title: ChIP-seq Lhx3.V5 in EB+8hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1

description:
Lhx3_8h_iNIL.bed
Lhx3_8h_iNIL.events

extract_protocol:
Cells were collected at different time points after NIL induction and fixed with 1 mM DSG (ProteoChem) followed by 1% formaldehyde (vol/vol) for 15 min at 20–25°C. Pellets containing ~25 × 10^6 cells were stored at −80 °C. Cells were thawed on ice, resuspended in 5 ml of Lysis Buffer  A (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol (vol/vol), 0.5% Igepal (vol/vol), 0.25% Triton X-100 (vol/vol)) and incubated for 10 min at 4°C in a rotating platform. Samples were spun down for 5 min at 1,350 g, resuspended in 5 ml Lysis Buffer B (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0) and incubated for 10 min at 4 °C in a rotating platform. Samples were spun down for 5 min at 1,350 g, resuspended in 3 ml of Sonication Buffer (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Trition X-100, 0.1% sodium deoxycholate (wt/vol), 0.1% SDS (wt/vol)). Nuclear extracts were sonicated on ice using a Branson 450 Sonifier (20% power amplitude; 18 cycles x 30 seconds pulses with 1 minute interval between each pulse) to sheer cross-linked DNA to an average fragment size of approximately 500 bp. Sonicated chromatin was incubated for 16 h at 4 °C with Dynabeads protein-G (Life Techologies) conjugated with either rabbit polyclonal antibody to V5 (ab15828, Abcam) to immunoprecipitate Lhx3 or a  combination of monoclonal antibodies (40.3A4, 39.3F7 and 40.206, DSHB) for Isl1. Ngn2 was immunoprecipitated by using a goat polyclonal antobody (sc-19233, Santa Cruz), whereas to immunoprecipitate Ebf2 and Onecut2, a rabbit polyclonal antibody (ab156999, Abcam) and a sheep polyclonal antibody (AF294, R&D Systems) were used, respectively. For histone modifications the following rabbit polyclonal antibodies were used: ab8895 (Abcam) for H3K4me1, ab7766 (Abcam) for H3K4me2, 39159 (Active Motif) for H3K4me3, ab4729 (Abcam) for H3K27ac and 39155 (Active Motif) for H3K27me3. After incubation, and with the aid of a magnetic device, beads were washed once with Sonication Buffer, than with Sonication buffer and 500 nM NaCl and once with LiCl Wash Buffer (20 mM Tris-HCl (pH 8.0), 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate) and 1 ml of TE (10 mM Tris, 1 mM EDTA, pH 8). Then, beads were centrifuged at 950 g for 3 min and the residual TE removed with a pipette. 210 µl of Elution Buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA (pH 8.0), 1% SDS) was added to the beads followed by incubation at 65°C for 45 min with a brief pulse of vortex every 10 min. 200 µl of supernatant was removed after a 1 min centrifugation at 16,000 g. The crosslink was reversed by 16 h incubation at 65°C. RNA was digested by the addition of 200 µl of TE and RNAse A (Sigma) at a final concentration of 0.2 mg/ml and incubated for 2 h at 37°C. Protein was digested by the addition of Proteinase K (Invitrogen) at a final concentration of 0.2 mg/ml, supplemented with CaCl2 followed by a 30-min incubation at 55°C. DNA was extracted with phenol:chloroform:isoamyl alcohol (25:24:1; vol/vol) (Invitrogen) and then recovered with an ethanol precipitation with glycogens as carrier. The pellets were suspended in 70 µl of water.
One third (24ul) of ChIP DNA was used to prepare llumina DNA sequencing libraries. Briefly, after end repair and A-tailing, Illumina-compatible Bioo Scientific multiplexed adapters were ligated and the unligated adapters removed through purification using Agencourt AmpureXP beads (Beckman Coulter). Adapter-ligated DNA was amplified by PCR using TruSeq Fw primer (AATGATACGGCGACCACCGAGATCTACAC) and TruSeq Rev primer (CAAGCAGAAGACGGCATACGAGAT), both from Sigma. DNA libraries between 300 and 500 bp in size were gel purified. KAPA SYBR FAST Roche LightCycler 480 2X qPCR Master Mix (Kapa Biosystems) was used in 20 μl reactions that were analyzed in a Roche LightCycler. Fifty base pair single-end sequencing was performed using Illumina HiSeq-2500 at the NYU Genome Core facility.


title: ChIP-seq Isl1 in EB+8hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

status: Public on Dec 07 2016

type: SRA

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

country: USA

institute: Penn State University

description:
Isl1_8h_iNIL.bed
Isl1_8h_iNIL.events

library_source: genomic

data_processing:
Basecall conversion to fastq files was performed using bcl2fastq for HiSeq runs and Picard for NextSeq runs.
Alignment: All transcription factor ChIP-Seq fastq files were aligned to mouse genome (version mm10) using Bowtie (1.0.1) (Langmead et al., 2009) with options “-q --best --strata -m 1 --chunkmbs 1024”.  Only uniquely mapped reads were considered for further analysis.
Binding event detection: Isl1 and Lhx3 binding sites were profiled using MultiGPS (Mahony et al., 2014), which enables the identification of differentially-enriched TF binding sites across multiple conditions. Our initial analysis showed that Isl1 and Lhx3 mostly bind to the same sets of regions genome-wide with similar ChIP enrichment. Hence we treated Isl1 and Lhx3 datasets at each time-point as different conditions in a single MultiGPS run. The discovered binding events were required to have a significant ChIP enrichment over input samples (q-value < 0.001) as assessed using binomial tests. Binding sites for Ngn2, Onecut2, and Ebf2 were identified using MultiGPS (Mahony et al., 2014) with different runs for each transcription factor. Binding events were required to have a significant ChIP enrichment over the input samples based on a binomial test (q-value < 0.001).
Genome_build: mm10
Supplementary_files_format_and_content: .events MultiGPS: MultiGPS output files
Supplementary_files_format_and_content: BED: Conversion of MultiGPS output files to BED format, centered on the MultiGPS binding event location
Supplementary_files_format_and_content: BIGWIG: WIG files were generated using custom software to summarize read counts overlapping genomic regions. All reads were artificially extended out to 200bp in length. A bin size of 10bp was used for calculating overlapping read counts. WIG files were converted to bigWig using wigToBigWig (UCSC)

molecule: genomic DNA

organism: Mus musculus

source_name: ES-derived embryoid bodies with induced transcription factors

growth_protocol: Generation of inducible lines: NIL (Ngn2-Isl1-Lhx3)-V5 and Flag-Ngn2 inducible ESC lines were generated as previously described (Mazzoni et al. 2013, Mazzoni et al. 2011). To generate IL (Isl1-Lhx3)-V5 inducible ESC lines, Isl1-Lhx3 open reading frames were amplified from p2Lox-NIL-V5 and inserted into the p2Lox-V5 plasmid (Iacovino M. et al., 2011). Phusion polymerase (New England Biolabs) was used to minimize the introduction of mutations during PCR amplification. Inducible cell lines were generated by treating the recipient ESCs for 16 h with 1 µg/ml Dox to induce Cre followed by electroporation of p2Lox-IL-V5 plasmid. After G418 selection (250ng/ml, Cellgro), four resistant clones were picked, characterized and expanded.   Cell culture and differentiation: All the inducible ESC lines were grown in 2-inhibitors medium (Advanced DMEM/F12:Neurobasal (1:1) Medium (Gibco), supplemented with 2.5% ESC-grade fetal bovine serum (vol/vol, Corning), N2 (Gibco), B27 (Gibco), 2mM L-glutamine (Gibco), 0.1 mM β-mercaptoethanol (Gibco), 1000 U/ml leukemia inhibitory factor (Millipore), 3µM CHIR (BioVision) and 1 µM PD0325901 (Sigma). For ChIP experiments, 3 x 10^6 cells were plated in each square dish (245mm x 245mm).

