title: splB_JK5_BL6

description:
Sample 19
Barcode: -
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait

value: 1 ug


title: MCK-NamptOE_24m_905

status: Public on Jul 22 2016

type: SRA

city: Philadelphia

first: Ian

middle: M

last: Silverman

state: Pennsylvania

address: 433 South University Ave, Room 104

department: Biology

country: USA

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
Reads were trimmed with Cutadapt (v1.4.2), mapped with Tophat2, and gene expression was quantified using HTseq (Trapnell et al. 2009; Martin 2011; Anders et al. 2015). DEseq2 was used perform differential expression analysis (Love et al. 2014).
Genome_build: mm10
Supplementary_files_format_and_content: counts.txt files: Gene Counts; number of reads mapped to ensemble gene IDs
Supplementary_files_format_and_content: DESeq_gencode.all.name.txt files: DESeq2 Output; differential expression analysis of RNA-seq data

molecule: polyA RNA

organism: Mus musculus

source_name: Quadricep muscle

growth_protocol: Mice were maintained under standard housing conditions on standard chow diet.

extract_protocol:
Total RNA was purified from the Quadricep muscle (Trizol reagent, Life Technologies). Poly(A)+ RNA was isolated using oligo dT beads (Life Technologies, Frederick, MD).
RNA was fragmented for 7 minutes using Fragmentation Reagent (Life Technologies, Waltham, MA).  mRNA-seq libraries were then generated using the Illumina mRNA-seq kit (illumina, San Diego, CA).

treatment_protocol: Mice were occassionally subjected to glucose and exercise tolerance tests before sacrifice.

tag: genotype

value: overexpressing Nampt in skeletal muscle

tag: tissue

value: quadricep muscle

tag: age

value: 24 months

tag: background strain


title: MCK-NamptOE_24m_906


title: MCK-NamptOE_4m_2035

value: 4 months


title: WT_24m_1279

value: wild type


title: Control

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava software used for basecalling
equenced reads were trimmed for adaptor sequence, and then mapped to mm9 whole genome using Tophat using default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (genes.fpkm tracking)

molecule: total RNA

source_name: control optic nerve

extract_protocol:
Optic nerves were removed, flash frozen on dry ice, and total RNA was harvested using Trizol reagent. Libraries were prepared according to Illumina's instructions accompanying Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: mixed

value: optic nerve


title: splB_JH4_mouse3_BL6

city: Boston

first: Jiazhi

last: Hu

state: MA

address: 300 Longwood Ave

department: PCMM

institute: Children's Hospital Boston

description:
Sample 18
Barcode: GTAC
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait

library_source: genomic

data_processing:
HTGTSrep pipeline was used for generating the processed files with "pass.xls" ends; Linear amplification-mediated (LAM)-HTGTS pipeline was used for generating processed files with "tlx" ends.
Paire-end sequenced reads were trimmed for barcode and adaptor sequence and joined
The trimmed reads then were searched against VDJ gene databases using igblast1.5 with default parameters and further processed by the HTGTSrep pipeline, or against LAM-HTGTS pipeline with default settings.
For HTGTSrep pipeline, reads can successfully aligned to V, D, J databases are reported and a statistic report including V gene usage and in-frame/non-productive information is created by the pipeline.
Genome_build: mm9, mm9_AJ851868ins (Based on the genome build of mm9, we replaced its chr12 between 114,493,850 and 115,696,909 with the reverse complement sequence of the GeneBank AJ851868.3)
Supplementary_files_format_and_content: tab-delimited text files include aligned V, D, J genes for each read and a V usage report for each sample.

molecule: genomic DNA

growth_protocol: Mice were bought from Jackson labs and kept in our mouse facility

extract_protocol:
Tissues were extracted and treated with RBC lysis, resuspended in PBS, and stained for FACS. Bone marrow-derived pro-B (B220+IgM-CD43+) cells were purified from 129SVE or C57BL/6 mice by sorting and after the depletion of erythrocytes. Single cell suspensions were stained with B220-APC, CD43-PE, and IgM-FITC antibodies. Splenic resting B cells were purified using biotin/streptavidin bead methods (B220 positive selection) or EasySep CD43-negative B cell selection.  Cells were then processed for genomic DNA extraction.
Libraries were prepared via HTGTS-Rep-seq protocols

treatment_protocol: No immunization, but the food and water are not germ-free

tag: strain

value: wild-type

tag: bait locus

tag: growth protocol

value: No immunization

value: 4-6 weeks

tag: cell type

value: Splenic B

tag: primer strategy

value: Individual

tag: dna amount

value: 2 ug


title: WT_24m_2372


title: WT_24m_1044


title: MCK-NamptOE_24m_1357


title: splB_JH4_mouse2_BL6

description:
Sample 17
Barcode: AACT
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: MCK-NamptOE_4m_2027


title: splB_mix_JK5_BL6

description:
Sample 20
Barcode: CA
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait

value: Combined with Jk1, Jk2, Jk4 primers in one library preparation


title: MCK-NamptOE_4m_2010


title: WT_4m_1971


title: WT_4m_1965


title: splB_JH3_mouse3_BL6

description:
Sample 15
Barcode: GCCAAT
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: MCK-NamptOE_24m_1242


title: WT_4m_1957


title: mNamptKO_4016

extract_protocol:
Total RNA was purified from the Quadricep muscle (miRNeasy; Qiagen, Valencia, CA). Poly(A)+ RNA was isolated using oligo dT beads (Life Technologies, Frederick, MD).
RNA was fragmented for 7 minutes using Fragmentation Reagent (Life Technologies, Waltham, MA).  mRNA-seq libraries were then generated using the Illumina mRNA-seq kit (illumina, San Diego, CA).

value: deficient for Nampt in skeletal muscle

value: 7 months


title: WT_24m_2373


title: splB_JH3_mouse1_BL6

description:
Sample 13
Barcode: -
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: mNamptKO_3696


title: splB_JH4_mouse1_BL6

description:
Sample 16
Barcode: -
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: WT_3790


title: splB_JH2_mouse2_BL6

description:
Sample 11
Barcode: CTGA
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: mNamptKO_3685


title: WT_3766


title: WT_3788


title: splB_JH1_mouse1_BL6

description:
Sample 7
Barcode: -
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_JH1_mouse3_BL6

description:
Sample 9
Barcode: GCCAAT
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: WT_3691


title: splB_mouse3_BL6

description:
Sample 6
Barcode: AGTG
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_JH1_mouse2_BL6

description:
Sample 8
Barcode: CTTGTA
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_mouse2_BL6

description:
Sample 5
Barcode: CAGATC
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: proB_mouse3_BL6

description:
Sample 3
Barcode: CTTGTA
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait

value: progenitor B


title: proB_mouse1_BL6

description:
Sample 1
Barcode: CTGG
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_mouse1_BL6

description:
Sample 4
Barcode: CTTGTA
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_JH3_mouse2_BL6

description:
Sample 14
Barcode: CTTGTA
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: Run80_L8_Input

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: 2% input

data_processing:
Sequence reads were aligned to the mouse mm9 genome using Bowtie.
Peak detection was performed using the HOMER base suite v4.3 with a false discovery rate filter of 5% utilizing the read from PBX1-ChIP-seq, normal IgG ChIP-seq normalized to inputs. The top 10% of the peaks were used for de novo motif finding using the MEME-ChIP tool from MEME suite (http://meme.nbcr.net/) with default settings and the HOMER based suite.
Peak-gene association was done using GREAT v2.0.2, associating a genomic region with the two nearest genes.
Genome_build: mm9
Supplementary_files_format_and_content: peaks from the HOMER analysis

molecule: nuclear RNA

source_name: ventral midbrain

growth_protocol: E12.5 embryos for ChIP-Seq were obtained from wild-type C57bl/6 mice.

extract_protocol:
Ventral midbrain E12.5 tissues were trypsinized to a single cell suspension using TrypLe (Invitrogen). Cells were filtered and washed using cold PBS with 1% BSA.
ChIP-Seq was performed following the manufacturer's instructions (Pierce, Agarose ChIP kit; 26156). The chipped fragmented DNA samples were end repaired and A-tailed. Illumina adapters were ligated and size selected (200-350 bp) on agarose gel before going to PCR amplification. PCR products were purified and size selected again on gel.

tag: antibody


title: Run80_L8_IgG

description: Control IgG

value: Control IgG


title: splB_JH2_mouse3_BL6

description:
Sample 12
Barcode: GCAT
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: CELF2_CLIPseq_stimulated_3.2

first: Kristen

last: Lynch

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Molecular Biophysics

description: stimulated JSL1 CELF2 CLIP-seq: third replicate, second PCR aliquot

data_processing:
Library strategy: CLIP-Seq
Trimming of 3' sequencing adapter oligonucleotide using cutadapat version 0.9.4.  Sequencing adapter was 'GTGTCAGTCACTTCCAGCGG'.
Alignment to hg19 genome with bowtie version 0.12.8
Collapsing of aligned reads within each individual library using Perl version 5.16.1, combining of aliquots from same cell cultures.
Calling of peaks with the program discover_peaks from the clipseq_analysis distribution, version 0.05.
Discarding of peaks with sequencing support from fewer than 2 out of 3 cell cultures using bedtools multicov.
Joining of peaks within 50nt of one another with bedtools slop.
Genome_build: hg19
Supplementary_files_format_and_content: BED format (six columns).  Score column (fifth column) of processed CLIP-seq reads denotes the copy number of the 5' coordinate (start coordinate for + strand, end coordinate for - strand) that was collapsed to one representative.

