title: Bisulfite-Seq analysis of WGBS_Lib 62 derived from human adult CD14 cells; WGBS_Lib 62

description:
sample_term_id: CL_0001054
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 62
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.17363
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.17377
****************
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: Adult Primary CD14+ cells; WGBS_Lib 62

value: BioSam 1234

value: CD14 Primary Cells

value: adult CD14

value: T4 Ligase (2,000U/ul) 16C o/n

value: Illumina paired end adapter

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: SPRI Beads

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of WGBS_Lib 67 derived from human fAdrenal cells; WGBS_Lib 67

status: Public on Jan 15 2014

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 67
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.16342
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.16344
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary fetal adrenal tissue; WGBS_Lib 67

extract_protocol: Library construction protocol: Genomic DNA (1.5~5µg) was fragmented to 100-500 bp using a Covaris S2. Purified DNA fragments were end-repaired. After A-tailing, the DNA fragments were ligated with methylated paired-end adapters. Adapter-attached DNA fragments of 300-400 bp, which contain 150-250 bp genomic DNA inserts, were gel-purified. The purified DNA fragments were subjected to two cycles of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen). Adapter-attached, bisulfite-converted DNA molecules were enriched by PCR using PfuTurboCx Hotstart DNA polymerase (Stratagene). The PCR amplified DNA fragments were subjected to a second gel size selection to remove PCR primers and adapter dimers. The enriched library was quantified using a Qubit fluorometer and Quant-iT dsDNA HS Assay Kit. Library sequencing was performed using 101 BP PE Illumina technology.

tag: sample alias

value: BioSam 1244

tag: sample common name

value: Fetal Adrenal Gland

value: Post-Mortem

value: presumed normal

tag: disease

value: Fetal Adrenal

value: Unknown

value: Male

value: Primary Tissue

value: Adrenal

value: University of Washington

value: 97.0 Days

value: 2x5hrs Epitect Kit

value: 5 ug

value: Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: Covaris S2 (TM)


title: Endogenous small RNAs from rice, control ROOTS (30')

city: Bellaterra (Cerdanyola del Vallés)

first: Sonia

last: Campo

state: Barcelona

address: Parc de Recerca UAB Edifici CRAG, Campus UAB

country: Spain

institute: Center for Research in Agricultural Genomics (CRAG)

description:
Total Endogenous small RNAs from rice, control leaves (30')
library strategy: Barcode

library_source: transcriptomic

data_processing: Small RNA sequences were parsed from FASTA formatted files containing reads from 454 sequencing and assigned to each one of the 8 specific libraries (leaf and root tissues, treated or not with elicitors for 30 min or 2h) through identification of the small RNA/adapter boundaries and barcode analysis. The adapter sequences in the 454 sequencing reads were removed and the remaining sequences were collected and mapped to the rice genome (Oryza sativa, version 5.0 - http://www.tigr.org/tdb/e2k1/osa1/pseudomolecules/info.shtml) using BLASTn. The unique RNA sequences that perfectly matched the genome were subjected to subsequent analysis.

molecule: total RNA

organism: Oryza sativa Japonica Group

source_name: Control Roots

growth_protocol:
Leaf tissues were collected from 15 day-old Nipponbare rice plants that had been grown at 28ÂºÂ±2ÂºC using a 16-h/8-h light/dark cycle
Root tissues were collected from rice seedings that had been grown in square-plates (24cmx24cm) containing Â½ MS agar medium for 8 days, grown at 28ÂºÂ±2ÂºC using a 16-h/8-h light/dark cycle. During this period, rice roots were allowed to grow over a piece of sterile paper placed over the agar medium.
Elicitors from the Magnaporthe oryzae strain 18.1 were prepared as previously described (Casacuberta JM, Raventos D, Puigdomenech P and Segundo BS. (1992). Expression of the Gene Encoding the PR-Like Protein PRms in Germinating Maize Embryos. Mol Gen Genet 234(1): 97-104.)

extract_protocol: Total RNA was extracted from tissues using TRIzol reagent according to manufacturerâs instructions (Invitrogen). 300 Âµg of total RNA were used for construction of small RNA libraries as described (Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Carrington JC. 2007. Genome-Wide Profiling and Analysis of Arabidopsis siRNAs. PLoS Biol 5(3): e57.; Donaire L, Wang Y, Gonzalez-Ibeas D, Mayer KF, Aranda MA, Llave C. 2009. Deep-sequencing of plant viral small RNAs reveals effective and widespread targeting of viral genomes. Virology 392(2): 203-214.)

treatment_protocol:
Elicitor treatment of rice leaves was performed by spraying the rice plants with 100 mL of a Magnaporthe oryzae 18.1 suspension (300 Âµg elicitor/mL) of sterile water containing 0.02% Tween-20 (v/v)
Elicitor treatment of rice roots was performed by covering the roots covered 30mL of a Magnaporthe oryzae 18.1 suspension (300 Âµg elicitor/mL) of sterile water containing 0.02% Tween-20 (v/v) and another piece of sterile paper

tag: age

value: 15-days old plants

tag: cultivar

value: Nipponbare


title: WT 6hr Rep 1

city: East Lansing

first: Quan

last: Zeng

state: MI

address: 578 Wilson Rd. CIPS103

department: Plant, Soil, and Microbial Sciences

institute: Michigan State University

data_processing:
Basecalls were performed by Illumina Real Time Analysis software v 1.13.48. Demultiplexing and FASTQ conversion by Illumian BCL2Fastq v1.8.2
Reads were trimmed of Illumina adapter and low quality bases with Trimmomatic v0.22
Reads were mapped to the  Erwinia amylovora ATCC 49946 genome (Accession NC_013971) and Erwinia amylovora ATCC 49946 plasmid 1 (Accession NC_013972) using TopHat (v2.0.4) with parmeters --mate-inner-dist 110 --mate-std-dev 60 --coverage-search --microexon-search --library-type fr-secondstrand --segment-length 12 --segment-mismatches 1 --min-intron-length 10 --max-intron-length 100 --min-coverage-intron 10 --max-coverage-intron 100 --min-segment-intron 10 --max-segment-intron 100 --b2-very-sensitive --transcriptome-index /Users/kmcarr/Documents/PublicGenomeData/Erwinia_amylovora/ATCC_49946/gbrowse/tophat_trxIndex
Read aligned to previously annotated rRNAs or tRNAs were filtered out
From the remaining reads aligned to previously unannotated regions putative transcripts were defined (XLOCS) with cufflinks/cuffmerge (v2.0.2)
Expression from each sample for each XLOC was estimated (FPKM) with cuffdiff (v2.0.2) with parameters -p 8 -u -b /usr/local/PUBLIC_DATA/Erwinia_amylovora/ATCC_49946/gbrowse/Eam_ATCC49964_pEA29.fasta -L Q-6,Q-12,WT-6,WT-12 --library-type fr-secondstrand --emit-count-tables --max-bundle-frags 1000000 merged.gtf <BAM file List>
Genome_build: NC_013971.1,  NC_013972.1
Supplementary_files_format_and_content: merged.gtf file generated by cuffmerge is standard GTF with definitions of putative transcripts identified by cufflinks, genes.fpkm_tracking tab delimited text with expression estimates generated by cuffdiff; FPKM values are averaged across biological replicates for each condition

organism: Erwinia amylovora

source_name: bacteria cells cultured in hrp inducing minimal medium

growth_protocol: Bacterial strains were cultured in LB broth supplemented with appropriate antibiotics overnight.  Cells were harvested by centrifugation, washed by 0.5XPBS, and were resuspended in hrp-inducing minimal medium.  The cell concentration of each strain in hrp-inducing minimal medium was adjusted to 0.5 (OD600). Cells were cultured for 6 and 12 hours prior to RNA isolation.

extract_protocol:
Total bacterial RNA including the sRNAs was isolated by miRNeasy kit from Qiagen following the kit instruction.  DNA was removed from an on column digestion using an Rnase-free Dnase set (Qiagen).
Libraries were constructed using the Illumina TruSeq small RNA Library Prep Kit (direct ligation of adapters to RNA) with slight modification. The final library size selection included a much larger range of fragment sizes than the usual narrow range mean to capture only miRNAs

tag: strain

tag: genotype

value: wild type

tag: time

value: 6 h

tag: sample type

value: small RNAs 50-350 nt


title: Whole Genome Sequencing analysis of  derived from human HUES64 cells; WGS_Lib 4

description:
sample_term_id: NTR_0000853
assay_term_id: OBI_0000124
nucleic_acid_term_id: SO_0000352
Design description: WGS REMC Sequencing on Illumina
Library name: WGS_Lib 4
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.18844
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.18849
****************
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: Harvard University ES Cell 64 AKA HUES 64; WGS_Lib 4

extract_protocol: Library construction protocol: Genomic DNA (0.5~1.5µg) was fragmented to 100-1,000 bp using a Covaris S2. Purified DNA fragments were end-repaired. After A-tailing, the DNA fragments were ligated with paired-end adapters. Adapter-attached DNA fragments of 470-570 bp, which contain 350-450 bp genomic DNA inserts, were gel-purified. The purified DNA fragments were utilized as templates for PCR enrichment (5-6 cycles) by using Phusion HF polymerase (NEB). The PCR amplified DNA fragments were purified using 1.5X of Agencourt AMPure XP beads (Beckman Coulter) to remove PCR primers. The enriched library was quantified using a Qubit fluorometer and Quant-iT dsDNA HS Assay Kit (Invitrogen). Library sequencing was performed using 101 BP PE Illumina

value: BioSam 1820

value: HUES64 Cell Line

tag: lineage

value: embrionic stem cell

tag: medium

value: HUES general media - KO DMEM, 20% KSR, bFGF (10ng/mL)

value: presumed normal

tag: passage

tag: line

value: adherence

tag: batch

value: BioSAli 2829

value: Cell Line

value: undifferentiated

tag: Sex

value: Harvard

value: Covaris shearing conditions:four cycles of two consecutive treatments (T1-Duty cycle 5%, Intensity  5, cycle per burst 200, duration 30 sec; T2-Duty cycle 1%, Intensity  5, cycle per burst 200, duration 5 sec).

value: Whole Genome Sequencing


title: Endogenous small RNAs from rice, elicitor-treated ROOTS (2h)

description:
Total Endogenous small RNAs from rice, elicitor leaves (2h)
library strategy: Barcode

source_name: Elicitor Roots

value: 15-days old plants


title: RNA-Seq analysis of cDNA_Lib 8 derived from human CD56+ ectoderm cells; cDNA_Lib 8

description:
sample_term_id: CL_0000221
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: mRNA-Seq for REMC on Illumina
Library name: cDNA_Lib 8
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15044
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15045
****************
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: CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; cDNA_Lib 8

extract_protocol: Library construction protocol: Direct RNA-seq method based on RNA 3' linker ligation, unpublished

value: BioSam 803

value: hESC Derived CD56+ Ectoderm Cultured Cells

value: ectoderm

value: Days 0-5:DMEM F12, 15% KSR, Dorsomorphin (2um), A83-01 (2um), PNU 74654 (2um)

value: CD56+ ectoderm

value: BioSAli 1011

value: Male

value: 3' cDNA ligation

value: Our protocol using T4 RNA ligase from NEB

value: ILLUMINA A1+B1, C1+D1, E1+F1, G1+H1

value: around 10ng

value: 3x RLT + 15/20 ul of Silane + 0.4x EtOn, eluted in 100ul, recleaned using 0.95X SPRI

value: yes

value: OligodT - Dynabeads mRNA purification kit (Invitrogen)

value: 98C 30 sec, 8 cycles of: 98C for 10 sec, 67C for 20 sec, 72C for 20 min, then 72C for 30 seconds, hold 4C

value: Qiagen AllPrep DNA/RNA/Protein Mini Kit

value: Adapter ligated cDNA made by reverse transcription of RNA

value: Phusion High Fidelity

value: 12 pmoles of each/50 ul of reaction

value: 70C for 4 min in Ambion Fragmentation Buffer

value: NO

value: mRNA-Seq

value: We synthesized first-strand cDNA using affinity-script reverse transcriptase


title: Bisulfite-Seq analysis of WGBS_Lib 63 derived from human CD19 cells; WGBS_Lib 63

