title: pcp2 TRAPSeq male 2

description: polysomal RNA

data_processing:
Library strategy: TRAP-Seq
Data were separatedly aligned to the mouse genome (mm9) downloaded from UCSC. TopHat  software (version 1.3.1) was used for processing reads. Segment size was set to 25bp with two mismatches to  the reference allowed, and the minimum anchor size was set to 10bp with no mismatches allowed.
differentially expressed genes were identified by performing a negative binomial test using the DESeq  package (Anders and Huber, 2010) of R/Bioconductor (Gentleman et al., 2004).

extract_protocol:
Single animals per replica were euthanized  with CO2 and cerebella were dissected. 4 cerebella was immediately homogenized in ice-cold  homogenization buffer (10 mM HEPES [pH 7.4], 150 mM KCl, 5 mM MgCl2, 0.5 mM dithiothreitol (DTT), 100  μg/ml cycloheximide, Complete-EDTA-free protease inhibitors (Roche) and RNasin RNase inhibitors  (Promega, Madison, WI) using a Teflon-glass homogenizer. Homogenates were centrifuged for 10 minutes at  2,000 × g, 4 °C, to pellet cell debris, and incubated with 1% IGEPAL CA-630 (NP-40, Sigma) and 30 mM  DHPC (Avanti Polar Lipids, Alabaster, AL) for 5 min. Lysates were centrifuged for 15 minutes at 20,000 × g to  pellet insoluble material. At this point, 30 μL of supernatant was saved as input sample. Two custom made  mouse anti-GFP (clones 19C8 and 19F7; see Heiman et al., 2008) antibodies were captured on Dynal  magnetic beads (Invitrogen Corporation, Carlsbad, CA) coupled with protein L (Pierce, Rockford, IL) . The  homogenate was incubated with antibody coupled beads at 4°C with end-over-end rotation for approximately  16 hours. Beads were subsequently collected on a magnetic rack, washed three times with high-salt wash  buffer (10 mM HEPES [pH 7.4], 350 mM KCl, 5 mM MgCl2, 1% NP-40, 0.5mM DTT, 100 μg/ml cycloheximide)  and RNA was released and purified using Rneasy Micro Kit (Qiagen, Valencia, CA) with in-column DNase  digestion. RNA quantity and quality were determined with a Nanodrop 1000 spectrophotometer (Wilmington,  DE) and Agilent 2100 Bioanalyzer using RNA 6000 Pico Chip. 4 biological replicas was produced per each cell  type. 10 ng of total RNA per IP or input sample were converted to cDNA using the NuGEN Ovation RNA-Seq  (NuGEN,San Carlos,CA,USA) following manufacturers’ instructions. The Single Primer Isothermal  Amplification (SPIA) method used in this protocol allows the amplification of RNA target in double stranded  cDNA under standardized conditions that markedly deplete rRNA without preselecting mRNA. cDNA obtained  was quality scored by RNA 6000 PicoChip for Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).
1 μg of cDNA per sample was sonicated using Covaris-S2 system (Covaris Inc., Woburn, MA, USA), cDNA  fragments of 200 bp were end-repaired and adapters were ligated for HiSeq 2000 (Ilumina Inc., San Diego,  CA, USA) technology using TruSeq DNA Sample kit (Illumina) and following manufacturer`s instructions.  Quality of libraries was assesed using HT DNA High Sensitivity Chip (Agilent) for 2100 Bioanalyzer.

value: 8 weeks

tag: library strategy

value: TRAP-Seq

tag: rna subtype

value: polysomal RNA


title: GC MeCP2 KO male 1

status: Public on Jan 14 2013

type: SRA

city: New York

first: Marian

last: Mellen

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

description: 5hmC IP DNA

library_source: genomic

data_processing:
Library strategy: 5hmC-Seq
Reads were aligned to mm9 mouse genome assembly using Bowtie v0.12.7  (-m1 --best).  (-m1 --best).
Further analysis was done using Bioconductor v2.9 using packages chipseq, biomaRt,  rtracklayer, MEDIPS and custom scripts.

molecule: genomic DNA

organism: Mus musculus

source_name: GRANULE CELLS

extract_protocol:
Isolation and sorting was performed as described in (Kriaucionis and  Heintz, 2009). Briefly, cerebella were dissected as described above and homogenized in homogenization  medium (0.25 M sucrose, 150 mM KCl, 5 mM MgCl2, 20 mM Tricine pH 7.8, 0.15 mM spermine,  0.5 mM spermidine, EDTA-free protease inhibitor cocktail (Roche) using loose (A) and tight (B) glassglass  dounce.Homogenate was supplemented with 50% iodixanol (OptiPrep, Axis-Shield,  Scotland), 150 mM KCl, 5 mM MgCl2, 20 mM Tricine pH 7.8; and laid on a 29% iodixanol cushion. GC nuclei from WT and Mecp2-null mice were sorted by selecting a specific FSC/SSC  population identified from GC EGFP+ mice. We observed that this FSC/SSC gated population in GC EGFP+  animals resulted >92% of the sorted nuclei being EGFP positive. Thus, the gate selected allows us  to enrich the sample from 65-70% to 92-96% on GC cells. .
5hmC was pulled down as described (Song et al., 2010). After  purification DNA was amplified as described in TruSeq DNA Sample kit. 1-0.5 μg of DNA was used for each experiment.  Sonicated DNA was end-repaired following by ligation to Illumina paired end sequencing adapters (Illumina,  PE‐ 102‐ 1003) following  by amplification with Illumina primers. Input samples were produced for  each cell types in both procedures. 5hmC enriched were then sequenced using Illumina platform obtaining more than 50 x10-6, 36-  bp single-end reads per sample. Reads were aligned to mm9 mouse genome assembly using Bowtie v0.12.7  (-m1 --best).Two biological replicas were done for each of the cell  type

tag: cell type

value: GRANULE CELLS

tag: strain

tag: age

value: 6 weeks

tag: genotype


title: Input Cerebellum tissue for pcp2 TRAPSeq male 2

description: total RNA

library_source: transcriptomic

data_processing:
Data were separatedly aligned to the mouse genome (mm9) downloaded from UCSC. TopHat  software (version 1.3.1) was used for processing reads. Segment size was set to 25bp with two mismatches to  the reference allowed, and the minimum anchor size was set to 10bp with no mismatches allowed.
differentially expressed genes were identified by performing a negative binomial test using the DESeq  package (Anders and Huber, 2010) of R/Bioconductor (Gentleman et al., 2004).

molecule: total RNA

source_name: Cerebellum

value: Cerebellum

value: RNA-Seq

value: total RNA


title: pcp2 TRAPSeq female 1

description: polysomal RNA

source_name: Purkinje cells

value: Purkinje cells


title: 5hmC-Seq PCP2 replica 1

extract_protocol:
Isolation and sorting was performed as described in (Kriaucionis and  Heintz, 2009). Briefly, cerebella were dissected as described above and homogenized in homogenization  medium (0.25 M sucrose, 150 mM KCl, 5 mM MgCl2, 20 mM Tricine pH 7.8, 0.15 mM spermine,  0.5 mM spermidine, EDTA-free protease inhibitor cocktail (Roche) using loose (A) and tight (B) glassglass  dounce.Homogenate was supplemented with 50% iodixanol (OptiPrep, Axis-Shield,  Scotland), 150 mM KCl, 5 mM MgCl2, 20 mM Tricine pH 7.8; and laid on a 29% iodixanol cushion. Cerebella  from 12 mice (6 males and 6 females) were used for PCs, 6 (3 males and 3 females) for BGs and 4 (2 males  and 2 females) for GCs. Nuclei were pelleted by centrifugation 30 min, 10,000 g, 4 °C in swinging  bucket rotor (SW41) in a Beckman Coulter XL-70 ultracentrifuge. The nuclear pellet was resuspended in  homogenization buffer and co-stained with DyeCycle Ruby (Invirogen) to 20 μM final concentration.  Nuclei were sorted in a BD FASCAria (BD Biosiences, San Jose, CA, USA) cell sorter using 635 nm and  488 nm excitation lasers and by gating with two parameters: high GFP signal (compared to wt mice)  indicating bacTRAP positive cells and lowest signal for DC Ruby, indicating singlets. Nuclei were fast frozen in  liquid nitrogen after sorting and kept at -80 C until analysis.
5hmC was pulled down as described (Song et al., 2010). After  purification DNA was amplified as described in TruSeq DNA Sample kit. 1-0.5 μg of DNA was used for each experiment.  Sonicated DNA was end-repaired following by ligation to Illumina paired end sequencing adapters (Illumina,  PE‐ 102‐ 1003) following  by amplification with Illumina primers. Input samples were produced for  each cell types in both procedures. 5hmC enriched were then sequenced using Illumina platform obtaining more than 50 x10-6, 36-  bp single-end reads per sample. Reads were aligned to mm9 mouse genome assembly using Bowtie v0.12.7  (-m1 --best).Two biological replicas were done for each of the cell  type

