title: 37EF3 - 252741411855

description: BaP Exposure


title: 37BM2 - 252741411895

status: Public on Apr 29 2019

type: genomic

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description: BaP Exposure

hyb_protocol: Hybridization was performed using the protocol recommended by the manufacturer.

scan_protocol: The hybridized slides were scanned using an Agilent C scanner and Feature Extraction v10.5 was used to extract the data.

data_processing:
Non-uniform features (outlier probes with signals influenced by array position) were removed from analysis. The algorithms previously used by Adewoye et al. were applied to detect autosomal CNVs as genomic segments with parent vs. offspring fluorescent signal log2 ratios above or below threshold values as described previously.
Following Feature Extraction, signal intensities (Cy3 and Cy5) were background subtracted and then normalized (Lowess normalization using Rank invariant probes). Log2 ratios of the Cy5/Cy3 were used for the analysis.

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse tissue

label_protocol: One µg of offspring DNA was labelled with Cy5 dye (5190-3400 SureTag DNA Labeling Kit). Five hundred ng of DNA from each respective parent were mixed together and labelled with Cy3 dye. As positive controls, and to identify existing strain differences, two additional arrays were used to compare MutaMouse with C57BL/6J DNA. DNA labelled with Cy3 and Cy5 were mixed together for hybridization onto the CGH array.

extract_protocol: DNA was extracted from the liver of each animal using the DNeasy Blood & Tissue Kit as per the manufacturer’s instructions.

treatment_protocol: Twelve MutaMouse males (BALB/C × DBA/2) approximately 15 weeks of age, were exposed daily to BaP (Sigma-Aldrich, Oakville, Ontario, Canada) dissolved in olive oil (Sigma-Aldrich; highly refined, low acidity) via oral gavage (approximately 150 µL) for 28 days (100 mg/kg body weight/day). Twelve concurrent males received olive oil and served as negative controls. Three days after the last treatment all males were mated with four C57Bl/6J females each over a two-week period to produce offspring

tag: treatment

value: BaP Exposure

tag: Sex

value: Male

tag: tissue

value: Liver

value: pooled male and female


title: 37HF1 - 252741410777

description: BaP Exposure

value: Female


title: 37BM3 - 252741411918

description: BaP Exposure


title: 37EF4 - 252741411802

description: BaP Exposure


title: 37HF3 - 252741411875

description: BaP Exposure


title: 37BF3 - 252741411901

description: BaP Exposure


title: 37BF2 - 252741411900

description: BaP Exposure


title: 37BM1 - 252741411894

description: BaP Exposure


title: 37BF1 - 252741411898

description: BaP Exposure


title: 37AM4 - 252741411762

description: BaP Exposure


title: 37AM2 - 252741411760

description: BaP Exposure


title: 37AM3 - 252741411761

description: BaP Exposure


title: 38AF2 - 252741411752

description: BaP Exposure


title: 37HM7 - 252741411874

description: BaP Exposure


title: 37AF3 - 252741411849

description: BaP Exposure


title: 37AM1 - 252741411759

description: BaP Exposure


title: 37AF1 - 252741411814

description: BaP Exposure


title: 35HM1 - 252741411862

description: BaP Exposure


title: 35HM3 - 252741411879

description: BaP Exposure


title: 35HF2 - 252741411881

description: BaP Exposure


title: 37EF2 - 252741411854

description: BaP Exposure


title: 35EM5 - 252741411768

description: BaP Exposure


title: 35EM3 - 252741411029

description: BaP Exposure


title: 35EM2 - 252741411028

description: BaP Exposure


title: 35EF3 - 252741411046

description: BaP Exposure


title: 35EF5 - 252741411861

description: BaP Exposure


title: 35EF4 - 252741411062

description: BaP Exposure


title: 35EM1 - 252741411027

description: BaP Exposure


title: 35EF6 - 252741411884

description: BaP Exposure


title: 35EF2 - 252741411056

description: BaP Exposure


title: 35EF1 - 252741411055

description: BaP Exposure


title: 35AM1 - 252741411803

description: BaP Exposure


title: 33GM3 - 252741411842

description: BaP Exposure


title: 35AF1 - 252741411821

description: BaP Exposure


title: 35AF2 - 252741411822

description: BaP Exposure


title: 37AF2 - 252741411763

description: BaP Exposure


title: 33GF1 - 252741411843

description: BaP Exposure


title: 33GF2 - 252741411859

description: BaP Exposure


title: 33GM1 - 252741411782

description: BaP Exposure


title: 35HM2 - 252741411885

description: BaP Exposure


title: 33FM3 - 252741410830

description: BaP Exposure


title: 35HF1 - 252741411880

description: BaP Exposure


title: 33FF5 - 252741411738

description: BaP Exposure


title: 33FM1 - 252741410665

description: BaP Exposure


title: 33FF3 - 252741410844

description: BaP Exposure


title: 35EM4 - 252741411063

description: BaP Exposure


title: 33FF1 - 252741410842

description: BaP Exposure


title: 33DF4 - 252741411889

description: BaP Exposure


title: 33DM1 - 252741411906

description: BaP Exposure


title: 33DM3 - 252741411925

description: BaP Exposure


title: 33DF3 - 252741411927

description: BaP Exposure


title: 33GM2 - 252741411841

description: BaP Exposure


title: 33DF2 - 252741411926

description: BaP Exposure


title: 33DF1 - 252741411907

description: BaP Exposure


title: 33DF5 - 252741411890

description: BaP Exposure


title: 33BM4 - 252741411751

description: BaP Exposure


title: 33BM1 - 252741411738

description: BaP Exposure


title: 33BF3 - 252741411935

description: BaP Exposure


title: 33BM3 - 252741411750

description: BaP Exposure


title: 33BM2 - 252741411749

description: BaP Exposure


title: 33FM2 - 252741410666

description: BaP Exposure


title: 33DM2 - 252741411924

description: BaP Exposure


title: 33BF2 - 252741411934

description: BaP Exposure


title: 32GM3 - 252741411767

description: BaP Exposure


title: 33BF1 - 252741411738

description: BaP Exposure


title: 32GM1 - 252741411747

description: BaP Exposure


title: 32GF2 - 252741411738

description: BaP Exposure


title: 32GF1 - 252741411737

description: BaP Exposure


title: 32EM5 - 252741411626

description: BaP Exposure


title: 33FF4 - 252741411610

description: BaP Exposure


title: 33FF2 - 252741410843

description: BaP Exposure


title: 32EM4 - 252741410829

description: BaP Exposure


title: 32EM3 - 252741410828

description: BaP Exposure


title: 32EM2 - 252741410827

description: BaP Exposure


title: 32EM1 - 252741410853

description: BaP Exposure


title: 32EF6 - 252741411740

description: BaP Exposure


title: 32CM4 - 252741411845

description: BaP Exposure


title: 32CM5 - 252741411846

description: BaP Exposure


title: 32EF5 - 252741411627

description: BaP Exposure


title: 32EF1 - 252741410835

description: BaP Exposure


title: 32CM6 - 252741411847

description: BaP Exposure


title: 32EF2 - 252741410867

description: BaP Exposure


title: 32CM2 - 252741411825

description: BaP Exposure


title: 32CF1 - 252741411826

description: BaP Exposure


title: 32EF3 - 252741410870

description: BaP Exposure


title: 32GM2 - 252741411743

description: BaP Exposure


title: 32CM3 - 252741411844

description: BaP Exposure


title: 32CM1 - 252741411824

description: BaP Exposure


title: 32BM4 - 252741411888

description: BaP Exposure


title: 32BM3 - 252741411887

description: BaP Exposure


title: 32BM2 - 252741411886

description: BaP Exposure


title: 31GM5 - 252741411923

description: BaP Exposure


title: 32BM1 - 252741411863

description: BaP Exposure


title: 31GM3 - 252741411903

description: BaP Exposure


title: 31GM2 - 252741411902

description: BaP Exposure


title: 31GM6 - 252741411756

description: BaP Exposure


title: 31GF4 - 252741411860

description: BaP Exposure


title: 31GF3 - 252741411905

description: BaP Exposure


title: 31GM1 - 252741411893

description: BaP Exposure


title: 31DM5 - 252741411827

description: BaP Exposure


title: 31DM4 - 252741411878

description: BaP Exposure


title: 31DM2 - 252741411876

description: BaP Exposure


title: 31DM3 - 252741411877

description: BaP Exposure


title: 32EF4 - 252741411745

description: BaP Exposure


title: 2FM1 - 252741411765

description: Control Exposure

value: Control Exposure


title: 31DF1 - 252741411828

description: BaP Exposure


title: 32CF2 - 252741411848

description: BaP Exposure


title: 31DF2 - 252741411931

description: BaP Exposure


title: 31DF3 - 252741411932

description: BaP Exposure


title: 31DM1 - 252741411823

description: BaP Exposure


title: 2EM3 - 252741411026

description: Control Exposure


title: 2EM4 - 252741411624

description: Control Exposure


title: 2EF3 - 252741411744

description: Control Exposure


title: 2EF2 - 252741410836

description: Control Exposure


title: 2EM5 - 252741411625

description: Control Exposure


title: 2EF1 - 252741410836

description: Control Exposure


title: 31GF1 - 252741411904

description: BaP Exposure


title: 12HM1 - 252741411840

description: Control Exposure


title: 2BM3 - 252741411978

description: Control Exposure


title: 12GM6 - 252741411838

description: Control Exposure


title: 12GM5 - 252741411837

description: Control Exposure


title: 2EM2 - 252741410869

description: Control Exposure


title: 12GM4 - 252741411836

description: Control Exposure


title: 12GM3 - 252741411773

description: Control Exposure


title: 12GM2 - 252741411069

description: Control Exposure


title: 12GM1 - 252741411067

description: Control Exposure


title: 2BF3 - 252741411958

description: Control Exposure


title: 12GF2 - 252741411061

description: Control Exposure


title: 2FF3 - 252741411734

description: Control Exposure


title: 12GF3 - 252741411917

description: Control Exposure


title: 12BM2 - 252741412069

description: Control Exposure


title: 12BM1 - 252741412068

description: Control Exposure


title: 12BM3 - 252741412070

description: Control Exposure


title: 12GF1 - 252741411060

description: Control Exposure


title: 2EM1 - 252741410868

description: Control Exposure


title: 12BF1 - 252741412071

description: Control Exposure


title: 12BF2 - 252741412072

description: Control Exposure


title: 2EF4 - 252741411739

description: Control Exposure


title: 11GM1 - 252741411781

description: Control Exposure


title: 12BF3 - 252741412002

description: Control Exposure


title: 11EM3 - 252741411059

description: Control Exposure


title: 11EF4 - 252741411834

description: Control Exposure


title: 11EF3 - 252741411772

description: Control Exposure


title: 11EF5 - 252741411835

description: Control Exposure


title: 11EM1 - 252741411057

description: Control Exposure


title: 11EM2 - 252741411058

description: Control Exposure


title: 11EF1 - 252741411045

description: Control Exposure


title: 11AM4 - 252741412023

description: Control Exposure


title: 11AM3 - 252741412022

description: Control Exposure


title: 12GF4 - 252741411779

description: Control Exposure


title: 11GM2 - 252741411839

description: Control Exposure


title: 11AM1 - 252741412081

description: Control Exposure


title: 11AF4 - 252741412026

description: Control Exposure


title: 11AM2 - 252741412001

description: Control Exposure


title: 11AF1 - 252741412082

description: Control Exposure


title: 11AF2 - 252741412024

description: Control Exposure


title: 10EM2 - 252741410871

description: Control Exposure


title: 11AF3 - 252741412025

description: Control Exposure


title: 10EF4 - 252741411771

description: Control Exposure


title: 10EM1 - 252741410859

description: Control Exposure


title: 10EF3 - 252741410874

description: Control Exposure


title: 10CM3 - 252741411997

description: Control Exposure


title: 10EF1 - 252741410872

description: Control Exposure


title: 10CM2 - 252741412079

description: Control Exposure


title: 10CF4 - 252741412000

description: Control Exposure


title: 11EF2 - 252741411047

description: Control Exposure


title: 10CF2 - 252741411998

description: Control Exposure


title: 10EF2 - 252741410873

description: Control Exposure


title: 10CF1 - 252741412080

description: Control Exposure


title: 10CF3 - 252741411999

description: Control Exposure


title: 10 week Socs3 cKO rep4

status: Public on Apr 28 2019

type: SRA

city: Tsurumi-ku, Yokohama City,

first: Archana

last: Bajpai

state: Kanagawa,

address: 1-7-22 Suehiro-cho,

department: IMS

country: Japan

institute: RIKEN Yokohama

library_source: transcriptomic

data_processing:
Fastq files having nucleotide and quality information were generated using Illumina offline basecaller (OLB) version 1.9.4.
Seqeunces were mapped on mouse genome (mm9) using TopHat2 (version 2.1.0) with parameters “—no-coverage-search -G genes.gtf”, genes.gtf is an annotation file provided Illumina database iGenomes (Trapnell et al., 2009.)
Mapped reads were counted and the fragments per kilobase per million reads (FPKM) of each gene is calculated using Cufflinks with the annotation described above (Mortazavi et al., 2008)
Genome_build: mm9
Supplementary_files_format_and_content: Mapped reads were counted and the fragments per kilobase per million reads (FPKM) of each gene

molecule: total RNA

source_name: keratinocytes

growth_protocol: The generation of keratin 5-specific Socs3 conditional knockout (Socs3 cKO) mice with a C57BL/6 background was described in a previous report [Uto-Konomi et al., 2012].

