR deletion mutant

tag: culture type

value: planktonic culture


title: FleQ_mutant_sample1

description: PA14 FleQ mutant ID 41540

source_name: FleQ_mutant_planktonic culture

value: FleQ transposon mutant


title: GacA_mutant_sample1

description: PA14 GacA mutant ID 34781

source_name: GacA_mutant_planktonic culture

value: GacA transposon mutant


title: GacA_mutant_sample2

description: PA14 GacA mutant ID 34781


title: LasR_mutant_sample1

description: PA14 LasR deletion mutant


title: FleQ_mutant_sample2

description: PA14 FleQ mutant ID 41540


title: Cbrb_mutant_sample1

description: PA14 Cbrb mutant ID 44074

source_name: Cbrb_mutant_planktonic culture

value: Cbrb transposon mutant


title: scTrio_mESC_1_RNA

description: single cell RNA seq


title: scTrio_mESC_1_RRBS

description: single cell RRBS


title: Cbrb_mutant_sample2

description: PA14 Cbrb mutant ID 44074


title: Anr_mutant_sample1

description: PA14 Anr mutant ID 26855

source_name: Anr_mutant_planktonic culture

value: Anr transposon mutant


title: Anr_mutant_sample2

description: PA14 Anr mutant ID 26855


title: RhlR_mutant_sample2

description: PA14 RhlR mutant ID 37943

source_name: RhlR_mutant_planktonic culture

value: RhlR transposon mutant


title: LadS_mutant_sample2

description: PA14 LadS mutant ID 38371

source_name: LadS_mutant_planktonic culture

value: LadS transposon mutant


title: scTrio_mESC_3_RNA

description: single cell RNA seq


title: LadS_mutant_sample1

description: PA14 LadS mutant ID 38371


title: Mutant rep4

first: Humphrey

middle: Hung-Chang

last: Yao

state: NC

address: 111 TW Alexander Drive

institute: NIEHS/NIH

data_processing:
Read pairs were filtered to retain only those with average base quality score >20.
Filtered read pairs were mapped against mm10 with TopHat v2.0.12, parameters as follows: --b2-sensitive --library-type fr-unstranded -g 10 --mate-inner-dist -60 --mate-std-dev 50.
Coverage tracks were generated by converting mapped reads to bedGraph (BEDtools2 genomeCoverageBed) then to bigWig (ucsc utlility script bedGraphToBigWig).
Analysis of differentially expressed genes was performed with Cuffdiff v2.1.1 using default parameters; based on reference annotations from RefSeq.
Analysis of differentially expressed repeat elements was performed with DESeq2, after converting mapped reads to counts-per-gene with HTseq-count; based on reference annotations from RepeatMasker.
Genome_build: mm10
Supplementary_files_format_and_content: Mapped read depth as bigWig; FPKM per gene (calculated byCuffllinks/Cuffnorm) as tab-delimited text file; read counts per RepeatMasker LINE/SINE/LTR element (caluclated by HTSeq-count; based on only uniquely-mapped reads) as tab-delimited text file.

extract_protocol:
RNA from a single pair of E14.5 testes (one biological replica) was extracted using the PicoPure extraction kit (Arcturus/Life Technologies).
RNA-Seq libraries were constructed from ~0.3 µg total RNA after rRNA depletion using Ribo-Zero GOLD (Illumina).   The Illumina TruSeq RNA Sample Prep V2 Kit was used according to manufacturer’s instructions except where noted.  The poly-A selection step was omitted and random primers were used for first-strand synthesis. The cDNAs were fragmented to ~275 bp using a Covaris E210. Amplification was performed using 16 cycles, which was optimized for the input amount and to minimize the chance of over-amplification.  Unique barcode adapters were applied to each library.

value: Glis3 mutant

value: testis

tag: molecule subtype

value: rRNA-depleted RNA


title: scTrio_mESC_2_RNA

description: single cell RNA seq


title: Mutant rep3


title: Mutant rep2


title: WT rep3

value: wild-type


title: WT rep2


title: WT rep1


title: YapTaz dCKO rep2

city: Houston

first: Min

last: Zhang

state: Texas

address: One Baylor Plaza Room 504E

department: Department of Molecular Physiology

institute: Baylor College of Medicine

data_processing:
Torrent_Suite 4.0.2 for basecalling with parameters: `BaseCaller --keypass-filter on --phasing-residual-filter=2.0 --trim-qual-cutoff 15 --trim-qual-window-size 30 --trim-adapter-cutoff 16 --num-unfiltered 1000 --calibration-training=100000 --flow-signals-type scaled-residual --max-phasing-levels 2`
Sequenced reads were aligned against mouse genome mm9 using Tmap version 3.0.1 with default RNA-Seq setting `map4`
Gene expression levels were measured by counting numbers of reads in all the exons using HTSeq version 0.5.4p3 with parameters: `htseq-count -m union -s yes -t exon -i gene_symbol`
Differential gene expression was measured using DESeq version 1.16.0
Genome_build: mm9
Supplementary_files_format_and_content: comma-separated values files for raw read counts
Supplementary_files_format_and_content: comma-separated values files for differential gene expressionprofiling

molecule: polyA RNA

source_name: YapTaz dCKO _Mandible

extract_protocol:
We dissected E10.5 mandibular tissues from Wnt1Cre Taz and Yap dKO mutant and control embryos in DEPC-treated PBS, then total RNA were extracted and treated for 30 min at 37˚C with RNAse free DNase I (Ambion). Poly(A) RNA was purified with the Micro Poly(A) purist Kit according to the manufacturer’s instructions (Ambion).
Purified RNA samples were processed for cDNA synthesis and library preparation following Ion Total RNA-Seq v2 (cat. #4475936) protocol.

value: C57BL/6J x CBA/J; 129SvEv

value: embryonic day 10.5

value: Wnt1Cre; Yapf/f, Tazf/f

value: mandible


title: control rep3

value: Yapf/f, Tazf/f


title: YapTaz dCKO rep1


title: control rep2


title: control rep1


title: I1 and I2 Seq

city: Qingdao

first: LI

last: Yang

state: Shandong

address: 6 Xian-Xia Ling Road

department: SOA

institute: The First Institute of Oceanography

data_processing:
Illumina Casava1.8  software used for basecalling.
Removed the adapter sequence of reads; Removed reads that did not contain at least 25 Q30 bases; Removed all reads that contained 10% ambiguous characters
Bowtie2 was used for the reads alignment
COG, KEGG, GO
Genome_build: JPMC00000000
Supplementary_files_format_and_content: annotation-table and genes-fpkm-matrix files include FPKM, GO, KEGG  and COG values for each sample

organism: Pseudoalteromonas sp. A2

source_name: Pseudoalteromonas sp. A2_1 mmol/L H2O2

growth_protocol: Pseudoalteromonas sp. A2 was cultured at 10 ℃ with rotation at a speed of 150 r/min in ZoBell 2216E medium consisting of 5 g of tryptone, 1 g of yeast extract in 1 L of seawater.

extract_protocol:
Total RNA was extracted using TRIzol® Reagent according the manufacturer’s instructions
RNA-Seq transcriptome libraries were prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) by using 5 μg of total RNA

value: an isolate from seawater with high activity against H2O2

tag: growth medium

value: ZoBell 2216E medium with a final concentration of 1 mmol/L H2O2


title: NTK8_1_RNAseq

city: Brookline

first: Yuting

last: Liu

state: MA

address: 82 Walnut St. Unit 3

department: Department of Genetics

institute: Harvard Medical School

description:
processed data file: SupTable_human_SCNT-derived_ESCs_genes_fpkm_140720.txt.gz
NTK8_1

data_processing:
Sequence reads were mapped against the human genome (hg19) with Tophat2. All programs were performed with default setting (unless otherwise specified). The unique mapped reads were subsequently assembled into transcripts guided by reference annotation (UCSC gene models) with Cufflinks v2.0.2. Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: SCNT derived human ES cells

extract_protocol:
Five 8-cell embryos for each group were directly lysed and used for cDNA synthesis using SMART-Seq v4 Ultra Low Input RNA Kit (Clontech). For MEF donor, 10 ng total RNA was used for cDNA synthesis using SMART-Seq v4 Ultra Low Input RNA Kit.
After amplification, the cDNA samples were fragmented using Covaris sonicator M220 to an average size of 150 bp (Covaris). Sequencing libraries were made with the fragmented DNA using NEBNext Ultra DNA Library Prep Kit for Illumina according to manufacturer’s instruction (New England Biolabs) with different barcodes. For each RNA-seq analysis of hESCs, 1 μg total RNA was used for mRNA purification. Barcoded RNA-seq libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs). Single end 50 bp sequencing was performed on a HiSeq 2500 sequencer (Illumina).

