title: Control-Stroma rep2

source_name: Control-Stroma

value: stromal (CD31-CD45-EpCAM-)


title: Ezh2KO-Stroma rep3

status: Public on May 11 2015

type: SRA

city: Parkville

first: Marie-Liesse

last: Asselin-Labat

state: VIC

address: 1G Royal Parade

department: Stem Cells and Cancer

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

library_source: transcriptomic

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v1.4.8 and Real Time Analysis (RTA) v1.12.4.2, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then Illumina CASAVA1.8 pipeline was used to generate the sequence data.
Reads were aligned to the mouse reference genome mm10 and mapped to known genomic features at the gene level using the Rsubread package (version 1.14.2) (Liao et al. 2013) from the Bioconductor software project (Gentleman et al. 2004). Reads were summarized at the gene level using the featureCounts (Liao et al. 2014) function in a strand-specific manner.
Genes with low counts were discarded, retaining only those with counts per million above 0.5 in at least 3 libraries. Predicted genes, genes without annotation and genes that mapped to Y or mitochondrial chromosomes were also removed from the analysis. After filtering, 14,831 genes remained available for the differential expression analysis.
Genome_build: NCBI mm10
Supplementary_files_format_and_content: Tab delimited count matrices containing read counts at gene level before (count.matrix.txt) and after (filtered.count.matrix.txt) filtering.

molecule: total RNA

organism: Mus musculus

growth_protocol: Lungs from ShhCre;Ezh2fl/fl and control ShhCre;Ezh2fl/+ embryos at day E16.5 were digested to a single cell suspesion, depleted by FACS for CD31 and CD45 positive cells and separated into epithelial and stromal cell populations based on expression of EpCAM marker.

extract_protocol:
EpCAM+ and EpCAM- cells from the Ezh2-deficient and control embryonic lungs at day E16.5 were pooled together as necessary to a minimum of 100000 cells per sample (3 samples per tissue-genotype combination). Total RNA was extracted and purified using Total RNA Purification Kit (Norgen) according to kit instructions.
150 ng of total RNA was subjected to NGS library preparation using TruSeq Stranded Total RNA with Ribo-Zero (Illumina) according to kit instructions. Completed libraries from different samples were pooled together at equimolar concentrations and sequenced on HiSeq 2000 with TruSeq SBS Kit v3- HS reagents (Illumina) as 100 bp single end reads at the Australian Genome Research Facility (AGRF).

tag: strain background

tag: genotype/variation

tag: age

tag: tissue

value: lung

tag: cell population

tag: library adapter

tag: sequencing depth

tag: mapped to genes before filtering

tag: mapped to genes after filtering


title: Ezh2KO-Stroma rep2


title: Control-Epithelium rep3

source_name: Control-Epithelium

value: Epithelial (CD31-CD45-EpCAM+)


title: Ezh2KO-Stroma rep1


title: Ezh2KO-Epithelium rep2


title: Control-Stroma rep3


title: Ezh2KO-Epithelium rep1


title: WT_RNAseq

city: Boston

first: Peng

last: Du

state: MA

address: 1 Blackfan Circle

country: USA

institute: Boston Children’s Hospital, Harvard Medical School

data_processing:
bowtie softare is used to map reads to mRNA with two mismatches permitted, and self-developed perl scripts were used to coculate the reads of each genes
For small RNA sequencing, after removal of the adaptor sequences, bowtie software was used to mapping the small RNAs into mature miRNA sequences (miRBase).
Genome_build: mm9
Supplementary_files_format_and_content: RNAseq.txt provided a matrix table, which contained five columns including the gene's name, cDNA's name, reads number in WT, DGCR8 and Dicer samples; small RNA seq.txt provided the reads number for each miRNAs.

source_name: mESCs

growth_protocol: Mouse ESCs (V6.5, Dgcr8-/- and Dicer-/-) were cultured in DMEM with ESGRO (1000 units/mL), supplemented with 15% (v/v) FBS and antibiotics

extract_protocol:
total RNAs were extracted using Trizol reagent
200 ng polyA(+) RNA isolated as described above was used for mRNA-seq. Sample preparation was with the TruSeq Stranded mRNA Sample Prep Kits (Illumina).10ug total RNAs was used for small RNA libraries preparaion fellowing small RNA Sample Prep Kits (Illumina)

tag: cell type

value: WT mESCs

tag: strain


title: Ezh2KO Epithelium rep1

library_source: genomic

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v1.4.8 and Real Time Analysis (RTA) v1.12.4.2, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then Illumina CASAVA1.8 pipeline was used to generate the sequence data.
Reads were aligned to the mouse reference genome mm10 using Rsubread package (version 1.13.25) (Liao et al. 2013).
We used a locally developed R software package (ChIP-seq analysis with windows, or csaw) based on a previously described approach (Lun and Smyth, 2014) to call H3K27me3 enriched regions. Reads from each library were counted into contiguous 2 kb bins spanning the entire genome. Similarly we counted reads into 10kb bins to capture background read levels. Reads in genomic regions annotated as repeat sequences according to RepeatMasker (Smit et al., 2010) from the UCSC server (http://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/chromOut.tar.gz) were excluded from counting.
Genome_build: NCBI RefSeq mm10
Supplementary_files_format_and_content: Tab delimited count matrix containing read counts in 2kb and 10kb bins. The counts exclude reads overlapping repeat regions.

molecule: genomic DNA

source_name: Ezh2KO Epithelium

growth_protocol: Lungs from ShhCre;Ezh2fl/fl and control ShhCre;Ezh2fl/+ embryos at day E16.5 were digested to a single cell suspesion, depleted by FACS for CD31 and CD45 positive cells and enriched for epithelial cells based on expression of EpCAM marker.

extract_protocol:
Freshly sorted EpCAM+ cells from Ezh2-deficient and control embryonic lungs at day E16.5 were cross-linked in 1 ml of freshly prepared 1% formaldehyde for 10 min at room temperature (RT). Cross-linking was stopped by adding 100 μl of 1.25M Glycine and 5 min incubation at RT. Cells were collected by centrifugation at 1000 x g for 5 min at 4C, resuspended in 200 ul of hypotonic buffer from Chromatrap Standard Pro-A ChIP spin column sonication kit (Chromatrap) containing 1 μl of proteinase inhibitor cocktail (PIC) (Sigma) and incubated on ice for 10 min. At this stage concentration of nuclei in the hypotonic buffer was estimated using a haemocytometer. Nuclei were collected by centrifugation at 5000 x g for 5 min at 4°C. Nuclear pellet was snap-frozen in dry ice and stored at -80°C. Nuclear pellets from several preparations were pooled together to a minimum of 400000-500000 cells per sample (2 samples per genotype) in 130 ul of cell lysis buffer (Chromatrap) containing 1 μl of PIC and incubated on ice for at least 10 min. The entire volume of lysate was transferred to a microTUBE (Covaris) and sonicated on Covaris S220 machine for 15 min under the following conditions: Duty Cycle 2%; Peak Incident Power 105 W; Cycles per Burst 200.    Sonicated lysate was centrifuged at 10000 x g for 5 min at 4°C and resulting supernatant was collected and stored at -80°C. A 25 μl aliquot of lysate was combined with 5 μl of 1M NaHCO3, 5 μl of 5M NaCl, 15 μl dH20 and 1 μl of 20 mg/ml Proteinase K (Roche). The mix was incubated at 65°C for 2 hours and Proteinase K was inactivated by heating the mix to 95°C for 10 min. DNA was isolated by Phenol-Chloroform extraction followed by DNA precipitation and resuspended in 30 ul of nuclease-free H2O. The fragment size and DNA concentration were determined using D1K Screentape on Tapestation instrument (Agilent).    50 μl of sonicated lysate was combined with 450 μl Chromatin Dilution Buffer (Millipore), 10 μg H3K27me3 antibody (Millipore #07-449), 2.25 μl PIC (Sigma) and 40 ul of Magna ChIP protein A magnetic beads (Millipore #16-661). The chromatin slurry was incubated overnight with rotation at 4°C and beads were washed according to Magna ChIP A kit instructions (Millipore #17-610). Chromatin was eluted from the beads by resuspension in 100 μl elution buffer (1% SDS, 0.1M NaHCO3) containing 1 μl of 20 mg/ml Proteinase K (Roche) followed by incubation at 62°C for 2 h with shaking and Proteinase K inactivation at 95°C for 10 min. 2 IP reactions were set up for each sample and eluted chromatin corresponding to the same sample was combined at this stage. DNA was isolated by phenol-chloroform extraction followed by precipitation and resuspended in 30 μl of nuclease free water.
20-30 ng of immunoprecipitated DNA from each of the samples were subjected to NGS library preparation using TruSeq Nano DNA Sample Preparation Kit (Illumina) following kit instructions with the following adjustments: fragmentation and size selection steps were omitted and 10 cycles of amplification were carried out during the fragment enrichment step. Resulting libraries were size selected using Pippin Prep DNA Size Selection System (Sage Science) to ensure fragment size below 900 bp. Libraries were pooled at equimolar concentrations and sequenced on HiSeq 2500 TruSeq SBS Kit v3 - HS reagents (Illumina) as 100 bp single end reads at AGRF.

value: epithelium

tag: chip antibody

value: H3K27me3 antibody

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #

tag: mapped reads

tag: molecule subtype

value: Immunoprecipitated DNA


title: Ezh2KO Epithelium rep2


title: Control Epithelium rep2

source_name: Control Epithelium


title: dgcr8-/-_RNAseq

value: dgcr8-/- mESCs


title: Control-Stroma rep1


title: Control-Epithelium rep1


title: Control Epithelium rep1


title: T cell wildtype rep2

status: Public on May 10 2015

city: New York

first: Yuheng

last: Lu

state: NY

address: 417 East 68th Street

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Paired-end RNA-Seq reads were first processed with Trimmomatic to remove TruSeq adaptor sequences and bases with quality scores below 20, and reads with less than 30 remaining bases were discarded.
Trimmed reads were then aligned to mm9 genome with the STAR aligner.
The number of uniquely mapped reads overlapping with each RefSeq gene was counted with HTSeq.
We used DESeq to evaluate the differences in expression between each pair of genotypes in the same cell type, which were represented with log2 fold change and Benjamini-Hocheberg corrected p-values.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including gene-wise read counts for each sample

source_name: OT1 specific CD8+ T cells

extract_protocol:
Total RNA was extracted from sorted cells using TRIzol LS Reagent (Invitrogen).
RNA libraries were prepared using TruSeq RNA Library Preparation Kit (Illumina).
About 20 millions of paired-end reads with 50-nucleotide length were generated for each sample and sequenced on Illumina Hi-Seq 2500 system (MSKCC iGO core facility).

tag: genotype

value: wild type

value: OT1 specific CD8+ T cells


title: T cell wildtype rep1


title: T cell wildtype rep3


title: T cell miR155 KO rep3

value: miR-155 KO


title: T cell miR155 KO rep2


title: T cell Socs1 KI rep3

value: Socs1 KI


title: T cell Socs1 KI rep2


title: T cell miR155 KO rep1


title: NK cell wildtype rep1

source_name: Natural Killer cells

value: Natural Killer cells


title: NK cell wildtype rep2


title: T cell Socs1 KI rep1


title: NK cell miR155 KO rep1


title: NK cell miR155 KO rep3


title: NK cell Socs1 KI rep2


title: NK cell miR155 KO rep2


title: NK cell Socs1 KI rep3


title: K562_g-H2AX_Topo_4hr_1

city: Palo Alto

first: Baoxu

last: Pang

state: CALIFORNIA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

description: processed data file: X_T.bedGraph

data_processing:
Reads were aligned to hg19 using BWA, duplicates and reads with mapping quality less than 60 were removed.
Biological replicates of respective treatment condition were pooled, and normalized based on the background regions against the input DNA.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated from the pooled biological replicates of respective treatment condition and normalized against the background regions of input DNA.

organism: Homo sapiens

source_name: chronic myelogenous leukemia

growth_protocol: K562 cells were maintained in RPMI 1640 media with penicillin/streptomycin and 8% FCS, according to the ENCODE recommended culture conditions. Cell density reached around 0.5x106/ml before treatment.

extract_protocol:
For FAIRE-seq, after fixation, lysates were cleared from sonicated nuclei and histone-free DNA were isolated by phenol-chloroform extraction.for ChIP samples. For ChIP-seq, after fixation, lysates were cleared from sonicated nuclei and antibodies against g-H2AX were used to IP the histone-DNA complexes.
Libraries were prepared according to the provider’s kits and protocols.

treatment_protocol: K562 cells were treated with indicated drugs for 4 hours then fixed and collected for processing.