value: 8-12 weeks

value: wt


title: Input Cerebellum tissue for pcp2 TRAPSeq female 1

description: total RNA


title: sept4 TRAPSeq male 2

description: polysomal RNA

source_name: Bergmann glia

extract_protocol:
Single animals per replica were euthanized  with CO2 and cerebella were dissected. 4 cerebella was immediately homogenized in ice-cold  homogenization buffer (10 mM HEPES [pH 7.4], 150 mM KCl, 5 mM MgCl2, 0.5 mM dithiothreitol (DTT), 100  μg/ml cycloheximide, Complete-EDTA-free protease inhibitors (Roche) and RNasin RNase inhibitors  (Promega, Madison, WI) using a Teflon-glass homogenizer. Homogenates were centrifuged for 10 minutes at  2,000 × g, 4 °C, to pellet cell debris, and incubated with 1% IGEPAL CA-630 (NP-40, Sigma) and 30 mM  DHPC (Avanti Polar Lipids, Alabaster, AL) for 5 min. Lysates were centrifuged for 15 minutes at 20,000 × g to  pellet insoluble material. At this point, 30 μL of supernatant was saved as input sample. Two custom made  mouse anti-GFP (clones 19C8 and 19F7; see Heiman et al., 2008) antibodies were captured on Dynal  magnetic beads (Invitrogen Corporation, Carlsbad, CA) coupled with protein L (Pierce, Rockford, IL) . The  homogenate was incubated with antibody coupled beads at 4°C with end-over-end rotation for approximately  16 hours. Beads were subsequently collected on a magnetic rack, washed three times with high-salt wash  buffer (10 mM HEPES [pH 7.4], 350 mM KCl, 5 mM MgCl2, 1% NP-40, 0.5mM DTT, 100 μg/ml cycloheximide)  and RNA was released and purified using Rneasy Micro Kit (Qiagen, Valencia, CA) with in-column DNase  digestion. RNA quantity and quality were determined with a Nanodrop 1000 spectrophotometer (Wilmington,  DE) and Agilent 2100 Bioanalyzer using RNA 6000 Pico Chip. 4 biological replicas was produced per each cell  type. 10 ng of total RNA per IP or input sample were converted to cDNA using the NuGEN Ovation RNA-Seq  (NuGEN,San Carlos,CA,USA) following manufacturers’ instructions. The Single Primer Isothermal  Amplification (SPIA) method used in this protocol allows the amplification of RNA target in double stranded  cDNA under standardized conditions that markedly deplete rRNA without preselecting mRNA. cDNA obtained  was quality scored by RNA 6000 PicoChip for Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).
1 μg  of cDNA per sample was sonicated using Covaris-S2 system (Covaris Inc., Woburn, MA, USA), cDNA  fragments of 200 bp were end-repaired and adapters were ligated for HiSeq 2000 (Ilumina Inc., San Diego,  CA, USA) technology using TruSeq DNA Sample kit (Illumina) and following manufacturer`s instructions.  Quality of libraries was assesed using HT DNA High Sensitivity Chip (Agilent) for 2100 Bioanalyzer.

value: Bergmann glia


title: pcp2 TRAPSeq male 1

description: polysomal RNA


title: kidney

city: shenzhen

first: zhiyong

last: huang

state: Guangdong

address: F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District

country: China

institute: BGI-Shenzhen, Shenzhen 518083, China

description: Sequenced reads were generated from kidney in Chinese tree shrew

data_processing:
use Chinese tree shrew genome as reference, sequenced reads were aligned onto the corresponding reference using TopHat v1.0.12 with default parameters except  -r 20 --mate-std-dev 10 -I 10000  --segment-mismatches 3  --segment-length 24 --solexa1.3-quals
Genome_build: This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession ALAR00000000. The version described in this paper is the first version, ALAR01000000.
Supplementary_files_format_and_content: sequenced reads were aligned onto the corresponding contig

organism: Tupaia chinensis

source_name: kidney

extract_protocol: For RNA-seq, poly-A+ RNA was isolated with 30 oligo-dT-coupled beads from 20 μg total RNA of each sample. First strand cDNA synthesis was performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. After end repair and addition of a 3’ dA overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200±20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using Illumina HiSeq 2000 and the paired-end sequencing module.

treatment_protocol: total RNA is extracted by TRIzol Reagent

tag: tissue

value: kidney


title: Input Cerebellum tissue for pcp2 TRAPSeq male 1

description: total RNA


title: pcp2 TRAPSeq female 2

description: polysomal RNA


title: Input Cerebellum tissue for pcp2 TRAPSeq female 2

description: total RNA


title: Input Cerebellum tissue for sept4 TRAPSeq female 2

description: total RNA


title: sept4 TRAPSeq male 1

description: polysomal RNA


title: sept4 TRAPSeq female 2

description: polysomal RNA


title: Input Cerebellum tissue for sept4 TRAPSeq male 1

description: total RNA


title: Cerebellum wt male 1


title: 5hmC-Seq ND1 replica 1

source_name: Cerebellar Granule cells

value: Cerebellar Granule cells


title: GC MeCP2 KO male 2

description: 5hmC IP DNA


title: Cerebellum MeCP2 KO male 4


title: Cerebellum MeCP2 KO male 3


title: Cerebellum MeCP2 KO male 2


title: nd1 TRAPSeq male 2

description: polysomal RNA

source_name: Granule cells

value: Granule cells


title: Cerebellum MeCP2 KO male 1


title: Input Cerebellum tissue for nd1 TRAPSeq male 2

description: total RNA


title: Input Cerebellum tissue for nd1 TRAPSeq female 2

description: total RNA


title: nd1 TRAPSeq female 1

description: polysomal RNA


title: nd1 TRAPSeq male 1

description: polysomal RNA


title: Input Cerebellum tissue for nd1 TRAPSeq male 1

description: total RNA


title: nd1 TRAPSeq female 2

description: polysomal RNA


title: Ventral tagmental area dopaminergic neurons, control 1

city: Stockholm

first: Daniel

last: Ramsköld

address: Nobels väg 3

country: Sweden

institute: Karolinska Institutet

description:
~200 TH-positive neurons from VTA of Nurr1-floxed Cre-less mice, sample 44.
PolyA+ RNA

data_processing:
Alignment by Bowtie version 0.12.7 to mm9 genome (excluding small contigs in _random files) and Ensembl transcriptome (version 11 Apr 2012).
Removal of non-unique alignments.
Gene expression values from 'rpkmforgenes' (http://sandberg.cmb.ki.se/rnaseq/) version 29 Nov 2011.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: BED files containing aligned reads, and tab-delimited text files containing gene expression values (RPKM/FPKM).

source_name: Ventral tagmental area TH1+ neurons, control

extract_protocol:
Pico RNA isolation kit (Arcturus Engineering, Inc.)
SMARTer Ultra Low Input RNA for Illumina Sequencing kit (Clontech #634935).

