title: CraY47D_2

city: Baltimore

first: Tracy

last: Hazen

address: 801 W. Baltimore St.

institute: Institute for Genome Sciences

data_processing:
Illumina reads were mapped to the EDL933 genome using Bowtie
The mapped reads were counted using HTSeq and normalized and then the differential expression of each gene for one sample compared to another was determined using DESeq v. 1.5.24, and statistical analyses were performed using R-2.15.2, and was represented as the log2 of the fold-change values.
Genome_build: EDL933

organism: Escherichia coli O157:H7 str. EDL933

source_name: Escherichia coli cells

growth_protocol: Overnight cultures of EHEC strain TUV93-0 ∆cra::FRT producing wild type Cra (pAMH257), non-phosphorylatable Cra Y47F (pAMH258) and phosphomimetic Cra Y47D (pAMH268) were grown in LB, and then diluted 1:100 in M9 with 0.4% glucose and grown aerobically at 37ºC to OD600 ~1.

extract_protocol:
RNA was isolated from pelleted cells using the hot phenol method and contaminating DNA was removed using the Ribopure Dnase I and also the Turbo DNA-free kit (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with RNA Later (Ambion) and then collected by centrifugation. Cell pellets were stored at -80C prior to RNA isolation.

value: phosphomimetic Cra Y47D


title: wt-3

status: Public on Feb 02 2018

type: SRA

city: Stanford

first: Sean

last: Beckwith

state: CA

address: 371 Serra Mall

department: Biology

country: USA

institute: Stanford University

description: WT Rap45 rep1

library_source: transcriptomic

data_processing:
Reads were aligned using Bowtie2 and analysed using DESeq2. Replicates were combined for analysis and genes with low reads (< 5 FPKM across all samples) were removed.
Genome_build: sacCer3 (April 2011)
Supplementary_files_format_and_content: FPKM

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: wild type

growth_protocol: Yeast were grown to mid-log-phase in YPD medium at 30C. (Asynchronous culture).

extract_protocol:
Pellets were collected, snap-frozen and then processed as per the RNA-seq protocol outlined. Two biological replicates were collected(-1,-2 or -3,-4 or -5,-6). RNA was prepared from samples (approximately 1.5 ODs) using the MasterPure™ Yeast RNA Purification Kit (Epicentre, MPY03100).
The sequencing libraries were prepared from 0.8 µg of RNA/sample using the Illumina TruSeq Stranded mRNA kit (Illumina, 15031047). The quality of the pooled library was checked using the Agilent Bioanalyser 2100 HS DNA assay. The library was sequenced on an Illumina HiSeq 2000 platform.

treatment_protocol: Asynchronous culture was treated with 30 nM rapamycin for 45 min, 90 min, or was untreated

tag: strain background

tag: genotype

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0

tag: growth protocol

value: Yeast liquid culture


title: CraY47F_1

state: MD

tag: genotype/variation

value: phosphorylatable Cra Y47F


title: CraY47F_2


title: ino80-3

description: ino80KO Rap45 rep1


title: RD_HNRNPH1_sin3_rep1

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Basecalling was performed using Illumina Casava 1.7
FASTQ sequences adapter trimmed (curtadapt) and mapped to the human hg19 genome by a pipeline that serially  employs STAR and BWA
Mapped reads were counted with HTSEQ
voom TMM normalized and contrasted using the empirical Bayes pipeline limma in R 3.2.3
Genome_build: hg19
Supplementary_files_format_and_content: count files are txt format files that contain raw read counts that map  to  transcripts for each defined gene.

organism: Homo sapiens

source_name: Rhabdomyosarcoma cell line

growth_protocol: The RD, RH30 and RH41 cell lines were cultured in RPMI1640, 100 units/ml penicillin and 100 mg/ml streptomycin, and 10% fetal bovine serum (Sigma).

extract_protocol:
RNA was extracted with a Maxwell simplyRNA Tissue kit and Maxwell Instrument (Promega, Madison, WI).
The total RNA stranded library prepared from the final PCR products of indexed samples was subjected to 300 bp paired-end sequencing

treatment_protocol: All siRNAs were dissolved in Ultra-pure distilled water (Invitrogen) to 20 µM as stocks.  Lipofectamine RNAiMAX (Invitrogen) was used to transfect siRNA (siRNA stock to Lipofectamine at 1:1 v/v ratio) and medium was replaced with fresh one after 6 hours. For cells harvested 2 and 4 days post transfection, 2×105 (RD and RH30) or 2.4×105 (RH41) cells were seeded per well of 6-well plate, 2 µl RNAiMAX and 2 µl of 20 µM siRNA were used for transfection in 2 ml culture medium.

tag: cell line

value: RD

tag: expression modification

value: HNRNPH1 sin3


title: RD_HNRNPH1_sin2_rep2

value: HNRNPH1 sin2


title: CraY47D_1


title: ino80-2

description: ino80KO Untreated rep2


title: RD_HNRNPH1_sin2_rep1


title: RD_HNRNPH1_sin2_rep3


title: RH30_HNRNPH1_sin2_rep1


title: Cra_WT_2

value: plasmid-encoded wild type Cra


title: RD_siControl_rep2

value: siControl


title: ino80-1

description: ino80KO Untreated rep1


title: wt-2

description: WT Untreated rep2


title: Cra_WT_1


title: arp5-3

description: arp5KO Rap45 rep1

value: BY4741 arp5::LEU2


title: ino80-4

description: ino80KO Rap45 rep2


title: RD_siControl_rep1


title: wt-1

description: WT Untreated rep1


title: 1SC4

status: Public on Feb 01 2018

city: Ithaca

first: Veronica

last: Guariglia

state: New York

address: 320 Stocking Hall

department: Food Science

institute: Cornell University

data_processing:
Raw data was generated by the Illumina pipeline software v1.8
the sequence reads were aligned to a 10403S genome using the BWA-MEM with default settings.The output was a SAM files for each sample. Used SAMTOOLS (Li, et al., PMID 1950593) to sort and index the SAM files obtained from BWA and convert them to BAM format. BAM files were converted to strand-specific base count files. Coverage at each base position along the chromosome was calculated by enumerating the number of reads that aligned to a given base for each DNA strand separately.
Differential expression of genes in different strains was statistically assessed using the BaySeq method implemented in the BaySeq 2.2.0 package available from Bioconductor. Genes were considered differentially expressed if they showed a false discovery rate (FDR) < 0.05 and a fold change (FC) ≥ 2.0 (meaning genes were upregulated on Prha-sigB) or FC ≤ 0.5 (meaning genes were downregulated on Prha-sigB).
Genome_build: 10403S genome (genebank accession number: NC_017544) or H7858 permanent draft (BioProject Accession number: PRJNA10752)
Supplementary_files_format_and_content: Each excel spreadsheet contains the normalized count data for each coding gene in 10403S or H7858, likelihood of being differentially expressed and False Discovery Rate (from Bayseq output), as well as the foldchange Bile/No Bile or WT/SigB depending on comparison.

organism: Listeria monocytogenes

source_name: BHI pH 5.5

growth_protocol: strains were streaked from frozen BHI stock, stored at -80°C in 15% glycerol, onto a BHI agar plate, followed by incubation at 37°C for 24 h. A single colony was subsequently inoculated into 5 ml of BHI broth in 16 mm tubes, followed by incubation at 37°C with shaking (230 rpm) for 18 h (Series 25 Incubator, New Brunswick Scientific, Edison, NJ). After 18 h, 50 μl BHI culture was inoculated into fresh 100 ml BHI broth and grown in flasks without shaking for 3h (to OD600 ~0.4) at 37°C.

extract_protocol:
Total RNA was extracted by using proteinase K, and lysozyme, followed by Tri reagent with bead-beating. Total RNA was incubated with DNase in the presence of RNasin to remove remaining DNA.
Preparation of cDNA fragment libraries was performed using the ScriptSeqTM Complete Kit (Bacteria)-Low Input (Epicentre, Madison, WI), which is composed of Ribo-ZeroTM rRNA Removal Reagents (Bacteria)-Low Input, Magnetic Core Kit-Low Input, and ScriptSeqTM v2 RNA-Seq Library Preparation Kit.

treatment_protocol:
Total RNA was treated with Ribo-ZeroTM rRNA Removal Reagents (Bacteria)-Low Input for removal of 16S and 23S ribosomal RNA and enriched for mRNA
Cultures were diluted into 100ml pH 5.5 BHI with or without 1.1% bile for 10 min.