tag: cell line

value: chronic myelogenous leukemia cell line

tag: treated with

value: Topotecan 10mM for 4hr

tag: chip antibody cat.#

tag: chip antibody lot #


title: K562_g-H2AX_Topo_4hr_2

description: processed data file: X_T.bedGraph


title: K562_g-H2AX_Daun_4hr_1

description: processed data file: X_Da.bedGraph

value: Daunorubucin 10mM for 4hr


title: K562_FAIRE_Daun_4hr_2

description: processed data file: FA_Da.bedGraph


title: K562_g-H2AX_Etop_4hr_1

description: processed data file: X_E.bedGraph

value: Etoposide 60mM for 4hr


title: K562_g-H2AX_untreated_1

description: processed data file: X_C.bedGraph

value: none (untreated control)


title: K562_g-H2AX_untreated_2

description: processed data file: X_C.bedGraph


title: K562_g-H2AX_Etop_4hr_2

description: processed data file: X_E.bedGraph


title: K562_FAIRE_Etop_4hr_2

description: processed data file: FA_E.bedGraph


title: K562_FAIRE_Etop_4hr_1

description: processed data file: FA_E.bedGraph


title: K562_FAIRE_untreated_2

description: processed data file: FA_C.bedGraph


title: NK cell wildtype rep3


title: K562_FAIRE_untreated_1

description: processed data file: FA_C.bedGraph


title: K562_FAIRE_Acla_4hr_1

description: processed data file: FA_A.bedGraph

value: Aclarubicin 20mM for 4hr


title: K562_FAIRE_Acla_4hr_2

description: processed data file: FA_A.bedGraph


title: K562_Whole_Cell_Extract

description: Whole Cell Extract


title: NK cell Socs1 KI rep1


title: K562_g-H2AX_Daun_4hr_2

description: processed data file: X_Da.bedGraph


title: Bre98p14_MBDCapSeq

status: Public on May 09 2015

city: Darlinghurst

first: Warwick

middle: James

last: Locke

state: NSW

address: 384 Victoria St

department: Cancer Deparment

institute: The Garvan Institute of Medical Research

data_processing:
Sequenced reads were aligned to hg18 genome assembly using bowtie. Reads with more than three mismatches and reads mapping to multiple positions were removed. Finally, multiple reads mapping to exactly the same genomic coordinate were eliminated and only one read was retained for downstream analysis.
For each MBDCap-Seq sample, fragment length was estimated using HOMER software, sequenced tags were shifted to the middle of estimated fragment lenght and the number of sequenced tags overlapping SssI regions was computed.
For each ChIP-seq sample, regions of enrichment were identified using the Homer peak calling algorithm. Large regions of enrichment were broken into non-overlapping 1000 bp tiles for the chromatin marks H3K27ac, H3K36me3 and H3K27me3 whereas, H3K4me3 exhibited smaller regions that did not need to be tiled. The density of sequence reads in regions of enrichment was assessed with edgeR. Where regions had to be tiled, adjacent statistically significant regions were combined into a single region and an aggregate statistic calculated using Fischer’s exact test.
Genome_build: hg18
Supplementary_files_format_and_content: For ChIP-seq, BED files containing peak coordinates. For MBD-seq, tab delimited (txt) files containing genomic coordinates of SssI regions and  the number of overlapping sequenced tags.

source_name: Human Mammary Epithelial Cell Line

growth_protocol: HMEC lines were generated from tissue taken from healthy women with informed donor consent as part of breast reduction mammoplasty (institutional ethics approval provided by the Sydney Adventist Hospital Ethics Committee, Project ID 06/03). At the time of surgery, all donors were aged between 23 and 43 years of age. Breast tissue was diced and then digested with collagenase to generate organoids. To establish HMEC lines, organoids were allowed to expand in MBD170 serum free basal medium (Life Technologies, Carlsbad CA, USA) until large colonies (1-2 cm) were observed (5-10 days). Organoid colonies were partially trypsinised to remove stromal cells and the remaining epithelial cells were transferred into a new tissue culture flask to generate passage 1 HMEC. vHMEC lines were then generated by serial passage of HMEC until proliferation slowed and the cells entered the selection phase. Selection phase HMEC were maintained with twice-weekly media changes until large, actively growing colonies (1-2 cm) were observed. Growing cells were trypsinised and transferred to a new culture vessel, generating the vHMEC lines.

extract_protocol:
Each capture utilised 1 μg genomic DNA sonicated to mean fragment size of ~500 bp using a Bioruptor® water bath sonicator. Methylated DNA was captured using the Methylminer® Methylated DNA Enrichment Kit (Life Technologies, Carlsbad CA, USA) according to the manufacturer’s protocol with a single high salt elution. Next generation sequencing was performed on 10 ng of MBD captured DNA at two commercial sequencing centres on the Illumina GAIIX sequencing platform.
10ng DNA of MBDCap enriched DNA was prepared for Ilumina sequencing using the Illumina ChIP-Seq DNA sample prep kit (IP-102-1001) according to the manufacturer’s instructions.  The library preparation was analyzed on Agilent High Sensitivity DNA 1000 Chip.

tag: tissue

value: Breast

tag: passage

tag: growth phase

value: vHMEC

value: Methylminer DNA enrichment Kit (Life Technologies)


title: Bre67p14_MBDCapSeq


title: Bre67p2_MBDCapSeq

value: HMEC


title: Bre67p7_MBDCapSeq


title: Bre98p7_MBDCapSeq


title: Bre98p2_MBDCapSeq


title: Bre38p7_MBDCapSeq


title: K562_FAIRE_Daun_4hr_1

description: processed data file: FA_Da.bedGraph


title: Bre38p26_MBDCapSeq


title: Bre12p3_MBDCapSeq


title: Bre12p14_MBDCapSeq


title: Bre98p9_H3K36me3_ChIPseq

extract_protocol:
ChIP experiments utilised ~2x10^6 cells (per immunoprecipitation) fixed for 10 minutes at 37°C in culture media containing 2.7% (w/v) formaldehyde (Sigma-Aldrich, St Louis MO, USA). Immunoprecipitation was performed using the Chromatin Immunoprecipitation Assay Kit (Merck Millipore, Billerica MA, USA) according to the manufacturers protocol withthe included salmon sperm DNA blocked agarose beads substituted with Protein A/G PLUS-Agarose Immunoprecipitation Reagent (Santa Cruz Biotechnology). Illumina 36 bp single end sequencing was performed on 5-12 ng of ChIP DNA.
10ng DNA of MBDCap enriched DNA was prepared for Ilumina sequencing using the Illumina ChIP-Seq DNA sample prep kit (IP-102-1001) according to the manufacturer’s instructions.  The library preparation was analyzed on Agilent High Sensitivity DNA 1000 Chip.

value: Anti-Histone H3 (tri methyl K36), abcam, #ab9050-100


title: Bre98p9_H3K27me3_ChIPseq

value: Anti-trimethyl-Histone H3 (Lys27), Millipore, #07-449


title: Bre12p7_MBDCapSeq


title: Bre38p3_MBDCapSeq


title: Bre98p2_H3K4me3_ChIPseq

description: H3K4me3 CHIP was performed in two donors, which were treated as biological replicates. Data from Sample GSM1421314 was used  together with data from Sample GSM1421312 to create the processed data file located on the record for Sample GSM1421312.

value: ChIPAb+ Trimethyl-Histone H3 (Lys4), Millipore, #17-614


title: Bre67p7_H3K4me3_ChIPseq


title: Bre98p8_H3K4me3_ChIPseq

description: H3K4me3 CHIP was performed in two donors, which were treated as biological replicates. Data from Sample GSM1421319 was used together with data from Sample GSM1421313 to create the processed data file located on the record for Sample GSM1421313.


title: Bre67p2_H3K4me3_ChIPseq


title: Bre98p4_H3K27me3_ChIPseq


title: SU_OUL_1_ac

city: Detroit

first: Stephen

last: Krawetz

state: MI

address: 275 E. Hancock

department: Center for Molecular Medicine and Genetics

institute: Wayne State University School of Medicine

description: Sample 16

data_processing:
Image analysis, base calling and FASTQ generation were performed using the genome analyzer pipeline software CASAVA (version 1.8.2).
Inline demultiplexing was performed using software fastq_multx (Aronesty 2011)
Sequencing reads were mapped to hg19 of the human reference genome (NCBI build 37.2) plus human ribosomal 5S, 18S and 28S sequences using Novoalign (Novocraft Technologies v.2.08, Selangor, Malaysia) paired-end base default parameters.
The relative abundance of each transcript was calculated using Genomatix software (www.genomatix.de) and presented as FPKM (fragments per kilobase exon per million fragments mapped).
Genome_build: hg19
Supplementary_files_format_and_content: bed files include each read's mapping location on reference genome

source_name: Sperm

extract_protocol:
Semen samples was treated with PureSperm gradient centrifugation through a 50% PureSperm cushion. RNA was isolated using the RNA isolation protocol as previously described [Goodrich et al. 2013]. In brief, a bead-based homogenization Qiazol protocol was applied to isolate the total RNA from each sample. An automated QiaCube extraction protocol specifically developed for sperm RNAs was used to extract the large RNA population. The residual DNA was removed by treating the isolated RNA with turbo-DNA Free (Ambion Inc.).
The RNA-Seq libraries for each sperm sample were prepared in two stages: cDNA amplification and RNA-Seq library preparation. In the first stage, four different amplification kits were studied: SMARTer™ Ultra Low RNA Kit for Illumina® Sequencing (Clontech Laboratories, Inc.), SeqPlex RNA Amplification Kit (Sigma-Aldrich Co.), Ovation® RNA-Seq System V2 and Ovation® RNA-Seq FFPE System from Nugen (NuGEN Technologies, Inc.). The RNA was reversed transcribed into cDNA then amplified. In the second stage, two library preparation kits were compared: Encore NGS Multiplex System I (NuGEN) and Ovation Ultralow Library Systems (NuGEN). The amplified cDNA is subject to sonication. Then the fragment ends are repaired before ligation of sequencing adaptors (with barcodes when necessary), followed by PCR amplification and library purification.

value: Fertile mature sperm

tag: cdna amplification kit

value: SMARTer Ultra Low RNA Kit (Clontech)

tag: rna-seq library preparation kit


title: SP_OUL_2_ac

description: Sample 14

tag: cell type

value: SeqPlex RNA Amplification Kit (Sigma-Aldrich)

value: Ovation Ultralow Library Systems (NuGEN)


title: SP_OUL_10_ac

description: Sample 13


title: SP_Enc_2_bc

description: Sample 12

value: Encore NGS Multiplex System I (NuGEN)


title: SU_OUL_10_ac

description: Sample 15


title: SP_Enc_10_bc_tr

description: Sample 10


title: SP_Enc_2_ac

description: Sample 11


title: SP_Enc_10_bc

description: Sample 9


title: SP_Enc_10_ac_tr

description: Sample 8


title: Ova_Enc_100_bc

description: Sample 6

value: Ovation RNA-Seq System V2 (NuGEN)


title: SP_Enc_10_ac

description: Sample 7


title: Ova_Enc_100_ac

description: Sample 5


title: Bre98p5_input_ChIPseq

value: none (input)


title: FFPE_Enc_100_bc_tr

description: Sample 4

value: Ovation RNA-Seq FFPE System (NuGEN)


title: Bre98p9_input_ChIPseq


title: FFPE_Enc_100_bc

description: Sample 3


title: FFPE_Enc_100_ac_tr

description: Sample 2


title: FFPE_Enc_100_ac

description: Sample 1


title: Bre98p5_H3K27ac_ChIPseq

value: Anti-Histone H3 (acetyl K27), abcam, ab4729


title: Medea_DPP (treatment with decapentaplegic (DPP))

status: Public on May 08 2015

first: Kevin

last: Van Bortle

state: CA

address: 3165 Porter Dr

data_processing:
ChIP-seq reads were aligned to the Drosophila (dm3) genome using bowtie 0.12.3, the data analysis did not include pairing of end reads.
Genome_build: dm3
Supplementary_files_format_and_content: wig files were generated running MACS 1.4.0alpha2

organism: Drosophila melanogaster

source_name: Drosophila Kc167 cells

growth_protocol: Kc167 cells were grown in HyClone SFX cell culture medium.

extract_protocol:
DPP and control lysates were extracted after 6 hr incubations
Libraries were prepared for paired-end sequencing with Illumina adaptors (cat# PE-102-1001)

treatment_protocol: Cells were split to density of 0.5 x 10^6 cells/mL and treated with 30 nM DPP the following morning.