tag: strain/background

tag: genotype/variation

value: homozygous Nurr1-floxed

value: ventral tagmental area

value: TH-positive neurons


title: Ventral tagmental area dopaminergic neurons, Nurr1 cKO 1

description:
~200 TH-positive neurons from VTA of Nurr1-floxed DAT-Cre mice, sample 20.
PolyA+ RNA

source_name: Ventral tagmental area TH1+ neurons, Nurr1 cKO

value: homozygous Nurr1-floxed, heterozygous BAC-DAT-CreER T2


title: Ventral tagmental area dopaminergic neurons, control 2

description:
~200 TH-positive neurons from VTA of Nurr1-floxed Cre-less mice, sample 47.
PolyA+ RNA


title: Ventral tagmental area dopaminergic neurons, Nurr1 cKO 3

description:
~200 TH-positive neurons from VTA of Nurr1-floxed DAT-Cre mice, sample 60.
PolyA+ RNA


title: Substantia nigra dopaminergic neurons, control 2

description:
~200 TH-positive neurons from SN of Nurr1-floxed Cre-less mice, sample 41.
PolyA+ RNA

source_name: Substantia nigra TH1+ neurons, control

value: substantia nigra


title: Cerebellum wt male 2


title: Substantia nigra dopaminergic neurons, control 1

description:
~200 TH-positive neurons from SN of Nurr1-floxed Cre-less mice, sample 32.
PolyA+ RNA


title: Substantia nigra dopaminergic neurons, control 3

description:
~200 TH-positive neurons from SN of Nurr1-floxed Cre-less mice, sample 43.
PolyA+ RNA


title: Input Cerebellum tissue for sept4 TRAPSeq male 2

description: total RNA

value: 8 weeks


title: Substantia nigra dopaminergic neurons, Nurr1 cKO 5

description:
~200 TH-positive neurons from SN of Nurr1-floxed DAT-Cre mice, sample 57.
PolyA+ RNA

source_name: Substantia nigra TH1+ neurons, Nurr1 cKO


title: Substantia nigra dopaminergic neurons, Nurr1 cKO 4

description:
~200 TH-positive neurons from SN of Nurr1-floxed DAT-Cre mice, sample 56.
PolyA+ RNA


title: Substantia nigra dopaminergic neurons, Nurr1 cKO 6

description:
~200 TH-positive neurons from SN of Nurr1-floxed DAT-Cre mice, sample 59.
PolyA+ RNA


title: Ventral tagmental area dopaminergic neurons, Nurr1 cKO 2

description:
~200 TH-positive neurons from VTA of Nurr1-floxed DAT-Cre mice, sample 53.
PolyA+ RNA


title: Substantia nigra dopaminergic neurons, Nurr1 cKO 2

description:
~200 TH-positive neurons from SN of Nurr1-floxed DAT-Cre mice, sample 48.
PolyA+ RNA


title: Substantia nigra dopaminergic neurons, Nurr1 cKO 3

description:
~200 TH-positive neurons from SN of Nurr1-floxed DAT-Cre mice, sample 52.
PolyA+ RNA


title: luminal 3 month tumor 6

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

data_processing:
Total RNA from prostate tissues was isolated using Nucleospin RNAII kit (Clontech).
The quantity and quality of each RNA sample was measured using an Agilent 2100 Bioanalyzer.
FPKM values for 22,310 genes were reported.
Genes with missing values (count of 0) in more than 10% of samples were eliminated from our analysis.
Missing values for the remaining genes were estimated by using impute.knn (impute package in R v2.11.1). ). The resulting dataset, having 14,063 genes, was normalized by using robust spline normalization (RSN) function of R-system v2.11.1 and was log transformed.
Supplementary_files_format_and_content: tab-delimited text or xls files include FPKM values for each Sample
build: mm9

source_name: prostate

extract_protocol: Prostate were removed, flash frozen on dry ice, and RNA was harvested using Nucleospin RNA II kit. Library construction was performed by the Columbia Genomic Sequencing Core Facility.

treatment_protocol: To induce tumor formation, mice were administered 9 mg per 40 g tamoxifen suspended in corn oil, or vehicle alone for negative controls, by oral gavage once daily for 4 consecutive days

value: prostate

tag: cell type origin

value: luminal cells

value: Nkx3.1-CreERT2/+; Pten flox/flox; R26R-YFP/+

value: tamoxifen induction at 2 months, wait 3 months


title: Ventral tagmental area dopaminergic neurons, control 3

description:
~200 TH-positive neurons from VTA of Nurr1-floxed Cre-less mice, sample 76.
PolyA+ RNA


title: luminal 3 month tumor 2


title: luminal 3 month tumor 5


title: luminal 3 month tumor 1


title: luminal 1 month tumor 3

value: tamoxifen induction at 2 months, wait 1 months


title: luminal 1 month tumor 2


title: luminal 3 month tumor 4


title: luminal 1 month tumor 5


title: luminal 1 month tumor 4


title: luminal 1 month tumor 6


title: luminal 1 month tumor 1


title: luminal control 6

value: 5 months, no tamoxifen induction


title: luminal control 1


title: basal 6 month tumor 5

value: basal cells

value: CK5-CreERT2; Pten flox/flox; R26R-YFP/+

value: tamoxifen induction at 2 months, wait 6 months


title: luminal control 2


title: luminal control 5


title: basal 6 month tumor 2


title: basal 6 month tumor 6


title: basal 6 month tumor 1


title: basal 6 month tumor 3


title: basal 3 month tumor 3


title: basal 3 month tumor 4


title: basal 3 month tumor 5


title: Substantia nigra dopaminergic neurons, Nurr1 cKO 1

description:
~200 TH-positive neurons from SN of Nurr1-floxed DAT-Cre mice, sample 21.
PolyA+ RNA


title: basal 3 month tumor 1


title: luminal 3 month tumor 3


title: basal 3 month tumor 2


title: basal control 6


title: basal control 4


title: basal control 2


title: basal control 3


title: basal control 5


title: MeDIP_SEQ SEPTIN4 replica1.1

data_processing:
Reads were aligned to mm9 mouse genome assembly using Bowtie v0.12.7  (-m1 --best).  (-m1 --best).
Further analysis was done using Bioconductor v2.9 using packages chipseq, biomaRt,  rtracklayer, MEDIPS and custom scripts.

extract_protocol:
Isolation and sorting was performed as described in (Kriaucionis and  Heintz, 2009). Briefly, cerebella were dissected as described above and homogenized in homogenization  medium (0.25 M sucrose, 150 mM KCl, 5 mM MgCl2, 20 mM Tricine pH 7.8, 0.15 mM spermine,  0.5 mM spermidine, EDTA-free protease inhibitor cocktail (Roche) using loose (A) and tight (B) glassglass  dounce.Homogenate was supplemented with 50% iodixanol (OptiPrep, Axis-Shield,  Scotland), 150 mM KCl, 5 mM MgCl2, 20 mM Tricine pH 7.8; and laid on a 29% iodixanol cushion. Cerebella  from 12 mice (6 males and 6 females) were used for PCs, 6 (3 males and 3 females) for BGs and 4 (2 males  and 2 females) for GCs. Nuclei were pelleted by centrifugation 30 min, 10,000 g, 4 °C in swinging  bucket rotor (SW41) in a Beckman Coulter XL-70 ultracentrifuge. The nuclear pellet was resuspended in  homogenization buffer and co-stained with DyeCycle Ruby (Invirogen) to 20 μM final concentration.  Nuclei were sorted in a BD FASCAria (BD Biosiences, San Jose, CA, USA) cell sorter using 635 nm and  488 nm excitation lasers and by gating with two parameters: high GFP signal (compared to wt mice)  indicating bacTRAP positive cells and lowest signal for DC Ruby, indicating singlets. Nuclei were fast frozen in  liquid nitrogen after sorting and kept at -80 C until analysis.
MeDIP was done as described in  (Weber et al., 2005) with the indicated modifications. 1-0.5 μg of DNA was used for each experiment.  Sonicated DNA was end-repaired following by ligation to Illumina paired end sequencing adapters (Illumina,  PE‐ 102‐ 1003). Enrichment was done using anti-methylC antibody (Eurogentech, BI-MECY-0100), following  by amplification with Illumina primers and size selection on an agarose gel. Input samples were produced for  each cell types in both procedures

value: Bergmann glia

value: 8-12 weeks


title: MeDIP_SEQ SEPTIN4 replica1.2


title: luminal control 4


title: basal control 1


title: mRNA from Arabidopsis Col-0 hae-3 hsl2-3  stage 15 flower receptacles 2

city: East Lansing

first: Chad

middle: E.

last: Niederhuth

state: M

address: 612 Wilson Road

department: Plant Biology

institute: Michigan State University

data_processing:
Reads were trimmed for quality using Fastx fastq quality trimmer with a min quality score of 13 and a min length of 32 bps. Reads were then trimmed for adaptor sequence from the 3' end using CUTADAPT with a overlap of 2bp and a min length of 32 bp. Trimmed reads were then aligned to the Arabidopsis TAIR10 genome using TOPHAT v 1.3.1 using standard settings. Reads were summed for each gene using HTseq-count and differential expression tested using DESeq v 1.5.6.
Genome Build:
h3h3_2.bed: TAIR10
h3h3_2_count.txt: TAIR10

organism: Arabidopsis thaliana

source_name: Stage 15 flower receptacles hae-3 hsl2-3 mutant

growth_protocol: Plants were grown in 16h light 8h dark at 22C

extract_protocol: Libraries were constructed from mRNA using the Illumina TruSeq RNA sample preparation kit (#RS-930-2001) following manufactuer's protocols.

