title: Control-T3

city: Granada

first: Raquel

last: Tobes

state: Granada

address: Plaza Campo Verde 3 Atico

department: Bioinformatics

institute: Era7 Bioinformatics

description: Healthy sister twin at the time point T1

data_processing:
Reads were mapped using Tophat v2.0.8b
Transcripts assembly and abundance estimation performed using Cufflinks
Analysis of differentially expressed genes was performed using Cufflinks
Genome_build: We used the Homo sapiens Ensembl GRCh37 genome (ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/Ensembl/GRCh37/Homo_sapiens_Ensembl_GRCh37.tar.gz) as the reference genome.
Supplementary_files_format_and_content: GTF files generated with Cufflinks, FPKM values are included in the last columns of the file

source_name: Healthy twin

extract_protocol:
PBMC were isolated by Ficoll gradient from blood samples and resuspended in nucleic acid preserving solution (TriZol, Invitrogen) and conserved at -80º C until used for RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: blood

value: peripheral blood mononuclear cells

tag: diagnosis

value: healthy

tag: gender

value: female


title: mRNA queen sample 5

status: Public on Sep 06 2015

type: SRA

city: Canberra

first: Sylvain

last: Foret

state: ACT

address: Gould Building #116

department: Research School of Biology

country: Australia

institute: The Australian National University

library_source: transcriptomic

data_processing:
Base calling: Cassave 1.8
Alignment of mRNAs: tophat 2.0.9, miRNAs: mirdeep2 2.0.0.5
Counts: htseq 0.5.4p3
Genome_build: Honey bee Apis mellifera genome assembly v4.5 official gene set v3.2
Supplementary_files_format_and_content: For mRNA: Official gene set 3.2 id (GB id), TAB, count; for miRNA, MiRBase ID (or if new, genomic coordinates and strand), TAB, count

molecule: total RNA

organism: Apis mellifera

source_name: L5 queen larvae

extract_protocol:
total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer.
Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip.

tag: developmental stage

value: L5 Larvae

tag: caste

value: Queen

tag: body part

value: Whole body


title: Control-T2

status: Public on Sep 05 2015

country: Spain

organism: Homo sapiens

tag: tissue

tag: cell type


title: OPC rep1

city: Rochester

first: FENG

last: CUI

state: NY

address: One Lomb Memorial Dr.

department: Thomas H. Gosnell School of Life Sciences

country: USA

institute: ROCHESTER INSTITUTE OF TECHNOLOGY

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence, then mapped to rnor5 whole genome using SHRiMP v2.2.3 with parameters -Q --qv-offset 33 -L ./<indexLocation>/<assemblyName> -N 8 –all-contigs
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. The software used to do this was Rsubread v1.16.1 (Liao et al., Nucleic Acids Research, 2011)
Genome_build: rnor5
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample.

organism: Rattus norvegicus

source_name: N7746-100 (Life Technologies)

extract_protocol:
RNA samples of the rat neurons, astrocytes and OPCs were prepared by the RNeasy Mini Kit of QIAGEN (Cat. 74104) following the instructions of the Kit. Cells were sheared using the Qiashredder (Cat. 79654). Isolated RNA was quantified using the Thermo Scientific NanoDrop (ND-1000). A total of 250 ng RNA was sent to the UR Genomics Research Center (Rochester, NY) for RNA sequencing using Illumina HiSeq2500 Sequencer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: oligodendrocyte precursor cells

tag: passages

tag: days

value: 8 days before passage and 6 days after passage


title: astrocyte rep2

source_name: N7745-100 (Life Technologies)

value: astrocyte


title: astrocyte rep1


title: mRNA queen sample 2


title: neuron rep1

source_name: A10840-01 (Life Technologies)

value: neuron


title: Control-T1


title: RNASeq_line C_L1_rep1

city: Seoul

first: Sumin

last: Oh

address: Cheongpa-ro 47-gil 100, Yongsan-gu

department: Department of Biological Science

country: South Korea

institute: Sookmyung Women's University

data_processing:
Basecalls performed using the CASAVA software
ChIP-seq reads were aligned to the mm9 genome assembly using the Bowtie2 program (Langmead et al., Nature method, 2012)
RNA-seq reads were aligned to the mm9 genome assembly using the STAR program (Dobin et al., Bioinformatics, 2012)
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: BedGraph files can be used to check ChIP-seq peaks through the UCSC genome browser.
Supplementary_files_format_and_content: RNA-Seq: Peak/bigWig files can be used to check RNA-seq peaks through the UCSC genome browser.

organism: Mus musculus

source_name: Mammary

growth_protocol: C57BL/6 mice were purchased from Charles River. All animals were handled and housed in accordance with the guidelines of the National Institutes of Diabetes, Digestive and Kidney Diseses Animal Care and Use Committee.

extract_protocol:
RNA-seq: Poly(A) RNA were purified twice with Trizol and RNeasy® Plus Mini Kit (Qiagen). cDNA was synthesized using SuperScript II (Invitrogen) and TruSeq RNA Sample Preparation Kit (Illumina).
Libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: Mixed C57BL/6J x CBA/J

value: Mammary gland

tag: state

value: lactation day of 1

tag: genotype

value: line C (GAS1 & GAS2 mutations at putative Stat5 enhancer)


title: GBS-T2

description: Guillain-Barré syndrome patient at the time point of passing to intermediate care  (T2)

source_name: Patient with GBS

value: Guillain-Barre Syndrome


title: GBS-T1

description: Guillain-Barré syndrome patient at the time point of hospitalization in the intensive care unit (T1)


title: RNASeq_line C_L1_rep2


title: RNASeq_line B_L1_rep2

value: line B (GAS1 mutation only at putative Stat5 enhancer)


title: RNASeq_WT_L1_rep1

extract_protocol:
Frozen-stored mammary tissues from L1 or p13 were broken into powder with mortar and pestle. Nuclei were extracted in Farnham lysis buffer (5mM PIPES pH8.0, 85mM KCl, 0.5% NP-40 and protease inhibitors). Antibodies against H3K27ac (Abcam, Ab4729), MED1 (Bethyl laboratory, A300-793A), RNA Pol II (Abcam, Ab5408), GR (Thermo Scientific, PA1-511A) were used for ChIP.
Libraries were prepared for sequencing using standard Illumina protocols.

value: wild type


title: ChIPSeq_WT_L1_RNA Pol II_rep1

library_source: genomic

molecule: genomic DNA

tag: chip antibody

value: RNA Pol II (Abcam, Ab5408)


title: ChIPSeq_WT_L1_input_rep1


title: ChIPSeq_WT_L1_MED1_rep1

value: MED1 (Bethyl lab, A300-793A)


title: Synechococcus 7002, unadapted wild type, irradiance 125:60

status: Public on Sep 04 2015

city: Boston

first: Ryan

last: McClure

address: 650 Albany St.

institute: Boston University

data_processing:
The 50-base short read sequences produced by the 5500XL SOLiD  sequencer were mapped in color space using SOLiD LifeScope software version 2.5 using the default parameters
Resulting BAM files were then examined with Rockhopper (McClure et al. 2013 Nucleic Acids Research) to determine RPKM levels of genes
Genome_build: Synechococcus 7002 NC_010474, NC_010475, NC_010476, NC_010477, NC_010478, NC_010479 and NC_010480
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Picosynechococcus sp. PCC 7002

source_name: Synechococcus 7002_unadapted wild type

growth_protocol: Synechococcus 7002 was routinely grown in modified A+ media (Stevens and Porter 1980) containing 17 mM NH4

extract_protocol:
RNA was extracted using Trizol following by DNAseI treatment using Qiagen RNAseay mini column
Template cDNA was prepared using the Applied Biosystems SOLiD® Total RNA-Seq Kit (Life Technologies, Carlsbad, CA) according to manufacturer's protocol. Sequencing was carried using the SOLiDTM 5500XL protocol (Life Technologies).

treatment_protocol: Synechococcus sp. PCC 7002 was grown in a turbidostat and subjected to six irradiance levels (33, 98, 164, 395, 610, and 760 µmol photons m-2 sec-1) with RNA being collected at each irradiance level

tag: genotype/variation

value: unadapted wild type

tag: light wavelength 630 nm/680 nm ratio

tag: irradiance level

value: 610 µmol photons m-2 sec-1.


title: him-8 mRNA rep2

city: Syracuse

first: Eleanor

middle: M

last: Maine

state: New York

address: 107 College Pl

department: Biology

institute: Syracuse University

data_processing:
Sequenced reads were mapped to the ce_WS220 genome using STAR version v2.3.0 with default parameters except that the --alignIntronMax was set to 5000.
Reads were counted, RPKM (Reads Per Kilobase of exon per Megabase of library size) were calculated and differentially expressed genes were identified using cuffdiff version 2.2.1
Genome_build: ce_WS220
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample; tab-delimited text files includes raw reads count for each sample

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: gonad

extract_protocol:
Gonads dissected from staged adults were collected and frozen on dry ice.  400 gonad arms were used per RNA prep.  RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Preparation Kit v2 (Cat#: RS-122-2001) was used with 1.2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: gonad

value: adult


title: Synechococcus 7002, unadapted wild type, irradiance 60:60

value: 395 µmol photons m-2 sec-1.


title: him-8 mRNA rep1


title: Synechococcus 7002, unadapted wild type, irradiance 25:25

value: 164 µmol photons m-2 sec-1.


title: met-2;him-8 mRNA rep1


title: Input DNA

data_processing:
ChIP-seq reads were aligned to the ce_WS220 genome assembly using bowtie version 1.0.0 with the following configurations -n 2 -l 30 -e 70 -M 1 --best --strata
Peak were called using MACS2 version v2.0.10.20130306-beta with default setting.
Data were normalized with BEADS version 1.1 and BigWiggle files were generated.
Peaks were revaluated manually.
Genome_build: ce_WS220
Supplementary_files_format_and_content: bw: BigWiggle format, normalized read count every 10bp; bed: bed format, H3K9me2-enriched sites; all processed data files are located on the series record and includes a description of the file contents.

source_name: whole animal

growth_protocol: We collected embryos from animals grown at 15°C, hatched them into M9 medium, collected the synchronized L1s, raised them in liquid medium with E. coli as a food source at 22°C for ~60 hr, and harvested adults.  For him-8 strains, hermaphrodites were separated from males using 35 micron nylon mesh (Sefar).

extract_protocol:
Tissue was disrupted and chromatin was sheared with a probe sonicator, and histone-DNA complexes were isolated with antibody.
DNA libraries were generated using the NEBNext® ChIP-seq Library Prep Master Mix Set for Illumina® (NEB #E6240) following the manufacturer’s protocol and using Qiagen column purification.

tag: antibody

value: whole animal


title: Input

city: Toulouse

first: Jean-Yves

last: Bouet

address: 169 avenue Marianne Grunberg-Manago

country: France

institute: CNRS

description: Total reads (PF): 48,502,096

data_processing:
Base-calling software : RTA-1.17.20.0
Data filtering steps : None (automatic Illumina quality filtering)
Read alignment : BWA-0.6.2
Additional processing software : Samtools and home-made script to generate density files.
Genome_build: ASM584v2 ; AP001918
Supplementary_files_format_and_content: All processed data files are in text format and represent the density tags for each DNA strand (F: forward; R:reverse)

organism: Escherichia coli

source_name: bacteria

growth_protocol: Samples were prepared from exponential growing phase cultures at 37°C in LB media (OD = 0.5)

extract_protocol:
Lysates were clarified from sonicated cell and protein-DNA complexes were isolated with anti SopB antibody
Library of precipitated DNA from ChIP preparation were constructed by adding 130-bp DNA adapters and sequenced with Illumina 50 cycles Truseq SBS kit v3 (FC-401-3002, Illumina); Library of precipitated DNA from ChIP preparation were constructed by adding 130-bp DNA adapters and sequenced with Illumina Library of precipitated DNA from ChIP preparation were constructed by adding 130-bp DNA adapters and sequenced with Illumina technology

treatment_protocol: Cells were treated with formalhedyde (1 %)

tag: strains

tag: plasmids


title: met-2;him-8 mRNA rep2

tag: developmental stage


title: GBS-T3

description: Guillain-Barré syndrome patient at the time point of the conclusion of locomotion rehabilitation program when the patient was close to abandon the hospital (T3)

value: blood

value: peripheral blood mononuclear cells

tag: diagnosis

tag: gender

value: female


title: Synechococcus 7002, unadapted wild type, irradiance 15:15

value: 98 µmol photons m-2 sec-1.