tag: cell-type

value: Late-stage embryonic plasmatocyte (Kc167)

tag: antibody

value: Medea rabbit polyclonal (gift from Dr. Laurel Raftery)


title: Schnurri_DPP (treatment with decapentaplegic (DPP))

value: Schnurri rabbit polyclonal (gift from Dr. Mark Biggin)


title: Medea_control (untreated)


title: Schnurri_control (untreated)


title: Medea_CTCFkd (RNAi depletion of CTCF)


title: Mad_control (untreated)

value: Mad rabbit polyclonal (gift from Dr. Lan Xu)


title: Mad_DPP (treatment with decapentaplegic (DPP))


title: Mad_CTCFkd (RNAi depletion of CTCF)


title: IgG_control (untreated)

value: IgG control


title: dSmad2_CTCFkd (RNAi depletion of CTCF)

value: dSmad2 sheep polyclonal (R&D systems cat#AF7948)


title: CTCF_DPP (treatment with decapentaplegic (DPP))

value: CTCF guinea-pig polyclonal


title: dSmad2_control (untreated)


title: mm1036_WT_mm9

city: Berlin

first: Darío

middle: G

last: Lupiáñez

address: Ihnestrasse 73

country: Germany

institute: Max Planck Institute for Molecular Genetics

data_processing:
Library strategy: 4C-Seq
Reads were mapped by Novoalign (Novoalign V2.07; www.novocraft.com)  to the reference sequences NCBI37/mm9.
To visualize the data, we created files in bedGraph track format for the readcounts of each fragment or in a specified window of fragments.
The viewpoint, adjacent undigested fragment and fragments 10 kb up and downstream were removed.
4C-seq contacts were analyzed in the mouse region chr1:73000000-79000000. A range of 5 fragments was used to normalize the data per million reads (RPM) over a sliding window and display the continuous-valued data in the figures. Log2 ratios were calculated by dividing fragment reads between different samples.
Genome_build: mm9
Supplementary_files_format_and_content: Smoothed/normalized data (bedGraph).

source_name: distal forelimb E11.5

growth_protocol: E11.5 mouse embryos were collected in ice cold 10% FCS in PBS

extract_protocol:
4C-seq libraries were generated from microdissected tissues or cells as described previously (van de Werken et al., 2012). BglII or HindIII (6-bp cutters) were used as primary restriction enzymes. Csp6I or DpnII were used as secondary restriction enzymes. For each viewpoint, a total of 1.6 mg of each library was amplified in 8 or 16 PCR reactions, depending on PCR efficiencies. Samples were multiplexed and sequenced with Ilumina Hi-Seq technology. The following primers were used: Wnt6_promoter_forward: CTACACGACGCTCTTCCGATCTCCACAGATGCCTACATCAG, Wnt6_promoter_reverse: CAGACGTGTGCTCTTCCGATCTCAGTTGGACAGCCTTCTACC,  Ihh promoter_forward: CTACACGACGCTCTTCCGATCTCTTGCTCGGGATTCAGAT, Ihh_promoter_reverse: CAGACGTGTGCTCTTCCGATCTGCATGTCTAGCATGGTGGTA, mm1036_forward: CTACACGACGCTCTTCCGATCTACCTTATCTTGGCCTTCAA,  mm1036_reverse: CAGACGTGTGCTCTTCCGATCTCCATAACCCAGACTGAGATG, Epha4_promoter_forward: CTACACGACGCTCTTCCGATCTTGGCTTTTACCGAAAATAAA, Epha4_promoter_reverse: CAGACGTGTGCTCTTCCGATCTTCGTAGTCTAGGTGGAGGAA Pax3_promoter_forward: CTACACGACGCTCTTCCGATCTTTCTATCTCCCCATGACACC, Pax3_promoter_reverse: CAGACGTGTGCTCTTCCGATCTTCCTCCAAACGTGCTCTG
Samples were multiplexed and sequenced with Ilumina Hi-Seq technology according to the manufacturer´s protocol.

treatment_protocol: Distal forelimbs were microdissected and dissociated using a Trypsin solution (0.05%).

tag: strain

value: distal forelimb

tag: age

value: wild type

tag: 1st restriction enzymes

value: BglII

tag: 2nd restriction enzymes

tag: viewpoint


title: Bre98p9_H3K27ac_ChIPseq

value: Breast

value: vHMEC

tag: chip antibody


title: Epha4_WT_mm9

tag: genotype


title: LT

city: Cambridge

first: Kate

middle: Mariel

last: Broadbent

address: FAS Center for Systems Biology Northwest Building, room 469 52 Oxford Street

department: Systems Biology

institute: Harvard University

description: processed data files: PlasmoDBv10_Expression_FPKMs.txt, Significant_Features.xlsx, LncRNA_Properties.xlsx

data_processing:
We trimmed the last base from reads passing Illumina filtering (PF) using Picard release 1.94 (SamToFastq).
We then aligned reads from each sample to the PlasmoDBv10.0 reference genome using TopHat v2.0.9 and the following parameters: -r 300 –mate-std-dev 100 –library-type fr-firststrand –i 70 –I 5000 –read-mismatches 0 –segment-mismatches 0 –max-segment-intron 5000 –max-coverage-intron 5000 –b2-very-sensitive –read-gap-length 0 –read-edit-dist 0 –read-realign-edit-dist 0 –max-deletion-length 0 –max-insertion-length 0 –max-multihits 2 –no-mixed –no-discordant. These parameters specified an average fragment size of 300 bp with a standard deviation of 100 bp, strand-specific reads prepared using the dUTP method, and an expected intron size of 70-5,000 bp. Also, to allow only perfect read pair mapping in the expected orientation, and to report only two alignments for non-unique read pairs.
To remove non-unique reads, we then used SAMtools v0.1.19 (view –q 10) to remove read pairs with a mapping quality of 10 or less, meaning at least a 10% chance that the read pair truly came from somewhere else in the genome.
We used Cufflinks v2.1.1 to assemble aligned reads from each sample into transfrags using the following parameters: –library-type fr-firststrand –max-intron-length 5000 –overlap-radius 1 –min-isoform-fraction .25 –pre-mrna-fraction .25 –min-frags-per-transfrag 50 –trim-3-dropoff-frac .2 –frag-bias-correct. These parameters specified strand-specific reads prepared using the dUTP method and a maximum intron size of 5,000 bp. Also, to not merge transfrags, to filter minor isoforms less than 25% as abundant as the major isoform, to ignore intronic alignments if not as abundant as specified, to require at least fifty aligned reads per assembled transfrag, to trim the 3’ end of assembled transfrags at 20% of average coverage, and to run the built-in bias correction algorithm prior to estimating transcript abundance. We also specified a set of 374 short (<300 bp) and/or structural RNAs (such as tRNAs, rRNAs, and snoRNAs) to exclude from assembly and abundance estimation.
We used Cuffmerge to parsimoniously merge assembled transfrags from each sample into a final transcriptome assembly, incorporating PlasmoDBv10.0 annotated transcript models (RABT). In sum, annotation-assisted Cufflinks RABT assembly predicted 9434 transcripts, including 660 un-annotated intergenic transcripts (647 unique loci) and 474 antisense transcripts (467 unique loci). The 467 unique antisense loci overlapped 462 annotated genes in an approximately 1:1 ratio. This encompassed transcription of at least 73% of the P. falciparum genome, a 13% increase compared to annotation alone, and included the prediction of high-confidence antisense transcripts from 8% of annotated genes.
We used TransDecoder release 2013-11-17 to predict coding regions in the Cufflinks RABT transcriptome. TransDecoder identifies regions in spliced transcript models that likely encode peptides greater than 100 amino acids based on (1) a match to a Pfam domain above the noise threshold or (2) a log-likelihood score of a Markov model for coding DNA that is greater than zero and greatest when calculated in the predicted open reading frame. Using this approach, we predicted coding regions in 11 out of 660 intergenic transcripts (1.7%) and 7 out of 474 antisense transcripts (1.4%), versus 5213 out of 5229 assembled protein-coding transcripts at least 100 amino acids long (99.7%)
To assess differential expression and regulation of both the PlasmoDBv10.0 and the Cufflinks RABT transcriptomes, we used Cuffdiff v2.1.1 and the following parameters: –library-type fr-firststrand –time-series –min-reps-for-js-test 1. These parameters specified strand-specific reads prepared using the dUTP method, time-course samples, and to not require all conditions to be replicated. We also instructed Cuffdiff to compare samples from the 56-hour time-course harvested approximately 8 hours apart (T6 vs. T14, T14 vs. T24, T20 vs. T28, T24 vs. T32, T28 vs. T36, T32 vs. T40, T36 vs. T44, T40 vs. T48, T48 vs. TT8) and to estimate biological variation across the blood stage using the four replicated conditions. Specifically, we considered the correlation matrix between sample profiles and paired R with T14 and T20, ET with T28, LT with T32, and S with T40. We then supplied these replicated conditions to Cuffdiff as samples in addition to specifying the desired sample comparisons described above. Finally, we used the Benjamini and Hochberg method and a FDR cut-off of .05 to threshold significance. After removing chimeric results, our analysis of the Cufflinks RABT transcriptome predicted 3815 differentially expressed genes, 127 alternative splicing events, and 81 cases of alternative promoter usage. This included 354 significant intergenic lncRNA loci (out of 647) and 69 significant antisense loci (out of 467). [See PlasmoDBv10_Expression_FPKMs.txt, Significant_Features.xlsx, LncRNA_Properties.xlsx].
Genome_build: PlasmoDB 10.0
Supplementary_files_format_and_content: We generated Gene Transfer Format (gtf) files using either Cufflinks or TransDecoder. Fields are as specified by UCSC; The abundance measurement tab-delimited text file contains FPKM values estimated by Cuffdiff for the 5,777 PlasmoDBv10.0 annotated transcripts. Masked transcripts (short or structural RNAs) have FPKMs of zero in every sample; The .xlsx matrix tables list properties as specified in the headers of each worksheet for the 3815 differentially expressed genes, 127 alternative splicing events, 81 cases of alternative promoter usage, 660 intergenic lncRNAs, and 474 antisense transcripts predicted in the Cufflinks RABT transcriptome. We assembled transcripts using Cufflinks/Cuffmerge RABT and computed significance using Cuffdiff.
Supplementary_files_format_and_content: Processed data files [PlasmoDBv10_Expression_FPKMs.txt, Significant_Features.xlsx, LncRNA_Properties.xlsx] are linked as supplementary files on the Series record.

organism: Plasmodium falciparum

source_name: blood stage

growth_protocol: In each experiment, we cultured a freshly thawed P. falciparum strain 3D7 clone in human RBCs using standard methods. We maintained cultures at 4% hematocrit and supplemented RPMI-HEPES medium with 5% human serum (O+) and 5% Albumax II (Gibco).