tag: strain

value: deltasigB

tag: condition

value: No Bile

tag: replicate


title: arp5-1

description: arp5KO Untreated rep1


title: 1SB4

value: Bile


title: 2SB4


title: 1WB4

value: WT


title: 1WC4


title: 2SC4


title: 2WC4


title: RD_siControl_rep3


title: 2WB4


title: 1SB2


title: 1SC3


title: 1SC2


title: 1WC3


title: 1WC2


title: 1SC1


title: 1SB3


title: 1WB2


title: 1WB3


title: 1SB1


title: 2SC2


title: 2SB3


title: 2SC3


title: 2SC1


title: 1WB1


title: 2SB2


title: 2SB1


title: 2WC3


title: 2WC1


title: 2WB3


title: 2WB2


title: 2WC2


title: 2WB1


title: 1WC1


title: Control time point 14 days replicate 1

city: Castanet-Tolosan

first: Christophe

last: Roux

address: Chemin de Borde Rouge

country: France

institute: University of Toulouse/CNRS

description:
RAW Ri GR24 14d vs GR24 14d ctrl
22_GAGTGG_L004

data_processing:
R. irregularis sample reads were mapped back to the Gloin1 genre repertoire to calculate gene expression as RPKM, using RNA-seq functionality in CLC software with the settings of minimum mapped read length fraction at 0.95 and minimum similarity at 0.98. To find the NRVTs significantly upregulated in response to plant signals, the RPKM of R. irregularis gene submitted to GR24 or root exudates were compared to their respective control using proportion-based test statistics with a False Discovery Rate (FDR) correction for multiple testing. R. irregularis genes were considered as significantly upregulated when meeting the requirements of RPKM fold change>5 and FDR corrected p value<0.05.
Selection of libraries: Pairwise Pearson correlations were calculated among each triplicates. Libraires with Pearson correlation lower than 0.9 were excluded: Library 4_GCCAAT_L004 (Control time point 1h replicate 1), Library 8_AGTTCC_L00 (GR24 time point 2 days replicate 2), Library 13_ATCACG_L004 (GR24 time point 7 days replicate 1), Library 18_GGCTAC_L004 (Control time point 7 days replicate 3).
Genome_build: GCA_000439145.2

organism: Rhizophagus irregularis DAOM 181602=DAOM 197198

source_name: germinating spores

growth_protocol: Spores (80,000) were germinated in 40ml of liquid M medium for 2 days in the dark with 2% CO2. To stimulate spores with root exudates, young carrot hairy roots (Daucus carota DC1 - Becard &Fortin, 1988) were transferred into fresh M medium petri-dishes (14.5cm in diameter) containing 1% of sucrose (Becard &Fortin, 1988), gelled with 0.3% of Phytagel (Sigma) and then covered with sterile cellophane membrane. The covered carrot roots were cultivated in growth chamber (22-25 degrees in dark) for around 1 weeks until they spread out. Then a suspension of in vitro cultured R. irregularis spores (60,000) were pipetted onto the cellophane membrane and incubate in a CO2 chamber (2% of CO2, in dark) for 14 days. The control samples were grown under the same conditions except the addition of carrot hairy roots.

extract_protocol:
Germinating spores were crushed with a motar and a pestle in liquid nitrogen and mRNA were extracted using RNeasy plant kit (Qiagen), according to the manufacturer instructions.
Samples were sequenced at the Genome and Transriptome platform (Toulouse, France - GeT). mRNA were isolated with polyT beads before processing, libraries were constructed according to the manufacturer's protocol.

treatment_protocol: Spores were treated with the strigolactone GR24 at a final concentration of 10-6M, and collected 1 hour, 2 days, 7 days and 14 days, after growing in the same previous conditions.

tag: treatment

value: Acetone 1/1000

tag: growth time post induction

value: 14 days


title: Root exudates time point replicate 1

description:
RAW Ri RE vs RE ctrl
34_CCGTCC_L004

value: Root exudates


title: Root exudates control time point replicate 1

description:
RAW Ri RE vs RE ctrl
37_ATCACG_L004


title: Root exudates control time point replicate 3

description:
RAW Ri RE vs RE ctrl
39_ACTTGA_L004


title: Root exudates time point replicate 2

description:
RAW Ri RE vs RE ctrl
35_GTCCGC_L004


title: Root exudates time point replicate 3

description:
RAW Ri RE vs RE ctrl
36_GTGAAA_L004


title: Root exudates control time point replicate 2

description:
RAW Ri RE vs RE ctrl
38_TTAGGC_L004


title: Control time point 7 days replicate 2

description:
RAW Ri GR24 7d vs GR24 7d ctrl
17_TAGCTT_L004

value: 7 days


title: GR24 time point 7 days replicate 3

description:
RAW Ri GR24 7d vs GR24 7d ctrl
15_ACTTGA_L004


title: GR24 time point 14 days replicate 1

description:
RAW Ri GR24 14d vs GR24 14d ctrl
19_GTGGCC_L004


title: GR24 time point 14 days replicate 2

description:
RAW Ri GR24 14d vs GR24 14d ctrl
20_GTTTCG_L004


title: Control time point 14 days replicate 3

description:
RAW Ri GR24 14d vs GR24 14d ctrl
24_ATTCCT_L004


title: Control time point 7 days replicate 1

description:
RAW Ri GR24 7d vs GR24 7d ctrl
16_GATCAG_L004


title: Control time point 14 days replicate 2

description:
RAW Ri GR24 14d vs GR24 14d ctrl
23_ACTGAT_L004


title: Control time point 2 days replicate 1

description:
RAW Ri GR24 2d vs GR24 2d ctrl
10_CCGTCC_L004

value: 2 days


title: GR24 time point 7 days replicate 1

description:
RAW Ri GR24 7d vs GR24 7d ctrl
13_ATCACG_L004


title: GR24 time point 2 days replicate 2

description:
RAW Ri GR24 2d vs GR24 2d ctrl
8_AGTTCC_L004


title: Control time point 2 days replicate 3

description:
RAW Ri GR24 2d vs GR24 2d ctrl
12_GTGAAA_L004


title: GR24 time point 7 days replicate 2

description:
RAW Ri GR24 7d vs GR24 7d ctrl
14_TTAGGC_L004


title: GR24 time point 2 days replicate 3

description:
RAW Ri GR24 2d vs GR24 2d ctrl
9_ATGTCA_L004


title: GR24 time point 2 days replicate 1

description:
RAW Ri GR24 2d vs GR24 2d ctrl
7_AGTCAA_L004


title: Control time point 1h replicate 3

description:
RAW Ri GR24 1h vs GR24 1h ctrl
6_CTTGTA_L004

value: 1 hour


title: Control time point 2 days replicate 2

description:
RAW Ri GR24 2d vs GR24 2d ctrl
11_GTCCGC_L004


title: GR24 time point 1h replicate 3

description:
RAW Ri GR24 1h vs GR24 1h ctrl
3_ACAGTG_L004


title: Control time point 1h replicate 2

description:
RAW Ri GR24 1h vs GR24 1h ctrl
5_CAGATC_L004


title: Control time point 1h replicate 1

description:
RAW Ri GR24 1h vs GR24 1h ctrl
4_GCCAAT_L004


title: GR24 time point 14 days replicate 3

description:
RAW Ri GR24 14d vs GR24 14d ctrl
21_CGTACG_L004


title: GR24 time point 1h replicate 1

description:
RAW Ri GR24 1h vs GR24 1h ctrl
1_CGATGT_L004


title: GR24 time point 1h replicate 2

description:
RAW Ri GR24 1h vs GR24 1h ctrl
2_TGACCA_L004


title: Control time point 7 days replicate 3

description:
RAW Ri GR24 7d vs GR24 7d ctrl
18_GGCTAC_L004


title: Small_RNA_Cells_01

city: Liege

first: Ingrid

last: Struman

address: Avenue de l'Hôpital, 1

department: BMGG

country: Belgium

institute: GIGA-R

data_processing:
All trimming was performed using Trimmomatic
Coding genes were identified after mapping Total RNA libraries using STAR against CRGh38
MicroRNAs were identified after mapping Small RNA libraries against miRbase v21 using bowtie2
PiwiRNAs were identified after mapping Small RNA libraries against piRbase using bowtie2
All the other ncRNA species were identified after mapping both Total and Small RNA libraries to non-coding genome available from ESEMBL using bowtie2
Species were separated using an inhouse script by RNA class
Genome_build: miRBase/piRbase/GRCh38/ncRNA genome