title: IP_F

description: Total reads (PF): 50,921,857

value: affinity purified anti-SopB


title: RNASeq_line B_L1_rep1

value: Mixed C57BL/6J x CBA/J

tag: tissue

value: Mammary gland

value: lactation day of 1


title: Synechococcus 7002, unadapted wild type, irradiance 5:5

value: 33 µmol photons m-2 sec-1.


title: H3K9me2_ChIPseq fer-1 rep1


title: H3K9me2_ChIPseq fer-1;him-8 rep1


title: RNASeq_WT_L1_rep2

value: wild type


title: H3K9me2_ChIPseq fer-1;him-8 rep2


title: bor 405min_rep3

city: Stanford

first: Thomas

last: Wandless

state: California

address: 318 Campus Dr. W350 Clark Ce

department: Chemical and Systems Biology

institute: Stanford University

data_processing:
uploaded to DNANexus and analyze for FPKM and read counts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM and read counts values for each sample

source_name: NIH3T3, bor 405min

extract_protocol:
RNA were collected using RNeasy mini kit from QIAGEN
RNA libraries were prepared for sequencing using Encore Complete RNA-seq kit from NuGEN

tag: cell line

tag: stress

value: bortezomib

tag: time


title: bor 405min_rep4


title: bor 135min_rep4

source_name: NIH3T3, bor 135min


title: bor 405min_rep1


title: bor 135min_rep2


title: ChIPSeq_WT_L1_H3K27ac

tag: strain

value: H3K27ac (Abcam, ab4729)


title: bor 135min_rep3


title: bor 405min_rep2


title: bor 135min_rep1


title: Synechococcus 7002, unadapted wild type, irradiance 170:60

value: unadapted wild type

value: 760 µmol photons m-2 sec-1.


title: bor 45min_rep4

source_name: NIH3T3, bor 45min


title: bor 45min_rep3


title: bor 45min_rep2


title: control 0min_rep3

source_name: NIH3T3, control 0min


title: bor 45min_rep1


title: control 0min_rep4


title: H3K9me2_ChIPseq fer-1 rep2

value: adult


title: control 0min_rep2


title: control 0min_rep1


title: MES-Mel18 [RNA-Seq]

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

institute: Center for Genomic Regulation (CRG)

description: (RNAseq) Mel18 Knock-Down

data_processing:
ChIPseq analysis: Alignment: Sequence reads were mapped to the Mouse genome (mm9, July 2007) using BOWTIE (PubMed ID 19261174) with the option -m 1. RNAseq analysis: Alignment: The reads were mapped against the mm9 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1.
Peak-calling: Peak detection was performed with MACS (PubMed ID: 18798982). ChIP profiles were produced by MACS in BedGraph. Peaks were reported in BED format.
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph files report genome-wide ChIP or RNAseq profiles.  BED files report signal enriched regions.

source_name: Mesoderm precursors

growth_protocol: E14Tg2A cells were cultured as previously described (Morey et al., 2012) in 2i media supplemented with LIF produced in house) as previously described (Ying et al., 2003) for at least two weeks (8 passages).  We took advantage of a recently reported protocol for differentiating ESC into a highly homogenous population of beating cardiomyocytes (CM) (Kattman et al., 2011). Interestingly, this protocol also permits early steps of cardiac differentiation, like formation of early cardiac-mesoderm precursors cells (MES) and cardiac precursor (CP) cells, to be studied.

extract_protocol:
Chromatin from ESC and MES was immunoprecipitated with 5 ug of antibody as described in Morey et al 2012. RNA was extracted with the RNA extraction kit (QIAGEN).
Libraries were prepared according to Illumina instructions.

treatment_protocol: In our hands, generation of highly‐enriched population of MES cells was strongly influenced both by the dose and the batch of BMP4. We performed full cardiomyocyte differentiation experiments using 32 different amounts of BMP4 from 0.1 to 0.8 ng/ml with every purchased BMP4. Typically, we obtained the best differentiation results with 0.1–0.3 ng/ml of BMP4. We also noticed that the amount of MES cells seeded to obtain cardiac precursor cells (CP) was crucial to obtain a high percentage of beating cardiomyocytes, with the best results obtained when 125,000–150,000 MES cells were seeded in a 96-well plate.

tag: cell type

value: Early cardiac mesoderm precursors cells (MES)

value: Mel18 Knock-Down


title: MES-CTR [RNA-Seq]

description: (RNAseq) Control

value: Control


title: NPC_Mel18

description: (RNAseq) Mel18 Knock-Down

data_processing:
ChIPseq analysis: Alignment: Sequence reads were mapped to the Mouse genome (mm9, July 2007) using BOWTIE (PubMed ID 19261174) with the option -m 1. RNAseq analysis: Alignment: The reads were mapped against the mm9 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1.
Peak-calling: Peak detection was performed with MACS (PubMed ID: 18798982). ChIP profiles were produced by MACS in BedGraph. Peaks were reported in BED format.
Genome_build: mm9
Supplementary_files_format_and_content: NPC_CTR_sense.bedgraph (BedGraph, genome-wide RNAseq profile)
Supplementary_files_format_and_content: NPC_CTR_antisense.bedgraph (BedGraph, genome-wide RNAseq profile)
Supplementary_files_format_and_content: NPC_Mel18_sense.bedgraph (BedGraph, genome-wide RNAseq profile)
Supplementary_files_format_and_content: NPC_Mel18_antisense.bedgraph (BedGraph, genome-wide RNAseq profile)

source_name: Neural progenitor cells

value: Neural progenitor cells

tag: treatment

value: Mel18 knockdown


title: ES-Ring1b [RNA-Seq]

description: (RNAseq) Ring1b Knock-Out

source_name: Undifferentiated ES cells

value: Embryonic stem cells (ESCs)

value: Ring1b Knock-Out


title: NPC_CTR

description: (RNAseq) Control

value: control


title: ES-CTR [RNA-Seq]

description: (RNAseq) Control


title: MES RYBP [ChIP-seq]

description: chromatin IP against RYBP

tag: chip antibody

value: RYBP (Millipore, catalog:Ab3637, lot:2066315)


title: ES-Mel18 [RNA-Seq]

description: (RNAseq) Mel18 Knock-Down

tag: genotype/variation


title: MES IgG [ChIP-seq]

description: chromatin IP against IgG


title: MES Cbx2 [ChIP-seq]

description: chromatin IP against Cbx2

value: Cbx2 (Bethyl, catalog:A302-524A, lot:A302-524A-1)


title: MES Mel18 [ChIP-seq]

description: chromatin IP against Mel18

value: Mel18 (Santa Cruz, catalog:H-115-X, lot:D0903)


title: MES Ring1b [ChIP-seq]

description: chromatin IP against Ring1b

value: Ring1b (Home-made)


title: Tun 405min rep3

data_processing:
uploaded to DNANexus and analyze for RPKM and read counts.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM and read counts values for each sample

source_name: Tun 405min

extract_protocol:
RNA were collected using RNeasy mini kit from QIAGEN
RNA libraries were prepared for sequencing using standard Illumina protocols

value: tunicamycin

tag: time (min)


title: Tun 405min rep1


title: Tun 135min rep1

source_name: Tun 135min


title: Tun 405min rep2


title: Tun 135min rep3


title: ESC Mel18 [ChIP-seq]

description: chromatin IP against Mel18


title: CM9_Mel18 [RNA-Seq]

description:
(RNAseq) Mel18 Knock-Down
paired-end, strand-specific

data_processing:
RNAseq analysis: Alignment: The reads were mapped against the mm9 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1.
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph, genome-wide RNAseq profile

source_name: Cardiomyocytes

growth_protocol: E14Tg2A cells were cultured as previously described (Morey et al., 2012) in 2i media supplemented with LIF produced in house as previously described (Ying et al., 2003) for at least two weeks (8 passages).  We took advantage of a recently reported protocol for differentiating ESC into a highly homogenous population of beating cardiomyocytes (CM) (Kattman et al., 2011). Interestingly, this protocol also permits early steps of cardiac differentiation, like formation of early cardiac-mesoderm precursors cells (MES) and cardiac precursor (CP) cells, to be studied.

extract_protocol:
RNA was extracted with the RNA extraction kit (QIAGEN).
Libraries were prepared according to Illumina instructions.

value: Cardiomyocytes


title: CM9_control [RNA-Seq]

description:
(RNAseq) Control
paired-end, strand-specific


title: HS 135min rep1

source_name: HS 135min

value: heat stress


title: Tun 45min rep2

source_name: Tun 45min


title: HS 45min rep3

source_name: HS 45min


title: HS 45min rep2


title: HS 135min rep3


title: HS 45min rep1


title: HS 135min rep2


title: control 0min rep2

source_name: control 0min


title: Tun 45min rep3


title: control 0min rep3


title: control 0min rep1


title: Tun 135min rep2


title: DD 405min rep4

value: unfolded DD


title: DD 405min rep1


title: DD 405min rep2


title: IK6-N-oleoylethanolamine-rep4

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

department: Pathology

institute: St Jude Children's Research Institute

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were mapped to mouse genome assembly mm9 using an in-house developed mapping pipeline, StrongArm, which uses multiple algorithms (bwa, version 0.5.9 and SIM4) (Florea et al., 1998; Li and Durbin, 2009) to map reads to the reference genome as well as all possible exon pairs based on RefSeq, Ensemble, UCSC known gene and AceView gene annotations (Rusch et al, unpublished).
read counts for each gene were estimated using HTseq with GTF file from Ensemble release 67
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample

source_name: pre-B cell from adult bone marrow

growth_protocol: Pre-B cells were derived from BM of adult Arf-/- mice by BCR-ABL1 transduction and subsequently transduced with an empty GFP-expressing vector (MIG) or MIG-IK6 expressing vector. Cells were grown in RPMI, 10% FCS, pen/strep/glut without addition of cytokines.

extract_protocol:
Trizol extraction of RNA
RNA libraries were prepared for sequencing using standard Illumina TruSeq RNA v2 protocols

treatment_protocol: Cells were treated with DMSO as a control or 1uM drug (dissolved in DMSO).