organism: Homo sapiens

source_name: JSL1 T cells, RPMI + PMA

growth_protocol: Either cell culture media alone (unstimulated) or PMA-supplemented media (stimulated)

extract_protocol:
UV crosslinking and CELF2 immunoprecipitation
CLIP-seq

value: JSL1 T cells

tag: detected molecule

value: CELF2-crosslinked RNA


title: Run80_L8_Pbx1

description: Pbx1 antibody

value: Pbx1 antibody


title: CELF2_CLIPseq_stimulated_3.3

description: stimulated JSL1 CELF2 CLIP-seq: third replicate, third PCR aliquot


title: CELF2_CLIPseq_stimulated_2.3

description: stimulated JSL1 CELF2 CLIP-seq: second replicate, third PCR aliquot


title: CELF2_CLIPseq_stimulated_2.2

description: stimulated JSL1 CELF2 CLIP-seq: second replicate, second PCR aliquot


title: CELF2_CLIPseq_stimulated_2.1

description: stimulated JSL1 CELF2 CLIP-seq: second replicate, first PCR aliquot


title: mNamptKO_3690

value: quadricep muscle


title: CELF2_CLIPseq_stimulated_1.1

description: stimulated JSL1 CELF2 CLIP-seq: first replicate, first PCR aliquot


title: CELF2_CLIPseq_stimulated_1.2

description: stimulated JSL1 CELF2 CLIP-seq: first replicate, second PCR aliquot


title: splB_JH2_mouse1_BL6

description:
Sample 10
Barcode: -
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: CELF2_CLIPseq_unstimulated_3.2

description: unstimulated JSL1 CELF2 CLIP-seq: third replicate, second PCR aliquot

source_name: JSL1 T cells, RPMI


title: CELF2_CLIPseq_unstimulated_3.3

description: unstimulated JSL1 CELF2 CLIP-seq: third replicate, third PCR aliquot


title: CELF2_CLIPseq_stimulated_1.3

description: stimulated JSL1 CELF2 CLIP-seq: first replicate, third PCR aliquot


title: CELF2_CLIPseq_unstimulated_2.3

description: unstimulated JSL1 CELF2 CLIP-seq: second replicate, third PCR aliquot


title: CELF2_CLIPseq_unstimulated_3.1

description: unstimulated JSL1 CELF2 CLIP-seq: third replicate, first PCR aliquot


title: CELF2_CLIPseq_unstimulated_2.2

description: unstimulated JSL1 CELF2 CLIP-seq: second replicate, second PCR aliquot


title: proB_mouse2_BL6

description:
Sample 2
Barcode: GCCAAT
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: CELF2_CLIPseq_stimulated_3.1

description: stimulated JSL1 CELF2 CLIP-seq: third replicate, first PCR aliquot


title: CELF2_CLIPseq_unstimulated_2.1

description: unstimulated JSL1 CELF2 CLIP-seq: second replicate, first PCR aliquot


title: CELF2_CLIPseq_unstimulated_1.3

description: unstimulated JSL1 CELF2 CLIP-seq: first replicate, third PCR aliquot


title: CELF2_CLIPseq_unstimulated_1.2

description: unstimulated JSL1 CELF2 CLIP-seq: first replicate, second PCR aliquot


title: Embryo-Stage 28-family 2-WTTS

city: Pullman

first: Zhihua

last: Jiang

state: WA

address: Veterinary and Biomedical Research Building, Room 151

department: Animal Science

institute: Washington State University

data_processing:
Illumina Casava1.7 software used for basecalling .Torrent Suite™ Software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Xenopus tropicalis genome using CLC genomics workbench. The Xenopus tropicalis genome contains both Xenopus tropicalis 7.1 genome annotation and NCBI Xenopus tropicalis refseq.
Genome_build: Xenopus tropicalis v7.1

organism: Xenopus tropicalis

source_name: Embryo_Stage 28_WTTS

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols and standard Ion Torrent protocols. WTTS libraries were prepared based on our protocol. The WTTS method includes several major steps: fragmentation, polyA+ RNA enrichment, 1st strand cDNA synthesis, size selection and PCR amplication.

value: Embryo

tag: developmental stage

value: Stage 28


title: Embryo-Stage 28-family 1-WTTS


title: Adult-RNAseq

source_name: Adult-RNAseq

value: Whole body

value: Adult


title: Embryo-Stage 15-family 2-WTTS

source_name: Embryo_Stage 15_WTTS

value: Stage 15


title: CELF2_CLIPseq_unstimulated_1.1

description: unstimulated JSL1 CELF2 CLIP-seq: first replicate, first PCR aliquot


title: Embryo-Stage 15-family 1-WTTS


title: Embryo-Stage 11-family 2-WTTS

source_name: Embryo_Stage 11_WTTS

value: Stage 11


title: Embryo-Stage 6-family 2-WTTS

source_name: Embryo_Stage 6_WTTS

value: Stage 6


title: Embryo-Stage 11-family 1-WTTS


title: Embryo-Stage 8-family 1-WTTS

source_name: Embryo_Stage 8_WTTS

value: Stage 8


title: Adult-Trial 7-WTTS

source_name: Adult_whole body_WTTS


title: Adult-Trial 6-WTTS


title: Female-Technical repeat 2-WTTS

source_name: Female_technical repeat_WTTS


title: Female-Technical repeat1-WTTS


title: Rep_3 9 DL

city: Stanford

first: Jose

middle: Ramon

last: Dinneny

state: United States

address: 260 Panama St

department: Plant Biology

institute: Carnegie Institution for Science, Department of Plant Biology

data_processing:
All RNA-Seq data was quality controlled via fastqc, adapters were filtered using cutadapt, low-quality 3’ sequences were filtered utilizing the fastx toolkit (discarding nucleotides < Q35, reads shorter than 50nt), and read singletons were discarded.
Read pairs which survived the above process were aligned against the Setaria viridis v1.1 genome
Alignments of RNA-Seq data were grouped by tissue/treatment/duration combinations (e.g. the three biological replicates derived from well-watered upper roots samples 6DAS were treated as a group).
Replicate groups were compared utilizing the cuffdiff algorithm
Differentially expressed genes were grouped by their directionality of differential expression, and analyzed for overrepresentation of Gene Ontology terms (GO terms) (Ashburner et al., 2000) utilizing the ‘topGO’ R package (Alexa, Rahnenführer, & Lengauer, 2006) from Bioconductor (Gentleman et al., 2004). GO-terms with a false-discovery corrected p-value <0.05 were deemed to be over-represented.
Genome_build: Setaria viridis v1.1 genome (http://phytozome.jgi.doe.gov/)
Supplementary_files_format_and_content: tab-delimited text files include log2 fold change values for each Sample
Supplementary_files_format_and_content: GO enrichment csv files include GO term, p-value and false discovery rate for each Sample (GO.tar.gz)

organism: Setaria viridis

source_name: drought_lower_9 days

growth_protocol: Seeds were grown in 25% sand, 75% peat in Deepots; 20 plants per sample were harvested.

extract_protocol:
Total RNA was purified by Zymo Plant RNA kit
Ribosomal RNA was depleted by Ribozero Plant Root/Seed kit, strand-specific libraries were made using NEBNext Ultra Directional kit for Illumina; libraries were amplified with 6 bp barcoded pcr primers
12 libraries were pooled per lane; aimed for 10 million reads per library.

tag: plant condition

value: drought (D) treated

value: Lower region (crown)

tag: harvest time point

value: 9 days after sowing

tag: biological replicate


title: Rep_3 9 WL

source_name: watered_lower_9 days

value: watered (W)


title: Rep_3 9 DU

source_name: drought_upper_9 days

value: Upper region (stem)


title: Adult-Trial 5-WTTS


title: Y5_3

city: Qingdao

first: Hao

last: Song

state: Shandong

address: 7 Nanhai Road

country: China

institute: Institute of Oceanology,Chinese Academy of Sciences

description: approximately 500mg larvae were collected for  RNA extraction

data_processing:
Raw image data file from highthroughput sequencing(Illumina HiSeqTM 2500) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality.
Raw reads filtering as follows:(1)Remove reads containing adaptors; (2)remove reads containing N > 10%; (3)remove low quality reads: The sQ(Quality value) of over 50% bases of the read is <= 5.
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.
Clean reads are assemblied into a transcriptome as the reference in the following analysis by Trinity. Taking the longest transcript of each gene as Unigene.

organism: Rapana venosa

source_name: larvae

extract_protocol:
larvae from six major developmental stage, viz., one spiral whorl stage, two spiral whorls stage, earlir stage of three spiral whorls, later stage of three spiral whorls, four spiral whorls stage(competent larva), post larva were collected under microscope, frozen in liquid nitrogen quickly till use. Each stage have three repeats for RNA extraction, every repeat contains approximately 500mg larvae.
RNA from six developmental stages of R. venosa （each stage have three replicates） was used for library consctruction.RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: development stage

value: post larva

value: whole larvae


title: Y5_1

tag: tissue


title: Adult-Trial 4-WTTS


title: Y5_2


title: Adult-Trial 3-WTTS


title: Rep_3 9 WU

source_name: watered_upper_9 days


title: Rep_3 6 DL

source_name: drought_lower_6 days

value: 6 days after sowing


title: Embryo-Stage 8-family 2-WTTS


title: Rep_3 6 WL

source_name: watered_lower_6 days


title: J4_1

value: four spiral whorls stage (competent larva)


title: Rep_3 6 DU

source_name: drought_upper_6 days


title: RBP-J KO with TNF for 24h rep2

city: New York

first: Baohong

last: Zhao

address: 535 E70th ST

institute: Hospital for Special Surgery

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Sequenced reads were mapped to mouse miRNAs from the miRBase release 21 using miRDeep2.
Number of raw counts was calculated using miRDeep2. The raw counts were then normalized by library size and multiplied by a factor of 1e6 which corresponds technically to counts per million (CPM) mapped miRNA reads.

source_name: bone marrow macrophages

growth_protocol: Murine bone marrow cells were harvested from tibiae and femora, and cultured overnight in Petri dishes (BD Biosciences) in a-MEM medium (Invitrogen) with 10% FBS (Invitrogen). Except where stated, CMG14-12 supernatant, which contained the equivalent of 20 ng/ml of recombinant M-CSF, were used as a source of M-CSF in experiments. Non-adherent cells were then re-plated into tissue culture dishes and cultured in the same medium for 3 days to obtain bone marrow derived macrophages.

extract_protocol: Illumina TruSeq Small RNA Library preparation

value: C57BL/6/129 mix background with C57BL/6 over 90%

value: bone marrow macrophages

tag: genotype

value: Rbpjf/f; LysM Cre

tag: treatment

value: with TNF for 24h


title: Rep_3 6 WU

source_name: watered_upper_6 days


title: G3_3

value: later stage of three spiral whorls


title: WT with TNF for 24h rep2

value: WT


title: G3_2


title: Embryo-Stage 6-family 1-WTTS

value: Embryo

value: Stage 6


title: G3_1


title: Rep_2 9 DU

value: drought (D) treated


title: RBP-J KO without stimulation rep 2

value: without stimulation


title: WT without stimulation rep2


title: J4_2


title: Adult-Trial 2-WTTS

value: Whole body

value: Adult


title: F3_3

value: earlier stage of three spiral whorls


title: RBP-J KO with TNF for 24h rep 1


title: J4_3


title: Rep_2 9 WL

value: watered (W)

value: Lower region (crown)

value: 9 days after sowing


title: Adult-Trial 1-WTTS


title: F3_2

value: whole larvae


title: WT with TNF for 24h rep1

value: C57BL/6/129 mix background with C57BL/6 over 90%


title: Rep_2 6 DL

value: 6 days after sowing


title: Rep_2 9 WU

value: Upper region (stem)


title: F3_1


title: RBP-J KO without stimulation rep 1

value: bone marrow macrophages

value: Rbpjf/f; LysM Cre


title: Rep_2 6 DU


title: D2_2

value: two spiral whorls stage


title: WT without stimulation rep1

value: WT


title: D2_1


title: Embryo-Stage 11-family 2-RNAseq

source_name: Embryo_Stage 11_RNAseq

value: Embryo

value: Stage 11


title: C1_3

value: one spiral whorl stage


title: Embryo-Stage 8-family 2-RNAseq

source_name: Embryo_Stage 8_RNAseq

value: Stage 8


title: Embryo-Stage 11-family 1-RNAseq


title: Rep_1 9 DL

value: drought (D) treated


title: Rep_2 9 DL


title: Rep_1 9 WL


title: Embryo-Stage 8-family 1-RNAseq


title: C1_1


title: Rep_1 9 DU


title: Embryo-Stage 6-family 2-RNAseq

source_name: Embryo_Stage 6_RNAseq

value: Stage 6


title: Rep 1_6 WL

value: watered (W)


title: LNCaP shFOXA1, hMe-Seal-seq

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: Enrichment of 5hmC by chemical pulldown

data_processing:
library strategy: hMe-Seal-seq
Reads were aligned to the hg19 reference human genome using bwa v0.6.1
Peak-calling by HOMER v4.1
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file and peak txt file

source_name: prostate cell line

growth_protocol: Cell lines were maintained in RPMI supplemented with 10% FBS.