Supplementary_files_format_and_content:
Files *.combined.txt → count table of genes post mapping and RNA class stratification found in all or any compartments
Files *.only_in_cells.txt → count table of genes post mapping and RNA class stratification found only in cells
Files *.only_in_exos.txt → count table of genes post mapping and RNA class stratification found only in exosomes
Files *Significantly_DOWN_in_Exos.txt → EdgeR results for relative enrichment; normalized data of Fold Change, Log count per million, p-value, FDR-corrected pvalue for genes significantly enriched in cells
Files *Significantly_UP_in_Exos.txt → EdgeR results for relative enrichment; normalized data of Fold Change, Log count per million, p-value, FDR-corrected pvalue for genes significantly enriched in exosomes

source_name: HUVEC cells

growth_protocol: HUVECs were cultured in Endothelial Cell Growth Media-2 (EGM2) (Lonza, Germany) supplemented with Supreme Serum (Lonza, US) 5% (v/v) exosome depleted (exosomes were depleted from the serum by overnight centrifugation at 110.000 g and 4ºC). Cells were incubated at 37ºC and 5% CO2 up to passage 10. For the exosome production, cells were seed in three T75 flasks in 10 ml of media so that 72 h later they would have reached 85-90% confluence. The supernatant was then recovered and exosomes were purified by sequential ultracentrifugation: the media was first centrifuged at 2000 g for 20 minutes at 4ºC to remove unattached cells followed by a second round of centrifugation at 12,000 g (45 minutes at 4ºC) to remove cell debris and large vesicles. The supernatant was then collected and passed through a 0.2 μm filter and ultracentrifuged at 110,000 g for 2h at 4ºC to pellet exosomes (Beckman Coulter  Opitima L-90K, SW32 Rotor). The pellet was washed with PBS to remove any possible co-precipitated protein complexes, and with a final round of centrifugation at 110,000 g for 2h at 4ºC, the pellet was recovered and stored in PBS at -80ºC.

extract_protocol:
miRNEASY RNA extraction kit, Quiagen
TruSeq Small RNA Library Prep Kit (IRS-200-0012, llumina) and TruSeq RNA Library Prep Kit (RS-122-2001, Illumina)

value: HUVEC

tag: source

value: Cells

tag: molecule subtype

value: Cellular RNA, small RNA


title: Total_RNA_Exos_03

source_name: HUVEC Exosomes

value: Exosomes

value: Exosomal RNA, Total RNA


title: Total_RNA_Exos_02


title: Total_RNA_Cells_01

value: Cellular RNA, Total RNA


title: Total_RNA_Cells_02


title: Small_RNA_Exos_01

value: Exosomal RNA, small RNA


title: Small_RNA_Exos_02


title: SOD1 2

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

data_processing:
Reads were trimmed to have a length of 25 nts
Genome_build: miRBase v19.0

source_name: Human neuroblastoma cells

growth_protocol: SH-SY5Y cells, either untransfected or stably transfected with cDNAs coding for wild type SOD1 or the mutant SOD1(G93A) were cultured in D-MEM high glucose medium, 10% fetal bovine serum (FBS), 2.5 mM L-glutamine, 100 U/ml penicillin, and 100 µg/ml streptomycin (all products were purchased by Euroclone) at 37°C with 5% CO2.

extract_protocol:
total RNA was extracted using TRIzol (Invitrogen) according to the manufacturer’s instructions.
Enriched RNA samples were processed using the Small RNA Expression Kit according to the manufacturer’s protocol (Small RNA expression kit, rev. C, Applied Biosystems). RNA was first hybridized and ligated with the adapter mix “A”, subsequently reverse transcribed and treated with RNAse H. The obtained cDNA libraries were PCR amplified, purified and size-selected by PAGE, resulting in libraries containing inserted small RNA sequences of 20–40 bp length. Size, integrity and purity of the libraries were verified by the Agilent 2100 Bioanalyzer (Agilent Technologies). cDNA libraries were barcoded using the Solid RNA barcoding kit and amplified onto beads using emulsion PCR.

tag: neuroblastoma cell line

value: wild type SOD1


title: Small_RNA_Cells_02


title: SOD1(G93A) 1

value: mutant SOD1(G93A)


title: SOD1 4


title: SOD1 1


title: SOD1 3


title: SOD1(G93A) 2


title: SOD1(G93A) 3


title: WT-mStromal-SVF-NT

city: San Diego

first: Ezra

last: Wiater

address: 10010 N Torrey Pines Rd

department: PBL

institute: Salk Institute For Biological Studies

data_processing:
MiSeq Generation of fastq files
tophat2 alignment
cuffdiff alignment
Genome_build: mm10
Supplementary_files_format_and_content: .diff file from cuffdiff comparing all four samples

molecule: polyA RNA

organism: Mus musculus

source_name: Primary SVF cells from bone stromal cells

extract_protocol:
total RNA extracted with Qiagen Rneasy kit
polyA RNA isolated and library prepared with NEBnext Ultra kit

value: Wild-type mice

tag: tissue

value: Primary bone marrow stromal SVF cells

value: Untreated


title: WT-mStromal-SVF-FSK

value: 2 hours FSK treatment


title: Het-mStromal-SVF-FSK

value: CRTC2-/- CRTC3-/+ mice


title: Het-mStromal-SVF-NT


title: OVCA_negative_supernatant

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were aligned to the transcriptome file with bwa v .0.5.9 with default parameters, converted to .bam format by samtools 0.1.19
Reads aligning to each transcript were counted with samtools v.0.1.19 idxstats,
Genome_build: transcripts as of March 2013, plus ERCC spike in probes and mitochondrial sequences.  File name included in submission is "human_refgu_ERCC.txt"
Supplementary_files_format_and_content: the total number of mapped reads per sample was used to convert the read counts for each transcript in each sample to RPM
Supplementary_files_format_and_content: mapped reads per million mapped reads per sample

source_name: OVCA (Ovarian Cancer Cell Line)

growth_protocol: NK cells were cultured in RPMI 1640 medium containing 10% fetal bovine serum (FBS) and supplemented with 10 ng/ml human IL-2 (Peprotech).  Generation of NK cell conditioned tissue culture supernatants: NK cells cultured in IL-2 were incubated with 250 ng/ml PDGF-DD (R&D Systems) in 24-well plates for 16h in the presence of 1 μg/ml IgG1 (NKDD+IgG supernatant) or blocking anti-NKp44 3.43.14 mAb (NKDD+αNKp44 supernatant). After 16h, supernatants were pooled, centrifuged and filtered to remove cellular debris, and then stored at -80°C until further use.

extract_protocol:
Total RNA was isolated using Trizol followed by Qiagen RNAeasy columns.
500 ng total RNA was used to make Illumina libraries using the TruSeq Stranded Total RNA library prep kit. Libraries were sequenced on an Illumina HiSeq 1000, single-end 50 bp run, to a sequencing depth of between 28 million and 60 million mapped reads per sample.

treatment_protocol: NK cell stimulations: NK cells were stimulated with 250 ng/ml PDGF-DD or PMA + ionomycin (PMA/i) for 8h or left unstimulated in 24-well plates prior to RNA isolation. Cancer cell-line treatments: Cancer cell-lines (Meljuso, Colo38, MCF7 and OVCA) were cultured in RPMI supplemented with 10% bovine calf serum (complete medium) or with NK cell-conditioned tissue culture supernatant (NKDD+IgG or NKDD+αNKp44) diluted 1:2 in complete medium for 48h before RNA isolation.

tag: cell type

value: tumor cell

value: control sup, RPMI + 10% BCS + 250ng/ml PDGF-DD

value: OVCA (Ovarian Cancer Cell Line)


title: Meljuso_NKDD_supernatant

source_name: Meljuso (Melanoma Cell Line)

value: sup from NK cells stimulated with 250 ng/ml PDGF-DD in RPMI + 10% BCS

value: Meljuso (Melanoma Cell Line)


title: OVCA_media

value: RPMI + 10% BCS


title: Meljuso_negative_supernatant


title: OVCA_NKDD_supernatant


title: MCF_NKDD_supernatant

source_name: MCF (Breast Cancer Cell Line)

value: MCF (Breast Cancer Cell Line)


title: Meljuso_media


title: MCF_negative_supernatant


title: COLO38_NKDD_supernatant

source_name: COLO38 (Melanoma Cell Line)

value: COLO38 (Melanoma Cell Line)


title: SOD1(G93A) 4


title: MCF_media


title: COLO38_media


title: COLO38_negative_supernatant


title: D5_NK_PMA_ionomycin

source_name: Donor 5

value: primary NK cells

value: 8h stimulation with PMA/ionomcyin


title: D5_NK_IL_2_media


title: D5_NK_PDGF_DD

value: 8h stimulation with 250ng/ml PDGF-DD (R&D Systems)


title: D4_NK_PMA_ionomycin

source_name: Donor 4


title: D4_NK_PDGF_DD_2


title: D4_NK_IL_2_media_2


title: D3_NK_IL_2_media

source_name: Donor 3


title: D3_NK_PDGF_DD


title: D3_NK_PMA_ionomycin


title: AF1_NK_PMA_ionomycin

source_name: Donor AF3


title: AF1_NK_PDGF_DD

source_name: Donor AF2


title: AF1_NK_IL_2_media

source_name: Donor AF1


title: ChIP Ad4BP/SF-1 cAMP

city: Fukuoka

first: Tetsuya

last: Sato

address: 3-1-1, Maidashi Higashi-ku

country: Japan

institute: Kyushu University

library_source: genomic

data_processing:
Read quality was checked for each sample using FASTQC version 0.11.5.
Reads of ChIP-seq samples were mapped to Mus. musculus reference genome (UCSC version mm10) using bowtie version 0.12.8 with the option ‘-m1 -e 100 -n 3 -l 30’.
The MACS program version 1.4.2 20120305 with the option '--nomodel --shiftsize=70' was then used to identify peaks and regions of Ad4BP/SF-1 enrichment.
Genome_build: mm10
Supplementary_files_format_and_content: bed file with peaks