tag: cell/tissue type

value: SCNT assisted by KDM4A derived human ES cells


title: NTK6_2_RNAseq

description:
processed data file: SupTable_human_SCNT-derived_ESCs_genes_fpkm_140720.txt.gz
NTK6_2


title: NTK7_2_RNAseq

description:
processed data file: SupTable_human_SCNT-derived_ESCs_genes_fpkm_140720.txt.gz
NTK7_2


title: IVF_8Cell_RNAseq

description:
processed data file: SupTable_human_SCNT_8Cell_genes_fpkm_140720.txt.gz
IVF_8Cell

source_name: 8-cell IVF embryos

value: 8-cell IVF embryos


title: CTR_hES15_1_RNAseq

description:
processed data file: SupTable_human_SCNT-derived_ESCs_genes_fpkm_140720.txt.gz
CTR_hES15_1

source_name: Control human ES cells

value: Control human ES cells


title: CTR_hES15_2_RNAseq

description:
processed data file: SupTable_human_SCNT-derived_ESCs_genes_fpkm_140720.txt.gz
CTR_hES15_2


title: Mutant rep1


title: ChIP-4b_mock-FLAG

city: Bunkyo-ku

first: Mizuo

last: Ando

state: Tokyo

address: 7-3-1 Hongo

department: Otolaryngology-Head and Neck Surgery

country: Japan

institute: The University of Tokyo

data_processing:
Basecalls performed using CASAVA version 1.6.0
Sequenced reads were selected for high-quality read (quality value >=30), and mapped to hg19 whole genome using bowtie v0.12.7 with parameters -q -n 0 -l 50 -p 30 --k 1 -X 500.
Mapped results were converted to ALN files by using bowtie2aln in CisGenome v2.0.
Peaks were calculated using CisGenome with the following setting: Read Extension Length E (0).
Motifs were calculated using CisGenome with the following setting: No.of Motifs (30), No. of MCMC iterations (1000).
Genome_build: hg19
Supplementary_files_format_and_content: Peaks (*.cod) were tab-delimited text files.

source_name: Oral cancer cell line

extract_protocol:
T3M-1 Cl-10 cells were infected with a mock retrovirus or virus generated from pMXS-ires-EGFP expressing FLAG-epitope–tagged ELF4 or ELF4(L211M). ChIP was conducted with anti-FLAG M2 antibody (Sigma-Aldrich). The precipitated DNA fragments were subjected to massively parallel sequencing with Genome Analyzer IIx (Illumina) for 51 bases from both ends of the fragments.
ChIP-seq libraries were prepared using Illumina NEBNext ChIP-Seq Library Prep Reagent Set following the manufacturer's protocols.

tag: cell

value: mock

tag: antibody vendor

value: SIGMA ALDRICH

tag: chip antibody

value: Monoclonal ANTI-FLAG M2, Clone M2

tag: antibody catalog

tag: antibody lot


title: ChIP-4b_mutant-FLAG

tag: genotype


title: CTR_hES6_2_RNAseq

description:
processed data file: SupTable_human_SCNT-derived_ESCs_genes_fpkm_140720.txt.gz
CTR_hES6_2


title: ChIP-4b_mutant-input


title: Donor_RNAseq

description:
processed data file: SupTable_human_SCNT_8Cell_genes_fpkm_140720.txt.gz
Donor

source_name: Fibroblast cells

value: Fibroblast cells


title: NTK6_1_RNAseq

description:
processed data file: SupTable_human_SCNT-derived_ESCs_genes_fpkm_140720.txt.gz
NTK6_1


title: SCNT_8Cell_RNAseq

description:
processed data file: SupTable_human_SCNT_8Cell_genes_fpkm_140720.txt.gz
SCNT_8Cell

source_name: 8-cell SCNT embryos

value: somatic cell nuclear transfer embryos at 8-cell stages


title: ChIP-4b_wild-FLAG

value: wild type


title: ChIP-4b_mock-input


title: SCNT_KDM4A_8Cell_RNAseq

description:
processed data file: SupTable_human_SCNT_8Cell_genes_fpkm_140720.txt.gz
SCNT_KDM4A_8Cell

value: SCNT assisted by KDM4A 8-cell embryos


title: NTK7_1_RNAseq

description:
processed data file: SupTable_human_SCNT-derived_ESCs_genes_fpkm_140720.txt.gz
NTK7_1


title: NTK8_2_RNAseq

description:
processed data file: SupTable_human_SCNT-derived_ESCs_genes_fpkm_140720.txt.gz
NTK8_2


title: C1 and C2 Seq

source_name: Pseudoalteromonas sp. A2_without H2O2

tag: strain

value: ZoBell 2216E medium without H2O2


title: ChIP-4b_wild-input


title: CTR_hES6_1_RNAseq

description:
processed data file: SupTable_human_SCNT-derived_ESCs_genes_fpkm_140720.txt.gz
CTR_hES6_1


title: Ca_13_RRBS

description: single cell RRBS

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Adapter sequence and low-quality sequences were trimmed.
For RNA seq data, TopHat (version 2.0.10) were used for sequence alignment to human hg19 genome. Gene expression level (FPKM) were calculated using Cufflinks (version 2.1.1).
For RRBS data, Bismark were used for sequence alignment to human (hg19) genome, and metlevel of each CpG site were calculated manually.
For gDNA seq data, bwa were used for sequence alignment to the human (hg19) genome, and the depth for each 10M window were calculated by summing the sequencing depth of all the positions in each window.
Genome_build: hg19

source_name: human adult cancer cell

growth_protocol: The hepG2 cell line were cultured in RPMI 1640 with 10% FBS, and digested with trypsin before single cell picking.

value: Male

tag: tissue

value: liver cancer


title: 3RiPSC4

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Basecalls performed using CASAVA version 1.8.4
Calculating insert size and standard deviation performed using Picard v.1.126
Reads were mapped to hg19 using TopHat v2.0.13 guided by GTF version GRCh37.70 with default parameters and calculated insert size and SD
read counting performed using HT-seq v0.6.0 (--mode=union --stranded=no --minaqual=30 --idattr=gene_name –type=exon)
Normalization and Deferential expression analysis performed using DEseq v3.0
BAM to bedgraph performed using bedtools v2.17.0
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.1.1
Genome_build: hg19
Supplementary_files_format_and_content: BigWig (coverage for mapped reads), count tables (read counts for genomic features) and normalized count tables

source_name: iPSC generated with OSK plus BRD3R

extract_protocol:
Cells were harvested with Trizol reagent and stored at -80 °C until use. Total RNA was extracted using the Direct-zolTM Miniprep kit (R2052).
The standard Agilent SureSelect Strand-Specific RNA sequencing protocol was followed. Briefly, the polyA fraction was purified using two rounds of oligo dT-magnetic bead purification. The resulting polyA fraction was fragmented and first strand cDNA was done with random primers in the presence of Actinomycin D using standard techniques. The resulting first stand cDNA was purified using AMPure Beads and second strand cDNA and end repair was done using standard techniques.  The blunt ended double stranded cDNA was incubated with exo- E.coli DNA polymerase to add an adenosine to the ends for T/A cloning of the adaptors. PCR amplification was done in the presence of uracil DNA glycosylase to generate strand specificity.  A second round of PCR amplification was done to add unique 6-bp barcodes to each sample and add sequences necessary for flow cell attachment.  The resulting mRNA libraries were quantitated using qPCR following the manufacturer's instructions (Kapa Biosystems, Woburn MA).