extract_protocol:
Chromatin was fixed in 1% formaldehyde, sheared to 200-700bp using a probe sonicator, immunoprecipitated using the indicated antibody or chemically labeled, purified and sequenced using Illumina Genome Analyzers following protocols recommended by the manufacturer.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: Cells were subjected to lentiviral infection by scramble or shFOXA1/shTET1.

tag: cell line

value: LNCaP

tag: genotype/variation

value: FoxA1 shRNA

tag: chemical labeling


title: Rep 1_6 WU


title: Rep_2 6 WU


title: abo4_3

city: evry

first: remi

last: bounon

state: essonne

address: 2 avenue Gaston Crémieux

department: BAP

country: France

institute: INRA

data_processing:
default parameters to Torrent Suite Software version 4.2.1
Mapping with Bowties2 on messager RNA TAIR 10 reference (parameters : no MultiHit, local reads mapping, TAIR 10 refrence with one gene model)
Genome_build: Arabidopsis thaliana TAIR 10
Supplementary_files_format_and_content: count by gene

organism: Arabidopsis thaliana

extract_protocol:
Qiagen_RNeasy.pdf
RNA libraries were prepared for sequencing using standard LifeTechnologies protocols for Ion Torrent Proton (4476286_Ion Total RNA-Seq Kit v2_UG_RevE.pdf)
RNA Seq in Stranded Single End, sizing 230bp, messager RNA selection (DynabeadsmRNADIRECTMicro_UG_Rev004.pdf)

treatment_protocol: no treatment

tag: organ

value: seedling

tag: ecotype


title: LNCaP shFOXA1, MeDIP-seq

description: Enrichment of 5mC by antibody pulldown

data_processing:
Reads were aligned to the hg19 reference human genome using bwa v0.6.1
Peak-calling by HOMER v4.1
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file and peak txt file


title: abo4_1


title: abo4_2


title: 12.1.5_3


title: Rep 1_6 DU


title: LNCaP shCtrl, MeDIP-seq, rep2

description: Enrichment of 5mC by antibody pulldown

value: control


title: 12.1.5_1


title: LNCaP shCtrl, hMe-Seal-seq

description: Enrichment of 5hmC by chemical pulldown


title: 1.11.2_3


title: D2_3

value: whole larvae


title: Rep_1 9 WU

value: Upper region (stem)

value: 9 days after sowing


title: C1_2


title: 1.11.2_2


title: LNCaP shCtrl (pLKO), hMe-Seal-seq

description: Enrichment of 5hmC by chemical pulldown


title: Tsc1cKO

source_name: Tsc1cKO optic nerve

tag: strain background

value: mixed

tag: age

value: optic nerve


title: Rep_2 6 WL

value: Lower region (crown)

value: 6 days after sowing


title: Embryo-Stage 6-family 1-RNAseq

value: Embryo


title: Rep 1_6 DL


title: LNCaP shTET1, hMe-Seal-seq

description: Enrichment of 5hmC by chemical pulldown


title: 1.11.2_1


title: Col-0_3

value: wild-type


title: LNCaP shTET1, MeDIP-seq

description: Enrichment of 5mC by antibody pulldown

tag: antibody


title: 12.1.5_2


title: first untagged control CRAC sample

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

country: United Kingdom

institute: University of Edinburgh

description: cross-linked RNA

data_processing:
Library strategy: CRAC
CRAC data processing steps: All processing steps were performed using the pyCRAC package version 1.2.2.5. Demultiplexing was performed using pyBarcodeFilter.py (version 2.3.4). 3' adapter removal and 3' end quality trimming (min Phred = 30) was performed using FlexBar (version 2.5). Reads were collapsed using random nucleotides present in 5' barcodes using pyFastqDuplicateRemover.py (version 0.0.2). Reads were mapped to the S. pombe genome (ASM294v2.19; source ENSEMBL) using novoalign (version 2.0.4) and feature counts were generated using pyReadCounters (version 0.5.3).
The gtf files were used to generate begraph files for viewing the data in the Integrated Genome Browser (bioviz.org).
Genome_build: ASM294v2.19
Supplementary_files_format_and_content: The data format of the processed data is the gene transfer format (gtf). This contains the genomic positions of the mapped reads. For the CRAC data mutation information was also included. PyReadCounters version 0.5.3 from the pyCRAC package (Webb et al Genome Biology, version 1.2.2.5) was used.

organism: Schizosaccharomyces pombe

source_name: first untagged control CRAC sample

growth_protocol: Schizosaccharonyces pombe were grown in YES medium to exponential phase at 30ºC

extract_protocol:
Cells (0.8-1g) were lysed in 1V (w/v) of TN150 (50 mM Tris pH 8.0, 0.1% NP-40, 150 mM NaCl, 5 mM beta-mercaptoethanol, Roche protease inhibitor cocktail) and 3V of 0.5 mm Zirkonia beas by vortexing for five minutes at full speed. Lysates were clarified by centrifugation and processed as previously described (Granneman et al 2009, PNAS).
Libraries were constructed using the CRAC library preparation method described in Granneman et al PNAS 2009 with small modifications to the adapter sequences (see sequences below)
PCR oligonucleotides for making CRAC libraries
3' adapter:
App_PE: 5’App-NAGATCGGAAGAGCACACGTCTG-ddC 3’
5' adapters:
L5Bb: 5'-invddT-ACACrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUrNrNrNrCrArCrUrArGrCrN-OH-3'
L5Bc: 5'-invddT-ACACrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUrNrNrNrGrUrGrArGrCrN-OH-3'
L5Cb: 5'-invddT-ACACrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUrNrNrNrUrGrGrArGrCrN-OH-3'
L5Cc: 5'-invddT-ACACrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUrNrNrNrArCrUrCrArGrCrN-OH-3'
P5_forward: 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’
P3_reverse: 5’-CAAGCAGAAGACGGCATACGAGAT(6nt barcode)GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’

treatment_protocol: Cells were UV-irradiated in the Megatron UV cross-linker (Granneman et al EMBO Journal 2011) for three minutes in YES medium and harvested by filtration. Cells were snap-frozen in liquid nitrogen and stored at -80ºC.

value: h+ ade6-M216 leu1-32 ura4-delta_18 his3delta_1


title: Col-0_2


title: LNCaP shTET1, FOXA1 ChIP-seq

description: Chromatin IP against FOXA1


title: P. chlororaphis_hfq_AB_rep2

city: Vernon Hills

first: DONGPING

last: WANG

state: IL

address: 777 Forest Edge Dr

department: Amlan

institute: OilDri Corporation of America

description:
strain: Pseudomonas chlororaphis 30-84 genotype: mutant, growing condition: AB minimal medium, Stage: late logarithm phase
Strand-specific cDNA libraries were constructed using the SOLiD Total RNA-Seq kit according to the manufacturer’s instructions with the following modifications: 1) For RNA fragmentation, 300 ng of rRNA-depleted RNA were incubated at 95˚C for 5 min. Bioanalyzer traces were used to confirm that the largest proportion of RNA fragments were around 200 bp. 2) Bioanalyzer traces following reverse transcription were used to confirm that hybrization and ligation of RNA adapters and subsequent reverse transcription of the RNA to cDNA was successful. 3) Amplification of cDNA was carried out following reverse transcription, but preceding the size-selection step. Samples were barcoded by replacing the SOLiD 3’ primer with the appropriate barcoding primer as directed in the SOLiD instructions. Size selection of DNA amplicons ranging from 200-300 bp was performed using an E-Gel iBase system (SYBR Safe 2% SizeSelect gel) (Life Technologies, Carlsbad, CA).  This step was repeated to ensure that adapter-adapter dimers were fully eliminated before sequencing. Paired-end sequencing was carried out by the University of Texas Genomic Sequencing and Analysis Facility (UTGSAF: http://www.ti3d.utexas.edu/facilities/gene-expression) on a Life Technologies SOLiD 5500xl sequencing system. Targeted sequencing depth was six-million paired-end reads per sample.

data_processing:
Paired-end sequencing was carried out by the Otogenetic company. Targeted sequencing depth was ten-million paired-end reads per sample.
Based on gene annotation information, the pipeline produced genome alignment results as a compressed binary version of the Sequence Alignment Map (BAM files).
Based on gene annotation information, the pipeline produced genome alignment results as a compressed binary version of the Sequence Alignment Map (BAM files).
Mapped reads were visualized using BamView in Artemis 13.2.0 (Rutherford et al. 2000).
The number of reads per kb of transcript per million mapped reads (RPKM) was used to normalize the raw data (Mortazavi et al., 2008), and mean RPKM values were determined for both the wild-type and mutant samples.
Genome_build: GenBank Accession #: PRJNA67533
Supplementary_files_format_and_content: RPKM values for each gene

organism: Pseudomonas chlororaphis subsp. aureofaciens 30-84

source_name: hfq mutant cells

growth_protocol: Two biological replicates of every strain were started from single colonies located on two separate plates containing AB + 2% CAA and then transferred to 1.5 ml AB + 2% CAA broth. All cultures were grown at 28˚C in static plates to an approximate OD600 = 1.8.

extract_protocol:
Transfer 700 μl lysate into RNeasy Mini column place in a 2 ml collection tube and centrifuge for 30 s at highest speed. Add 350 μl Buffer RW1 to the column and centrifuge for 30 s. Discard flow-through and reuse the collection tube. Add 10 μl DNase stock solution to 70 μ l RDD Buffer. Add the DNase I solution into the column and incubate at RT for 15 min. Add 350 μl Buffer RW1 to the column and wait for 5 min, centrifuge for 30 s. Discard the flow-through and collection tubes. Place the RNeasy Mini spin column in a new 2 ml collection tube. Add 500 μl Buffer RPE to the column. Centrifuge for 30 s. Place the column in a new 1.5 ml tube, and centrifuge for 1 min to eliminate any residue ethanol. Place the column in a new collection tube. Add 50 μl RNase free water, centrifuge for 1 min. Store RNA samples at -20°C
Strand-specific cDNA libraries were constructed using Illumina TruSeq RNA Sample Preparation Kits.