extract_protocol:
Total RNA was isolated with a TRIzol (Thermo Fisher Scientific, Waltham, MA) from ear specimens. cDNA libraries were synthesized with TruSeq RNA Library Preparation Kit v2 (Illumina, San Diego, CA) according to the manufacturer's instruction. Sequencing data were obtained using the HiSeq 1000 system (Illumina)  which could read a 50 bp sequence (single-ended 50–base pair reads).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Ear

tag: age

value: 10 week after birth

tag: genotype

value: Socs3 cKO


title: 8 week Socs3 cKO rep3

value: 8 week after birth


title: 10 week WT rep3

value: Wild Type


title: 2 week Socs3 cKO rep1

value: 2 week after birth


title: 8 week Socs3 cKO rep4


title: 10 week Socs3 cKO rep2


title: 2 week Socs3 cKO rep4


title: 8 week Socs3 cKO rep2


title: 10 week Socs3 cKO rep1


title: 10 week WT rep2


title: 10 week WT rep1

value: 10  week after birth


title: 8 week Socs3 cKO rep1


title: 10CM1 - 252741412078

description: Control Exposure


title: 10 week Socs3 cKO rep3


title: 2 week Socs3 cKO rep2


title: 8 week WT rep3


title: 2 week WT rep2


title: 2 week WT rep1


title: 2 week WT rep4


title: 2 week WT rep3


title: 8 week WT rep1


title: PAG_48h_2

status: Public on Apr 27 2019

city: Beijing

first: Wen

last: Zhong

address: Datun Road

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
Fastq files were aligned with Bowtie (v1.1.1)  to merged transcript sequences from the UCSC RefGene database. The parameter for the mapping program Bowtie was “-l25 -n2 –M3 -e 200 --best --strata --phred33-quals --trim5 4”.
The unmapped tags in the first round were then mapped to the rat genome (rn6)
For each gene, only tags uniquely mapped and localized in exons or exon-exon junctions were counted
Genome_build: rn6
Supplementary_files_format_and_content: bigwig files

molecule: polyA RNA

organism: Rattus norvegicus

extract_protocol:
For RNA extraction, we used Trizol kit by following manufacturer's instructions
Trizol-isolated RNA was enriched for Poly(A+) RNA with biotinylated oligo(dT), converted to cDNA with Superscript III (Invitrogen). Next, a terminal transferase (NEB, cat.no.M0315S) was used to add a ddNTP to the 3’-end of the cDNA. After the second-strand cDNA synthesis, 23 cycles of PCR were performed to amplify the cDNA. The length of 200-400nt PCR product was subjected to deep sequencing.

tag: cell line

tag: cell type

value: Insulin secreting beta cell derived line

tag: treated with

value: 0.5 mM palmitate with 27.8 mM glucose

tag: time


title: PAG_24h_2


title: PAG_48h_1


title: PAG_16h_3


title: PAG_16h_2


title: 2 week Socs3 cKO rep3


title: PAG_16h_1


title: PA_24h_1

value: 0.5 mM palmitate


title: PAG_8h_3


title: 8 week WT rep2


title: PA_48h_2


title: PA_48h_1


title: PA_16h_3


title: PAG_8h_1


title: PA_24h_2


title: PAG_48h_3


title: PAG_24h_1


title: PAG_8h_2


title: PA_8h_2


title: PA_16h_1


title: PA_8h_1


title: BSA_24h_3

value: BSA


title: BSA_24h_2


title: BSA_48h_3


title: BSA_16h_3


title: BSA_16h_1


title: PA_8h_3


title: BSA_48h_1


title: BSA_8h_3


title: BSA_8h_1


title: BSA_24h_1


title: BSA_16h_2


title: PA_16h_2


title: BSA_48h_2


title: PA_48h_3


title: Mino8253_S9

status: Public on Apr 26 2019

city: Houston

first: Kapil

last: Bhalla

state: TX

address: 1515 Holcombe Blvd

department: Leukemia

country: USA

institute: MD Anderson Cancer Center

data_processing:
Reads were mapped with TopHat 2.0. Only uniquely mapping reads were allowed.
The mapped reads were then assembled into transcripts with Cufflinks 2.0 and the UCSC RefSeq gene model.
Gene expression (FPKM) was quantile normalized using the R statistical system.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include quantile normalized FPKM values for each Sample

organism: Homo sapiens

source_name: Mantle cell lymphoma

growth_protocol: Cells were grown in RPMI-1640 media with 20% FBS

extract_protocol:
Total RNA was isolated from MCL cells utilizing an RNA mini kit from Ambion. Isolated RNA was treated with DNAse 1 at 37°C for 20 minutes. The RNA was quantified and checked for purity and integrity prior to library construction.
RNA was prepared for sequencing utilizing a kit from Illumina

treatment_protocol: MCL Mino cells were treated with 500 nM of OTX015, 500 nM of ARV-825, or ARV-771 for 4 hours

tag: agent

value: ARV-825 treated

tag: agent concentration


title: MinoOTX2_S5

value: OTX015 treated


title: Minocontrol3_S3

value: Control cells

value: no treatment


title: Minocontrol1_S1


title: MinoOTX3_S6


title: Mino8252_S8


title: Mino7713_S12

value: ARV-771 treated


title: MinoOTX1_S4


title: Mino7712_S11


title: BSA_8h_2


title: Mino7711_S10


title: H1_D90_2

city: Singapore

first: Aida

last: Moreno-Moral

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

description: Cells maintained on LN-521+LN-221

data_processing:
All reads were assessed for quality and (when necessary) adaptors were removed using Cutadapt.
RNA-Seq reads were aligned to hg38 (Ensembl Gene annotation build 79) using STAR 2.5.2b
Reads were quantified using RSEM 1.2.31
Genome_build: hg38 (Ensembl Gene annotation build 79)
Supplementary_files_format_and_content: H1_timecourse_TPM.txt: tab separated file with TPM values for each gene and sample; H1_timecourse_gene_raw_counts.txt: tab separated file with raw gene expression counts for each gene and sample

source_name: H1 from WiCell International

growth_protocol: Cells were cultured in triplicates wells coated with LN-521 and LN-221. Cells at day 0 were cultured with Nutristem medium. Cells at Day 1 and 3 were cultured in RMPI 1640 with B27 without insulin supplement and CHIR99021. Cells at day 5 were cultured in RMPI 1640 with B27 without insulin supplement and IWP2. Cells at day 7 and 9 were cultured in RMPI 1640 with B27 without insulin supplement. Cells at day 11 to 90 were cultured in RPMI 1640 supplemented with CTS B-27 Supplement.

extract_protocol:
RNA was isolated with Norgen Biotek's Single-cell RNA-isolation kit according to manufacturer's protocol. 700 ng of total RNA was used for library construction.
Libraries were constructed with TruSeq stranded total RNA library Prep Kit (Illumina).
Samples were multiplexed with 10 samples per lane and sequenced in Illumina HiSeq 3000 RNA sequencing platform (150bp pair-end reads)

treatment_protocol: At day 0, medium was supplemented with 10 mg of CHIR99021 and at day 3, medium was supplemented with 5 mg IWP2

tag: cellline

tag: biological replicate

value: day 90


title: H1_D90_4

description: Cells maintained on LN-521+LN-221


title: H1_D90_5

description: Cells maintained on LN-521+LN-221


title: H1_D14_2

description: Cells maintained on LN-521+LN-221

value: day 14


title: H1_D14_6

description: Cells maintained on LN-521+LN-221


title: H1_D30_3

description: Cells maintained on LN-521+LN-221

value: day 30


title: H1_D20_2

description: Cells maintained on LN-521+LN-221

value: day 20


title: H1_D11_2

description: Cells maintained on LN-521+LN-221

value: day 11


title: H1_D20_1

description: Cells maintained on LN-521+LN-221


title: H1_D30_10

description: Cells maintained on LN-521+LN-221


title: H1_D20_3

description: Cells maintained on LN-521+LN-221


title: H1_D11_5

description: Cells maintained on LN-521+LN-221


title: H1_D14_3

description: Cells maintained on LN-521+LN-221


title: H1_D11_1

description: Cells maintained on LN-521+LN-221


title: Minocontrol2_S2


title: H1_D11_7

description: Cells maintained on LN-521+LN-221


title: H1_D30_1

description: Cells maintained on LN-521+LN-221


title: H1_D9_4

description: Cells maintained on LN-521+LN-221

value: day 9


title: H1_D9_2

description: Cells maintained on LN-521+LN-221


title: H1_D9_1

description: Cells maintained on LN-521+LN-221


title: H1_D7_3

description: Cells maintained on LN-521+LN-221

value: day 7


title: H1_D9_10

description: Cells maintained on LN-521+LN-221


title: H1_D7_4

description: Cells maintained on LN-521+LN-221


title: H1_D11_6

description: Cells maintained on LN-521+LN-221


title: H1_D7_10

description: Cells maintained on LN-521+LN-221


title: H1_D7_1

description: Cells maintained on LN-521+LN-221


title: H1_D7_2

description: Cells maintained on LN-521+LN-221


title: Mino8251_S7


title: H1_D5_3

description: Cells maintained on LN-521+LN-221

value: day 5


title: H1_D5_1

description: Cells maintained on LN-521+LN-221


title: H1_D5_2

description: Cells maintained on LN-521+LN-221


title: H1_D3_3

description: Cells maintained on LN-521+LN-221

value: day 3


title: H1_D5_5

description: Cells maintained on LN-521+LN-221


title: H1_D0_2

description: Cells maintained on LN-521+LN-221

value: day 0


title: H1_D3_1

description: Cells maintained on LN-521+LN-221


title: H1_D0_1

description: Cells maintained on LN-521+LN-221


title: H1_D1_2

description: Cells maintained on LN-521+LN-221

value: day 1


title: H1_D5_4

description: Cells maintained on LN-521+LN-221


title: H1_D1_1

description: Cells maintained on LN-521+LN-221


title: H1_D9_3

description: Cells maintained on LN-521+LN-221


title: H1_D1_3

description: Cells maintained on LN-521+LN-221


title: LN521-221_3

description: Human embryonic stem cells were cultured in wells coated with LN-521 or LN-521+LN-221 using nutristem medium.