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 63
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.17371
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.17382
****************
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: Adult Primary CD19+ cells; WGBS_Lib 63

value: BioSam 1235

value: CD19 Primary Cells

value: presumed normal

tag: markers

value: Unknown

value: Male

value: Primary Cell

value: UW

value: 37.0 Years

value: 2x5hrs Epitect Kit

value: 5 ug

value: Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes

value: T4 Ligase (2,000U/ul) 16C o/n

value: Illumina paired end adapter

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: SPRI Beads

value: Pfu Turbo Cx hot start

value: Covaris S2 (TM)


title: Bisulfite-Seq analysis of WGBS_Lib 68 derived from human fPlacenta cells; WGBS_Lib 68

description:
sample_term_id: UBERON_0001987
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 68
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.17367
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.17376
****************
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: Primary fetal placenta tissue; WGBS_Lib 68

value: BioSam 1239

value: Fetal Placenta

value: Post-Mortem

value: presumed normal

value: Female

value: Primary Tissue

value: Placenta

value: University of Washington


title: RNA-Seq analysis of cDNA_Lib 7 derived from human CD56+ ectoderm cells; cDNA_Lib 7

description:
Design description: mRNA-Seq for REMC on Illumina
Library name: cDNA_Lib 7
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15043
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15045
****************
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: CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; cDNA_Lib 7

value: BioSam 803

value: hESC Derived CD56+ Ectoderm Cultured Cells

value: ectoderm

value: Days 0-5:DMEM F12, 15% KSR, Dorsomorphin (2um), A83-01 (2um), PNU 74654 (2um)

value: CD56+ ectoderm

value: adherence

value: BioSAli 1011

value: Cell Line

value: Male

value: Harvard

value: 3' cDNA ligation

value: Our protocol using T4 RNA ligase from NEB

value: ILLUMINA A1+B1, C1+D1, E1+F1, G1+H1

value: around 10ng

value: 3x RLT + 15/20 ul of Silane + 0.4x EtOn, eluted in 100ul, recleaned using 0.95X SPRI

value: yes

value: OligodT - Dynabeads mRNA purification kit (Invitrogen)

value: 98C 30 sec, 8 cycles of: 98C for 10 sec, 67C for 20 sec, 72C for 20 min, then 72C for 30 seconds, hold 4C

value: Qiagen AllPrep DNA/RNA/Protein Mini Kit

value: Adapter ligated cDNA made by reverse transcription of RNA

value: Phusion High Fidelity

value: 12 pmoles of each/50 ul of reaction

value: 70C for 4 min in Ambion Fragmentation Buffer

value: NO

value: mRNA-Seq

value: We synthesized first-strand cDNA using affinity-script reverse transcriptase


title: Endogenous small RNAs from rice, control ROOTS (2h)

description:
Total Endogenous small RNAs from rice, control leaves (2h)
library strategy: Barcode

value: 15-days old plants

value: Nipponbare


title: Bisulfite-Seq analysis of WGBS_Lib 54 derived from human IMR-90 cells; WGBS_Lib 54

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 54
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.17366
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.17374
****************
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: Cell line derived from human fetal lung; WGBS_Lib 54

value: IMR90 cells

value: BioSam 1502

value: IMR90 Cell Line

value: DMEM/FBS

value: presumed normal

value: BioSAli 2350

value: Cell Line

value: Female

value: ATCC American Type Culture Collection

value: 2x5hrs Epitect Kit

value: 5 ug

value: Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes

value: T4 Ligase (2,000U/ul) 16C o/n

value: Illumina paired end adapter

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: SPRI Beads

value: Pfu Turbo Cx hot start

value: Covaris S2 (TM)


title: Bisulfite-Seq analysis of WGBS_Lib 70 derived from human fMuscle_Trunk  cells; WGBS_Lib 70

description:
sample_term_id: UBERON_0001774
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 70
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.17364
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.17381
****************
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: Primary fetal trunk muscle tissue; WGBS_Lib 70

value: BioSam 1241

value: Fetal Muscle, Trunk

value: Post-Mortem

value: Unknown

value: Primary Tissue

value: Trunk

value: University of Washington


title: Endogenous small RNAs from rice, elicitor-treated LEAVES (30')

description:
Total Endogenous small RNAs from rice, elicitor leaves (30')
library strategy: Barcode

source_name: Elicitor Leaves

value: 15-days old plants

value: Nipponbare


title: Endogenous small RNAs from rice, elicitor-treated LEAVES (2h)


title: Bisulfite-Seq analysis of WGBS_Lib 61 derived from human adult CD3 cells; WGBS_Lib 61

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 61
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.17362
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.17379
****************
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: Adult Primary CD3+ cells; WGBS_Lib 61

value: BioSam 1236

value: CD3 Primary Cells

value: presumed normal

value: adult CD3

value: Male

value: Primary Cell

value: UW

value: 37.0 Years

value: 2x5hrs Epitect Kit

value: 5 ug

value: Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes

value: T4 Ligase (2,000U/ul) 16C o/n


title: tumor tissue with Transcatheter Arterial Infusion chemotherapy

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

country: China

institute: Yunnan Agricultural University

description:
The T_with_TAI column and norm_T_with_TAI(RPTM) columns show the raw and normalized (Reads Per Ten Million transcripts) read numbers, respectively.
RNA-Seq (18-28nt)

data_processing:
Reads with low scored nucleotides < 15 were removed.
3' adapters were removed and the small RNA sequences were extracted from the raw reads.
The reads with at least 18nt were maintained in the final results.
The unique sequences and their counts were calculated from the extracted sequences.
The unique sequences were aligned to mature miRNAs of human in miRBase (v19) to calcualte their frequencies.
Supplementary_files_format_and_content: unique sequence and count; human mature miRNAs and their raw and normalized (Reads Per Ten Million transcripts) frequency

source_name: tumor tissue of stage III CRC patient who received Transcatheter Arterial Infusion chemotherapy one week before surgical resection

extract_protocol: Total RNA of the collected tissues were extracted using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. The integrity of the RNA was checked with an ultraviolet spectrophotometry and 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA). Construction of small RNA libraries from size fractionated RNA was carried out by following Solexa protocol and the obtained libraries were sequenced by Illumina HiSeq 2000 sequencer.

treatment_protocol: In Transcatheter Arterial Infusion, we used transfemoral intervention (also known as Seldinger technique) and performed this operation under Digital Subtraction Angiography (DSA) surveillance. 5 Fr-RH catheter was used for chemotherapeutics delivery, catheter tip was inserted into common hepatic artery and mesenteric artery respectively, 1~2 cm deep into target vessel. Ultravist-300 (Schering, Iodine quantity 300mg/mL) was used for angiography, 5~7 ml/s total volume 20~25 ml per time for common hepatic artery angiography and 5~10 ml/s total volume 20~40 ml per time for mesenteric artery angiography. Tumor support artery was chosen for drug delivery according to angiographic images. 1 gram of Tegafur was dissolved in 200 ml of normal saline, 100 mg of Eloxatine was dissolved in 200 ml of 5% Glucose Injection, 10 mg of Mitomycin was dissolved in 100 ml of normal saline. Then 500 mg of Tegafur, 50 mg of Eloxatine and 5mg of Mitomycin were injected into common hepatic artery and tumor support artery separately.

tag: country/location

value: Chinese in eastern China

tag: tissue

value: tumor tissue of colorectal cancer

tag: tumor stage

value: stage III

tag: therapy


title: Endogenous small RNAs from rice, control LEAVES (2h)

source_name: Control Leaves

tag: age

value: 15-days old plants


title: adjacent normal tissue without Transcatheter Arterial Infusion chemotherapy

description:
The ANT_no_TAI column and norm_ANT_no_TAI(RPTM) columns show the raw and normalized (Reads Per Ten Million transcripts) read numbers, respectively.
RNA-Seq (18-28nt)

source_name: adjacent normal tissue of stage III CRC tumor

value: adjacent normal tissue of colorectal cancer

value: no therapy


title: adjacent normal tissue with Transcatheter Arterial Infusion chemotherapy

description:
The ANT_with_TAI column and norm_ANT_with_TAI(RPTM) columns show the raw and normalized (Reads Per Ten Million transcripts) read numbers, respectively.
RNA-Seq (18-28nt)

source_name: adjacent normal tissue of stage III CRC patient who received Transcatheter Arterial Infusion chemotherapy one week before surgical resection


title: tumor tissue without Transcatheter Arterial Infusion chemotherapy

description:
The T_no_TAI column and norm_T_no_TAI(RPTM) columns show the raw and normalized (Reads Per Ten Million transcripts) read numbers, respectively.
RNA-Seq (18-28nt)

source_name: tumor tissue of stage III CRC


title: Dmel_F_BR4_TR2

city: Gainesville

first: Lauren

last: McIntyre

state: FL

address: 2033 Mowry Rd

institute: University of Florida

data_processing:
Primer and adapter sequences were trimmed using custom perl scripts.
Each sample was first evaluated with TopHat to create a set of read-supported junctions.
Reads were aligned to D. melanogaster genome FB (FlyBase v5) using Bowtie ( --best, --tryhard, --paired end).  Reads aligning more than 10 times were removed from consideration.
Unaligned reads were then unpaired and realigned using Bowtie.
Remaining unaligned reads were mapped to the junctions from TopHat.
Expression was then quantified for each exonic region using Reads Per Kilobase Per Million Mapped Reads (RPKM), Average Number of Reads Per Nucleotide (APN).
Genome_build: Flybase 5
Supplementary_files_format_and_content: Are in the CSV format. With the following columns: common contig id, number of reads in the common region, total mappable reads, length of the common region in bp, RPKM. See Series supplementary file for location of contig on the genome.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Adult Head Tissue

growth_protocol: Flies were raised on standard food medium at 25C on a 12 hour light dark cycle.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen).
Solexa/Illumina libraries were constructed according to manufacturer's instructions.

tag: biological replicate

tag: technical replicate

value: female

tag: developmental stage

value: adult

value: Berlin (BDSC 8522)

value: head


title: RNA-Seq analysis of cDNA_Lib 6 derived from human CD56+ ectoderm cells; cDNA_Lib 6

description:
sample_term_id: CL_0000221
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: mRNA-Seq for REMC on Illumina
Library name: cDNA_Lib 6
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15042
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15046
****************
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: CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; cDNA_Lib 6

tag: sample alias

value: BioSam 802

tag: sample common name

value: hESC Derived CD56+ Ectoderm Cultured Cells

value: ectoderm

value: Days 0-5:DMEM F12, 15% KSR, Dorsomorphin (2um), A83-01 (2um), PNU 74654 (2um)

tag: disease

value: presumed normal

value: CD56+ ectoderm

value: adherence

value: BioSAli 1010

value: Cell Line

value: Male

value: Harvard

value: 3' cDNA ligation

value: Our protocol using T4 RNA ligase from NEB

value: ILLUMINA A1+B1, C1+D1, E1+F1, G1+H1

value: around 10ng

value: 3x RLT + 15/20 ul of Silane + 0.4x EtOn, eluted in 100ul, recleaned using 0.95X SPRI

value: yes

value: OligodT - Dynabeads mRNA purification kit (Invitrogen)

value: 98C 30 sec, 8 cycles of: 98C for 10 sec, 67C for 20 sec, 72C for 20 min, then 72C for 30 seconds, hold 4C

value: Qiagen AllPrep DNA/RNA/Protein Mini Kit

value: Adapter ligated cDNA made by reverse transcription of RNA

value: Phusion High Fidelity

value: 12 pmoles of each/50 ul of reaction

value: 70C for 4 min in Ambion Fragmentation Buffer

value: NO

value: mRNA-Seq

value: We synthesized first-strand cDNA using affinity-script reverse transcriptase


title: Dmel_F_BR4_TR1

value: female

value: adult

tag: strain

value: Berlin (BDSC 8522)

value: head


title: Dmel_F_BR3_TR1


title: Bisulfite-Seq analysis of WGBS_Lib 34 derived from human fetal heart cells; WGBS_Lib 34