tag: ecotype

value: hae-3 hsl2-3 mutant

value: Flower Receptacles, from base of flower to slightly above attachment point of floral organs, including petal, sepal, and stamen tissue in between.

tag: developmental stage

value: Stage 15 Flowers


title: mRNA from Arabidopsis Col-0 hae-3 hsl2-3  stage 15 flower receptacles 3

data_processing:
Reads were trimmed for quality using Fastx fastq quality trimmer with a min quality score of 13 and a min length of 32 bps. Reads were then trimmed for adaptor sequence from the 3' end using CUTADAPT with a overlap of 2bp and a min length of 32 bp. Trimmed reads were then aligned to the Arabidopsis TAIR10 genome using TOPHAT v 1.3.1 using standard settings. Reads were summed for each gene using HTseq-count and differential expression tested using DESeq v 1.5.6.
Genome Build:
h3h3_3.bed: TAIR10
h3h3_3_count.txt: TAIR10


title: MeDIP_SEQ PCP2 replica2

value: Purkinje cells


title: basal 6 month tumor 4


title: MeDIP_SEQ PCP2 replica1


title: MeDIP_SEQ ND1 replica2

source_name: Cerebellar granule cells

value: Cerebellar granule cells


title: MeDIP_SEQ ND1 replica1.1


title: mRNA from Arabidopsis Col-0 Wild Type stage 15 flower receptacles 3

data_processing:
Reads were trimmed for quality using Fastx fastq quality trimmer with a min quality score of 13 and a min length of 32 bps. Reads were then trimmed for adaptor sequence from the 3' end using CUTADAPT with a overlap of 2bp and a min length of 32 bp. Trimmed reads were then aligned to the Arabidopsis TAIR10 genome using TOPHAT v 1.3.1 using standard settings. Reads were summed for each gene using HTseq-count and differential expression tested using DESeq v 1.5.6.
Genome Build:
Col_WT_3.bed: TAIR10
Col_WT_3_count.txt: TAIR10

source_name: Stage 15 flower receptacles Col-0 WT

value: Wild Type


title: mRNA from Arabidopsis Col-0 Wild Type stage 15 flower receptacles 2

data_processing:
Reads were trimmed for quality using Fastx fastq quality trimmer with a min quality score of 13 and a min length of 32 bps. Reads were then trimmed for adaptor sequence from the 3' end using CUTADAPT with a overlap of 2bp and a min length of 32 bp. Trimmed reads were then aligned to the Arabidopsis TAIR10 genome using TOPHAT v 1.3.1 using standard settings. Reads were summed for each gene using HTseq-count and differential expression tested using DESeq v 1.5.6.
Genome Build:
Col_WT_2.bed: TAIR10
Col_WT_2_count.txt: TAIR10


title: mRNA from Arabidopsis Col-0 Wild Type stage 15 flower receptacles 1

data_processing:
Reads were trimmed for quality using Fastx fastq quality trimmer with a min quality score of 13 and a min length of 32 bps. Reads were then trimmed for adaptor sequence from the 3' end using CUTADAPT with a overlap of 2bp and a min length of 32 bp. Trimmed reads were then aligned to the Arabidopsis TAIR10 genome using TOPHAT v 1.3.1 using standard settings. Reads were summed for each gene using HTseq-count and differential expression tested using DESeq v 1.5.6.
Genome Build:
Col_WT_1.bed: TAIR10
Col_WT_1_count.txt: TAIR10


title: Jurkat_H3K27me3_ChipSeq_replicate2

status: Public on Jan 12 2013

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Chromatin IP against H3K27me3 in Jurkat

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

organism: Homo sapiens

source_name: T-ALL cell line

growth_protocol: Human Jurkat cells were purchased from the American Type Culture Collection (ATCC), Manassas, VA. Cells were maintained under typical conditions in RPMI media with 10% Bovine Calf Serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 20 min.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 1000 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: chip antibody

tag: antibody catalog number

tag: cell line

value: Jurkat E6-1

tag: cell number

value: 50 million

tag: antibody manufacturer

value: Abcam


title: vim3 BS-seq

status: Public on Jan 11 2013

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

data_processing:
BS-Seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics) to TAIR10 chr1..5/C/M, allowing up to 2 mismatches and retaining only uniquely-mapping reads. Identical reads were collapsed into single reads. Only reference genome cytosines covered with at least 4 reads were considered for analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: Presented as a single base-pair resolution UCSC genome browser wiggle file for each nuclear genome (1-5), where column 1 is the genomic coordinate of the cytosine and column 2 is the methylation level #C/(#C+#T).
Supplementary_files_format_and_content: For each genotype, three wiggle files were generated. Where each file represents data of methylation levels in three sequence contexts (CG, CHG, CHH)

source_name: 3wk-old leaf tissue

extract_protocol: Fragmented genomic DNA library as described in Cokus et al., Nature 2008, except directly with pre-methylated final adapters (see Feng et al., Methods Mol. Biol. 2011;733:223-38 for further information)

treatment_protocol: Genomic DNA was extracted using Qiagen DNeasy Mini Kit.

value: Columbia


title: suvr1 BS-seq


title: suvr5 BS-seq


title: vim1 BS-seq


title: suvh9 BS-seq


title: suvh4/5/6 BS-seq


title: suvh8 BS-seq


title: suvr2 BS-seq


title: vim2 BS-seq


title: suvr1/2/3/4/5 BS-seq


title: suvr3 BS-seq


title: suvh4/kyp BS-seq


title: Mouse mammary gland whole cell extract

city: Amsterdam

first: Wilbert

last: Zwart

address: Plesmanlaan 121

country: Netherlands

institute: NKI

description: whole cell extract

data_processing:
Reads were aligned to mm9 using BWA with the default settings
Peak calling was done using chip sample versus whole cell extract by two different packages
Peaks were called using MACS version 1.4.1 using a p-value cutoff of 1e-7
Peaks were called using CCAT version 3.0 using the supplied histone config file
Genome_build: mm9
Supplementary_files_format_and_content: bed and peak

source_name: C57BL/6J mouse mammary gland

growth_protocol: The mice used in this study were backcrossed several generations to the C57BL/6J background. All animal studies were carried out in accordance with the United Kingdom Home Office guidelines. A minimum of 6 pairs of mouse mammary gland pads from mice at 5-6 weeks of age were excised washed with phosphate buffered saline (PBS) and minced.

extract_protocol:
After tissue fixation and cell lysis, lysates were clarified from sonicated nuclei.Lysate was immunoprecipitated for Estrogen Receptor and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: genetic background

value: mammary gland


title: mRNA from Arabidopsis Col-0 hae-3 hsl2-3  stage 15 flower receptacles 1

data_processing:
Reads were trimmed for quality using Fastx fastq quality trimmer with a min quality score of 13 and a min length of 32 bps. Reads were then trimmed for adaptor sequence from the 3' end using CUTADAPT with a overlap of 2bp and a min length of 32 bp. Trimmed reads were then aligned to the Arabidopsis TAIR10 genome using TOPHAT v 1.3.1 using standard settings. Reads were summed for each gene using HTseq-count and differential expression tested using DESeq v 1.5.6.
Genome Build:
h3h3_1.bed: TAIR10
h3h3_1_count.txt: TAIR10


title: suvh3 BS-seq


title: suvh2 BS-seq


title: suvh5 BS-seq


title: suvh6 BS-seq


title: MeDIP_SEQ SEPTIN4 replica2


title: MeDIP_SEQ ND1 replica1.2


title: Mouse mammary gland Estrogen Receptor ChIp-seq

description: Chromatin IP  for Estrogen Receptor alpha, pooled samples from 6 mice