data_processing:
All reads were assessed for quality and (when necessary) adaptors were removed using Cutadapt.
RNA-Seq reads were aligned to hg38 (Ensembl Gene annotation build 79) using STAR 2.5.2b
Reads were quantified using RSEM 1.2.31
Genome_build: hg38 (Ensembl Gene annotation build 79)
Supplementary_files_format_and_content: LN221_TPM.txt: tab separated file with TPM values for each gene and sample; LN221_gene_raw_counts.txt: tab separated file with raw gene expression counts for each gene and sample

growth_protocol: Cells were cultured in triplicates wells coated with LN-521 or LN-521+LN-221 in nutristem medium for 4 days.

treatment_protocol: Nutristem medium was changed daily for 4 days.


title: H1_Pluri_1

description: Cells maintained on LN-521


title: H1_D0_3

description: Cells maintained on LN-521+LN-221


title: H1_Pluri_3

description: Cells maintained on LN-521


title: H1_Pluri_2

description: Cells maintained on LN-521


title: H1_D3_2

description: Cells maintained on LN-521+LN-221


title: LN521-221_1


title: LN521_3


title: LN521_2


title: LN521_1


title: LN521-221_2


title: 1001D30_2

description: Cells maintained on LN-521+LN-221

data_processing:
All reads were assessed for quality and (when necessary) adaptors were removed using Cutadapt.
RNA-Seq reads were aligned to hg38 (Ensembl Gene annotation build 79) using STAR 2.5.2b
Reads were quantified using RSEM 1.2.31
Genome_build: hg38 (Ensembl Gene annotation build 79)
Supplementary_files_format_and_content: HS1001_timecourse_TPM.txt: tab separated file with TPM values for each gene and sample; HS1001_timecourse_gene_raw_counts.txt: tab separated file with raw gene expression counts for each gene and sample

source_name: HS1001 from Dr. Hovatta’s laboratory (Rodin et al., 2014)

value: Human embryonic stem cells


title: 1001D90_2

description: Cells maintained on LN-521+LN-221


title: 1001D90_1

description: Cells maintained on LN-521+LN-221


title: 1001D20_2

description: Cells maintained on LN-521+LN-221


title: 1001D30_1

description: Cells maintained on LN-521+LN-221


title: 1001D14_3

description: Cells maintained on LN-521+LN-221


title: 1001D11_3

description: Cells maintained on LN-521+LN-221


title: 1001D14_2

description: Cells maintained on LN-521+LN-221


title: 1001D11_1

description: Cells maintained on LN-521+LN-221


title: 1001D20_1

description: Cells maintained on LN-521+LN-221


title: 1001D11_2

description: Cells maintained on LN-521+LN-221


title: 1001D9_3

description: Cells maintained on LN-521+LN-221


title: 1001D14_1

description: Cells maintained on LN-521+LN-221


title: 1001D5_3

description: Cells maintained on LN-521+LN-221


title: 1001D9_2

description: Cells maintained on LN-521+LN-221


title: 1001D7_4

description: Cells maintained on LN-521+LN-221


title: 1001D7_1

description: Cells maintained on LN-521+LN-221


title: 1001D9_1

description: Cells maintained on LN-521+LN-221


title: 1001D1_3

description: Cells maintained on LN-521+LN-221


title: 1001D1_2

description: Cells maintained on LN-521+LN-221


title: 1001D7_3

description: Cells maintained on LN-521+LN-221


title: 1001D3_3

description: Cells maintained on LN-521+LN-221


title: 1001D1_1

description: Cells maintained on LN-521+LN-221


title: 1001D3_1

description: Cells maintained on LN-521+LN-221


title: 1001D0_3

description: Cells maintained on LN-521+LN-221


title: 1001D0_2

description: Cells maintained on LN-521+LN-221


title: 1001D5_1

description: Cells maintained on LN-521+LN-221


title: 1001D3_2

description: Cells maintained on LN-521+LN-221


title: 1001D5_2

description: Cells maintained on LN-521+LN-221


title: 1001_pluri_1

description: Cells maintained on LN-521


title: 1001_pluri_3

description: Cells maintained on LN-521


title: 1001D0_1

description: Cells maintained on LN-521+LN-221


title: 1001_pluri_2

description: Cells maintained on LN-521


title: 6A

city: Urbana

first: Christopher

middle: V

last: Rao

state: IL

address: 600 S Mathews Ave

department: Chemical and Biomolecular Engineering

institute: University of Illinois Urbana Champaign

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v1.8.4 Conversion Software.
Sequenced reads were trimmed for adaptors and low quality reads using trimmomatic-0.30. Then they were mapped to ASM252v1 build using tophat2/2.0.10 with parameters -p 4 --library-type fr-firststrand
Read counts were generated by htseq with parameters -f bam -s no -r name -m intersection-nonempty -t exon.
Raw counts were treated in EdgeR. CPM (counts per million) were normalized by effective library size built in edgeR.
Genome_build: ASM252v1
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample, normalized by effective library size (TMM method)

organism: Yarrowia lipolytica

source_name: Yarrowia lipolytica W29

growth_protocol: Yarrowia lipolytica W29 cells were cultivated in bioreactors in medium (glucose 50 g/L, yeast nitrogen base without amino acid and ammonium sulfate 1.7 g/L, yeast extract 1.5 g/L and ammonium sulfate 1 g/L), pH controlled at 2.0, 4.0 and 6.0 in triplicates. Cells were harvested at hour 50.

extract_protocol:
Total RNA was extracted with RNeasy mini kit (Qiagen), homogenized using FastPrep-24 with glass beads (425-600 μm). The extracted total RNA were treated with Turbo RNase-free DNase kit (ThermoFisher), purified again with RNeasy mini kit protocol “RNA clean up”.
The stranded RNAseq libraries were prepared with Illumina's TruSeq Stranded RNA Sample Prep kit.  The libraries were pooled in equimolar concentration, and sequenced  for 101 cycles from each single end of the fragments on a HiSeq2500 (Illumina).

tag: medium ph


title: 6C


title: 6B


title: 8A_50 biotype2_15 biotype1_Day1

city: Brookings

first: Madhav

middle: P.

last: Nepal

state: South Dakota

address: Northern Plains Biostress 249D

department: Biology and Microbiology

institute: South Dakota State University

data_processing:
Quality control of reads was assessed using FastQC program (version 0.11.3) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The FastQC results were visualized using MultiQC v1.3 9. Low quality bases (QC value < 20) and adapters were removed by trimming using the program Trimmomatic (version 0.36). The coding sequences  (Gmax: Gmax_275_Wm82.a2.v1.transcript_primaryTranscriptOnly.fa.gz) were obtained from the Phytozome database and aligned using Salmon ver.0.9.1 accessed from Bioconda.
Genome_build: Gmax: Gmax_275_Wm82.a2.v1.transcript_primaryTranscriptOnly.fa.gz
Supplementary_files_format_and_content: tab-delimited matrix text file include transcript abundance values for each sample

organism: Glycine max

source_name: Leaves

extract_protocol:
RNA was extracted from the leave samples from resistant and susceptible cultivars treated with no aphids, biotype 2: biotype1 collected at day 1 and no aphids, biotype 2: biotype1 and no aphids: biotype1 at day 11 using PureLink RNA mini kit (Invitrogen, USA). RNA samples were treated with TURBOTM DNase (Invitrogen, USA) to remove any DNA contamination following the manufacturer’s instructions. Assessment of the isolated RNA integrity was performed by 1% agarose gel electrophoresis, and RNA concentration was measured by Nanodrop 2000 (Thermo Fisher Scientific, USA). Three replicates from these treatments in resistant and susceptible cultivars were pooled in equimolar concentration.
RNAseq library construction was prepared using Illumina’s TruSeq Stranded mRNA Kit v1 (San Diego, CA). The libraries were quantified by QuBit dsDNA HS Assay (Life Technologies, Carlsbad, CA) and pooled in equimolar concentrations. The libraries were sequenced on an Illumina NextSeq 500 using a NextSeq 500/550 High Output Reagent Cartridge v2 (San Diego, CA) at 75 cycles.

tag: protocol

value: 50 biotype2_ 15 biotype1

tag: time point

value: Leaves

value: not applicable


title: 4A_50 biotype 2_15 biotype1_Day1

value: 50 biotype 2_ 15 biotype1


title: 4C_50 biotype 2_15 biotype1_Day11


title: 11C_Control_Susceptible_Day11

value: Control


title: 5C_No Inducer_15 biotype1_Day11

value: No Inducer_ 15 biotype1


title: 12C_Control_Resistant_Day11


title: 4C


title: 12A_Control_Resistant_Day1


title: 11A_Control_Susceptible_Day1


title: 4B


title: 4A


title: 2C


title: 2A


title: 8C_50 biotype2_15 biotype1_Day11


title: 1C_No Inducer_15 biotype1_Day11


title: Col0_pWER_HF-RPL18-IP Rep1

status: Public on Apr 24 2019

city: Zürich

first: Alexis

last: Sarazin

address: Universitätstrasse 2

country: Switzerland

institute: ETH

description:
Immunoprecipitated RNA
GMD-89

data_processing:
Basecalling pipeline: MiSeq Control Software 2.4; RTA 1.18.54.0; CASAVA-1.8.2
FASTQ file generation and demultiplexing was done by Fasteris.
Reads were trimmed and clipped using FASTX-Toolkit (fastx_trimmer options: -f 11 –l 121; fastx_clipper options –a AGATCGGAAGAGC). Remaining pairs were then aligned on the Arabidopsis thaliana TAIR10 reference genome using Tophat (v2.0.11) and Bowtie (v2.2.1.0)
Counts for annotated gene (Ensembl TAIR10) were generated using the featureCounts function from the Subread package with options -s -p -O –M
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text file of reads count values.

organism: Arabidopsis thaliana

source_name: roots

growth_protocol: plants were grown vertically on ½ MS media covered in mesh (Sefear nitrex 03-65125) under long day light conditions at 22°C for 6 days

extract_protocol:
For each sample, ~20 different plates were frozen and ground in liquid nitrogen. Supernatants were precleared and incubated with EZview Red ANTI-FLAG M2 affinity Gel (Sigma). The beads were removed by spinning and RNA was then extracted using phenol:chloroform.
Extracted RNA was processed into sequencing libraries and sequenced at Fasteris (http://www.fasteris.com, Switzerland) using the Illumina MiSeq sequencer

tag: strain and genotype

value: Columbia-0 containing pWER::HF:RPL18 transgene

value: roots

tag: development stage

value: 6 days after putting in light


title: hyl1_pCO2_HF-RPL18-IP Rep1

description:
Immunoprecipitated RNA
GMD-237

value: Columbia-0 hyl1 mutant containing pCO2::HF:RPL18 transgene

tag: tissue


title: Col0_pSHR_HF-RPL18-IP Rep1

description:
Immunoprecipitated RNA
GMD-320

value: Columbia-0 containing pSHR::HF:RPL18 transgene


title: hyl1_pSHR_HF-RPL18-IP Rep2

description:
Immunoprecipitated RNA
GMD-323

value: Columbia-0 hyl1 mutant containing pSHR::HF:RPL18 transgene


title: Col0_pSHR_HF-RPL18-IP Rep2

description:
Immunoprecipitated RNA
GMD-321


title: hyl1_pSHR_HF-RPL18-IP Rep1

description:
Immunoprecipitated RNA
GMD-322


title: 2B

tag: strain


title: hyl1_pCO2_HF-RPL18-IP Rep2

description:
Immunoprecipitated RNA
GMD-238


title: hyl1_pWER_HF-RPL18-IP Rep1

description:
Immunoprecipitated RNA
GMD-91

value: Columbia-0 hyl1 mutant containing pWER::HF:RPL18 transgene


title: Col0_pCO2_HF-RPL18-IP Rep2

description:
Immunoprecipitated RNA
GMD-236

value: Columbia-0 containing pCO2::HF:RPL18 transgene


title: Col0_pCO2_HF-RPL18-IP Rep1

description:
Immunoprecipitated RNA
GMD-235


title: hyl1_pSCR_HF-RPL18-IP Rep1

description:
Immunoprecipitated RNA
GMD-233

value: Columbia-0 hyl1 mutant containing pSCR::HF:RPL18 transgene


title: hyl1_pWER_HF-RPL18-IP Rep2

description:
Immunoprecipitated RNA
GMD-92


title: hyl1_pACR4_HF-RPL18-IP Rep1

description:
Immunoprecipitated RNA
GMD-229

value: Columbia-0 hyl1 mutant containing pACR4::HF:RPL18 transgene


title: Col0_pWER_HF-RPL18-IP Rep2

description:
Immunoprecipitated RNA
GMD-90


title: hyl1_pACR4_HF-RPL18-IP Rep2

description:
Immunoprecipitated RNA
GMD-230


title: Col0_pACR4_HF-RPL18-IP Rep1

description:
Immunoprecipitated RNA
GMD-227

value: Columbia-0 containing pACR4::HF:RPL18 transgene


title: Col0_pACR4_HF-RPL18-IP Rep2

description:
Immunoprecipitated RNA
GMD-228


title: hyl1_p35S_HF-RPL18-IP Rep2

description:
Immunoprecipitated RNA
GMD-226

value: Columbia-0 hyl1 mutant containing p35S::HF:RPL18 transgene


title: Col0_p35S_HF-RPL18-IP Rep2

description:
Immunoprecipitated RNA
GMD-224

value: Columbia-0 containing p35S::HF:RPL18 transgene


title: Col0_pSCR_HF-RPL18-IP Rep2

description:
Immunoprecipitated RNA
GMD-232

value: Columbia-0 containing pSCR::HF:RPL18 transgene


title: hyl1_p35S_HF-RPL18-IP Rep1

description:
Immunoprecipitated RNA
GMD-225


title: Col0_p35S_HF-RPL18-IP Rep1

description:
Immunoprecipitated RNA
GMD-223


title: SAB-21 (smallRNA-Seq)