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 34
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.16338
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.16343
****************
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: Cardiac tissue obtained from fetus and confirmed normal by pathology examination,sample based on pool from two donors; WGBS_Lib 34

value: BioSam 1119

value: Fetal Heart

value: Post-Mortem

value: presumed normal

value: Unknown

value: Primary Tissue

value: Heart

value: University of Washington

value: 2x5hrs Epitect Kit

value: 5 ug

value: Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes

value: T4 Ligase (2,000U/ul) 16C o/n

value: Illumina paired end adapter

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: SPRI Beads

value: Pfu Turbo Cx hot start

value: Covaris S2 (TM)


title: RNA-Seq analysis of cDNA_Lib 5 derived from human CD56+ ectoderm cells; cDNA_Lib 5

description:
Design description: mRNA-Seq for REMC on Illumina
Library name: cDNA_Lib 5
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15041
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15046
****************
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: CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; cDNA_Lib 5

value: BioSam 802

value: hESC Derived CD56+ Ectoderm Cultured Cells

tag: lineage

value: ectoderm

tag: medium

value: Days 0-5:DMEM F12, 15% KSR, Dorsomorphin (2um), A83-01 (2um), PNU 74654 (2um)

tag: passage

value: CD56+ ectoderm

value: adherence

value: BioSAli 1010

value: Cell Line

value: Male

value: Harvard

value: 3' cDNA ligation

value: Our protocol using T4 RNA ligase from NEB

value: ILLUMINA A1+B1, C1+D1, E1+F1, G1+H1

value: around 10ng

value: 3x RLT + 15/20 ul of Silane + 0.4x EtOn, eluted in 100ul, recleaned using 0.95X SPRI

value: yes

value: OligodT - Dynabeads mRNA purification kit (Invitrogen)

value: 98C 30 sec, 8 cycles of: 98C for 10 sec, 67C for 20 sec, 72C for 20 min, then 72C for 30 seconds, hold 4C

value: Qiagen AllPrep DNA/RNA/Protein Mini Kit

value: Adapter ligated cDNA made by reverse transcription of RNA

value: Phusion High Fidelity

value: 12 pmoles of each/50 ul of reaction

value: 70C for 4 min in Ambion Fragmentation Buffer

value: NO

value: mRNA-Seq

value: We synthesized first-strand cDNA using affinity-script reverse transcriptase


title: Dmel_F_BR2_TR1

tag: Sex

value: female

value: adult

value: Berlin (BDSC 8522)

value: head


title: Dmel_F_BR3_TR2


title: HEK293 mRNAseq library

city: Berlin

first: Markus

last: Landthaler

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max-Delbrück-Center for Molecular Medicine

data_processing:
Read demultiplexing, read filtering and adapter trimming was done using flexbar (Dodt et al, 2012).
We used TopHat2 (version 2.06) (Trapnell et al., 2009 and Kim et al. 2013) for spliced alignment of reads to the human reference genome sequence (hg18).
We used Cuffdiff (version 2.0.2)(Trapnell et al., 2010) to generate FPKM values
Genome_build: hg18
Supplementary_files_format_and_content: FPKM table

source_name: HEK293 cell culture

growth_protocol: MCF-7 cells were grown in D-MEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v) 10,000 U/ml penicillin/10,000 µg/ml streptomycin.

extract_protocol: oligodT-purified RNA converted into cDNA by TruSeq™ RNA Sample Preparation Kit

tag: cell line

tag: purification

value: oligo(dT) beads


title: Dmel_F_BR2_TR2

tag: tissue


title: MCF7 mRNAseq library

source_name: MCF7 cell culture


title: ChIP-seq_AcH4-HeLa

status: Public on Jan 14 2014

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

description: AcH4 ChIP-seq in HeLa cells

data_processing:
Basecalls performed using CASAVA version 1.4
reads were aligned to the hg18 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18
Supplementary_files_format_and_content: bigwig files report normalized total tags

source_name: HeLa cell

growth_protocol: HEK293T and HeLa cells were cultured in DMEM and MEM alpha medium supplemented with 10% FBS, respectively.

extract_protocol:
For ChIP-seq, fixation was stopped by adding Glycine (0.125M) and incubating for 5 min at RT, followed by washing with PBS twice. Chromatin DNA was sheared to 300500 bp average in size through sonication. Resultant was immunoprecipitated with control IgG or specific antibodies overnight at 4°C, followed by incubation with protein G magnetic beads (Invitrogen) for an additional 2 h. After washing and elution, the proteinDNA complex was reversed by heating at 65°C overnight. For samples fixed with glutaraldehyde, proteinase K (0.3mg/ml) (Ambion) was added during de-crosslinking. Immunoprecipitated DNA was purified by using QIAquick spin columns (Qiagen) ; 7SK snRNA ChIRP was performed with an single anti-sense DNA oligonucleotide (5-accttgagagcttgtttggagg-3) following the protocol exactly as described previously (Chu et al., 2012). This DNA oligonucleotide sequence has been shown to specifically target to and efficiently pull down 7SK snRNA (Yang et al., 2001).
the libraries were constructed following Illuminaâ€™s Chip-Seq Sample prep kit. Briefly, Chip DNA was end-blunted and added with an â€˜Aâ€™ base so the adaptors from Illumina with a â€˜Tâ€™ can ligate on the ends. Then 200â€“400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

treatment_protocol: For experiments not involving siRNA transfection, cells grown to ~90% confluent were fixed directly; For experiments involving siRNA transfection, cells were subjected to two rounds of siRNAs transfection in 3 days, followed by fixation.

value: HeLa cervical cancer cells

tag: chip antibody

tag: chip antibody details

value: 06-598 (Millipore)


title: ChIP-seq_AcH3-HeLa

description: AcH3 ChIP-seq in HeLa cells

value: 06-599 (Millipore)


title: ChIP-seq_Brd4-HeLa

description: Brd4 ChIP-seq in HeLa cells

value: ab46199 (Abcam)


title: ChIP-seq_JMJD6-HeLa

description: JMJD6 ChIP-seq in HeLa cells

value: ab10526 (Abcam)


title: ChIRP-seq_7SK-siBrd4-2-HEK293T

description: 7SK snRNA ChIRP in HEK293T cells transfected with siRNA specific against Brd4 (Dharmacon)

source_name: HEK293T cell

value: Human Embryonic Kidney 293 cells

tag: oligonucletides used for chirp

value: accttgagagcttgtttggagg

tag: sirna transfection


title: MB11-H3K4me1 (S00658)

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

description: ChIP-DNA

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 2.1.0 with default parameters.
These data were normalized by total reads (mapped reads per million reads per kilobase).
Bedgraph files were generated using our in-house program and converted to TDF files using IGVTools version 2.2.1.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph and TDF files contain identical summary data.

organism: Mus musculus

source_name: midbrain

extract_protocol:
Lysates were clarified from sonicated nuclei and HISTONE-DNA complexes were isolated with antibody.
Libraries were prepared according to NEB's instructions accompanying the DNA Sample Kit (NEB# E6240L). 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 Illumina HiSeq 1000 following the manufacturer's protocols.

value: midbrain

tag: age

value: 11 dpc

tag: antibody

value: H3K4me1 (Abcam ab8895)


title: ChIRP-seq_7SK-siJMJD6-2-HEK293T

description: 7SK snRNA ChIRP in HEK293T cells transfected with siRNA specific against JMJD6 (Dharmacon)


title: ChIP-seq_CDK9-siJMJD6-HEK293T

description: CDK9 ChIP-seq in HEK293T cells transfected with siRNA specific against JMJD6

value: 2316S (Cell Signaling Technology)


title: ChIP-seq_CDK9-siCTL-HEK293T

description: CDK9 ChIP-seq in HEK293T cells transfected with control siRNA

value: siCTL


title: ChIP-seq_Pol II-siBrd4-re2-HEK293T

description: Pol II ChIP-seq in HEK293T cells transfected with siRNA specific against Brd4 (repeat)

value: Pol II

value: SC-899 (Santa Cruz Biotechnology)


title: ChIP-seq_Pol II-siJMJD6-re2-HEK293T

description: Pol II ChIP-seq in HEK293T cells transfected with siRNA specific against JMJD6 (repeat)


title: ChIP-seq_P300-HEK293T

description: P300 ChIP-seq in HEK293T cells

value: SC-585 (Santa Cruz biotechnology)


title: ChIP-seq_H3K27Ac-HEK293T

description: H3K27Ac ChIP-seq in HEK293T cells

value: ab4729 (Abcam)


title: ChIP-seq_H3K4me1-07-436-HEK293T

description: H3K4me1 ChIP-seq in HEK293T cells

value: 07-436 (Millipore)


title: ChIP-seq_H3K4me1-ab8895-HEK293T

description: H3K4me1 ChIP-seq in HEK293T cells

value: ab8895 (Abcam)


title: MB11-H3K27ac (S00657)

description: ChIP-DNA

value: H3K27ac(Active Motif 39134)


title: ChIP-seq_Pol II-siCTL-re2-HEK293T

description: Pol II ChIP-seq in HEK293T cells transfected with control siRNA (repeat)


title: ChIP-seq_Brd4-re2-HEK293T

description: Brd4 ChIP-seq in HEK293T cells (repeat)


title: ChIP-seq_Brd4-re1-HEK293T

description: Brd4 ChIP-seq in HEK293T cells


title: ChIP-seq_H3K4me3-HEK293T

description: H3K4me3 ChIP-seq in HEK293T cells

value: ab8580 (Abcam)


title: Endogenous small RNAs from rice, control LEAVES (30')

description:
Total Endogenous small RNAs from rice, control leaves (30')
library strategy: Barcode

value: 15-days old plants

tag: cultivar

value: Nipponbare


title: ChIP-seq_JMJD6-re2-HEK293T

description: JMJD6 ChIP-seq in HEK293T cells (repeat)

value: Human Embryonic Kidney 293 cells

value: ab10526 (Abcam)


title: ChIP-seq_H3K4me2-HEK293T

description: H3K4me2 ChIP-seq in HEK293T cells

value: ab7766 (Abcam)


title: ChIRP-seq_7SK-siJMJD6-1-HEK293T

description: 7SK snRNA ChIRP in HEK293T cells transfected with siRNA specific against JMJD6 (Qiagen)

value: accttgagagcttgtttggagg


title: ChIP-seq_AcH3-HEK293T

description: AcH3 ChIP-seq in HEK293T cells

value: 06-599 (Millipore)


title: ChIP-seq_JMJD6-re1-HEK293T

description: JMJD6 ChIP-seq in HEK293T cells


title: ChIRP-seq_7SK-siCTL-HEK293T

description: 7SK snRNA ChIRP in HEK293T cells transfected with control siRNA


title: ChIP-seq_CDK9-siBrd4-HEK293T

description: CDK9 ChIP-seq in HEK293T cells transfected with siRNA specific against Brd4

value: 2316S (Cell Signaling Technology)


title: Ly2 HoxC11_Untreated

city: Dublin

first: Leonie

last: Young

address: York Street

department: Surgery

country: Ireland

institute: Royal College of Surgeons, Ireland

data_processing:
The DNA sequencing was carried out on the Illumina GAII using Illumina pipeline v1.6.0.
The alignment was carried out using bowtie v0.12.5 with parameters: -m 1 -v 2 —strata —best
Peak calling was carried out by MACS 1.4.0Beta (--shiftsize=60)
Genome_build: hg19
Supplementary_files_format_and_content: Wiggle files from the MACS analysis were converted to BigWig using the wigToBigWig tool.