treatment_protocol: wild type and mutant strains

value: hfq mutant

tag: strain


title: P. chlororaphis_hfq_AB_rep1


title: Col-0_1

tag: developmental stage


title: LNCaP shCtrl, H3K4me2 ChIP-seq

description: Chromatin IP against H3K4me2

value: shCtrl


title: first tagged Seb1 CRAC sample

description: cross-linked RNA

source_name: first tagged Seb1 CRAC sample

value: h+ ade6-M216 leu1-32 ura4-delta_18 his3delta_1 Seb1-HTP::KAN


title: second tagged Seb1 CRAC sample

description: cross-linked RNA

source_name: second tagged Seb1 CRAC sample


title: LNCaP, hMe-Seal-seq

description: Enrichment of 5hmC by chemical pulldown

value: LNCaP

value: Normal


title: Third replicate of X. Retroflexus and M. oxydansin dual species biofilm

city: Lyngby

first: Lea Benedicte

middle: Skov

last: Hansen

address: Kemitorvet 208

department: Center for Biological Sequence Analysis

country: Denmark

institute: Technical University of Denmark

data_processing:
As a quality control, only reads approved by the CASAVA v1.8.2 (Illumina, San Diego, CA, USA) was included and adaptor remnants were removed. End nucleotides with a quality Phred score below 20 were removed. After the end trim process, sequences shorter than 45 nt were removed from the metatranscriptomic libraries. Reads were discarded if they displayed a mean Phred score below 15 in a sliding window of 5 nt for the metatranscriptomes. The quality filtering was carried out using Biopieces (https://github.com/maasha/biopieces).
To create a mapping template for the transcriptomes all four genomes were sequences and assemblied. All metatranscriptome libraries were mapped to the four genomes using Bowtie2 v.2.0.5
An expression table was created by counting number of nt mapping to each gene in the gene catalogue for every sample.
Genome_build: Custom genome catalogue
Supplementary_files_format_and_content: There are two processed data files: custom genome catalogue (all_contigs500.fasta - fasta file format) and a gene expression matrix (matrix_sum.txt - tab separated table in text format).Only reads approved by the CASAVA v1.8.2 (Illumina, San Diego, CA, USA) was included and adaptor remnants were removed. End nucleotides with a quality Phred score below 20 were removed. After the end trim process, sequences shorter than 50 nt were removed from the genomic. Reads were discarded if they displayed a mean Phred score below 10 in a sliding window of 10 nt for the genomic libraries. The quality filtering was carried out using Biopieces (https://github.com/maasha/biopieces). Velvet v.1.2.07 was used to assemble the genomic data (Zerbino and Birney, 2008) and Prodigal v2.50 was used for gene calling (Hyatt et al., 2010) and all contigs above 500 nt was concatenated into a custom genome catalogue. The transcripts were mapped to this catalogue and the information from the gene calling about the position of the genes were used to count how many nt mapped to a specific gene. This information was collected in a gene expression matrix.
Supplementary_files_format_and_content: Please note that the 'prodigal_all_new.txt' contains gene  names (which are listed in the matrix_sum.txt) and their position in the genomes, which are included in the file 'all_contigs_500.fasta'.

organism:
Microbacterium oxydans
Xanthomonas retroflexus

source_name: dual species biofilm

growth_protocol: Over night cultures of each strain were subcultured to exponential phase and adjusted to an optical density at 600nm (OD600nm) of 0.15 in fresh tryptic soy broth

extract_protocol:
For RNA extraction, planktonic cells from biofilm-containing wells were gently removed, wells were rinsed three times using phosphate buffer saline (PBS) and then the biofilms were scraped with sterile pipette tips into 1ml of PBS. The biofilm suspensions were immediately centrifuged at 5000g for 5 min and resuspended in 100μl of PBS followed by addition of 500μl Ambion RNAlater (Thermo Fisher Scientific, Waltham, MA, USA). The RNAlater-preserved samples were kept at 4°C ON, after which RNAlater was removed by adding 600μl cold PBS and centrifuged at 8000g for 5 min at 4°C. The pellet was resuspended in 200μl lysozyme solution (20μg/ml) and incubated at room temperature for 10 min with vortexing for 10s every 2 min. After adding 700μl RLT buffer and vortexing for 10s, the obtained solution was transferred into bead-beating tubes (provided by the FastDNA SPIN Kit for soil) and bead beaten using the Savant FastPrep FP120 (Qbiogene) for 30s at setting 5.0, followed by centrifugation at 13000g for 8 min at 4°C. 850μl of supernatant were transferred to a new microcentrifuge tube. 470μl of 100% ethanol was added and mixed by pipetting. 700μl lysate was transferred to an RNeasy mini spin column. Total RNA was then further purified from each biofilm sample using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions. DNase treatment to remove genomic DNA was conducted according to the instructions in Ambion DNAfree Kit (Thermo Fisher Scientific), except the incubation time was extended to 1h. The complete removal of DNA was confirmed by RT-qPCR using 20µl SYBR Green reactions on Mx 3000 (Stratagene, Cedar Creek, Texas). The qPCR targeted the 16S rRNA gene with the eubacterial primers EUB338 and EUB518. All qPCR reactions were run in technical duplicates and contained 10µl Brilliant III SYBR Green QPCR Master Mix (Stratagene, Cedar Creek, Texas), 1µl forward primer (final concentration 385 nM), 1µl reverse primer (final concentration 385 nM), 1µl template DNA (100x diluted to avoid PCR inhibitors. The program combined the annealing and extension step: 95°C for 3 min followed by 40 cycles of 95°C for 10s, 60°C for 20s, and a final dissociation curve. The standard curve for bacteria was made from a pure culture of Pseudomonas putida kt2440 (Park and Crowley, 2005; VanGuilder et al., 2008). mRNA was subsequently isolated using the Ambion MicroExpress Bacterial mRNA Purification Kit (Thermo Fisher) following the manufacturer’s instructions.
The RNA transcripts were prepared using ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies, Madison, WI, USA)
50bp single reads on an Illumina HiSeq 2000 (Illumina)

treatment_protocol: A total of 4ml of single-species, dual-species or four-species diluted cultures (mixtures of each species at equal cell density) were inoculated in six-well polystyrene plates (Greiner Bio-One, Frickenhausen, Germany) and allowed to grow for 24h at 24°C.

tag: biofilm type

value: Dual species


title: PrEC, hMe-Seal-seq

description: Enrichment of 5hmC by chemical pulldown

value: PrEC LHS


title: P. chlororaphis_WT_AB_rep1 (hfq)

description:
strain: Pseudomonas chlororaphis 30-84 genotype: wild type, growing condition: AB minimal medium, Stage: late logarithm phase
Strand-specific cDNA libraries were constructed using the SOLiD Total RNA-Seq kit according to the manufacturer’s instructions with the following modifications: 1) For RNA fragmentation, 300 ng of rRNA-depleted RNA were incubated at 95˚C for 5 min. Bioanalyzer traces were used to confirm that the largest proportion of RNA fragments were around 200 bp. 2) Bioanalyzer traces following reverse transcription were used to confirm that hybrization and ligation of RNA adapters and subsequent reverse transcription of the RNA to cDNA was successful. 3) Amplification of cDNA was carried out following reverse transcription, but preceding the size-selection step. Samples were barcoded by replacing the SOLiD 3’ primer with the appropriate barcoding primer as directed in the SOLiD instructions. Size selection of DNA amplicons ranging from 200-300 bp was performed using an E-Gel iBase system (SYBR Safe 2% SizeSelect gel) (Life Technologies, Carlsbad, CA).  This step was repeated to ensure that adapter-adapter dimers were fully eliminated before sequencing. Paired-end sequencing was carried out by the University of Texas Genomic Sequencing and Analysis Facility (UTGSAF: http://www.ti3d.utexas.edu/facilities/gene-expression) on a Life Technologies SOLiD 5500xl sequencing system. Targeted sequencing depth was six-million paired-end reads per sample.

source_name: wild type bacterial cells

value: wild type


title: Second replicate of X. Retroflexus and M. oxydansin dual species biofilm


title: PC-3M, hMe-Seal-seq

description: Enrichment of 5hmC by chemical pulldown


title: P. chlororaphis_WT_AB_rep2 (hfq)


title: Second replicate of four species biofilm

organism:
Paenibacillus amylolyticus
Microbacterium oxydans
Stenotrophomonas rhizophila
Xanthomonas retroflexus

source_name: four species biofilm

value: Four species


title: Fifth replicate of four species biofilm


title: PC-3M, TAmC-seq

description: Enrichment of 5mC by chemical pulldown

data_processing:
library strategy: TAmC-seq
Reads were aligned to the hg19 reference human genome using bwa v0.6.1
Peak-calling by HOMER v4.1
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file and peak txt file


title: second untagged control CRAC sample

description: cross-linked RNA

source_name: second untagged control CRAC sample


title: LNCaP shCtrl, FOXA1 ChIP-seq

description: Chromatin IP against FOXA1


title: LNCaP shTET1, H3K4me2 ChIP-seq

description: Chromatin IP against H3K4me2


title: LNCaP, TAmC-seq

description: Enrichment of 5mC by chemical pulldown


title: Third replicate of X. Retroflexus and P. amylolyticus in dual species biofilm

organism:
Paenibacillus amylolyticus
Xanthomonas retroflexus


title: First replicate of X. Retroflexus and M. oxydansin dual species biofilm


title: First replicate of X. Retroflexus in single species biofilm

organism: Xanthomonas retroflexus

source_name: single species biofilm

value: Single species


title: Third replicate of X. Retroflexus and S. rhizophila in dual species biofilm

organism:
Stenotrophomonas rhizophila
Xanthomonas retroflexus


title: Third replicate of X. Retroflexus in single species biofilm


title: Third replicate of four species biofilm


title: Fourth replicate of four species biofilm


title: First replicate of X. Retroflexus and P. amylolyticus in dual species biofilm


title: First replicate of X. Retroflexus and S. rhizophila in dual species biofilm


title: Neat RNA Sequins Flat Mix

status: Public on Jul 21 2016

city: Darlinghurst

first: Simon

middle: Andrew

last: Hardwick

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
Sequenced reads were trimmed to remove standard Illumina adapter sequences using CutAdapt with Trim Galore wrapper script.
Reads were mapped using TopHat2 to genome co-index comprising hg38, ERCCs and our in silico chromosome.
Transcripts were assembled using StringTie, using reference annotations to calculate gene expression values (FPKMs).
Genome_build: hg38
Supplementary_files_format_and_content: GTF files for transcript assemblies, including quantitative expression values.

organism: synthetic construct

source_name: Neat RNA Sequins Flat Mix

extract_protocol:
Total RNA was extracted from K562 using TRIzol (Invitrogen). DNAse treatment was performed with TURBO DNase (Life Technologies) followed by a cleanup with RNA Clean and Concentrator-25 Kit (Zymo Research).
RNA was ribo-depleted using Ribo-Zero™ Magnetic Kit (Human/Mouse/Rat) (Epicentre), libraries were prepared using KAPA Stranded RNA-Seq Library Preparation Kit (KAPA Biosystems).

tag: molecule subtype

value: Neat RNA spike-in (no natural RNA)


title: Second replicate of X. Retroflexus and S. rhizophila in dual species biofilm


title: LNCaP shCtrl, MeDIP-seq

description: Enrichment of 5mC by antibody pulldown

value: control


title: Neat RNA Sequins Mix B

source_name: Neat RNA Sequins Mix B


title: PrEC, TAmC-seq

description: Enrichment of 5mC by chemical pulldown


title: Neat RNA Sequins Mix A

source_name: Neat RNA Sequins Mix A


title: K562 spiked with Sequins Mix A rep3

source_name: Blood

tag: cell line source

value: Female CML patient

tag: biopsy source

value: Peripheral vein

value: 53 yo


title: First replicate of four species biofilm


title: OVCAR5 500 nM JQ1 2

city: PHILADELPHIA

first: yuesheng

last: Li

state: PA

address: 333 Cottman Ave.