city: Luxembourg

first: Arnaud

last: Muller

address: 84 Val Fleuri

department: DONC

country: Luxembourg

institute: LIH

data_processing:
Base calling was performed with CASAVA 1.8.2 pipeline (Illumina).
Small RNA-Seq reads of 15 to 40 nt in length were then mapped to the human genome (assembly version hg19 - UCSC repository) using Bowtie v0.12.8, (Langmead et al. 2009).
Small RNAs were annotated and quantified using ncPRO-seq software version 1.5.1 as described (Chen et al. 2012).
Genome_build: hg19
Supplementary_files_format_and_content: Text file that contains the raw sequence counts.

source_name: NCH601 ctl

growth_protocol: hNSC.100 neural stem cell line and NCH644 were cultured in Neurobasal medium (Life technologies, 21103-049) with B27 - VitA (Life technologies,12587010) supplements whereas NCH421k and NCH601 cell lines were cultured as non-adherent spheres in DMEM-F12 medium (Lonza) containing 1xBIT100 (Provitro). In addition, both media contained 2mM L-Glutamine (Lonza), 30U/ml Pen-Step (Lonza), 1U/ml Heparin (SIGMA), 20ng/ml bFGF (Miltenyi, 130-093-841) and 20ng/ml EGF (Provitro, 1325950500).

extract_protocol:
Total RNA was extracted with Trizol and quantified using Nanodrop. RNA quality was checked using bioanalyzer (Agilent). Total RNAs were depleted from Ribosomal RNAs using RiboMinus™ technology.
Libraries were prepared according to the Illumina standard protocol using TruSeq Stranded RNA Kits. Single stranded sequencing of 50bp reads was performed using Hiseq2500 (Illumina)

treatment_protocol: Cells were treated with 500uM TMZ or DMSO.

tag: treatment


title: SAB-22 (smallRNA-Seq)

source_name: NCH601 TMZ

value: TMZ


title: SAB-23 (smallRNA-Seq)


title: SAB-24 (smallRNA-Seq)


title: SAB-19 (smallRNA-Seq)

value: Control


title: SAB-14 (smallRNA-Seq)

source_name: NCH421k ctl


title: SAB-17 (smallRNA-Seq)

source_name: NCH421k TMZ


title: SAB-18 (smallRNA-Seq)


title: SAB-20 (smallRNA-Seq)


title: SAB-13 (smallRNA-Seq)


title: SAB-12 (smallRNA-Seq)

source_name: NCH644 TMZ


title: Col0_pSCR_HF-RPL18-IP Rep1

description:
Immunoprecipitated RNA
GMD-231


title: SAB-11 (smallRNA-Seq)


title: SAB-10 (smallRNA-Seq)


title: hyl1_pSCR_HF-RPL18-IP Rep2

description:
Immunoprecipitated RNA
GMD-234


title: SAB-09 (smallRNA-Seq)

source_name: NCH644 ctl


title: SAB-06 (smallRNA-Seq)

source_name: hNSC100 TMZ


title: SAB-08 (smallRNA-Seq)


title: SAB-05 (smallRNA-Seq)


title: SAB-03 (smallRNA-Seq)

source_name: hNSC100 ctl


title: SAB-22 (RNA-seq)

data_processing:
Base calling was performed with CASAVA 1.8.2 pipeline (Illumina).
RNA-Seq reads of 50 nt in length were further submitted to TopHat v.2.0.9 (Trapnell et al. 2009) using bowtie2 (Langmead and Salzberg) v.2.1.0 with default parameters for mapping on the human genome (assembly version GCRh37 release 69 - Ensembl repository).
Corresponding BAM file have been used for gene counting using HTSeq v.0.6.1 (Anders et al.).
Genome_build: GRCh37.69
Supplementary_files_format_and_content: Text file that contains the raw sequence counts for each gene (Ensembl gene identifier) produced by the program HTSeq-count.


title: SAB-02 (smallRNA-Seq)


title: SAB-23 (RNA-seq)


title: SAB-04 (smallRNA-Seq)


title: SAB-16 (smallRNA-Seq)


title: SAB-15 (smallRNA-Seq)


title: SAB-24 (RNA-seq)


title: SAB-20 (RNA-seq)


title: SAB-19 (RNA-seq)


title: SAB-21 (RNA-seq)


title: SAB-16 (RNA-seq)


title: SAB-17 (RNA-seq)


title: SAB-18 (RNA-seq)


title: SAB-15 (RNA-seq)


title: SAB-13 (RNA-seq)


title: SAB-12 (RNA-seq)


title: SAB-07 (smallRNA-Seq)


title: SAB-10 (RNA-seq)


title: SAB-14 (RNA-seq)


title: SAB-09 (RNA-seq)


title: SAB-01 (smallRNA-Seq)


title: SAB-11 (RNA-seq)


title: SAB-05 (RNA-seq)


title: SAB-06 (RNA-seq)


title: SAB-07 (RNA-seq)


title: SAB-04 (RNA-seq)


title: SAB-03 (RNA-seq)


title: 1001D90_5

description: Cells maintained on LN-521+LN-221

value: Human embryonic stem cells

value: day 90


title: pWER_FLAG-AGO1-IP

description: Immunoprecipitated RNA

data_processing:
Basecalling pipeline: HiSeq Control Software 1.5.15.1; RTA 1.13.48.0; CASAVA-1.8.2
FASTQ file generation and demultiplexing and adapter removal was done by Fasteris.
15-to-44-nt reads with identical sequence were grouped using the processReads function from the ncPRO-seq pipeline and aligned against A.thaliana’s genome (TAIR10) using bowtie2.
Genome_build: TAIR10
Supplementary_files_format_and_content: For each sample, tab-delimited text files including distinct sequences and reads count values.

extract_protocol:
For each FLAG-AGO1 allele, ~5 different plates were frozen and ground in liquid nitrogen. Supernatants were precleared and incubated with EZview Red ANTI-FLAG M2 affinity Gel (Sigma). The beads were removed by spinning and RNA was then extrafcted using Trizol reagent (Life Technologies).
Extracted RNA was processed into sequencing libraries using adapted Illumina protocols and sequenced at Fasteris (http://www.fasteris.com, Switzerland) using the Illumina HiSeq sequencer

value: Columbia-0 dcl234 triple mutant expressing pWER_FLAG-AGO1

value: roots


title: pSHR_FLAG-AGO1-IP

description: Immunoprecipitated RNA

value: Columbia-0 dcl234 triple mutant expressing pSHR_FLAG-AGO1

value: 6 days after putting in light


title: pCO2_FLAG-AGO1-IP

description: Immunoprecipitated RNA

value: Columbia-0 dcl234 triple mutant expressing pCO2_FLAG-AGO1


title: RNA-seq_ETV4KO1_DMSO

status: Public on Apr 23 2019

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

data_processing:
Reads were aligned to the human genome using HISAT2
Sam files were then converted to bam files and sorted via Samtools
Read counts for each gene were determined from alignments to hg19 UCSC knownGene gene models using featuresCounts from the SubRead package
Normalization and differential expression analysis were performed using DeSeq2
Genome_build: hg19
Supplementary_files_format_and_content: Gene counts in a text file

source_name: Endometrioid adenocarcinoma_1 hr 0.1% DMSO

growth_protocol: Ishikawa cells (Sigma-Aldrich) were grown in full media (RPMI-1640 (Gibco), 10% fetal bovine serum (Gibco), and 1% penicillin-streptomycin (Gibco)).  Five days prior to induction, cells were moved to hormone-depleted media with phenol-red free RPMI-1640(Gibco), 10% charcoal-dextran treated fetal bovine serum (Sigma-Aldrich), and 1% penicillin-streptomycin(Gibco).

extract_protocol:
Cells were harvested from 10cm dishes in 600mL RLT Plus (Qiagen) supplemented with 1% beta-mercaptoethanol after an 8 hour induction with 10nM E2 or DMSO.  RNA purification was performed using RNA Clean and Concentrator (Zymo Research) with the optional DNase I treatment.
The KAPA Stranded mRNA-seq kit (Kapa Biosystems) was used to create Poly(A) selected libraries from 1mg total RNA.

treatment_protocol: Inductions involved treating cells with 0.1% DMSO, as a vehicle control, or 10nM E2 (Sigma-Aldrich) for 8 hours

value: Ishikawa ETV4 KO clone 1

value: Endometrioid adenocarcinoma

value: 1 hr 0.1% DMSO


title: papaya control

city: Tokyo

first: Minaho

last: Kawamura

address: BLICK GATE Suidobashi F2, Chiyodaku-kandamisakicho

data_processing:
Samples were sequenced using Illlumina HiSeq2500 instrument with paired-end 2 x 100-bp cycle
Base calls were performed on bcl2fastq2 version 2.17
Pre-processing of sequence reads using sickle version 1.200 with threshold for trimming based on average quality in a window:30. threshold to keep a read based on length after trimming:40. as command option.
assemble using Trinity version 2.0.6
The gene expression level (FPKM) were determined using RSEM version 1.2.19
Genome_build: de novo
Supplementary_files_format_and_content: tab-delimited text files including FPKM from RSEM

organism: Carica papaya

source_name: leaf

extract_protocol:
Total RNA was extracted with the NucleoSpin RNA Plant  (MACHEREY-NAGEL, Germany).
Libraries were prepared for sequencing using library creation kits (TruSeq Stranded mRNA sample prep kit, Illumina, San Diego, CA, USA)

treatment_protocol: Place the leaves in a cytoprotective solution composed of dimethyl sulfoxide, glycerin, glycol and trehalose at room temperature (26 ° C) for 72 hours, then put in a freezer and cool the temperature down by 0.5 ° C daily for 180 days. After the temperature was finally lowered to -60 ° C, it was returned to room temperature and naturally thawed was used for the test.

