title: SC3-iPS

status: Public on Jan 01 2013

city: Toronto

first: Yu

last: Liu

state: ON

address: 600 University Ave

department: Molecular Genetics

country: Canada

institute: University of Toronto

data_processing:
Illumina CASAVA 1.8 was used to perform basecalling
The first 15 bases of each read were trimmed
Top-Hat 1.3 was used to align to mm9 genome
Reads mapped to multiple location in the genome were dicarded
RPKM were calculated for protein coding gene using exon union model.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited text file of RPKM

source_name: secondary iPS cells

growth_protocol: Secondary MEFs were isolated and treated with doxycycline to induce reprogramming

extract_protocol:
mRNA was purified using Qiagen RNAeasy kit with on-column DNAse treatment
RNA libraries were prepared for sequencing using standard Illumina Truseq kit protocols

treatment_protocol: Secondary MEFs were treated with doxycycline for 14, 21, 22, 23 or 27 days

tag: day of dox treatment

tag: days cultured without doxycycline

value: secondary iPS cells


title: Filter development, replicate 1, hour 03

status: Public on Apr 21 2015

type: SRA

city: Houston

first: Gad

last: Shaulsky

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

country: USA

institute: Baylor College of Medicine

description:
Sample 4
FDrep1_hr03

library_source: transcriptomic

data_processing:
After demultiplexing, the data was mapped to the D. discoideum genome with bowtie version 0.12.7. Read qualities were used. Other parameters: seed length = 28, allowed mismatches = 2, allowed up to 1 alignment per read, with bowtie options -a, --strata, --best. Unmapped reads were trimmed from 3' by 2 nucleotides, which was repeated 5 times.
Raw expression values were computed as the number of reads that were uniquely mapped to gene exons.
Normalized expression were scaled with mappable exon lengths. This normalization is similar to the RPKM normalization (Reads Per Kilobase of exon per Megabase of library size), but instead of dividing by exon lengths we used the uniquely mappable parts of the exon. To obtain uniquely mappable parts, all possible subsequences of the reference genome (of the same length as reads in raw data) are mapped back to the reference genome, obtaining the number of uniquely mapped sequences to the exons (Exon_mappable). As a library size we used the total number of all uniquely mapped reads from the experiment, excluding the non-polyadenylated genes (N_unique). Normalized expressions were computed as follows: Exp = 10^9*raw/(N_unique * Exon_mappable).
Genome_build: D. discoideum Chromosomal DNA: 1,2,3,4,5,6,M, and floating contigs (created: 05-13-2009 13:53) from the DictyBase (chromosomes 1,2,3,4,5,6 and mitochondrial DNA are the same as on NCBI assembly "dicty_2.7"). Regions [3016085, 3768655] from chr2, [64985, 72996] from chrBF and [42801, 78150] from chrR were masked.
Supplementary_files_format_and_content: Processed data files are tab-separated files with two columns: the first containing gene names (DDB_G ids) and the second its expression. Files ending with "_raw.txt" contain raw expression values while files ending with "_nor.txt" contain normalized expression values.

molecule: polyA RNA

organism: Dictyostelium discoideum

source_name: Cells developing on nitrocellulose filters

growth_protocol: Dictyostelium discoideum cells were grown in nutrient media (HL-5) to mid-log phase prior to collection for development.

extract_protocol:
TriZol (Life Sciences) -- Cells were scraped (filter) or pelleted (suspension) and disrupted in TriZol. Total RNA was extracted by phenol/chloroform as per manufacturer's instructions.
mRNA was enriched by 2x polyA bead selection (Ambion, Life Sciences). Multiplexed libraries were constructed as outlined in Miranda et al (2013), PMID #23494306.

tag: strain

tag: growth

tag: treatment

value: Development on 5 cm nitrocellulose filters

tag: time point (hour)

tag: replicate


title: Filter development, replicate 1, hour 02

description:
Sample 3
FDrep1_hr02


title: iPS1-C3 day 0

status: Public on Oct 06 2011

city: bronx

first: Mingyan

last: Lin

state: ny

address: 1300 Morris Park Avenue

institute: Albert Einstein college of medicine

description: amplified cDNA (The average fragment length : 250bp,  the standard deviation : 50bp)

data_processing: iPS cell and neuron RNA-Seq reads were separately aligned to the human genome (GRCh37/hg19) using the software TopHat (version 1.2.0).