treatment_protocol: To obtain Embryoid bodies (EBs) ESC were trypsinized (Gibco) and seeded in AK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout SR (vol/vol) (Gibco), Pen/Strep (Gibco), 2mM L-glutamine and 0.1 mM 2-mercaptoethanol) (day -2).  After 2 days, EBs were passed 1:2 and the inducible cassette was induced by adding 3 µg/ml of Doxycycline (Sigma) to the culture medium (EBs 0h).

tag: strain

tag: chip target

tag: chip antibody

value: anti-Isl1 combination (DSHB 40.3A4, 39.3F7, 40.206)

tag: treatment

tag: cell type

value: Embryoid Bodies


title: ChIP-seq Isl1 in EB+8hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1

description:
Isl1_8h_iNIL.bed
Isl1_8h_iNIL.events


title: Scerevisiae_YEPD_aF_225min

city: Hanover

first: Christina

middle: M

last: Kelliher

state: NH

address: 7400 Hinman

department: Molecular & Systems Biology

institute: Geisel School of Medicine at Dartmouth

library_source: transcriptomic

data_processing:
Sequenced reads mapped to the respective yeast genome using STAR with parameters --outFilterType BySJout --alignIntronMin 10 --alignIntronMax 3000 --outFilterIntronMotifs RemoveNoncanonical
Transcripts were quantified in Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using Cufflinks with the respective transcriptome GTF file (i.e. quantify one transcript per annotated gene, not gene isoforms). Values were normalized by gene size and by library size.
Time point samples from the respective yeasts were normalized together using the cuffnorm feature of Cufflinks (default parameters for stranded RNA-Seq)
A value of "1" was added to every FPKM value in each dataset; see manuscript for details
Genome_build: Saccharomyces cerevisiae S288C Ensembl R64-1-1 downloaded from Illumina iGenomes on 3-2-16; Cryptococcus neoformans var. grubii H99 (Serotype A) downloaded from the Broad Institute on 3-2-16
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae culture, wild-type, 225 min

growth_protocol: YEPDextrose at 30c

extract_protocol:
Illumina TruSeq Stranded mRNA Library Prep Kit was used for the construction of sequencing libraries
Cells were removed at each time point and flash frozen on dry ice. RNA was harvested using standard yeast methods.
see SAMPLES section; RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
synchronous G1 populations collected by alpha-factor mating pheromone (30 ng/ml, 110 minutes) arrest-release
see SAMPLES section

value: BF264-15D MATa bar1

tag: genotype/variation

value: wild type

tag: time

value: 225 min


title: Scerevisiae_YEPD_aF_220min

source_name: S. cerevisiae culture, wild-type, 220 min

value: 220 min


title: Input-DNA in EB(iNgn2.Isl1.Lhx3.V5) replicate 1

value: Input


title: ChIP-seq Lhx3.V5 in EB+48hrDox(iIsl1.Lhx3.V5) replicate 1

description:
Lhx3_48h_iIL.bed
Lhx3_48h_iIL.events

value: anti-V5 (Abcam ab15828)


title: ChIP-seq Lhx3.V5 in EB+12hrDox(iIsl1.Lhx3.V5) replicate 2

description:
Lhx3_12h_iIL.bed
Lhx3_12h_iIL.events


title: Scerevisiae_YEPD_aF_210min

source_name: S. cerevisiae culture, wild-type, 210 min

value: 210 min


title: Input-DNA in EB+48hrDox(iIsl1.Lhx3.V5) replicate 1


title: Scerevisiae_YEPD_aF_230min

source_name: S. cerevisiae culture, wild-type, 230 min

value: 230 min


title: polyA mRNA RNA-seq from K562 (ENCLB555AQT)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR000COK/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000COK
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AQT
size range: >200
spikeins used: /references/ENCSR402QNO/

data_processing: See GSM*_README.txt supplementary file linked below

organism: Homo sapiens

source_name: Homo sapiens K562 immortalized cell line cytosolic fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/1b708d74-8022-4880-a167-5a42555ca167/@@download/attachment/LID8465.pdf

tag: line

value: immortalized cell line

tag: description

value: leukemia, The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

tag: biosample encode accession

tag: dev stage

value: adult

tag: Sex

value: female

tag: age

value: 53 year

tag: health state

value: chronic myelogenous leukemia (CML)

tag: lab

value: Thomas Gingeras, CSHL

tag: subcellular fraction term name

value: cytosol

tag: link

value: ENCBS721AAA at ENCODE; https://www.encodeproject.org/ENCBS721AAA/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ENCODE dbxrefs K562; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=K562

value: ATCC sample source; http://www.atcc.org/products/all/CCL-243.aspx


title: Scerevisiae_YEPD_aF_215min

source_name: S. cerevisiae culture, wild-type, 215 min

tag: strain

value: BF264-15D MATa bar1

value: wild type

value: 215 min


title: MeRIP1

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

country: Switzerland

institute: University of Lausanne

description: library strategy: MeRIP-Seq

data_processing:
The samples were sequenced on two flowcells on the Illumina MiSeq (MiSeq Control Software Version 2.6.1.1). Readlength was 68 bp SR
Mapping was done using Star (v. 2.4.0h), secondary alignments were filtered. Mapping was done against BDGP6 (ensembl release 79).
After mapping peaks were called using MACS (v.1.4.1, parameters: "--nomodel --shiftsize 65 --to-small -w -S --keep-dup all --call-subpeaks --nolambda -g 90464385 ).
After peakcalling peaks were split into subpeaks using PeakSplitter (v.1.0).
Consensus peaks were obtained by intersecting subpeaks of both replicates ( using BEDTools (v.2.25.0)).
For each consensus peak the coverage was calculated as counts per million (CPM) for each of the samples and averaged for input and MeRIP samples. Foldchanges for MeRIP vs Input were calculated based on these.
Genome_build: BDGP6 Ensembl release 79
Supplementary_files_format_and_content: bigwig tracks

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: MeRIP, S2R+ cells

growth_protocol: S2R+ cells were grown on standard conditions at room temperature