molecule: genomic DNA

source_name: mouse Leydig cells

growth_protocol: Mouse Leydig cells prepared from 9-week-old male ICR mice were cultured in DMEM supplemented with 10% FBS and 1 x penicillin-streptomycin on collagen type I-coated dishes.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample prep master mix set 1 Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 12 cycles and library fragments of 300 - 700 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: ICR

tag: Sex

value: Male

tag: age

value: testis

value: Leydig


title: Input DNA


title: 2Pseq_Pabpn1_dox-3day_rep1

city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

institute: Nagoya University

data_processing:
library strategy: 2P-seq
2P-seq samples were analyzed by Illumina NextSeq.
(2P-seq read processing) Reads were first quality filtered by trimmed of adapters with Trimmomatic (Bolger et al., 2014) and A stretches (>5 As)  were removed if they were immediately downstream of first sequenced nucleotide. We interpreted these events as polyA tails that due to reverse transcription errors or biological reasons had a non-As added to the cDNA. Next, we mapped either filtered reads (set A) or filtered reads with the first 15 nts trimmed (set B) to the mm9 genome using STAR aligner, end-to-end mode. The trimming of first 15 nt was done to ensure that reads were not going to be lost due to mismatches at the 5’ end, which may involve non-templated nucleotides (such as uridines), which are added to some termination events. For both sets, the first mapped nucleotide was considered the cleavage site. The two mapped libraries were combined as follows. If the read only aligned in set A or set B, the cleavage site was used as is. If the read aligned in both set A and set B, we subjected the mapped site to one further test. If the mapped cleavage site in set A overlaps the mapped cleavage site minus 15 nucleotides in set B, the position in set A was used. However, if the mapped cleavage site in set A differed substantially from the read in set B, we chose the site in set A as the mapped site. We attributed changes for this subset to the shorter read being harder to find exact matches, so preferred the mapped position of the longer read. With the combined mapped cleavage sites, we then applied an internal priming filter, in which we removed reads with at least 7 adenosines in the 10 nucleotides 3’ of the cleavage site, or 13 adenosines in the downstream 20 nucleotides. The remaining cleavage sites were filtered so that it must have at least 2 different reads mapping to it and also to not overlap B2 SINE elements. Finally, we scored reads as PAS containing or not PAS containing by surveying the 80 nucleotides upstream of the cleavage site for the presence of the top 36 PAS motifs, as described in (Almada et al., 2013). Specifically, the top 2 canonical PAS motifs are AATAAA or ATTAAA. Next, we also look for known variants, AGTAAA or TATAAA. We subsequently look for the next 8 most frequent sites or PAS8 (AATATA, AATACA, CATAAA, GATAAA, AATGAA, ACTAAA, AAGAAA, AATAGA). Finally we look for the remaining 24 PAS variants.
(Cleavage cluster pipeline) Cleavage sites from biological replicates of 2P-seq datasets were collapsed. Sites within 25 nucleotides of each other on the same strand were merged using Bedtools mergeBed (Langmead et al., 2009). The tentative clusters were further merged across all 2P-seq datasets to create a combined cluster set with mergeBed, but this time only if they overlapped, creating a combined list of cleavage clusters. Next we assigned whether the cleavage cluster was a PAS-linked or PAS independent cluster. To do this, the most abundant cleavage site within a cluster was called the max site. We looked up to 100 nucleotides upstream of the max site and looked for one of PAS 36 motifs. Those with PAS36 motifs were called PAS-linked clusters whereas those without were not PAS-independent clusters. Robust clusters were those where at least two independent libraries had non-zero reads; genes with premature clusters were defined as genes with robust clusters overlapped intron 1 of the gene.
Genome_build: mm9
Supplementary_files_format_and_content: Bw files for both strands.

source_name: Pabpn1 CKO, dox- (Pabpn1-), 3day

growth_protocol: V6.5 mouse embryonic stem cells were grown under standard conditions without feeders. Pabpn1 CKO clones derived from V6.5 mESCs were maintained in 1 μg/ml of doxycycline.

extract_protocol:
Total RNA was isolated with TRIzol Reagent.
2P-Seq was performed as described in (Spies et al., 2013). Briefly, total RNA is poly(A) selected using oligo-dT dynabeads. Subsequently, RNA was cleaved with trace levels of RNase T1 for 20 minutes at 22oC, inactivated, and cleaned up with an ethanol precipitation. The resulting RNA was reverse transcribed using IW-RT1p and the size selected for 200-400 nts on a polyacrylamide gel. Next the cDNA was circularized using CircLigase II (Epicentre), PCR amplified with primers IW-PCR-F.1 and IW-PCR-RPI, and further size selected to remove adapters, before sequencing from the poly(A) tail using IW-Seq-PE1.1 in single end read mode on the Illumina NEXT-Seq.

treatment_protocol: Cells were maintained or removed from doxycycline for 3 days.

value: Embryonic stem cells

tag: genotype and drug

value: Pabpn1 CKO


title: 2Pseq_Pabpn1_dox-3day_rep2


title: 2Pseq_Pabpn1_dox+3day_rep2

source_name: Pabpn1 CKO, dox+ (Pabpn1+), 3day

tag: treated with

value: doxycycline for 3 days


title: 2Pseq_Pabpn1_dox+3day_rep1


title: 2Pseq_dox-_U1AMO_rep2

description: Exosc3 CKO, dox- (Exosc3-), 2day, U1 AMO

data_processing:
Library strategy: 2P-seq
2P-seq samples were analyzed by Illumina NextSeq.
(2P-seq read processing) Reads were first quality filtered by trimmed of adapters with Trimmomatic (Bolger et al., 2014) and A stretches (>5 As)  were removed if they were immediately downstream of first sequenced nucleotide. We interpreted these events as polyA tails that due to reverse transcription errors or biological reasons had a non-As added to the cDNA. Next, we mapped either filtered reads (set A) or filtered reads with the first 15 nts trimmed (set B) to the mm9 genome using STAR aligner, end-to-end mode. The trimming of first 15 nt was done to ensure that reads were not going to be lost due to mismatches at the 5’ end, which may involve non-templated nucleotides (such as uridines), which are added to some termination events. For both sets, the first mapped nucleotide was considered the cleavage site. The two mapped libraries were combined as follows. If the read only aligned in set A or set B, the cleavage site was used as is. If the read aligned in both set A and set B, we subjected the mapped site to one further test. If the mapped cleavage site in set A overlaps the mapped cleavage site minus 15 nucleotides in set B, the position in set A was used. However, if the mapped cleavage site in set A differed substantially from the read in set B, we chose the site in set A as the mapped site. We attributed changes for this subset to the shorter read being harder to find exact matches, so preferred the mapped position of the longer read. With the combined mapped cleavage sites, we then applied an internal priming filter, in which we removed reads with at least 7 adenosines in the 10 nucleotides 3’ of the cleavage site, or 13 adenosines in the downstream 20 nucleotides. The remaining cleavage sites were filtered so that it must have at least 2 different reads mapping to it and also to not overlap B2 SINE elements. Finally, we scored reads as PAS containing or not PAS containing by surveying the 80 nucleotides upstream of the cleavage site for the presence of the top 36 PAS motifs, as described in (Almada et al., 2013). Specifically, the top 2 canonical PAS motifs are AATAAA or ATTAAA. Next, we also look for known variants, AGTAAA or TATAAA. We subsequently look for the next 8 most frequent sites or PAS8 (AATATA, AATACA, CATAAA, GATAAA, AATGAA, ACTAAA, AAGAAA, AATAGA). Finally we look for the remaining 24 PAS variants.
(Cleavage cluster pipeline) Cleavage sites from biological replicates of 2P-seq datasets were collapsed. Sites within 25 nucleotides of each other on the same strand were merged using Bedtools mergeBed (Langmead et al., 2009). The tentative clusters were further merged across all 2P-seq datasets to create a combined cluster set with mergeBed, but this time only if they overlapped, creating a combined list of cleavage clusters. Next we assigned whether the cleavage cluster was a PAS-linked or PAS independent cluster. To do this, the most abundant cleavage site within a cluster was called the max site. We looked up to 100 nucleotides upstream of the max site and looked for one of PAS 36 motifs. Those with PAS36 motifs were called PAS-linked clusters whereas those without were not PAS-independent clusters. Robust clusters were those where at least two independent libraries had non-zero reads; genes with premature clusters were defined as genes with robust clusters overlapped intron 1 of the gene.
Genome_build: mm9
Supplementary_files_format_and_content: Bw files for both strands. Summary txt file includes information of 2P sites.

source_name: Exosc3 CKO mESC

growth_protocol: V6.5 mouse embryonic stem cells were grown under standard conditions without feeders. Exosc3 CKO clones derived from V6.5 mESCs were maintained in 0.1 μg/ml of doxycycline.