molecule: total RNA

organism: Homo sapiens

source_name: hiPSCs

growth_protocol: Stem cell lines were maintained on irradiated mouse embryonic fibroblasts (MEFs) in hES medium consisting of knockout (KO)-DMEM, 1mM pen/strep, 1 mM Gluta-MAX, 1X nonessential amino acids (NEAA), 55 μM β-mercaptoethanol (β-ME) (Gibco, Carlsbad, CA), 10% Knockout (KO) serum replacement (Invitrogen, Carlsbad, CA), 10% plasmanate (Talecris Biotherapeutics, Research Triangle Park, NC), and 10 ng/ml FGF2 (R&D Systems Inc., Minneapolis, MN).

extract_protocol: Total RNA (25 ng) was converted to cDNA using the NuGEN Ovation RNA-Seq System according to the manufacturer's protocol (NuGEN, San Carlos, CA, USA). The protocol employs a single primer isothermal amplification (SPIA) method to amplify RNA target into double stranded cDNA under standardized conditions that markedly deplete rRNA without preselecting mRNA. cDNA was then used for Illumina sequencing library preparation using Encore NGS Library System I. NuGEN-amplified double-stranded cDNA was fragmented into ,300 base pair (bp) using a Covaris-S2 system. DNA fragments (200 ng) were then end-repaired to generate blunt ends with 59 phosphatase and 39 hydroxyls and adapters were ligated for paired end sequencing on Illumina HiSeq 2000. The average fragment length is 250bp and the standard deviation is 50bp.

treatment_protocol: To support glutamatergic differentiation, adherent colonies were treated on day 10 with WNT3A (100ng/ml) (R&D Systems, Minneapolis, MN) in neural induction medium. Cells were fed every other day for 2 weeks. On day 25, medium was changed to neuronal differentiation medium, which consists of Neurobasal medium, 1X N2 supplement, 2X B27, 0.1 mM NEAA, supplemented with cAMP (1 μM), BDNF, GDNF, and IGF1 (10 ng/ml each, PeproTech, Rocky Hill, NJ). The concentration of WNT3A was reduced to 10ng/ml.

tag: cell type

value: hiPSCs

tag: passages

tag: clone


title: Filter development, replicate 1, hour 08

description:
Sample 9
FDrep1_hr08


title: SC1-iPS

organism: Mus musculus


title: RNA H1, i

status: Public on Oct 31 2012

city: New Haven

first: Flora

last: Vaccarino

state: CT

address: 230 South Frontage Road

department: Child Study Center

institute: Yale University

description: ILLUMINA HiSeq sequencing reads

data_processing:
Base calling: Illumina CASAVA
Alignment: Tophat 1.3.1, parameters --solexa1.3-quals --coverage-search --no-novel-indels --microexon-search [extra parameter "-r 100" for PE 2x100 data, "-r 150" for 2x75 data and without "-r" parameter for SE data]
Conversion from BAM to SAM: SAMtools 0.1.11
Conversion SAM to MRF: sam2mrf (part of RSEQtools, couldn't find RSEQtools version, it is whatever version was available as of August 2011)
RPKM computation: mrfQuantifier (part of RSEQtools, same note about version)
Genome_build: hGRC37 (hg19)

source_name: iPS

growth_protocol: Fibroblast were growth under standar condition in DMEM high Glucose media containing 10% FBS. iPSCs were mantained on matrigel coated plates in DMEM/F12 media containing 1% N2 supplement, 2% B27 supplement, 2 mM L-glutamine, 0.1 mM non-essential amino acids, 1% penicillin/ streptomycin, 0.5 mg/mL BSA Fraction V, 0.12 mM monothioglycerol. Colonies were passed using dispase.

extract_protocol:
Cells were treated with Accutase and pelleted. Total RNA was extracted using PicoPure kit (Life Technologies catalog # KIT0204).
Fibroblast  RNA libraries for both families (03 and 1123) were prepared for sequencing using standard Illumina protocols using 5 ug of total RNA. iPSC RNA libraries for family 03 were prepare as well using standard Illumina protocols using 2.5 ug of total RNA.   Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2.5 ug of total RNA for the construction of multiplex sequencing libraries for all iPSC for  members of family S1123. In all cases, library fragments of ~300 bp were band isolated from an agarose gel.

tag: passage number

value: iPS


title: RNA 03-03, i4

description: ILLUMINA HiSeq sequencing reads


title: Filter development, replicate 2, hour 14

description:
Sample 33
FDrep2_hr14