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen). mRNA was purified by using two rounds of purification with Dynabeads Oligo (dT)25 (Invitrogen)
NEBNext Ultra directional Kit (NEB) was used omitting RNA fragmentation step for recovered m6A-RIP samples and following the manufacturer`s protocol for input samples.

treatment_protocol: no treatment

tag: cell line

value: S2R+ cells

value: embryonic cells

tag: rip antibody


title: Scerevisiae_YEPD_aF_195min

source_name: S. cerevisiae culture, wild-type, 195 min

value: 195 min


title: Input-DNA in EB+12hrDox(iIsl1.Lhx3.V5) replicate 1

tag: chip target

value: Input

tag: chip antibody

tag: treatment

value: Embryoid Bodies


title: ChIP-seq Lhx3.V5 in EB+12hrDox(iIsl1.Lhx3.V5) replicate 1

description:
Lhx3_12h_iIL.bed
Lhx3_12h_iIL.events

value: anti-V5 (Abcam ab15828)

tag: cell type


title: Scerevisiae_YEPD_aF_200min

source_name: S. cerevisiae culture, wild-type, 200 min

tag: genotype/variation

tag: time

value: 200 min


title: Input-DNA in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1


title: ChIP-seq Ngn2 in EB+12hrDox(iFlag.Ngn2) replicate 2

description:
Ngn2_12h_iN.bed
Ngn2_12h_iN.events

value: anti-Ngn2 (Santa Cruz sc-19233)


title: Scerevisiae_YEPD_aF_185min

source_name: S. cerevisiae culture, wild-type, 185 min

value: 185 min


title: Scerevisiae_YEPD_aF_240min

source_name: S. cerevisiae culture, wild-type, 240 min

value: 240 min


title: ChIP-seq Ngn2 in EB+12hrDox(iFlag.Ngn2) replicate 1

description:
Ngn2_12h_iN.bed
Ngn2_12h_iN.events


title: Scerevisiae_YEPD_aF_180min

source_name: S. cerevisiae culture, wild-type, 180 min

value: 180 min


title: Input-DNA in EB+12hrDox(iFlag.Ngn2) replicate 1


title: Scerevisiae_YEPD_aF_175min

source_name: S. cerevisiae culture, wild-type, 175 min

value: 175 min


title: Scerevisiae_YEPD_aF_170min

source_name: S. cerevisiae culture, wild-type, 170 min

value: 170 min


title: DNase-seq from MN1 (ENCLB347XWH)

description:
https://www.encodeproject.org/experiments/ENCSR732IZK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR732IZK
assay title: DNase-seq
assembly: mm10
encode release date: 2016-07-15
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB347XWH

source_name: Mus musculus strain B6NCrl MN1 immortalized cell line

tag: line

value: immortalized cell line

tag: biosample encode accession

value: unknown

value: not collected

value: John Stamatoyannopoulos, UW

value: ENCBS861BIB at ENCODE; https://www.encodeproject.org/ENCBS861BIB/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/

value: ENCODE dbxrefs Cellosaurus CVCL_U508; http://web.expasy.org/cellosaurus/CVCL_U508


title: Scerevisiae_YEPD_aF_165min

source_name: S. cerevisiae culture, wild-type, 165 min

value: BF264-15D MATa bar1

value: wild type

value: 165 min


title: Scerevisiae_YEPD_aF_205min

source_name: S. cerevisiae culture, wild-type, 205 min

value: 205 min


title: PWD26 Rep1

city: Irvine

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

institute: University of California, Irvine

description: protocol: SMART-seq2

data_processing:
RSEM was used for alignment, mapping and quantification
Reads were not trimmed for adaptor sequence. Sequenced reads were aligned, mapped and quantified to the mouse genome (mm10/vM4) using RSEM v1.12.2 with standard parameters. (B. Li, C. N. Dewey, RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC bioinformatics 12, 323 (2011).).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file Supplement_Table_S6.xlsx includes FPKM values for each sample with a pseudocount of 1. Supplement_Table_S5.xlsx includes data clustering with fold-changes and gene ontology.

source_name: Cutaneous wound myofibroblast

extract_protocol:
Cutaneous wound tissues were harvested and dissegragated into single cell suspensions with collagenase. Cells were FACS sorted as viable tdTomatoHi directly into lysis buffer. Total RNA was isolated using RNEasy Micro Kit as per manufacturer's protocols. RNAs with optimal quality (RIN>8.8) were considered for library construction.
RNA libraries were prepared for sequencing using standard SMART-seq2 protocols. 1. S. Picelli et al., Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nature methods 10, 1096-1098 (2013).  2. S. Picelli et al., Full-length RNA-seq from single cells using Smart-seq2. Nature protocols 9, 171-181 (2014).

tag: background strain

value: Mixed background

value: Cutaneous wound myofibroblast

tag: post-wounding day

tag: genotype


title: PWD21 Rep2

description: protocol: SMART-seq2


title: PWD21 Rep1

description: protocol: SMART-seq2


title: PWD15 Rep2

description: protocol: SMART-seq2


title: Scerevisiae_YEPD_aF_190min

source_name: S. cerevisiae culture, wild-type, 190 min

value: 190 min


title: Scerevisiae_YEPD_aF_155min

source_name: S. cerevisiae culture, wild-type, 155 min

value: 155 min


title: Scerevisiae_YEPD_aF_150min

source_name: S. cerevisiae culture, wild-type, 150 min

value: 150 min


title: Scerevisiae_YEPD_aF_160min

source_name: S. cerevisiae culture, wild-type, 160 min

value: 160 min


title: PWD12 Rep2

description: protocol: SMART-seq2


title: Scerevisiae_YEPD_aF_145min

source_name: S. cerevisiae culture, wild-type, 145 min

value: 145 min


title: PWD15 Rep1

description: protocol: SMART-seq2


title: Scerevisiae_YEPD_aF_140min

source_name: S. cerevisiae culture, wild-type, 140 min

value: 140 min


title: Scerevisiae_YEPD_aF_135min

source_name: S. cerevisiae culture, wild-type, 135 min

value: 135 min


title: Scerevisiae_YEPD_aF_130min

source_name: S. cerevisiae culture, wild-type, 130 min

value: 130 min


title: PWD12 Rep1

description: protocol: SMART-seq2


title: 48h ATAC-Seq - Replicate 1

data_processing:
Library strategy: ATAC-Seq
Basecalling conversion to fastq files was performed using bcl2fastq version 2
ATAC-Seq fastq files were aligned to mm10 genome build using bowtie2 (Langmead and Salzberg, 2012) in paired-end mode (parameters: -X 2000 --no-mixed –no-overhang) after trimming forward and reverse transposase sequence using flexbar (Dodt et al. 2012). Potential PCR duplicates were removed using samtools rmdup (Li et al., 2009). Resulting BAM files were converted to single-end BED files using bedtools bamtobed (Quinlan and Hall, 2010). Replicates from the same time-point were concatenated for all further analysis.
After concatenating replicate files, JAMM's SignalGenerator script was used to obtain depth-normalized, smoothed signal for ATAC-Seq data using the 5' ends of all reads (Ibrahim et al. 2015). Peaks were called on all ATAC-Seq reads using JAMM (parameters: -f1 -b 100 -e auto)
Genome_build: mm10
Supplementary_files_format_and_content: Data provided included signal data (bigwig) and peak files (narrowPeak)