value: ERalpha

tag: chip antibody catalog #

tag: chip antibody manufacturer

value: Santa Cruz


title: vim1/2/3 BS-seq


title: sgs3 BS-seq


title: suvh1 BS-seq


title: suvh10 BS-seq


title: sdg2 BS-seq


title: sdg8 BS-seq


title: sde3 BS-seq


title: suvh7 BS-seq


title: ros3 BS-seq


title: rdd BS-seq

value: rdd


title: rdm1 BS-seq


title: nrpe1 BS-seq


title: rdr1 BS-seq


title: nrpb2 BS-seq


title: ref6 BS-seq


title: rdr6 BS-seq


title: rdr2 BS-seq


title: rpa2 BS-seq


title: nrpd1 BS-seq


title: mom1 BS-seq


title: msi1 BS-seq


title: idnl1 idnl2 BS-seq

value: idnl1 idnl2


title: idn2 BS-seq


title: met1 cmt3 BS-seq

value: met1 cmt3


title: met2 BS-seq


title: met1 het BS-seq

value: met1 het


title: met1 BS-seq


title: ktf1 BS-seq


title: ibm1 BS-seq


title: met1 WT BS-seq

value: met1 WT


title: fpa BS-seq

value: fpa


title: fld BS-seq

value: fld


title: idn2 idnl1/2 BS-seq

value: idn2 idnl1/2


title: sde5 BS-seq


title: fve BS-seq

value: fve


title: fca fpa BS-seq

value: fca fpa


title: fca BS-seq

value: fca


title: hen1 BS-seq


title: fas2 BS-seq


title: drm1/2 cmt3 BS-seq

value: drm1/2 cmt3


title: drm1/2 BS-seq


title: dcl2/3/4 BS-seq


title: dms4 BS-seq


title: dcl4 BS-seq


title: dnmt2 cmt3 BS-seq

value: dnmt2 cmt3


title: drm3 BS-seq

value: Columbia


title: dcl3 BS-seq


title: cmt1 BS-seq


title: drd1 BS-seq


title: dms3 BS-seq


title: dcl2 BS-seq


title: bru1 BS-seq


title: ddm1 BS-seq


title: dnmt2 drm12 BS-seq

value: dnmt2 drm12


title: clsy1 BS-seq


title: atxr56 BS-seq


title: ago7  BS-seq


title: ago8  BS-seq


title: cmt2 BS-seq


title: cmt3 BS-seq


title: ago10  BS-seq


title: ago6  BS-seq


title: ago9  BS-seq


title: ago2  BS-seq


title: ago5 BS-seq


title: ago3  BS-seq


title: ago4  BS-seq


title: ago1  BS-seq


title: dcl2/4 BS-seq


title: WT replicate 3 BS-seq

value: Wild type


title: yoon_ypgal_rep2

status: Public on Jan 10 2013

city: Oxford

first: Aino

middle: Inkeri

last: Järvelin

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

description: B.subtillis capped IVT  spike-ins added

data_processing:
Base-calling was performed using Illumina CASAVA pipeline and standard parameters.
3' sequences were extracted from demultiplexed sequencing reads for poly(A) site mapping protocols.
Reads were aligned to the S288c reference R63 genome assembly using the GSNAP aligner.
Transcript poly(A) sites were identifed from data as the base before the start of the poly(A) tail.
Reads and poly(A) sites were mapped to the annotated S.cerevisae transcriptome from Xu et al. 2009 lifted-over to match with genome version (very minor changes)
Genome_build: Saccharomyces cerevisiae S288C reference genome R63 downloaded from SGD(http://www.yeastgenome.org/)
Supplementary_files_format_and_content: Bedgraph and gff files contain poly(A) site calls from the 3'T-fill protocol.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: mid-log phase cells, OD 1

growth_protocol: Yeast cells were grown to mid-log phase (OD1) using either YPAD (1% yeast extract, 2% peptone, 1% glucose) or YPGal (1% yeast extract, 2% peptone, 1% galactose).

extract_protocol: Total RNA was isolated by a standard hot phenol method and contaminant DNA was removed by DNase I treatment. The sample was subject to different alternative transcript end or poly(A) site mapping protocol in order to map the poly(A) sites of each transcript. 3T-fill: Starting from total RNA, poly(A) RNA is reverse transcribed using a biotinylated adapter containing an anchored oligo-dT primer. After second strand synthesis, fragments are captured by streptavidin beads, end-repaired, adenylated, and ligated to a second adapter The final library is then loaded into an Illumina cluster station where the poly(A) stretch is filled in with dTTPs before the sequencing reaction starts. This enables the sequencing to start immediately after the poly(A) tail. Internal: The library was prepared as the 3T-fill but using different oligos that allows the sequencing into the poly(A) tail (from the body of the cDNA) and omitting the T-fill step on the illumina clustering station. In this case a stringent library size selection (200bp was performed). BpmI: The library was prepared as the previous one but, introducing a restriction site on the priming oligo that allows the cleavage off the poly(A) tail. RNASeq: strand specific RNASeq protocol usong dUTP digestion as previously described (PMID:21943893). Yoon: RNA-Seq protocol enriching for poly(A) containing fragments after RNA fragmentation, as previously descrived (PMID:20421314).

tag: strain

value: SLS045 (diploid, S288c background)

tag: media

value: YPGal media

tag: forward side barcode

value: CGAAAC(T)

tag: reverse side barcode

tag: protocol

value: yoon


title: yoon_ypd_rep2

description: B.subtillis capped IVT  spike-ins added

value: YPAD media


title: yoon_ypd_rep1

description: B.subtillis capped IVT  spike-ins added

value: AGCGCT(T)


title: yoon_ypgal_rep1

description: B.subtillis capped IVT  spike-ins added


title: internal_ypgal_rep3

description: B.subtillis capped IVT  spike-ins added

value: TACAAG(T)

value: internal


title: rnaseq_ypd_rep3

description: B.subtillis capped IVT  spike-ins added

value: TCCGTC(T)

value: rnaseq


title: rnaseq_ypd_rep1

description: B.subtillis capped IVT  spike-ins added

value: ATAGAT(T)


title: rnaseq_ypd_rep2

description: B.subtillis capped IVT  spike-ins added

value: GAATGA(T)


title: yoon_ypd_rep3

description: B.subtillis capped IVT  spike-ins added

value: GTATAG(T)


title: rnaseq_ypgal_rep2

description: B.subtillis capped IVT  spike-ins added


title: internal_ypgal_rep2

description: B.subtillis capped IVT  spike-ins added

value: GCCTAA(T)


title: internal_ypd_rep1

description: B.subtillis capped IVT  spike-ins added

value: ACATCG(T)


title: bpmI_ypgal_rep2

description: B.subtillis capped IVT  spike-ins added

value: CGTGAT(T)

value: bpmI


title: internal_ypgal_rep1

description: B.subtillis capped IVT  spike-ins added

value: SLS045 (diploid, S288c background)


title: bpmI_ypd_rep2

description: B.subtillis capped IVT  spike-ins added


title: rnaseq_ypgal_rep1

description: B.subtillis capped IVT  spike-ins added

value: YPGal media


title: bpmI_ypd_rep3

description: B.subtillis capped IVT  spike-ins added

value: GTAGCC(T)


title: bpmI_ypgal_rep1

description: B.subtillis capped IVT  spike-ins added

value: AAGCTA(T)


title: bpmI_ypgal_rep3

description: B.subtillis capped IVT  spike-ins added


title: rnaseq_ypgal_rep3

description: B.subtillis capped IVT  spike-ins added


title: 3tfill_ypgal_rep3

description: B.subtillis capped IVT  spike-ins added


title: bpmI_ypd_rep1

description: B.subtillis capped IVT  spike-ins added

value: YPAD media


title: 3tfill_ypgal_rep2

description: B.subtillis capped IVT  spike-ins added


title: 3tfill_ypgal_rep1

description: B.subtillis capped IVT  spike-ins added


title: 3tfill_ypd_rep3

description: B.subtillis capped IVT  spike-ins added


title: yoon_ypgal_rep3

description: B.subtillis capped IVT  spike-ins added

value: yoon


title: 3tfill_ypd_rep2

description: B.subtillis capped IVT  spike-ins added


title: 3tfill_ypd_rep1

description: B.subtillis capped IVT  spike-ins added


title: internal_ypd_rep3

description: B.subtillis capped IVT  spike-ins added

value: TACAAG(T)


title: internal_ypd_rep2

description: B.subtillis capped IVT  spike-ins added

value: internal


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency second long time course - t=12h

city: Los Angeles

first: Sabeeha

last: Merchant

state: California

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

institute: University of California Los Angeles

description: Illumina's RNA-Seq whole transcriptome analysis

library_source: non-genomic

data_processing:
RNAs were sequenced at Illumina and Los Alamos National Laboratory on a GAIIx system for estimating transcript abundance in each of the three N-deficiency time course experiments. The reads were aligned using bowtie  in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates.
Processed files correpond to the bowtie standard output format.