source_name: Ly2 HoxC11_Untreated

growth_protocol: Endocrine-resistant MCF-7–derived LY2 were maintained in MEM (Eagle) with 2 mmol/L L-glutamine and supplemented with 10% fetal bovine serum (Invitrogen). All cell lines were incubated at 37°C, under 5% CO2.

extract_protocol: DNA libraries were generated from 10 ng of ChIP output DNA by adaptor ligation, gel purification, and cycles of PCR as described by Illumina.

treatment_protocol: Cells were maintained in steroid-depleted medium for 72 hours before being treated for 45 mins with vehicle or tamoxifen [4-hydroxytamoxifen (4-OHT), 10-7 mol/L; Sigma-Aldrich].

tag: cell type

value: breast cancer

tag: treatment

value: Untreated


title: Ly2 Input_control

source_name: Ly2 Input_control


title: Ly2 HoxC11_Tamoxifen

source_name: Ly2 HoxC11_Tamoxifen

value: Tamoxifen


title: Melanocyte control

city: Stanford

first: Paul

last: Khavari

state: CA

address: 269 Campus Drive

institute: Stanford University

description:
ChIP DNA
mc_ctrl_mitf_chipseq

data_processing:
MITF ChIP-seq data was mapped to the hg19 genome assembly by bowtie using the following command line execution: bowtie -p 7 -a -m 1 --best --strata --quiet -S -t /indexes/hg19 FILENAME.fastq | samtools view -bS -o FILENAME.bam -
Peaks were called using MACS(Feng et al. 2012) with a p-value cutoff of 1e-10. For comparative analysis, MITF peaks were selected that were present in both primary melanocytes and COLO829 cells, but the called peak did not need to be present in both datasets for a given cell type
Genome_build: hg19
Supplementary_files_format_and_content: Called peaks for MITF present in primary melanocytes and COLO829 melanoma cells (see supplementary file linked to Series record)

source_name: Primary human melanocytes infected with a lentivirus for RFP (control)

growth_protocol: Primary human melanocytes were obtained through an Institutional Review Board–approved protocol and cultured as described previously (Flockhart et al. 2012). COLO829 cells were grown in RPMI 1640 medium with 10% FBS and Pen/Strep.

extract_protocol:
20-50 million cells were used. Cells were trypsinized, washed, and cross-linked as described previously(Sen et al. 2008). Lysis with a modified RIPA buffer (1% NP40/Igepal, 0.5% Sodium Deoxycholate, 0.1% SDS, 100uM EDTA in PBS), nuclei were isolated and DNA was sonicated to ~150bp and overnight pulldown was performed with an antibody to MITF (Sigma HPA003259)
ChIP-sequencing libraries were prepared with a modified version of NEBNext ChIP-seq library prep kit (NEB) using Ampure beads (Agencourt) for purification. Barcodes were introduced and these libraries were sequenced with 1x50bp reads on the Illumina HiSeq platform.

treatment_protocol: Primary human melanocytes were treated with lentiviral RFP (control) or BRAFV600E for 48 hours prior to harvest.  COLO829 cells were treated for 24hr with DMSO or PLX4032 before harvest.

value: Primary Melanocyte

tag: genotype/variation

value: control (lentiviral RFP )

tag: braf signaling status

value: OFF

value: anti-MITF (Sigma, HPA003259, lot# A08324)


title: Melanocyte BRAFV600E

description:
ChIP DNA
mc_braf_mitf_chipseq

source_name: Primary human melanocytes infected with a lentivirus for BRAFV600E

value: BRAFV600E overexpression

value: ON


title: ChIP-seq_Pol II-siBrd4-HEK293T

description: Pol II ChIP-seq in HEK293T cells transfected with siRNA specific against Brd4

value: Pol II

value: SC-899 (Santa Cruz Biotechnology)


title: ChIP-seq_Pol II-siCTL-HEK293T

description: Pol II ChIP-seq in HEK293T cells transfected with control siRNA

value: Human Embryonic Kidney 293 cells

value: siCTL


title: COLO829 PLX4032

description:
ChIP DNA
colo829_plx4032_mitf_chipseq

source_name: COLO829 human melanoma cell line treated with PLX4032

value: COLO829 melanoma cell line

value: BRAF inhibitor PLX4032 (Vemurafenib)


title: COLO829 DMSO

description:
ChIP DNA
colo829_dmso_mitf_chipseq

source_name: COLO829 human melanoma cell line treated with DMSO

value: DMSO (control)


title: ChIP-seq_Pol II-siJMJD6-HEK293T

description: Pol II ChIP-seq in HEK293T cells transfected with siRNA specific against JMJD6


title: ChIP-seq_AcH4-HEK293T

description: AcH4 ChIP-seq in HEK293T cells

value: 06-598 (Millipore)


title: LM11-RING1B

description: forelimb bud from mouse 11dpc embryos, antibody: RING1B

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Botwie2 (version 2.0.5) with default parameters.
Processed files in wiggle format were generated using in-house program.
Genome_build: mm9 (NCBI version 37.2)
Supplementary_files_format_and_content: wiggle

source_name: forelimb

growth_protocol: ES cells were cultured in standard conditions.

extract_protocol:
Lysates were clarified from sonicated nuclei and RING1B-DNA complexes were isolated with antibody.
Libraries were prepared according to NEB's instructions accompanying the DNA Sample Kit (NEB# E6240L). 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: strain

value: forelimb

value: 11 dpc

value: anti-RING1B antibody

tag: chip antibody info


title: FB11-RING1B

description: forebrain from mouse 11dpc embryos, antibody: RING1B

source_name: forebrain

value: forebrain


title: MB11-RING1B

description: midbrain from mouse 11dpc embryos, antibody: RING1B

value: midbrain


title: CEL_seq_AA100_50pg_TR1

status: Public on Jan 13 2014

city: la jolla

first: vipul

last: bhargava

state: California

address: 9500 gilman drive

institute: ucsd

description: addition of Activin A (100 ng/mL); mRNA used=50pg; CEL-seq method, Technical Replicate 1; paired-end run

data_processing:
Basecalls performed using Illumina Casava1.8
Sequence reads obtained from Illumina HiSEQ2000 were trimmed of first 7 bp and next 32 bp were used for mapping with mus musculus REFSEQ database (mRNA) using in-house mapping code allowing upto 2 mismatches
Sequencing libraries prepared from same dilution of mRNA were pooled together by using CEL-seq primers # 37,38,39 and 40. The primers 37 and 38 were used for technical replicates derived from serum free media control while primers 39 and 40 were used for technical replicates derived from Activin A (100 ng/mL) samples. CEL-seq reads were de-multiplexed by using CEL-seq primers # 37,38,39,40 as mentioned in Hashimshony et al. 2012.
Genome_build: mus musculus REFSEQ database of RNA
Supplementary_files_format_and_content: tab-delimited text files include REFSEQ gene id and Unique Reads

source_name: embryoid body

growth_protocol: Differentiating ESCs were grown in serum free conditions.

extract_protocol:
At day4 of differentiation, cells were harvested and total RNA was extracted using Trizol. Poly 'A' enriched mRNA was isolated using Dynabeads mRNA purification kit (Invitrogen) from each sample.
Std. RNA-seq libraries were prepared as described by Mortazavi et al. 2008. Smart-seq libraries were prepared as described by Ramsköld et al. 2012. CEL-seq libraries were prepared as described by Hashimshony et al. 2012.

treatment_protocol: At day2 of differentiation, embryoid bodies were dispersed and treated with/without Activin A (100 ng/mL) compound for two days.

value: mouse embryonic stem cells

tag: developmental stage

value: day 4 of differentiation


title: CEL_seq_AA100_25pg_TR2

description: addition of Activin A (100 ng/mL); mRNA used=25pg; CEL-seq method, Technical Replicate 2; paired-end run


title: CEL_seq_SFM_25pg_TR2

description: serum free media control; mRNA used=25pg; CEL-seq method, Technical Replicate 2; paired-end run


title: CEL_seq_SFM_50pg_TR1

description: serum free media control; mRNA used=50pg; CEL-seq method, Technical Replicate 1; paired-end run


title: CEL_seq_AA100_100pg_TR1

description: addition of Activin A (100 ng/mL); mRNA used=100pg; CEL-seq method, Technical Replicate 1; paired-end run


title: CEL_seq_SFM_25pg_TR1

description: serum free media control; mRNA used=25pg; CEL-seq method, Technical Replicate 1; paired-end run


title: ChIRP-seq_7SK-siBrd4-1-HEK293T

description: 7SK snRNA ChIRP in HEK293T cells transfected with siRNA specific against Brd4 (Qiagen)

tag: cell line

value: accttgagagcttgtttggagg


title: CEL_seq_AA100_1ng_TR2

description: addition of Activin A (100 ng/mL); mRNA used=1ng; CEL-seq method, Technical Replicate 2; paired-end run


title: CEL_seq_AA100_1ng_TR1

description: addition of Activin A (100 ng/mL); mRNA used=1ng; CEL-seq method, Technical Replicate 1; paired-end run


title: CEL_seq_SFM_100pg_TR1

description: serum free media control; mRNA used=100pg; CEL-seq method, Technical Replicate 1; paired-end run


title: CEL_seq_SFM_100pg_TR2

description: serum free media control; mRNA used=100pg; CEL-seq method, Technical Replicate 2; paired-end run


title: CEL_seq_SFM_1ng_TR2

description: serum free media control; mRNA used=1ng; CEL-seq method, Technical Replicate 2; paired-end run


title: CEL_seq_AA100_25pg_TR1

description: addition of Activin A (100 ng/mL); mRNA used=25pg; CEL-seq method, Technical Replicate 1; paired-end run


title: CEL_seq_SFM_50pg_TR2

description: serum free media control; mRNA used=50pg; CEL-seq method, Technical Replicate 2; paired-end run


title: CEL_seq_AA100_100pg_TR2

description: addition of Activin A (100 ng/mL); mRNA used=100pg; CEL-seq method, Technical Replicate 2; paired-end run


title: DP_seq_AA100_25pg_TR2

description: addition of Activin A (100 ng/mL); mRNA used=25pg; DP-seq method, Technical Replicate 2


title: CEL_seq_SFM_1ng_TR1

description: serum free media control; mRNA used=1ng; CEL-seq method, Technical Replicate 1; paired-end run


title: DP_seq_AA100_25pg_TR1

description: addition of Activin A (100 ng/mL); mRNA used=25pg; DP-seq method, Technical Replicate 1


title: DP_seq_SFM_25pg_TR1

description: serum free media control; mRNA used=25pg; DP-seq method, Technical Replicate 1


title: DP_seq_AA100_50pg_TR2

description: addition of Activin A (100 ng/mL); mRNA used=50pg; DP-seq method, Technical Replicate 2


title: DP_seq_SFM_25pg_TR2

description: serum free media control; mRNA used=25pg; DP-seq method, Technical Replicate 2


title: DP_seq_AA100_50pg_TR1

description: addition of Activin A (100 ng/mL); mRNA used=50pg; DP-seq method, Technical Replicate 1


title: DP_seq_SFM_50pg_TR2

description: serum free media control; mRNA used=50pg; DP-seq method, Technical Replicate 2


title: CEL_seq_AA100_50pg_TR2

description: addition of Activin A (100 ng/mL); mRNA used=50pg; CEL-seq method, Technical Replicate 2; paired-end run


title: P21_Nrl_rep1

city: Saclay

first: Jerome

middle: Eric

last: Roger

state: Please select

address: 151 Route de la Rotonde, Campus CEA Saclay - Bat 151

department: CERTO

country: France

institute: CNRS-Universite Paris Sud

data_processing:
Single read sequence-by-synthesis of 76 base length using TruSeq SBS v5 reagents was carried out on Genetic Analyzer IIx running SCS2.9 software (Illumina).
RNA-seq reads passing chastity filter were analyzed using Genomatix Software Suite (Genomatix Software GmbH, Munich Germany).
Sequences were aligned to NCBI mouse reference genome Build 37 on Genomatix Mining Station with Genomatix Mapper 3.5.1.
Alignments were annotated on Genomatix Genome Analyzer using ElDorado 08-2011 database, and differential expression analysis was performed using DEseq
Genome_build: NCBI build 37 Eldorado version 08-2011
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample, fold change, adjusted p-value