source_name: ES-derived embryoid bodies with induced transcription factors

extract_protocol:
50,000 cells were harvested and washed in ice-cold PBS buffer. After centrifugation the supernatant was aspirated and the cell pellet was resuspended in a master mix of 22.5 µl RNase-free water, 25 µl TD buffer and 2.5 µl TDE1 (transposase enzyme, both Illumina Nextera DNA Library Prep kit), followed by incubation for 60 minutes at 37oC. The reaction was then cleaned using the DNA Clean and Concentrator-5 kit (Zymo Research). The optimal number of PCR cycles was determined to be Ct+4.
qPCR reactions were performed using 10% of a master mix of sample, forward and reverse (barcode) primers, 1X SYBR Green I (Biozym) and 1X NEBNext PCR MasterMix (New England Biolabs). Following PCR amplification, the library was cleaned using the DNA Clean and Concentrator-5 kit and eluted in 15 µl 10 mM Tris-Cl pH 8.0. Sample was quantified using Qubit (Life Technologies) measurement and the fragment length distribution was determined using the Bioanalyzer DNA High Sensitivity assay (Agilent). Sequencing was performed on an Illumina NextSeq 500 using V2 chemistry for 150 cycles (paired-end 75nt).

value: Embryoid Bodies


title: 48h ATAC-Seq - Replicate 2


title: Scerevisiae_YEPD_aF_125min

source_name: S. cerevisiae culture, wild-type, 125 min

value: 125 min


title: Scerevisiae_YEPD_aF_120min

source_name: S. cerevisiae culture, wild-type, 120 min

value: 120 min


title: Scerevisiae_YEPD_aF_115min

source_name: S. cerevisiae culture, wild-type, 115 min

value: BF264-15D MATa bar1

value: 115 min


title: 0h ATAC-Seq - Replicate 1


title: ChIP-seq Oct4 in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1

description:
Oct4_12h_iNIL.bed
Oct4_12h_iNIL.events

value: anti-Oct4 (Santa Cruz sc-5279)


title: PWD 26 Rep2

description: protocol: SMART-seq2


title: Scerevisiae_YEPD_aF_110min

source_name: S. cerevisiae culture, wild-type, 110 min

value: wild type

value: 110 min


title: ChIP-seq Oct4 in EB(iNgn2.Isl1.Lhx3.V5) replicate 1

description:
Oct4_0h_iNIL.bed
Oct4_0h_iNIL.events


title: Scerevisiae_YEPD_aF_105min

source_name: S. cerevisiae culture, wild-type, 105 min

value: 105 min


title: ChIP-seq Lhx3.V5 in EB+48hrDox(iIsl1.Lhx3.V5) replicate 4

description:
Lhx3_48h_iIL.bed
Lhx3_48h_iIL.events

value: anti-V5 (Abcam ab15828)


title: Scerevisiae_YEPD_aF_100min

source_name: S. cerevisiae culture, wild-type, 100 min

value: 100 min


title: ChIP-seq Lhx3.V5 in EB+48hrDox(iIsl1.Lhx3.V5) replicate 3

description:
Lhx3_48h_iIL.bed
Lhx3_48h_iIL.events


title: Scerevisiae_YEPD_aF_95min

source_name: S. cerevisiae culture, wild-type, 95 min

value: 95 min


title: ChIP-seq Lhx3.V5 in EB+48hrDox(iIsl1.Lhx3.V5) replicate 2

description:
Lhx3_48h_iIL.bed
Lhx3_48h_iIL.events


title: Scerevisiae_YEPD_aF_90min

source_name: S. cerevisiae culture, wild-type, 90 min

value: 90 min


title: Cneoformans_YEPD_elut_230min

organism: Cryptococcus neoformans

source_name: C. neoformans culture, wild-type, 230 min

extract_protocol:
KAPA Stranded mRNA Library Prep Kit was used for the construction of sequencing libraries
Cells were removed at each time point and flash frozen on dry ice. RNA was harvested using standard yeast methods.
see SAMPLES section; RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
synchronous G1 populations collected by centrifugal elutriation
see SAMPLES section

value: 230 min


title: Cneoformans_YEPD_elut_220min

source_name: C. neoformans culture, wild-type, 220 min

value: 220 min


title: Scerevisiae_YEPD_aF_75min

source_name: S. cerevisiae culture, wild-type, 75 min

value: 75 min


title: Scerevisiae_YEPD_aF_80min

source_name: S. cerevisiae culture, wild-type, 80 min

value: 80 min


title: Scerevisiae_YEPD_aF_85min

source_name: S. cerevisiae culture, wild-type, 85 min

value: 85 min


title: ChIP-seq Oct4 in EB+12hrDox(iFlag.Ngn2) replicate 1

description:
Oct4_12h_iN.bed
Oct4_12h_iN.events

value: Embryoid Bodies


title: Cneoformans_YEPD_elut_200min

source_name: C. neoformans culture, wild-type, 200 min

value: 200 min


title: Cneoformans_YEPD_elut_210min

source_name: C. neoformans culture, wild-type, 210 min

value: 210 min


title: EB+12hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me1.rep1

description: ChIP-seq H3K4me1 in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) replicate 1

data_processing:
Basecalling conversion to fastq files was performed using bcl2fastq for HiSeq runs and Picard for NextSeq runs
Alignment: All transcription factor ChIP-Seq fastq files were aligned to mouse genome (version mm10) using Bowtie (1.0.1) (Langmead et al., 2009) with options “-q --best --strata -m 1 --chunkmbs 1024”.  Only uniquely mapped reads were considered for further analysis.
All histone modification ChIP-Seq fastq files were aligned to mm10 genome build using bowtie2 (Ben Langmead & Salzberg, 2012) with default parameters. After filtering for uniquely-aligned reads that had 2 or less mismatches, potential PCR duplicates were removed using samtools rmdup (parameters: -s) (H. Li et al., 2009). Resulting BAM files were converted to BED format using bedtools bamtobed command when necessary (Quinlan & Hall, 2010). For H3K4me1, replicates files were concatenated for all further analysis. JAMM was used to obtain the average fragment length for each experiment (Ibrahim et al. 2015).
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-Seq replicate experiments were concatenated and converted to bigwig files using deepTools bamCoverage at 10bp resolution (parameters: --normalizeUsingRPKM)(Ramirez et al. 2014), using the average fragment length predicted by JAMM (Ibrahim et al. 2015).