treatment_protocol: Seed BJ cells into 6-well plate at 100,000 cells/well. Twenty-four hours post plating, add OSK (OCT4, 10 MOI; SOX2, 5 MOI and KLF4, 5 MOI) viruses with or without GFP or BRD3R viruses into respective wells. Incubate  overnight. Next morning, remove viruses by replacing virus-containing media with fresh fibroblast media. Seventy-two hour post transduction, harvest RNA.

tag: cell type

value: iPSC generated with OSK plus BRD3R

tag: lentiviral transgenes

value: no

tag: passage number

value: passage 20

value: induced pluripotent stem cells

tag: harvest time

value: 80% confluence


title: BJ-OSK-BRD3R-B

source_name: Human forskin fibroblast, BJ (ATCC, CRL-2522)

tag: cell line

value: BJ

value: OCT4 (10 MOI), SOX2 (5 MOI), KLF4 (5 MOI), BRD3R (25 ul virus)

value: passage 8

value: reprogramming cells

value: day 3 post transduction


title: BJ-OSK-BRD3R-A

value: OCT4 (10 MOI), SOX2 (5 MOI), KLF4 (5 MOI), BRD3R(2.5 ul/35000 cells)

value: passage 7


title: keratinocyte

source_name: human keratinocyte from donor

value: human keratinocyte from donor

value: passage 4

value: keratinocyte

tag: culture protocols

value: Human keratinocyte was cultured with DermaLife K serum-free human keratinocyte medium (Lifeline Cell Technology, LL-0007) per manufacturer¡Å™s instruction.


title: BJ-OSK-GFP-A

value: OCT4 (10 MOI), SOX2 (5 MOI), KLF4 (5 MOI), GFP (8 MOI)


title: BJ-OSK-GFP-B

value: OCT4 (10 MOI), SOX2 (5 MOI), KLF4 (5 MOI), GFP (25 ul virus)


title: 3RiPSC3

value: iPSC generated with OSK plus BRD3R

value: no


title: cancer_bulk_RNA

description: bulk RNA seq

source_name: human adult cancer tissue

tag: gender

value: Male

value: liver cancer

tag: passage


title: cancer_bulk_RRBS

description: bulk RRBS


title: liver_bulk_RRBS

description: bulk RRBS

source_name: human adult liver tissue

value: adult liver


title: liver_bulk_genome

description: genome DNA seq


title: cancer_bulk_genome

description: genome DNA seq


title: BJ-OSK-A

value: BJ

value: OCT4 (10 MOI), SOX2 (5 MOI), KLF4 (5 MOI)

value: cells were cultured in human fibroblast media as described in fibroblast culture protocol.


title: BJ-OSK-B

value: passage 8

value: reprogramming cells

value: day 3 post transduction


title: WT 10 months Male Striatum miRNA rep2 (Q50)

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling
Genome mapped via Omnisoft OSA 4.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using fastq-mcf sequence quality filter, clipping and processor with following settings for Omnisoft: Trimming  /Mode=TrimByQuality /ReadTrimQuality=2;  Options  /ParallelJobNumber=4 /PairedEnd=True /FileFormat=FASTQ /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=False /MaxMiddleInsertionSize=10 /MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /ExcludeNonUniqueMapping=False /ReportCutoff=10 /WriteReadsInSeparateFiles=True /GenerateSamFiles=False /ThreadNumber=6 /InsertSizeStandardDeviation=40 /ExpectedInsertSize=300 /MatePair=False /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic /CompressionMethod=Gzip /Gzip=True /SearchNovelExonJunction=False /ExcludeUnmappedInBam=False /KeepFullRead=False /Replace=False /Platform=ILLUMINA /CompressBam=False;
Genome_build: Genome version Mouse B.38, gene models version Ensembl miRBase.R21
Supplementary_files_format_and_content: Excel files include FPKM and Count values for each Sample

source_name: Striatum

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen miRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Striatum

value: Wild Type

tag: age

value: 10 months

tag: Sex

tag: housing condition

value: housed with Wild Type and Het (Q50) mice


title: WT 6 months Male Striatum miRNA rep3 (Q50)

value: 6 months


title: WT 10 months Male Striatum miRNA rep4 (Q50)


title: WT 10 months Male Striatum miRNA rep1 (Q50)


title: WT 6 months Male Striatum miRNA rep4 (Q20)

value: housed with Wild Type and Het (Q20) mice


title: WT 6 months Male Striatum miRNA rep1 (Q50)


title: WT 6 months Male Striatum miRNA rep3 (Q20)


title: WT 10 months Male Striatum miRNA rep3 (Q50)


title: WT 10 months Male Striatum miRNA rep4 (Q20)


title: WT 6 months Male Striatum miRNA rep2 (Q20)


title: WT 6 months Male Striatum miRNA rep1 (Q20)


title: WT 10 months Male Striatum miRNA rep3 (Q20)


title: WT 10 months Male Striatum miRNA rep2 (Q20)


title: WT 6 months Male Striatum miRNA rep2 (Q50)


title: WT 6 months Male Striatum miRNA rep4 (Q50)


title: WT 6 months Female Striatum miRNA rep3 (Q50)

value: Female


title: WT 6 months Female Striatum miRNA rep2 (Q50)


title: WT 10 months Female Striatum miRNA rep4 (Q50)


title: WT 6 months Female Striatum miRNA rep2 (Q20)


title: WT 10 months Female Striatum miRNA rep1 (Q50)


title: WT 10 months Female Striatum miRNA rep2 (Q50)


title: WT 10 months Female Striatum miRNA rep3 (Q20)


title: WT 6 months Female Striatum miRNA rep3 (Q20)


title: WT 6 months Female Striatum miRNA rep1 (Q20)


title: Het (Q92) 6 months Male Striatum miRNA rep4

value: Het (Q92) Knock-In

value: housed with Het (Q92) mice


title: WT 10 months Female Striatum miRNA rep3 (Q50)


title: WT 10 months Female Striatum miRNA rep2 (Q20)


title: Het (Q92) 10 months Male Striatum miRNA rep4

value: Male


title: WT 6 months Female Striatum miRNA rep4 (Q20)


title: Het (Q92) 10 months Male Striatum miRNA rep3


title: Het (Q92) 6 months Male Striatum miRNA rep2


title: Het (Q92) 10 months Male Striatum miRNA rep2


title: Het (Q92) 6 months Male Striatum miRNA rep3


title: Het (Q92) 10 months Male Striatum miRNA rep1


title: WT 10 months Male Striatum miRNA rep1 (Q20)


title: Het (Q92) 6 months Female Striatum miRNA rep3


title: WT 6 months Female Striatum miRNA rep1 (Q50)


title: Het (Q92) 6 months Female Striatum miRNA rep2


title: WT 10 months Female Striatum miRNA rep4 (Q20)


title: Het (Q92) 6 months Female Striatum miRNA rep4


title: Het (Q92) 6 months Female Striatum miRNA rep1


title: Het (Q92) 10 months Female Striatum miRNA rep4


title: Het (Q92) 10 months Female Striatum miRNA rep3


title: Het (Q92) 10 months Female Striatum miRNA rep2


title: Het (Q50) 6 months Male Striatum miRNA rep4

value: Het (Q50) Knock-In


title: R50_4

city: Bellville

first: Abhilasha

last: Madhvi

state: Western Cape

address: Francie van Zijl Drive. Tygerberg

country: South Africa

institute: Stellenbosch University

description: Differentiated to macrophages using L-CSF

data_processing:
Basecalling by SOLiD
Mapped using Lifescope, export .BAM files for mapped reads
Quantified to transcriptome in Partek (EM method)
Differential expression, Normalise RPKM, (Gene Specific Analysis- Partek), read count of 0 reset to 1.0E-4
Filer for data with FDR<0.05 and fold change >|2| Remove genes with less than 60 reads
Genome_build: Mus Musculus mm10
Supplementary_files_format_and_content: text files containing unfiltered gene counts and RPKM values

source_name: BMDMs infected with R1507 M.tb

growth_protocol: BMDMs were allowed 7 days to differentiate prior to infection with M.tb.