value: bone marrow

value: pre-B cell

tag: genotype

tag: drug

value: N-oleoylethanolamine


title: DD 135min rep3


title: DD 405min rep3


title: IK6-N-oleoylethanolamine-rep2


title: IK6-Bexarotene-rep3

value: Bexarotene


title: IK6-N-oleoylethanolamine-rep1


title: DD 45min rep3


title: IK6-N-oleoylethanolamine-rep3


title: DD 135min rep2


title: DD 135min rep1


title: IK6-Bexarotene-rep2


title: Tun 45min rep1


title: IK6-Bexarotene-rep1


title: IK6-Carbacyclin-rep3

value: Carbacyclin


title: DD 45min rep2


title: IK6-ATRA-rep4

value: all-trans retinoic acid (ATRA)


title: IK6-Carbacyclin-rep1


title: cont rep3


title: IK6-ATRA-rep3


title: IK6-Carbacyclin-rep2


title: cont rep2


title: cont rep5


title: IK6-ATRA-rep2


title: IK6-DMSO-rep4

value: DMSO


title: IK6-ATRA-rep1


title: IK6-DMSO-rep3


title: cont rep1


title: IK6-DMSO-rep1


title: IK6-DMSO-rep2


title: MIG-N-oleoylethanolamine-rep4


title: MIG-N-oleoylethanolamine-rep1


title: 8_Wild_Type_#2_CD34-

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

data_processing:
Reads were created by CASAVA 1.8.2 from the  HiSeq2000, and these are all reads which pass filter
Reads were filtered from the adapter sequences using FAR software (Dodt, M, Ahmed R, Dieterich C. FAR – flexible adapter remover. FAR project website (2011)( http://sourceforge.net/projects/theflexibleadap/).
Reads were aligned to whole genome using the bismark(http://www.bioinformatics.babraham.ac.uk/projects/bismark/) alignment tool with a maximum of 2 mismatches in a directional manner and only uniquely aligning reads were retained.
In order to call methylation score for a base position, we required that read bases aligning to that position have at least 20 phred quality score and the base position should have at least 10X coverage. Only CpG dinucleotides that satisfy these coverage and quality criteria were retained for subsequent analysis. *myCpG.txt files are constructed for each CpG position in the genome. The file contains location of the CpG, total read coverage on the C base, percentage of bisulfite converted Cs (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The pipeline that aligns and calls for methylation percentage per base is available at http://code.google.com/p/amp-errbs
Genome_build: mm9
Supplementary_files_format_and_content: myCpG.txt = tab delimited file with the following column heades: chrBase chr base strand coverage freqC freqT

source_name: CD34 negative cells

extract_protocol: ERRBS libraries were constructed as described in 18. Akalin A et al. Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in Acute Myeloid Leukemia. PLOS Genetics 8, in press (2012).

value: Wild-Type

value: CD34 negative cells

tag: flowcell id

tag: lane #

tag: genetic background

value: FVB/n


title: 15_Wild_Type_#2_CD34+

source_name: CD34 positive cells

value: CD34 positive cells


title: 13_PML-RARa_#1_CD34+

value: PML-RARa


title: 10_Wild_Type_#1_CD34-


title: 9_Wild_Type_#1_CD34+


title: 11_PML-RARa_#2_CD34+


title: MIG-N-oleoylethanolamine-rep2


title: 7_Wild_Type_#2_CD34+


title: 12_PML-RARa_#2_CD34-


title: MIG-Bexarotene-rep3


title: DD 45min rep1


title: 5_PML-RARa_#1_CD34+


title: cont rep4


title: MIG-Bexarotene-rep1


title: MIG-Carbacyclin-rep4


title: 4_PML-RARa_#2_CD34-


title: 2_Wild_Type_#1_CD34-


title: MIG-Bexarotene-rep2


title: 3_PML-RARa_#2_CD34+


title: 1_Wild_Type_#1_CD34+


title: MIG-Carbacyclin-rep3


title: MIG-Carbacyclin-rep1


title: MIG-N-oleoylethanolamine-rep3


title: 20_PML-RARa_#2_CD34-


title: 19_PML-RARa_#2_CD34+


title: MIG-ATRA-rep4


title: MIG-ATRA-rep2


title: 18_Wild_Type_#1_CD34-


title: MIG-DMSO-rep3


title: MIG-DMSO-rep1


title: 17_Wild_Type_#1_CD34+


title: 14_PML-RARa_#1_CD34-


title: MIG-Carbacyclin-rep2


title: MIG-DMSO-rep2


title: Restricted 7 TP2 [muscle]

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

description:
Experimental: day 15 with ad libitum diet following 125 days of restricted diet Period 2
KKM9-56

data_processing:
Basecalls performed using CASAVA version 1.4
RNAseq reads were aligned to UMD3.1 genome using Tophat
Raw counts were enumerated using HTSEQ-count (settings: mode = union)
The raw read counts were normalized using scaling factors estimated by the Trimmed mean of M-Values (TMM) method implemented  the edgeR software package. The normalised values represent read counts per million mapped reads, adjusted for sample library size.
Genome_build: Bos_taurus_UMD_3.1
Supplementary_files_format_and_content: [Raw counts] Tab delimited txt files (First row contains the ENSEMBL gene IDs and second row the raw number of reads that map to each gene)
Supplementary_files_format_and_content: [Normalized counts] Tab delimited txt files (First row contains the ENSEMBL gene IDs and second row the normalized values that map to each gene)

organism: Bos taurus

source_name: Muscle

growth_protocol: Purebred Holstein Friesian bulls (n=20) were assigned to one of two feeding treatments (i) restricted feed allowance for 125 days (n=10) followed by ad libitum access to feed for a further 55 days or (ii) a control group with ad libitum access to feed through out the 180 days trial (n=10).  The first 125 days of the trial were denoted as Peirod 1, during which treatment groups were fed differentially. the subsequent 55 days, denoted as Period 2 during which all bulls were fed ad libitum. All bulls received the same diet of 70% concentrate 30% grass silage through out the experimental trial,with the amount of feed provided different dependnet on each treatment group. restricted fed animals were fed to grow at 0.6 kg /day during Peirod 1, with ad libitum animals expected to gain in excess of 1.5 to 2 kg/day

extract_protocol:
Total RNA was extracted from frozen muscle tissue by homogenisation in Trizol. RNA was then DNAse treated and purified using Quiagen RNeasy mini kit.
Single-end mRNA-seq libraries were constructed using the Illumina Truseq sample prep kit.

treatment_protocol: 20 bulls fed a restricted diet for 125 days to grow at 0.6kg/day, after which they were fed ad libitum for a further 55 days. The remaining 20 bulls in the control group were fed ad libitum throughout

tag: breed

value: Holstein-Friesian

value: male

tag: diet

value: 70% concentrate, 30% grass silage diet

value: Muscle

tag: biopsy day

value: day 15 of Period 2

tag: feeding period

value: Realimentation period

tag: restriction model

value: Undergoing compensatory growth


title: Restricted 9 TP2 [muscle]

description:
Experimental: day 15 with ad libitum diet following 125 days of restricted diet Period 2
KKM7-59

tag: gender

tag: tissue


title: Restricted 8 TP2 [muscle]

description:
Experimental: day 15 with ad libitum diet following 125 days of restricted diet Period 2
KKM3-58


title: Restricted 6 TP2 [muscle]

description:
Experimental: day 15 with ad libitum diet following 125 days of restricted diet Period 2
KKM10-47


title: Restricted 5 TP2 [muscle]

description:
Experimental: day 15 with ad libitum diet following 125 days of restricted diet Period 2
KKM9-44


title: Restricted 10 TP2 [muscle]

description:
Experimental: day 15 with ad libitum diet following 125 days of restricted diet Period 2
KKM6-60


title: Restricted 3 TP2 [muscle]

description:
Experimental: day 15 with ad libitum diet following 125 days of restricted diet Period 2
KKM4-35


title: Restricted 1 TP2 [muscle]

description:
Experimental: day 15 with ad libitum diet following 125 days of restricted diet Period 2
KKM4-31


title: B6 Liver, +MegaFasL

first: Alexander

last: Poltorak

state: Massachusetts

address: 150 Harrison avenue

institute: Tufts University

description:
7_S3
MegaFasL_genes.fpkm_tracking.txt

data_processing:
MiSeq Basecalls - data untrimmed - 75bp paired-end reads
Tophat; tophat -p 4 -o
cuffdiff 2.2.1; cuffdiff -p 4 -L
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited txt containg FPKM values

organism: Mus musculus domesticus

source_name: Liver

extract_protocol:
Liver and Thymus were removed and immediately TriPure reagent (Roche)
TruSeq RNA Sample Preparation Kit

tag: strain

tag: age

value: 8 weeks

value: MegaFasL

value: Liver


title: Restricted 4 TP2 [muscle]

description:
Experimental: day 15 with ad libitum diet following 125 days of restricted diet Period 2
KKM8-38


title: Restricted 10 TP1 [muscle]

description:
Experimental: day 120 with restricted diet Period 1
KKM2-30

value: day 120 of Period 1

value: Differential feeding

value: Undergoing restricted feed intake


title: B6 Liver, Unstimulated

description:
3_S3
Untreated_genes.fpkm_tracking.txt

tag: treatment

value: Unstimulated


title: MIG-ATRA-rep3

value: bone marrow

tag: cell type

value: pre-B cell

value: all-trans retinoic acid (ATRA)


title: Restricted 9 TP1 [muscle]

description:
Experimental: day 120 with restricted diet Period 1
KKM5-29

value: Holstein-Friesian


title: B6 Thymus, +MegaFasL

description:
5_S1
MegaFasL_genes.fpkm_tracking.txt

source_name: Thymus

value: Thymus


title: B6 Thymus, Unstimulated

description:
1_S1
Untreated_genes.fpkm_tracking.txt


title: Restricted 8 TP1 [muscle]

description:
Experimental: day 120 with restricted diet Period 1
KKM3-28

value: male

value: 70% concentrate, 30% grass silage diet


title: 16_Wild_Type_#2_CD34-

value: Wild-Type

value: CD34 negative cells

value: FVB/n


title: 6_PML-RARa_#1_CD34-

value: PML-RARa


title: MIG-DMSO-rep4

value: DMSO


title: MIG-ATRA-rep1


title: Restricted 7 TP1 [muscle]

description:
Experimental: day 120 with restricted diet Period 1
KKM8-26

value: Muscle


title: MSM Liver, +MegaFasL

description:
8_S4
MegaFasL_genes.fpkm_tracking.txt

organism: Mus musculus molossinus

value: MSM/Ms

value: 8 weeks

value: MegaFasL

value: Liver


title: Restricted 4 TP1 [muscle]

description:
Experimental: day 120 with restricted diet Period 1
KKM2-08

value: day 120 of Period 1

value: Differential feeding

value: Undergoing restricted feed intake


title: Restricted 5 TP1 [muscle]

description:
Experimental: day 120 with restricted diet Period 1
KKM10-14

value: Holstein-Friesian


title: Restricted 2 TP2 [muscle]

description:
Experimental: day 15 with ad libitum diet following 125 days of restricted diet Period 2
KKM9-34

value: day 15 of Period 2

value: Realimentation period

value: Undergoing compensatory growth


title: Restricted 3 TP1 [muscle]

description:
Experimental: day 120 with restricted diet Period 1
KKM10-05

value: male

value: 70% concentrate, 30% grass silage diet


title: Restricted 1 TP1 [muscle]

description:
Experimental: day 120 with restricted diet Period 1
KKM6-01


title: MSM Thymus, Unstimulated

description:
2_S2
Untreated_genes.fpkm_tracking.txt

value: Unstimulated

value: Thymus


title: Restricted 2 TP1 [muscle]

description:
Experimental: day 120 with restricted diet Period 1
KKM4-04


title: Control 10 TP2 [muscle]

description:
Control: day 15 with ad libitum diet Period 2
KKM8-57

value: Control


title: Control 7 TP2 [muscle]

description:
Control: day 15 with ad libitum diet Period 2
KKM3-46

value: Muscle


title: Control 9 TP2 [muscle]

description:
Control: day 15 with ad libitum diet Period 2
KKM9-49


title: Control 6 TP2 [muscle]

description:
Control: day 15 with ad libitum diet Period 2
KKM2-45


title: Control 8 TP2 [muscle]

description:
Control: day 15 with ad libitum diet Period 2
KKM5-48


title: Control 3 TP2 [muscle]

description:
Control: day 15 with ad libitum diet Period 2
KKM5-40


title: Control 2 TP2 [muscle]

description:
Control: day 15 with ad libitum diet Period 2
KKM6-39


title: Control 4 TP2 [muscle]

description:
Control: day 15 with ad libitum diet Period 2
KKM4-41


title: HCEC-B4G12_83

city: Los Angeles

first: Anthony

middle: J.