value: Abcam ab8895


title: 0h ATAC-Seq - Replicate 2


title: Cneoformans_YEPD_elut_190min

source_name: C. neoformans culture, wild-type, 190 min

value: 190 min


title: Scerevisiae_YEPD_aF_60min

source_name: S. cerevisiae culture, wild-type, 60 min

value: BF264-15D MATa bar1

value: wild type

value: 60 min


title: Scerevisiae_YEPD_aF_70min

source_name: S. cerevisiae culture, wild-type, 70 min

value: 70 min


title: Cneoformans_YEPD_elut_180min

source_name: C. neoformans culture, wild-type, 180 min

value: 180 min


title: cells_OS-2_B

city: Minneapolis

first: Milcah

last: Scott

state: MN

address: 2101 6th Street Se

department: Department of Microbiology and Immunology

institute: University of Minnesota

description: canine osteosarcoma cell line derivative OS-2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to a HISAT2 index for mapping which was built from a multi-sequence fasta file containing both the canine (canFam3) and murine (mm10) genomes with the HISAT2 aligner (2.0.2-beta) using default parameters.
Rsubread featureCounts (1.4.6) was used to estimate transcript abundance using default parameters.
Genome_build: mm10 and canFam3
Supplementary_files_format_and_content: tab-delimited text file include count values for each sample and includes data for both dog and mouse genes.

organism: Canis lupus familiaris

extract_protocol:
Total RNA was extracted from primary intratibial tumors and from cell lines using Qiagen miRNeasy Mini Kit.
Sequencing libaries were prepared using Illumina TruSeq Library Preparation Kits

tag: tissue

value: osteosarcoma cell line


title: Scerevisiae_YEPD_aF_65min

source_name: S. cerevisiae culture, wild-type, 65 min

value: 65 min


title: cells_OS-2_A

source_name: canine osteosarcoma cell line derivative OS-2


title: Scerevisiae_YEPD_aF_55min

source_name: S. cerevisiae culture, wild-type, 55 min

value: 55 min


title: Cneoformans_YEPD_elut_160min

source_name: C. neoformans culture, wild-type, 160 min

value: 160 min


title: cells_OS-1_B

description: canine osteosarcoma cell line derivative OS-1


title: Scerevisiae_YEPD_aF_45min

source_name: S. cerevisiae culture, wild-type, 45 min

value: 45 min


title: Scerevisiae_YEPD_aF_50min

source_name: S. cerevisiae culture, wild-type, 50 min

value: 50 min


title: Cneoformans_YEPD_elut_150min

source_name: C. neoformans culture, wild-type, 150 min

value: 150 min


title: Scerevisiae_YEPD_aF_40min

source_name: S. cerevisiae culture, wild-type, 40 min

value: 40 min


title: Cneoformans_YEPD_elut_140min

source_name: C. neoformans culture, wild-type, 140 min

value: 140 min


title: Clone 34 day4 Replicate 2

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
Human fibroblast RNA-seq reads were aliged to the Human genome (hg19) using Tophat v2.0.8 using Ensembl gene v72 as gene model.
RNA-Seq reads from hF x mESC fusion were aligned independently to Human (hg19, Ensembl v72) and Mouse (mm9, Ensembl v67) using Tophat v2.0.8. Reads aligned to both Human and Mouse were excluded from the further anlaysis.
Reads overlapping with each gene was counted using  HTSeq and differentially expressed genes were identified using edgeR
FPKM values were estimated using R script
Genome_build: hg19; mm9
Supplementary_files_format_and_content: hg19 FPKM values

organism: Homo sapiens x Mus musculus hybrid cell line

source_name: hF x mESC fusion_day4

growth_protocol: Human fibroblast (hF) clones were maintainedat 3% O2  in DMEM supplemented with 10% FCS, 1% non-essential amminoacids, 2mM L-glutammine and antibiotics (10 µg/ml penicillin and streptomycin). After hF x mESC fusion, heterokaryons and hybrids were cultured in mouse ESC medium (KO-DMEM supplemented with 10% FCS, 1% non-essential amminoacids, 2mM L-glutammine, 50μM β-mercaptoethanol, antibiotics (10 µg/ml penicillin and streptomycin) and LIF) and selected 12hrs after by adding puromycin (1.5 μg/ml) and HAT (20μM hypoxantine, 0.08 mM aminopterin, and 3.2 mM thymidine; Sigma).

extract_protocol:
Total RNA was exacted by RNABee (Amsbio) accordingly to manifacturer instructions
RNA-seq libraries were prepared from 0.6μg total RNA accordingly to Illumina True-seq RNA sample preparation v2 guide (Illumina). Libraries were amplified 14 cycles before deep-sequencing.

treatment_protocol: hF clones were fused with mESC by PEG (Roche)

value: human fibroblast clone (derived from TERT-immortalised NHDF17914) fused with mouse ESC (E14Tg2a:puroR)

tag: time point

value: day 4 after fusion with mouse ESC


title: Clone 34 day6 Replicate 2

source_name: hF x mESC fusion_day6

value: day 6 after fusion with mouse ESC


title: Cneoformans_YEPD_elut_130min

source_name: C. neoformans culture, wild-type, 130 min

value: 130 min


title: Cneoformans_YEPD_elut_120min

source_name: C. neoformans culture, wild-type, 120 min

value: wild type

value: 120 min


title: Scerevisiae_YEPD_aF_35min

source_name: S. cerevisiae culture, wild-type, 35 min

value: BF264-15D MATa bar1

value: 35 min


title: Clone 34 day4 Replicate 1


title: Scerevisiae_YEPD_aF_25min

source_name: S. cerevisiae culture, wild-type, 25 min

value: 25 min


title: Cneoformans_YEPD_elut_110min

source_name: C. neoformans culture, wild-type, 110 min

value: 110 min


title: Cneoformans_YEPD_elut_100min

source_name: C. neoformans culture, wild-type, 100 min

value: 100 min


title: Cneoformans_YEPD_elut_170min

source_name: C. neoformans culture, wild-type, 170 min

value: 170 min


title: Scerevisiae_YEPD_aF_20min

source_name: S. cerevisiae culture, wild-type, 20 min

value: 20 min


title: Clone 34 day0 Replicate 1

source_name: hF x mESC fusion_day0

value: day 0 after fusion with mouse ESC


title: Cneoformans_YEPD_elut_90min

source_name: C. neoformans culture, wild-type, 90 min

value: 90 min


title: Clone 12 day6 Replicate 2


title: Scerevisiae_YEPD_aF_10min

source_name: S. cerevisiae culture, wild-type, 10 min

value: 10 min


title: Cneoformans_YEPD_elut_70min

source_name: C. neoformans culture, wild-type, 70 min

value: 70 min


title: Clone 12 day4 Replicate 2

value: human fibroblast clone (derived from TERT-immortalised NHDF17914) fused with mouse ESC (E14Tg2a:puroR)