extract_protocol:
BMDM RNA was extracted using the RNeasy® Plus Mini Kit and mRNA enrichment was performed using the Dynabeads® mRNA DIRECT™ Kit (Cat. No. 61012, Ambion, Life Technologies, Oslo, Norway)
AB Library Builder™ Whole Transcriptome Core Kit for 5500 Genetic Analysis Systems (Cat. No. 4472690, Applied Biosystems, Life Technologies), SOLiD® EZ Bead™ System (Cat. No. 4448419, Applied Biosystems, Life Technologies)
Paired end (75/35)

treatment_protocol: On day 7, BMDMs were infected with either R5527 or R1507 M.tb for 12 hours

value: bone marrow derived macrophages (BMDMs)

tag: m.tb strain

value: R1507 Beijing M.tb

tag: infection period

tag: m.tb culturing coonditions

value: Detergent-free medium


title: R55_3

source_name: BMDMs infected with R5527 M.tb

value: R5527 Beijing M.tb


title: Het (Q50) 6 months Male Striatum miRNA rep1

tag: genotype


title: Het (Q50) 6 months Male Striatum miRNA rep2

tag: strain


title: Het (Q50) 10 months Male Striatum miRNA rep3

tag: tissue


title: Het (Q50) 6 months Male Striatum miRNA rep3


title: R55_2


title: Het (Q50) 10 months Male Striatum miRNA rep4


title: R55_1


title: Het (Q50) 10 months Male Striatum miRNA rep2


title: Het (Q92) 6 months Male Striatum miRNA rep1


title: C3

source_name: Uninfected BMDMs


title: C2


title: Het (Q50) 6 months Female Striatum miRNA rep3


title: Het (Q50) 6 months Female Striatum miRNA rep2


title: C1


title: Het (Q50) 6 months Female Striatum miRNA rep4


title: Het (Q50) 10 months Female Striatum miRNA rep4


title: Het (Q50) 6 months Female Striatum miRNA rep1


title: Het (Q92) 10 months Female Striatum miRNA rep1


title: R50_1


title: Het (Q20) 6 months Male Striatum miRNA rep4

value: Het (Q20) Knock-In


title: Het (Q50) 10 months Female Striatum miRNA rep1


title: R50_2


title: Het (Q20) 6 months Male Striatum miRNA rep3


title: Het (Q50) 10 months Female Striatum miRNA rep3


title: Het (Q20) 10 months Male Striatum miRNA rep3


title: Het (Q20) 6 months Male Striatum miRNA rep1


title: Het (Q20) 10 months Male Striatum miRNA rep1


title: Het (Q20) 6 months Male Striatum miRNA rep2


title: Het (Q20) 6 months Female Striatum miRNA rep3


title: Het (Q50) 10 months Female Striatum miRNA rep2


title: Het (Q20) 6 months Female Striatum miRNA rep2


title: Het (Q20) 6 months Female Striatum miRNA rep1


title: Het (Q50) 10 months Male Striatum miRNA rep1


title: Het (Q20) 6 months Female Striatum miRNA rep4


title: Het (Q20) 10 months Female Striatum miRNA rep4


title: Het (Q20) 10 months Female Striatum miRNA rep3


title: Het (Q20) 10 months Female Striatum miRNA rep2


title: Het (Q140) 6 months Male Striatum miRNA rep4

value: Het (Q140) Knock-In

value: housed with Het (Q140) mice


title: Het (Q140) 6 months Male Striatum miRNA rep3

value: Striatum


title: Het (Q20) 10 months Female Striatum miRNA rep1

value: 10 months


title: Het (Q140) 6 months Male Striatum miRNA rep2


title: Het (Q140) 6 months Male Striatum miRNA rep1


title: Het (Q140) 10 months Male Striatum miRNA rep4


title: Het (Q140) 10 months Male Striatum miRNA rep3


title: Het (Q20) 10 months Male Striatum miRNA rep2


title: Het (Q140) 10 months Male Striatum miRNA rep2


title: Het (Q140) 6 months Female Striatum miRNA rep4


title: Het (Q140) 10 months Male Striatum miRNA rep1


title: Het (Q20) 10 months Male Striatum miRNA rep4


title: Het (Q140) 6 months Female Striatum miRNA rep3


title: Het (Q140) 10 months Female Striatum miRNA rep3


title: Het (Q140) 10 months Female Striatum miRNA rep2


title: Het (Q140) 6 months Female Striatum miRNA rep2


title: Het (Q140) 10 months Female Striatum miRNA rep4


title: Het (Q140) 6 months Female Striatum miRNA rep1


title: (-7d) sequencing

city: Tai'an

first: yuanyuan

last: gao

address: Daizong Street 61#

institute: Shandong Agricultural University

data_processing:
Illumina HiSeqTM 2000 Systerm was used to sequencing
Raw sequences were transformed into clean tags after filtering low-quality sequences and impurities.
Alignment statistics of the clean tags were performed.
Gene expression annotation was performed. All clean tags were mapped to the bovine reference sequences. And the number of unambiguous clean tags for each gene was normalized to TPM.
Genome_build: Bos taurus genome 3.1
Supplementary_files_format_and_content: txt files include TPM values for each Sample ...

organism: Bos taurus

source_name: Mammary gland

extract_protocol:
Mammary tissue was removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina Gene Expression Sample Prep Kit was used with 6μg of total RNA for the construction of sequencing libraries.
Libraries were prepared for sequencing using standard Illumina protocols

value: mammary tissue

tag: Stage

value: day 7 before parturition

value: the second parity


title: (-35d) sequencing

value: day 35 before parturition


title: Het (Q140) 10 months Female Striatum miRNA rep1

value: Female


title: (+3d) sequencing

value: day 3 after parturition


title: WT 6 months Male Liver miRNA rep4 (Q50)

source_name: Liver

value: Liver

value: Wild Type

value: 6 months

value: Male

value: housed with Wild Type and Het (Q50) mice


title: WT 6 months Male Liver miRNA rep3 (Q50)


title: EWS-FLI1-HA-ChipSeq

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

data_processing:
Basecalls was performed using BaseSpace.
Sequenced data was trimmed for adaptor sequence  by Cutadapt softweare to remove adapter sequences with parameter -q 20 -m 20 .
Chip-seq reads were aligned to the mm9 genome assembly using Bowtie2 version 2.2.0 -p 4 -q .
Genome_build: mm9
Supplementary_files_format_and_content: MACS called peaks

source_name: SCOS#2 Dox ON 72h_ChIP

growth_protocol: DMEM+10%FBS+PS (SCOS#2 and #12)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. We used anti HA antibody(Monoclonal Mouse IgG 1-κ):Nacalai cat# 06340-54 Lot#M4H0340.
Libraries were prepared according to illumina'sTrueseq ChIP sample prep kit set A(Part#IP-202-1012)

treatment_protocol: SCOS#2 Dox ON samples were treated with Dox (2µg/ml) containing medium for 72hours.