last: Aldave

state: CA

address: 200 Stein Plaza DSERC 3-143

department: Ophthalmology

institute: Stein Eye Institute, UCLA

description: Sample 15

data_processing:
The FASTQ files containing the RNA-sequencing data were uploaded to the Partek Flow servers for alignment to the hg38 genome using the TopHat aligner, which output the results in BAM files
The BAM files were uploaded to the Partek Genomics Suite software and the reads and read-depth were transformed to reads per kilobase per million (RPKM) values, a normalized quantity that accounts for gene size.
These data were annotated using the Ensemble 77 transcript database.
Genome_build: hg38
Supplementary_files_format_and_content: The processed data file is a txt file with Ensemble 77 gene symbol ID in the first column. Sample names are given on the first row with RPKM values for each gene running down the column.

source_name: corneal endothelial cell line

growth_protocol: Cultured cells were either grown in F99 or Human Endothelial SFM.

extract_protocol:
TriReagent extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNeasy Clean-Up Kit.
Enrichment for poly(A) RNAs was performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module, followed by library preparation using the PrepX Complete ILM DNA Library Kit. Libraries were prepared as per the manufacturer's instructions.

value: endothelial

tag: imortalization

value: SV40 TAg

tag: culture medium

value: Human Endothelial-SFM


title: Control 1 TP2 [muscle]

description:
Control: day 15 with ad libitum diet Period 2
KKM7-37


title: Control 10 TP1 [muscle]

description:
Control: day 120 with ad libitum diet Period 1
KKM3-27


title: HCEC-B4G12_82

description: Sample 14


title: Restricted 6 TP1 [muscle]

description:
Experimental: day 120 with restricted diet Period 1
KKM7-17


title: HCEC-B4G12_81

description: Sample 13


title: HCEC-12_77

description: Sample 12


title: Control 9 TP1 [muscle]

description:
Control: day 120 with ad libitum diet Period 1
KKM2-19


title: HCEC-12_76

description: Sample 11


title: MSM Thymus, +MegaFasL

description:
6_S2
MegaFasL_genes.fpkm_tracking.txt

value: MSM/Ms

value: 8 weeks

value: MegaFasL


title: Control 8 TP1 [muscle]

description:
Control: day 120 with ad libitum diet Period 1
KKM1-18

value: day 120 of Period 1

value: Differential feeding


title: Control 6 TP1 [muscle]

description:
Control: day 120 with ad libitum diet Period 1
KKM6-15

value: Holstein-Friesian


title: Control 7 TP1 [muscle]

description:
Control: day 120 with ad libitum diet Period 1
KKM1-16


title: HCEC-12_75

description: Sample 10


title: MSM Liver, Unstimulated

description:
4_S4
Untreated_genes.fpkm_tracking.txt

value: Liver


title: 96_bap_rep1

city: Gainesville

first: Xiefan

last: Fang

state: Florida

address: 1200 Newell Drive, ARB R1-148

department: Pediatrics

institute: University of Florida

data_processing:
RNA-seq reads were uploaded to the galaxy platform https://main.g2.bx.psu.edu/. RNA-seq reads were trimmed, filtered, and mapped to the zebrafish genome (Danio_rerio.Zv9.68) with the Tophat for Illumina tool. mRNA quantification was performed with Partek Genomics Suite (GS) version 6.11 (Partek, St. Louis, MO). Refseq Transcripts (2013-04-10) and Ensembl Transcripts release 70 databases were used for gene and transcript annotation. EdgeR was used for normalized abundance measurements.
Genome_build: ZV9
Supplementary_files_format_and_content: Tab-delimited text files include EdgeR normalized read counts for each gene or transcript annotated to the UCSC Refseq Transcripts (2013-04-10) or Ensembl Transcripts release 70 databases. Each file contains data for either 3.3 hpf or 96 hpf samples.

organism: Danio rerio

source_name: whole organism_96hpf_bap

extract_protocol:
Pooled embryos or larvae were homogenized with pellet pestles cordless motor (Sigma-Aldrich) in RNAzol (Molecular Research Center, Cincinnati, OH). RNA was isolated and purified with RNeasy Mini Kit (Qiagen, Valencia, CA) by following the manufacturer’s protocols.  TruSeq RNA Sample Prep Kit was used with 1 mg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared by following standard Illumina protocols

value: AB line

value: whole organism

value: 96 hours post fertilization

value: BaP (50 μg/L)


title: 96_bap_rep2


title: 96_con_rep2

source_name: whole organism_96hpf_control

value: control (0.1 mL/L )


title: Control 5 TP2 [muscle]

description:
Control: day 15 with ad libitum diet Period 2
KKM7-42

value: male

value: 70% concentrate, 30% grass silage diet

value: day 15 of Period 2

value: Realimentation period

value: Control


title: Control 5 TP1 [muscle]

description:
Control: day 120 with ad libitum diet Period 1
KKM1-12

value: Muscle


title: HCEnC-21T_86

description: Sample 9

value: endothelial

value: telemorase


title: HCEnC-21T_84

description: Sample 7


title: 3.3_bap_rep3

source_name: whole organism_3.3hpf_bap

value: 3.3 hours post fertilization


title: Control 4 TP1 [muscle]

description:
Control: day 120 with ad libitum diet Period 1
KKM8-11

value: day 120 of Period 1

value: Differential feeding


title: Control 3 TP1 [muscle]

description:
Control: day 120 with ad libitum diet Period 1
KKM1-10

value: Holstein-Friesian


title: 3.3_con_rep3

source_name: whole organism_3.3hpf_control

value: AB line


title: pHCEnC_65

description: Sample 5

source_name: primary corneal endothelial cells


title: 96_con_rep1

value: whole organism


title: pHCEnC_68

description: Sample 6


title: 3.3_con_rep2


title: 3.3_bap_rep2


title: Young4

city: Daejeon

first: sujin

last: Baek

address: Gwahank-ro 125

department: MGRC

institute: KRIBB

description: myoblast young4

data_processing:
Illumina Casava1.7 software used for basecalling.
mapped to mm10 whole genome using bwa.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated  using a standard protocol. The rpkm values are on log2 scale.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values

source_name: myoblast young-mouse4

extract_protocol:
mirVana miRNA isolation kit (Ambion, Austin, TX) by the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: myoblast

tag: rna fraction

value: small RNA

tag: developmental stage

value: young


title: Control 2 TP1 [muscle]

description:
Control: day 120 with ad libitum diet Period 1
KKM5-09

value: male


title: 3.3_bap_rep1

value: BaP (50 μg/L)


title: Young3

description: myoblast young3

source_name: myoblast young-mouse3


title: pHCEnC_60

description: Sample 4


title: Young2

description: myoblast young2

source_name: myoblast young-mouse2


title: evHCEnC_58

description: Sample 3

source_name: ex vivo corneal endothelium


title: 3.3_con_rep1

value: control (0.1 mL/L )


title: evHCEnC_56

description: Sample 2


title: HCEnC-21T_85

description: Sample 8


title: evHCEnC_48

description: Sample 1


title: Old4

description: myoblast old4

source_name: myoblast old-mouse4

value: old


title: Young1

description: myoblast young1

source_name: myoblast young-mouse1


title: id1 root

city: Ames

last: Peterson

state: IA

address: 2288 Molecular Biology Building

department: Genetics, Development and Cell Biology

institute: Iowa state University

description: small RNA

data_processing:
Raw reads were firstly treated by BGI to remove the adaptors and low-quality reads.
Clean reads were uniquely and perfectly mapped to the maize B73 reference genome by Bowtie.
Small RNAs expression level was represented as the amount of mapped reads per 100-kb window, per chromosome.
Genome_build: ZmB73_RefGen_V2
Supplementary_files_format_and_content: tab-delimited text files include totally mapped reads per 100-kb window

organism: Zea mays

source_name: 14-day old seedling

growth_protocol: Plants were grown in the PGW-40 growth chamber, which has 15 h of light and 9 h of dark.

extract_protocol:
Total RNAs were extracted by using the PureLink Reagent, and then were treated with Dnase.
Small RNA libraries were prepared for sequencing by Beijing Genomics Institute (BGI) while using standard Illumina protocols

value: root

tag: development stage

value: 14-day old

tag: genotype


title: id4 root

description: small RNA


title: 9d9a root

description: small RNA


title: ASC_Day2_RNA-Seq

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

data_processing:
reads aligned with tophat v2.0.8b with parameter –-b2-very-sensitive,
transcript abundance estimated with cufflinks v2.1.1 with parameter -–GTF-guide
reference gtf with cuffmerge v2.1.1 with parameters -g, -s
differential expression analysis with cuffdiff v2.1.1 with parameters -b, -s, -u
csv file created from cuffdiff output file genes.fpkm_tracking
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for viewing in Genome Browser; bed files with four columns: chromosome, start position, end position and score; csv file created from cuffdiff output file genes.fpkm_tracking

source_name: Pre-adipocytes from liposuction material, cultured, 9 days after adipogenic stimulation (Day 2).

growth_protocol: Primary ASCs isolated from liposuction material were cultured in T175 flasks under proliferative conditions in high-glucose DMEM (4.5 g/l; Life Technologies-BRL) containing 20% FBS and 2 ng/ml basic fibroblast growth factor (Sigma-Aldrich). Cells at passage 5-7 were used for adipogenic induction. When cells reached confluency, adipogenic differentiation was induced by replacing growth medium with DMEM/F12 containing 10% FBS and by addition of 0.5 µM 1-methyl-3 isobutylxanthine (Dumex Alpharma), 1 µM dexamethasone (Dumex Alpharma), 10 µg/ml insulin (Novo Nordisk) and 100 µM (Dumex Alpharma) indomethacin for up to 9 days.

extract_protocol:
For RNA-seq: 10e6 cells were cultured. Total RNA was isolated using the Ambion TRIzol® Reagent RNA extraction kit (Life Technologies), quality checked using a BioAnalyzer 2100 and processed for library preparation.
Sequencing library was prepared according to the Illumina protocol, and sequenced on an Illumina HiSeq2500 at the Norwegian Sequencing Center.

tag: passages

value: Cells in passage 5-7

tag: initial cell type

value: pre-adipocytes

tag: cell differentiation status

value: Non-proliferating, differentiated for 9 days


title: Old2

description: myoblast old2

source_name: myoblast old-mouse2


title: 714H leaf

description: small RNA

value: seedling


title: ASC_Day1_RNA-Seq

source_name: Pre-adipocytes from liposuction material, cultured, 3 days after adipogenic stimulation (Day 1).

value: Non-proliferating, differentiated for 3 days


title: B73 root

description: small RNA


title: LMNA_Day3

data_processing:
Reads aligned to reference using bowtie version 1.0.0 using parameters –best
bigWig files were generated by getting a ratio of IP over Input in 1 kb bins
Peaks called using Enriched Domain Detector
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for viewing in Genome Browser; bed files with four columns: chromosome, start position, end position and score; csv file created from cuffdiff output file genes.fpkm_tracking

source_name: Pre-adipocytes from liposuction material, cultured, 3 days after adipogenic stimulation (Day 3).

extract_protocol:
For ChIP-seq: Cells (10e7 cells/ChIP) were harvested and fixed with 1% formaldehyde for 10 min before quenching with 125 mM glycine. Cells were lysed for 30 min at 4C on a rotator in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% deoxycholate, 1 mM PMSF, protease inhibitor cocktail) adjusted to 1% SDS, and sonicated 3 times 15 min in a Bioruptor® (Diagenode). After sedimentation at 10,000 g for 10 min, the supernatant was collected and diluted 10x in RIPA buffer without SDS to constitute input chromatin. Chromatin was incubated overnight at 4oC on a rotator with antibodies coupled to magnetic Dynabeads Protein G. ChIP samples were washed 3 times in ice-cold RIPA buffer. Crosslinks were reversed and DNA eluted for 6 h at 37C in 50 mM NaCl, 20 mM Tris-HCl pH 7.5, 5 mM EDTA, 1% SDS, 0.5 µg/ml RNase A, and 2 µg/ml Proteinase K added twice. DNA was purified and dissolved in H2O.
Sequencing library was prepared according to the Illumina protocol, and sequenced on an Illumina HiSeq2500 at the Norwegian Sequencing Center.