extract_protocol:
We centrifuged 50 mL aliquots of harvested culture at 2400 rpm in a Sorval RT6000B to obtain at least 2 mL of packed RBCs per time-point. For time-course 1, we stored packed RBCs in 15 mL of Buffer RLT (with BME added) at -80°C prior to RNA extraction. For time-course 2, we lysed packed RBCs using a .05% saponin solution, washed liberated parasites using phosphate-buffered saline (pH 7.4), pelleted parasites at 13.2 RPM in a micro-centrifuge, and stored parasites in 1 mL of TRIZOL reagent at -80°C prior to RNA extraction. For time-course 1, we thawed RBC samples stored in Buffer RLT, added one volume of 70% ethanol, and immediately loaded the mixture onto RNeasy Midi columns (Qiagen). For time-course 2, we thawed parasite samples stored in TRIZOL reagent, performed TRIZOL-chloroform extraction, and immediately applied the aqueous layer to RNeasy Mini columns (Qiagen). During both RNeasy Midi and Mini RNA extraction procedures, we performed the optional on-column DNase I digestion for thirty minutes to remove genomic DNA. We stored isolated total RNA aliquots at -80°C with 1 unit/uL RNaseOUT (Invitrogen), and validated RNA quality using an Agilent Bioanalyzer RNA 6000 Pico Kit.
We began library preparation with a second DNase treatment (Ambion TURBO DNase) using 20 units of SUPERase-In (Ambion) and 40 units of RNaseOUT (Invitrogen) to protect RNA from degradation. Each DNase reaction was incubated at 25°C for 30 minutes followed by 1.8X RNAclean SPRI bead purification (Agencourt). Second, we used a Human/Mouse/Rat Ribo-Zero Magnetic Kit (Epicentre) to deplete 18S and 28S rRNA from DNase-treated total RNA. We used 3.5-5 ug of DNase-treated total RNA for all samples except T6, T14, and TT8. In these cases, we used .4 ug, 1 ug, and .7 ug of DNase-treated total RNA, respectively. Furthermore, for T6 we mixed 4 and 8 hpi total RNA 1:1, and for T14 we mixed 12 and 16 hpi total RNA 1:1. Third, we fragmented rRNA-depleted RNA at 85°C for 8 minutes using Mg2+ Fragmentation Buffer (New England Biolabs), followed by 1.8X RNAclean SPRI bead purification (Agencourt). Fourth, we reverse-transcribed the fragmented RNA using SuperScript III (Invitrogen), 200 ng/uL of freshly prepared Actinomycin D (Sigma-Aldrich), 3 ug of 76% AT-biased random hexamers (Integrated DNA Technologies), and a gradually ramping up thermocycler program. Specifically, we set the ramp speed of a PTC-225 DNA Engine Tetrad (MJ Research) to .1°C/second, and used the following program: 5°C, 10°C, 15°C, 20°C, 25°C, 30°C, 35°C for 5 minutes each, 42°C for 30 minutes, 45°C, 50°C, 55°C for 10 minutes each. We cleaned up first strand synthesis (FSS) reactions using both Micro Bio-Spin P-30 Rnase-free columns (Bio-Rad) and 1.8X RNAclean SPRI bead purification (Agencourt). Fourth, we performed second strand synthesis (SSS) using a biased dACG-TP/dU-TP mix (Fermentas), 10 units of E. coli DNA ligase (Invitrogen), 160 units of E. coli DNA polymerase (Invitrogen), and 2 units of E. coli RNase H (Invitrogen), followed by 1.8X AmpureXP SPRI bead purification (Agencourt). Fifth, we used an Illumina series KAPA Library Preparation Kit (Kapa Biosystems) and barcoded Y-adapters developed by the Broad Institute to end repair, A-tail, and ligate adapters to each library. We added adapters in approximately 15-fold excess of library targets, and removed un-ligated adapters and adapter-dimers using 1.0X AmpureXP SPRI bead purification (Agencourt). Sixth, we digested the dUTP-marked second strand at 37°C for 30 minutes, followed by 25°C for 15 minutes, using Uracil-Specific Excision Reagent (USER) enzyme (New England Biolabs). Seventh, we amplified libraries for as few cycles as necessary using a KAPA Real-Time PCR Library Amplification Kit (Kapa Biosystems) and PCR primers developed by the Broad Institute. Each library except for T6, T14, and TT8 required only four PCR cycles, while T14 and TT8 required eight PCR cycles, and T6 required twelve PCR cycles. Following a 2 minute denaturation step at 98°C, we cycled libraries using an ABI 7900 Real-Time PCR machine and the following 2-step program: (1) denaturation at 98°C for 20 seconds, (2) annealing and extension at 55°C for 190 seconds. Finally, we quantified libraries using a KAPA Library Quantification Kit (Kapa Biosystems) and combined barcoded libraries into two pools. We sequenced each pool on an Illumina Hiseq machine (one lane per pool) using 101-bp, paired-end read technology. We prepared the fifteen libraries used in this study in parallel (except for real-time amplification).

treatment_protocol: We synchronized cultures using multiple 5% sorbitol solution treatments, and expanded cultures to accommodate harvesting of at least 50 mL of culture at each planned time-point (time-course 1: every ~4 hours for 56 hours; time course 2: ~4 hours before and after the ring to trophozoite and trophozoite to schizont morphological stage transitions).

tag: developmental stage

value: late trophozoite


title: S

value: schizont


title: R

value: ring


title: ET

value: early trophozoite


title: T48

value: 48 hpi


title: T44

value: 44 hpi


title: T40

value: 40 hpi


title: T36

value: 36 hpi


title: dFB_N_02

city: Fribourg

first: Rüegg

last: Curzio

address: Albert-Gockel 1

department: Département de Médecine 3

country: Switzerland

institute: Université de Fribourg

data_processing:
Sequencing data was processed using the Illumina Pipeline Software version 1.82.
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.3, Martin 2011) and filtered for low complexity with seq_crumbs (v. 0.1.8).
Reads were aligned against Homo sapiens.GRCh38.76 genome using STAR (v. 2.4.0f1, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1, Anders et al. 2014) using Homo sapiens.GRCh38.76 gene annotation.
Genome_build: Homo sapiens.GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include gene counts for each Sample.

source_name: Dermal Normal Fibroblasts

growth_protocol: After sample dissociation, cells were grown for 4-7 passages (to confluency) on plastic dishes from NUNC in corresponding medium (DMEM for fibroblasts, M199 for HUVECs)

extract_protocol:
Machery-Nagel mRNA NucleoSpin was used following manufacturer's instructions
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA protocol

treatment_protocol: Medium was removed, cells were washed with ice cold PBS and harvested on ice in lysis buffer

tag: tissue source

value: skin

value: Fibroblast

tag: cell subtype

value: Dermal Normal Fibroblasts


title: HU_02

source_name: HUVEC

value: Human Umbilical Vein Cell

tag: passage

value: control HUVEC


title: cFB_T_03

source_name: Colon Tumor Fibroblasts

value: colon tumor

value: Colon Tumor Fibroblasts


title: cFB_T_02


title: cFB_N_03

source_name: Colon Normal Fibroblasts

value: normal colon

value: Colon Normal Fibroblasts


title: T24

value: 24 hpi


title: dFB_N_01


title: cFB_T_01


title: T28

value: 28 hpi


title: cFB_N_02


title: HU_03


title: T20

value: 20 hpi


title: T6

value: 6 hpi


title: T32

value: 32 hpi


title: T14

value: 14 hpi


title: TT8

value: TT8 hpi


title: Chicken-DT40-Lig4

city: Charlottesville,

first: Anindya

last: Dutta

email: ad8q@virginia.edu, pk7z@virginia.edu

state: VA

address: Room no. 1232, Jordan Hall

department: MD-BIOC BC/Mole Genetics~School of medicine

institute: University of Virginia

description:
Circular DNA
Extrachromosomal circular DNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Identification of microDNA by paired-end sequencing of MDA products: microDNA were computationally identified by two different methods: Island method and split read method (in-house developed). All sequence tags were mapped on the reference genome (build mm10 for mouse and hg19 for human galGal4 for chicken) by using the Novoalign software. Only those paired tags that could be mapped uniquely and in opposite orientation to each other were considered for the identification of islands in the "island method". The sequence coverage of each base pair was profiled for each chromosome, and islands (potential circles) delineated where there were two consecutive sequenced bases. In other words an "island" is a contiguous portion of the genome where a cluster of PE-tags were mapped uniquely and in the opposite orientation to its pair. Paired End tags that had one tag mapping uniquely to an island, while the other was unmapped but passed the sequence quality filter, were considered separately for the validation of circles. We generated a database of hypothetical junctional tags that could be created by ligation of the ends of islands to generate circles. The unmapped tags described above were matched against these hypothetical junctional tags. If the mapped tag of a PE read falls in an island and the un-mapped tag matches with a hypothetical junctional tag generated by ligation of the ends of the island, we annotated that island as a circle. This approach underestimates the number of true microDNAs because further sequence coverage is likely to reveal more junctional tags ligating the ends of islands. The "split read" method extracted the paired end tags where one end was mapped (M) and other end was un-mapped (UM) but had good base quality score. The UM tags were split into two equal halves and mapped individually by using Novoalign software. Those split pairs which were mapped on the same strand (F-F or R-R) with no mismatch were considered for the identification of circles.  The "Island method" and the "split-read method" both are dependent on the junctional tags for the identification of circles. >80% of the circles were identified by both algorithms. The "Island method" failed to detect circles 1) with low base coverage, 2) with the start and the end of the circle contaminated by reads from contaminating linear DNA or lost due to sequencing errors and 3) that were overlapping with each other. On the other hand the "Split-read method" failed to detect circles if the two split reads do not map uniquely to the genome. Processed data include the microDNA co-ordinate (chromosome name, start position of circle and end position of circle) mm9 assembly for mouse and hg19 assembly for human samples. The fourth column in the processed data is base pair coverage (abundance).
Genome_build: mm10 for mouse and hg19 for human galGal4 for chicken
Supplementary_files_format_and_content: Processed data include the microDNA co-ordinate (chromosome name, start position of circle and end position of circle) mm10 assembly for mouse, hg19 assembly for human and galGal4 for chicken samples. The fourth column in the processed data is base pair coverage (abundance).

molecule: other

organism: Gallus gallus

source_name: DT40-Chicken cell line-mutated Lig4

extract_protocol: Nuclei were extracted from tissues and cell lines. All the reagents used were pre-chilled and the entire procedure was performed on ice. Tissues and cells were homogenized by douncing 50 times in 10 mL of Nuclear Extraction Buffer. After homogenization, samples were layered on 18 mL of Sucrose Cushion in 40 mL ultracentrifuge tubes (Beckman, 25 × 89 mm, 344058) and spun at 30,000 x g for 45 min at 4°C (Beckman, L8-70M, SW28 rotor). Supernatant, including debris, was removed, and 200 μl of chilled 1 × PBS was added to the tube. After 20 min incubation on ice, the nuclei were dissociated by pipetting, and recovered by centrifugation at 500 x g for 5 min.

tag: cell line


title: Chicken-DT40-Rad54

description:
Genomic DNA
Extrachromosomal circular DNA

source_name: DT40-Chicken cell line-mutated Rad54


title: Chicken-DT40-WT

source_name: DT40-Chicken cell line-mutated WT


title: Chicken-DT40-NBS1

source_name: DT40-Chicken cell line-mutated NBS1


title: Chicken-DT40-Ku70

source_name: DT40-Chicken cell line-mutated Ku70


title: Chicken-DT40-CtIP

source_name: DT40-Chicken cell line-mutated CtIP


title: Chicken-DT40-BRCA1

source_name: DT40-Chicken cell line-mutated BRCA1


title: HU_01


title: dFB_N_03


title: YPS163 Biological Replicate 2

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425-G Henry Mall

institute: University of Wisconsin - Madison

data_processing:
Sequencing reads were processed with Trimmomatic version 0.30
Trimmed sequencing reads were mapped to a reference genome with strain-specific SNPs (for YPS163, YPS1009, NCYC110, NCYC3290, and W303) or to the S288c reference 58 for all other strains, using BWA version 0.7.3
HTseq version 0.5.4 was used to sum read counts per gene
Read counts per gene were normalized for gene size and the number of reads generated per library via RPKM
Genome_build: reference genome with strain-specific SNPs (for YPS163, YPS1009, NCYC110, NCYC3290, and W303) or to the S288c reference 58 for all other strains
Supplementary_files_format_and_content: Tab-delimited text file includes RPKM values for each sample

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae cells

growth_protocol: All strains were grown in YPD for 7-10 generations to OD600 ~0.3

extract_protocol:
RNA was extracted with hot phenol protocol; RNA was rRNA-depleted with Epicentre's Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat)
cDNA library was prepared with Epicentre's Script-seq V2 H/M/R Complete Kit (Human/Mouse/Rat)

tag: strain id

tag: wild or lab strain

value: wild

tag: ploidy

value: diploid

tag: euploid or aneuploid

value: euploid


title: Bre98p4_H3K36me3_ChIPseq

source_name: Human Mammary Epithelial Cell Line

tag: tissue

value: Breast

tag: growth phase

value: HMEC

value: Anti-Histone H3 (tri methyl K36), abcam, #ab9050-100


title: YPS1009_ChrXII.3n Biological Replicate 3

value: aneuploid


title: YPS1009_ChrXII.3n Biological Replicate 2


title: YPS163 Biological Replicate 1


title: YPS1009_ChrXII.2n Biological Replicate 3


title: YPS1009_ChrXII.4n Biological Replicate 3


title: YPS1009_ChrXII.4n Biological Replicate 1


title: YPS1009_ChrXII.4n Biological Replicate 2


title: cFB_N_01

tag: cell type

value: Fibroblast


title: YPS1009_ChrXII.2n Biological Replicate 2


title: leaf

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

country: China

institute: Yunnan Agricultural University

data_processing:
Reads with low scored nucleotids < 15 were removed.
3' adapters were removed and the small RNA sequences were extracted from the raw reads.
5' barcodes GT were removded.
The reads with at least 18nt were maintained in the final results.
The unique sequences and their counts were calculated from the extracted sequences.
Genome_build: The obtained unique sequences were aligned to the genome of Cicer arietinum,  GenBank Assembly ID: GCA_000347275.1.
Supplementary_files_format_and_content: unique sequence and count

organism: Cicer arietinum

source_name: pooled leaf tissue

growth_protocol: The chickpeas were grown in soil under glass house conditions with a temp of 25C/21c (day/night)

extract_protocol:
Total RNA was isolated from selected tissues using TRIzol reagent with the manufacture's protocol.
Small RNA libraries were prepared by following the Illumina's protocol.