source_name: Nrl-/- mouse retina at age postnatal day 21

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for directional next-generation sequencing using a modified TruSeq RNA Sample Preparation Kit protocol as described (Brooks et al. 2012). The protocol utilizes the labeling of the second strand of cDNA with uracil, which allows the degradation of this strand prior to sequencing

tag: genotype

value: Nrl-/-

value: Retina

value: post natal day 21


title: P21_Crx_rep2

source_name: Crx-/- mouse retina at age postnatal day 21

value: Crx-/-

tag: tissue


title: P21_Hom_rep1

source_name: CrxRip/Rip mouse retina at age postnatal day 21

value: CrxRip/Rip


title: DP_seq_SFM_50pg_TR1

description: serum free media control; mRNA used=50pg; DP-seq method, Technical Replicate 1


title: P21_Hom_rep2


title: DP_seq_AA100_1ng_TR2

description: addition of Activin A (100 ng/mL); mRNA used=1ng; DP-seq method, Technical Replicate 2


title: DP_seq_SFM_100pg_TR2

description: serum free media control; mRNA used=100pg; DP-seq method, Technical Replicate 2


title: DP_seq_AA100_1ng_TR1

description: addition of Activin A (100 ng/mL); mRNA used=1ng; DP-seq method, Technical Replicate 1


title: P21_WT_rep1

source_name: wild type mouse retina at age postnatal day 21

value: wild type


title: P21_WT_rep2


title: P21_Het_rep2

source_name: CrxRip/+ mouse retina at age postnatal day 21

value: CrxRip/+


title: P2_Nrl_rep2

source_name: Nrl-/- mouse retina at age postnatal day 2

value: post natal day 2


title: DP_seq_SFM_1ng_TR2

description: serum free media control; mRNA used=1ng; DP-seq method, Technical Replicate 2


title: DP_seq_SFM_1ng_TR1

description: serum free media control; mRNA used=1ng; DP-seq method, Technical Replicate 1


title: P2_Nrl_rep1


title: Smart_seq_AA100_25pg_TR2

description: addition of Activin A (100 ng/mL); Smart-seq method, Technical Replicate 2


title: P21_Het_rep1


title: P2_Crx_rep2

source_name: Crx-/- mouse retina at age postnatal day 2


title: P21_Nrl_rep2


title: Smart_seq_SFM_25pg_TR2

description: serum free media control; mRNA used=25pg; Smart-seq method, Technical Replicate 2


title: P2_Crx_rep1


title: P2_Hom_rep2

source_name: CrxRip/Rip mouse retina at age postnatal day 2


title: Smart_seq_SFM_25pg_TR1

description: serum free media control; mRNA used=25pg; Smart-seq method, Technical Replicate 1


title: DP_seq_SFM_100pg_TR1

description: serum free media control; mRNA used=100pg; DP-seq method, Technical Replicate 1


title: DP_seq_AA100_100pg_TR2

description: addition of Activin A (100 ng/mL); mRNA used=100pg; DP-seq method, Technical Replicate 2


title: DP_seq_AA100_100pg_TR1

description: addition of Activin A (100 ng/mL); mRNA used=100pg; DP-seq method, Technical Replicate 1


title: Smart_seq_AA100_50pg_TR2

description: addition of Activin A (100 ng/mL); mRNA used=50pg; Smart-seq method, Technical Replicate 2


title: P21_Crx_rep1


title: Smart_seq_AA100_50pg_TR1

description: addition of Activin A (100 ng/mL); mRNA used=50pg; Smart-seq method, Technical Replicate 1


title: Smart_seq_SFM_50pg_TR2

description: serum free media control; mRNA used=50pg; Smart-seq method, Technical Replicate 2


title: P2_Het_rep1

source_name: CrxRip/+ mouse retina at age postnatal day 2


title: Smart_seq_AA100_100pg_TR2

description: addition of Activin A (100 ng/mL); mRNA used=100pg; Smart-seq method, Technical Replicate 2


title: P2_WT_rep1

source_name: wild type mouse retina at age postnatal day 2


title: embryo_16-30h

city: Pasadena

first: Maria

last: Ninova

address: 1200 E California Blvd

department: Division of Biology and Biological Engineering

institute: Calfironia Institute of Technology

description:
Sample 11
small RNA profiling

data_processing:
3' adapters (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC) were trimmed using the cutadapt tool with default parameters and reads shorter than 17 nt were discarded.
Reads mapping to known rRNAs (including the 2S rRNA), tRNAs and sn(o)RNAs were filtered out.
Filtered reads were mapped to the genome using Bowtie allowing 1 mismatch; reads mapping to more than 5 loci were discarded.
Different runs of the same sample were merged.
Genome_build: dvir_r1.2_FB2011_07
Supplementary_files_format_and_content: Tab-delimited tables (.txt) with small RNA counts

organism: Drosophila virilis

source_name: whole embryo

growth_protocol: D. virilis were maintained on standard fly media at 25°C. Embryos were collected on apple juice agar plates and allowed to age for the desired times.

extract_protocol:
Samples were disrupted in 1 ml Trizol (Invitrogen) and total RNA was extracted according to the manufacturer's instructions.
Librarires were constructed using the Illumina TruSeq™ Small RNA Kit

value: 16-30h embryo


title: larvae

description:
Sample 9
small RNA profiling

source_name: 3rd instar larvae

value: larva


title: Smart_seq_SFM_100pg_TR2

description: serum free media control; mRNA used=100pg; Smart-seq method, Technical Replicate 2


title: Smart_seq_AA100_1ng_TR1

description: addition of Activin A (100 ng/mL); mRNA used=1ng; Smart-seq method, Technical Replicate 1


title: embryo_14-16h

description:
Sample 8
small RNA profiling

value: 14-16 h embryo


title: Smart_seq_SFM_100pg_TR1

description: serum free media control; mRNA used=100pg; Smart-seq method, Technical Replicate 1


title: Smart_seq_AA100_1ng_TR2

description: addition of Activin A (100 ng/mL); mRNA used=1ng; Smart-seq method, Technical Replicate 2


title: Smart_seq_SFM_1ng_TR2

description: serum free media control; mRNA used=1ng; Smart-seq method, Technical Replicate 2


title: P2_Hom_rep1


title: embryo_10-12h

description:
Sample 6
small RNA profiling

value: 10-12 h embryo


title: Smart_seq_SFM_1ng_TR1

description: serum free media control; mRNA used=1ng; Smart-seq method, Technical Replicate 1


title: embryo_8-10h

description:
Sample 5
small RNA profiling

value: 8-10 h embryo


title: Smart_seq_AA100_100pg_TR1

description: addition of Activin A (100 ng/mL); mRNA used=100pg; Smart-seq method, Technical Replicate 1


title: Std_RNA-seq_SFM_TR2

description: serum free media control; mRNA used=50ng; Std. RNA-seq method, Technical Replicate 2


title: embryo_12-14h

description:
Sample 7
small RNA profiling

value: 12-14 h embryo


title: Std_RNA-seq_SFM_TR1

description: serum free media control; mRNA used=50ng; Std. RNA-seq method, Technical Replicate 1

value: mouse embryonic stem cells


title: embryo_6-8h

description:
Sample 4
small RNA profiling

value: 6-8 h embryo


title: embryo_4-6h

description:
Sample 3
small RNA profiling

value: 4-6 h embryo


title: Std_RNA-seq_AA100_TR2

description: addition of Activin A (100 ng/mL); mRNA used=50ng; Std. RNA-seq method, Technical Replicate 2

value: day 4 of differentiation


title: embryo_2-4h

description:
Sample 2
small RNA profiling

value: 2-4 h embryo


title: P2_WT_rep2

value: Retina


title: Std_RNA-seq_AA100_TR1

description: addition of Activin A (100 ng/mL); mRNA used=50ng; Std. RNA-seq method, Technical Replicate 1


title: embryo_0-2h

description:
Sample 1
small RNA profiling

value: 0-2 h embryo


title: adults

description:
Sample 10
small RNA profiling

source_name: whole body, mixed males and females

value: adult


title: Sample_T10

status: Public on Jan 12 2014

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

institute: University of Pennsylvania

data_processing:
Illumina Casava 1.8.1 and 1.8.2 software used for basecalling.
We trimmed reads for adapter and poly-A contamination using in-house software before aligning to the mouse genome and transcriptome using RNA-Seq Unified Mapper and mouse genome build mm9.
Using uniquely aligned reads and UCSC known gene annotations, we assigned read counts to genes using HTSeq and htseq-count. Only exonic reads were counted, with overlap assigned using the intersection non-empty method. Known isoforms were combined into single entities for read counting.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw counts for UCSC known genes

source_name: Hippocampus; single neuron from tissue; TIVA captured

growth_protocol: Coronal brain slices (220-270 mm) were prepared from 8 - 10 day old C57BL/6 mice (Charles River) with a Leica VT2000 vibratome.  Acutely isolated tissues were transferred to artificial cerebrospinal fluid (aCSF)(in mM: NaCl 122, NaHCO3 28, glucose 5.5, HEPES 10, KCl 3.5, MgCl2 1, CaCl2 2, pH 7.4 with 5% CO2/ 95% O2 gas mixture) for 90 min.

extract_protocol:
Individual cells were collected by TIVA. Imaging and photolysis were performed in the CA1 area of the hippocampus immediately on cells using a confocal microscope (Zeiss 710 Meta, 40x water objective, N.A. 1.0). Photolysis was performed using the 405 nm laser for uncaging at 80% power and 100.85 µs per pixel. Loading was confirmed by detecting Cy5 signal in the emission range excited by 561 nm, and uncaging was performed using the 405 nm laser while recording FRET excited by 514 nm and simultaneous capturing in Cy3 (538-599nm) and Cy5 (637-704nm) emission ranges. In some experiments, a line-scan analysis was performed using a 4-pixel-width line and averaging pixel values. After uncaging a single cell in the tissue, the imaged field and surrounding area, including the photolysed cell, was isolated by aspiration using a wide bore glass pipette, and further processed for mRNA analysis. Collected samples were individually amplified using 3 rounds of a linear in vitro-transcription-based method.
Protocols applicable only to a subset of Samples. Included as a column of the SAMPLES section above, labelled "protocol: extract protocol"
Samples were prepared for multiplexed paired-end Illumina sequencing using  TruSeq according to manufacturer instructions.

treatment_protocol: Loaded with TIVA-tag (30 µM in aCSF) for 90 min at rt.

value: Hippocampus

value: Neuron


title: Sample_T9


title: Sample_T7


title: Sample_Tiva_2F


title: Sample_Tiva_2E


title: HPs5a

source_name: Hippocampus; bulk tissue;

extract_protocol:
Bulk samples were individually amplified using 3 rounds of a linear in vitro-transcription-based method.
Protocols applicable only to a subset of Samples. Included as a column of the SAMPLES section above, labelled "protocol: extract protocol"
Samples were prepared for multiplexed paired-end Illumina sequencing using  TruSeq according to manufacturer instructions.

treatment_protocol: No treatment

value: Tissue


title: Sample_DL-cs7

source_name: Hippocampus; single neuron from culture; TIVA captured

growth_protocol: Cultured neurons from C57BL/6 mice were grown on coverslips for 7-9 days as described in Cummings, D. D., Wilcox, K. S. & Dichter, M. A. Calcium-dependent paired-pulse facilitation of miniature EPSC frequency accompanies depression of EPSCs at hippocampal synapses in culture. J Neurosci. 16, 5312-5323 (1996).