tag: chip antibody

value: anti-Lamin A/C Santa Cruz sc7292


title: LMNA_Day1

source_name: Pre-adipocytes from liposuction material, cultured, 1 day after adipogenic stimulation (Day 1).

value: Non-proliferating, differentiated for 1 day


title: Old1

description: myoblast old1

source_name: myoblast old-mouse1


title: LMNA_Day9

source_name: Pre-adipocytes from liposuction material, cultured, 9 days after adipogenic stimulation (Day 9).


title: 9d9a leaf

description: small RNA


title: 714 leaf

description: small RNA


title: id4 leaf

description: small RNA


title: EPI5.2

city: London

first: paul

last: blakeley

address: 215 Euston Road

country: United Kingdom

institute: Crick Institute

data_processing:
Reads alligned to the human genome sequence using TopHat2
Read counts were generated using HTSeq-count
Genome_build: GRCh37.74
Supplementary_files_format_and_content: count files

source_name: Human Embryo

extract_protocol:
Single cells were isolated from blastocyst stage embryos (6-7 days post fertilisation) for subsequent analysis by micromanipulation, with a duration of less than 20 minutes. Embryos were placed in drops of G-MOPS solution (Vitrolife) on a petri dish overlaid with mineral oil. The plate was placed on a microscope stage (Olympus IX70) and the embryos were held with an opposing holding pipette and blastomere biopsy pipette (Research Instruments) using Narishige micromanipulators (Narishige, Japan). The biopsy mode of a Saturn 5 laser (Research Instruments) was used to separate the majority of the mural TE from the ICM and polar TE. The ICM and polar TE were washed quickly in PBS without Ca2+ and Mg2+ (Invitrogen) then placed in 0.05% trypsin/EDTA (Invitrogen) for 5 minutes at room temperature. Trypsin was quenched using Global Media supplemented with 5 mg/mL LifeGlobal Protein Supplement. After quenching, the cell clump was placed back on the stage in a drop of G-MOPS solution and pipetted up and down several times using the blastomere biopsy pipette.
cDNA was generated from single cells using the SMARTer Ultra Low Input RNA kit for Illumina Sequencing–HV (Clontech Laboratories, Inc.) according to maunfacturers’ guidelines. Single cells were picked using 100 μm inner diameter Stripper pipette (Origio) and transferred to individual low bind RNAse-free tube containing 0.25 μl RNase inhibitor, 4.75 μl Dilution buffer and 5 μl nuclease-free water on a -80°C pre-chilled CoolRack (Biocision, CA). Samples were stored at -80°C until ready to be processed. 1 μl of 3’ SMART CDS Primer II A was added to the sample, mixed well and incubated at 72°C for 3 min. First strand cDNA was synthesised by adding 4 μl 5X First-Strand Buffer, 0.5 μl 100 mM DTT, 1 μl 20 mM dNTP mix, 1 μl SMARTer IIA Oligonucleotide, 0.5 μl RNase Inhibitor and 2 μl SMARTScribe Reverse Transcriptase (100 U/μl) directly to a tube containing the sample and incubating at 42°C for 2 hours followed by 10 min at 70°C.    First strand cDNA was purified by adding 36 μl of room temperature SPRI Ampure XP beads (Beckman Coulter Genomics), mixing well and incubating at room temperature for 8 min. Tubes were placed on a MagnaBot II Magnetic Separation device (Promega) and allowed to stand until all beads were immobilised into a pellet. The supernatant was removed and discarded. Tubes were briefly spun and any residual liquid was removed.     Double stranded cDNA was amplified from the template bound to the beads using Advantage 2 PCR kit (Clontech Laboratories, Inc.). 5 μl 10X Advantage 2 PCR Buffer, 2 μl 10 mM dNTP Mix, 2 μl IS PCR Primer, 2 μl 50X Advantage 2 Polymerase Mix and 39 μl Nuclease-Free water were added to the tube containing the sample to give a total volume of 50 μl. PCR amplification was performed at 95°C for 1 min, followed by 18 cycles of 15 sec at 95°C, 30 sec at 65°C and 6 min at 68°C followed by final extension step of 10 min at 72°C. Amplified cDNA was purified by adding 90 μl SPRI Ampure XP beads, mixing well and incubating at room temperature for 8 min to allow amplified cDNA bind to the beads. Sample tubes were placed on the magnet and allowed to stand until all beads had been immobilised. Supernatant was removed and discarded and beads were washed twice by adding 200 μl freshly prepared 80% ethanol and leaving for 30 sec before discarding the supernatant. Tubes were spun briefly to collect residual liquid. The bead pellet was allowed to air dry. 12 μl of purification buffer was added to rehydrate the pellet and incubated for 2 min at room temperature. cDNA was eluted by pipetting up and down 10 times before returning the tube to the magnet. The clear supernatant containing the cDNA was removed from the immobilised beads and transferred to a new low-bind tube. cDNA was stored at -80°C until library preparation.     cDNA quality was assessed by High Sensitivity DNA assay on an Agilent 2100 Bioanalyser with good quality cDNA showing a broad peak from 300 to 9000 bp. cDNA concentration was measured using QuBit dsDNA HS kit (Life Technologies UK Ltd.) Typical yields from a single cell ranged from 1 ng to 9 ng.
In preparation for library generation cDNA was sheared using Covaris S2 to achieve cDNA in 200-500 bp range. 10 μl of cDNA sample and 65 μl purification buffer was added to Covaris AFA Fiber Pre-Slit Snap Cap microTUBE. cDNA was sheared using the settings 10% Duty, Intensity 5, Burst Cycle 200 for 2 min. Sheared cDNA was transferred to a new 0.2 ml low-bind tube.    Libraries were prepared using Low Input Library Prep Kit (Clontech Laboratories, Inc.) according to manufacturer’s instructions. The amount of input cDNA was calculated from the concentration measured by the Bioanalyser assay prior to shearing, taking into account the dilution involved in the shearing step. The appropriate amplification cycle number was selected according to manufacturer’s guidelines. Library quality was assessed by Bioanalyser and the concentration was measured by QuBit assay.  The molar concentration of library was calculated thus:   Library molecular weight = average size in bp (from Bioanalyser) x 650 g/mol per bp   Molar concentration = library concentration from QuBit/library molecular weight  Libraries with a molar concentration greater than 2nM were submitted for 50-bp paired-end sequencing on Illumina HiSeq 2000.

value: Blastocyst

tag: lineage

value: Epiblast

tag: embryo number

value: Embryo 5


title: id1 leaf

description: small RNA

tag: tissue


title: EPI4.3

value: Embryo 4


title: EPI6.1

value: Embryo 6


title: LMNA_Day-2

source_name: Pre-adipocytes from liposuction material, cultured, undifferentiated, proliferating, 2 days before adipogenic stimulation.

value: Proliferating, undifferentiated


title: B73 leaf

description: small RNA


title: H2BGlcNAc_Day9

value: anti-H2B (glcnac S112) Abcam ab130951


title: EPI5.1


title: EPI4.2


title: H2BGlcNAc_Day3


title: 714 rep2

data_processing:
Reads were trimmed by FASTX toolkit
Trimmed reads were mapped to maize B73 reference genome by Tophat
Expression of each gene was counted by HTSeq
Genome_build: ZmB73_RefGen_V2
Supplementary_files_format_and_content: A comma seperated file includes raw read counts for each sample

growth_protocol: Plants were grown in SB 300 Universal Soil in the PGW-40 growth chamber, which has 15 h of light and 9 h of dark.

extract_protocol:
Total RNAs were extracted by using the Rneasy Plant Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Old3

description: myoblast old3

source_name: myoblast old-mouse3

value: myoblast

value: small RNA

value: old

tag: strain


title: LMNA_Day0

source_name: Pre-adipocytes from liposuction material, cultured, undifferentiated, confluent, on day of adipogenic stimulation (Day 0).

value: Cells in passage 5-7


title: EPI2.1

value: Embryo 2


title: H2BGlcNAc_Day0

value: pre-adipocytes


title: EPI4.1


title: H2BGlcNAc_Day1


title: 714 rep1

value: seedling

value: 14-day old


title: TE4.1

value: Trophectoderm


title: H2BGlcNAc_Day-2


title: B73 rep3


title: PE5.1

value: Primitive Endoderm


title: PE5.2

value: Blastocyst


title: 714H rep3


title: PE4.1


title: DT40_WT_RNAseq

city: Bethesda

first: Andrew

middle: J

last: Oler

state: MD

address: 31 Center Drive, Room 3B62E

department: Bioinformatics and Computational Biosciences Branch (BCBB)

institute: NIAID/NIH

data_processing:
Basecalls performed using CASAVA version 1.7
RNA-seq reads were aligned to the Ensembl 73 (galGal4) version of the chicken genome with TopHat version 2.0.8b with options --read-realign-edit-dist 0 -o tophat2_RNASEQ_WT_out --mate-std-dev 50 --solexa1.3-quals -p 10 --bowtie-n.  A previously built transcriptome index (made from GTF Annotation from Ensembl 73) was used as input for --transcriptome-index parameter.
bigWig coverage tracks were made using bam2wig.pl (part of Bio::ToolBox Perl package) with options --pos span --rpm --split --bw; the height represents a normalized Read Coverage Per Million Mapped Reads (RPM).
Genome_build: galGal4
Supplementary_files_format_and_content: bigWig file reporting normalized Read Coverage Per Million Mapped Reads (RPM).

organism: Gallus gallus

source_name: B lymphocyte

growth_protocol: The DT40 CL18 chicken B lymphoma cell line was grown exponentially at 37 °C in RPMI containing 9% FBS, 1% chicken serum, 100 μM β-mercaptoethanol, and antibiotics.  Cell density was maintained at 0.2–1.0 × l0E6 per mL by splitting the cultures daily.

extract_protocol:
Cells were harvested for total RNA extraction using Trizol per manufacturer's instructions.
RNA concentration was determined using the Qubit RNA broad range assay in the Qubit Fluorometer (Invitrogen) and RNA integrity was determined using Eukaryote Total RNA Nano Series II ChIP on a 2100 Bioanalyzer (Agilent). RNA-seq libraries were prepared from 4 ug of total RNA using the TruSeq RNA sample prep kit following manufacturer’s protocol (Illumina). Briefly, oligo-dT purified mRNA was fragmented and subjected to first and second strand cDNA synthesis. cDNA fragments were blunt-ended, ligated to Illumina adaptors, and PCR amplified to enrich for the fragments ligated to adaptors. The resulting cDNA libraries were verified and quantified on Agilent Bioanalyzer and sequenced using the GAIIx Genome Analyzer (Illumina).