department: Genomic Facility

institute: Fox Chase Cancer Center

description:
OVCAR5 Wild Type 500 nM JQ1 Replicate 2 48h
OVCAR5 500 nM JQ1 2

data_processing:
Illumina Hiseq Control software version 2.2.58 for base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to homo sapiens UCSC hg19 (RefSeq) reference genome using TopHat alignment v1.0.0 from Illumina Basespace Apps
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using the Illumina BaseSpace apps Cufflinks Assembly and Differential Expression v1.1.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Ovarian Cancer Cell Line

growth_protocol: Cells were grown in RPMI-1640 + 10% FBS, 5 ug/ml Insulin, 10 U/ml Penicillin-Streptomycin and 2mM GlutaMAX at 37°C, 5% CO2 in 6 well plates.

extract_protocol:
RNA was extracted using the GeneJET RNA purification kit (Thermo Scientific) according to manufacturer's instructions.
RNA libraries were prepared for sequencing using the TruSeq Stranded mRNA Library Prep Kit according to Illumina protocol.

treatment_protocol: Cells were treated with DMSO or 500 nM JQ1 for 48 hours prior to harvesting.


title: WT_4m_1959

data_processing:
Reads were trimmed with Cutadapt (v1.4.2), mapped with Tophat2, and gene expression was quantified using HTseq (Trapnell et al. 2009; Martin 2011; Anders et al. 2015). DEseq2 was used perform differential expression analysis (Love et al. 2014).
Genome_build: mm10
Supplementary_files_format_and_content: counts.txt files: Gene Counts; number of reads mapped to ensemble gene IDs
Supplementary_files_format_and_content: DESeq_gencode.all.name.txt files: DESeq2 Output; differential expression analysis of RNA-seq data

source_name: Quadricep muscle

extract_protocol:
Total RNA was purified from the Quadricep muscle (Trizol reagent, Life Technologies). Poly(A)+ RNA was isolated using oligo dT beads (Life Technologies, Frederick, MD).
RNA was fragmented for 7 minutes using Fragmentation Reagent (Life Technologies, Waltham, MA).  mRNA-seq libraries were then generated using the Illumina mRNA-seq kit (illumina, San Diego, CA).

tag: tissue

value: quadricep muscle

value: 4 months

tag: background strain


title: Second replicate of X. Retroflexus and P. amylolyticus in dual species biofilm


title: Second replicate of X. Retroflexus in single species biofilm


title: K562 spiked with Sequins Mix A rep1


title: OVCAR5 DMSO 1

description:
OVCAR5 Wild Type DMSO Control Replicate 1 48h
OVCAR5 DMSO 1


title: A1847 DMSO 2

description:
A1847 Wild Type DMSO Control Replicate 2 48h Expt 2
A1847 DMSO 2


title: A2780_JQ1R_1

description:
A2780 Wild Type 500 nM JQ1 48h
A2780_JQ1R_1


title: A2780_DMSO_2_48h

description:
A2780 Wild Type DMSO Control  48h
A2780_DMSO_2_48h


title: A2780_JQ1_2_48h

description:
A2780 JQ1R 48h
A2780_JQ1_2_48h


title: A1847 DMSO 1

description:
A1847 Wild Type DMSO Control Replicate 1 48h Expt 2
A1847 DMSO 1


title: A1847 500 nM JQ1 1

description:
A1847 Wild Type 500 nM JQ1 Replicate 1 48h Expt 2
A1847 500 nM JQ1 1


title: OVCAR5 500 nM JQ1 1

description:
OVCAR5 Wild Type 500 nM JQ1 Replicate 1 48h
OVCAR5 500 nM JQ1 1


title: K562 spiked with Sequins Mix A rep2


title: Neat RNA Fusion Sequins Mix

source_name: Neat RNA Fusion Sequins Mix


title: A1847 500 nM JQ1 2

description:
A1847 Wild Type 500 nM JQ1 Replicate 2 48h Expt 2
A1847 500 nM JQ1 2


title: A1847_JQ1_1_48h

description:
A1847 Wild Type DMSO Control  48h Expt 1
A1847_JQ1_1_48h


title: single cell H1 hESC cell [H1_Exp3.290]

city: Madison

first: Ning

last: Leng

state: WI

address: 330 N Orchard St

institute: Morgridge Institute for Research

description:
GSM1562598
sc_cell_type_ec.csv
H1_Exp3.290

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequencing reads were mapped to hg19 using bowtie 0.12.8
Gene expected counts were calculated using RSEM 1.2.3
Genome_build: hg19
Supplementary_files_format_and_content: Expected counts

source_name: undifferentiated human embryonic stem cells

growth_protocol: Growth can treatment conditions were listed in additional columns in the SAMPLE section

extract_protocol:
Single-cell suspentions were loaded onto a medium size (10-17 μm) C1 Single-Cell Auto Prep IFC (Fluidigm), and cell-loading script was performed according to the manufacturer’s instructions. Full-length single-cell cDNA libraries generated by the SMARTer PCR cDNA Synthesis kit (Clontech) and the Advantage 2 PCR kit (Clontech) performed in the C1 system.
For scRNA-seq, diluted single-cell cDNA libraries were fragmented and amplified using the Nextera XT DNA Sample Preparation Kit and the Nextera XT DNA Sample Preparation Index Kit (Illumina). Libraries were multiplexed at 24 libraries per lane, and single-end reads of 67-bp sequencing was performed on an Illumina HiSeq 2500 system. For bulk RNAseq, mRNA is isolated from purified 100 ng total RNA using oligo-dT beads. Isolated mRNA is fragmented in reverse transcription buffer with heat and then reverse-transcribed with SmartScribe reverse transcriptase using a random hexamer oligo.After reverse transcription, RNA is removed by RNaseA and RNaseH treatment. A partial Illumina 5′ adaptor is then ligated to the single stranded cDNA using T4 RNA ligase 1 and incubated overnight at 22°C. After purification, ligated cDNA is amplified by 18 cycles of PCR using oligos that contain full Illumina adaptors. Indexed cDNA libraries are pooled and sequenced on an Illumina HiSeq2500 with a single 51 bp read and a 10 bp index read.

tag: passage

value: passage 30-35

tag: facs sorting

value: not sorted


title: single cell H1 hESC cell [H1_Exp3.291]

description:
GSM1562599
sc_cell_type_ec.csv
H1_Exp3.291

treatment_protocol: Growth can treatment conditions were listed in additional columns in the SAMPLE section


title: OVCAR5 DMSO 2

description:
OVCAR5 Wild Type DMSO Control Replicate 2 48h
OVCAR5 DMSO 2

tag: cell line


title: single cell H1 hESC cell [H1_Exp3.289]

description:
GSM1562597
sc_cell_type_ec.csv
H1_Exp3.289


title: single cell H1 hESC cell [H1_Exp3.287]

description:
GSM1562595
sc_cell_type_ec.csv
H1_Exp3.287


title: A1847_JQ1R_2

description:
A1847 Wild Type 500 nM JQ1 48h Expt 1
A1847_JQ1R_2


title: single cell H1 hESC cell [H1_Exp3.286]

description:
GSM1562594
sc_cell_type_ec.csv
H1_Exp3.286


title: single cell H1 hESC cell [H1_Exp3.284]

description:
GSM1562592
sc_cell_type_ec.csv
H1_Exp3.284


title: single cell H1 hESC cell [H1_Exp3.283]

description:
GSM1562591
sc_cell_type_ec.csv
H1_Exp3.283


title: single cell H1 hESC cell [H1_Exp3.285]

description:
GSM1562593
sc_cell_type_ec.csv
H1_Exp3.285


title: single cell H1 hESC cell [H1_Exp3.288]

description:
GSM1562596
sc_cell_type_ec.csv
H1_Exp3.288


title: single cell H1 hESC cell [H1_Exp3.282]

description:
GSM1562590
sc_cell_type_ec.csv
H1_Exp3.282


title: single cell H1 hESC cell [H1_Exp3.279]

description:
GSM1562587
sc_cell_type_ec.csv
H1_Exp3.279


title: single cell H1 hESC cell [H1_Exp3.278]

description:
GSM1562586
sc_cell_type_ec.csv
H1_Exp3.278


title: single cell H1 hESC cell [H1_Exp3.277]

description:
GSM1562585
sc_cell_type_ec.csv
H1_Exp3.277


title: single cell H1 hESC cell [H1_Exp3.274]

description:
GSM1562582
sc_cell_type_ec.csv
H1_Exp3.274


title: single cell H1 hESC cell [H1_Exp3.280]

description:
GSM1562588
sc_cell_type_ec.csv
H1_Exp3.280


title: single cell H1 hESC cell [H1_Exp3.281]

description:
GSM1562589
sc_cell_type_ec.csv
H1_Exp3.281


title: single cell H1 hESC cell [H1_Exp3.276]

description:
GSM1562584
sc_cell_type_ec.csv
H1_Exp3.276


title: single cell H1 hESC cell [H1_Exp3.275]

description:
GSM1562583
sc_cell_type_ec.csv
H1_Exp3.275


title: single cell H1 hESC cell [H1_Exp3.272]

description:
GSM1562580
sc_cell_type_ec.csv
H1_Exp3.272


title: single cell H1 hESC cell [H1_Exp3.273]

description:
GSM1562581
sc_cell_type_ec.csv
H1_Exp3.273


title: single cell H1 hESC cell [H1_Exp3.271]

description:
GSM1562579
sc_cell_type_ec.csv
H1_Exp3.271


title: single cell H1 hESC cell [H1_Exp3.269]

description:
GSM1562577
sc_cell_type_ec.csv
H1_Exp3.269


title: single cell H1 hESC cell [H1_Exp3.270]

description:
GSM1562578
sc_cell_type_ec.csv
H1_Exp3.270


title: single cell H1 hESC cell [H1_Exp3.267]

description:
GSM1562575
sc_cell_type_ec.csv
H1_Exp3.267


title: A1847_DMSO_1_48h

description:
A1847 JQ1R 48h
A1847_DMSO_1_48h


title: single cell H1 hESC cell [H1_Exp3.265]

description:
GSM1562573
sc_cell_type_ec.csv
H1_Exp3.265


title: single cell H1 hESC cell [H1_Exp3.266]

description:
GSM1562574
sc_cell_type_ec.csv
H1_Exp3.266


title: single cell H1 hESC cell [H1_Exp3.263]

description:
GSM1562571
sc_cell_type_ec.csv
H1_Exp3.263


title: single cell H1 hESC cell [H1_Exp3.262]

description:
GSM1562570
sc_cell_type_ec.csv
H1_Exp3.262


title: single cell H1 hESC cell [H1_Exp3.264]

description:
GSM1562572
sc_cell_type_ec.csv
H1_Exp3.264


title: single cell H1 hESC cell [H1_Exp3.260]

description:
GSM1562568
sc_cell_type_ec.csv
H1_Exp3.260


title: single cell H1 hESC cell [H1_Exp3.258]

description:
GSM1562566
sc_cell_type_ec.csv
H1_Exp3.258


title: single cell H1 hESC cell [H1_Exp3.261]