treatment_protocol: No treatment

value: leaf


title: YJM428 Biological Replicate 1


title: wildtype H37Rv experiment 2 replicate 2

city: Worcester

first: Scarlet

last: Shell

address: 60 Prescott St

department: Biology and Biotechnology

institute: Worcester Polytechnic Institute

description:
library construction: RNAseq strand-specific expression library
supplementary file: Shell experiment 2 expression RPKM.txt

data_processing:
Data were de-multiplexed and Ssaha2 was used to map and create SAM and BAM files
Read pairs that were not correctly oriented with respect to each other were filtered out, unpaired reads were filtered out, and the region encoding the rRNA was filtered out
For expression libraries, coverage at each genome coordinate on each strand was determined using Samtools and Mpileup. Missing values were replaced with 0.
For expression libraries, RPKMs were calculated from BAM files using Artemis
1st nt identification (5' end mapping libraries only): The first nt of each "read 1" was extracted from BAM files, and 1st nt coverage at each position on each strand was determined.
5' end calling (5' end mapping libraries only): for any position with a 1st nt read depth greater than 10 times the 1st nt read depth at the position 10 nt before OR 10 nt after on the same strand, a 5' end was reported in table "Shell 5 prime end mapping coverage peaks".
Genome_build: NC_000962
Supplementary_files_format_and_content: RPKM files contain RPKM data from RNAseq expression libraries
Supplementary_files_format_and_content: Expression coverage files contain mapped read depth at each genome coordinate from RNAseq expression libraries
Supplementary_files_format_and_content: 5-prime-end peak files contain read depth at each RNA 5' end identified in 5' end mapping libraries

organism: Mycobacterium tuberculosis

growth_protocol: Cultures were grown to log phase (OD 0.5-1) in 7H9 supplemented with OADC, 0.05% Tween-80, and 0.2% glycerol in roller bottles

extract_protocol:
Cultures were inactivated with RNAlater, disrupted with bead-beating in the presence of Trizol, and total RNA was extracted according to the manufacturer's instructions. RNA was then treated with Dnase and re-purified with RNeasy.
Expression libraries were constructed using either the dUTP method or a ligation-based method to maintain strand specificity. 5' end mapping libraries were constructed by direct ligation of adapters to RNA 5' ends after differential treatment with or without 5' polyphosphatase.

tag: strain

tag: growth condition

value: aerobic log phase


title: YPS1009_ChrXII.2n Biological Replicate 1


title: YPS1009_ChrXII.3n Biological Replicate 1


title: wildtype H37Rv experiment 2 replicate 1


title: wildtype H37Rv experiment 2 replicate 3


title: YJM308 Biological Replicate 2


title: YJM308 Biological Replicate 1


title: Y2209 Biological Replicate 2


title: Chicken-DT40-BRCA2

source_name: DT40-Chicken cell line-mutated BRCA2


title: YPS163 Biological Replicate 3


title: Y2189 Biological Replicate 1


title: Y2189 Biological Replicate 2


title: NCYC3290 Biological Replicate 3


title: NCYC3290 Biological Replicate 2


title: NCYC3290 Biological Replicate 1


title: YJM428 Biological Replicate 2


title: Y2209 Biological Replicate 1


title: flower

source_name: pooled flower tissue

value: flower


title: NCYC110_ChrVIII.4n Biological Replicate 3


title: NCYC110_ChrVIII.3n Biological Replicate 3


title: NCYC110_ChrVIII.4n Biological Replicate 2


title: NCYC110_ChrVIII.2n Biological Replicate 3


title: NCYC110_ChrVIII.3n Biological Replicate 2


title: NCYC110_ChrVIII.2n Biological Replicate 1


title: NCYC110_ChrVIII.2n Biological Replicate 2


title: W303_ChrXII.4n Biological Replicate 3

value: lab


title: W303_ChrXII.4n Biological Replicate 2


title: W303_ChrXII.4n Biological Replicate 1


title: W303_ChrXII.3n Biological Replicate 2


title: W303_ChrXII.2n Biological Replicate 3


title: W303_ChrXII.3n Biological Replicate 1


title: W303_ChrXII.3n Biological Replicate 3


title: W303_ChrXII.2n Biological Replicate 2


title: K10 Biological Replicate 1


title: K9 Biological Replicate 1


title: W303_ChrXII.2n Biological Replicate 1


title: Mouse-AMThymus.Rep1

source_name: 6 Months old adult mice

value: Thymus


title: K1 Biological Replicate 1


title: Mouse-AMSpleen.Rep1

value: Spleen


title: Mouse-AMSperm.Rep1

value: Sperm


title: Mouse-AMSMuscle.Rep1

value: Skeletal Muscle


title: NCYC110_ChrVIII.3n Biological Replicate 1


title: Mouse-AMLiver.Rep1

value: Liver


title: NCYC110_ChrVIII.4n Biological Replicate 1

value: wild


title: Mouse-AMKidney.Rep1

value: Kidney


title: Mouse-AMBrain.Rep1

value: Brain


title: Mouse-AMHeart.Rep1

value: Heart


title: wildtype H37Rv experiment 1 replicate 2 5' end mapping library without triphosphate conversion

description:
library construction: RNAseq 5' end mapping library. There was no treatment to 5' ends before adapter ligation.
supplementary file: Shell 5 prime end mapping coverage peaks.txt


title: wildtype H37Rv experiment 1 replicate 2 5' end mapping library with triphosphate conversion

description:
library construction: RNAseq 5' end mapping library. 5' triphosphates were converted to 5' monophosphates before adapters were ligated to RNA 5' ends.
supplementary file: Shell 5 prime end mapping coverage peaks.txt


title: wildtype H37Rv experiment 1 replicate 2 expression library

description:
library construction: RNAseq strand-specific expression library
supplementary file: Shell experiment 1 expression RPKM.txt


title: Human-PC-3


title: s_5_CB9_input.fastq.gz

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description: Sample 4

data_processing:
Libraries were sequenced on an Illumina GAIIx using the default RTA analysis software.
The reads were aligned using the allele-specific alignment pipeline (ASAP; http://www.bioinformatics.babraham.ac.uk/projects/ASAP/) utilising the Bowtie short read aligner. Briefly, each read was simultaneously aligned to BL6 and Cast genome sequences and best alignments for each genome were reported. Sequences that aligned equally well to both genomes were put into common alignments, others were partitioned into either BL6 or Cast genome specific alignments depending on the number of mismatches to the two genome sequences. Sequences having more than one chromosomal alignment (non-unique) were discarded and up to a maximum of one mismatch was tolerated. The Mus musculus cast genome was constructed by injecting 20,443,889 SNPs into the BL6 reference genome. SNPs were sourced from the Biomart Mus musculus variation database (dbSNP128, Ensembl) (6,270,609) and further complemented by 17,259,893 high-confidence flagged SNPs in the Sanger mouse strain database (data was downloaded from the Mouse Genomes Project page (http://www.sanger.ac.uk/resources/mouse/genomes/). We excluded SNPs close to indels, repeat element or those having two possible base calls for each genome. In order to reduce potential biases towards the reference BL6 genome assembly arising from falsely annotated SNPs, a condition was applied where each SNP had to have at least one BL6- and one Cast- specific read being aligned to it from across all four sequenced libraries (2 ChIPs & 2 inputs).
Genome_build: NCBIM37
Supplementary_files_format_and_content: text file cotaining chromosome (column 1), start (column 2) and end (column 3) positions of all called peaks, as well as a number of different fields detailing the allel-specific nature of the peaks (obvious from the column titles).

source_name: ES cells_input

growth_protocol: Reciprocal hybrid mouse ES cells were cultured in N2B27 media supplemented with 500 U/ml LIF, 1µM PD0325901 and 3 µM CHIR99021 (2i) to maintain ground state pluripotency. Monolayer neural differentiation was induced by withdrawal of 2i and LIF supplements. Derived Neural Stem Cells (NSCs) were maintained in RHB-A media supplemented with10 ng/ml of FGF-2 and EGF.

extract_protocol:
ChIP assays were performed using formaldehyde cross-linked chromatin isolated from ten 10 cm dishes of hybrid ES cells grown to ~70% confluency. Crosslinking was performed by adding formaldehyde to cell media in the dish to a final concentration of 1% and incubation at room temperature for 10 minutes. The reactions were stopped with glycine to a final concentration of 125 mM. The cells were washed in PBS and re-suspended in cell lysis buffer (0.25 % Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH 8.0) to isolate nuclei. Chromatin was extracted in nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 0.5 % SDS) and sheared to an average size of 200-500 bp using Bioruptor sonicator. Chromatin from ~5x106 cells was diluted 5 fold with IP buffer (1.1 % TX-100, 1.2 mM EDTA, 16.7 mM Tris pH 8.1, 167 mM NaCl) and pre-cleared with 10 µg non-immune rabbit IgG and 50 µl of protein A magnetic beads for 3 hours at 4˚C on a rotating wheel. Anti-Zfp57 antibody (4 µg, Abcam ab45341) was added to pre-cleared chromatin and incubated overnight at 4˚C on a rotating wheel. Chromatin was precipitated with protein magnetic A beads (25 µl slurry in X-ChIP) for further 3 hours at 4 oC with rotation. The beads were washed in each of the following:  buffer 1 (1% Triton X-100, 0.1% SDS, 2 mM EDTA, 150 mM NaCl and 20 mM Tris pH 8), buffer 2 (1% Triton X-100, 0.1% SDS, 2 mM EDTA, 500 mM NaCl and 20 mM Tris pH 8), buffer 3 (0.25 M LiCl, 1% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA, 10 mM Tris pH 8) and twice with TE buffer (10 mM Tris pH 8, 1 mM EDTA). The bound chromatin was eluted into elution buffer (1% SDS, 0.1 M NaHCO3), crosslinks reversed and protein digested. DNA was extracted by phenol/chloroform and ethanol precipitated in the presence of 10 µg of glycogen. One tenth of ChIP reactions was used for qPCR and SNP-Pyrosequencing analysis to control for ChIP efficiency. The remainder was used for Illumina library preparation.
Sequencing libraries were prepared from ~10ng of ChIP and 1 µg of input DNA using NEBnext® kit (E6260, NEB) according to manufacturer's protocol. The PCR amplified library was purified using Agencourt AMPure magnetic beads and gel size selected for 150-400 bp. Each ChIP and input libraries were sequenced from a single end to a length of 40nt on individual lanes of an Illumina Genome Analyzer IIx.

value: Cast/EiJ x C57BL/6J

value: hybrid ES cells


title: s_4_BC8_input.fastq.gz

description: Sample 3

value: C57BL/6J x Cast/EiJ


title: Human-OVCAR8


title: s_2_BC8_Zfp57.fastq.gz

description: Sample 1

source_name: ES cells_Zfp57 ChIP-seq

value: Anti-Zfp57 antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: wildtype H37Rv experiment 1 replicate 1 5' end mapping library with triphosphate conversion

value: aerobic log phase


title: s_3_CB9_Zfp57.fastq.gz

description: Sample 2

tag: chip antibody


title: Mouse-AMTestis.Rep1

value: Testis


title: wildtype H37Rv experiment 1 replicate 1 expression library


title: Human-C4-2


title: Human-ES2


title: IHH_DupP1_hg19

data_processing:
Library strategy: 4C-Seq
Reads were mapped by Novoalign (Novoalign V2.07; www.novocraft.com)  to the reference sequences GRCh37/hg19.
To visualize the data, we created files in bedGraph track format for the readcounts of each fragment or in a specified window of fragments.
The viewpoint, adjacent undigested fragment and fragments 10 kb up and downstream were removed.
4C-seq contacts were analyzed in the human region chr2:217000000-225000000. A range of 5 fragments was used to normalize the data per million reads (RPM) over a sliding window and display the continuous-valued data in the figures. Log2 ratios were calculated by dividing fragment reads between different samples.
Genome_build: hg19
Supplementary_files_format_and_content: Smoothed/normalized data (bedGraph).

source_name: human adult fibroblasts

growth_protocol: Skin fibroblasts were cultured in DMEM (Lonza) supplemented with 10% fetal calf serum (Gibco), 1% ultraglutamine (Lonza) and 1% penicillin/streptomycin (Lonza).