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas cultured cells

growth_protocol: Chlamydomonas reinhardtii strains CC-3269/ 2137 (wild-type nit2 mt+) were cultured at 24°C (180 rpm, ~90 mmol/m2/s, cool white fluorescent bulbs at 4100K and warm white fluorescent bulbs at 3000K were used in the ratio of 2:1) in TAP medium, -N TAP or TAP suppemented with various amounts of NH4

extract_protocol: Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced  by whole transcriptome analysis.

treatment_protocol: N-starved cells were grown to approximately 4x10^6 cells/mL, collected by centrifugation (2170 xg, room temperature, 5 min), washed and resuspended in the same medium to 2 x 10^6 cells/mL. For growth in reduced nitrogen, N-free TAP medium supplemented with NH4Cl to 7, 3.5, 1.75, 0.7 or 0.35 mM. Cultures were inoculated to 1x10^5 cells/mL and collected for RNA at 1 x 10^6 cells/mL, when the growth rates of all cultures were identical

tag: group

value: 2nd long time course

tag: treatment

value: Nitrogen deficiency

tag: time

tag: medium

value: TAP

tag: sequencing cycles / read length

tag: library type

value: paired-end

tag: mean/std insert size


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency second long time course - t=24h


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency second long time course - t=48h


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency first long time course - t=8h

value: 1st long time course


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency second long time course - t=2h


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency second long time course - t=0h


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency second long time course - t=8h


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency first long time course - t=8h (2)

value: single-end


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency first long time course - t=30m


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency first long time course - t=30m (2)


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency first long time course - t=0


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency first long time course - t=4h


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency short time course - t=60m

value: short time course


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency short time course - t=12m


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency short time course - t=30m


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency short time course - t=45m


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency short time course - t=18m


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency short time course - t=8m


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency short time course - t=24m


title: CcPri-5SAGE

city: Shatin

first: CHI KEUNG

last: CHENG

address: Rm 386, Science Center South Block

department: Life Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
Accuracy of all sequence reads were checked using a Phred-equivalent quality score
Perl scripts were written to remove low quality sequences, extract valid ditags and individual tags
Individual tags were mapped to the Coprinopsis cinerea okayama7#130 genomic sequence without a single mismatch
Expression level of individual genes was assessed by summing up the occurrence of all the tags mapped to the putative 5'-UTR and divided this number by the total occurrence of all genome-mapped tags, then multiplied by 100,000 and expressed as tags per hundred thousand in the corresponding stage

Genome_build: Coprinopsis cinerea okayama7#130; GCF_000182895.1
Supplementary_files_format_and_content: Tab-delimited text file containing genes expressed in either developmental stages, myc1 and pri1 denotes respective normalized tag counts

organism: Coprinopsis cinerea

source_name: Stage 1 primordium

growth_protocol: The mycelium of the dikaryotic C. cinerea strain was grown at 37C on solid YMG medium and harvested after 7 days. Stage 1 primordium was grown at 25C under a light/dark regime of 14/10hr and harvested when the primordium reached about 5mm.

extract_protocol:
Total RNA was extracted using Trizol reagent.
mRNA was isolated from the total RNA and subsequently reverse-transcribed using a template switching approach. Double stranded cDNA was synthesized and digested with MmeI. 50bp digested fragments were excised and purified from 15% polyacrylamide gel. The tags were ligated using T4 DNA ligase to form 100bp ditags.

tag: developmental stage

value: Stage 1 primordium


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency short time course - t=4m


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency short time course - t=0'


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency short time course - t=0


title: JLDDhoBV05TS2

description: Chlamydomonas reinhardtii hmox1 mutant

data_processing:
Illumina Casava1.8 software used for basecalling.
The reads were aligned using bowtie  in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome.
Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates.
Genome_build: version 4.0 assembly of the Chlamydomonas genome
Supplementary_files_format_and_content: Tab-delimited table with all genes (rows) and expression estimates (columns, in RPKMs) for every single library (or raw file, for a total or 16).

growth_protocol: All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness.

extract_protocol: Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina.

treatment_protocol: Cells (4A+ or hmox1) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit.

value: hmox1 mutant

tag: light

value: 0.5h white light


title: CcMyc-5SAGE

source_name: Vegetative mycelium

value: Vegetative mycelium


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency short time course - t=2m


title: JLDDhoBV05TS1

description: Chlamydomonas reinhardtii hmox1 mutant


title: JLDDhoBV0TS2

description: Chlamydomonas reinhardtii hmox1 mutant

value: dark


title: JLDDhoBV0TS1

description: Chlamydomonas reinhardtii hmox1 mutant


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency first long time course - t=4h (2)


title: JLDDhoNT05TS2

description: Chlamydomonas reinhardtii hmox1 mutant

value: 0 mM


title: Chlamydomonas reinhardtii 2137 - Nitrogen deficiency first long time course - t=0 (2)


title: JLDD4ABV05TS2

description: Chlamydomonas reinhardtii 4A+ wild-type

value: 4A+ wild-type


title: JLDDhoNT0TS2

description: Chlamydomonas reinhardtii hmox1 mutant


title: JLDD4ABV0TS1

description: Chlamydomonas reinhardtii 4A+ wild-type


title: JLDD4ABV0TS2

description: Chlamydomonas reinhardtii 4A+ wild-type


title: JLDD4ABV05TS1

description: Chlamydomonas reinhardtii 4A+ wild-type


title: NAc_withdrawal_rep2

city: Farmington

first: Jodi

last: Eipper-Mains

state: CT

address: 263 Farmington Ave.

department: Genetics & Developmental Biology

institute: University of Connecticut Health Center

data_processing:
Sequences and quality scores were extracted from image files using GAPipeline software v1.0 or v1.3.2.
Sequences were aligned to the Mus musculus genome (2007, mm9; NCBI Build 37) using Bowtie v0.12.7 permitting multi-alignment and allowing up to two mismatches. Ambiguous alignments were resolved using the Spliced Paired-end Aligner Perl script (Brooks et al. 2011).
Normalized mRNA expression was calculated as RPKM (reads per kilobase gene model per million mapped reads) (Mortazavi et al. 2008) from aligned sequence reads.
Z-scores were computed from frequency data using the following equation: (x − μ)/ σ; x, sample frequency; μ, mean across all samples; σ, standard deviation across all samples.
Gene expression data (Z-scores) were hierarchically clustered using Gene Cluster v3.0; heat maps were generated using Java Treeview v1.1.6r2.
Genome_build: mm9, NCBI Build 37
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each replicate and composite files of all RPKM values.

source_name: Nucleus accumbens

growth_protocol: Adult male C57BL/6 mice (Jackson Laboratories, Bar Harbor, ME; 2–5months old) were group-housed in the animal facility at the University of Connecticut Health Center on a 12h light/dark cycle (lights, 0700–1900h) and handled in accordance with Institutional Animal Care and Use Committee guidelines. After acclimation for 1 week, animals were handled for 1min/day for 2–3days prior to injections. On each treatment day, animals were allowed to acclimate to the behavior room for 45–60min before beginning injections.

extract_protocol:
Nucleus accumbens punches were taken from individual mice (at least eight animals/treatment group). Total RNA was prepared using TRIzol. Total RNA used for NAc library preparation consisted of equal amounts of RNA from eight individual mice for each treatment. One Saline, one Cocaine and one 8-day Withdrawal mRNA-Seq library was prepared from each pooled RNA sample according to manufacturer’s specifications (Illumina, San Diego, CA, USA). Briefly, total RNA was treated with DNase I; poly(A)+ RNA purified using Dynal magnetic beads (Invitrogen) was fragmented by partial alkaline hydrolysis (Ambion, Grand Island, CA, USA) and reverse-transcribed using random primers and SuperScript II (Invitrogen). cDNA was size-selected (∼200bp insert) on 2% agarose gels.
Libraries were prepared for sequencing using the Paired-End DNA Sample Prep Kit (Illumina). Nucleus accumbens libraries were sequenced in nine lanes (three technical replicates per sample) on an Illumina GAIIx using a 37-cycle paired-end sequencing protocol.

treatment_protocol: Animals were given Saline (10 ml/kg/day) or Cocaine (10 or 20mg/kg/day) intraperitoneally for 7days and locomotor activity was monitored daily using a 15′′ × 15′′ Plexiglas chamber; after the seventh injection, locomotor activity was threefold higher in mice receiving Cocaine than in mice receiving Saline. Animals were sacrificed by decapitation 24h after the final injection with the exception of mice in the Withdrawal groups, which were kept in the home cage for 8 days after the final Cocaine dose prior to tissue harvest.