value: Freeze thaw awakening -


title: pACR4_FLAG-AGO1-IP

description: Immunoprecipitated RNA

value: Columbia-0 dcl234 triple mutant expressing pACR4_FLAG-AGO1


title: papaya treatment

value: Freeze thaw awakening +


title: SAB-08 (RNA-seq)


title: SAB-01 (RNA-seq)


title: SAB-02 (RNA-seq)


title: PREM34

city: london

first: kaiyu

last: lei

state: London

address: ducan road

department: Surgery and Cancer

country: United Kingdom

institute: imperial college london

description: RNA-seq

data_processing:
RNA-Seq reads was aligned to the GRCh38 Homo sapiens reference genome downloaded from Ensembl (release 81) with HISAT version 2.0.1 using parameters of --known-splicesite-infile --dta-cufflinks --rna-strandness RF --phred33 –p 4 -q
Reads per kilobase per million mapped reads (RPKM) were calculated and then normalized with DESeq2 (version 1.6.3). In short, exons labeled as ‘retained_intron’ were first excluded, and overlapping interval exons of each genes were merged and a final gene level model was produced in GFF  format.
Differentially expressed genes (DEGs) between two groups of samples were identified with DESeq2 (version 1.6.3), edgeR (version 3.8.6) and Cuffdiff (version 2.2.1). The transcript with a q value <0.05 in at least two methods and an expression FC >1.5 between two groups was defined as a shared differentially expressed gene (DEG)
Gene ontology (GO) enrichment analysis.
Genome_build: GRCh38 release 81
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: lower segment myometrial tissue

extract_protocol:
60-100 mg of frozen tissues per sample, which had been treated with RNAlater® (Sigma) overnight at 2-4oC prior to -80oC storage, were mechanically homogenised in TRIzol® (Life Technologies), using a Precellys 24 bead-based homogeniser, and total RNA was extracted from the aqueous phase of chloroform-treated and centrifuged homogenates using the TRIzol® Plus RNA Purification kit (Life Technologies) with on-column DNase treatment prior to elution with RNase-free water.
Sample libraries were made using the TruSeq Stranded mRNA Sample Preparation kit, following the high-throughput sample (HT) protocol (Illumina); quality assessment of RNA samples and their cDNA libraries were assessed using a Life Technologies Qubit fluorimeter and Agilent Technologies Bioanalyser 2100

tag: labour status; term no labour (tnl), term early labour (teal), term established labour (tesl)

value: TEaL

tag: gestation (weeks)

tag: gravida

tag: parity

tag: cervical dilation (cm)

tag: repture of membranes (rom) status; spontaneous (srom), artificial (arm)

value: no ROM

tag: cs reason

value: Breech


title: PREM39

description: RNA-seq

value: TEsL

value: SROM (9 hours before CS)


title: PREM28

description: RNA-seq


title: PREM07

description: RNA-seq

value: Undiagnosed breech


title: PREM47

description: RNA-seq

value: ARM (26 hours before CS)

value: Fetal distress (abnormal CTG)


title: PREM49

description: RNA-seq

value: TNL

value: Maternal request


title: PREM13

description: RNA-seq

value: SROM (21 hours before CS)

value: Previous third degree tear


title: PREM27

description: RNA-seq

value: ARM (26 minutes before CS)


title: PREM21

description: RNA-seq

value: Breech & previous CS


title: PREM35

description: RNA-seq

value: Previous CS


title: PREM37

description: RNA-seq

value: SROM (12 hours before CS)


title: PREM09

description: RNA-seq

value: Tocophobia


title: PREM38

description: RNA-seq

value: SROM (4 hours before CS)


title: PREM48

description: RNA-seq

value: no ROM


title: PREM31

description: RNA-seq

value: Previous rectal and vaginal prolapse


title: PREM16

description: RNA-seq

value: TEaL

value: Breech


title: PREM43

description: RNA-seq


title: PREM14

description: RNA-seq


title: pSCR_FLAG-AGO1-IP

description: Immunoprecipitated RNA

value: Columbia-0 dcl234 triple mutant expressing pSCR_FLAG-AGO1

value: roots

value: 6 days after putting in light


title: PREM04

description: RNA-seq

value: TNL

value: Previous traumatic delivery


title: PREM05

description: RNA-seq


title: PREM20

description: RNA-seq

value: SROM (10 hours before CS)


title: CHD4_2

city: Philadelphia

first: yasuyuki

last: okamoto

state: pa

address: 3307 N. Broad Street

department: fels

institute: temple university

description: Sample 18

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to the hg19 genome assembly using TopHat 2.0.9 with these parameters: -p 28 --b2-fast -G /UCSC/hg19/Annotation/Genes/genes.gtf --segment-length 20
Fragments Per Kilobase of exon per Megabase of library size (FPKM) and DE genes were calculated using cuffdiff v 2.1.1 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: human colon_CHD4

growth_protocol: SW48 were cultured in L-15 medium containd,10% FBS.

extract_protocol:
Total  RNA wasextracted  using either Trizol reagent(Life Technologies) or RNeasy (Qiagen). Illumina TruSeq Stranded Total RNA with Ribo-zero Gold kits  (RS-122-2301 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNA single treatment (siRNA on day1, day3 and day6, RNA extraction on day8), siDNMT1 combination (siDNMT1 on day1, day3 and day5, TEST siRNA on day7 and day8, RNA extraction on day11) and DAC combination (DAC 50nM on day1, day2 and day3, TEST siRNA on day1 and day2, RNA extraction on day5).

tag: cell line

value: SW48 (Human colon adenocarcinoma cell line)

value: siCHD4 treatment


title: CHD4_1

description: Sample 17


title: CHD4_0

description: Sample 16


title: CHD4_DAC_2

description: Sample 15

source_name: human colon_CHD4_DAC

value: siCHD4 plus decitabine treatment


title: CHD4_DAC_1

description: Sample 14


title: PREM22

description: RNA-seq

value: Previous third degree tear


title: CHD4_DNMT1_2

description: Sample 12

source_name: human colon_CHD4_DNMT1

value: siCHD4 plus siDNMT1 treatment


title: CHD4_DAC_0

description: Sample 13


title: con_2

description: Sample 9

source_name: human colon_con

value: Control


title: CHD4_DNMT1_1

description: Sample 11


title: con_1

description: Sample 8


title: con_DAC_2

description: Sample 6

source_name: human colon_con_DAC

value: decitabine treatment


title: con_DNMT1_1

description: Sample 2

source_name: human colon_con_DNMT1

value: siDNMT1 treatment


title: con_DNMT1_0

description: Sample 1


title: con_DNMT1_2

description: Sample 3


title: BAP1-KO-INPUT

status: Public on Apr 22 2019

city: South San Francisco

first: Rohit

last: Reja

state: CA

address: 1 DNA Way

institute: Genentech

library_source: genomic

data_processing:
Illumina v1.8 software used for basecalling
Raw reads were aligned to the mouse reference (GRCm38-mm10) using GSNAP (with parameters -M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap). Reads were filtered to include only uniquely mapped reads.
ChIP-seq peaks were called for each dataset with matched input using MACS2.
Genome_build: mm10
Supplementary_files_format_and_content: Peak files are in text format

source_name: Embryonic stem cells

extract_protocol:
ES cells were treated with 100 nM 4-OHT and 10 μM emricasan (Cayman Chemical) for 4 days.  For RNF2 ChIP, nuclear extracts were prepared from 2×107 cells using the truChIP High Cell  Chromatin Shearing Kit (Covaris).Chromatin was sheared to 200-700 bp with a Covaris E220 sonicator (settings: duty cycle 5%, peak incident power 140 W, cycles per burst 200, processing  time 12 min, temperature 4oC, degassing mode continuous, volume 1.0 ml in TC12x12 AFA  tubes). Bap1C91A/- cells were crosslinked in 2 mM disuccinimidyl glutarate (Thermo Fisher Scientific) at room temperature for 30 min prior to nuclear extracts following the process above.Sheered nuclear extracts were centrifuged at 16000×g for 5 min, and then the soluble fractions were supplemented with 1 % Triton X-100, 2 mM EDTA, 150 mM NaCl, 20mM Tris-HCl pH 8.1 and 1× protease inhibitor cocktail (Sigma). Next, anti-RNF2 (Abcamab3832), or anti-BAP1 (Genentech, PRO424270) antibodies were added that had been pre-coupled to protein A-Dynabeads (Life Technologies).
Libraries were prepared using standard protocols for the Ovation Ultralow System. Briefly, samples were PCR-amplified and sized using the Agilent 2100Bioanalyzer. Barcoded libraries were sequenced 50 bp single end on HiSeq 2500 (Illumina).

tag: background

tag: age

tag: genotype

value: BAP1 knockout

tag: cell type

value: Embryonic stem cells (ESC)

tag: chip antibody

value: none (input)


title: Ctrl2_WGBS

status: Public on Apr 21 2019

city: Davis

first: Keith

last: Dunaway

address: 3318 Tupper Hall

department: MMI

institute: UC Davis

description: Post-mortem brain

data_processing:
Filter using Illumina flag
Separate and trim reads based on adapter contamination
Align to rn6 using BSSeeker2
Combine aligned reads, both trimmed and no adapter contamination
Convert sam files to percent methylation bed files
Combine all chromosome percent methylation bed files into a single file
Genome_build: rn6
Supplementary_files_format_and_content: Percent Methylation Bed file containing single base methylation information with ranged color coding

source_name: hypothalamus

extract_protocol:
Extracted and purified using the Qiagen Puregene kit
Five (5) μg of DNA was fragmented to ~300 bp using 28 cycles of 15 seconds on/15 seconds off on a Diagenode Bioruptor. DNA was end-repaired using 1× T4 DNA ligase buffer, 400 μM dNTPs, 15 U T4 DNA polymerase (NEB), and 50 U PNK (NEB) for 30 min at 20°C. After PCR purifying (Qiagen), adenine bases were appended to the ends using 1× NEB 2 buffer, 200 μM dATP, and 15 U Klenow Fragment (3′ to 5′ exo-, NEB) for 30 min at 37°C. After another DNA purification using the PCR MinElute kit (Qiagen), 3 μL of Illumina's methylated sequencing adapters were ligated on using 1× ligase buffer and 5 μL Quick T4 DNA Ligase (NEB) for 30 min at room temperature. After a final PCR purification, 500 ng of library was bisulfite converted using Zymo's EZ DNA Methylation-Direct kit according to the manufacturer's instructions. The library was then amplified using 2.5 U PfuTurbo Cx Hotstart DNA Polymerase (Stratagene) for 12 cycles using Illumina's standard amplification protocol.

value: hypothalamus

tag: gender

value: Male

value: postnatal day 9

value: control


title: AMC2_WGBS

description: Post-mortem brain

tag: tissue

value: augmented maternal care


title: con_0

description: Sample 7


title: PV

city: Nanjing

first: Shaowu

last: Yin

state: jiangsu

address: College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road,  210023, China.

institute: Nanjing Normal University

data_processing:
After removing adaptor sequences, ambiguous ‘N’ nucleotides (with the ratio of ‘N’ greater than 5%) and low quality sequences (with quality score less than 20), the remaining clean reads were assembled using trinity software (v2013-02-25) as described for de novo transcriptome assembly without a reference genome.
The quality of the assembly was critically assessed by Hanyu Bio-Tech before subsequent analysis.
The coding sequences for assembly sequences were predicted using GetORF by EMBOSS Wiki (http://emboss.sourceforge.net/apps/cvs/emboss/apps/getorf.html).
For homology annotation, the predicted protein coding sequences were annotated based on the following databases: Nr (NCBI non-redundant protein sequences); GO (gene ontology); KEGG (KEGG Ortholog database); KOG (euKaryotic Ortholog Groups); Swiss-Prot (a manually annotated and reviewed protein sequence database) using the BLASTx algorithm (E-value <1E-5). If the results from different databases conflicted, a priority was determined by the best match.
Supplementary_files_format_and_content: processed data (mrna-seq GENE).xlsx
Supplementary_files_format_and_content: processed data (mrna-seq Trinity gene).fasta

organism: Tachysurus vachellii

source_name: Pelteobagrus vachelli

growth_protocol: P. vachelli (654 ± 89 g in body weight) were randomly transferred to three aquaria with bio-filtered water recirculation systems (equipped with cooling and heating functions and a volume of 200 L and flow rate of 5 L/min) and fed with artificial compound feed, including more than 42.0% protein (Zhenjiang Jiaji Feed Co. Ltd., China). Normal oxygen concentration was 6.8 mg/L (measured with an HQd portable meter and LDO101 probe).