treatment_protocol: Cells were maintained or removed from doxycycline for 3 days. For U1 experiments, Exosc3 CKO cells were either kept in doxycycline or removed from doxycycline for 1 day and 16 hours. Cells were subsequently trypsinized, washed twice in PBS, and 5 million cells were nucleofected with 15 μM concentration of U1 AMO or Scr AMO. Cells were seeded onto 10 cm dishes, and total RNA was harvested 8 hours later in TRIzol Reagent.

tag: genotype

value: Exosc3 CKO

value: dox-, 2day, U1 AMO


title: 2Pseq_dox-_U1AMO_rep1


title: 2Pseq_dox+_U1AMO_rep1

description: Exosc3 CKO, dox+ (Exosc3+), 2day, U1 AMO

value: dox+, 2day, U1 AMO


title: 2Pseq_dox+_U1AMO_rep2


title: D4_NK_PDGF_DD


title: 2Pseq_dox-_ScrAMO_rep2

description: Exosc3 CKO, dox- (Exosc3-), 2day, Scr AMO

value: dox-, 2day, Scr AMO


title: D4_NK_IL_2_media


title: D4_NK_PMA_ionomycin_2


title: 2Pseq_dox-3day_rep1

description: Exosc3 CKO, dox- (Exosc3-), 3day

value: dox-, 3day


title: 2Pseq_dox+3day_rep2

description: Exosc3 CKO, dox+ (Exosc3+), 3day

value: dox+, 3day


title: 2Pseq_dox-3day_rep2

description: Exosc3 CKO, dox- (Exosc3-), 3day


title: 2Pseq_dox+_ScrAMO_rep1

description: Exosc3 CKO, dox+ (Exosc3+), 2day, Scr AMO

value: dox+, 2day, Scr AMO


title: 2Pseq_dox+3day_rep1

description: Exosc3 CKO, dox+ (Exosc3+), 3day


title: RNAseq_Exosc3_CKO_dox-_rep2

description: Exosc3 CKO, dox- (Exosc3-) 3 days

data_processing:
RNA-seq samples were analyzed by Illumina NextSeq.
All analyses were carried out using UCSC (NCBI37/mm9) mouse gene annotations. Paired end reads were first mapped to ribosomal RNA and various repetitive sequences such as U1 snRNA using Bowtie2 (Langmead and Salzberg, 2012), and then subsequently mapped to the mouse UCSC transcriptome and genome using STAR aligner (Dobin et al., 2013). The ensuing reads were filtered for uniquely mapping, properly paired reads, and subsequently potential PCR duplicates were removed using the Picard Suite MARKDUP (http://broadinstitute.github.io/picard). In genome browser shots, the reads are displayed. For metaplot alignments, we further processed the reads by selecting read 2 of the paired-end read (same direction as the RNA), and filtered away any overlapping miRNAs, tRNAs, repeats from repeatMasker, or snoRNA.
The number of reads per transcript was counted by using intersectBed of the Bedtools suite (Quinlan and Hall, 2010), only allowing for exonic or spliced reads. After filtering out for intervals with low numbers, differential transcripts were called using edgeR, where we normalized libraries using UQ normalization.
Genome_build: mm9
Supplementary_files_format_and_content: Bw files for both strands. Summary txt file includes normalized FPKM gene counts.

extract_protocol:
Total RNA was isolated with TRIzol Reagent and treated with DNase Turbo (Ambion AM2238).
RNAs that passed a Bioanalyzer RIN score of 8.5 were subsequently used to prepare libraries. RNAs were depleted of ribosomal RNAs using the RiboZero rRNA removal kit (Epicentre MRZH116), converted into stranded RNA-Seq libraries with the Illumina Tru-Seq kit (Illumina RS-122-2101), and sequenced in paired end read mode using the Illumina NEXT-Seq.

value: dox-, 3 day


title: RNAseq_Exosc3_CKO_dox+_rep2

description: Exosc3 CKO, dox+ (Exosc3+) 3 days

value: dox+, 3 day


title: WT_Lsd1_IP

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC mm9 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC mm9 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

source_name: embryonic stem cell

growth_protocol: ESCs were grown in N2B27 media supplemented with MEK inhibitor, GSK3 inhibitor, and LIF (2i/LIF).

extract_protocol:
RNA was extracted using Trizol reagent (Life technologies). RNAse free DNaseI (Sigma) was used to eliminate DNA contamination and the treated RNA was purified with RNeasy mini kit (Qiagen).
For ChIP, ESCs were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin were sonicated using a E220 focused-ultrasonicator (Covaris). 100 µg sheared chromatin, 5 µg antibody, and 50 µl protein A/G beads (Santa Cruz) were used for each immunoprecipitation. Immunoprecipitated DNA were purified after washing, eluting, and reverse-crosslinking and submitted for library preparation.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit

treatment_protocol:
For induction of the exit of naive pluripotency, 2i+LIF cultured ESCs were passaged to 0.1% gelatin (Stem cell technologies) coated plates and cultured for more than 2 passages in FBS+LIF media containing Dulbecco's modified Eagle's medium (DMEM) (Corning) supplemented with 15% FBS (Gemini), 1×Penicillin-Streptomycin (Life technologies), 1× Glutamax (Life technologies), 1× MEM non-essential amino acids (Life technologies), 1× β-mercaptoethanol (Life technologies), and 1.8×103 U/ml of LIF (Gemini).
For shRNA knockdown, ESCs were infected with lentivial shRNA in the presense of 10ug/ml polybrene for 12 hours and then selected with 2 ug/ml puromycin for 48h before harvest for ChIP-seq or RNA-seq experiments.

value: embryonic stem cell

tag: cell line

tag: genotype/variation

value: Wildtype/WT

tag: chip antibody

value: Lsd1 (Abcam 17721)


title: WT_FBS_nonTsh_RNA_2

tag: shRNA

value: nonTsh


title: WT_Mll4_1

value: Mll4 (Homemade, #825)


title: WT_Lsd1_input


title: ChIP Ad4BP/SF-1 veh

tag: strain

value: ICR

value: Male

value: testis

value: Leydig


title: WT_FBS_input


title: WT_FBS_nonTsh_RNA_1


title: WT_FBS_RNA_3


title: 2Pseq_dox+_ScrAMO_rep2

value: Embryonic stem cells

value: Exosc3 CKO

tag: treatment


title: WT_FBS_RNA_2


title: WT_FBS_RNA_1


title: WT_FBS_H3K4me2

value: H3K4me2 (Homemade, #27)


title: WT_FBS_H3K4me3

value: H3K4me3 (Homemade, #28)


title: WT_FBS_H3K4me1

value: H3K4me1 (Homemade, #24)