title: input DNA

source_name: SCOS#2 Dox ON 72h_input


title: WT 6 months Male Liver miRNA rep2 (Q50)


title: WT 10 months Male Liver miRNA rep4 (Q50)


title: WT 6 months Male Liver miRNA rep1 (Q50)


title: WT 10 months Male Liver miRNA rep3 (Q50)


title: WT 10 months Male Liver miRNA rep2 (Q50)


title: WT 10 months Male Liver miRNA rep1 (Q50)


title: WT 6 months Male Liver miRNA rep4 (Q20)

value: housed with Wild Type and Het (Q20) mice


title: Wild-type (N2)-Replicate-2

city: Delhi

first: Arnab

last: Mukhopadhyay

state: Delhi

address: Aruna asaf ali marg

country: India

institute: National Institute of Immunology

data_processing:
Demultiplexing and conversion of BCL file format reads to FASTQ file format was done with Illumina CASAVA v1.8.2 software package
Reads were trimmed off to remove adapter sequence, if any, and to filter out the reads ≤ 15 bp using CLC Genomics Workbech v6.5.1
Quality filtered reads were aligned to the C. elegans annotated reference genome (W230) using CLC Genomics Workbench v6.5.1
RPKM (Reads Per Kilobase of exon model per Million mapped reads) were calculated using default parameters. Biological replicates of different samples were compared  with two group comparison as independent measurement (one group of genes are controls and another group of genes as treat) by using the gene RPKM. Significant fold changes (P≤ 0.05, fold change ≥ 2) were selected by applying beta-binomial Baggerley’s test
Supplementary_files_format_and_content: abundance measurement

organism: Caenorhabditis elegans

source_name: mix stage culture

growth_protocol: Wild-type (N2), daf-2 (e1370), daf-16(mgDf50);daf-2(e1370) and daf-2(e1370);daf-12(m20)mutant worm strains were obtained from Caenorhabditis Genetics Centre (Minneapolis,  MN, USA). Mixed culture of worms were grown on 15-20 OP50 E coli. seeded 150 X 15 mm NGM (Nematode Growth Media)  petri-plates maintained at 20 °C.

extract_protocol:
Worms were grown for mixed culture from different strains on OP50 E coli. seeded 90 mm plates for RNA isolation.  The pellet was forzen in 250 µl TRIzol reagent (Invitrogen part # 15596-026) and kept at -80 °C after washing four times in M9 buffer. Total RNA was isolated as per manufacturer protocol from the frozen pellet
RNA quality was checked on a 2100 Bioanalyzer by using the RNA 6000 Nano Kit (Agilent Technologies, USA). RNA with RNA integrity number (RIN) > 9 was selected for library preparation.  The RNA library was prepared using the TrueSeq RNA SamplePrep V2 kit (Illumina, USA) according to manufacturer-provided specifications.

tag: culture

value: Mix Culture

tag: temperature

value: 20 °C

value: Wild-type (N2)


title: Wild-type (N2)-Replicate-1


title: daf-2(-)-Replicate-2


title: daf-16(-);daf-2(-)-Replicate-2


title: WT 6 months Male Liver miRNA rep2 (Q20)


title: DAF-16 input_daf-16(-)

data_processing:
Demultiplexing and conversion of BCL file format reads to FASTQ file format was done with Illumina CASAVA v1.8.2 software package
Quality filtered reads were aligned to the C. elegans annotated reference genome (W230) using Bowtie v.0.12.7 with parameters: -q -m 1 --best --strata
Peak calling was done with uniquely aligned reads containing no more than one mismatch using peak calling algorithm MACS v1.4.2 with parameters: --mfold=5,30 --bw=175 -w
Genome_build: C. elegans annotated reference genome (W230)
Supplementary_files_format_and_content: peak and summit file

growth_protocol: Wild-type (N2), daf-2 (e1370), daf-16(mgDf50);daf-2(e1370) and daf-16(mgDf50)mutant worm strains were obtained from Caenorhabditis Genetics Centre (Minneapolis,  MN, USA). Mixed culture of worms were grown on 15-20 OP50 E coli. seeded 150 X 15 mm NGM (Nematode Growth Media)  petri-plates maintained at 20 °C.

extract_protocol:
Worms were harvested from plates with 1 X PBS buffer and washed four times. The compact worm slurry (250 µl) was resuspended in 4 ml cross-linking buffer (1% formaldehyde in 1 X PBS) followed by homogenization with 7 ml glass Dounce homogenizer.
A total of 5 ng of DNA was used as a starting material for library preparation according to the Illumina, Inc. ( San Diego, CA, USA) protocol, "Preparing Samples for ChIP Sequencing of DNA".

tag: developmental stage


title: daf-2(-)-Replicate-1


title: DAF-16 input_daf-16(-);daf-2(-)


title: WT 6 months Male Liver miRNA rep1 (Q20)


title: DAF-16 chip_daf-16(-)


title: WT 6 months Male Liver miRNA rep3 (Q20)


title: daf-16(-);daf-2(-)-Replicate-1


title: WT 10 months Male Liver miRNA rep2 (Q20)


title: DAF-16 input_wild-type (N2)


title: WT 10 months Male Liver miRNA rep3 (Q20)


title: DAF-16 chip_wild-type (N2)


title: DAF-16 chip_daf-16(-);daf-2(-)


title: WT 6 months Female Liver miRNA rep3 (Q50)


title: WT 6 months Female Liver miRNA rep4 (Q50)


title: DAF-16 input_daf-2 (e1370)

data_processing:
Demultiplexing and conversion of BCL file format reads to FASTQ file format was done with Illumina CASAVA v1.8.2 software package
Quality filtered reads were aligned to the C. elegans annotated reference genome (W235) using Bowtie v.0.12.7 with parameters: -q -m 1 --best --strata
Peak calling was done with uniquely aligned reads containing no more than one mismatch using peak calling algorithm MACS v1.4.2 with parameters: --mfold=5,30 --bw=175 -w
Genome_build: C. elegans annotated reference genome (W235)
Supplementary_files_format_and_content: Tag density file

growth_protocol: daf-2 (e1370)mutant worm strains were obtained from Caenorhabditis Genetics Centre (Minneapolis,  MN, USA). Mixed culture of worms were grown on 15-20 OP50 E coli. seeded 150 X 15 mm NGM (Nematode Growth Media)  petri-plates maintained at 20 °C.

tag: chip antibody

value: input


title: DAF-16 chip_daf-2 (e1370)


title: WT 6 months Female Liver miRNA rep2 (Q50)


title: WT 6 months Female Liver miRNA rep1 (Q50)


title: WT 10 months Female Liver miRNA rep4 (Q50)

value: 10 months


title: WT 10 months Male Liver miRNA rep4 (Q20)


title: cKO ctrl-b

city: Columbus

first: Katelin

middle: Libby

last: Hansen

state: OH

address: 333 W. 10th Ave

department: Neuroscience

institute: The Ohio State University

description: Processed data in: miR132Normal_vs_miR132KO_PairWiseCommon_AllFilteredGenes.txt

data_processing:
Base-calling was conducted with the standard Illumina Analysis Pipeline 1.0 (Firescrest-Bustard)
FASTQ sequence files (sequencing reads plus quality information) were generated and mapped to the mouse genome (UCSC mm9) using the Bowtie algorithm with default settings.
A C++ program was used to count the number of uniquely mapped reads within exons of Ref-Seq genes (UCSC Genome Browser mm9 annotation)
RefSeq gene sequence counts were median normalized and overlapping gene IDs were discarded.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files with raw and normalized reads for each sample, as well as fold change values