tag: cell line

value: B lymphocyte cells

tag: cell density


title: S. pombe Δdbr diauxic short 1

status: Public on Sep 03 2015

city: Ithaca

first: Jeffrey

middle: A

last: Pleiss

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

description: custom non-stranded lariat sequencing, short gel

organism: Schizosaccharomyces pombe

source_name: S. pombe Δdbr diauxic

growth_protocol: 30 C, unless heatshock

extract_protocol:
phenol chloroform extraction
RNAseq, lariat sequencing

value: delta dbr 972h-


title: 714H rep2


title: H3K4me3_ChIP-Seq_Maturing zone

city: Hannover

first: Christoph

last: Peterhansel

address: Herrenhaeuser Strasse 2

department: Botany

country: Germany

institute: Leibniz-Universitaet-Hannover

data_processing:
GATC-Biotech used Casava 1.8.2 for basecalling
Trimmomatic 0.32 was used to trim the raw reads. (adapter clipper [Adapter: TruSeq3-SE], leading trimmer, trailing trimmer and sliding window trimmer modules were used with their default settings)
RNA-Seq: with CLC Genomics Workbench 7.5.1: RNA-seq analysis including read mapping was carried out with the "RNA-Seq Analysis" tool. Reads were mapped with default settings only to regions that were covered by gene annotations of the maize reference genome . Reads which mapped equally to multiple positions were ignored. Raw read counts were chosen as expression values. RPKM values were calculated for each gene to quantify absolute expression. Statistical evaluation of differentially expressed genes was carried out with the "Empirical Analysis of DGE" tool which implements EDGE analysis and Benjamini Hochberg correction of p-values.
ChIP-Seq: with CLC Genomics Workbench 7.5.1: Duplicated reads were removed with the tool “Remove Duplicate Reads” using default settings. The reads were mapped to the reference genome using default parameters with two exceptions: Reads were mapped without masking and reads which mapped equally to multiple positions were ignored. The “Peak Shape” tool from the CLC Genomics workbench was used to call peaks: Peaks were initially called with a p-value of 0.0001. Afterwards, the "Advanced Peak Shape Tools" were used to optimize peak calling according to the manual: For each sample, a subset of 1000 called peaks with highest p-values were used as positive regions to define a new filter with the tool "Learn Peak Shape Filter". Number of bins was calculated for each sample as: Number of bins = window size / size of bins (35 bp). This optimized filter was used for the definite peak calling with the tool "Apply Peak Shape Filter" again with a p-value of 0.0001.
ChIP-Seq: differential analysis and annotation of peaks: Differential analysis of regulated peaks between the maturing zone and the base of the maize leaf was carried out with the R Bioconductor package DiffBind 1.10.0 following the manual. Only peaks which were found in at least two samples were included for further analyses. Quantitative differences of the normalized peaks were statistically evaluated using the implemented R package edgeR. Peaks were annotated to the next gene with PeakAnalyzer 1.4 using the next TSS option. Transcript IDs were manually transformed into Gene_IDs
Genome_build: Zea_mays.AGPv3.21.dna.toplevel from Ensemble
Supplementary_files_format_and_content: RNA_Seq: Tab-delimited text files include feature ID, Gene annotation class, fold-change and FDR values from EDGE analysis, total exon reads and RPKM values for each sample
Supplementary_files_format_and_content: H3K9ac and H3K4me3_ChIP-Seq: Tab-delimited text files include coordinates of DiffBind consensus peaks (Crom, ChromStart, ChromEnd), average normalized reads from the base and the maturing zone, fold-changes and FDR-values from the edgeR analysis and the Feature ID and gene annotation class of the next gene.

source_name: Third leaf

growth_protocol: Zea mays cv. B73 was grown in growth chambers with a photoperiod of 16h light at 25°C and 8h darkness at 20°C. The photon flux intensity was adjusted to 130 µmol m-2 s-1. Water soaked seeds were transferred to soil and plants were harvested when the third leaf was fully expanded (13 to 14 days after sowing)

extract_protocol:
Leaf material of 10 plants was pooled for each replicate. Cross-linked chromatin was isolated, sonicated and precipitated with indicated antibodies. Pricipitates were treated with RNase A (# R4642, Sigma-Aldrich) and purified with the MiniElute PCR purification Kit (# 428004, Qiagen)
10 ng of precipitated DNA were submitted to sequencing on an Illumina HiSeq2000 instrument with 50 bp single end reads (GATC Biotech, Konstanz, Germany). The service included quality assessment on a 2500 Bioanalyzer and library preparation.
4 cm from the middle of the illuminated area of the third leaf were harvested for analysis of the maturing zone. Base samples were isolated from the same leaves. Plants were cut 0.5 cm above soil and the lowest 1-2 cm of the leaf area without light access were harvested. For isolation of molecules see SAMPLES section

value: Maturing zone of the leaf

value: H3K4me3:04-745, Merck Millipore


title: 714H rep1


title: S. pombe Δdbr diauxic short 2


title: PE5.4

value: Embryo 5


title: PE5.3


title: S. pombe Δdbr diauxic long 1

description: custom non-stranded lariat sequencing, long gel


title: Control 1 TP1 [muscle]

description:
Control: day 120 with ad libitum diet Period 1
KKM10-07

source_name: Muscle

tag: breed

value: Holstein-Friesian

tag: gender

value: male

tag: diet

value: 70% concentrate, 30% grass silage diet

value: Muscle

tag: biopsy day

value: day 120 of Period 1

tag: feeding period

value: Differential feeding

tag: restriction model

value: Control


title: S. pombe Δdbr heatshock short 2

source_name: S. pombe Δdbr heatshock


title: S. pombe Δdbr heatshock long 2


title: B73 rep2

source_name: 14-day old seedling

value: seedling

tag: development stage

tag: genotype


title: TE3.6

tag: developmental stage

value: Embryo 3


title: 714 rep3

value: 14-day old


title: B73 rep1


title: S. pombe Δdbr diauxic shift

description: Trueseq RNAseq

source_name: S. pombe Δdbr diauxic shift


title: S. pombe wt diauxic shift

description: Trueseq RNAseq

source_name: S. pombe wt diauxic shift


title: S. pombe Δdbr heatshock

description: Trueseq RNAseq


title: S. pombe Δdbr rich media short 2

source_name: S. pombe Δdbr rich media


title: S. pombe Δdbr diauxic long 2


title: S. pombe Δdbr heatshock short 1


title: S. pombe Δdbr heatshock long 1


title: S. pombe wt rich media

description: Trueseq RNAseq

source_name: S. pombe wt rich media


title: H3K4me3_ChIP-Seq_Base

value: Base of the leaf


title: S. pombe ED668 Δupf1 1

description: Trueseq RNAseq

source_name: S. pombe ED668 Δupf1

value: ED668 delta upf1


title: S. pombe Δdbr rich media short 1


title: S. pombe ED668 1

description: Trueseq RNAseq

source_name: S. pombe ED668


title: S. pombe wt heatshock

description: Trueseq RNAseq

source_name: S. pombe wt heatshock


title: S. pombe ED668 Δupf1 2

description: Trueseq RNAseq


title: Small RNA 6 d s4U elution 2

city: Boston

first: Erin

middle: Elizabeth

last: Duffy

state: MA

address: 200 Longwood Ave, Goldenson 405

department: Neurobiology

institute: Harvard Medical School

description:
processed data files: miRNA_quantifications_s4U.xlsx
processed data files: miRNA_differential_expression_edgeR.xlsx

data_processing:
Sequencing reads had adapters removed using Fastx-clipper (version 0.0.13).
Reads were then mapped using Bowtie2 (version 2.2.3) separately to synthetic spikes, UniVec laboratory contaminants, and rRNAs.
Remaining reads were mapped directly to mature miRNA sequencess (miRBase 21) and then to the human genome, using sRNAbench.
Differentially expression of miRNAs between samples was evaluated using edgeR (version 3.2.4).
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files for forward and reverse strands for each sample are separated
Supplementary_files_format_and_content: Excel tables of mature miRNA quatifications and of differential expression results using edgeR package.

source_name: HEK 293T cells

growth_protocol: HEK293T cells were cultured in high glucose DMEM media supplemented with 10% (v/v) fetal bovine serum, and 1% (v/v) 2 mM L-glutamine.

extract_protocol:
Cells were resuspended in TRIzol reagent, flash frozen, and stored overnight at -80°C. Long RNA: Cell lysates were chloroform extracted once and total RNA purified by the RNeasy mini kit (Qiagen). Small RNA  Cell lysates were chloroform extracted once and total RNA purified by the mirVana kit. Long and short RNA: Biotinylation and s4U-RNA enrichment with HPDP-biotin was carried out based on protocols by Gregersen et al. and adapted for MTS-biotin. Reactions were carried out in a total volume of 250 μL, containing 70 μg total RNA, 10 mM HEPES [pH 7.5], 1 mM EDTA, and 5 mg (MTSEA biotin-XX, Biotinum) or 50 mg (HPDP-biotin, Pierce) biotin dissolved in DMF (final concentration of DMF = 20%). Reactions were incubated at room temperature for 2 h (HPDP) or 30 min (MTS) in the dark. Following biotinylation, excess of free biotin was removed by phenol:chloroform extraction of the RNA using Phase-Lock-Gel tubes. RNA was precipitated at 20,000 x g for 20 min with a 1:10 volume of 5 M NaCl and an equal volume of isopropanol. The pellet was washed with an equal volume of 75% ethanol and precipitated again at 20,000 x g for 10 min. Purified RNA was dissolved in 50 uL RNase-free water and denatured at 65 °C for 10 min, followed by rapid cooling on ice for 5 min. Biotinylated RNA was separated from non-labeled RNA using μMacs Streptavidin Microbeads (Miltenyi). 200 μL beads were added to each sample and incubated for 15 min at room temperature. In the meantime, μColumns placed in the magnetic field of the μMacs separator were equilibrated with nucleic acid wash buffer supplied with the beads (Miltenyi). Reactions were applied to the μColumns and flow-through was collected as the pre-existing RNA fraction. μColumns were washed twice with 500 μL high salt wash buffer (100 mM Tris-HCl [pH 7.4], 10 mM EDTA, 1 M NaCl, and 0.1% Tween20). s4U-RNA was eluted from μColumns with 100 μL freshly prepared 100 mM DTT followed by a second elution with an additional 100 μL 5 min later. RNA was recovered from the flow-through and eluted fractions using the MinElute Spin columns (Qiagen) according to the instructions of the manufacturer. Samples were spiked with 11 ng S. pombe total RNA (a generous gift from Julien Berro) for downstream normalization.
Long RNA: 5 μg input and RNA collected from flow-through and eluted fractions were used for polyA library preparation. Sequencing libraries were constructed by standard mRNA-seq protocols by the Yale Center for Genomic Analysis (YCGA). Small RNA: 10% input from no s4U sample, along with eluted fractions were used for small RNA library preparation. Sequencing libraries were constructed by standard smRNA-seq protocols from the YCGA.

treatment_protocol: Long RNA: Cultured cells at 80% confluence were labeled with 700 μM s4U for 60 min, followed by PBS wash, trypsinization, and harvest. Small RNA: cultured cells were split 1:8 and labeled with 100 uM s4U for 22d, 6d, 3d, 1d, 9h, 3h, 1h, 20 min, or no s4U, followed by PBS wash, trypsinization, and harvest

value: HEK 293T

tag: biotin reagent

value: MTS-biotin

tag: s4u feed

value: 100 µM, 6 days

tag: sample type

value: biochemically enriched small RNA


title: S. pombe ED668 2

description: Trueseq RNAseq


title: Small RNA 3 d s4U elution 2

description: processed data files: miRNA_quantifications_s4U.xlsx

value: 100 µM, 3 days


title: S. pombe Δdbr rich media long 2

value: delta dbr 972h-


title: Small RNA 3 d s4U elution


title: Small RNA 6 d s4U elution


title: Small RNA 1 d s4U elution

value: 100 µM, 1 day


title: S. pombe Δdbr rich media long 1


title: Small RNA 1 hr s4U elution 2


title: Small RNA 9 hr s4U elution


title: Small RNA 3 hr s4U elution 2


title: Small RNA 1 d s4U elution 2


title: Small RNA 20 min s4U elution 2


title: Small RNA 1 hr s4U elution


title: Small RNA no s4U Input

value: total small RNA


title: Small RNA 20 min s4U elution


title: Long RNA no s4U 22d Input

data_processing:
Sequencing reads were aligned used Tophat2 (version 2.0.12; Bowtie2 version 2.2.3) to align RNA-Seq reads simultaneously to the human and S. pombe genomes (hg19/PomBase v22) and transcriptomes (GENCODE v19/Ensembl Fungi v22)
Cufflinks (version 2.2.1) to quantify annotated human and S. pombe transcripts, using only reads that were uniquely mapped and that aligned within up to two mismatches to the reference.
Normalized expression values to S.  pombe spike-ins by multiplying raw FPKM's by the slope of the linear regression line of raw S. pombe gene FPKMs with the normalizing sample on the y-axis sand the sample of interest on the X-axis.
Genome coverage tracks were generated using IGVTools (version 2.0)
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files for forward and reverse strands for each sample are separated
Supplementary_files_format_and_content: Excel tables of mature miRNA quatifications and of differential expression results using edgeR package.