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s protocol. The total RNA quantity and purity were analysed with Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 100ng of total RNA was used for cDNA library constructions. The library for sequencing was generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB, USA). Transcriptome sequencing was carried out on an Illumina HiSeq 2500 platform that generated approximately 125-bp paired-end (PE) raw reads by Hanyu Bio-Tech (Shanghai, China).

treatment_protocol: Fish were killed by dissection after mild anaesthetisation in a eugenol bath (1:10,000), after which eight tissues (brain, liver, gill, spleen, intestine, heart, muscle and kidney) were frozen in liquid nitrogen and stored at -80°C. Three fish were pooled to create a sample.

value: adult fish

value: heart, liver, brain, spleen and kidney

tag: tag

value: fish


title: Ctrl1_WGBS

description: Post-mortem brain

tag: treatment


title: BAP1-KO

value: anti-BAP1 (Genentech, PRO424270)


title: Ctrl3_WGBS

description: Post-mortem brain


title: AMC1_WGBS

description: Post-mortem brain


title: Ctrl6_RNAseq

description: Post-mortem brain

data_processing:
The Hi-Seq 2500 reads were trimmed using Trimmomatic and Illuminaclip single end adapter trimming
final quality was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
RNA-seq reads were aligned to the current UCSC rat genome rn6 using the splicing-aware aligner Tophat2 (v2.0.14, stranded, Single End).
Differential expression was analyzed using cufflinks (v2.2.1) with bias, multi-read, and length corrections.
Cuffdiff was performed using a Cuffmerge generated gtf from all assembled transcripts and RefSeq UCSC genes using a genometric pooled dispersion model and minimum alignment of 10 fragments.
Genome_build: rn6
Supplementary_files_format_and_content: Strand specific RNAseq bigwig showing read coverage over the genome

extract_protocol:
Extracted and purified using the Qiagen RNeasy kit
Total RNA was isolated from AMC and control hypothalamus using the RNeasy Kit (Qiagen, Valencia, CA). Total RNA samples were then processed with a Gene Read ribosomal RNA depletion kit (Qiagen, Germantown PA) prior to Illumina Hi-Seq library preparation using a directional RNA-seq library kit (NEB, Ipswich, MA). Libraries were checked by Bioanalyzer analysis (Agilent, Santa Clara, CA) for quality, then 50 base pair, single end reads were acquired on a Hi-Seq 2500 (Illumina, San Diego, CA) at the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkley.


title: Ctrl5_RNAseq

description: Post-mortem brain


title: AMC6_RNAseq

description: Post-mortem brain


title: Ctrl4_RNAseq

description: Post-mortem brain


title: AMC5_RNAseq

description: Post-mortem brain


title: ebf3: GFP+ rep3

status: Public on Apr 20 2019

city: Paris

first: Emilie

last: Dambroise

address: 24 bd Montparnasse

country: France

institute: Institut Imagine

data_processing:
Basecalls performed using Illumina script BclToFastq version 1.8.3
Data were demultiplexed using the distribution of CASAVA software (CASAVA-1.8.2)
Data quality was checked with FastQC 0.10.1
Reads were mapped to the genome of Oryzias latipes oryLat2 (downloaded from UCSC) using TopHat2
Differential expression analysis of RNA-seq and gene expression profiles with biological replication was performed using the Bioconductor package DESeq
Differential expression statistics classified each gene as up, down or not significant according a |log2-transformed fold change| >1, with adjusted p-values less than 0.05, and computed FDR from resulting p-values using a Benjamini Hochberg multiple test
DE statistics classified each gene as up/down/not significant according a |log2-transformed fold change| >1, with adjusted p-values less than 0.05
FDR from resulting p-values using a Benjamini Hochberg multiple test (FDR <= 0.05)
Selection of genes up regulated and downregulated in wdr12:GFP+ compared both to wdr12:GFP- and ebf3:GFP+ cells (refered as controls)
Genome_build: Oryzias latipes oryLat2
Supplementary_files_format_and_content: wdr12: GFP+ referred as wdr12GFP
Supplementary_files_format_and_content: wdr12: GFP- referred as wdr12GFPm
Supplementary_files_format_and_content: ebf3: GFP+ referred as ebf3GFP
Supplementary_files_format_and_content: ebf3: GFP+ union wdr12:GFP- referred as controls
Supplementary_files_format_and_content: raw counts: ebf3GFP_tot-count.xlsx
Supplementary_files_format_and_content: raw counts: wdr12GFPmvsebf3GFP.xls
Supplementary_files_format_and_content: raw counts: wdr12GFPmvswdr12GFP.xls
Supplementary_files_format_and_content: raw counts: wdr12GFPvsebf3GFP.xls

organism: Oryzias latipes

source_name: optic tectum

extract_protocol:
RNA isolation was performed using the PicoPureTM Isolation kit according to the manufacturer's protocol. Total RNA concentration and quality were checked in an Agilent Bioanalyser.
4ng of RNA were used for each library construction (Epicentre). Library construction was performed with TotalScript™ RNA-Seq Kit according to the manufacter’s protocol.
Libraries were sequenced on an Illumina Hiseq 1000 instrument, using a TruSeq SR Cluster Kit v3-cBot-HS (Illumina) and TruSeq SBS Kit v3-HS - 50 cycles (Illumina), using a Single Read 50 bp protocol. Libraries have been pooled in equimolar proportions and diluted to a final concentration of 12pM, according to Illumina recommandations.

treatment_protocol: Thirty one-month optic tecta were quickly dissected out and placed in ice-cold calcium-free RINGER solution. Cells were dissociated in FACSmax Cell Dissociation Solution (AMS Biotechnology, Abingdon, UK; T200100). A mechanical dissociation step was performed with a plunger from a 1-mL syringe. Tectums were squished through a strainer (40-μm mesh) into a Petri dish and the cell suspension was transferred into another tube. Cells were sorted on a MoFlo Astrios (Beckman-Coulter) cytometer

tag: line

value: 1 month

value: optic tectum


title: ebf3: GFP+ rep2


title: wdr12: GFP+ rep3


title: ebf3: GFP+ rep1


title: con_DAC_0

description: Sample 4

value: SW48 (Human colon adenocarcinoma cell line)


title: con_DAC_1

description: Sample 5

value: decitabine treatment


title: AMC3_WGBS

description: Post-mortem brain


title: wdr12: GFP+ rep2


title: wdr12: GFP+ rep1


title: wdr12: GFP- rep2


title: TSChomo2_S14

status: Public on Apr 17 2019

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

data_processing:
Raw reads (fastq files) were quality-trimmed and adapters removed with cutadapt (version 1.12).
The processed fastq files were mapped to the mouse transcriptome and genome using TopHat (v2.0.14).
Quantification was done using htseq-count (version 0.6.0).
Genes with a sum of counts less than 10 over all samples were filtered out.
Normalization was done with the DESeq2 package (version 1.16.1).
Genome_build: GRCm38
Supplementary_files_format_and_content: iTS_genes.htseq_counts_per_sample: tab-delimited text file, containing read counts per gene per sample generated by htseq-count. iTS_DESeq2_normc_htseq.txt:  tab-delimited text file, containing normalized read counts per gene per sample, generated by DESeq2.

source_name: Embryo-derived mouse trophoblast stem cells

growth_protocol: Mouse embryonic fibroblasts were grown in DMEM supplemented with 10% FBS, 2 mM L-glutamine, and antibiotics. TSCs were grown in TX medium supplemented  with FGF4 (25 ng/ml), heparin (1 μg/ml), and Tgfβ1 (2 ng/ml) on Matrigel as described previously (Kubaczka et al., 2014) . Blastocyst-derived TSC (bdTSC) were isolated as described (Oda et al., 2006).

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy kit
RNA libraries were prepared for sequencing using the SENSE mRNA-seq library prep kit V2 (Lexogen), and pooled libraries were sequenced on an Illumina NextSeq 500 platform to generate 75-bp paired-end reads

treatment_protocol: Stable colonies

tag: strain background

value: Blastocyst derived trophoblast stem cell line

tag: genotype/variation

value: knock-in reporter Oct-4-GFP


title: NT12

status: Public on Apr 19 2019

city: yinchuan

last: Xiaofan

state: Ningxia

address: Helanshan west road

department: school of life science

institute: Ningxia univertisty

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Prior to differential gene expression analysis for each sequenced library, the read counts were adjusted by edger program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the DEGSeq R package (1.12.0). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.005 and log2 (Fold change) of 1 were set as the threshold for significantly differential expression.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: narciclasine treated_root cells

growth_protocol: Seeds were surface sterilized with 70% ethanol containing 0.05% Tween 20 for 30 seconds and then 15% sodium hypochlorite for 15 min, and rinsed at least three times with sterilized water before sowing on agar plates of 1/2 × MS medium (pH5.7) containing 1% (W/V) sucrose, 0.8% (W/V) agar. After stratification for 4 days at 4 ℃, the plates were placed vertically in a climate chamber at 21～22 ℃ under 200 µM m-2s-1 light conditions (16/8 h light cycle) for 5 days.

extract_protocol:
At each time point, total RNA was extracted with Trizol (Invitrogen) from 3 mm samples of excised root tips (100 mg), and RNA quality was monitored on 1% agarose gels. RNA purity was analyzed with a NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Narciclasine was purchased from Sigma-Aldrich (http://www.sigmaaldrich.com/catalog/product/ sigma/n9789?lang=zh&region=CN) with the CAS number 29477-83-6. For narciclasine treatment, 5 day-old seedlings were transferred to the plates containing 1/2 MS medium with or without 0.5 µM narciclasine and incubated for 2 or 12 hr.

tag: ecotype

value: wild type

tag: treated with

value: 0.5 µM narciclasine for 12 hrs

value: root


title: CK12

source_name: control_root cells

value: none (control)


title: NT2

value: 0.5 µM narciclasine for 2 hrs


title: TSChomo1_S13


title: Sf9

city: Nanyang

first: Dandan

last: Li

state: Henan

address: 1638 Wolong Road

institute: Nanyang Normal University

data_processing:
Transcriptome de novo assembly is carried out with short reads assembling program – Trinity
Unigenes were annotated with the databases of NR, NT, Swiss-Prot, KEGG, COG and GO
WEGO software was used to do GO functional classification for all Unigenes
Unigene pathway analysis is used by KEGG
SNP analysis was analyzed by SOAP, SSR detection is done with software MicroSAtellite(MISA)
Genome_build: from SPODOBASE, All ESTs sequences (254639) come from 10 different libraries
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Spodoptera frugiperda

source_name: Spodoptera frugiperda Ovary cells line Sf9

growth_protocol: Sf9 cells were maintained in Grace medium (Gibco) containing 10% fetal bovine serum (FBS) (Gibco) at 28°C and routinely passaged every third day.

extract_protocol:
Total RNA was extracted from different samples of Sf9 cells with the TRIzol (Thermo Fisher Scientific) method.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA or by removing rRNAs from the total RNA. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. The suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeq™ 2000.

treatment_protocol: For transient expression, cells were grown in 24-well plates to 70%-80% confluency and further transfected with 2μg of plasmid DNA or antisense oligonucleotides employing Lipofectamine LTX and Plus Reagents (Thermo Fisher Scientific). Cells were harvested at different time-points after transfection and subjected to further analysis.