description:
GSM1562569
sc_cell_type_ec.csv
H1_Exp3.261


title: single cell H1 hESC cell [H1_Exp3.254]

description:
GSM1562562
sc_cell_type_ec.csv
H1_Exp3.254


title: single cell H1 hESC cell [H1_Exp3.257]

description:
GSM1562565
sc_cell_type_ec.csv
H1_Exp3.257


title: single cell H1 hESC cell [H1_Exp3.253]

description:
GSM1562561
sc_cell_type_ec.csv
H1_Exp3.253


title: single cell H1 hESC cell [H1_Exp3.252]

description:
GSM1562560
sc_cell_type_ec.csv
H1_Exp3.252


title: single cell H1 hESC cell [H1_Exp3.251]

description:
GSM1562559
sc_cell_type_ec.csv
H1_Exp3.251


title: single cell H1 hESC cell [H1_Exp3.255]

description:
GSM1562563
sc_cell_type_ec.csv
H1_Exp3.255


title: single cell H1 hESC cell [H1_Exp3.249]

description:
GSM1562557
sc_cell_type_ec.csv
H1_Exp3.249


title: single cell H1 hESC cell [H1_Exp3.248]

description:
GSM1562556
sc_cell_type_ec.csv
H1_Exp3.248


title: single cell H1 hESC cell [H1_Exp3.268]

description:
GSM1562576
sc_cell_type_ec.csv
H1_Exp3.268


title: single cell H1 hESC cell [H1_Exp3.246]

description:
GSM1562554
sc_cell_type_ec.csv
H1_Exp3.246


title: single cell H1 hESC cell [H1_Exp3.244]

description:
GSM1562553
sc_cell_type_ec.csv
H1_Exp3.244


title: single cell H1 hESC cell [H1_Exp3.243]

description:
GSM1562552
sc_cell_type_ec.csv
H1_Exp3.243


title: single cell H1 hESC cell [H1_Exp3.242]

description:
GSM1562551
sc_cell_type_ec.csv
H1_Exp3.242


title: single cell H1 hESC cell [H1_Exp3.237]

description:
GSM1562546
sc_cell_type_ec.csv
H1_Exp3.237


title: single cell H1 hESC cell [H1_Exp3.240]

description:
GSM1562549
sc_cell_type_ec.csv
H1_Exp3.240


title: single cell H1 hESC cell [H1_Exp3.239]

description:
GSM1562548
sc_cell_type_ec.csv
H1_Exp3.239


title: single cell H1 hESC cell [H1_Exp3.241]

description:
GSM1562550
sc_cell_type_ec.csv
H1_Exp3.241


title: single cell H1 hESC cell [H1_Exp3.259]

description:
GSM1562567
sc_cell_type_ec.csv
H1_Exp3.259


title: single cell H1 hESC cell [H1_Exp3.233]

description:
GSM1562542
sc_cell_type_ec.csv
H1_Exp3.233


title: single cell H1 hESC cell [H1_Exp3.230]

description:
GSM1562539
sc_cell_type_ec.csv
H1_Exp3.230


title: single cell H1 hESC cell [H1_Exp3.231]

description:
GSM1562540
sc_cell_type_ec.csv
H1_Exp3.231


title: single cell H1 hESC cell [H1_Exp3.229]

description:
GSM1562538
sc_cell_type_ec.csv
H1_Exp3.229


title: single cell H1 hESC cell [H1_Exp3.256]

description:
GSM1562564
sc_cell_type_ec.csv
H1_Exp3.256


title: single cell H1 hESC cell [H1_Exp3.238]

description:
GSM1562547
sc_cell_type_ec.csv
H1_Exp3.238


title: single cell H1 hESC cell [H1_Exp3.236]

description:
GSM1562545
sc_cell_type_ec.csv
H1_Exp3.236


title: single cell H1 hESC cell [H1_Exp3.226]

description:
GSM1562535
sc_cell_type_ec.csv
H1_Exp3.226


title: single cell H1 hESC cell [H1_Exp3.247]

description:
GSM1562555
sc_cell_type_ec.csv
H1_Exp3.247


title: single cell H1 hESC cell [H1_Exp3.232]

description:
GSM1562541
sc_cell_type_ec.csv
H1_Exp3.232


title: single cell H1 hESC cell [H1_Exp3.217]

description:
H1 cells were routinely maintained at the undifferentiated state in E8 medium on Matrigel
sc_cell_type_ec.csv
H1_Exp3.217


title: single cell H1 hESC cell [H1_Exp3.219]

description:
GSM1562528
sc_cell_type_ec.csv
H1_Exp3.219


title: single cell H1 hESC cell [H1_Exp3.228]

description:
GSM1562537
sc_cell_type_ec.csv
H1_Exp3.228


title: single cell H1 hESC cell [H1_Exp3.227]

description:
GSM1562536
sc_cell_type_ec.csv
H1_Exp3.227


title: single cell H1 hESC cell [H1_Exp3.250]

description:
GSM1562558
sc_cell_type_ec.csv
H1_Exp3.250


title: single cell H1 hESC cell [H1_Exp3.224]

description:
GSM1562533
sc_cell_type_ec.csv
H1_Exp3.224


title: single cell H1 hESC cell [H1_Exp3.225]

description:
GSM1562534
sc_cell_type_ec.csv
H1_Exp3.225


title: single cell H1 hESC cell [H1_Exp2.153]

description:
GSM1562525
sc_cell_type_ec.csv
H1_Exp2.153


title: single cell H1 hESC cell [H1_Exp2.154]

description:
GSM1562526
sc_cell_type_ec.csv
H1_Exp2.154


title: single cell H1 hESC cell [H1_Exp3.234]

description:
GSM1562543
sc_cell_type_ec.csv
H1_Exp3.234


title: single cell H1 hESC cell [H1_Exp3.223]

description:
GSM1562532
sc_cell_type_ec.csv
H1_Exp3.223


title: single cell H1 hESC cell [H1_Exp2.151]

description:
GSM1562523
sc_cell_type_ec.csv
H1_Exp2.151


title: single cell H1 hESC cell [H1_Exp2.147]

description:
GSM1562519
sc_cell_type_ec.csv
H1_Exp2.147


title: single cell H1 hESC cell [H1_Exp3.222]

description:
GSM1562531
sc_cell_type_ec.csv
H1_Exp3.222


title: single cell H1 hESC cell [H1_Exp2.149]

description:
GSM1562521
sc_cell_type_ec.csv
H1_Exp2.149


title: single cell H1 hESC cell [H1_Exp2.148]

description:
GSM1562520
sc_cell_type_ec.csv
H1_Exp2.148


title: single cell H1 hESC cell [H1_Exp3.221]

description:
GSM1562530
sc_cell_type_ec.csv
H1_Exp3.221


title: single cell H1 hESC cell [H1_Exp2.150]

description:
GSM1562522
sc_cell_type_ec.csv
H1_Exp2.150


title: single cell H1 hESC cell [H1_Exp3.235]

description:
GSM1562544
sc_cell_type_ec.csv
H1_Exp3.235


title: single cell H1 hESC cell [H1_Exp2.142]

description:
GSM1562515
sc_cell_type_ec.csv
H1_Exp2.142


title: single cell H1 hESC cell [H1_Exp3.220]

description:
GSM1562529
sc_cell_type_ec.csv
H1_Exp3.220


title: single cell H1 hESC cell [H1_Exp3.218]

description:
GSM1562527
sc_cell_type_ec.csv
H1_Exp3.218


title: single cell H1 hESC cell [H1_Exp2.152]

description:
GSM1562524
sc_cell_type_ec.csv
H1_Exp2.152


title: single cell H1 hESC cell [H1_Exp2.144]

description:
GSM1562516
sc_cell_type_ec.csv
H1_Exp2.144


title: single cell H1 hESC cell [H1_Exp2.141]

description:
GSM1562514
sc_cell_type_ec.csv
H1_Exp2.141


title: single cell H1 hESC cell [H1_Exp2.130]

description:
GSM1562504
sc_cell_type_ec.csv
H1_Exp2.130


title: single cell H1 hESC cell [H1_Exp2.133]

description:
GSM1562506
sc_cell_type_ec.csv
H1_Exp2.133


title: single cell H1 hESC cell [H1_Exp2.132]

description:
GSM1562505
sc_cell_type_ec.csv
H1_Exp2.132


title: single cell H1 hESC cell [H1_Exp2.128]

description:
GSM1562502
sc_cell_type_ec.csv
H1_Exp2.128


title: single cell H1 hESC cell [H1_Exp2.139]

description:
GSM1562512
sc_cell_type_ec.csv
H1_Exp2.139


title: single cell H1 hESC cell [H1_Exp2.135]

description:
GSM1562508
sc_cell_type_ec.csv
H1_Exp2.135


title: single cell H1 hESC cell [H1_Exp2.145]

description:
GSM1562517
sc_cell_type_ec.csv
H1_Exp2.145


title: single cell H1 hESC cell [H1_Exp2.134]

description:
GSM1562507
sc_cell_type_ec.csv
H1_Exp2.134


title: single cell H1 hESC cell [H1_Exp2.137]

description:
GSM1562510
sc_cell_type_ec.csv
H1_Exp2.137


title: single cell H1 hESC cell [H1_Exp2.124]

description:
GSM1562498
sc_cell_type_ec.csv
H1_Exp2.124


title: single cell H1 hESC cell [H1_Exp2.121]

description:
GSM1562495
sc_cell_type_ec.csv
H1_Exp2.121


title: single cell H1 hESC cell [H1_Exp2.146]

description:
GSM1562518
sc_cell_type_ec.csv
H1_Exp2.146


title: single cell H1 hESC cell [H1_Exp2.117]

description:
GSM1562492
sc_cell_type_ec.csv
H1_Exp2.117


title: single cell H1 hESC cell [H1_Exp2.118]

description:
GSM1562493
sc_cell_type_ec.csv
H1_Exp2.118


title: single cell H1 hESC cell [H1_Exp2.140]

description:
GSM1562513
sc_cell_type_ec.csv
H1_Exp2.140


title: single cell H1 hESC cell [H1_Exp2.116]

description:
GSM1562491
sc_cell_type_ec.csv
H1_Exp2.116


title: single cell H1 hESC cell [H1_Exp2.129]

description:
GSM1562503
sc_cell_type_ec.csv
H1_Exp2.129


title: single cell H1 hESC cell [H1_Exp2.127]

description:
GSM1562501
sc_cell_type_ec.csv
H1_Exp2.127


title: single cell H1 hESC cell [H1_Exp2.126]

description:
GSM1562500
sc_cell_type_ec.csv
H1_Exp2.126


title: single cell H1 hESC cell [H1_Exp2.123]

description:
GSM1562497
sc_cell_type_ec.csv
H1_Exp2.123


title: single cell H1 hESC cell [H1_Exp2.120]

description:
GSM1562494
sc_cell_type_ec.csv
H1_Exp2.120


title: single cell H1 hESC cell [H1_Exp2.122]

description:
GSM1562496
sc_cell_type_ec.csv
H1_Exp2.122


title: single cell H1 hESC cell [H1_Exp2.138]