value: total long RNA


title: MTS-biotin, no s4U

description: biochemically enriched RNA

data_processing:
Sequencing reads were aligned used Tophat2 (version 2.0.12; Bowtie2 version 2.2.3) to align RNA-Seq reads simultaneously to the human and S. pombe genomes (hg19/PomBase v22) and transcriptomes (GENCODE v19/Ensembl Fungi v22)
Cufflinks (version 2.2.1) to quantify annotated human and S. pombe transcripts, using only reads that were uniquely mapped and that aligned within up to two mismatches to the reference.
Normalized expression values to S. pombe spike-ins by multiplying raw FPKM's by the slope of the linear regression line of raw S. pombe gene FPKMs with the normalizing sample on the y-axis sand the sample of interest on the X-axis.
Genome coverage tracks were generated using BEDTools
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files for forward and reverse strands for each sample are separated

extract_protocol:
Cells were resuspended in TRIzol reagent, flash frozen, and stored overnight at -80°C. Cell lysates were chloroform extracted once and total RNA purified by the RNeasy mini kit (Qiagen). Biotinylation and s4U-RNA enrichment with HPDP-biotin was carried out based on protocols by Gregersen et al. and adapted for MTS-biotin. Reactions were carried out in a total volume of 250 μL, containing 70 μg total RNA, 10 mM HEPES [pH 7.5], 1 mM EDTA, and 5 mg (MTSEA biotin-XX, Biotinum) or 50 mg (HPDP-biotin, Pierce) biotin dissolved in DMF (final concentration of DMF = 20%). Reactions were incubated at room temperature for 2 h (HPDP) or 30 min (MTS) in the dark. Following biotinylation, excess of free biotin was removed by phenol:chloroform extraction of the RNA using Phase-Lock-Gel tubes. RNA was precipitated at 20,000 x g for 20 min with a 1:10 volume of 5 M NaCl and an equal volume of isopropanol. The pellet was washed with an equal volume of 75% ethanol and precipitated again at 20,000 x g for 10 min. Purified RNA was dissolved in 50 uL RNase-free water and denatured at 65 °C for 10 min, followed by rapid cooling on ice for 5 min. Biotinylated RNA was separated from non-labeled RNA using μMacs Streptavidin Microbeads (Miltenyi). 200 μL beads were added to each sample and incubated for 15 min at room temperature. In the meantime, μColumns placed in the magnetic field of the μMacs separator were equilibrated with nucleic acid wash buffer supplied with the beads (Miltenyi). Reactions were applied to the μColumns and flow-through was collected as the pre-existing RNA fraction. μColumns were washed twice with 500 μL high salt wash buffer (100 mM Tris-HCl [pH 7.4], 10 mM EDTA, 1 M NaCl, and 0.1% Tween20). s4U-RNA was eluted from μColumns with 100 μL freshly prepared 100 mM DTT followed by a second elution with an additional 100 μL 5 min later. RNA was recovered from the flow-through and eluted fractions using the MinElute Spin columns (Qiagen) according to the instructions of the manufacturer. Samples were spiked with 11 ng S. pombe total RNA (a generous gift from Julien Berro) for downstream normalization.
5 μg input and RNA collected from flow-through and eluted fractions were used for polyA library preparation. Sequencing libraries were constructed by standard mRNA-seq protocols by the Yale Center for Genomic Analysis (YCGA).

treatment_protocol: Cultured cells at 80% confluence were labeled with 700 μM s4U for 60 min, followed by PBS wash, trypsinization, and harvest.


title: Small RNA 22d s4U Input

value: 100 µM, 22 days


title: Long RNA s4U 22d Input


title: MTS-biotin 1

description: biochemically enriched RNA

value: 700 μM, 60 minutes


title: Small RNA 22 d s4U elution 2


title: MTS-biotin 2

description: biochemically enriched RNA


title: Input 2


title: Input 1


title: S. pombe Δdbr rich media

description: Trueseq RNAseq


title: ERRγ-ChIP

city: La Jolla

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

data_processing:
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline 1.7 and mapped to the mouse genome (mm9, NCBI Build 37) using Bowtie. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows.
Peaks: Peak detection was performed with the HOMER software suite (http://biowhat.ucsd.edu/homer/).
Genome_build: mm9
Supplementary_files_format_and_content: bowtie files are alignments made from fastq files with the Bowtie aligner; bedGraph files were generated on Homer and can be visualized on the UCSC genome browser; peak files were generated using Homer.

source_name: mouse ES-cell derived neurons

growth_protocol: ES-D3 cells from ATCC were differentiated to neurons as described in (Bibel et al.  Nature protocols 2, 1034-1043 (2007)).

extract_protocol: Standard Illumina DNA library construction

tag: originating cell type

value: ES-D3 from ATCC

tag: chip antibody

value: ERRγ (Dufour et al. Cell Metab 5, 345-356 (2007))


title: Small RNA 3 hr s4U elution


title: input


title: Hyperactivated MYC and depleted BUD31, replicate 1

city: Houston

first: Chad

middle: A.

last: Shaw

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: BCM

description:
Sample name: 9-Myc_LowBUD31
rRNA-depleted RNA

data_processing:
RNA-seq NGS reads were mapped using STAR RNASeq aligner (version 2.3.1). In order to improve mapping accuracy, splice junctions’ database file (gencode.v.14.annotation.gtf.sjdb) was supplied at the genome index generation step with command line option –sjdbOverhang 74 together with hg19_Gencode14.overhang75/hg19_chrOnly.fa and default parameters. Duplicate reads were marked with the MarkDuplicates function of the Picard-tools software package (version 1.107) using default settings.
Duplicates were marked for each sample, using picard-tools-1.107.
Intron-exon junctions were obtained using the University of California Santa Cruz Genome Browser “knownGene” table (downloaded 06/04/2014). Constitutive junctions were defined as junctions that 1) appeared in each transcript annotated to a given gene symbol and 2) did not overlap with any transcript annotated to a different gene symbol and 3) failed to mark the start or stop of a transcript
We used R together with the Rsamtools package to calculate intron retention (IR). Briefly, for each intron-exon junction, we extracted all non-duplicate reads overlapping this junction. Next, we assigned these reads into two categories: 1) “intronic” if the read mapped to at least the first base of the intron, 2) “exonic” if none of the bases of the read mapped to the first base of the intron. We counted the total number of reads assigned into each category for each junction. IR was calculated as described in the paper.
Genome_build: hg19
Supplementary_files_format_and_content: [IntronRetentionScores.txt] Tab-delimited text file containing intron retention scores, where rows correspond to junctions and column correspond to samples.

source_name: MYC-ER HMECs with dox-inducible shBUD31

growth_protocol: Immortalized mammary epithelial cells are grown in 6cm plastic plates in MEGM medium (Lonza).

extract_protocol:
Total RNA was isolated using the Rneasy kit (Qiagen).
RNA samples were rRNA depleted, and RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MYC-ER HMECs with dox-inducible shBUD31 (pINDUCER-shBUD31-3'UTR) were cultured for 72 hours -/+ 16 ng/ml doxycycline and 48 hours -/+ 300 nM tamoxifen in triplicates.

tag: cell type

value: Immortalized mammary epithelial cell

tag: passages

tag: condition

value: Hyperactivated MYC and depleted BUD31


title: Depleted BUD31, replicate 3

description:
Sample name: 8-LowBUD31
rRNA-depleted RNA

tag: cell line

value: MYC-ER HMECs with dox-inducible shBUD31 (pINDUCER-shBUD31-3'UTR)

value: Depleted BUD31


title: Hyperactivated MYC and depleted BUD31, replicate 3

description:
Sample name: 11-Myc-LowBUD31
rRNA-depleted RNA


title: Hyperactivated MYC, replicate 3

description:
Sample name: 5-Myc
rRNA-depleted RNA

value: Hyperactivated MYC


title: Hyperactivated MYC, replicate 1

description:
Sample name: 3-Myc
rRNA-depleted RNA


title: Hyperactivated MYC, replicate 2

description:
Sample name: 4-Myc
rRNA-depleted RNA


title: Control, replicate 2

description:
Sample name: 2-Control
rRNA-depleted RNA

value: Control


title: Control, replicate 1

description:
Sample name: 1-Control
rRNA-depleted RNA


title: Sonoran 3_Saguaro

city: Colorado Springs

first: Jeremy

last: Bono

state: CO

address: 1420 Austin Bluffs Parkway

department: Biology

institute: University of Colorado Colorado Springs

data_processing:
Low quality sequences were filtered out by removing any reads with unknown nucleotides >5%, or reads with more than 20% of base quality scores <10
Trinity was used for de novo transcriptome assembly using default parameters, combining all 18 libraries
Abundance of transcripts was estimated by mapping reads back to the assembly using RNA-seq by Expectation Maximization software package bundled with Trinity
Differential expression analysis was conducted using EdgeR; Genes with low counts were excluded by selecting only those with 1 read per million in at least three libraries
Supplementary_files_format_and_content: Tab delimited text file includes count abundance data for each sample under each experimental condition

organism: Drosophila mettleri

extract_protocol:
10 larvae from each sample/food combination were pooled and RNA was extracted following a Tri-reagent protocol
Libraries were constructed by BGI Americas
Each library was split and sequenced on both lanes to avoid lane artifiacts

treatment_protocol: Larvae representing each sample were reared in three food treatments: saguaro cactus, coastal prickly pear cactus, or Drosophila 4-24 Instant food

tag: population

value: Sonoran

tag: strain

value: 8 day old larvae

tag: food type

value: saguaro cactus


title: Sonoran 3_PP

value: coastal prickly pear cactus


title: Sonoran 3_lab food

source_name: Sonoran_larvae_lab food

value: Drosophila 4-24 Instant food


title: Sonoran 2_PP


title: HPDP-biotin

description: biochemically enriched RNA

value: HEK 293T

value: HPDP-biotin


title: Sonoran 1_lab food


title: Sonoran 1_PP


title: Sonoran 1_Saguaro


title: Santa Catalina Island 2_Saguaro

source_name: Santa Catalina island_larvae_Saguaro

value: Santa Catalina Island


title: Sonoran 2_lab food


title: Santa Catalina Island 3_Saguaro


title: Santa Catalina Island 3_PP

source_name: Santa Catalina island_larvae_PP


title: Santa Catalina Island 3_lab food

source_name: Santa Catalina island_larvae_lab food


title: Hyperactivated MYC and depleted BUD31, replicate 2

description:
Sample name: 10-Myc_LowBUD31
rRNA-depleted RNA


title: Santa Catalina Island 2_lab food


title: Santa Catalina Island 1_Saguaro

description: CMSaguaro

value: C-M


title: Santa Catalina Island 1_PP

description: CMPP


title: Santa Catalina Island 2_PP


title: Santa Catalina Island 1_lab food

description: CMlabfood


title: Depleted BUD31, replicate 2

description:
Sample name: 7-LowBUD31
rRNA-depleted RNA


title: H3K9ac_ChIP-Seq_Maturing zone

source_name: Third leaf

extract_protocol:
Leaf material of 10 plants was pooled for each replicate. Cross-linked chromatin was isolated, sonicated and precipitated with indicated antibodies. Pricipitates were treated with RNase A (# R4642, Sigma-Aldrich) and purified with the MiniElute PCR purification Kit (# 428004, Qiagen)
10 ng of precipitated DNA were submitted to sequencing on an Illumina HiSeq2000 instrument with 50 bp single end reads (GATC Biotech, Konstanz, Germany). The service included quality assessment on a 2100 Bioanalyzer and library preparation.
4 cm from the middle of the illuminated area of the third leaf were harvested for analysis of the maturing zone. Base samples were isolated from the same leaves. Plants were cut 0.5 cm above soil and the lowest 1-2 cm of the leaf area without light access were harvested. For isolation of molecules see SAMPLES section