title: WT_FBS_H3K27ac


title: RNAseq_Exosc3_CKO_dox-_rep1

description: Exosc3 CKO, dox- (Exosc3-) 3 days


title: WT_Mll4_2


title: RNAseq_Exosc3_CKO_dox+_rep1

description: Exosc3 CKO, dox+ (Exosc3+) 3 days


title: 2Pseq_dox-_ScrAMO_rep1

value: dox-, 2day, Scr AMO


title: WT_2i_nonTsh_RNA_1


title: WT_2i_input


title: WT_2i_RNA_3


title: WT_2i_nonT_RNA_2


title: WT_2i_RNA_1


title: WT_2i_H3K4me3


title: WT_2i_H3K4me2_2


title: WT_2i_H3K4me1_2


title: WT_2i_H3K4me2


title: WT_2i_H3K27ac


title: Mll4dSET_Mll4

value: MLL4 SET deletion/MLL4dSET


title: Mll4dSET_FBS_input


title: Mll4dSET_FBS_RNA_4


title: Mll4dSET_FBS_RNA_3


title: Mll4dSET_FBS_RNA_2


title: Mll4dSET_FBS_RNA_1


title: Mll4dSET_FBS_H3K4me2


title: Mll4dSET_2i_RNA_4


title: Mll4dSET_2i_RNA_3


title: Mll4dSET_FBS_H3K4me1


title: Mll4dSET_FBS_H3K27ac


title: Mll4dSET_2i_RNA_2


title: Mll4dSET_2i_H3K4me3


title: Mll4dSET_2i_H3K4me2_2


title: Mll4dSET_2i_RNA_1


title: WT_2i_H3K4me1


title: Mll4dSET_2i_H3K4me1_2


title: Mll4dNT_FBS_input

value: Mll4 NT deletion/Mll4dNT


title: Mll4dSET_2i_H3K4me2

value: embryonic stem cell


title: Mll4dSET_2i_H3K4me1


title: Mll4dNT_FBS_RNA_4


title: Mll4dSET_2i_H3K27ac


title: Mll4dNT_Mll4


title: Mll4dNT_FBS_RNA_2


title: Mll4dNT_FBS_RNA_3


title: Mll4dNT_FBS_H3K4me2


title: Mll4dNT_FBS_H3K4me3


title: Mll4dNT_FBS_RNA_1


title: Mll4dSET_FBS_H3K4me3


title: Mll4dNT_2i_input


title: Mll4dNT_FBS_H3K4me1


title: Mll4dNT_FBS_H3K27ac


title: Mll4dSET_2i_input


title: Mll4dNT_2i_RNA_3


title: Mll4dNT_2i_RNA_4


title: Mll4dNT_2i_RNA_2


title: Mll4dNT_2i_RNA_1


title: Mll4dNT_2i_H3K4me3


title: Mll4dNT_2i_H3K4me2_2


title: Mll4dNT_2i_H3K4me1_2


title: Mll4dNT_2i_H3K4me1


title: Mll4dNT_2i_H3K27ac


title: Mll4KO_Mll4_2

value: Mll4 knockout/Mll4KO


title: Mll4KO_Mll4_1


title: WT_2i_RNA_2

value: Wildtype/WT


title: Mll4KO_FBS_RNA_3


title: Mll4KO_FBS_input


title: Mll4KO_FBS_RNA_4


title: Mll4KO_FBS_Lsd1sh_H3K4me1


title: Mll4KO_FBS_nonTsh_RNA_1

value: nonTsh


title: Mll4KO_FBS_nonTsh_H3K4me1


title: Mll4KO_FBS_Lsd1sh_RNA_2


title: Mll4KO_FBS_nonTsh_H3K27ac


title: Mll4KO_FBS_Lsd1sh_RNA_1


title: Mll4KO_FBS_nonTsh_RNA_2


title: Mll4dNT_2i_H3K4me2


title: Mll4KO_FBS_Lsd1sh_H3K27ac


title: Mll4KO_FBS_H3K4me3


title: Mll4KO_FBS_RNA_2


title: Mll4KO_FBS_RNA_1


title: Mll4KO_FBS_H3K4me2


title: Mll4KO_FBS_H3K4me1


title: Mll4KO_2i_nonTsh_RNA_1


title: Mll4KO_FBS_H3K27ac


title: Mll4KO_2i_nonTsh_H3K4me1_2


title: Mll4KO_2i_nonTsh_H3K27ac_2


title: Mll4KO_2i_nonTsh_H3K4me1


title: Mll4KO_2i_input


title: Mll4KO_2i_RNA_3


title: Mll4KO_2i_RNA_2


title: Mll4KO_2i_RNA_4


title: Mll4KO_2i_RNA_1


title: Mll4KO_2i_nonTsh_RNA_2


title: Mll4KO_2i_Lsd1sh_RNA_1


title: Mll4KO_2i_Lsd1sh_H3K27ac_2


title: Mll4KO_2i_H3K27ac


title: Mll4KO_2i_H3K4me2


title: Mll4KO_2i_H3K4me3


title: Mll4KO_2i_Lsd1sh_H3K4me1


title: LNCaP HS-5 CM, 3

city: Richardson

first: Nikki

last: Delk

address: 800 West Campbell Road

department: Biological Sciences

institute: University of Texas at Dallas

data_processing:
Single-end 76 bp read length Fastq files were checked for quality using fastqc/v0.11.2 and fastq_screen/v0.4.4
Reads were quality trimmed using fastq-mcf (ea-utils/v1.1.2-806).
Trimmed fastq files were mapped to hg19 (UCSC version from igenomes)
Duplicates were marked using picard-tools/v1.127
Read counts were generated using featureCounts (subread/v1.4.6).
Normalized read counts and differentially expressed genes found using edgeR/v3.2.4
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited txt files that includes raw read counts for each sample per gene

source_name: LNCaP

growth_protocol: All cells  were cultured in DMEM (Gibco/Thermo Scientific; 1185-092) supplemented with 10% (v/v) fetal bovine serum essence (FBS; Seradigm; 3100-500), 0.4mM L-glutamine (L-glut; Gibco/Invitrogen; 25030-081), and 10U/ml penicillin G sodium and 10 mg/ml streptomycin sulfate (pen-strep; Gibco/ Invitrogen; 15140-122).

extract_protocol:
RNA was harvested using GeneJET RNA Purification Kit according to the manufacturer’s instructions (Thermo Scientific; K0732), RNA quantitiy and quality was then verified useng Biotek plate reader Gen 5 software, microspots protocol.
One microgram of total DNAse-treated RNA was prepared with DNAse 1, RNase-free(Thermo, #EN0521)

treatment_protocol: PCa cell lines were treated with vehicle control (PBS) or 25 ng/ml IL-1β (R&D Systems; 201-LB-005); or PCa cell lines were grown in bone marrow stromal cell conditioned medium (CM) from HS-5 bone marrow stromal cells for 3 days and DMEM served as the growth control. At Day 3, total RNA was extracted from 3 biological replicates (1, 2, 3 ) for RNA-sequencing.

value: Prostate

value: LNCaP

tag: time

value: 3 days


title: PC3 CM (control), 3

value: grown in DMEM medium (control)


title: Mll4KO_2i_H3K4me2_2


title: PC3 CM (control), 1


title: PC3 CM (control), 2


title: US-1501136_PID21071_IDH1_RNA-Seq_17Jun2015.Human

city: Kenilworth

first: Diane

last: Levitan

state: NJ

address: 2015 Galloping Hill Road

department: Translational Medicine

institute: Merck

data_processing:
Data was analyzed using the OmicSoft QC and FPKM pipeline. Data was normalized to the number of reads (FKPM), Upper Quartile normalized and Log2 transformed.
Genome_build: hg19
Supplementary_files_format_and_content: UMI corrected read counts per gene for each sample.

source_name: MRK-A 30mpk mouse 35 GB10

extract_protocol: TruSeq Stranded Total RNA RiboZero protocol

value: Xenograft tumor

value: Treated MRK-A 30 mpk

tag: model

tag: tumor type

value: Glioma

tag: mrna

value: mRNA

tag: bar code


title: US-1501147_PID21071_IDH1_RNA-Seq_17Jun2015.Human

source_name: MRK-A 30mpk mouse 36 GB10

tag: tissue


title: LNCaP CM (control), 3


title: LNCaP CM (control), 2


title: US-1501151_PID21071_IDH1_RNA-Seq_17Jun2015.Human

source_name: Vehicle mouse 6 GB10

value: Treated vehicle


title: LNCaP CM (control), 1


title: US-1501134_PID21071_IDH1_RNA-Seq_17Jun2015.Human

source_name: Vehicle mouse 15 GB10


title: Mll4KO_2i_Lsd1sh_RNA_2

tag: cell type


title: US-1501121_PID21071_IDH1_RNA-Seq_17Jun2015.Human

source_name: MRK-A 30mpk mouse 30 GB10


title: Mll4KO_2i_Lsd1sh_H3K27ac


title: Mll4KO_2i_H3K4me1_2

value: H3K4me1 (Homemade, #24)


title: US-1501111_PID21071_IDH1_RNA-Seq_17Jun2015.Human

source_name: Vehicle mouse 13 GB10


title: Mll4KO_2i_Lsd1sh_H3K4me1_2


title: PC3 PBS (Vehicle control), 2

value: phosphate buffered saline (PBS, vehicle control)


title: US-1501105_PID21071_IDH1_RNA-Seq_17Jun2015.Human

source_name: Vehicle mouse 17 GB10


title: US-1501142_PID21071_IDH1_RNA-Seq_17Jun2015.Human

source_name: MRK-A 30mpk mouse 37 GB10


title: LnCAP 25 ng/ml IL-1β, 2

value: 25 ng/ml IL-1β (R&D Systems; 201-LB-005)


title: DS-96106_PID21071_IDH1_RNA-Seq_17Jun2015.Human

source_name: 13 VEHICLE BT142


title: DS-96093_PID21071_IDH1_RNA-Seq_17Jun2015.Human

source_name: 19 VEHICLE BT142


title: LnCAP 25 ng/ml IL-1β, 3


title: LNCaP HS-5 CM, 2

value: grown in bone marrow stromal cell conditioned medium (CM) from HS-5 bone marrow stromal cells


title: LnCAP 25 ng/ml IL-1β, 1


title: DS-96083_PID21071_IDH1_RNA-Seq_17Jun2015.Human

source_name: 12 VEHICLE BT142


title: DS-96087_PID21071_IDH1_RNA-Seq_17Jun2015.Human

source_name: 30 MRK-A 30mpk BT142


title: LnCAP PBS (Vehicle control), 2


title: DS-96081_PID21071_IDH1_RNA-Seq_17Jun2015.Human

source_name: 26 MRK-A 30mpk BT142


title: LnCAP PBS (Vehicle control), 1


title: DS-96074_PID21071_IDH1_RNA-Seq_17Jun2015.Human

source_name: 20 VEHICLE BT142


title: DDX21 irCLIP from HeLa with ActD Biological replicate 2

city: Cambridge

first: Eliezer

last: Calo

state: MASSACHUSETTS

institute: Massachusetts Institute of Technology

description:
Protein enriched RNA
HS_HeLa_irCLIP_DDX21_ActD_minus.bw,HS_HeLa_irCLIP_DDX21_ActD_plus.bw

data_processing:
Sequencing reads were trimmed of 3' adaptors, collapsed for PCR duplicates, stripped of the 5' barcode, and mapped to the mouse (GRCh38) genome using STAR
RT stop identificaiton, gene assignment, and peak calling was performed as in FAST-iCLIP (PMID: 25411354)
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig file containing unique RT stops from the high confidence intersection of biological replicates of DDX21 irCLIP

source_name: HeLa Cells

growth_protocol: HeLa cells were cultured in DMEM with 10% FBS. DMSO or ActD treatments were carried out for 1 hour at 37C.