tag: tissue

value: Nucleus accumbens

value: Withdrawal


title: NAc_cocaine_rep3

value: Cocaine


title: NAc_saline_rep3

value: Saline


title: JLDD4ANT0TS1

description: Chlamydomonas reinhardtii 4A+ wild-type


title: JLDD4ANT05TS1

description: Chlamydomonas reinhardtii 4A+ wild-type


title: NAc_withdrawal_rep1


title: JLDDhoNT05TS1

description: Chlamydomonas reinhardtii hmox1 mutant


title: NAc_cocaine_rep2


title: RNA-Seq (Total RNA) CD4 Primary Cells; RNA.RS19124

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) CD4 Primary Cells
Library name: lib-RNA.RS19124
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15261
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7018
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing: Various levels of processed data files will be made available as this project proceeds.

source_name: flow sorted CD4+ Cells, year 37; RNA.RS19124

extract_protocol: Library construction protocol: Illumina TruSeq RNA PART# 15008136 REVISION A

tag: sample alias

tag: sample common name

value: CD4 Primary Cells

tag: disease

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: year 37

value: Male

value: Hispanic

value: mRNA-Seq

value: Ambion Ribopure

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: Random Primers(hexamers)

value: TruSeq RNA

value: cDNA

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: RNA-Seq (Total RNA) Fetal Adrenal Gland; RNA.RS20008

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Adrenal Gland
Library name: lib-RNA.RS20008
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15273
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14474
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Adrenal Gland primary tissue, day 85; RNA.RS20008

value: Fetal Adrenal Gland

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: day 85

value: Female

value: Ambion mirVana miRNA isolation kit


title: NAc_saline_rep1

value: Nucleus accumbens

tag: strain

value: Saline


title: RNA-Seq (Total RNA) CD8 Primary Cells; RNA.RS19125

description:
sample_term_id: CL_0000625
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) CD8 Primary Cells
Library name: lib-RNA.RS19125
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15257
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7035
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: flow sorted CD8+ Cells, year 37; RNA.RS19125

value: CD8 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: year 37

value: Male

value: Hispanic

value: mRNA-Seq

value: Ambion Ribopure


title: RNA-Seq (Total RNA) CD8 Primary Cells; RNA.RS19107

description:
sample_term_id: CL_0000625
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) CD8 Primary Cells
Library name: lib-RNA.RS19107
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15259
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5352
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: flow sorted CD8+ Cells,year 21; RNA.RS19107

value: year 21

value: Caucasian

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: Random Primers(hexamers)

value: TruSeq RNA

value: cDNA

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: NAc_cocaine_rep1

value: Nucleus accumbens

value: Cocaine


title: Digital Genomic Footprinting assay of Fetal Placenta Tissue; DGF.DS20346

description:
sample_term_id: UBERON_0001987
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS20346
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14997
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11433
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Placenta primary tissue, day 113; DGF.DS20346

extract_protocol: Library construction protocol: Single read - Illumina

value: Fetal Placenta

tag: molecule

value: genomic DNA

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: day 113

value: Female

value: Digital Genomic Footprinting

value: Qiagen minElut


title: Digital Genomic Footprinting assay of Fetal Spinal Cord; DGF.DS20351

description:
sample_term_id: UBERON_0002240
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS20351
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15017
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11311
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Spinal, Cord primary tissue, day 113; DGF.DS20351

value: Fetal Spinal Cord


title: Digital Genomic Footprinting assay of Fetal Muscle, Leg; DGF.DS20239

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS20239
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15027
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11453
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Muscle, Leg primary tissue, day 113; DGF.DS20239

value: Fetal Muscle, Leg


title: Digital Genomic Footprinting assay of Fetal Muscle, Trunk; DGF.DS20242

description:
sample_term_id: UBERON_0001774
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS20242
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15022
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11446
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Muscle, Trunk primary tissue, day 113; DGF.DS20242

value: Fetal Muscle, Trunk


title: Digital Genomic Footprinting assay of Fetal Stomach Tissue; DGF.DS17878

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS17878
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14993
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7168
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal primary tissue, day 98; DGF.DS17878

value: Fetal Stomach

value: day 98


title: JLDD4ANT0TS2

description: Chlamydomonas reinhardtii 4A+ wild-type

value: 4A+ wild-type

value: 0 mM

value: dark


title: Digital Genomic Footprinting assay of Fetal Muscle, Back; DGF.DS17767

description:
sample_term_id: UBERON_0002324
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS17767
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15032
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8377
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Muscle, Back primary tissue, day 91; DGF.DS17767

value: Fetal Muscle, Back

value: genomic DNA

value: day 91

value: Male


title: Digital Genomic Footprinting assay of CD4 Primary Cells; DGF.DS17212

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS17212
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14987
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5345
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: flow sorted CD4+ Cells,year 21; DGF.DS17212

value: CD4 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: year 21

value: Caucasian


title: JLDDhoNT0TS1

description: Chlamydomonas reinhardtii hmox1 mutant

value: hmox1 mutant


title: RNA-Seq (Total RNA) Fetal Renal Cortex, Left; RNA.RS19411

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Renal Cortex, Left
Library name: lib-RNA.RS19411
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15220
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10021
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Kidney, renal, cortex, Left primary tissue, day 105; RNA.RS19411

value: Fetal Renal Cortex, Left

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: day 105

value: mRNA-Seq

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: Random Primers(hexamers)

value: TruSeq RNA

value: cDNA

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: RNA-Seq (Total RNA) Fetal Renal Pelvis; RNA.RS19410

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Renal Pelvis
Library name: lib-RNA.RS19410
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15180
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8347
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Kidney, renal, pelvis primary tissue, day 105; RNA.RS19410

value: Fetal Renal Pelvis

value: Female


title: JLDD4ANT05TS2

description: Chlamydomonas reinhardtii 4A+ wild-type

source_name: Chlamydomonas cultured cells

value: 4A+ wild-type

value: 0 mM

value: 0.5h white light


title: RNA-Seq (Total RNA) Fetal Adrenal Gland; RNA.RS20009

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Adrenal Gland
Library name: lib-RNA.RS20009
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15271
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14470
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Adrenal Gland primary tissue, day 101; RNA.RS20009

value: Fetal Adrenal Gland

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: day 101

value: Male


title: RNA-Seq (Total RNA) Fetal Kidney, Left; RNA.RS19027

description:
sample_term_id: UBERON_0004538
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Kidney, Left
Library name: lib-RNA.RS19027
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15184
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10029
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Kidney, Left primary tissue, day 96; RNA.RS19027

value: Fetal Kidney, Left

value: UW

value: fetal

value: day 96

value: mRNA-Seq

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit


title: RNA-Seq (Total RNA) Fetal Adrenal Gland; RNA.RS19024

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Adrenal Gland
Library name: lib-RNA.RS19024
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15253
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10067
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Adrenal Gland primary tissue, day 108; RNA.RS19024

value: day 108

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: Random Primers(hexamers)

value: TruSeq RNA

value: cDNA

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: RNA-Seq (Total RNA) Fetal Kidney; RNA.RS18774

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Kidney
Library name: lib-RNA.RS18774
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15170
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15169
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Kidney primary tissue, day 108; RNA.RS18774

value: Fetal Kidney

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Female


title: RNA-Seq (Total RNA) Fetal Intestine, Large; RNA.RS18768

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Intestine, Large
Library name: lib-RNA.RS18768
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15236
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8426
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Intestine, Large primary tissue, day 105; RNA.RS18768

value: Fetal Intestine, Large

value: Primary Tissue

value: day 105


title: RNA-Seq (Total RNA) Fetal Intestine, Small; RNA.RS18767

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Intestine, Small
Library name: lib-RNA.RS18767
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15226
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15225
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Intestine, Small primary tissue, day 98; RNA.RS18767

value: Fetal Intestine, Small

value: UW

value: fetal

value: day 98


title: RNA-Seq (Total RNA) Fetal Intestine, Large; RNA.RS18762

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Intestine, Large
Library name: lib-RNA.RS18762
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15242
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8446
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Intestine, Large primary tissue, day 115; RNA.RS18762

value: day 115

value: Male

value: mRNA-Seq

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit


title: RNA-Seq (Total RNA) Fetal Intestine, Large; RNA.RS18764

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Intestine, Large
Library name: lib-RNA.RS18764
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15240
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8434
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Intestine, Large primary tissue, day 91; RNA.RS18764

value: day 91

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: Random Primers(hexamers)

value: TruSeq RNA

value: cDNA


title: RNA-Seq (Total RNA) Fetal Intestine, Small; RNA.RS18763

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Intestine, Small
Library name: lib-RNA.RS18763
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15230
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7059
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal primary tissue, day 115; RNA.RS18763