extract_protocol:
Individual cells were collected by TIVA. Imaging and photolysis were performed immediately on cells using a confocal microscope (Zeiss 710 Meta, 40x water objective, N.A. 1.0). Loading was confirmed by detecting Cy5 signal in the emission range excited by 561 nm, and uncaging was performed using the 405 nm laser while recording FRET excited by 514 nm and simultaneous capturing in Cy3 (538-599nm) and Cy5 (637-704nm) emission ranges.  Photolysis was performed using the 405 nm laser at 30% power and 50 µs per pixel. In some experiments, a line-scan analysis was performed using a 4-pixel-width line and averaging pixel values. After uncaging a single cell in the tissue, the imaged field and surrounding area, including the photolysed cell, was isolated by aspiration using a wide bore glass pipette, and further processed for mRNA analysis. Collected samples were individually amplified using 3 rounds of a linear in vitro-transcription-based method.
Protocols applicable only to a subset of Samples. Included as a column of the SAMPLES section above, labelled "protocol: extract protocol"
Samples were prepared for multiplexed paired-end Illumina sequencing using  TruSeq according to manufacturer instructions.

treatment_protocol: The coverslips were rinsed in prewarmed cell saline buffer (in mM: NaCl 140, KCl 5.4, MgCl2 1, CaCl2 2, glucose 16, HEPES 10), and then placed in an empty Petri dish in a humidified chamber. Immediately after, 50 µL of 10 µM TIVA-tag in cell saline buffer was added to the coverslip. After 15 min incubation and two rinses of cell saline buffer the coverslip was transferred to an imaging chamber with cell saline buffer. Imaging and photolysis were performed immediately on cells using a confocal microscope (Zeiss 710 Meta, 40x water objective, N.A. 1.0). FRET was recorded under the same configuration as the tissue imaging experiments described below. Photolysis was performed using the 405 nm laser at 30% power and 50 µs per pixel.


title: Sample_DL-cs8


title: Smart_seq_AA100_25pg_TR1

description: addition of Activin A (100 ng/mL); mRNA used=25pg; Smart-seq method, Technical Replicate 1

source_name: embryoid body


title: Sample_DL-cs6


title: HPs4b


title: Sample_40H

source_name: Hippocampus; single neuron from culture; pipette collected

extract_protocol:
Individual cells were collected by Pipette. Collected samples were individually amplified using 3 rounds of a linear in vitro-transcription-based method.
Protocols applicable only to a subset of Samples. Included as a column of the SAMPLES section above, labelled "protocol: extract protocol"
Samples were prepared for multiplexed paired-end Illumina sequencing using  TruSeq according to manufacturer instructions.


title: Sample_DL-cs10


title: Sample_DL-cs4

source_name: Cortex; single neuron from culture; TIVA captured

value: Cortex


title: Sample_36H


title: Sample_DL-cs5


title: CTX_10

source_name: Cortex; single neuron from culture; pipette collected


title: Sample_DL-cs2


title: Sample_Tiva_46

source_name: Hippocampus; single neuron from tissue; pipette collected


title: Sample_Tiva_44


title: Sample_Tiva_45


title: CTX_8


title: CTX_7


title: Sample_3T19

source_name: Cortex; single neuron from tissue; TIVA captured


title: P2_Het_rep2

value: CrxRip/+

value: post natal day 2


title: Sample_DL-HP3b


title: Sample_3T5


title: D14_Pregnant_SmallRNA

status: Public on Jan 11 2014

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

data_processing:
Sequence files from Ion Torrent PGM imported into CLC Genomics Workbench 6.5.1
Sequence tags were extracted and counted keeping reads between 15 and 55 bases
Small RNA samples were annotated using miRBase (release 19) with Bos taurus species, counts were grouped by mature miRNA and a list of unannotated reads was generated
Sub samples were generated from each sample with a threshold of 10 counts per mature miRNA
Pregnant and cyclic samples were compared using the experiment tool in CLC Genomics Workbench
Genome_build: miRBase release 19
Supplementary_files_format_and_content: Spreadsheets were exported from CLC Genomics Workbench in .xls format. Feature ID is the sequence of the miRNA with the Small RNA column grouped by mature miRNA. Expression values are set to mature 5' counts.

organism: Ovis aries

source_name: Microvesicles from uterine luminal fluid

extract_protocol:
Total RNA, extracted from extracellular vesicles isolated from ULF of cyclic (n=4) and pregnant (n=4) ewes using the miRNeasy kit (Qiagen) , was pooled for a total of 5-10 ng small RNA with less than 1 µg of total RNA per sample.  Small RNA sequencing was performed by the Washington State University Genomics Core using an Ion Torrent PGM (Life Technologies).
Hybridization, RNA ligation and reverse transcription were performed using Ion Total RNA-Seq Kit v2 (Cat # 4475936, Life Technologies) according to the manufacturer’s instructions for small RNA sequencing.  Purification and size selection of the cDNA was conducted using AMPureXP beads (Beckmann-Coulter Genomics, Brea, CA).  Libraries were quantified by real-time quantitative PCR (qPCR) and pooled into a single emulsion PCR reaction performed using an Ion One Touch instrument (Life Technologies).  Sequencing bead numbers, quality and enrichment for DNA carrying beads was assessed by flow cytometry using a Millipore Guava (EMD Millipore Corporation, Billerica, MA).

tag: breed

value: rambouillet

tag: status

value: pregnant

tag: type

value: extracellular vesicles


title: CTX_11


title: Sample_43H


title: Smart_seq_SFM_50pg_TR1

description: serum free media control; mRNA used=50pg; Smart-seq method, Technical Replicate 1

value: mouse embryonic stem cells


title: RNAseq_mouse_hippocampus_pAminus

status: Public on Jan 10 2014

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

data_processing:
Basecalling using Illumina Casava1.8.2 software.
combine three technical replicates RNAseq_mouseESC_pAminus_1.txt, RNAseq_mouseESC_pAminus_2.txt, RNAseq_mouseESC_pAminus_3.txt to RNAseq_mouseESC_pAminus.txt for further analysis
combine three technical replicates RNAseq_mouseESC_pAplus_1.txt, RNAseq_mouseESC_pAplus_2.txt, RNAseq_mouseESC_pAplus_3.txt to RNAseq_mouseESC_pAplus.txt for further analysis
Map to mouse genome mm9 or rhesus genome rheMac3 using Tophat (v 2.0.8)
Bam to Bedgraph using genomeCoverageBed
Bedgraph to bigwig using UCSC bedGraphToBigWig
For visualization, Bigwig files were generated using UCSC bedGraphToBigWig from Bedgraph files, which were generated using genomeCoverageBed from Tophat generated .bam. A UCSC browser session with uploaded Bigwig (.bw) track files is used for visualizing gene expression, etc.
Genome_build: mm9 for mouse samples or for rheMac3 rhesus samples
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

source_name: mouse hippocampus tissue

growth_protocol: hES cells were maintained on plates coated with Matrigel (BD Biosciences) in either defined mTeSR medium (StemCell Technologies Inc.) or conditioned medium (CM) with irradiated mouse embryo fibroblasts supplemented with 4 ng/mL human Basic Fibroblast Growth Factor (bFGF)

extract_protocol:
Total RNAs were prepared using Trizol Reagent and treatment with DNase I. 20μg of total RNAs were separated into polyadenylated and nonpolyadenylated fraction by oligo(dT) magnetic beads (Invitrogen). Ribosomal RNAs were further depleted in nonpolyadenylated fractionby using RiboMinus kit (Invitrogen) o get the poly(A)-/ribo- RNA population. Poly(A)-/ribo- RNAs were further incubated with 5U of RNase R (Epicentre) for 3h at 37℃ and then were subjected to Trizol extraction (Invitrogen).
An aliquot of poly(A)-/ribo- enriched and RNase R digested RNA was used for library preparation with Illumina TruSeq Stranded Total RNA HT Sample Prep Kit (P/N 15031048), and then subjected to 1x100 deep sequencing with Illumina HiSeq 2000

value: hippocampus

tag: chromosome

value: diploid


title: RNAseq_mouse_hippocampus_pAplus


title: RNAseq_mouseESC_pAminus

description: three technical replicates and combined together for further mapping analysis

source_name: embryonic stem cells

value: embryonic stem cells

tag: passages


title: fibroblast_9_CxB

city: Stockholm

first: Daniel

last: Ramsköld

address: Nobels väg 3

country: Sweden

institute: Karolinska Institutet

description: fibroblast 9 genotype C57xCAST

data_processing:
For expression values, we aligned reads using bowtie 0.12.7, option --best, against the genome and transcriptome (Ensembl, version 16 May 2011) with the genotype of both strains, in mm9 coordinates (but for Smart-seq2 samples we used rna-star against the genome)
Non-uniquely mapped reads were removed
Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE.
For allelic ratios, we aligned using gsnap version 2012-07-20, with tolerance for known SNP positions  (but for Smart-seq2 samples we used rna-star)
We used samtools mpileup to extract allelic counts
Genome_build: mm9
Supplementary_files_format_and_content: gene expression values (tab-delimited text)

source_name: fibroblast (primary culture from tail)

extract_protocol:
We used lysis buffer of the kit 'SMARTer Ultra Low Input RNA for Illumina Sequencing' from Clontech
We used Smart-seq2, as described by Picelli et al. Nature methods 2013 (PMID 24056875)

value: CAST/EiJ(mother) x C57BL/6J(father)

tag: cross

value: first generation cross

value: fibroblast (primary culture from tail)


title: fibroblast_21_BxC

description: fibroblast 21 genotype CASTxC57

value: C57BL/6J(mother) x CAST/EiJ(father)


title: fibroblast_20_BxC

description: fibroblast 20 genotype CASTxC57


title: Sample_DL-cs3


title: fibroblast_19_BxC

description: fibroblast 19 genotype CASTxC57


title: RNAseq_mouseESC_pAplus


title: fibroblast_17_BxC

description: fibroblast 17 genotype CASTxC57


title: fibroblast_14_CxB

description: fibroblast 14 genotype C57xCAST


title: fibroblast_15_CxB

description: fibroblast 15 genotype C57xCAST


title: 8cell_split4b

description: 8-cell stage blastomere 4 split b

source_name: 8-cell stage blastomere

value: 8-cell stage blastomere


title: fibroblast_13_CxB

description: fibroblast 13 genotype C57xCAST


title: 8cell_split3b

description: 8-cell stage blastomere 3 split b


title: 8cell_2pooled_split9a

description: Two 8-cell stage blastomeres 9 split a


title: 8cell_split4a

description: 8-cell stage blastomere 4 split a


title: 8cell_split3a

description: 8-cell stage blastomere 3 split a


title: 8cell_2pooled_split9b

description: Two 8-cell stage blastomeres 9 split b


title: D14_Cyclic_SmallRNA

value: cyclic


title: 8cell_2pooled_split7b

description: Two 8-cell stage blastomeres 7 split b


title: 8cell_2pooled_split5b

description: Two 8-cell stage blastomeres 5 split b


title: 8cell_2pooled_split7a

description: Two 8-cell stage blastomeres 7 split a


title: 8cell_14-4_smartseq2

description: 8-cell stage embryo 14 cell 4


title: 8cell_14-2_smartseq2

description: 8-cell stage embryo 14 cell 2


title: 8cell_12-4_smartseq2

description: 8-cell stage embryo 12 cell 4


title: fibroblast_22_BxC

description: fibroblast 22 genotype CASTxC57


title: 8cell_14-1_smartseq2

description: 8-cell stage embryo 14 cell 1


title: 8cell_12-2_smartseq2

description: 8-cell stage embryo 12 cell 2


title: 8cell_12-3_smartseq2

description: 8-cell stage embryo 12 cell 3


title: 8cell_2pooled_split5a

description: Two 8-cell stage blastomeres 5 split a


title: 8cell_12-1_smartseq2

description: 8-cell stage embryo 12 cell 1


title: 8cell_13-1_smartseq2

description: 8-cell stage embryo 13 cell 1


title: fibroblast_16_CxB

description: fibroblast 16 genotype C57xCAST


title: 16cell_split1a

description: Two 16-cell stage blastomere 1 split a

source_name: 16-cell stage blastomere

value: 16-cell stage blastomere


title: 16cell_2pooled_split8b

description: Two 16-cell stage blastomeres 8 split b


title: 16cell_split2a

description: Two 16-cell stage blastomere 2 split a


title: 16cell_2pooled_split8a

description: Two 16-cell stage blastomeres 8 split a


title: 16cell_2pooled_split6a

description: Two 16-cell stage blastomeres 6 split a


title: 16cell_2pooled_split6b

description: Two 16-cell stage blastomeres 6 split b


title: midblast_3-5

description: Mid blastocyst 3 cell 5

data_processing:
For expression values, we aligned reads using bowtie 0.12.7, option --best, against the genome and transcriptome (Ensembl, version 16 May 2011) with the genotype of both strains, in mm9 coordinates
Non-uniquely mapped reads were removed
Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE.
For allelic ratios, we aligned using gsnap version 2012-07-20, with tolerance for known SNP positions
We used samtools mpileup to extract allelic counts
Genome_build: mm9
Supplementary_files_format_and_content: gene expression values (tab-delimited text)