extract_protocol:
Lysates were clarified from sonicated HeLa cells and DDX21-RNA complexes were isolated with anti-DDX21 (Novus Bio: NB100-1718) antibody.
Libraries were prepared according to the irCLIP protocol (PMID: 27111506)

treatment_protocol: Cells were UV crosslinked at 254nm for 0.3J/cm^2 to in vivo fix RNA-RBP interactions

tag: agent

value: ActD

value: HeLa

tag: gender

value: female


title: DS-96057_PID21071_IDH1_RNA-Seq_17Jun2015.Human

source_name: 21 MRK-A 30mpk BT142


title: DDX21 irCLIP from HeLa with ActD Biological replicate 1


title: DDX21 irCLIP from HeLa with DMSO Biological replicate 2

description:
Protein enriched RNA
HS_HeLa_irCLIP_DDX21_DMSO_minus.bw,HS_HeLa_irCLIP_DDX21_DMSO_plus.bw

value: DMSO


title: DS-96028_PID21071_IDH1_RNA-Seq_17Jun2015.Human

source_name: 23 MRK-A 30mpkn BT142


title: DDX21 irCLIP from HeLa with DMSO Biological replicate 1


title: DS-96009_PID21071_IDH1_RNA-Seq_17Jun2015.Human

source_name: 28 MRK-A 30mpk BT142


title: D17-105114_K_d_S4

city: West Lafayette

first: Jyothi

last: Thimmapuram

state: IN

address: YONG 1022, 155 S. Grant Street

department: Bioinformatics Core

institute: Purdue University

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned against hg19 / ENSEMBL 75 using STAR v. 2.5.1b with the following flags -runThreadN 8 --runMode alignReads  with default ENCODE options except --alignIntronMin 10
Gene expression was quantitated using RSEM v. 1.2.30 with the following flags for all libraries: rsem-calculate-expression --paired-end --calc-pme --alignments -p 8  --forward-prob 0 against an annotation matching the STAR SA reference, with the exception of the positively-stranded CZ libraries, for which --forward-prob was set to 1. Posterior mean estimates (pme) of counts were retrieved, ribosomal RNA counts removed and expression in reads per kilobase of modeled exon per million mapped reads (RPKM) or transcripts per million (TPM) were computed on the remaining count matrices. Similar scripts and pipelines were used for ERCC and SIRV mapping and quantitation.
Genome_build: hg19 / ENSEMBL 75

source_name: Universal Human Reference RNA_K_d_S4

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: kit

value: Kapa RiboErase (K)

tag: state

value: heat degraded

tag: site


title: shBLACAT2#2

city: Guangzhou

first: Wang

last: He

state: Guangdong

address: 107th, Yanjiangxi Road

department: Urology

country: China

institute: Sun Yat-sen Memorial Hospital

description: polyA+ RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using TopHat v2.0.9
FPKM were calculated using a protocol from Anders S, et al., Bioinformatics 2015, 31(2):166-169 and Robinson MD, et al. Genome Biol 2010, 11(3):R25. 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.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM and count values for each Sample

source_name: bladder cancer cell line UM-UC-3

growth_protocol: UM-UC-3 cells were cultured in Dulbecco's modiﬁed eagle's medium (DMEM) (Hyclone). All culture medium were supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin, and 100 μg/ml streptomycin (HyClone, Thermo, USA). All cells were cultured in a humidified air atmosphere incubator with 5% CO2 at 37°C.

extract_protocol:
Total RNA from cells was isolated using Trizol reagent (Life techologies) and puriﬁed with GeneJET RNA purification kit (Thermo) and RNase-free DNase set (QIAGEN) following manufacturer’s instructions.RNA electrophoresis was conducted to inspect RNA integration.
The library was prepared with TruSeq Stranded mRNA LT Sample Prep Kit (Cat. No.15032612,Illumina) according to manufacturer’s instructions.

treatment_protocol: UM-UC-3 cells were infected by lentivirus expressing scramble shRNA or shRNAs targeting BLACAT2 with the presence of polybrene (Sigma-Aldrich) and selected by puromycin (Sigma-Aldrich) for 2 weeks to obtain stable expression cell lines.

value: BLACAT2 was depleted with shRNA#2

tag: cell line

value: bladder cancer cell line UM-UC-3


title: shBLACAT2#1

description: polyA+ RNA

value: BLACAT2 was depleted with shRNA#1


title: shControl

description: polyA+ RNA

value: Negative control


title: LnCAP PBS (Vehicle control), 3

source_name: LNCaP

value: Prostate

value: LNCaP

value: 3 days


title: D17-105112_K_i_S4

source_name: Universal Human Reference RNA_K_i_S4

value: intact


title: D17-105106_RZ_d_S4

source_name: Universal Human Reference RNA_RZ_d_S4

value: RiboZero Gold (RZ)


title: D17-105113_K_d_S4


title: Pineal Gland Night 42

city: New York

first: Marjan

last: Bozinoski

state: NY

address: 1305 York Avenue, Box 140

department: Physiology and Biophysics

institute: Weill Cornell Medicine

data_processing:
Illumina Casava 1.8.2. software used for basecalling.
Reads were aligned with the RNA-STAR aligner (v. 2.3.0e) , using the GRCh37/hg19  genome build. STAR aligner parameters used: --runThreadN 8  --outFilterMultimapNmax 1 --outSAMunmapped Within --outStd SAM. Quality control metrics were calculated and visualized using FastQC software and in-house written scripts, and no major artifacts or abnormalities were found. Gencode 19 annotation was used to qunatify the reads overlapping the genes.
Gene read counts were provided by R subreads package, (featureCounts function) with parameters specifying: paired-end reads, and reverse-complement for the second strand (-p, -S2).  Annotation for assigning the reads was derived from Gencode 19 annotation for GRCh37/hg19 genome build.  Differential expression analysis was performed using DESeq2 software package.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: human_FPKM.xlsx file includes FPKM values for all of the Samples

source_name: died at mid-night (23:00-01:00)

extract_protocol:
Pineal glands were obtained from NDRI (National Disease Research Interchange  (Pennsylvania Medical Center, Philadelphia, PA). Two glands were from individuals that died atmid-day (11:00-13:00) and four from deaths occurring at mid-night (23:00-01:00). Sampleswere stored at -80 o C until use. RNA was extracted from individual glands with Trizol (Invitrogen, Carlsbad,CA) and subsequently cleaned up using an RNeasy Micro Kit with on-column DNase treatment(Qiagen, Valencia, CA). The amount and quality of RNA were determined using a NanoDropspectrophotometer (NanoDrop, Wilmington, DE) and an Agilent 2100 Bioanalyzer (AgilentTechnologies, Santa Clara, CA), respectively. RIN values ranged from 7.3-8.7.
Ribodepleted Total RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pineal Gland


title: D17-105105_RZ_d_S4


title: Pineal Gland Night 39


title: Mll4KO_2i_nonTsh_H3K27ac

source_name: embryonic stem cell

value: embryonic stem cell

tag: genotype/variation

value: Mll4 knockout/Mll4KO

value: nonTsh

tag: chip antibody


title: Pineal Gland Night 41


title: Pineal Gland Day 38


title: D17-105104_RZ_i_S4

source_name: Universal Human Reference RNA_RZ_i_S4


title: D17-105103_RZ_i_S4


title: DS-96032_PID21071_IDH1_RNA-Seq_17Jun2015.Human

source_name: 15 VEHICLE BT142

value: Xenograft tumor

value: Treated vehicle

value: Glioma

value: mRNA


title: Pineal Gland Day 37


title: D17-105101_CR_d_S4

source_name: Universal Human Reference RNA_CR_d_S4

value: Takara/Clontech Ribogone (CR)

value: heat degraded


title: imb_koenig_2015_17_010307_JKRS17_KD_3

city: Mainz

first: Stefanie

last: Ebersberger

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

description:
bam from 2 instrument models: Illumina HiSeq 2500 and NextSeq 500
merge of 3 sequencing runs