extract_protocol:
4C-seq libraries were generated from microdissected tissues or cells as described previously (van de Werken et al., 2012). BglII or HindIII (6-bp cutters) were used as primary restriction enzymes. Csp6I or DpnII were used as secondary restriction enzymes. For each viewpoint, a total of 1.6 mg of each library was amplified in 8 or 16 PCR reactions, depending on PCR efficiencies. Samples were multiplexed and sequenced with Ilumina Hi-Seq technology. The following primers were used: WNT6_promoter_forward: CTACACGACGCTCTTCCGATCTGCAGCACTCACTCTAGCC, WNT6_promoter_reverse: CAGACGTGTGCTCTTCCGATCTGTTCGGAACCCAGACAGT, IHH_promoter_forward: CTACACGACGCTCTTCCGATCTAGAGTTGTTGAAAGGGTTAAAA, IHH_promoter_reverse: CAGACGTGTGCTCTTCCGATCTCTTGTCTGGTTGTGGCTTAC, PAX3_promoter_forward: CTACACGACGCTCTTCCGATCTGATGAATGTTCAAACCCAGAT, PAX3_promoter_reverse: CAGACGTGTGCTCTTCCGATCTGCGTGGAGTCAGAAGGAGT
Samples were multiplexed and sequenced with Illumina Hi-Seq technology according to the manufacturer´s protocol.

treatment_protocol: Single cell suspension was generated using a Trypsin solution (0.05%).

value: fibroblasts

tag: age

value: adult

tag: genotype

value: duplication P1

tag: 1st restriction enzymes

value: HindIII

tag: 2nd restriction enzymes

value: DpnII

tag: viewpoint

value: IHH


title: IHH_Control_hg19

value: control


title: WNT6_Control_hg19

value: BglII


title: WNT6_DupF2_hg19

value: duplication F2


title: PAX3_DelB1_hg19

value: deletion B1


title: PAX3_Control_hg19


title: Mouse-AMLung.Rep1

value: Lung


title: AA+GSK-J4

city: White Plains

first: Mary

middle: E

last: Donohoe

address: 785 Mamaroneck

department: Burme Medical Research Institute

institute: Weill Cornell Medical College

description: total RNA

data_processing:
TopHat2 was used with default setting to map the sequence tags after removal of duplicates.
Fragments Per Kilobase of exon per Million base reads (FPKM) was calculated as described in the manuscript
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and statistics for differential gene expression

source_name: Female ES cells_L-ascorbic acid_and_GSK-J4

growth_protocol: LF2 female ESCs were cultured on the feeder cells and passed twice without feeder before treatments.

extract_protocol:
Total RNA was extracted using TRIzol reagent and RNeasy column (Qiagen) was used for purification.
The Illumina TrueSeq DNA Sample Prep Kit was used for library construction.

treatment_protocol: LF2 ESCs were cultured with DMSO or GSK-J4 (10 µM) in the absence or presence of 50 µg/ml of L-ascorbic acid (AA) for 24 hr.

tag: cell line

tag: gender

value: female

value: embryonic stem cells


title: PBS+GSK-J4

description: total RNA

source_name: Female ES cells_GSK-J4


title: AA+DMSO

description: total RNA

source_name: Female ES cells_L-ascorbic acid_and_DMSO


title: PBS+DMSO

description: total RNA

source_name: Female ES cells_DMSO


title: PKR_WT_PA_C

city: Salt Lake City

first: Osama

middle: A

last: Youssef

state: UT

address: 15 N medical Dr

institute: University of Utah

description: immunoprecipitated RNA

data_processing:
CASAVA 1.7.0 and CASAVA 1.8.2 were used for basecalling
Reads were aligned to the mm9 genome assembly using Novoalign (Novocraft) with default parameters except greater than or equal 100 alignments per read was allowed
Aligned reads were analyzed with USeq (www.sourceforge.net/projects/Useq). FPKM and RPKM were calculated using DRDS and DRSS applications respectively from Useq package
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM or RPKM values for each Sample

source_name: embryonic fibroblasts

extract_protocol:
Immunoprecipitations were performed on cell lysate and IPed RNAs were extracted using Trizol
Illumina small TruSeq RNA sample preparation kit was used after RNA fragmentation

treatment_protocol: 0.1 mM palmitic acid

value: MEF

value: Wildtype

tag: cell treatment

value: 0.1 mM palmitic acid


title: wildtype H37Rv experiment 1 replicate 1 5' end mapping library without triphosphate conversion

value: aerobic log phase


title: PKR_WT_C

description: immunoprecipitated RNA

value: Mock


title: PKR_RM3_PA_B

description: immunoprecipitated RNA

value: PKR dsRBD mutant


title: Chicken-DT40-MSH3

source_name: DT40-Chicken cell line-mutated MSH3


title: PKR_RM2_PA_B

description: immunoprecipitated RNA


title: PKR_RM1_PA_B

description: immunoprecipitated RNA


title: PKR_RM_C

description: immunoprecipitated RNA


title: Human-LnCap

source_name: Human-LnCap

value: Human-LnCap


title: PKR_RM3_B

description: immunoprecipitated RNA


title: PKR_RM_PA_C

description: immunoprecipitated RNA


title: PKR_RM1_B

description: immunoprecipitated RNA


title: PKR_WT3_PA_B

description: immunoprecipitated RNA


title: RNAi_rep3_zt15

city: Waltham

first: Sebastian

last: Kadener

address: 415 South Street

institute: Brandeis University

description:
3' RNA-seq
processed data file: RNAi_data_all_final.csv

data_processing:
Removal of rRNA reads using alignment to drosophila rRNA reference with bowtie
Tophat alignment to Drosophila genome dm3
Quantification of the signal in each annotated transcript (at the 3' end) by normalized read counts.
Genome_build: dm3
Supplementary_files_format_and_content: .csv files with list of transcripts and the RNA-seq quantification of each sample.

extract_protocol:
Fly heads of the indicated genotypes were collected and RNA was extracted using TRI reagent (SIGMA).
RNA-seq libraries were prepared as previously described (Engreitz et al., 2013) by performing polyA selection after fragmentation.

value: head

tag: genotype/variation

value: cabut RNAi  (Tim-gal4, UAS-cbt RNAi)

tag: time


title: RNAi_rep3_zt23

tag: tissue


title: PKR_WT1_PA_B

description: immunoprecipitated RNA

tag: cell type


title: RNAi_rep3_zt19


title: RNAi_rep3_zt3


title: PKR_RM2_B

description: immunoprecipitated RNA


title: RNAi_rep3_zt7


title: PKR_WT2_B

description: immunoprecipitated RNA


title: RNAi_rep2_zt7


title: PKR_WT3_B

description: immunoprecipitated RNA


title: RNAi_rep2_zt3


title: PKR_WT1_B

description: immunoprecipitated RNA


title: RNAi_rep3_zt11


title: RNAi_rep2_zt23


title: RNAi_rep2_zt19


title: PKR_RM3_PA_A

description: immunoprecipitated RNA


title: PKR_RM1_PA_A

description: immunoprecipitated RNA


title: RNAi_rep2_zt11


title: RNAi_rep2_zt15


title: RNAi_rep1_zt7


title: PKR_WT2_PA_B

description: immunoprecipitated RNA


title: PKR_RM3_A

description: immunoprecipitated RNA


title: PKR_RM2_A

description: immunoprecipitated RNA


title: RNAi_rep1_zt3


title: RNAi_rep1_zt23


title: PKR_WT3_PA_A

description: immunoprecipitated RNA


title: PKR_WT1_PA_A

description: immunoprecipitated RNA


title: PKR_RM1_A

description: immunoprecipitated RNA


title: PKR_WT3_A

description: immunoprecipitated RNA


title: RNAi_rep1_zt15


title: PKR_WT2_PA_A

description: immunoprecipitated RNA


title: RNAi_rep1_zt11


title: OE_rep2_zt7

description:
3' RNA-seq
processed data file: OE_data_all_final.csv

value: cabut OE (Tim-gal4; UAS-cbtFLAG)


title: PKR_WT1_A

description: immunoprecipitated RNA


title: Wnt6_WT_mm9

source_name: distal forelimb E11.5

tag: strain

value: distal forelimb

value: wild type


title: Wnt6_InvF_mm9

value: InvF

value: BglII


title: OE_rep2_zt19


title: OE_rep2_zt23


title: OE_rep2_zt15


title: PKR_RM2_PA_A

description: immunoprecipitated RNA


title: OE_rep1_zt7


title: Pax3_DelB_mm9

value: DelB


title: RNAi_rep1_zt19


title: mm1036_InvF_mm9


title: mm1036_DelBs_mm9

value: DelBs


title: OE_rep1_zt3


title: OE_rep1_zt23


title: PKR_WT2_A

description: immunoprecipitated RNA


title: mm1036_Dbfs_mm9

value: Dbfs


title: Ihh_WT_mm9

value: Ihh


title: mm1036_DelB_mm9


title: OE_rep1_zt11


title: conRNAi_rep3_zt3

value: control for cabut RNAi (Tim-gal4;UAS-Dcr2)


title: OE_rep2_zt3


title: mm1036_Dbf_mm9

value: Dbf


title: OE_rep2_zt11


title: Pax3_DelBs_mm9


title: Pax3_WT_mm9


title: conRNAi_rep3_zt19


title: Ihh_Dbf_mm9


title: conRNAi_rep3_zt15


title: WT_rep2

data_processing:
Reads were mapped to the mouse reference genome (mm10) using the STAR mapper (Dobin et al., 2013) (splice junctions based on RefSeq ;options: --alignIntronMin 20 --alignIntronMax 500000 --outFilterMismatchNmax 10).
More than 87% of read pairs mapped uniquely and these reads were subsequently used for expression analysis via the Cufflinks package (Trapnell et al., 2012) (version 2.2.1; default settings).
In a first step, transcripts of each sample were assembled using Cufflinks provided with reference gene annotations from Ensembl. The resulting assemblies were then merged via Cuffmerge and finally differential gene expression was determined by applying Cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: Density file (bigWig)

extract_protocol:
Tissue samples were lysed (RLT +2-mercaptoethanol, Qiagen), and RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol.
Sequencing libraries were prepared from total RNA (300 ng), multiplexed and sequenced with Ilumina Hi-Seq technology according to the manufacturer´s protocol (TruSeq RNA Sample Prep ,Ver. A).

treatment_protocol: E11.5 distal limbs were microdissected from wild type or mutant embryos


title: WT_rep1


title: InvF_rep2

value: InvF/InvF


title: conRNAi_rep3_zt23


title: OE_rep1_zt15


title: C6 [adult male]

city: Swansea

first: Tamsyn

last: Uren Webster

address: Wallace Building

institute: Swansea University

data_processing:
The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit) was used to clip Illumina adapter sequences and to trim the first 12 bp at the 5’ end.
Quality trimming of the 3' end of the reads using a sliding window  trimmer was performed (http://wiki.bioinformatics.ucdavis.edu/index.php/Trim.slidingWindow.pl).
Digital normalisation using khmer (Brown et al. 2012, arXiv:1203.4802 [q-bio.GN]) was performed, and retained reads were paired using a custom script.
De novo transcriptome assembly was performed using Trinity (version R2013-02-25; (Grabherr et al. 2011))
Transcripts were annotated using Blast and all available Ensembl cDNA sequences for zebrafish (Danio rerio), medaka (Oryzias latipes), nile tilapia (Oreochromis niloticus), stickleback (Gasterosteus aculeatus), human and mouse (Release 71), RefSeq RNA, non-redundant nucleotides (nt) and proteins (nr) databases. Top hits with an e-value of < 1e-15 were retained. When no annotation could be found, the Trinity-generated transcript ID was given.
Sequence reads were mapped against the transcriptome assembly using Bowtie2 (version 2.1.0, (Langmead and Salzberg 2012)), using the -k 1 parameter. Count data was extracted using idxstats in samtools (version 0.1.18, (Li et al. 2009)) and differential expression analysis was conducted in edgeR (Robinson et al. 2010).
Genome_build: n/a
Supplementary_files_format_and_content: The edgeR results file for each treatment group versus the control group was merged with the annotation results, and is provided in a tab delimited text file. For each transcript, raw count data for each replicate is included together with the log fold change, P values and FDR values from the expression analysis for that treatment.

organism: Salmo trutta

extract_protocol:
Liver samples were snap frozen with liquid nitrogen and stored at -80 C. Total RNA was extracted using Quiagen RNeasy columns
Libraries were constructed with Illumina TruSeq RNA sample preparation kit.