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: RNA-Seq (Total RNA) Fetal Renal Cortex; RNA.RS18155

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Renal Cortex
Library name: lib-RNA.RS18155
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15208
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7112
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal primary tissue, day 120; RNA.RS18155

value: Fetal Renal Cortex

value: Primary Tissue

value: day 120

value: Female


title: RNA-Seq (Total RNA) Fetal Intestine, Small; RNA.RS18765

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Intestine, Small
Library name: lib-RNA.RS18765
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15228
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8408
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Intestine, Small primary tissue, day 120; RNA.RS18765

value: Fetal Intestine, Small

value: UW

value: fetal


title: RNA-Seq (Total RNA) Fetal Renal Cortex, Left; RNA.RS18153

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Renal Cortex, Left
Library name: lib-RNA.RS18153
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15223
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7227
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal primary tissue, day 105; RNA.RS18153

value: Fetal Renal Cortex, Left

value: day 105

value: Male

value: mRNA-Seq


title: RNA-Seq (Total RNA) Fetal Renal Pelvis, Left; RNA.RS18154

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Renal Pelvis, Left
Library name: lib-RNA.RS18154
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15201
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7261
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal primary tissue, day 105; RNA.RS18154

value: Fetal Renal Pelvis, Left

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: Random Primers(hexamers)


title: RNA-Seq (Total RNA) Fetal Kidney; RNA.RS18152

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Kidney
Library name: lib-RNA.RS18152
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15172
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7065
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal primary tissue, day 85; RNA.RS18152

value: Fetal Kidney

value: University of Washington, Congenital Defects Lab. Ian Glass

value: day 85

value: TruSeq RNA

value: cDNA

value: Proprietary


title: RNA-Seq (Total RNA) Fetal Intestine, Small; RNA.RS18148

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Intestine, Small
Library name: lib-RNA.RS18148
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15232
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7062
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal primary tissue, day 91; RNA.RS18148

value: Fetal Intestine, Small

value: Primary Tissue

value: day 91

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: RNA-Seq (Total RNA) Fetal Intestine, Small; RNA.RS18147

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Intestine, Small
Library name: lib-RNA.RS18147
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15234
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8412
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Intestine, Small primary tissue, day 108; RNA.RS18147

value: UW

value: fetal

value: day 108

value: Female


title: Digital Genomic Footprinting assay of Moblized CD34 Primary Cells; DGF.DS12734

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS12734
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15010
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2401
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: flow sorted CD34+ cells from cord blood; DGF.DS12734

value: CD34 Primary Cells

value: genomic DNA

value: FHCRC HEIMFELD

value: Primary Cell

value: 33 years

value: Caucasian

value: Digital Genomic Footprinting

value: Qiagen minElut


title: RNA-Seq (Total RNA) Fetal Kidney; RNA.RS18150

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Kidney
Library name: lib-RNA.RS18150
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15165
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10033
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Kidney primary tissue, day 105; RNA.RS18150

value: Fetal Kidney

value: University of Washington, Congenital Defects Lab. Ian Glass

value: day 105

value: mRNA-Seq

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: Random Primers(hexamers)

value: TruSeq RNA

value: cDNA

value: Proprietary


title: RNA-Seq (Total RNA) Fetal Kidney; RNA.RS18151

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Kidney
Library name: lib-RNA.RS18151
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15175
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15174
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Kidney primary tissue, day 87; RNA.RS18151

value: Primary Tissue

value: UW

value: fetal

value: day 87

value: Male

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: RNA-Seq (Total RNA) Fetal Renal Pelvis, Left; RNA.RS20100

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Renal Pelvis, Left
Library name: lib-RNA.RS20100
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15195
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9973
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Kidney, renal, pelvis, Left primary tissue, day 120; RNA.RS20100

value: Fetal Renal Pelvis, Left

value: day 120

value: Ambion mirVana miRNA isolation kit


title: RNA-Seq (Total RNA) Fetal Adrenal Gland; RNA.RS18144

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Adrenal Gland
Library name: lib-RNA.RS18144
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15255
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10073
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Adrenal Gland primary tissue, day 108; RNA.RS18144

value: Fetal Adrenal Gland

value: University of Washington, Congenital Defects Lab. Ian Glass

value: day 108


title: RNA-Seq (Total RNA) Fetal Intestine, Large; RNA.RS18149

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Intestine, Large
Library name: lib-RNA.RS18149
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15244
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7048
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal primary tissue, day 120; RNA.RS18149

value: Fetal Intestine, Large

value: Female

value: mRNA-Seq

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit


title: RNA-Seq (Total RNA) Fetal Renal Pelvis, Right; RNA.RS20089

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Renal Pelvis, Right
Library name: lib-RNA.RS20089
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15188
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9945
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Kidney, renal, pelvis, Right primary tissue, day 105; RNA.RS20089

value: Fetal Renal Pelvis, Right

value: Primary Tissue

value: day 105

value: Random Primers(hexamers)

value: TruSeq RNA

value: cDNA

value: Proprietary


title: RNA-Seq (Total RNA) Fetal Renal Pelvis, Left; RNA.RS20099

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Renal Pelvis, Left
Library name: lib-RNA.RS20099
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15197
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9964
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Kidney, renal, pelvis, Left primary tissue, day 105; RNA.RS20099

value: Fetal Renal Pelvis, Left

value: UW

value: fetal

value: Male

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: RNA-Seq (Total RNA) Fetal Renal Pelvis, Right; RNA.RS20090

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Renal Pelvis, Right
Library name: lib-RNA.RS20090
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15186
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9954
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Kidney, renal, pelvis, Right primary tissue, day 120; RNA.RS20090

value: University of Washington, Congenital Defects Lab. Ian Glass

value: day 120

value: Ambion mirVana miRNA isolation kit


title: RNA-Seq (Total RNA) Fetal Renal Pelvis, Right; RNA.RS20088

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Renal Pelvis, Right
Library name: lib-RNA.RS20088
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15190
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7266
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal primary tissue, day 105; RNA.RS20088

value: mRNA-Seq


title: RNA-Seq (Total RNA) Fetal Renal Pelvis; RNA.RS18775

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Renal Pelvis
Library name: lib-RNA.RS18775
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15182
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8352
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Kidney, renal, pelvis primary tissue, day 91; RNA.RS18775

value: Fetal Renal Pelvis

value: day 91

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit


title: RNA-Seq (Total RNA) Fetal Intestine, Large; RNA.RS18766

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Intestine, Large
Library name: lib-RNA.RS18766
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15238
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8430
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Intestine, Large primary tissue, day 98; RNA.RS18766

value: Fetal Intestine, Large

value: Primary Tissue

value: day 98

value: Female

value: Random Primers(hexamers)


title: RNA-Seq (Total RNA) Fetal Renal Cortex, Right; RNA.RS20087

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Renal Cortex, Right
Library name: lib-RNA.RS20087
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15210
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9994
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Kidney, renal, cortex, Right primary tissue, day 105; RNA.RS20087

value: Fetal Renal Cortex, Right

value: UW

value: day 105

value: TruSeq RNA

value: cDNA

value: Proprietary


title: RNA-Seq (Total RNA) Fetal Renal Cortex, Right; RNA.RS20086

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Renal Cortex, Right
Library name: lib-RNA.RS20086
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15212
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7231
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal primary tissue, day 105; RNA.RS20086

value: University of Washington, Congenital Defects Lab. Ian Glass

value: fetal

value: Male

value: Ambion mirVana miRNA isolation kit

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: RNA-Seq (Total RNA) Fetal Renal Cortex; RNA.RS20085

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Renal Cortex
Library name: lib-RNA.RS20085
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15203
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11588
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Kidney, renal, cortex primary tissue, day 97; RNA.RS20085

value: Fetal Renal Cortex

value: day 97

value: mRNA-Seq

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit


title: RNA-Seq (Total RNA) Fetal Heart; RNA.RS20083

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Heart
Library name: lib-RNA.RS20083
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15249
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10060
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Heart primary tissue, day 91; RNA.RS20083

value: Fetal Heart

value: Primary Tissue

value: day 91

value: Female