title: Clone 12 day6 Replicate 1


title: cells_OS-1_A

source_name: canine osteosarcoma cell line derivative OS-1

value: osteosarcoma cell line


title: Clone 12 day4 Replicate 1

value: day 4 after fusion with mouse ESC


title: Cneoformans_YEPD_elut_60min

source_name: C. neoformans culture, wild-type, 60 min

value: 60 min


title: Scerevisiae_YEPD_aF_0min

source_name: S. cerevisiae culture, wild-type, 0 min

value: wild type

value: 0 min


title: Scerevisiae_YEPD_aF_5min

source_name: S. cerevisiae culture, wild-type, 5 min

value: BF264-15D MATa bar1

value: 5 min


title: 2.3

city: Rennes

first: Hélène

last: Falentin

address: 65 rue de St Brieuc

department: Microbiologie

country: France

institute: INRA

description: mRNA from stationary growth phase 6

data_processing:
Libraries were sequenced on an Illumina HiSeq 2000 as 50 pb reads using the Sequence By Synthesis technique at the Montpellier GenomiX facility.
Image analyses and basecalling were performed using the Illumina HiSeq Control Software and Real-Time Analysis component.
Demultiplexing was performed using Illumina's sequencing analysis software (CASAVA 1.8.2). The quality of the data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
reads were mapped using bowtie
mapped reads were counted using htseq-count with union parameter
Genome_build: GCA_000945235.1
Supplementary_files_format_and_content: Tab-delimited file with a first column for gene identification. The next columns correspond to the gene counts for each sample.

organism: Propionibacterium freudenreichii

source_name: bacterial culture

growth_protocol: Planktonic culture in Yeast Extract Lactate medium (Malik) grown under microaerophilic conditions at 30°C without addition of any nutrient

extract_protocol:
Total RNA was extracted using Rneasy Mini Kit (Qiagen) and Dnase treatment. Ribosomic RNA were depleted using Ribozero for Gram plus (Epicentre). Quality was checked using Nanodrop and Nanochips for Bioanalyseur (Agilent).
The RNA-seq libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit according to the manufacturer's instructions.

treatment_protocol: Bacterial cells were recovered by a centrifugation step and incubated into RNA protect (Qiagen).

value: CIRM-BIA 138 alias ITG P20

tag: growth phase

value: stationary


title: Cneoformans_YEPD_elut_50min

source_name: C. neoformans culture, wild-type, 50 min

tag: strain

value: 50 min


title: Clone 12 day0 Replicate 2


title: Scerevisiae_YEPD_aF_30min

source_name: S. cerevisiae culture, wild-type, 30 min

value: 30 min


title: 2.2

description: mRNA from stationary growth phase 5


title: 2.1

description: mRNA from stationary growth phase 4


title: Cneoformans_YEPD_elut_40min

source_name: C. neoformans culture, wild-type, 40 min

value: 40 min


title: Cneoformans_YEPD_elut_30min

source_name: C. neoformans culture, wild-type, 30 min


title: Clone 34 day0 Replicate 2

value: day 0 after fusion with mouse ESC


title: Clone 12 day0 Replicate 1


title: Scerevisiae_YEPD_aF_15min

source_name: S. cerevisiae culture, wild-type, 15 min

value: 15 min


title: 1.3

description: mRNA from exponential growth phase 3

value: exponential


title: Cneoformans_YEPD_elut_20min

source_name: C. neoformans culture, wild-type, 20 min

value: 20 min


title: Cneoformans_YEPD_elut_10min

source_name: C. neoformans culture, wild-type, 10 min

value: 10 min


title: Cneoformans_YEPD_elut_80min

source_name: C. neoformans culture, wild-type, 80 min

value: 80 min


title: 1.1

description: mRNA from exponential growth phase 1


title: Cneoformans_YEPD_elut_0min

source_name: C. neoformans culture, wild-type, 0 min


title: Organophosphate 1

city: Madurai

first: Velmurugan

last: Ganesan

state: Tamilnadu

address: Palkalainagar

department: Department of Molecular Biology, School of Biological Sciences

country: India

institute: Madurai Kamaraj University

description: Mice gut metatranscriptome

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The reads were mapped with mouse genome, murine mRNAs, tRNAs and rRNAs by Bowtie 2 and the annotated sequences were removed.
Then the reads were mapped with reference database of human microbiome that includes 538 draft and finished bacterial geneomes using bowtie 2 (http://www.hmpdacc.org).
Differential expression was studied by DeSeq
Genome_build: Reference human microbiome genome (http://www.hmpdacc.org/)
Supplementary_files_format_and_content: Excel files with read count

organism: mouse gut metagenome

source_name: Mice gut metatranscriptome

growth_protocol: Mice were maintained at 25°-28° C, 40-60% humidity with 12 h day/night cycles. The animals were fed with deionized water and standard rat chow ab libitum.

extract_protocol:
After treatment period, the mice were sacrificed and the cecum tissue was collected. The total RNA was isolated using TRIZOL and the eukaryotic eukaryotic and bacterial rRNAs were removed by using MicrobExpress and MicrobEnrich kits (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with organophosphate (monocrotophos 28 ug/kg body weight/day) directly in drinking water for 180 days.

tag: sample type

value: Cecal bacteria


title: Control 2

description: Mice gut metatranscriptome


title: 1.2

description: mRNA from exponential growth phase 2


title: H9_amnion_58698

status: Public on Dec 06 2016

city: Detroit

first: Katherine

last: Gurdziel

address: 6135 Woodward Ave.

department: Institute of Environmental Health Sciences

institute: Wayne State University

description: Cultured H9 colonies were first incubated with Accutase at 37°C for 10 min before triturated and suspended in PBS as single cells. H9s were then centrifuged and the cell pellet was resuspended in mTeSR1 containing 10 µM Y27632. H9 cells were plated as single cells at 30,000 cells cm-2 onto the a thick Geltrex gel bed (> 100 μm thick). After 24 hr (on day 1), culture medium was changed to fresh mTeSR1 without Y27632. 4% (v : v) GeltrexTM was also supplemented in mTeSR1 medium on day 1 to provide a 3D ECM environment. Thereafter, mTeSR1 medium was replenished daily, and 4% (v : v) GeltrexTM was supplemented daily. The culture was continued to day 5.

data_processing:
Reads were mapped to the human reference genome (Build hg19) using STAR (Dobin 2013)
Counts for each gene were tabulated using HTSeq (Andres 2015)
Differntial expression between conditions was determined using edgeR (Robinson 2010)
Genome_build: hg19
Supplementary_files_format_and_content: Tabulated Excel and TXT files, listing the raw RNA reads for each sample, and the fold change of expression levels in hPSC_amnion relative to hPSCs.

source_name: hESC-derived amnion-like cells

growth_protocol: For hESC maintenance, H9 cells were maintained in a standard feeder-free culture system using mTeSR1 medium and lactate dehydrogenase-elevating virus (LDEV)-free hESC-qualified reduced growth factor basement membrane matrix GeltrexTM per the manufacturers' instructions. All cultures were visually examined during every passage to ensure the absence of spontaneously differentiated, mesenchymal-like cells in the culture. All hESCs were used before reaching P70.