source_name: Mid blastocyst cell (92-94h post-fertilization)

extract_protocol:
We used lysis buffer of the kit 'SMARTer Ultra Low Input RNA for Illumina Sequencing' from Clontech
We used the kit 'SMARTer Ultra Low Input RNA for Illumina Sequencing' from Clontech


title: midblast_3-8

description: Mid blastocyst 3 cell 8

value: Mid blastocyst cell (92-94h post-fertilization)


title: midblast_3-7

description: Mid blastocyst 3 cell 7


title: zy2

description: Zygote 2

source_name: Zygote

value: Zygote


title: midblast_3-9

description: Mid blastocyst 3 cell 9


title: midblast_3-6

description: Mid blastocyst 3 cell 6


title: midblast_3-4

description: Mid blastocyst 3 cell 4


title: zy3

description: Zygote 3


title: zy1

description: Zygote 1


title: midblast_3-3

description: Mid blastocyst 3 cell 3


title: midblast_3-18

description: Mid blastocyst 3 cell 18


title: midblast_3-23

description: Mid blastocyst 3 cell 23


title: 16cell_split2b

description: Two 16-cell stage blastomere 2 split b


title: midblast_3-2

description: Mid blastocyst 3 cell 2


title: 16cell_split1b

description: Two 16-cell stage blastomere 1 split b


title: midblast_3-17

description: Mid blastocyst 3 cell 17


title: midblast_3-12

description: Mid blastocyst 3 cell 12


title: midblast_3-14

description: Mid blastocyst 3 cell 14


title: midblast_3-11

description: Mid blastocyst 3 cell 11


title: midblast_3-13

description: Mid blastocyst 3 cell 13


title: zy4

description: Zygote 4


title: midblast_3-15

description: Mid blastocyst 3 cell 15


title: midblast_2-9

description: Mid blastocyst 2 cell 9


title: midblast_3-1

description: Mid blastocyst 3 cell 1


title: midblast_2-8

description: Mid blastocyst 2 cell 8


title: midblast_3-10

description: Mid blastocyst 3 cell 10


title: midblast_2-5

description: Mid blastocyst 2 cell 5


title: midblast_2-7

description: Mid blastocyst 2 cell 7


title: midblast_2-6

description: Mid blastocyst 2 cell 6


title: 8cell_14-3_smartseq2

description: 8-cell stage embryo 14 cell 3


title: midblast_2-3

description: Mid blastocyst 2 cell 3


title: midblast_2-18

description: Mid blastocyst 2 cell 18


title: midblast_2-24

description: Mid blastocyst 2 cell 24


title: midblast_2-15

description: Mid blastocyst 2 cell 15


title: midblast_2-2

description: Mid blastocyst 2 cell 2


title: midblast_2-17

description: Mid blastocyst 2 cell 17


title: midblast_2-16

description: Mid blastocyst 2 cell 16


title: midblast_2-12

description: Mid blastocyst 2 cell 12


title: midblast_2-13

description: Mid blastocyst 2 cell 13


title: midblast_2-4

description: Mid blastocyst 2 cell 4


title: midblast_2-23

description: Mid blastocyst 2 cell 23


title: midblast_1-9

description: Mid blastocyst 1 cell 9


title: midblast_2-10

description: Mid blastocyst 2 cell 10


title: midblast_2-1

description: Mid blastocyst 2 cell 1


title: midblast_2-11

description: Mid blastocyst 2 cell 11


title: midblast_1-8

description: Mid blastocyst 1 cell 8


title: midblast_1-5

description: Mid blastocyst 1 cell 5


title: midblast_1-3

description: Mid blastocyst 1 cell 3


title: midblast_1-4

description: Mid blastocyst 1 cell 4


title: midblast_1-22

description: Mid blastocyst 1 cell 22


title: midblast_1-23

description: Mid blastocyst 1 cell 23


title: midblast_1-2

description: Mid blastocyst 1 cell 2


title: midblast_1-24

description: Mid blastocyst 1 cell 24


title: midblast_1-20

description: Mid blastocyst 1 cell 20


title: midblast_1-17

description: Mid blastocyst 1 cell 17


title: midblast_1-18

description: Mid blastocyst 1 cell 18


title: midblast_1-16

description: Mid blastocyst 1 cell 16


title: midblast_2-14

description: Mid blastocyst 2 cell 14


title: midblast_1-11

description: Mid blastocyst 1 cell 11


title: midblast_1-15

description: Mid blastocyst 1 cell 15


title: midblast_1-10

description: Mid blastocyst 1 cell 10


title: midblast_1-12

description: Mid blastocyst 1 cell 12


title: midblast_1-1

description: Mid blastocyst 1 cell 1


title: midblast_1-13

description: Mid blastocyst 1 cell 13


title: mid2cell_6-2

description: Mid 2-cell stage embryo 6 cell 2

source_name: Mid 2-cell stage blastomere (34-40h post-fertilization)


title: mid2cell_7-1

description: Mid 2-cell stage embryo 7 cell 1

value: Mid 2-cell stage blastomere (34-40h post-fertilization)


title: mid2cell_5-2

description: Mid 2-cell stage embryo 5 cell 2


title: mid2cell_5-1

description: Mid 2-cell stage embryo 5 cell 1


title: mid2cell_4-1

description: Mid 2-cell stage embryo 4 cell 1


title: mid2cell_4-2

description: Mid 2-cell stage embryo 4 cell 2


title: mid2cell_7-2

description: Mid 2-cell stage embryo 7 cell 2


title: midblast_1-6

description: Mid blastocyst 1 cell 6


title: mid2cell_3-2

description: Mid 2-cell stage embryo 3 cell 2


title: mid2cell_0-2

description: Mid 2-cell stage embryo 0 cell 2


title: mid2cell_3-1

description: Mid 2-cell stage embryo 3 cell 1


title: mid2cell_0-1

description: Mid 2-cell stage embryo 0 cell 1


title: lateblast_2-9

description: Late blastocyst 2 cell 9

source_name: Late blastocyst cell (100-102h post-fertilization)


title: mid2cell_6-1

description: Mid 2-cell stage embryo 6 cell 1


title: midblast_1-19

description: Mid blastocyst 1 cell 19


title: lateblast_2-3

description: Late blastocyst 2 cell 3

value: Late blastocyst cell (100-102h post-fertilization)


title: lateblast_2-8

description: Late blastocyst 2 cell 8


title: lateblast_2-7

description: Late blastocyst 2 cell 7


title: lateblast_2-2

description: Late blastocyst 2 cell 2


title: lateblast_2-5

description: Late blastocyst 2 cell 5


title: lateblast_2-16

description: Late blastocyst 2 cell 16


title: lateblast_2-17

description: Late blastocyst 2 cell 17


title: midblast_1-14

description: Mid blastocyst 1 cell 14


title: lateblast_2-14

description: Late blastocyst 2 cell 14


title: lateblast_2-12

description: Late blastocyst 2 cell 12


title: lateblast_2-1

description: Late blastocyst 2 cell 1


title: lateblast_1-9

description: Late blastocyst 1 cell 9


title: lateblast_1-8

description: Late blastocyst 1 cell 8


title: lateblast_1-6

description: Late blastocyst 1 cell 6


title: lateblast_1-5

description: Late blastocyst 1 cell 5


title: lateblast_1-26

description: Late blastocyst 1 cell 26


title: lateblast_1-4

description: Late blastocyst 1 cell 4


title: lateblast_1-24

description: Late blastocyst 1 cell 24


title: lateblast_1-23

description: Late blastocyst 1 cell 23


title: lateblast_1-27

description: Late blastocyst 1 cell 27


title: lateblast_1-21

description: Late blastocyst 1 cell 21


title: lateblast_1-2

description: Late blastocyst 1 cell 2


title: lateblast_1-19

description: Late blastocyst 1 cell 19


title: lateblast_1-20

description: Late blastocyst 1 cell 20


title: late2cell_9-2

description: Late 2-cell stage embryo 9 cell 2

source_name: Late 2-cell stage blastomere (46-48h post-fertilization)


title: late2cell_9-1

description: Late 2-cell stage embryo 9 cell 1

value: Late 2-cell stage blastomere (46-48h post-fertilization)


title: lateblast_1-14

description: Late blastocyst 1 cell 14


title: lateblast_1-11

description: Late blastocyst 1 cell 11


title: lateblast_1-10

description: Late blastocyst 1 cell 10


title: late2cell_7-2

description: Late 2-cell stage embryo 7 cell 2


title: late2cell_8-2

description: Late 2-cell stage embryo 8 cell 2


title: late2cell_8-1

description: Late 2-cell stage embryo 8 cell 1


title: late2cell_7-1

description: Late 2-cell stage embryo 7 cell 1


title: late2cell_6-2

description: Late 2-cell stage embryo 6 cell 2


title: late2cell_6-1

description: Late 2-cell stage embryo 6 cell 1


title: lateblast_1-7

description: Late blastocyst 1 cell 7


title: late2cell_5-2

description: Late 2-cell stage embryo 5 cell 2


title: late2cell_5-1

description: Late 2-cell stage embryo 5 cell 1


title: earlyblast_4-8

description: Early blastocyst 4 cell 8

source_name: Early blastocyst cell (86-88h post-fertilization)


title: earlyblast_4-9

description: Early blastocyst 4 cell 9

value: Early blastocyst cell (86-88h post-fertilization)