value: Maturing zone of the leaf

value: H3K9ac:07-352, Merck Millipore


title: H3K9ac_ChIP-Seq_Base

value: Base of the leaf


title: RNA-Seq_Maturing zone

extract_protocol:
Leaf material of 6 plants was pooled for each replicate and RNA was extracted using Trizol followed by DNase digestion (RNase Free DNase Set # 79254, Qiagen) and purification of RNA (RNeasy MiniElute Cleanup kit # 74204, Qiagen)
2 µg of total RNA per biological replicate were submitted to sequencing on an Illumina HiSeq2000 instrument with 50 bp single end reads (GATC Biotech, Konstanz, Germany). The service included quality assessment on a 2100 Bioanalyzer, cDNA synthesis from fragmented poly(A)+ RNA and library preparation.
4 cm from the middle of the illuminated area of the third leaf were harvested for analysis of the maturing zone. Base samples were isolated from the same leaves. Plants were cut 0.5 cm above soil and the lowest 1-2 cm of the leaf area without light access were harvested. For isolation of molecules see SAMPLES section


title: TG2

status: Public on Sep 02 2015

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

description:
VSFP2.3 transgenic mouse replicate 2
Mouse 595

data_processing:
Illumina Casava 1.8.2 software used for basecalling. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics)
The Alignment was performed using STAR 2.3.0 to mm10. Reads per gene were counted via htseq version 0.6.1. Data analysis was performed using R/Bioconductor (3.0.2/2.12) loading DESeq, gplots and goseq packages.
Candidate genes were filtered to a minimum of 2x fold change, RPKM > 1, and FDR-corrected pvalue<0.05. For functional analysis gene ontology enrichment was tested accounting for gene length via R-package goseq.
Genome_build: mm10

source_name: Left ventricular free wall

extract_protocol:
RNA was extracted using NucleoSpin RNA kit, Macherey-Nagel. All samples exhibited a RIN value of >7.
Library preparation for RNA-Seq was performed using the TruSeq Stranded Total RNA Sample Prep Kit, Illumina starting from 500 ng of total RNA according to Illumina's instructions. Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000  following the manufacturer's protocols.

treatment_protocol: No treatment

tag: Sex

value: Female

tag: age

value: 19 weeks

tag: parents

value: VSFP2.3 transgenic


title: RNA-Seq_Base


title: WT2

description:
Wild-type mouse replicate 2
Mouse 594

tag: genotype

value: WT


title: TG1

description:
VSFP2.3 transgenic mouse replicate 1
Mouse 553

value: Male

value: 35 weeks


title: WT1

description:
Wild-type mouse replicate 1
Mouse 552


title: Prdm9 Affinity-seq

city: Bar Harbor

first: Petko

last: Petkov

state: Maine

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

description: Processed data file: Affinity-Seq_B6_combined4.bedgraph.gz

data_processing:
ChIP-Seq reads were aligned to the mm9 genome assembly using BWA v1.2.3.
ChIP-Seq reads were filtered to keep only uniquely mapped reads.
ChIP-Seq peaks were called using MACS v2.0.9 and RSEG 0.4.8.
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph files were generated using bedtools v2.17.0.

source_name: spleen

extract_protocol:
Genomic DNA sonicated to an average of 200bp using a high speed digital sonicating waterbath. Paired with bacterial extract protein that had gone through a single step of purification. Captured particles with streptavadin beads.
Libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: spleen

value: adult


title: Prdm9_ChIPSeq

description: Processed data file: P9_1b_4b_combined.bedgraph.gz

source_name: spermatocytes

extract_protocol:
Nuclei were isolated from cells using hypotonic lysis. Chromatin was fragmented either by MNase digestion. After high speed spin, soluble chromatin was removed and used for ChIP.
Libraries were prepared for sequencing using standard Illumina protocols

tag: antibody

value: spermatocytes

value: 12 days post-partum


title: Affinity-seq Input DNA

source_name: liver

value: liver


title: Prdm9 Input DNA


title: H3K9me3 Input DNA

description: Processed data file: B6_h3k9me3_log2ratio_mm9_4kb.bedgraph.gz


title: H3K9me3_ChIPSeq


title: Sonoran 2_Saguaro

value: Sonoran

tag: developmental stage

value: 8 day old larvae

value: saguaro cactus


title: 444wt_3

data_processing:
ChIP-Seq reads were aligned to the mm9 genome assembly using BWA v1.2.3
ChIP-Seq reads were filtered to keep only uniquely mapped reads
ChIP-Seq peaks were called using MACS v1.4.2
RNA-Seq reads were aligned to mm9 with BowTie 0.12.9
Normalized RNA expression level per gene was calculated in fragments per kilobase of transcript per million mapped reads (FPKM) using RSEM version 1.2.8 using the following parameters: --fragment-length-mean 280 and --fragment-length-sd 50.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample generated from rsem. Bedgraph files were generated using bedtools

extract_protocol:
Enriched germ cells were collected after collagenase and trypsin digestion. Total RNA was extracted using  Qiagen RNeasy Micro Kit (cat# 74004).
Libraries were prepared for sequencing using standard Illumina protocols


title: AM2 _GES14_rep 1

data_processing:
ChIP-seq We utilized the 2nd biological replicate (AO2 _GES14) to confirm the first (AM2 _GES14), but derived our results from the original sample only (AM2 _GES14) along with the control data.
ChIP-Seq reads were aligned to the mm9 genome assembly using BWA v1.2.3
ChIP-Seq reads were filtered to keep only uniquely mapped reads
ChIP-Seq peaks were called using MACS v1.4.2
RNA-Seq reads were aligned to mm9 with BowTie 0.12.9
Normalized RNA expression level per gene was calculated in fragments per kilobase of transcript per million mapped reads (FPKM) using RSEM version 1.2.8 using the following parameters: --fragment-length-mean 280 and --fragment-length-sd 50.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample generated from rsem. Bedgraph files were generated using bedtools

extract_protocol:
Nuclei were isolated from cells using hypotonic lysis. Chromatin was fragmented either by Mnase digestion. After high speed spin soluble chromatin was removed and used for ChIP
Libraries were prepared for sequencing using standard Illumina protocols


title: Input DNA


title: 456wt_1


title: 456wt_2


title: 343wt_3


title: 444wt_2


title: AO2 _GES14_rep2


title: 343wt_2


title: 456wt_3


title: 186wt_1


title: 186wt_3


title: 186wt_2


title: WT rep3

first: Laurent

last: Dupays

address: The Ridgeway, Mill Hill

institute: The Francis Crick Institute

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the mm9 genome assembly using Tophat.
Differential expressed genes were analysed using Avadis suite.
Genome_build: mm9
Supplementary_files_format_and_content: Avadis differential expression result file

source_name: E11.5 heart, WT

extract_protocol:
E11.5 embryonic hearts from the Nkx2-5 hypomorphic line were dissected and stored in RNAlater (Qiagen). After genotyping, 3 control and 3 hypomorphic samples were selected for total RNA extraction using Trizol and purified on RNeasy column (Qiagen).
Total RNA was converted to a library of template molecule suitable for high throughput DNA sequencing using Truseq kit (Illumina).

value: heart


title: Hypomorph rep3

source_name: E11.5 heart, Hypomorph

value: hypomorphic heart


title: Hypomorph rep1


title: Hypomorph rep2


title: WT rep2


title: 12qDOX1A_XIST_rna

city: Vancouver

first: Carolyn

last: Brown

state: BC

address: 2350 Health Sciences Mall

department: Medical Genetics

country: Canada

institute: University of British Columbia

description: processed data file: FPKM_genes_all_NextSeq.txt

data_processing:
Fastq reads from RNA-seq were mapped to hg18 using Tophat with UCSC hg18 gene annotations, outputting only uniquely mapped reads.
FPKM values were obtained through Cufflinks.
Fastq reads from ChIP-seq were mapped to hg18 using Bowtie, keeping only uniquely mapped reads. PCR-duplicates were excluded.
ChIP-seq bam files were analyzed using SeqMonk to obtain normalized levels of H3K27ac and H3K27me3. Read Count Quantitation was done using All Reads and correcting for total count per million reads. Sites pertaining to the higest and lowest 5% in the input samples were excluded in the analysis.
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each gene in each RNA-seq samples; and RPM values for H3K27ac and H3K27me3 levels in 1Mb windows for each ChIP-seq samples.

source_name: fibroscarcoma cell line HT1080

extract_protocol:
Total RNA was extracted using Trizol.
PolyA-selected RNA library was constructed with Illumina TruSeq Stranded mRNA library prep kit.

value: fibroscarcoma cell line

tag: dox treatment

value: 5day DOX

tag: integration


title: WT rep1


title: 12qND1A_XIST_rna

value: No DOX


title: 1pDOX2A_XIST_rna


title: 1pND1A_XIST_rna


title: ROZ12 TFH

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina Casava1.8.2 software used for basecalling and demultiplexing.
Reads were mapped to Macaca_mulatta UNMC_v7.6 genome assembly with the STAR (v2.3.0e) aligner args: --outFileterMultimapNmax 1 --outFilterType BySJout --outSJfilterReads Unique --sjdbGTFfile UNMC_rhesus_annotation_v7.6 --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Per sample annotated transcript models were quantitated with Cufflinks (v2.1.1) args: -G UNMC_rhesus_annotation_v7.6.gtf
Sample transcript models were merged with Cuffmerge (v2.1.1)
FPKM (Fragments per kilobase of exon per million reads mapped) abundance estimates and differential expression was caluclated with Cuffdiff (v2.1.1)
Genome_build: UNMC_v7.6 is a presubmission version of the MacaM GCA_000772875.1 assembly. (MaSuRCA_Rhesus_Genome_v7_20130927.fasta, UNMC_rhesus_annotation_v7.6.gtf)
Supplementary_files_format_and_content: tab delimited text file containing FPKM for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: Splenocyte

extract_protocol:
Total RNA was prepared using the QIAGEN RNEasy Micro Kit.
Libraries were generated using the CLONTECH SMARTer HV kit, barcoding and sequencing primers were added using NexteraXT DNA kit.  Libraries were validated by microelectrophoresis, quantified, pooled and clustered on Illumina TruSeq v3 flowcell.  Clustered flowcell was sequenced on an Illumina HiSeq 1000 in 100-base single-read reactions.

tag: infection status

value: SIV positive

tag: time point

value: 24 weeks post infection

tag: cell population

value: TFH


title: 444wt_1

tag: cell type


title: ROZ12 TREG

value: TREG


title: 343wt_1


title: REi9 CD4

value: BULK CD4


title: REi9 TREG


title: ROZ12 TFR

value: TFR


title: REi9 TFH


title: RLI8 TREG


title: REi9 TFR


title: RQu8 CD4


title: RQu8 TREG


title: RQu8 TFH


title: RQu8 TFR


title: RLI8 TFH


title: RLI8 TFR


title: RZH8 CD4


title: RZH8 TFR


title: RZH8 TREG


title: RZH8 TFH


title: ROZ12 CD4


title: RII9 TREG

value: SIV negative

value: uninfected


title: RII9 CD4


title: RLM7 TFH


title: RII9 TFH


title: RII9 TFR


title: RLM7 TFR