extract_protocol:
Samples were collected and prepared for RNA isolation following a protocol commonly used for processing in vivo tissues. In brief, samples were washed with DMEM/F12. Cysts (ca. 5,000 or more per sample) or colonies were then scraped from the culture substrate, before being spun down at 1,000 rpm for 3 min in a conical tube. RNA was isolated from the cell pellet using an RNeasy Micro Kit as suggested by the manufacturer. RNA quality and quantity were determined using a NanoDrop 1000 spectrophotometer, as well as an Agilent 2100 Bioanalyzer.
Performed by the University of Michigan DNA Sequencing Core following Illumina guidelines.

value: Derived from H9 line

tag: differentiation

value: differentiated, squamous cells


title: Control 1

description: Mice gut metatranscriptome


title: H9_amnion_58697


title: H9_amnion_58696


title: H9_58693

description: Cultured H9 colonies were first incubated with Accutase at 37°C for 10 min before triturated and suspended in PBS as single cells. hPSCs were then centrifuged and the cell pellet was resuspended in mTeSR1 containing 10 µM Y27632. H9 cells were plated as single cells at 30,000 cells cm-2 onto the a glass coverlsip thinnly coated with 1% Geltrex for 1 h at room temperature. After 24 hr (on day 1), culture medium was changed to fresh mTeSR1 without Y27632. The culture was continued till day 5. Medium was changed daily with fresh mTeSR1.

source_name: undifferentiated hESC (H9 line), feeder free

value: H9 line

value: undifferentiated


title: H9_58689


title: Organophosphate 2

description: Mice gut metatranscriptome


title: S34673_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C66

city: Seattle

first: Scott

last: Presnell

state: WA

address: 1201 Ninth Avenue

institute: Benaroya Research Institute

data_processing:
Base-calling was performed automatically in Illumina BaseSpace after sequencing; FASTQ reads were trimmed in Galaxy in three steps: 1) hard-trimming to remove 1 3'-end base (FASTQ Trimmer tool, v.1.0.0); 2) adapter trimming to remove SMARTer adapter sequences (FastqMcf tool, v1.0.0); 3) quality trimming from both ends until minimum base quality for each read >= 30 (FASTQ Quality Trimmer tool, v.1.0.0).
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and ht-seq-count.
Samples were selected for further analysis by using these criteria: log10(PF_ALIGNED_BASES)>6.5, MEDIAN_CV_COVERAGE<2 & MEDIAN_CV_COVERAGE >0.4; PCT_USABLE_BASES>0.35; and at least one in frame TCR CDR3 junction identified by IMGT/HighV-QUEST.
Genome_build: GRCh38
Supplementary_files_format_and_content: AbATE_single_cell_profile_raw_counts.txt is a tab-delimited matrix. The first column contains Ensembl gene IDs. The remaining columns include raw read counts assigned for each library. Outlier samples have been removed but data have not been gene filtered or normalized.
Supplementary_files_format_and_content: metrics_AbATE_single_cell_libs.txt is a tab-delimited matrix. The first column contains library ID, remaining columns include RNA sequencing and alignment metrics.

source_name: CD8+ sorted T-cells

extract_protocol:
Single cells were captured on a C1 system, using a 5-10 um mRNA Seq IFC according to manufacturer’s instructions (Fluidigm, South San Francisco, CA).  Full-length cDNA was prepared using SMARTer Ultra Low RNA Kit for the Fluidigm C1 System (Clontech, Mountain View, CA).
Libraries were prepared from amplified cDNA using the NexteraXT kit according to manufacturer’s instructions (Illumina, San Diego, CA).

tag: samplelabel

tag: sampleID

tag: status

value: R

tag: itn name

tag: studysiteshort

value: YALE

tag: age

tag: gender

value: Male

tag: treatmentgroup

tag: race

value: White; White

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: sortmarkers

value: CD8+ CD45R0+ TIGIT- KLRG1-

tag: stim

value: anti-CD3 anti-CD28 Stimulated

tag: numcellssorted

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis

value: C1+SMARTer v1

tag: libraryprep

tag: projectid

tag: seqsite

value: BRI

value: single cell +debris

tag: flowcellid

tag: runchemistry

value: HiSeq SBS Kit v4

tag: lane


title: S34671_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C54

tag: samplelabel

tag: sampleID

tag: status

tag: itn name

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup


title: S34654_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C36

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: sortmarkers

tag: stim

tag: numcellssorted

tag: samplebarcode

value: single cell


title: S34650_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C35

tag: libraryid

tag: cdnasynthesis

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: S34659_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C96

tag: samplelabel

tag: sampleID

tag: status

tag: itn name

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup


title: S34657_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C70

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: sortmarkers

tag: stim

tag: numcellssorted

tag: samplebarcode


title: S34660_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C59

tag: libraryid

tag: cdnasynthesis

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: S34669_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C71

tag: samplelabel

tag: sampleID

tag: status

tag: itn name

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup


title: S34652_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C16

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: sortmarkers

tag: stim

tag: numcellssorted

tag: samplebarcode


title: S34653_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C22

tag: libraryid

tag: cdnasynthesis

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: S34649_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C23

tag: samplelabel

tag: sampleID

tag: status

tag: itn name

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup


title: S34663_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C65

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: sortmarkers

tag: stim

tag: numcellssorted

tag: samplebarcode


title: S34645_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C46

tag: libraryid

tag: cdnasynthesis

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: S34640_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C18

tag: samplelabel

tag: sampleID

tag: status

tag: itn name

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup


title: S34635_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C63

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: sortmarkers

tag: stim

tag: numcellssorted

tag: samplebarcode


title: S34638_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C06

tag: libraryid

tag: cdnasynthesis

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: S34637_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C91

tag: samplelabel

tag: sampleID

tag: status

tag: itn name

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup


title: S34633_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C92

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: sortmarkers

tag: stim

tag: numcellssorted

tag: samplebarcode


title: S34632_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C74

tag: libraryid

tag: cdnasynthesis

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: S34639_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C12

tag: samplelabel

tag: sampleID

tag: status

tag: itn name

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup


title: S34630_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C62

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: sortmarkers

tag: stim

tag: numcellssorted

tag: samplebarcode


title: H9_58692

tag: cell type

tag: differentiation


title: S34330_618372_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C87

tag: samplelabel

tag: sampleID

value: Female

value: White

tag: libraryid

tag: cdnasynthesis

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title: S32749_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr_C59

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber


title: S32748_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr_C48

tag: samplelabel

tag: sampleID

tag: sortmarkers

tag: stim

tag: numcellssorted

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis


title: S32752_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr_C76

tag: status

tag: itn name

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: S32746_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr_C22

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber


title: S32745_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr_C04

tag: samplelabel

tag: sampleID

tag: sortmarkers

tag: stim

tag: numcellssorted

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis


title: S32744_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr_C35

tag: status

tag: itn name

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: S32742_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr_C18

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber


title: S32747_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr_C36

tag: samplelabel

tag: sampleID

tag: sortmarkers

tag: stim

tag: numcellssorted

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis


title: S32845_106306_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C33

tag: status

tag: itn name

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: S32762_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr_C27