treatment_protocol: Fish were exposed to three concentrations of each chemical for 14 days using a flow-through system

tag: developmental stage

value: adult

tag: Sex

value: male

tag: exposed to

value: water (control) for 4 days

value: liver


title: OE_rep1_zt19

value: head


title: C5 [adult male]


title: InvF_rep1


title: conRNAi_rep3_zt7


title: C4 [adult male]


title: conRNAi_rep2_zt3


title: conRNAi_rep2_zt23


title: DelB_rep1

value: DelB/+


title: C3 [adult male]


title: conRNAi_rep2_zt7


title: Ihh_Dbfs_mm9

value: distal forelimb


title: C1 [adult male]


title: DelB_rep2


title: Dbf_WT_rep2

value: wild type


title: conRNAi_rep2_zt15


title: conRNAi_rep2_zt11


title: Dbf_Het_rep2

value: Dbf/+


title: HL3

description: processed data file: C_HL_transcript_expression_results.txt

source_name: 225.9 ug linuron_liver

value: 225.9 µg/L linuron for 4 days


title: conRNAi_rep2_zt19


title: Dbf_WT_rep1


title: conRNAi_rep1_zt7


title: Dbf_Het_rep1


title: HL2


title: HL1


title: ML3

description: processed data file: C_ML_transcript_expression_results.txt

source_name: 15.3 ug linuron_liver

value: 15.3 µg/L linuron for 4 days


title: conRNAi_rep1_zt23


title: conRNAi_rep1_zt3


title: conRNAi_rep1_zt19


title: YJM428_ChrXVI.4n Biological Replicate 1

data_processing:
Sequencing reads were processed with Trimmomatic version 0.30
Trimmed sequencing reads were mapped to the S288c reference V64-1-1, using BWA mem version 0.7.12-r1039
HTseq version 0.6.0 was used to sum read counts per gene
Saccharomyces cerevisiae sequencing reads normalized by reads from Schizosaccharomyces pombe spike-in control
Supplementary_files_format_and_content: Tab-delimited text file includes normalized values for each gene in each sample

source_name: S. cerevisiae cells

tag: wild or lab strain

value: wild

tag: ploidy

value: diploid

tag: euploid or aneuploid

value: aneuploid


title: YJM428_ChrXVI.4n Biological Replicate 2


title: ML2


title: NCYC110_ChrVIII.4n Biological Replicate 4


title: ML1


title: YJM428_ChrXVI.2n Biological Replicate 2

value: euploid


title: YJM428_ChrXVI.2n Biological Replicate 1


title: conRNAi_rep1_zt15

value: control for cabut RNAi (Tim-gal4;UAS-Dcr2)


title: NCYC110_ChrVIII.3n Biological Replicate 4


title: NCYC110_ChrVIII.2n Biological Replicate 4


title: conOE_rep2_zt3

value: control for cabut OE (Tim-gal4 )


title: conOE_rep2_zt23


title: conOE_rep2_zt7


title: LL1

description: processed data file: C_LL_transcript_expression_results.txt

source_name: 1.7 ug linuron_liver

value: adult

value: 1.7 µg/L linuron for 4 days


title: NCYC3290 Biological Replicate 4


title: LL2

value: male


title: conOE_rep2_zt15


title: T73_ChrVIII.4n Biological Replicate 2


title: C2 [adult male]

value: water (control) for 4 days

value: liver


title: HE2

description: processed data file: C_HE_transcript_expression_results.txt

source_name: 34.4 ng E2_liver

value: 34.4 ng/L E2 for 4 days


title: T73_ChrVIII.2n Biological Replicate 2


title: conOE_rep2_zt19

value: head


title: HE3


title: HE1


title: conOE_rep2_zt11


title: LL3


title: conRNAi_rep1_zt11


title: T73_ChrVIII.2n Biological Replicate 1


title: conOE_rep1_zt7


title: YPS163_ChrVIII.2n Mat a Biological Replicate 2

value: haploid


title: ME2

description: processed data file: C_ME_transcript_expression_results.txt

source_name: 18.1 ng E2_liver

value: 18.1 ng/L E2 for 4 days


title: conOE_rep1_zt3


title: YPS163_ChrVIII.1n Mat a Biological Replicate 2


title: YPS163_ChrVIII.2n Mat a Biological Replicate 1


title: LE3

description: processed data file: C_LE_transcript_expression_results.txt

source_name: 1.9 ng E2_liver

value: 1.9 ng/L E2 for 4 days


title: ME1


title: YPS163_ChrVIII.1n Mat a Biological Replicate 1


title: LE2


title: conOE_rep1_zt19


title: conOE_rep1_zt15


title: LE1


title: conOE_rep1_zt11


title: T73_ChrVIII.4n Biological Replicate 1


title: ME3


title: Ex vivo2

city: Barcelona

first: BERNARDO

last: BELLO ORTI

state: Barcelona

address: Bellaterra

department: Bacteriology

country: Spain

institute: CReSA

data_processing:
For both in vivo and ex vivo experiments, bioinformatic analysis was performed following the count-based differential expression method (Anders et al., 2013), with some modifications.
Genome_build: Haemophilus parasuis str. Nagasaki
Supplementary_files_format_and_content: Tab-delimited text files include counts for each gene.

organism: Glaesserella parasuis str. Nagasaki

source_name: ex vivo incubation

growth_protocol: 24h chocolate agar plate culture at 37ºC

extract_protocol:
Sequencing library was generated using an Ion Torrent RNA-Seq v2 kit (Life Technologies) and RNA was sequenced using an Ion Torrent PGM instrument (Life Technologies) with an Ion 316 chip (Life technologies) at the Centre for Research in Agricultural Genomics (CRAG, Campus de Bellaterra-UAB, Spain). As control, RNA from the Nagasaki strain grown overnight on chocolate agar plates was purified and sequenced in the same manner.
Bacteria were recovered by centrifugation and pellets were used for RNA extraction. An additional low speed centrifugation step was added to ex vivo and in vivo samples in order to eliminate mammalian cells. All bacterial samples were processed for RNA extraction as follows. Pellets were resuspended in 2% SDS 16 mM EDTA 10 mM TRIS (pH XX) and incubated for 5 min at 100 ºC. Afterwards, samples were processed by two hot acid phenol-chloroform extractions, followed by two chloroform/ isoamyl alcohol extractions. RNA was then precipitated with 0.6 volumes of isopropanol 0.1 volumes of 5M ammonium acetate and 1μL of glycogen. After centrifugation the pellet was washed with 70% ethanol, dried and resuspended in warmed RNase-free water. To ensure that contaminating bacterial DNA was eliminated from the samples, treatment with RNase-free DNase (Qiagen) was performed. In addition, ribosomal RNA was eliminated with the Ribo-Zero rRNA removal kit (Epicentre Biotechnologies, Madison, WI, USA) following manufacturer’s instructions. PCR reactions using primers specific for H. parasuis 16S rRNA gene were carried out to ensure that no bacterial DNA was left in the sample.

value: Nagasaki

tag: culture time

tag: genotype

value: wild type


title: Plate2

source_name: agar plate culture


title: RNAi_25_con

data_processing:
Removal of rRNA reads using alignment to drosophila rRNA reference with bowtie
Tophat alignment to Drosophila genome dm3
Quantification of the signal in each annotated transcript (at the 3' end) by normalized read counts.
Genome_build: dm3; GCF_000001215.2
Supplementary_files_format_and_content: Excel file with list of transcripts and the RNA-seq quantification of each sample.

tag: strain background

value: Canton-S

value: Control (+/cbtE1-UAS-cbt RNAi)

tag: sucrose conc. (%)

value: fly heads


title: RNAi_100_rep2

source_name: cabut RNAi_sucrose_100%_18h

value: cabut RNAi  (Tim-gal4, UAS-cbt RNAi)


title: RNAi_50_con


title: RNAi_100_rep1


title: RNAi_100_con


title: RNAi_0_con


title: RNAi_50_rep2

source_name: cabut RNAi_sucrose_50%_18h


title: conOE_rep1_zt23

value: control for cabut OE (Tim-gal4 )


title: RNAi_50_rep1


title: RNAi_25_rep2

source_name: cabut RNAi_sucrose_25%_18h


title: RNAi_0_rep1

source_name: cabut RNAi_sucrose_0%_18h


title: RNAi_0_rep2


title: Control Experiments Set 3

status: Public on May 07 2015

city: Tucson

first: Darren

middle: A.

last: Cusanovich

state: AZ

address: 1230 N Cherry Avenue, BSRL 421

department: Cellular and Molecular Medicine

institute: University of Arizona

description: Controls Set 3

data_processing:
library strategy: ATAC-seq
qseq files generated with OLB v1.9.3
barcodes updated and fastq files generated with custom perl script
Adapters trimmed with Trimmomatic v0.32
Reads mapped with BWA v0.7.8-r749-dirty
Unmapped reads and mitochondrial reads filtered out.
Duplicate fragments removed with picard v1.105
Reads overlapping known hypersensitive sites were counted for each barcode to generate DHS matrix with custom python script
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: tab-separated vector - first 4 columns contain location information for each hypersensitivity site, remaining columns include counts of reads overlapping that site assigned to each barcode. Please see 'readme.txt' for detailed description..

source_name: Mixture of GM12878 and HL-60

growth_protocol: Cells grown under standard conditions. Patski and HEK293T were cultured in DMEM supplemented with 10% FBS. GM12878 and HL-60 were grown in RPMI 1640 supplemented with 15% FBS.

extract_protocol:
Intact nuclei were isolated with ATAC-seq cold lysis buffer suplemented with protease inhibitors.
Genomic DNA in intact nuclei was simultaneously molecularly tagged and fragmented. Nuclei tagged with 1 of 96 barcodes were pooled and then redistributed into wells of a PCR plate (15-25 nuclei per well) using a cell sorter.  A second barcode was introduced during library amplification.

tag: cell line

value: Mixture of GM12878 and HL-60

tag: molecule subtype

value: Accessible genomic DNA


title: RNAi_25_rep1

tag: genotype/variation


title: 4 hr FGF + LY294002 Rep2

city: San Francisco

first: Harish

last: Vasudevan

address: 555 Mission Bay Blvd South, Room 452H

department: Radiation Oncology

institute: University of California San Francisco

description:
Poly A selected RNA
50 ng/mL FGF1 + 1 μg/mL heparin + 10 μM LY294002

data_processing:
Library construction and sequencing were performed at MSSM Genomics Core.  Illumina CASAVA software was used for basecalling.
Sequence reads were trimmed and Tophat was used to align FastQ files to reference genome. The resulting alignments were used to perform abundance estimates and differential exprsesion analysis using CuffDiff
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file including FPKM values for each sample

source_name: E13.5 Palate Cells (MEPM)

growth_protocol: Cells were grown in DMEM  + 10%FBS and serum starved overnight in 0.1% FBS

extract_protocol:
RNA was isolated from cells using the Qiagen RNeasy kit and polyA selected (MSSM Genomics Core)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Palate

tag: age

tag: treatment


title: 1 hr FGF + LY294002 Rep2

tag: tissue

value: 50 ng/mL FGF1 + 1 μg/mL heparin + 10 μM LY294002


title: 1 hr FGF + LY294002 Rep1


title: 4 hr PDGF + LY294002 Rep2

description:
Poly A selected RNA
30 ng/mL PDGFA + 10 μM LY294002

value: 30 ng/mL PDGFA + 10 μM LY294002


title: GM12878 and HL-60 Mixture


title: 4 hr FGF + LY294002 Rep1


title: GM12878 and HEK293T Mixture

source_name: Mixture of GM12878 and HEK293T

value: Mixture of GM12878 and HEK293T


title: 4 hr PDGF + LY294002 Rep1


title: 1 hr PDGF + LY294002 Rep2


title: Control Experiments Set 1

description: Controls Set 1


title: conRNAi_rep3_zt11

value: head

value: control for cabut RNAi (Tim-gal4;UAS-Dcr2)

tag: time


title: 1 hr PDGF + LY294002 Rep1


title: Control Experiments Set 2

description: Controls Set 2


title: 4 hr FGF + PD325901 Rep2

description:
Poly A selected RNA
50 ng/mL FGF1 + 1 μg/mL heparin + 1 μM PD325901


title: 1 hr FGF + PD325901 Rep2

value: 50 ng/mL FGF1 + 1 μg/mL heparin + 1 μM PD325901


title: 4 hr PDGF Rep3

description:
Poly A selected RNA
30 ng/mL PDGFA

value: 30 ng/mL PDGFA


title: 4 hr FGF Rep1

description:
Poly A selected RNA
50 ng/mL FGF1 + 1 μg/mL heparin

value: 50 ng/mL FGF1 + 1 μg/mL heparin


title: 4 hr FGF Rep2


title: 1 hr PDGF + PD325901 Rep2

description:
Poly A selected RNA
30 ng/mL PDGFA + 1 μM PD325901

value: 30 ng/mL PDGFA + 1 μM PD325901


title: 4 hr FGF Rep3


title: 4 hr PDGF + PD325901 Rep1


title: 4 hr PDGF Rep1

description:
Poly A selected RNA
30 ng/mL PDGFA


title: WT OE female

city: Bochum

first: Claudia

last: Haering

address: Universitätsstr. 150

department: Biology

institute: Ruhr University Bochum

description: RNA sample was prepared from the OE of three different mice

data_processing:
Illumina sequencing was performed on a HiSeq-2000 using paired end 101-bp reads.
RNA-Seq reads were aligned to version mm9 of mouse reference genome and transcriptome using TopHat (v2.0.7) which utilizes the ultra-fast short–read mapping program Bowtie to arrange the alignment
Aligned RNA-Seq reads for each sample were assembled into transcripts and their abundance was estimated by the program Cufflinks (v1.3.3) using the RefSeq mm9 reference transcriptome in Gene Transfer Format (GTF) obtained from the UCSC Genome Bioinformatics database (University of California Santa Cruz). For differential gene expression analysis between wild type and NKCC1-deficient mice, we analyzed the three OE transcriptome raw datasets for each condition (wild type/NKCC1-deficient) in Cuffdiff.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited file includes FPKM values