title: earlyblast_4-6

description: Early blastocyst 4 cell 6


title: earlyblast_4-5

description: Early blastocyst 4 cell 5


title: lateblast_1-16

description: Late blastocyst 1 cell 16


title: earlyblast_4-17

description: Early blastocyst 4 cell 17


title: earlyblast_4-12

description: Early blastocyst 4 cell 12


title: earlyblast_4-3

description: Early blastocyst 4 cell 3


title: earlyblast_4-18

description: Early blastocyst 4 cell 18


title: earlyblast_4-13

description: Early blastocyst 4 cell 13


title: earlyblast_4-14

description: Early blastocyst 4 cell 14


title: lateblast_1-13

description: Late blastocyst 1 cell 13


title: earlyblast_4-16

description: Early blastocyst 4 cell 16


title: earlyblast_3-9

description: Early blastocyst 3 cell 9


title: earlyblast_4-1

description: Early blastocyst 4 cell 1


title: earlyblast_3-4

description: Early blastocyst 3 cell 4


title: earlyblast_3-3

description: Early blastocyst 3 cell 3


title: earlyblast_3-17

description: Early blastocyst 3 cell 17


title: earlyblast_3-16

description: Early blastocyst 3 cell 16


title: earlyblast_3-15

description: Early blastocyst 3 cell 15


title: earlyblast_3-8

description: Early blastocyst 3 cell 8


title: earlyblast_3-13

description: Early blastocyst 3 cell 13


title: earlyblast_3-7

description: Early blastocyst 3 cell 7


title: earlyblast_3-1

description: Early blastocyst 3 cell 1


title: earlyblast_3-12

description: Early blastocyst 3 cell 12


title: earlyblast_4-2

description: Early blastocyst 4 cell 2


title: earlyblast_2-6

description: Early blastocyst 2 cell 6


title: earlyblast_3-10

description: Early blastocyst 3 cell 10


title: earlyblast_2-8

description: Early blastocyst 2 cell 8


title: earlyblast_2-7

description: Early blastocyst 2 cell 7


title: earlyblast_2-3

description: Early blastocyst 2 cell 3


title: earlyblast_2-5

description: Early blastocyst 2 cell 5


title: earlyblast_2-2

description: Early blastocyst 2 cell 2


title: earlyblast_3-2

description: Early blastocyst 3 cell 2


title: earlyblast_2-16

description: Early blastocyst 2 cell 16


title: earlyblast_2-15

description: Early blastocyst 2 cell 15


title: earlyblast_2-22

description: Early blastocyst 2 cell 22


title: earlyblast_2-4

description: Early blastocyst 2 cell 4


title: earlyblast_2-10

description: Early blastocyst 2 cell 10


title: earlyblast_2-17

description: Early blastocyst 2 cell 17


title: earlyblast_3-6

description: Early blastocyst 3 cell 6


title: early2cell_3-2

description: Early 2-cell stage embryo 3 cell 2

source_name: Early 2-cell stage blastomere (31-32h post-fertilization)


title: early2cell_2-2

description: Early 2-cell stage embryo 2 cell 2

value: Early 2-cell stage blastomere (31-32h post-fertilization)


title: earlyblast_2-19

description: Early blastocyst 2 cell 19


title: earlyblast_3-14

description: Early blastocyst 3 cell 14


title: earlyblast_2-12

description: Early blastocyst 2 cell 12


title: early2cell_1-2

description: Early 2-cell stage embryo 1 cell 2


title: early2cell_3-1

description: Early 2-cell stage embryo 3 cell 1


title: earlyblast_2-1

description: Early blastocyst 2 cell 1


title: early2cell_1-1

description: Early 2-cell stage embryo 1 cell 1


title: early2cell_2-1

description: Early 2-cell stage embryo 2 cell 1


title: early2cell_0-2

description: Early 2-cell stage embryo 0 cell 2


title: early2cell_0-1

description: Early 2-cell stage embryo 0 cell 1


title: C57twocell_18-2

description: 2-cell stage embryo 18 cell 2

source_name: 2-cell stage blastomere

value: 2-cell stage blastomere


title: C57twocell_18-1

description: 2-cell stage embryo 18 cell 1


title: C57twocell_22-2

description: 2-cell stage embryo 22 cell 2


title: C57twocell_22-1

description: 2-cell stage embryo 22 cell 1


title: C57twocell_20-2

description: 2-cell stage embryo 20 cell 2


title: C57twocell_16-2

description: 2-cell stage embryo 16 cell 2


title: BXC_liver_cell_4

description: Liver cell 4

source_name: Liver cell

value: adult

value: liver cell


title: BXC_liver_cell_2

description: Liver cell 2


title: BXC_liver_cell_6

description: Liver cell 6


title: C57twocell_16-1

description: 2-cell stage embryo 16 cell 1


title: BXC_liver_cell_1

description: Liver cell 1


title: BXC_liver_cell_5

description: Liver cell 5


title: BXC_30pg_liver_RNA_0

description: 30 pg total RNA, from pool of liver RNA, technical replicate

source_name: Liver

extract_protocol:
We used Trizol (Ambion catalog number 15596-026)
We used the kit 'SMARTer Ultra Low Input RNA for Illumina Sequencing' from Clontech

value: liver (pooled)


title: BXC_10pg_liver_RNA_1

description: 10 pg total RNA, from pool of liver RNA, technical replicate

value: first generation cross


title: BXC_1ng_liver_RNA_1

description: 1 ng total RNA, from pool of liver RNA, technical replicate


title: BXC_100pg_liver_RNA_2

description: 100 pg total RNA, from pool of liver RNA, technical replicate


title: BXC_100pg_liver_RNA_1


title: BXC_1ng_liver_RNA_0


title: BXC_10pg_liver_RNA_2


title: 8cell_8-8

description: 8-cell stage embryo 8 cell 8

value: CAST/EiJ(mother) x C57BL/6J(father)


title: 8cell_8-7

description: 8-cell stage embryo 8 cell 7


title: 8cell_8-6

description: 8-cell stage embryo 8 cell 6


title: C57twocell_20-1

description: 2-cell stage embryo 20 cell 1


title: 8cell_8-3

description: 8-cell stage embryo 8 cell 3


title: 8cell_8-2

description: 8-cell stage embryo 8 cell 2


title: 8cell_5-8

description: 8-cell stage embryo 5 cell 8


title: CL37_11-12_A

first: Kevin

middle: M

last: Carr

address: Plant Biology Lab, 612 Wilson Rd., Rm. S-20 A

department: Research Technology Support Facility

description: fae1 with the castor hydroxylase (RcFAH12) expressed in seeds (Lu, C. F., Fulda, M., Wallis, J. G., and Browse, J. (2006) The Plant Journal 45, 847-856)

data_processing:
Basecalls were performed by Illumina Real Time Analysis software v 1.13.48. Demultiplexing and FASTQ conversion by Illumian BCL2Fastq v1.8.2
Reads were trimmed of Illumina adapter and low quality bases with Trimmomatic v0.22
Reads were mapped to the  Arabidopsis thalian genome, vTAIR10 using TopHat (v2.0.3). Only reads aligning to annotated genes were accepted.
Raw counts of reads aligning to each gene within each sample were determined with htseq-count (v0.5.4p3). Output is reported in processed data files.
Normalized expression (FPKM) was determined using Cufflinks (v2.0.1). Output is reported in supplementary matrix file, averaged FPKM across all biological replicates per condition.
Genome_build: TAIR10
Supplementary_files_format_and_content: Count files are tab delimited text output by htseq-count reporting TAIR10 gene ID, raw count. Supplementary matrix file is tab delimited text output by cufflinks reporting TAIR10 gene ID, short gene name, gene locus (<chr#>:<start>-<stop>), normalized (FPKM) expression values for each plant line/developmental stage, average of three biological replicates each.

organism: Arabidopsis thaliana

growth_protocol: All plant lines were grown randomized across a growth chamber under constant ~100-170 μE light, ~22° C and ~60% humidity.

extract_protocol:
Developing siliques of 7-8, 9-10, or 11-12 DAF were collected from a single shoot of ~50 plants of each plant line, frozen in liquid nitrogen and developing seeds removed by (Bates, P., Jewell, J., and Browse, J. (2013) Plant Methods 9, 9). Approximately 100 mg of frozen seed samples (three biological replicates for each plant line/ developmental stage) were ground to a fine power,  RNA extracted Suzuki, Y., Kawazu, T., and Koyama, H. (2004) BioTechniques 37, 542-544 , and DNA removed (DNA-Free RNA Kit, Zymo Research).
Libraries were constructed using the Illumina TruSeq mRNA Library Preparation Kit v2

value: Seeds

tag: age (days after flowering)


title: CL37_11-12_C


title: 8cell_5-4

description: 8-cell stage embryo 5 cell 4

value: 8-cell stage blastomere


title: 8cell_5-7

description: 8-cell stage embryo 5 cell 7


title: CL37_11-12_B


title: BXC_30pg_liver_RNA_2

value: C57BL/6J(mother) x CAST/EiJ(father)


title: 8cell_5-2

description: 8-cell stage embryo 5 cell 2


title: 8cell_2-6

description: 8-cell stage embryo 2 cell 6


title: 8cell_2-8

description: 8-cell stage embryo 2 cell 8


title: CL37_9-10_C


title: CL37_9-10_B


title: 8cell_2-7

description: 8-cell stage embryo 2 cell 7


title: 8cell_2-4

description: 8-cell stage embryo 2 cell 4


title: CL37_7-8_C


title: 8cell_5-1

description: 8-cell stage embryo 5 cell 1


title: 8cell_2-2

description: 8-cell stage embryo 2 cell 2


title: 8cell_2-3

description: 8-cell stage embryo 2 cell 3


title: CL37_9-10_A


title: 8cell_8-1

description: 8-cell stage embryo 8 cell 1


title: 8cell_2-1

description: 8-cell stage embryo 2 cell 1


title: CL37_7-8_B


title: 8cell_1-8

description: 8-cell stage embryo 1 cell 8


title: 8cell_1-7

description: 8-cell stage embryo 1 cell 7


title: 8cell_5-6

description: 8-cell stage embryo 5 cell 6


title: CL37_7-8_A


title: 8cell_1-6

description: 8-cell stage embryo 1 cell 6


title: 8cell_1-5

description: 8-cell stage embryo 1 cell 5


title: 8cell_1-4

description: 8-cell stage embryo 1 cell 4


title: 8cell_1-2

description: 8-cell stage embryo 1 cell 2


title: 8cell_1-1

description: 8-cell stage embryo 1 cell 1


title: fae1_11-12_A

description: fae1 mutant (Kunst, L., Taylor, D. C., and Underhill, E. W. (1992) Plant Physiol. Biochem. 30, 425-434)


title: fae1_11-12_B


title: 8cell_5-3

description: 8-cell stage embryo 5 cell 3


title: 4cell_4-4

description: 4-cell stage embryo 4 cell 4

source_name: 4-cell stage blastomere

value: 4-cell stage blastomere


title: 4cell_4-3

description: 4-cell stage embryo 4 cell 3


title: 4cell_4-2

description: 4-cell stage embryo 4 cell 2


title: fae1_7-8_C


title: fae1_9-10_C


title: 4cell_4-1

description: 4-cell stage embryo 4 cell 1


title: 4cell_3-4

description: 4-cell stage embryo 3 cell 4


title: fae1_9-10_A


title: fae1_9-10_B


title: 4cell_3-3

description: 4-cell stage embryo 3 cell 3


title: fae1_7-8_B


title: 4cell_2-3

description: 4-cell stage embryo 2 cell 3


title: 4cell_2-1

description: 4-cell stage embryo 2 cell 1


title: 4cell_2-2

description: 4-cell stage embryo 2 cell 2


title: 4cell_3-1

description: 4-cell stage embryo 3 cell 1


title: fae1_7-8_A


title: 4cell_1-1

description: 4-cell stage embryo 1 cell 1


title: 16cell_6-9

description: 16-cell stage embryo 6 cell 9

value: 16-cell stage blastomere


title: fae1_11-12_C


title: 4cell_1-2

description: 4-cell stage embryo 1 cell 2


title: 16cell_6-6

description: 16-cell stage embryo 6 cell 6


title: 4cell_1-4

description: 4-cell stage embryo 1 cell 4


title: 16cell_6-8

description: 16-cell stage embryo 6 cell 8


title: 16cell_6-7

description: 16-cell stage embryo 6 cell 7


title: 16cell_6-5

description: 16-cell stage embryo 6 cell 5


title: 16cell_6-4

description: 16-cell stage embryo 6 cell 4


title: 16cell_6-3

description: 16-cell stage embryo 6 cell 3


title: 16cell_6-2

description: 16-cell stage embryo 6 cell 2


title: 4cell_2-4

description: 4-cell stage embryo 2 cell 4


title: 16cell_5-9

description: 16-cell stage embryo 5 cell 9


title: 16cell_6-10

description: 16-cell stage embryo 6 cell 10


title: 16cell_6-11

description: 16-cell stage embryo 6 cell 11


title: 16cell_6-1

description: 16-cell stage embryo 6 cell 1


title: 16cell_5-5

description: 16-cell stage embryo 5 cell 5