source_name: Hippocampus

extract_protocol:
Animals were sacrificed by cervical dislocation and hippocampi were removed bilaterally and subjected to total RNA extraction by TRIzol (Invitrogen #15596-018) as per manufacturer instructions. Polyadenylated RNA was purified by Dynabeads® mRNA purification kit (Life Technologies #61006). As per manufacturer protocol, 1µg of total RNA was incubated at 50°C for 2 min and placed on ice. The sample was added to Dynabeads® with 50µL binding buffer, mixed thoroughly at room temperature for 5 min, washed twice, and then eluted into 10 µL 10 mM Tris-HCl (pH 7.5) by heating to 70°C for 2 min. Purified mRNA was treated with DNase I (Life Technologies #18068015) at 37°C for 30 min followed by 70°C for 5 min. For first strand synthesis, 10µL of the digestion product, 1µL oligo(dT)18 (500 ug/ml), and 1μl 10 mM dNTP mix were mixed. Samples were heated to 65°C for 5 minutes and incubated on ice. Four microliters of 5X First-Strand Buffer, 2μl of 0.1 M DTT, and 1μl of RNaseOUT Recombinant RNase Inhibitor (Life Technologies #10777-019) were added and incubated at 37°C for 2 min. One microliter of MMLV reverse transcriptase (Life Technologies #26025) was added to samples, which were then incubated at 37°C for 50 minutes, followed by a five-minute inactivation at  70°. cDNA was then treated with NEBNEXT mRNA second strand synthesis  mix (neb #e6112) and incubated for 2.5 hours at  16°C, followed by sonication for 10 seconds.  Samples were purified on a PCR column (Fermentas #K0702) and eluted in 22µl 10 mM Tris pH 8.
Blunt ends were prepared using the DNATerminator® End Repair Kit (Lucigen #40035). Samples were purified using AMPure xp beads (Beckman #A63880) and A-tailing of 3’ ends of eluted cDNA was performed using Exo-minus Klenow DNA polymerase (Epicentre #KL0810259) at 37°C for 30 min. Uniquely tagged Illumina genomic adopters were ligated by Enzymatics T4 DNA ligase (Invitrogen #15224) at RT for 2hrs.  Size visualization was performed using a 2% agarose gel, yielding cDNA libraries ranging in size from 200–250 bp, which were amplified by PCR (5 sec at 98°C; 10 sec at 72°C; 10-20 cycles) using Phusion High-Fidelity DNA Polymerase (ThermoScientific #F530) .

tag: genotype/variation

value: cKO non-transgenic control


title: cKO ctrl-c


title: WT 10 months Female Liver miRNA rep2 (Q50)


title: miR132212 cKO-c


title: cKO ctrl-a


title: WT 10 months Female Liver miRNA rep3 (Q50)


title: miR132212 cKO-b


title: miR132212 cKO-a


title: WT 10 months Male Liver miRNA rep1 (Q20)


title: WT 6 months Female Liver miRNA rep3 (Q20)


title: WT 6 months Female Liver miRNA rep4 (Q20)


title: WT 6 months Female Liver miRNA rep2 (Q20)


title: miR132 ctrl-b

description: Processed data in: miR132OverExpression_vs_Control_PairWiseCommon_AllFilteredGenes.txt

value: miR132 non-transgenic control


title: WT 6 months Female Liver miRNA rep1 (Q20)


title: WT 10 months Female Liver miRNA rep4 (Q20)


title: miR132 ctrl-a


title: WT 10 months Female Liver miRNA rep3 (Q20)


title: WT 10 months Female Liver miRNA rep2 (Q20)


title: WT 10 months Female Liver miRNA rep1 (Q20)


title: tTA:miR132-a


title: miR212 ctrl-c

description: Processed data in: 212_tran1to3_vs_212_con1to3_30_DESeq2_AllFilteredGenes.xls

value: miR212 non-transgenic control


title: miR212 ctrl-b


title: Het (Q92) 6 months Male Liver miRNA rep4

value: Het (Q92) Knock-In

value: housed with Het (Q92) mice


title: miR212 ctrl-a


title: tTA:miR212-c


title: Het (Q92) 6 months Male Liver miRNA rep3


title: WT 10 months Female Liver miRNA rep1 (Q50)

value: Female


title: Het (Q92) 6 months Male Liver miRNA rep2

value: Liver


title: tTA:miR212-b


title: Het (Q92) 6 months Male Liver miRNA rep1


title: Het (Q92) 10 months Male Liver miRNA rep4


title: tTA:miR132-c


title: miR132 ctrl-c


title: Het (Q92) 10 months Male Liver miRNA rep1


title: tTA:miR212-a


title: Het (Q92) 6 months Female Liver miRNA rep2


title: Het (Q92) 10 months Male Liver miRNA rep2


title: Het (Q92) 10 months Female Liver miRNA rep2


title: Het (Q92) 10 months Male Liver miRNA rep3


title: Het (Q92) 6 months Female Liver miRNA rep3


title: Het (Q92) 10 months Female Liver miRNA rep1


title: Het (Q92) 6 months Female Liver miRNA rep4


title: tTA:miR132-b


title: Het (Q92) 6 months Female Liver miRNA rep1


title: Het (Q92) 10 months Female Liver miRNA rep3


title: Het (Q50) 6 months Male Liver miRNA rep4

value: Het (Q50) Knock-In


title: Het (Q50) 6 months Male Liver miRNA rep2

value: 6 months


title: Het (Q50) 6 months Male Liver miRNA rep1

value: Male


title: Het (Q50) 6 months Male Liver miRNA rep3

value: housed with Wild Type and Het (Q50) mice


title: Het (Q50) 10 months Male Liver miRNA rep4


title: Het (Q50) 10 months Male Liver miRNA rep3


title: Het (Q50) 6 months Female Liver miRNA rep4


title: Het (Q50) 6 months Female Liver miRNA rep3


title: Het (Q50) 10 months Male Liver miRNA rep1


title: Het (Q50) 6 months Female Liver miRNA rep2


title: Het (Q50) 10 months Male Liver miRNA rep2


title: Het (Q92) 10 months Female Liver miRNA rep4


title: Het (Q50) 6 months Female Liver miRNA rep1


title: Het (Q50) 10 months Female Liver miRNA rep3


title: Het (Q50) 10 months Female Liver miRNA rep2


title: Het (Q50) 10 months Female Liver miRNA rep4


title: Het (Q50) 10 months Female Liver miRNA rep1


title: Het (Q20) 6 months Male Liver miRNA rep3

value: Het (Q20) Knock-In

value: housed with Wild Type and Het (Q20) mice


title: Het (Q20) 6 months Male Liver miRNA rep1


title: Het (Q20) 10 months Male Liver miRNA rep4


title: Het (Q20) 6 months Male Liver miRNA rep4


title: Het (Q20) 6 months Male Liver miRNA rep2


title: Het (Q20) 10 months Male Liver miRNA rep3


title: Het (Q20) 10 months Male Liver miRNA rep1


title: Het (Q20) 6 months Female Liver miRNA rep3


title: Day 14 Reporter Positive H441 Cells IAV Secondary Infection (Fig 2 A-E)

city: Durham

first: Nicholas

last: Heaton

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

data_processing:
The reads were mapped to the mouse or human transcriptome as well as the influenza genome using Bowtie
Read numbers were normalized across samples.

source_name: Cell Culture

growth_protocol: Cells were grown under standard laboratory conditions.

extract_protocol:
Cells were sorted by a facs aira into wells of a 96 well plate containing RNA protection buffer.
TruSeq Nano DNA sample Preparation Kit (Illumina) was used as per the manufacturer’s instructions.

treatment_protocol: Mice or cells were infected for the indicated times.