source_name: Olfactory Epithelium

extract_protocol:
Olfactory Epithelia were prepared and pooled from individuals for each condition. Subsequently RNA was isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer´s protocol including the optional on-column DNaseI digestion.
Libraries for NGS sequencing were prepared from RNA and subjected to DSN normalization by standard Illumina protocols

tag: strain

value: NMRI

value: Olfactory Epithelium

value: wildtype


title: 1 hr PDGF + PD325901 Rep1


title: 4 hr PDGF + PD325901 Rep2


title: 4 hr FGF + PD325901 Rep1


title: WT OE male


title: 4 hr PDGF Rep2

description:
Poly A selected RNA
30 ng/mL PDGFA


title: KO OE female


title: WT OE mixed gender

description: RNA sample was prepared from two OE of each gender


title: PD10_TFC_mES-G45-DKO-6

city: Beijing

first: xiaomeng

last: liu

state: Beijing

address: Yiheyuan Road No.5

institute: Biodynamics Optical Imaging Center (BIOPIC), Peking University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to refference genome (mm9) using bismark and bowtie
Genome_build: mm9
Supplementary_files_format_and_content: wig files indicate the 5mC level at the site with coverage >= 5

source_name: ES cells

growth_protocol: V6.5 ES cells were cultured on feeder cells with standard ES cell culture conditions.

extract_protocol:
The genomic DNA of mouse ES cells was extracted with the DNeasy Blood & Tissue Kit (Qiagen).
1 μg genomic DNA plus 0.1% of unmethylated lambda DNA spike-in was digested by 10 U MspI (Fermentas). Then the digested DNA was end repaired and dA tailed with Klenow Fragment. Next, the DNA fragments was ligated with the Illumina TruSeq adapters using T4 DNA ligase (Fermentas) overnight. Size selection of the 200-500 bp DNA fragments were performed on a 2% agarose gel. After that, bisulphite conversion of the library was performed using a MethylCode DNA Methylation Kit (Invitrogen). The bisulphite-converted DNA was amplified by 15 cycles of PCR using PfuTurbo Cx polymerase (Agilent Technologies) and then purified by AMPure XP beads (Beckman).Finally, the libraries were sequenced on an Illumina HiSeq 2000.

tag: cell type

value: embryonic stem cells

value: Gadd45a/b DKO


title: KO OE male


title: PD10_TFC_mES-WT

value: wild type


title: 1 hr FGF + PD325901 Rep1


title: KO OE mixed gender


title: PD10_TFC_mES-G45-DKO-2


title: PD10_TFC_mES-WT-8


title: HL-60 RNA-seq Replicate 2

data_processing:
Reads generated with standard Illumina pipeline
Reads mapped with Bowtie2
Differential expression determined with CuffDiff2
Genome_build: hg19
Supplementary_files_format_and_content: standard outputs from CuffDiff2 and GFF for gene models used including  the differential expression test output from CuffDiff (gene_exp.diff).

source_name: Promyelocytic cell line HL-60

growth_protocol: Cells grown under standard conditions in RPMI 1640 supplemented with 15% FBS.

extract_protocol:
Qiagen RNeasy Kit
Standard Illumina TruSeq protocol

value: Promyelocytic cell line


title: HL-60 RNA-seq Replicate 3


title: HL-60 RNA-seq Replicate 1


title: GM12878 RNA-seq Replicate 2

source_name: Lymphoblastoid cell line GM12878

value: Lymphoblastoid cell line


title: GM12878 RNA-seq Replicate 3


title: GM12878 RNA-seq Replicate 1


title: Organoid 4 derived from patient 31

city: Utrecht

first: Lennart

last: Kester

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: mRNA

data_processing:
After sequencing, read 1 was aligned to the hg19 RefSeq human transcriptome downloaded from the UCSC genome browser (Meyer et al., 2013) using bwa (Li and Durbin, 2010) with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL-seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Samples with less than 500.000 reads were discarded after which the remaining samples were rpm normalized.
Genome_build: hg19
Supplementary_files_format_and_content: mRNA count data for all samples, each column is a sample each row is a gene

source_name: Colonic Adenocarcinoma derived organoid

growth_protocol: Organoids derived from colorectal cancer cases were resuspended in matrigel. Subseqeuntly, droplets of matrigel (10 ul), were put in a dish. After letting the Matrigel solidy, Human Intestinal  Stem Cell medium (HISC) (Basal culture medium with 50% Wnt conditioned medium, 20% R-Spondin conditioned medium, 10% Noggin conditioned medium,  1 x B27, 1,25 mM n-Acetyl Cysteine, 10 mM Nicotinamide, 50 ng/ml human EGF, 10 nM Gastrin, 500 nM A83-01, 3 uM SB202190, 10 nM Prostaglandine E2 and 1 x Primocin (Vivogen)) minus Wnt was added and the cells were incubated at 37 oC.

extract_protocol:
For single organoid mRNA sequencing, organoids were hand-picked and deposited into trizol (life technologies).
The RNA was extracted using chloroform and precipitated with iso-propanol. The RNA-pellet was then processed using the CEL-seq protocol (Hashimshony et al., 2012) and sequenced on an Illumina Nextseq using 75bp paired end sequencing.

tag: sample type

value: Organoid culture

value: Colonic Adenocarcinoma derived organoid

tag: protocol

value: CEL-seq (Hashimshony et al., Cell reports 2012)

tag: subject

value: patient 31


title: Organoid 3 derived from patient 31

description: mRNA


title: Organoid 11 derived from patient 31

description: mRNA


title: Organoid 12 derived from patient 31

description: mRNA


title: Organoid 5 derived from patient 31

description: mRNA


title: Organoid 6 derived from patient 31

description: mRNA


title: Organoid 1 derived from patient 31

description: mRNA


title: Organoid 7 derived from patient 26

description: mRNA

value: patient 26


title: Organoid 7 derived from patient 31

description: mRNA


title: Organoid 5 derived from patient 26

description: mRNA


title: Organoid 6 derived from patient 26

description: mRNA


title: Organoid 8 derived from patient 31

description: mRNA


title: Organoid 9 derived from patient 31

description: mRNA


title: Organoid 8 derived from patient 26

description: mRNA


title: Organoid 4 derived from patient 26

description: mRNA


title: Organoid 10 derived from patient 26

description: mRNA


title: Organoid 12 derived from patient 26

description: mRNA


title: Organoid 2 derived from patient 26

description: mRNA


title: Organoid 11 derived from patient 26

description: mRNA


title: Organoid 9 derived from patient 23

description: mRNA

value: patient 23


title: Organoid 5 derived from patient 23

description: mRNA


title: Organoid 7 derived from patient 23

description: mRNA


title: Organoid 6 derived from patient 23

description: mRNA


title: Organoid 4 derived from patient 23

description: mRNA


title: Organoid 10 derived from patient 31

description: mRNA


title: Organoid 2 derived from patient 31

description: mRNA


title: Organoid 9 derived from patient 26

description: mRNA


title: Organoid 2 derived from patient 23

description: mRNA


title: Organoid 3 derived from patient 23

description: mRNA


title: Organoid 12 derived from patient 23

description: mRNA


title: Organoid 9 derived from patient 20

description: mRNA

value: patient 20


title: Organoid 11 derived from patient 23

description: mRNA


title: Organoid 3 derived from patient 26

description: mRNA


title: Organoid 1 derived from patient 23

description: mRNA


title: Organoid 8 derived from patient 20

description: mRNA


title: Organoid 10 derived from patient 23

description: mRNA


title: Organoid 5 derived from patient 20

description: mRNA


title: Organoid 7 derived from patient 20

description: mRNA


title: Organoid 6 derived from patient 20

description: mRNA


title: Organoid 3 derived from patient 20

description: mRNA


title: Organoid 4 derived from patient 20

description: mRNA


title: Organoid 8 derived from patient 23

description: mRNA


title: Organoid 10 derived from patient 20

description: mRNA


title: Organoid 2 derived from patient 20

description: mRNA


title: Organoid 9 derived from patient 19b

description: mRNA

value: patient 19b


title: Organoid 1 derived from patient 20

description: mRNA


title: Organoid 12 derived from patient 20

description: mRNA


title: Organoid 11 derived from patient 20

description: mRNA


title: Organoid 7 derived from patient 19b

description: mRNA


title: Organoid 6 derived from patient 19b

description: mRNA


title: Organoid 1 derived from patient 26

description: mRNA


title: Differentiated cells (G0/G1)

first: Gustavo

last: Rodriguez-Esteban

state: Catalonia

address: C. Baldiri Reixac, 4; Barcelona Science Park

department: Development

institute: Centro Nacional de Análisis Genómico

description: Tag count: 1168399

data_processing:
Image analysis and base calling were performed using the Illumina pipeline.
Sequence tags were obtained after purity filtering. This was followed by sorting and counting the unique tags.
Genome_build: n/a
Supplementary_files_format_and_content: tab-delimited text files include count values for each tag.

organism: Schmidtea mediterranea

source_name: Xin isolated cells

extract_protocol:
Total RNA was extracted from FACS isolated cells using TRIzol LS Reagent (Life Technologies).
Sequence tag preparation was done using Illumina's Digital Gene Expression Tag Profiling Kit according to the manufacturer's protocol.  Anchor enzyme: NlaIII. Tag length: 17bp. Barcodes: X1, ACGT;  X2, AATG; Xin,  AGCA. Cluster generation was performed with the Illumina 1G Analyzer.

value: Differentiated cells (G0/G1)

value: asexual

tag: clonal line

tag: regeneration time

value: 2 days

tag: cell cycle phase


title: Organoid 8 derived from patient 19b

description: mRNA


title: Organoid 5 derived from patient 19b

description: mRNA


title: Proliferating stem cells and stem cell progeny (G0/G1)

description: Tag count: 3488712

source_name: X2 isolated cells


title: Proliferating stem cells (S/G2/M)

description: Tag count: 3641099

source_name: X1 isolated cells

value: Proliferating stem cells (S/G2/M)


title: Organoid 3 derived from patient 19b

description: mRNA


title: Organoid 4 derived from patient 19b

description: mRNA


title: Organoid 2 derived from patient 19b

description: mRNA


title: Organoid 11 derived from patient 19b

description: mRNA


title: Organoid 12 derived from patient 19b

description: mRNA


title: Organoid 10 derived from patient 19b

description: mRNA


title: Organoid 9 derived from patient 8

description: mRNA

value: patient 8


title: Organoid 8 derived from patient 8

description: mRNA


title: Organoid 1 derived from patient 19b

description: mRNA


title: Organoid 7 derived from patient 8

description: mRNA


title: Organoid 6 derived from patient 8

description: mRNA


title: Organoid 5 derived from patient 8

description: mRNA


title: Organoid 4 derived from patient 8

description: mRNA


title: Organoid 10 derived from patient 8

description: mRNA


title: Organoid 3 derived from patient 8

description: mRNA


title: Organoid 9 derived from patient 7

description: mRNA

value: patient 7


title: Organoid 1 derived from patient 8

description: mRNA


title: Organoid 12 derived from patient 8

description: mRNA


title: Organoid 11 derived from patient 8

description: mRNA


title: Organoid 6 derived from patient 7

description: mRNA


title: Organoid 5 derived from patient 7

description: mRNA


title: Organoid 2 derived from patient 7

description: mRNA


title: Organoid 4 derived from patient 7

description: mRNA


title: Organoid 3 derived from patient 7

description: mRNA


title: Organoid 11 derived from patient 7

description: mRNA


title: Organoid 10 derived from patient 7

description: mRNA


title: Organoid 12 derived from patient 7

description: mRNA


title: Organoid 8 derived from patient 19a

description: mRNA

value: patient 19a


title: Organoid 9 derived from patient 19a

description: mRNA