description:
GSM1562511
sc_cell_type_ec.csv
H1_Exp2.138


title: single cell H1 hESC cell [H1_Exp2.125]

description:
GSM1562499
sc_cell_type_ec.csv
H1_Exp2.125


title: single cell H1 hESC cell [H1_Exp2.111]

description:
GSM1562486
sc_cell_type_ec.csv
H1_Exp2.111


title: single cell H1 hESC cell [H1_Exp2.112]

description:
GSM1562487
sc_cell_type_ec.csv
H1_Exp2.112


title: single cell H1 hESC cell [H1_Exp2.136]

description:
GSM1562509
sc_cell_type_ec.csv
H1_Exp2.136


title: single cell H1 hESC cell [H1_Exp2.103]

description:
GSM1562478
sc_cell_type_ec.csv
H1_Exp2.103


title: single cell H1 hESC cell [H1_Exp2.109]

description:
GSM1562484
sc_cell_type_ec.csv
H1_Exp2.109


title: single cell H1 hESC cell [H1_Exp2.115]

description:
GSM1562490
sc_cell_type_ec.csv
H1_Exp2.115


title: single cell H1 hESC cell [H1_Exp2.101]

description:
GSM1562476
sc_cell_type_ec.csv
H1_Exp2.101


title: single cell H1 hESC cell [H1_Exp2.107]

description:
GSM1562482
sc_cell_type_ec.csv
H1_Exp2.107


title: single cell H1 hESC cell [H1_Exp2.098]

description:
GSM1562473
sc_cell_type_ec.csv
H1_Exp2.098


title: single cell H1 hESC cell [H1_Exp2.113]

description:
GSM1562488
sc_cell_type_ec.csv
H1_Exp2.113


title: single cell H1 hESC cell [H1_Exp2.114]

description:
GSM1562489
sc_cell_type_ec.csv
H1_Exp2.114


title: single cell H1 hESC cell [H1_Exp2.096]

description:
GSM1562471
sc_cell_type_ec.csv
H1_Exp2.096


title: single cell H1 hESC cell [H1_Exp2.110]

description:
GSM1562485
sc_cell_type_ec.csv
H1_Exp2.110


title: single cell H1 hESC cell [H1_Exp2.108]

description:
GSM1562483
sc_cell_type_ec.csv
H1_Exp2.108


title: single cell H1 hESC cell [H1_Exp2.106]

description:
GSM1562481
sc_cell_type_ec.csv
H1_Exp2.106


title: single cell H1 hESC cell [H1_Exp2.093]

description:
GSM1562469
sc_cell_type_ec.csv
H1_Exp2.093


title: single cell H1 hESC cell [H1_Exp2.091]

description:
GSM1562467
sc_cell_type_ec.csv
H1_Exp2.091


title: single cell H1 hESC cell [H1_Exp2.092]

description:
GSM1562468
sc_cell_type_ec.csv
H1_Exp2.092


title: single cell H1 hESC cell [H1_Exp2.105]

description:
GSM1562480
sc_cell_type_ec.csv
H1_Exp2.105


title: single cell H1 hESC cell [H1_Exp2.090]

description:
GSM1562466
sc_cell_type_ec.csv
H1_Exp2.090


title: single cell H1 hESC cell [H1_Exp2.104]

description:
GSM1562479
sc_cell_type_ec.csv
H1_Exp2.104


title: single cell H1 hESC cell [H1_Exp2.100]

description:
GSM1562475
sc_cell_type_ec.csv
H1_Exp2.100


title: single cell H1 hESC cell [H1_Exp2.102]

description:
GSM1562477
sc_cell_type_ec.csv
H1_Exp2.102


title: single cell H1 hESC cell [H1_Exp2.088]

description:
GSM1562464
sc_cell_type_ec.csv
H1_Exp2.088


title: single cell H1 hESC cell [H1_Exp2.097]

description:
GSM1562472
sc_cell_type_ec.csv
H1_Exp2.097


title: single cell H1 hESC cell [H1_Exp2.089]

description:
GSM1562465
sc_cell_type_ec.csv
H1_Exp2.089


title: single cell H1 hESC cell [H1_Exp2.099]

description:
GSM1562474
sc_cell_type_ec.csv
H1_Exp2.099


title: single cell H1 hESC cell [H1_Exp2.087]

description:
GSM1562463
sc_cell_type_ec.csv
H1_Exp2.087


title: single cell H1 hESC cell [H1_Exp2.084]

description:
GSM1562460
sc_cell_type_ec.csv
H1_Exp2.084


title: single cell H1 hESC cell [H1_Exp2.085]

description:
GSM1562461
sc_cell_type_ec.csv
H1_Exp2.085


title: ddm1 ago6

city: Athens

first: Robert

middle: J

last: Schmitz

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description: library strategy: MethylC-seq

data_processing:
Data were mapped to the TAIR10 reference genome
MethylC-seq analysis were performed as described in Schmtiz et al. Epigenome-wide inheritance of DNA methylation variants in a recombinant inbred population. Genome Research (2013).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab delimited text file, see metafile for column headers

source_name: stage 1-9 inflorescence tissue

growth_protocol: All mutants used in this study are in the Col-0 ecotype background of Arabidopsis thaliana. Plants were grown in long-day (18 hour light) conditions at 23℃ and stage 1-12 inflorescence tissue was used for all experiments and sequencing.

extract_protocol: DNA was isolated using fractional precipitation followed by phenol-chloroform extraction and RNase A treatment. 1ug of DNA was used to prepare libraries as previously described (Urich et al. 2015).

tag: genotype/variation

value: ddm1 ago6


title: single cell H1 hESC cell [H1_Exp2.083]

description:
GSM1562459
sc_cell_type_ec.csv
H1_Exp2.083


title: single cell H1 hESC cell [H1_Exp2.079]

description:
GSM1562455
sc_cell_type_ec.csv
H1_Exp2.079


title: single cell H1 hESC cell [H1_Exp2.077]

description:
GSM1562453
sc_cell_type_ec.csv
H1_Exp2.077


title: single cell H1 hESC cell [H1_Exp2.080]

description:
GSM1562456
sc_cell_type_ec.csv
H1_Exp2.080


title: single cell H1 hESC cell [H1_Exp2.094]

description:
GSM1562470
sc_cell_type_ec.csv
H1_Exp2.094


title: single cell H1 hESC cell [H1_Exp2.082]

description:
GSM1562458
sc_cell_type_ec.csv
H1_Exp2.082


title: single cell H1 hESC cell [H1_Exp2.078]

description:
GSM1562454
sc_cell_type_ec.csv
H1_Exp2.078


title: single cell H1 hESC cell [H1_Exp2.076]

description:
GSM1562452
sc_cell_type_ec.csv
H1_Exp2.076


title: single cell H1 hESC cell [H1_Exp2.075]

description:
GSM1562451
sc_cell_type_ec.csv
H1_Exp2.075


title: single cell H1 hESC cell [H1_Exp2.081]

description:
GSM1562457
sc_cell_type_ec.csv
H1_Exp2.081


title: single cell H1 hESC cell [H1_Exp1.068]

description:
GSM1562446
sc_cell_type_ec.csv
H1_Exp1.068


title: single cell H1 hESC cell [H1_Exp2.074]

description:
GSM1562450
sc_cell_type_ec.csv
H1_Exp2.074


title: single cell H1 hESC cell [H1_Exp2.073]

description:
GSM1562449
sc_cell_type_ec.csv
H1_Exp2.073


title: single cell H1 hESC cell [H1_Exp1.064]

description:
GSM1562443
sc_cell_type_ec.csv
H1_Exp1.064


title: single cell H1 hESC cell [H1_Exp1.070]

description:
GSM1562448
sc_cell_type_ec.csv
H1_Exp1.070


title: single cell H1 hESC cell [H1_Exp1.062]

description:
GSM1562441
sc_cell_type_ec.csv
H1_Exp1.062


title: single cell H1 hESC cell [H1_Exp1.066]

description:
GSM1562445
sc_cell_type_ec.csv
H1_Exp1.066


title: single cell H1 hESC cell [H1_Exp1.063]

description:
GSM1562442
sc_cell_type_ec.csv
H1_Exp1.063


title: single cell H1 hESC cell [H1_Exp1.061]

description:
GSM1562440
sc_cell_type_ec.csv
H1_Exp1.061


title: single cell H1 hESC cell [H1_Exp1.060]

description:
GSM1562439
sc_cell_type_ec.csv
H1_Exp1.060


title: single cell H1 hESC cell [H1_Exp2.086]

description:
GSM1562462
sc_cell_type_ec.csv
H1_Exp2.086


title: single cell H1 hESC cell [H1_Exp1.058]

description:
GSM1562437
sc_cell_type_ec.csv
H1_Exp1.058


title: single cell H1 hESC cell [H1_Exp1.057]

description:
GSM1562436
sc_cell_type_ec.csv
H1_Exp1.057


title: single cell H1 hESC cell [H1_Exp1.055]

description:
GSM1562435
sc_cell_type_ec.csv
H1_Exp1.055


title: single cell H1 hESC cell [H1_Exp1.065]

description:
GSM1562444
sc_cell_type_ec.csv
H1_Exp1.065


title: single cell H1 hESC cell [H1_Exp1.054]

description:
GSM1562434
sc_cell_type_ec.csv
H1_Exp1.054


title: single cell H1 hESC cell [H1_Exp1.053]

description:
GSM1562433
sc_cell_type_ec.csv
H1_Exp1.053


title: single cell H1 hESC cell [H1_Exp1.051]

description:
GSM1562431
sc_cell_type_ec.csv
H1_Exp1.051


title: single cell H1 hESC cell [H1_Exp1.050]

description:
GSM1562430
sc_cell_type_ec.csv
H1_Exp1.050


title: single cell H1 hESC cell [H1_Exp1.049]

description:
GSM1562429
sc_cell_type_ec.csv
H1_Exp1.049


title: single cell H1 hESC cell [H1_Exp1.048]

description:
GSM1562428
sc_cell_type_ec.csv
H1_Exp1.048


title: single cell H1 hESC cell [H1_Exp1.047]

description:
GSM1562427
sc_cell_type_ec.csv
H1_Exp1.047


title: single cell H1 hESC cell [H1_Exp1.052]

description:
GSM1562432
sc_cell_type_ec.csv
H1_Exp1.052


title: single cell H1 hESC cell [H1_Exp1.045]

description:
GSM1562426
sc_cell_type_ec.csv
H1_Exp1.045


title: single cell H1 hESC cell [H1_Exp1.044]

description:
GSM1562425
sc_cell_type_ec.csv
H1_Exp1.044


title: single cell H1 hESC cell [H1_Exp1.043]

description:
GSM1562424
sc_cell_type_ec.csv
H1_Exp1.043


title: single cell H1 hESC cell [H1_Exp1.042]

description:
GSM1562423
sc_cell_type_ec.csv
H1_Exp1.042


title: single cell H1 hESC cell [H1_Exp1.041]

description:
GSM1562422
sc_cell_type_ec.csv
H1_Exp1.041


title: single cell H1 hESC cell [H1_Exp1.035]

description:
GSM1562417
sc_cell_type_ec.csv
H1_Exp1.035


title: single cell H1 hESC cell [H1_Exp1.036]