tag: sequencing

value: Double Lane

tag: sample type


title: Day 2 IAV Infected H441 Cells (Fig 2 A-E)

value: Day 2 IAV Infected H441 Cells


title: WT 6 months Female Striatum miRNA rep4 (Q50)

value: Striatum

value: Wild Type

tag: age


title: Het (Q20) 6 months Female Liver miRNA rep2

tag: Sex


title: Het (Q20) 10 months Male Liver miRNA rep2

value: 10 months

tag: housing condition


title: Naïve Reporter- H441 Cells (Fig 2 A-E)

value: Naïve Reporter- H441 Cells


title: WT 10 months Female Striatum miRNA rep1 (Q20)


title: Day 14 Reporter Positive H441 Cells No Secondary Infection (Fig 2 A-E)


title: Het (Q20) 6 months Female Liver miRNA rep1


title: Het (Q20) 10 months Female Liver miRNA rep4


title: Day 14 Reporter+ H441 Cells (Fig 1 C-I)

value: Single Lane

value: Day 14 Reporter+ H441 Cells


title: Day 24 Reporter+ H441 Cells (Fig 1 C-I)

value: Day 24 Reporter+ H441 Cells


title: Day 7 Reporter+ H441 Cells (Fig 1 C-I)

value: Day 7 Reporter+ H441 Cells


title: Day 5 Reporter+ H441 Cells (Fig 1 C-I)

value: Day 5 Reporter+ H441 Cells


title: Het (Q20) 10 months Female Liver miRNA rep3

value: Liver

value: Female


title: Het (Q20) 10 months Female Liver miRNA rep2


title: Day 2 Reporter+ H441 Cells (Fig 1 C-I)

value: Day 2 Reporter+ H441 Cells


title: Naïve Reporter- H441 Cells (Fig 1 C-I)


title: Het (Q140) 6 months Male Liver miRNA rep4

value: Het (Q140) Knock-In

value: 6 months

value: Male

value: housed with Het (Q140) mice


title: Het (Q140) 6 months Male Liver miRNA rep2


title: Het (Q140) 6 months Male Liver miRNA rep3


title: Het (Q20) 6 months Female Liver miRNA rep4

value: Het (Q20) Knock-In

value: housed with Wild Type and Het (Q20) mice


title: Het (Q140) 6 months Male Liver miRNA rep1


title: Het (Q140) 10 months Male Liver miRNA rep3


title: Het (Q140) 10 months Male Liver miRNA rep4


title: MAP_7

city: CAPE TOWN

first: DAN

last: STEIN

address: Rondebosch

department: DEPARTMENT OF PSYCHIATRY

institute: UNIVERSITY OF CAPE TOWN

data_processing:
Illumina Casavav1.8.2 software used for basecalling.
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence using Trimmomatic options SLIDINGWIDOW:90:10 MINLEN:90 CROP:90. Remaining reads were then mapped to hg19 UCSC human genome using TopHat v2.0.0 with estimated mean inner distance and standard deviation between mate paired-ends as the -r and --mate-std-dev parameters, respectively.
Genes with low counts were removed by unspecific filtering. Following, voom transformation was performed on raw counts as described by Law et al., Genome Biology 2014.
Htseq v0.6.0 was used to count all of the mapped reads by htseq-count using parameters -stranded=reverse-q.
Unspecific filtering removed lowly expressed genes and genes with more than 20 reads in at least 10 subjects were retained and normalied with EgeR VOOM normalization.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include raw count values and VOOM transformed values for each sample are provided as two seperate matrices.

source_name: Human peripheral blood

extract_protocol:
RNA was extracted and purified in accordance with the PAX gene RNA kit per manufacterer's instructions. Globin mRNA was depleted from samples using GLOBINclear - Human Kit (Life Technologies, USA).
RNA libraries were prepared for sequencing using stranded Illumina Tru-Seq protocols using the Illumina HiSeq 2000.

treatment_protocol: Blood was collected in PAXgene tubes (Qiagen, CA, USA).

tag: condition

value: METH-Associated Psychosis

value: blood


title: MAP_6


title: MAP_4


title: MAP_9


title: MAP_5


title: Het (Q140) 10 months Male Liver miRNA rep1

value: 10 months


title: MAP_8


title: Het (Q140) 10 months Male Liver miRNA rep2


title: Het (Q140) 6 months Female Liver miRNA rep4


title: MAP_3


title: MAP_2


title: Het (Q140) 6 months Female Liver miRNA rep3


title: Het (Q140) 6 months Female Liver miRNA rep2


title: Het (Q140) 6 months Female Liver miRNA rep1


title: MA_10

value: METH-Dependency without Psychosis


title: MAP_1


title: Het (Q140) 10 months Female Liver miRNA rep3


title: MA_8


title: MA_9


title: MA_7


title: Het (Q140) 10 months Female Liver miRNA rep4


title: Het (Q20) 10 months Female Liver miRNA rep1


title: Het (Q140) 10 months Female Liver miRNA rep2


title: MAP_10


title: WT 6 months Male Cortex miRNA rep4 (Q50)

source_name: Cortex

value: Cortex

value: Wild Type

value: housed with Wild Type and Het (Q50) mice


title: MA_5


title: MA_4


title: WT 6 months Male Cortex miRNA rep1 (Q50)


title: WT 10 months Male Cortex miRNA rep3 (Q50)


title: WT 10 months Male Cortex miRNA rep4 (Q50)


title: MA_3


title: WT 6 months Male Cortex miRNA rep2 (Q50)


title: MA_2


title: WT 6 months Male Cortex miRNA rep4 (Q20)


title: CONTROL_9

value: Control


title: CONTROL_7


title: Het (Q140) 10 months Female Liver miRNA rep1

value: Liver


title: CONTROL_8


title: WT 6 months Male Cortex miRNA rep3 (Q20)


title: WT 6 months Male Cortex miRNA rep1 (Q20)


title: WT 10 months Male Cortex miRNA rep4 (Q20)


title: WT 10 months Male Cortex miRNA rep1 (Q50)


title: WT 6 months Male Cortex miRNA rep2 (Q20)


title: CONTROL_3


title: CONTROL_2


title: CONTROL_4


title: CONTROL_5


title: MA_6


title: WT 10 months Male Cortex miRNA rep3 (Q20)


title: WT 6 months Male Cortex miRNA rep3 (Q50)


title: WT 10 months Male Cortex miRNA rep2 (Q20)


title: CONTROL_1


title: WT 10 months Male Cortex miRNA rep1 (Q20)


title: CONTROL_10


title: MA_1


title: WT 10 months Male Cortex miRNA rep2 (Q50)


title: WT 6 months Female Cortex miRNA rep4 (Q50)

value: Female


title: WT 6 months Female Cortex miRNA rep3 (Q50)


title: K562, siRNA aCP1/2 combined knockdown, rep2

city: Los Angeles

first: Yu-Ting

last: Tseng

state: California

address: 650 Charles E. Young Drive South

department: Department of Microbiology, Immunology, & Molecular Genetics

institute: University of California, Los Angeles

description: aCP KD

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to Ensembl human transcript (release 72) then hg19 whole genome using tophat v1.4.1 with parameters -a 8 -m 0 -I 300000 -p 8 -g 20 --library-type fr-unstranded -initial-read-mismatches 3 --segment-mismatches 2
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using cuffdiff v2.2.0 with uniquely and properly mapped reads.
Genome_build: hg19

source_name: K562, siRNA aCP1/2 combined knockdown

extract_protocol:
K562 cells were harvested 72 hours after the siRNA transfection and RNAs were purified using Absolutely RNA miniprep Kit (Stratagene) according to manufacturer’s instruction.
Libraries for RNA-seq analysis were constructed using the TruSeq RNA Sample Preparation Kit V1 according to manufacturer’s instruction. The libraries corresponded to the 3 control siRNA depletions  and 3 aCP1/2 co-depletions. These libraries were multiplexed and sequenced on a single channel on the Hiseq-2000 platform using a 100nt paired-end sequencing protocol by NGSC at University of Pennsylvania.