value: Ovary cells

tag: passage

value: normal


title: TSChetero1_S15


title: TSChetero2_S16


title: BYKEMEF1_S11

source_name: Embryo-derived BYKE mouse embryonic fibroblast

value: Embryonic fibroblast

value: Quadruple knock-in reporters Nanog-2A-EGFP, Elf5-EYFP-NLS, Utf1-2A-tdTomato and Esrrb-2A-TagBFP


title: ASO

source_name: Sf9 cells with Bm-15 repression

value: Bm-15 repression


title: 5F_22_S24

source_name: GETMS transgenes

value: induced Trophoblast stem cell line

value: knock-in  reporter Oct-4-GFP


title: Bm_15

source_name: Sf9 cells with Bm-15 overexpression

value: Bm-15 overexpression


title: 5F_21_S23


title: AMC4_RNAseq

description: Post-mortem brain

value: hypothalamus

value: Male

value: postnatal day 9

value: augmented maternal care


title: 5F_11_S21

value: knock-in reporter Oct-4-GFP


title: 4F_52_S20

source_name: GETM transgenes


title: 4F_51_S19


title: CK2

value: wild type


title: mES_v6-5_1

description: processed data file: genes.htseq_counts_per_sample.txt, DESeq2_normc_htseq.txt

data_processing:
Raw reads (fastq files) were quality-trimmed and adapters removed with cutadapt (version 1.12).
The processed fastq files were mapped to the mouse transcriptome and genome using TopHat (v2.0.14).
Quantification was done using htseq-count (version 0.6.0).
Genes with a sum of counts less than 10 over all samples were filtered out.
Normalization was done with the DESeq2 package (version 1.16.1).
Genome_build: GRCm38
Supplementary_files_format_and_content: genes.htseq_counts_per_sample: tab-delimited text file, containing read counts per gene per sample generated by htseq-count. DESeq2_normc_htseq.txt:  tab-delimited text file, containing normalized read counts per gene per sample, generated by DESeq2.

growth_protocol: Mouse embryonic fibroblasts were grown in DMEM supplemented with 10% FBS, 2 mM L-glutamine, and antibiotics. ESCs were grown in DMEM supplemented with 10% FBS, 1% nonessential amino acids, 2 mM L-glutamine, home-made mouse Leukemia inhibitory factor (mLif), 0.1 mM b-mercaptoethanol (Sigma), and antibiotics with or without 2i- PD0325901 (1 mM) and CHIR99021 (3 mM) (Tocris). Blastocyst-derived TSC (bdTSC) were isolated as described (Oda et al., 2006). For reprogramming, Doxycyclin was added to the media.

treatment_protocol: For samples in reprogramming, cells from stable colonies were harvested

tag: strain

value: Inner cell mass


title: wdr12: GFP- rep1

value: 1 month

value: optic tectum


title: BYKE_iPS_OSKM_C3_1

source_name: Induced pluripotent stem cells

value: Embryonic-like stem cell line

value: OSKM transgenes


title: mES_v6-5_2


title: 4F_31_S17

tag: cell line


title: 4F_32_S18


title: BYKE_iPS_OSKM_C3_2


title: BYKE_iPS_OSKM_C1_2


title: BYKE_iPS_5F_c10_1

value: GETMS transgenes


title: BYKE_iPS_OSKM_C1_1


title: BYKEMEF2_S12

value: Embryonic fibroblast

value: Quadruple knock-in reporters Nanog-2A-EGFP, Elf5-EYFP-NLS, Utf1-2A-tdTomato and Esrrb-2A-TagBFP


title: BYKE_iPS_5F_C12_2


title: 5F_12_S22

value: induced Trophoblast stem cell line


title: BYKE_MEF_1


title: BYKE_ES_2

source_name: Modified KH2 embryonic stem cells

value: Embryonic stem cell line


title: BYKE_MEF_2


title: BYKE_iPS_5F_c10_-2


title: MEF GETMS H3K27ac ChIP-seq

description: Paired-end ChIP-seq

data_processing:
ChIP-seq: Paired-end reads were mapped to the genome (mm9) using bowtie using max insert size of 1000, mapping unique hits with up to 3 mismatches.
genome build: mm9
processed data files format and content: ChIP-seq: bigwig files were created by calculating the genomic coverage of mapped paired-end reads and normalized to 20M pairs. Peaks were called using MACS, using a p-value threshold of 1e-3, shift size of 2Kb, short local window of 10Kb and long local window of 50Kb.

source_name: GETMS

growth_protocol: Mouse embryonic fibroblasts (MEFs) were isolated as previously described (Wernig et al., 2008). MEFs were grown in DMEM supplemented with 10% FBS, 2 mM L-glutamine, and antibiotics. ESCs were grown in DMEM supplemented with 10% FBS, 1% nonessential amino acids, 2 mM L-glutamine, home-made mouse Leukemia inhibitory factor (mLif), 0.1 mM b-mercaptoethanol (Sigma), and antibiotics with or without 2i- PD0325901 (1 mM) and CHIR99021 (3 mM) (Tocris). Blastocyst-derived TSC (bdTSC) were isolated as described (Oda et al., 2006). TSCs were grown in TSC culturing medium, combined of 30% TSC medium containing RPMI supplemented with 20% FBS, 0.1 mM b-mercaptoethanol (Sigma) , 2 mM L-glutamine, 25 ng/ml homemade mouse FGF4 and 1 mg/ml heparin (Sigma-Aldrich), and 70% MEF conditioned TSC media (MEF-CM) with the same supplements. For reprogramming, Doxycyclin was added to the media.

extract_protocol: ChIP-seq: Chromatin immunoprecipitation (ChIP) assay was performed as previously described (Mendenhall et al., 2013) using H3K27ac antibody (Abcam, ab4729) and H3K4me2 antibody (Millipore, 07-030).

treatment_protocol: For samples in reprogramming, cells were harvested at day 3.

value: Mouse Embryonic Fibroblasts (MEF)

value: 3 days of reprogramming by GETSM

value: H3K27ac (Abcam, ab4729)


title: BYKE_ES_1


title: MEF GTMS H3K27ac ChIP-seq

description: Paired-end ChIP-seq

source_name: GTMS

value: 3 days of reprogramming by GTMS


title: MEF GTMS H3K4me2 ChIP-seq

description: Paired-end ChIP-seq

value: H3K4me2 (Millipore, 07-030)


title: MEF GETMS H3K4me2 ChIP-seq

description: Paired-end ChIP-seq


title: MEF+S H3K27ac ChIP-seq

description: Paired-end ChIP-seq

source_name: MEF + S

value: 3 days of reprogramming by Esrrb


title: MEF+S H3K4me2 ChIP-seq

description: Paired-end ChIP-seq


title: TSCendo-B6#1_RNA-seq_re-analyzed

description:
Single-end RNA-seq
This re-analyzed sample is associated with two raw data files which represent technical duplicates.
[processed data files:]
FPKM.txt
FPKM.bed.gz

data_processing:
RNA-seq: Reads were mapped using TopHat to the mouse genome (mm9), and expression levels were calculated using cufflinks (with default parameters).
genome build: mm9
processed data files format and content: RNA-seq: Processed files include a tab-separated text file with FPKM values for each gene/condition, as well as a .bed version visualizing expression levels. Replicates were combined for a single value per cell type. FPKM values are available on the series record.

source_name: endogenous trophoblast stem cells

growth_protocol: TSCs and iTSCs were cultured under TX medium condition as decribed in PMID:24527396. mESCs were cultured in 2i medium and MEFs with DMEM supplemenated with 10% FBS medium

extract_protocol:
Cells were homogenized and RNA was harvested using the RNeasy kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: endogenous trophoblast stem cells


title: TSCendo#1_RNA-seq_re-analyzed


title: mESC_RNA-seq_re-analyzed

source_name: embryonic stem cells

value: embryonic stem cells


title: MEF GETMS-TSC RNA-seq_rep2

description:
Single-end RNA-seq
[processed data files:]
FPKM.txt
FPKM.bed.gz

source_name: MEF GETMS-TSC

extract_protocol:
RNA-seq: RNA extraction was done using the RNesay kit (Qiagen) according to the manufacturer’s instructions. Six RNA libraries were prepared: MEFs, and MEFS at three days of reprogramming by OSKM, GETM, GTMS or GETMS. ESC and TSC samples were re-analyzed from GSE64684.
RNA-seq: Library preparation was done with QuantSeq 3′ mRNA-Seq Library Prep Kit by Lexogen. Libraries were subjected to single-end sequencing using Illumina Next-Seq 500 platform.

value: TSC reprogramming medium


title: MEF GETM RNA-seq_rep2

source_name: MEF GETM

value: 3 days of reprogramming by GETM


title: MEF GETMS-ESC RNA-seq_rep1

source_name: MEF GETMS-ESC

value: ESC reprogramming medium


title: MEF GETM RNA-seq_rep1


title: MEF GETMS-TSC RNA-seq_rep1


title: BYKE_iPS_5F_C12_1

value: Embryonic-like stem cell line


title: MEF OSKM RNA-seq_rep1

source_name: MEF OSKM

value: 3 days of reprogramming by OSKM


title: MEF GTMS RNA-seq_rep2

source_name: MEF GTMS

value: 3 days of reprogramming by GTSM


title: MEF GETMS-ESC RNA-seq_rep2


title: MEF RNA-seq_rep2

source_name: MEF


title: MEF OSKM RNA-seq_rep2


title: MEF GTMS RNA-seq_rep1


title: iPSC ATAC-seq_rep1

description:
Paired-end ATAC-seq
[processed data files:]
iPSC_25_coverage.macs2.bed
iPSC.norm.bigwig

data_processing:
ATAC-seq: Paired-end reads were mapped using Bowtie to the mouse genome (mm9), using max insert size of 2000. Mapping only unique hits with up to 3 mismatches within first 38 bases.
genome build: mm9
processed data files format and content: ATAC-seq: bigwig files were created by calculating the genomic coverage of mapped paired-end reads and normalized to total primary data size (bigWigInfo) of 150M bases. Peaks were called using MACS2 bdgpeakcall, with min-length and max-gap paramters set to 500 bp. The ATAC-seq replicate samples were combined in order to produce the processed data files. ATAC-seq processed data files are available on the series record.

source_name: iPSC

extract_protocol:
ATAC-seq: Eight ATAC libraries were prepared: iPSCs, TSCs, MEFs, and MEFS at three days of reprogramming by OSKM, GETM, GTMS or GETMS.
ATAC-seq: Library preparation was performed as previously described (Buenrostro et al., 2016). Libraries were subjected to paired-end sequencing using Illumina Next-Seq 500 platform.

value: iPSC

value: induced pluripotant stem cells


title: MEF RNA-seq_rep1


title: iTSC ATAC-seq_rep1

description:
Paired-end ATAC-seq
[processed data files:]
TSC_25_coverage.macs2.bed
TSC.norm.bigwig

source_name: iTSC

value: iTSC

value: induced trophoblast stem cells


title: MEF GETMS-TSC ATAC-seq_rep2

description:
Paired-end ATAC-seq
[processed data files:]
GETSM-TSC_25_coverage.macs2.bed
GETSM-TSC.norm.bigwig

value: Mouse Embryonic Fibroblasts (MEF)

value: 3 days of reprogramming by GETSM in TSC medium


title: MEF GETMS-ESC ATAC-seq

description:
Paired-end ATAC-seq
[processed data files:]
GETSM-ESC_25_coverage.macs2.bed
GETSM-ESC.norm.bigwig

value: 3 days of reprogramming by GETSM in ESC medium


title: MEF GETM ATAC-seq_rep1

description:
Paired-end ATAC-seq
[processed data files:]
GETM_25_coverage.macs2.bed
GETM.norm.bigwig


title: MEF GETMS-TSC ATAC-seq_rep1


title: iPSC ATAC-seq_rep2

description:
Paired-end ATAC-seq
[processed data files:]
ESC_25_coverage.macs2.bed
ESC.norm.bigwig


title: MEF GTMS ATAC-seq_rep2

description:
Paired-end ATAC-seq
[processed data files:]
GTSM_25_coverage.macs2.bed
GTSM.norm.bigwig


title: MEF GTMS ATAC-seq_rep1


title: MEF OSKM ATAC-seq_rep2

description:
Paired-end ATAC-seq
[processed data files:]
OSKM_25_coverage.macs2.bed
OSKM.norm.bigwig


title: MEF OSKM ATAC-seq_rep1


title: MEF ATAC-seq

description:
Paired-end ATAC-seq
[processed data files:]
MEF_25_coverage.macs2.bed
MEF.norm.bigwig


title: Tumor_11659 (RNA-seq)

city: Gothenburg

first: Toshima

middle: Z.