description:
GSM1562418
sc_cell_type_ec.csv
H1_Exp1.036


title: single cell H1 hESC cell [H1_Exp1.040]

description:
GSM1562421
sc_cell_type_ec.csv
H1_Exp1.040


title: single cell H1 hESC cell [H1_Exp1.039]

description:
GSM1562420
sc_cell_type_ec.csv
H1_Exp1.039


title: single cell H1 hESC cell [H1_Exp1.029]

description:
GSM1562412
sc_cell_type_ec.csv
H1_Exp1.029


title: single cell H1 hESC cell [H1_Exp1.032]

description:
GSM1562415
sc_cell_type_ec.csv
H1_Exp1.032


title: single cell H1 hESC cell [H1_Exp1.031]

description:
GSM1562414
sc_cell_type_ec.csv
H1_Exp1.031


title: single cell H1 hESC cell [H1_Exp1.033]

description:
GSM1562416
sc_cell_type_ec.csv
H1_Exp1.033


title: single cell H1 hESC cell [H1_Exp1.026]

description:
GSM1562410
sc_cell_type_ec.csv
H1_Exp1.026


title: single cell H1 hESC cell [H1_Exp1.027]

description:
GSM1562411
sc_cell_type_ec.csv
H1_Exp1.027


title: single cell H1 hESC cell [H1_Exp1.030]

description:
GSM1562413
sc_cell_type_ec.csv
H1_Exp1.030


title: single cell H1 hESC cell [H1_Exp1.023]

description:
GSM1562407
sc_cell_type_ec.csv
H1_Exp1.023


title: single cell H1 hESC cell [H1_Exp1.024]

description:
GSM1562408
sc_cell_type_ec.csv
H1_Exp1.024


title: single cell H1 hESC cell [H1_Exp1.021]

description:
GSM1562405
sc_cell_type_ec.csv
H1_Exp1.021


title: single cell H1 hESC cell [H1_Exp1.022]

description:
GSM1562406
sc_cell_type_ec.csv
H1_Exp1.022


title: single cell H1 hESC cell [H1_Exp1.025]

description:
GSM1562409
sc_cell_type_ec.csv
H1_Exp1.025


title: single cell H1 hESC cell [H1_Exp1.020]

description:
GSM1562404
sc_cell_type_ec.csv
H1_Exp1.020


title: single cell H1 hESC cell [H1_Exp1.019]

description:
GSM1562403
sc_cell_type_ec.csv
H1_Exp1.019


title: single cell H1 hESC cell [H1_Exp1.018]

description:
GSM1562402
sc_cell_type_ec.csv
H1_Exp1.018


title: single cell H1 hESC cell [H1_Exp1.016]

description:
GSM1562400
sc_cell_type_ec.csv
H1_Exp1.016


title: single cell H1 hESC cell [H1_Exp1.038]

description:
GSM1562419
sc_cell_type_ec.csv
H1_Exp1.038


title: single cell H1 hESC cell [H1_Exp1.015]

description:
GSM1562399
sc_cell_type_ec.csv
H1_Exp1.015


title: single cell H1 hESC cell [H1_Exp1.012]

description:
GSM1562397
sc_cell_type_ec.csv
H1_Exp1.012


title: single cell H1 hESC cell [H1_Exp1.014]

description:
GSM1562398
sc_cell_type_ec.csv
H1_Exp1.014


title: single cell H1 hESC cell [H1_Exp1.008]

description:
GSM1562393
sc_cell_type_ec.csv
H1_Exp1.008


title: single cell H1 hESC cell [H1_Exp1.010]

description:
GSM1562395
sc_cell_type_ec.csv
H1_Exp1.010


title: single cell H1 hESC cell [H1_Exp1.006]

description:
GSM1562391
sc_cell_type_ec.csv
H1_Exp1.006


title: single cell H1 hESC cell [H1_Exp1.003]

description:
GSM1562389
sc_cell_type_ec.csv
H1_Exp1.003


title: single H9 hESCs differentiated for 96 hours [H9.96h_189]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_189

source_name: H9 cells differentiated for 96 hours


title: single H9 hESCs differentiated for 96 hours [H9.96h_188]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_188


title: single cell H1 hESC cell [H1_Exp1.002]

description:
GSM1562388
sc_cell_type_ec.csv
H1_Exp1.002


title: single cell H1 hESC cell [H1_Exp1.004]

description:
GSM1562390
sc_cell_type_ec.csv
H1_Exp1.004


title: single cell H1 hESC cell [H1_Exp1.009]

description:
GSM1562394
sc_cell_type_ec.csv
H1_Exp1.009


title: single H9 hESCs differentiated for 96 hours [H9.96h_186]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_186


title: single cell H1 hESC cell [H1_Exp1.001]

description:
GSM1562387
sc_cell_type_ec.csv
H1_Exp1.001


title: single cell H1 hESC cell [H1_Exp1.017]

description:
GSM1562401
sc_cell_type_ec.csv
H1_Exp1.017


title: single H9 hESCs differentiated for 96 hours [H9.96h_185]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_185


title: single H9 hESCs differentiated for 96 hours [H9.96h_184]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_184


title: single H9 hESCs differentiated for 96 hours [H9.96h_190]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_190


title: single H9 hESCs differentiated for 96 hours [H9.96h_183]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_183


title: single cell H1 hESC cell [H1_Exp1.007]

description:
GSM1562392
sc_cell_type_ec.csv
H1_Exp1.007


title: single H9 hESCs differentiated for 96 hours [H9.96h_179]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_179


title: single H9 hESCs differentiated for 96 hours [H9.96h_187]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_187


title: single cell H1 hESC cell [H1_Exp1.011]

description:
GSM1562396
sc_cell_type_ec.csv
H1_Exp1.011


title: single H9 hESCs differentiated for 96 hours [H9.96h_174]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_174


title: single H9 hESCs differentiated for 96 hours [H9.96h_173]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_173


title: single H9 hESCs differentiated for 96 hours [H9.96h_175]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_175


title: single H9 hESCs differentiated for 96 hours [H9.96h_176]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_176


title: single H9 hESCs differentiated for 96 hours [H9.96h_182]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_182


title: single H9 hESCs differentiated for 96 hours [H9.96h_192]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_192


title: single H9 hESCs differentiated for 96 hours [H9.96h_171]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_171


title: single H9 hESCs differentiated for 96 hours [H9.96h_170]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_170


title: single H9 hESCs differentiated for 96 hours [H9.96h_167]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_167


title: single H9 hESCs differentiated for 96 hours [H9.96h_165]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_165


title: single H9 hESCs differentiated for 96 hours [H9.96h_168]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_168


title: single H9 hESCs differentiated for 96 hours [H9.96h_180]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_180


title: single H9 hESCs differentiated for 96 hours [H9.96h_163]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_163


title: single H9 hESCs differentiated for 96 hours [H9.96h_160]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_160


title: single H9 hESCs differentiated for 96 hours [H9.96h_158]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_158


title: single H9 hESCs differentiated for 96 hours [H9.96h_164]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_164


title: single H9 hESCs differentiated for 96 hours [H9.96h_156]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_156


title: single H9 hESCs differentiated for 96 hours [H9.96h_162]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_162


title: single H9 hESCs differentiated for 96 hours [H9.96h_178]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_178


title: single H9 hESCs differentiated for 96 hours [H9.96h_159]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_159


title: single H9 hESCs differentiated for 96 hours [H9.96h_153]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_153


title: single H9 hESCs differentiated for 96 hours [H9.96h_155]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_155


title: single H9 hESCs differentiated for 96 hours [H9.96h_166]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_166


title: single H9 hESCs differentiated for 96 hours [H9.96h_177]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_177


title: single H9 hESCs differentiated for 96 hours [H9.96h_152]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_152


title: single H9 hESCs differentiated for 96 hours [H9.96h_154]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_154


title: single H9 hESCs differentiated for 96 hours [H9.96h_150]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_150


title: single H9 hESCs differentiated for 96 hours [H9.96h_149]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_149


title: single H9 hESCs differentiated for 96 hours [H9.96h_148]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_148


title: single H9 hESCs differentiated for 96 hours [H9.96h_169]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_169


title: single H9 hESCs differentiated for 96 hours [H9.96h_147]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_147


title: single H9 hESCs differentiated for 96 hours [H9.96h_144]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_144


title: ddm1 pol IV rdr6

description: library strategy: MethylC-seq

value: ddm1 pol IV rdr6


title: single H9 hESCs differentiated for 96 hours [H9.96h_146]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_146


title: single H9 hESCs differentiated for 96 hours [H9.96h_151]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_151


title: single H9 hESCs differentiated for 96 hours [H9.96h_157]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_157


title: single H9 hESCs differentiated for 96 hours [H9.96h_161]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_161


title: single H9 hESCs differentiated for 96 hours [H9.96h_142]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_142


title: single H9 hESCs differentiated for 96 hours [H9.96h_143]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_143


title: single H9 hESCs differentiated for 96 hours [H9.96h_145]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_145


title: single H9 hESCs differentiated for 96 hours [H9.96h_141]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_141


title: single H9 hESCs differentiated for 96 hours [H9.96h_140]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_140


title: single H9 hESCs differentiated for 96 hours [H9.96h_139]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_139


title: single H9 hESCs differentiated for 96 hours [H9.96h_138]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_138


title: single H9 hESCs differentiated for 96 hours [H9.96h_135]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_135


title: single H9 hESCs differentiated for 96 hours [H9.96h_136]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_136


title: single H9 hESCs differentiated for 96 hours [H9.96h_134]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_134


title: single H9 hESCs differentiated for 96 hours [H9.96h_133]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_133


title: single H9 hESCs differentiated for 96 hours [H9.96h_132]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_132


title: single H9 hESCs differentiated for 96 hours [H9.96h_129]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_129


title: single H9 hESCs differentiated for 96 hours [H9.96h_131]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_131


title: single H9 hESCs differentiated for 96 hours [H9.96h_130]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_130


title: single H9 hESCs differentiated for 96 hours [H9.96h_126]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_126


title: single H9 hESCs differentiated for 96 hours [H9.96h_125]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_125


title: single H9 hESCs differentiated for 96 hours [H9.96h_128]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_128


title: single H9 hESCs differentiated for 96 hours [H9.96h_127]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_127


title: single H9 hESCs differentiated for 96 hours [H9.96h_122]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_122


title: single H9 hESCs differentiated for 96 hours [H9.96h_121]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_121


title: single H9 hESCs differentiated for 96 hours [H9.96h_120]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_120


title: single H9 hESCs differentiated for 96 hours [H9.96h_124]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_124


title: single H9 hESCs differentiated for 96 hours [H9.96h_118]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_118


title: single H9 hESCs differentiated for 96 hours [H9.96h_119]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_119


title: single H9 hESCs differentiated for 96 hours [H9.96h_137]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_137


title: single H9 hESCs differentiated for 96 hours [H9.96h_123]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_123


title: single H9 hESCs differentiated for 96 hours [H9.96h_117]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_117


title: single H9 hESCs differentiated for 96 hours [H9.96h_113]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
sc_time_course_ec.csv
H9.96h_113