tag: cell line

tag: diagnosis

value: Leukemia


title: K562, siRNA aCP1/2 combined knockdown, rep1

description: aCP KD


title: K562, siRNA aCP1/2 combined knockdown, rep3

description: aCP KD


title: CONTROL_6


title: WT 6 months Female Cortex miRNA rep2 (Q50)

tag: genotype


title: K562, control siRNA knockdown, rep2

description: aCP CTRL

source_name: K562, control siRNA knockdown


title: WT 10 months Female Cortex miRNA rep3 (Q50)

tag: strain


title: K562, control siRNA knockdown, rep1

description: aCP CTRL


title: Ca_26_RNA

city: Beijing

first: Yu

last: Hou

address: No.5 Yiheyuan Street

institute: Peking University

description: single cell RNA seq

source_name: human adult cancer cell

extract_protocol:
The RNA and DNA of each single cell were separated and extracted by Trio-seq.
For RNA seq and genome DNA seq data, we constructed the sequencing libraries using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #7370L). RRBS libraries were constructed using RRBS protocol as described in 2013 (Guo et al. 2013)

tag: gender

tag: tissue

value: liver cancer

tag: passage


title: WT 10 months Female Cortex miRNA rep2 (Q50)


title: WT 10 months Female Cortex miRNA rep1 (Q50)


title: WT 10 months Female Cortex miRNA rep4 (Q50)


title: K562, control siRNA knockdown, rep3

description: aCP CTRL


title: Ca_26_RRBS

description: single cell RRBS


title: Ca_25_RRBS

description: single cell RRBS


title: Ca_25_RNA

description: single cell RNA seq


title: WT 6 months Female Cortex miRNA rep4 (Q20)

value: 6 months


title: Ca_24_RNA

description: single cell RNA seq

value: Male


title: Ca_24_RRBS

description: single cell RRBS


title: Ca_23_RNA

description: single cell RNA seq


title: WT 6 months Female Cortex miRNA rep2 (Q20)


title: WT 6 months Female Cortex miRNA rep1 (Q20)


title: Ca_22_RNA

description: single cell RNA seq


title: Ca_23_RRBS

description: single cell RRBS


title: WT 6 months Female Cortex miRNA rep3 (Q20)


title: WT 6 months Female Cortex miRNA rep1 (Q50)


title: WT 10 months Female Cortex miRNA rep3 (Q20)


title: WT 10 months Female Cortex miRNA rep2 (Q20)


title: Ca_22_RRBS

description: single cell RRBS


title: Het (Q92) 6 months Male Cortex miRNA rep4

value: Het (Q92) Knock-In

value: housed with Het (Q92) mice


title: Ca_21_RRBS

description: single cell RRBS


title: Het (Q92) 6 months Male Cortex miRNA rep3


title: Ca_20_RNA

description: single cell RNA seq


title: WT 10 months Female Cortex miRNA rep4 (Q20)

value: housed with Wild Type and Het (Q20) mice


title: Het (Q92) 6 months Male Cortex miRNA rep1


title: Ca_19_RNA

description: single cell RNA seq


title: Ca_19_RRBS

description: single cell RRBS


title: Het (Q92) 10 months Male Cortex miRNA rep2


title: Het (Q92) 10 months Male Cortex miRNA rep3


title: Ca_18_RNA

description: single cell RNA seq


title: Ca_18_RRBS

description: single cell RRBS


title: Het (Q92) 10 months Male Cortex miRNA rep1


title: Ca_17_RNA

description: single cell RNA seq


title: Ca_17_RRBS

description: single cell RRBS


title: WT 10 months Female Cortex miRNA rep1 (Q20)


title: Ca_16_RRBS

description: single cell RRBS


title: Ca_21_RNA

description: single cell RNA seq


title: Ca_15_RNA

description: single cell RNA seq


title: Ca_16_RNA

description: single cell RNA seq


title: Ca_15_RRBS

description: single cell RRBS


title: Ca_14_RRBS

description: single cell RRBS


title: Ca_20_RRBS

description: single cell RRBS


title: Ca_14_RNA

description: single cell RNA seq


title: Het (Q92) 10 months Male Cortex miRNA rep4


title: Het (Q92) 10 months Female Cortex miRNA rep4


title: Het (Q92) 6 months Female Cortex miRNA rep2


title: Het (Q92) 6 months Female Cortex miRNA rep4


title: Het (Q92) 10 months Female Cortex miRNA rep1


title: Het (Q92) 6 months Female Cortex miRNA rep3


title: Het (Q92) 10 months Female Cortex miRNA rep3


title: Het (Q92) 10 months Female Cortex miRNA rep2


title: Het (Q92) 6 months Female Cortex miRNA rep1


title: Ca_12_RNA

description: single cell RNA seq


title: Ca_12_RRBS

description: single cell RRBS


title: Het (Q50) 6 months Male Cortex miRNA rep2

value: Het (Q50) Knock-In


title: Ca_11_RRBS

description: single cell RRBS


title: Het (Q50) 6 months Male Cortex miRNA rep1


title: Het (Q50) 10 months Male Cortex miRNA rep4


title: Ca_10_RNA

description: single cell RNA seq


title: Het (Q50) 10 months Male Cortex miRNA rep3


title: Het (Q92) 6 months Male Cortex miRNA rep2


title: Ca_10_RRBS

description: single cell RRBS


title: Het (Q50) 10 months Male Cortex miRNA rep2


title: Ca_13_RNA

description: single cell RNA seq


title: Ca_09_RNA

description: single cell RNA seq


title: Het (Q50) 10 months Male Cortex miRNA rep1


title: Ca_09_RRBS

description: single cell RRBS


title: Ca_08_RNA

description: single cell RNA seq


title: Het (Q50) 6 months Male Cortex miRNA rep4


title: Het (Q50) 6 months Female Cortex miRNA rep4


title: Ca_11_RNA

description: single cell RNA seq


title: Ca_08_RRBS

description: single cell RRBS


title: Ca_07_RRBS

description: single cell RRBS


title: Het (Q50) 10 months Female Cortex miRNA rep3


title: Het (Q50) 6 months Female Cortex miRNA rep2


title: Ca_06_RNA

description: single cell RNA seq


title: Ca_06_RRBS

description: single cell RRBS


title: Het (Q50) 6 months Female Cortex miRNA rep1


title: Het (Q50) 10 months Female Cortex miRNA rep2


title: Ca_07_RNA

description: single cell RNA seq


title: yjm789_ypd_S1

city: Morgantown

first: Xiaoqing

last: Rong-Mullins

state: West Virginia

address: 53 Campus Dr

institute: West Virginia University

data_processing:
Base-calling was performed via Illumina CASAVA version 1.7.
Tophat v2.0.12 (Kim et al. 2013; Trapnell et al. 2009) was used to map the RNA-Seq reads to the S288c genome and to generate .bam files for mapped reads. The reads were first mapped to ribosomal RNA and transfer RNA genes; 1.05-1.94 million read pairs per sample were not matched to those RNA genes, and 91.2-95.5% of those unmatched reads were then matched to the whole gene pool of S288c. The reads matched to rRNA and tRNA were excluded because these RNAs tend to be extracted at high and/or variable abundances across replicates, thus may bias the calculation of FPKM (fragments per kb gene per million mapped fragments).
The following approach was used to quantify gene expression from the mapped reads in .bam files. The R-package Rsubread v1.18.0 (Liao et al. 2013) was used to generate count tables based on the annotations of S288c genome release R64-1-1. Then DESeq2 v1.8.1 (Anders and Huber, 2010) was used to quantify differential expression.
Genome_build: sacCer3
Supplementary_files_format_and_content: Table S1 as a single .xlsx file with multiple worksheets: Read counts and differential expression data from RNA-Seq. In each comparison for differential expression in the format of 'condition_A...condition_B', condition_A is the denominator and condition_B is the numerator when calculating fold change. • Rsubread_count_table: count table generated by Rsubread package, input for differential expression analysis by DESeq2 package. • Rsubread_FPKM: FPKM data calculated based on 'Rsubread_count_table'. • DESeq: differential expression data generated by DESeq2 package.

organism: Saccharomyces cerevisiae

source_name: yeast cells

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

extract_protocol:
Total RNA was extracted from each sample and multiplexed unstranded paired-end cDNA libraries were prepared using Illumina TruSeq RNA Sample Prep Kit v2.
RNA libraries were prepared for sequencing on Illumina MiSeq using standard Illumina protocols

value: S96 YRR1_delta

tag: yrr1_ allele transformed

tag: growth medium

value: YPD


title: yjm789_ypd_S2


title: Ca_05_RNA

description: single cell RNA seq


title: yjm789_nqo_S8

value: YPD + 4NQO


title: Het (Q50) 10 months Female Cortex miRNA rep1

value: Cortex

value: 10 months