last: Parris

address: Medicinaregatan 1G, 6th floor

department: Department of Oncology

country: Sweden

institute: University of Gothenburg

data_processing:
Quality control of raw RNA-seq reads was performed prior to assembly using FastQC (0.11.5), followed by trimming and filtering of the reads with TrimGalore (0.3.3) to remove adapter sequences and reads with Phred quality scores below 20.
Counts and Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using HtSeq (0.6.1)(60) and Cufflinks (2.2.1)(61).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Human breast tumor

extract_protocol:
Total RNA was extracted with RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer and RNA quantification with Nanodrop and Qubit.
Illumina TruSeq strand-specific RNA libraries (Ribosomal depletion using RiboZero human) containing 125 bp pair-end reads were obtained for each sample on a HiSeq2000 sequencer (Illumina) using standard Illumina protocols.

value: breast tumor

tag: 8p11-p12 amplification

value: Amplified

tag: pt status

tag: lymph node status

tag: er status

value: pos

tag: pgr status

value: neg

tag: her2 status


title: Tumor_11378 (RNA-seq)

tag: tissue

tag: age


title: Tumor_11372 (RNA-seq)


title: iTSC ATAC-seq_rep2

tag: cell type

tag: treatment


title: MEF GETM ATAC-seq_rep2


title: Tumor_10408 (RNA-seq)


title: Tumor_10068 (RNA-seq)


title: Tumor_8901 (RNA-seq)


title: Tumor_10415 (RNA-seq)


title: Tumor_9494 (RNA-seq)


title: Tumor_10400 (RNA-seq)


title: Tumor_9493 (RNA-seq)


title: Tumor_8931 (RNA-seq)


title: Tumor_10569 (RNA-seq)


title: Tumor_11315 (RNA-seq)


title: Tumor_8828 (RNA-seq)


title: Tumor_8652 (RNA-seq)


title: Tumor_8860 (RNA-seq)


title: Tumor_7631 (RNA-seq)


title: Tumor_8842 (RNA-seq)


title: Tumor_8629 (RNA-seq)


title: Tumor_8472 (RNA-seq)


title: Sample_96H_2_20160508

city: Shanghai

first: Mengzhu

last: Xue

address: No.100, Haike Road

institute: Shanghai Advanced Research Institute

data_processing:
Fastqc was utilized to check the RNA sequencing quality
mirdeep2 was used to complete the analysis. Mapper.pl was used to cut adapters,discard reads shorted than 15 and do alignment;quantifier.pl was used for abundance calculation with miRBase reference miRNA sequences.
In details, data determined on April 21 and May 8 (or May 4) were analyzed respectively, then read count and normalized count values were combined together.
Genome_build: hg19
Supplementary_files_format_and_content: text files include raw and normalized count values for each Sample

source_name: EMT, 96H

extract_protocol:
RNA was harvested using Trizol reagent.
After 3' and 5' adapter introduced, RNA libraries were quatified with Qubit agents.

value: adenocarcinomic human alveolar basal epithelial cells

tag: protocol

value: EMT induced

tag: time

value: 96 hr

tag: data determined on


title: Sample_96H_2_20160421


title: Sample_96H_1_20160508


title: Tumor_7253 (RNA-seq)


title: Sample_24H_2_20160504

source_name: EMT, 24H

value: 24 hr


title: Sample_24H_2_20160421


title: Sample_96H_1_20160421


title: Sample_24H_1_20160504


title: Tumor_10823 (RNA-seq)


title: CHD4_DNMT1_0

description: Sample 10

source_name: human colon_CHD4_DNMT1

value: SW48 (Human colon adenocarcinoma cell line)

value: siCHD4 plus siDNMT1 treatment


title: Sample_0H_2_20160504

source_name: EMT, 0H

value: 0 hr


title: Sample_24H_1_20160421


title: Inhibitory-1 total RNAseq

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

country: South Korea

institute: Chung-Ang University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: vGAT-positive brain neurons

growth_protocol: αCaMKII-Cre and vGAT-IRES-Cre transgenic mouse colonies were maintained by breeding transgenic mice to wild-type C57Bl/6J mice. Mice used for experiments were bred in the Seoul National University (SNU) Specific Pathogen Free center (LML08-404). Male mice (3-5 months) were used.

extract_protocol:
Fluorescent cells were manually collected by using glass pipette. After washing in HBSS, collected cells were directly lysed with cell lysis buffer containing RNase inhibitor as follow manufacturer’s instruction of SMART-seq v4 (Ultra low input RNA kit, Clontech Laboratories, Inc.).
After generation of cDNA from homogenous cell-type samples, the construction of library was performed by using Nextera XT DNA library prep kit (Illumina, Inc., USA) according to the manufacturer’s instructions. The double-stranded library was purified by using magnetic beads to remove all reaction components. The library was amplified to add the complete adapter sequences required for cluster generation. The finished library is purified from PCR components.

value: brain

value: vGAT-positive brain neurons

tag: number of cells

value: 100 Single cells


title: Sample_0H_1_20160421


title: Excitatory-2 total RNAseq

source_name: aCaMKII-positive brain neurons

value: aCaMKII-positive brain neurons


title: Sample_0H_2_20160421


title: Sample_0H_1_20160508


title: Tumor_7325 (RNA-seq)


title: Inhibitory-2 total RNAseq


title: Excitatory-1 total RNAseq


title: siControl-Dex_RNAseq

city: Toronto

first: Carolyn

middle: L

last: Cummins

address: 144 College St.

institute: University of Toronto

data_processing:
Splicing analysis: Detailed description of the analysis pipeline can be found in [Irimia et al. Cell 159, 1511-1523 (2014)]. A summary of the main steps is provided here. An RNA-Seq dataset is first aliged to the genome using Bowtie. Reads that map to the genome are discarded from further analysis since exon-exon junctions (EEJs) are absent from genomic sequence. Reads that failed to align to the genome are aligned to a custom library of EEJs using Bowtie. To quantify splicing, the combination of EEJs that define each splicing event was created. For the case of single exon skipping events, we generated EEJs for C1A, AC2 and C1C2 (A represents the alternative exon and C1 and C2 represent the neighboring constitutive exons), requiring a minimum of eight positions from each exon. For multi-exon events we generated all possible forward combinations from C1 to C2 exons. If multiple alternative 5’ and/or 3’ splice sites were associated with any alternative, C1 or C2 exons, they were also included in the combinations. Read counts for each EEJ were then used to calculate the Percent Spliced In (PSI) of each event. A  simplified format of the formula is: PSI = 100% * (reads supporting inclusion / total reads).
Gene expression analysis (cRPKM): RNA-seq reads were aligned back to the mouse genome (Ensembl release 67) and transcript levels were quantified as reads per kilobase (of target gene) per million (of total reads) and corrected for transcript length and sequence redundancy (cRPKM)
Genome_build: mm9
Supplementary_files_format_and_content: 2014-03-13_cassette_all.txt, 2014-03-13_5altSS_all.txt, and 2014-03-13_3altSS_all.txt: 3 tab delimited text files summarizing the splicing analysis in N2a cells, where the tables contain, cassette exon, 5 prime splice site, and 3 prime splice site events, respectively. For all tables, each row corresponds to a unique splicing event. The table has the following columns: GENE - gene ID, EVENT - unique event ID containing the ENSEMBL gene ID, COORD - genomic coordinates of the alternative exon, LENGTH - nucleotide length of the alternative exon, FullCO - genomic coordinates of alternative exon as well as the coordinates of the last and first base pairs of the upstream and downstream exons, respectively, COMPLEX - refers to type of splicing event (S/C1/C2/C3: alternative cassette exon > 15 nucleotides, ME: mutually exclusive exons, Alt3: alternative 3´ splice site, Alt5: alternative 5´ splice site, MIC: alternative micro cassette exon ≤ 15 nucleotides), siArg_Dex_R1 - PSI in cells treated with siArglu1 + 100nM Dexamethasone, SiArg_Veh_R1 - PSI in cells treated with siArglu1 + Vehicle (ethanol), siCon_Dex_R1 - PSI in cells treated with control siRNA + 100nM Dexamethasone, siCon_Veh_R1 - PSI in cells treated with control siRNA + Vehicle (ethanol), siArg_Dex.Q + siArg_Veh.Q + siCon_Dex.Q + siCon_Veh.Q - quality scores for the corresponding PSI values, see  [Irimia et al. Cell 159, 1511-1523 (2014)] for details.
Supplementary_files_format_and_content: 2014-03-13_cRPKMs_all.txt: tab delimited text file summarizing gene expression analysis in N2a cells. Each row corresponds to a single gene. The table has the following columns: Gene - gene ID, external_gene_id - ENSEMBL gene ID, description – full gene name, cRPKM_siCon_Dex_R1 - cRPKMs in cells treated with control siRNA + 100nM Dexamethasone, cRPKM_siCon_Veh_R1 - cRPKMs in cells treated with control siRNA + Vehicle (ethanol), cRPKM_siArg_Dex_R1 - cRPKMs in cells treated with siArglu1 + 100nM Dexamethasone, cRPKM_siArg_Veh_R1 - cRPKMs in cells treated with siArglu1 + Vehicle (ethanol), reads_siCon_Dex_R1 - reads in cells treated with control siRNA + 100nM Dexamethasone, reads_siCon_Veh_R1 - reads in cells treated with control siRNA + Vehicle (ethanol), reads_siArg_Dex_R1 - reads in cells treated with siArglu1 + 100nM Dexamethasone, reads_siArg_Veh_R1 - reads in cells treated with siArglu1 + Vehicle (ethanol), see  [Labbéet al. Stem Cells 30, 1734–1745 (2012)] for details.

source_name: Neuro-2a cells

growth_protocol: Monolayer growth in DMEM with 10% FBS

extract_protocol:
Total RNA was extracted from cultured cells using RNA-STAT60 reagent (Tel-Test Inc)
mRNA enriched Illumina TruSeq V2 RNA libraries were constructed using standard illumina protocol following DNAse treatment.

treatment_protocol: siRNA transfection with Lipofectamine RNAiMax (Life Technologies)

value: Neuro-2a; N2a

value: neuroblastoma cell line

tag: transfected with

value: non-targeting control siRNAs for 48 hrs

tag: treated with

value: 100 nM Dexamethasone for 4 hrs


title: siARGLU1-Veh_RNAseq

tag: cell line

value: ARGLU1 siRNAs for 48 hrs

value: Vehicle (EtOH) for 4 hrs


title: siARGLU1-Dex_RNAseq


title: FCRL5+#3

status: Public on Apr 16 2019

city: San Francisco

first: Charlie

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

data_processing:
Bases were called and reads were demultiplexed with Illumina CASAVA 1.8.2 and read quality assessed using FastQC
Reads were aligned to the transcriptome using STAR version 2.4.2a with default parameters
Gene expression per sample was modeled with RSEM version 1.2.21
Genome_build: release GRCm38 of the mouse genome
Supplementary_files_format_and_content: Tab delimited text files showing tpm for all genes

source_name: Blood leukocytes

extract_protocol:
Class-switched B cells (IgM- IgD- CD19+) that were either FCRL5+ or FCRL5- were isolated from the blood of P. chabaudi-infected mice by double-sorting on a FACS AriaII.  Total RNA was isolated, converted to cDNA, and pre-amplified as described in the SMARTer Ultra-low input kit (Clontech PN 634833) but with modified procedures for low cell number analysis (Fluidigm)
RNA libraries were prepared for sequencing following Illumina protocols.  cDNA libraries were diluted to 0.25ng/ul, fragmented with the Nextera XT DNA kit (Illumina PN FC-131-1024), multiplexed, and sequenced on a Hi-Seq2500

value: blood

value: CD19+ B cells

tag: cell surface markers

value: CD19+ IgM- IgD- FCRL5+


title: FCRL5-#5

value: CD19+ IgM- IgD- FCRL5-


title: FCRL5-#3


title: FCRL5+#1


title: FCRL5+#4


title: FCRL5+#5


title: FCRL5+#2


title: FCRL5-#2


title: FCRL5-#4


title: FCRL5-#1