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber


title: S32763_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr_C39

tag: samplelabel

tag: sampleID

tag: sortmarkers

tag: stim

tag: numcellssorted

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis


title: S32740_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr_C57

tag: status

tag: itn name

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: S32737_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr_C39

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber


title: S32738_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr_C75

tag: samplelabel

tag: sampleID

tag: sortmarkers

tag: stim

tag: numcellssorted

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis


title: S32764_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr_C45

tag: status

tag: itn name

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: S32739_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr_C92

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber


title: S32735_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr_C20

tag: samplelabel

tag: sampleID

tag: sortmarkers

tag: stim

tag: numcellssorted

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis


title: S32732_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr_C25

tag: status

tag: itn name

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: S32734_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr_C08

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber


title: WT_4154_H5

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Libraries were sequenced on the Illumina HiSeq2500 platform using the default RTA analysis software.
Reads were trimmed using trim galore v0.4 using default parameters to remove standard illumina adapters. Reads were mapped to the GRCh38 human genome assembly plus the ERCC spike in control sequences using HiSat v2.0.1b guided by splice junctions imported from the gene models in Ensembl v78. Uniquely mapping reads were imported into SeqMonk v0.32.1 for analysis. Quantitation was performed on a gene set of annotated models with a biotype of protein_coding or lincRNA at a gene level counting reads overlapping any valid exon in each gene. Counts were expressed as log2 reads per million reads of library (log2RPM).
Genome_build: GRCh38
Supplementary_files_format_and_content: Quantitated RNA-Seq data file is tab delimited and contains the following columns: (1) Chromosome; (2) Start; (3) End; (4) Strand; (5) mRNA Name; (6) mRNA ID (Ensembl) (7) Description (Ensembl); (8-228) log2 RPM value

source_name: single cell transcriptome EZH2 +/+ wildtype  human ESC

growth_protocol: Human ESC (WA09; obtained from WiCell) were cultured on CF1 irradiated mouse embryonic fibroblasts (MEF) in Advanced DMEM containing 20% Knockout Serum Replacement (Life Technologies) supplemented with 2mM L-Glutamine (Life Technologies), 0.1mM B-Mercaptoethanol (Sigma-Aldrich), 1x Penicillin/Streptomycin (Life Technologies), 1x Non-Essential Amino Acids (Life Technologies) and 4ng/ml FGF2 (WT-MRC Cambridge Stem Cell Institute). Cells were passaged using 1mg/ml Collagenase IV (Life Technologies).

extract_protocol:
SSEA4-positive live hESC were deposited by FACS directly into 96-well plates. Poly-A cDNA from single cells was obtained as described by Picelli et al.
Illumina Nextera DNA LT library preparation kit was used following the Fluidigm protocol described for cDNA generation using the Fluidigm C1 machine (available online). Spike-ins (ERCC RNA Spike-in Mix, Ambion) were added in a final dilution of 1:10E6.

treatment_protocol: All samples were flow sorted for SSEA4.

tag: cell type

value: H9 embryonic stem cell (ESC)

tag: genotype


title: WT_4154_H8


title: WT_4154_H3


title: WT_4154_H9


title: WT_4154_H2


title: WT_4154_H11


title: S32743_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr_C46

tag: samplelabel

tag: sampleID

tag: status

value: R

tag: itn name

tag: sortmarkers

tag: stim

tag: numcellssorted

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis


title: WT_4154_G1


title: WT_4154_G3


title: S32741_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr_C06

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: WT_4154_F9

tag: cell type

tag: genotype


title: WT_4154_F7


title: WT_4154_F5


title: WT_4154_G11


title: S32736_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr_C33

tag: samplelabel

tag: sampleID

tag: status

tag: itn name

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: sortmarkers

tag: stim


title: WT_4154_G10


title: WT_4154_F3


title: WT_4154_F12


title: WT_4154_F10


title: WT_4154_F2


title: WT_4154_E9


title: WT_4154_E8


title: WT_4154_F1


title: WT_4154_E6


title: WT_4154_E10


title: WT_4154_E11


title: WT_4154_E12


title: WT_4154_H7


title: WT_4154_D1


title: WT_4154_D3


title: WT_4154_C7


title: WT_4154_C8


title: WT_4154_F8


title: WT_4154_C5


title: S32846_106306_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr_C39

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

tag: numcellssorted

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis

tag: libraryprep

tag: projectid


title: WT_4154_C3

tag: cell type

tag: genotype


title: WT_4154_C2


title: TYP140815-02

city: Charleston

first: Marion

last: Neely

state: SC

address: 331 Ft. Johnson Rd

department: NCCOS

institute: National Ocean Services

data_processing:
Illumina BCL output files were converted to FASTQ-sanger file format in Galaxy with FASTQ Groomer. Sequence quality trimming was performed using Trimmomatic  with a minimum quality score of phred >20 over the length of the reads.  The trimmed reads were then quality checked using the FASTQC tool.
Reads were mapped to the Ensembl T. truncatus genome, version turTru1 v76.1, with Bowtie2 v 2.2.4 as the alignment engine within the package RNA-Seq by Expectation Maximization (RSEM), generating mapped read counts as FPKM (fragments per kilobase of transcript per million mapped reads).
A table of summarized FPKMs for all samples was created.

organism: Tursiops truncatus

source_name: skin

extract_protocol:
Qiagen RNeasy Lipid Tissue Mini Kit with on-column DNase digestion.
NEBNext Ultra Directional RNA Library Prep Kit for Illumina, indexed with the NEBNextMulitplex Oligos for Illumina.

tag: tissue

value: skin

tag: Sex

value: male

value: USA:Cooper, Ashley, Wando, and Stono River Basin (CAWS), South Carolina


title: TYP140808-01


title: TYP140808-05


title: WT_4154_C4


title: TYP140730-05


title: TYP140806-01


title: TYP140801-04


title: WT_4154_B6


title: WT_4154_B5


title: TYP140716-01


title: WT_4154_B4


title: WT_4154_B3


title: TYP140715-04


title: TYP140227-06


title: WT_4154_B1


title: TYP140715-01


title: TYP140807-01


title: TYP140227-05


title: TYP140716-05


title: WT_4154_B12


title: WT_4154_B2


title: WT_4154_B11


title: WT_4154_B9


title: TYP140717-03


title: TYP140227-04


title: TYP140227-02


title: TYP140227-03


title: TYP131204-05


title: TYP131206-01


title: WT_4154_A7


title: WT_4154_A6


title: WT_4154_A5


title: TYP131204-04


title: TYP131204-02


title: WT_4154_A4


title: TYP120824-02

value: USA:Ashepoo, Combahee, Edisto River Basin, South Carolina


title: WT_4154_A3


title: TYP120816-01


title: TYP120823-03


title: TYP120816-02


title: WT_4154_A2


title: TYP120814-05


title: TYP120814-03


title: TYP131122-01


title: WT_4154_A9


title: TYP120824-04


title: TYP120731-04


title: WT_4154_A12