data_processing:
Basic quality checks were applied to all sequenced reads using FastQC  (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Afterwards, iCLIP reads were filtered based on sequencing quality (Phred score) in the barcode region. Only reads with at most one position with a Phred score < 20 in the experimental barcode (positions 4 to 7) and without any position with a Phred score < 17 in the random barcode (positions 1 to 3 and 8 to 9) were kept for further analysis. The reads were then de-multiplexed based on the experimental barcode at positions 4 to 7 using Flexbar (version 2.4) without allowing mismatches (Dodt et al., 2012).  The following analysis steps were applied to all individual samples: Remaining adapter sequences were trimmed from the read ends using Flexbar (version 2.4) allowing one mismatch in 10 nt, requiring a minimal overlap of 1 nt between read and adapter as well as removing all reads with a remaining length of less than 24 nt (including the 9-nt barcode). After adapter trimming, quality checks were repeated on individual samples using FastQC. Afterwards, the first 9-nt of each read containing the barcode were trimmed off and added to the header of the read in the fastq file, such that the information is kept for downstream analysis.  Filtered and trimmed reads were mapped to the human genome (hg19/GRCh37) and its annotation (GENCODE release 19) (Harrow et al., 2012) using STAR (version 2.4.0h) (Dobin et al., 2013). When running STAR, up to two mismatches were allowed, soft-clipping was prohibited and only uniquely mapped, unspliced reads were kept for further analysis. Un-spliced reads were defined as reads mapping without N-stretches longer than 5 in the CIGAR string. The nucleotide position upstream of each aligned read was considered as the ‘crosslink nucleotide’, with each read counted as individual ‘crosslink event’.   After mapping and filtering, duplicate reads were marked in selected samples using the dedup function from bamUtil (version 1.0.7) (https://github.com/statgen/bamUtil), which defines duplicates as reads whose 5' ends map to the same position in the genome. We then removed all marked duplicates with an identical random barcode representing technical duplicates, while all real biological duplicates with different random barcodes were kept.  Samtools (Li et al., 2009) was used to sort and index the resulting bam files. Based on the bam files, bedgraph files were created, considering only the position upstream of the 5' mapping position of the read. bedgraph files were then transformed to bigWig format using bedGraphToBigWig of the UCSC tool suite (Kent et al., 2010).
Genome_build: hg19/GRCh37

source_name: U2AF65 knockdown replicate 3

extract_protocol:
Hela was lysed in 1ml lysis buffer followed by immunoprecipitation as described on previously published protocol (Huppertz et al., 2014; Sutandy et al., 2016)
in vivo iCLIP libraries were prepared from HeLa cells under U2AF65 KD and wild-type conditions according to the previously published protocol (Huppertz et al., 2014; Sutandy et al., 2016). For immunoprecipitation, we used 7.5 µg monoclonal anti-U2AF65 antibody produced in mouse (Sigma cat. no. U4758) per sample. Each iCLIP library was done in triplicates. The libraries were sequenced as single-end reads on an Illumina HiSeq 2500 and NextSeq 500 sequencing system.

value: HeLa

tag: technique

value: in vivo iCLIP

tag: iped-protein

tag: barcode

value: TACG


title: D17-105100_CR_i_S4

source_name: Universal Human Reference RNA_CR_i_S4


title: D17-105099_CR_i_S4


title: imb_koenig_2015_17_010307_JKRS17_KD_2

source_name: U2AF65 knockdown replicate 2

value: AGAA


title: D17-105098_CZ_d_S4

source_name: Universal Human Reference RNA_CZ_d_S4

value: SMARTer Pico (CZ)


title: D17-105111_K_i_S4

value: Kapa RiboErase (K)

value: intact


title: imb_koenig_2015_17_010307_JKRS17_KD_1

source_name: U2AF65 knockdown replicate 1

value: CGCC


title: D17-105097_CZ_d_S4


title: Pineal Gland Night 40

value: Pineal Gland


title: D17-105094_LX_d_S4

source_name: Universal Human Reference RNA_LX_d_S4

value: Lexogen RiboCop (LX)


title: imb_koenig_2015_17_010307_JKRS17_control_KD_2

source_name: wild type replicate 2

value: TTAA


title: imb_koenig_2015_17_010307_JKRS17_control_KD_3

source_name: wild type replicate 3

value: GGTC


title: D17-105093_LX_d_S4


title: D17-105095_CZ_i_S4

source_name: Universal Human Reference RNA_CZ_i_S4


title: D17-105102_CR_d_S4


title: imb_koenig_2015_17_010307_JKRS17_control_KD_1

source_name: wild type replicate 1

value: CGAG


title: previous_koenig_lujh32-combined_STAR_sample3

source_name: wild type replicate 3_3

value: CGGA


title: previous_koenig_lujh32-combined_STAR_sample2

source_name: wild type replicate 3_2

value: TGGC


title: imb_koenig_2015_12_01_JKRS13_Hela_RT30

source_name: replicate 1

value: ATCG


title: D17-105092_LX_i_S4

source_name: Universal Human Reference RNA_LX_i_S4


title: D17-105085_K_d_S3

source_name: Universal Human Reference RNA_K_d_S3

value: heat degraded


title: D17-105086_K_d_S3


title: D17-105091_LX_i_S4


title: previous_koenig_lujh32-combined_STAR_sample4

source_name: wild type replicate 3_4

value: HeLa


title: D17-105083_K_i_S3

source_name: Universal Human Reference RNA_K_i_S3


title: 9260B_Tissue

first: Jun

last: Zhu

address: 1 Gustave L. Levy Pl

department: Genetics and genomic sciences

institute: Icahn school of medicine at mount sinai

data_processing:
Sequencing reads were aligned to the human reference genome hg19 using TopHat.
Rresulting aligned reads were analyzed by Cufflinks with reference genome.
Cufflinks assembled the aligned reads into transcripts with reference genome and reported the expression of those transcripts in Fragments Per Kilobase of exon per Million fragments mapped (FPKM).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: GBM tumor tissue

extract_protocol:
Cells were lysed with Trizol reagent, and RNA was extracted according to manufacture instructions (Life Technologies). RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep Kit .
Poly-A enrichment library prep method was used. RNA libraries were prepared for sequencing using standard Illumina protocols.

value: GBM tumor tissue

tag: tumor stage

value: stage IV glioma tumors


title: 9260B_Sphere

source_name: GBM stem cells

value: GBM stem cells


title: D17-105084_K_i_S3


title: 9217_B_sphere


title: D17-105082_Q_d_S3

source_name: Universal Human Reference RNA_Q_d_S3

value: Qiagen GeneRead rRNA Depletion (Q)


title: D17-105080_Q_i_S3

source_name: Universal Human Reference RNA_Q_i_S3


title: 9217_A_tissue


title: D17-105081_Q_d_S3


title: D17-105079_Q_i_S3


title: 9217_B_tissue


title: 9217_A_sphere


title: 9212_B_tissue


title: D17-105076_LX_i_S2

source_name: Universal Human Reference RNA_LX_i_S2


title: 9212_B_sphere


title: D17-105075_LX_i_S2


title: previous_koenig_lujh32-combined_STAR_sample1

source_name: wild type replicate 3_1

value: in vivo iCLIP

value: GGTT


title: 9212_A_tissue


title: D17-105074_NE_d_S4

source_name: Universal Human Reference RNA_NE_d_S4

value: New England Biolabs NEBNext rRNA Depletion (NE)


title: D17-105072_NE_i_S4

source_name: Universal Human Reference RNA_NE_i_S4

value: intact


title: D17-105073_NE_d_S4


title: 7653_B_sphere


title: 10647C_Tissue


title: 7653_B_tissue


title: 9212_A_sphere


title: 10647C_Sphere


title: D17-105061_LX_i_S1

source_name: Universal Human Reference RNA_LX_i_S1

value: Lexogen RiboCop (LX)


title: 10647B_Tissue


title: D17-105054_RZ_i_S3

source_name: Universal Human Reference RNA_RZ_i_S3

value: RiboZero Gold (RZ)


title: D17-105062_LX_i_S1


title: PC3 PBS (Vehicle control), 3

value: Prostate

tag: time

value: 3 days

tag: treatment

value: phosphate buffered saline (PBS, vehicle control)


title: 10647B_Sphere


title: D17-105053_RZ_i_S3


title: 10647A_Tissue


title: D17-105051_RZ_d_S3

source_name: Universal Human Reference RNA_RZ_d_S3


title: D17-105052_RZ_d_S3


title: D17-105049_K_d_S2

source_name: Universal Human Reference RNA_K_d_S2

value: Kapa RiboErase (K)


title: 10647A_Sphere


title: HeLa Input iPOL2

data_processing:
Sequences were mapped to the respective genomes using Bowtie2 and analyzed by QuEST and MACS2
ChIP-seq reads were alingned to the hg19 genome
For QuEST ChIP-seq peaks were determined using a kernel density estimate bandwidth of 30, a ChIP candidate threshold of = 20, a ChIP extension fold enrichment of 3, and a ChIP-to-background fold enrichment of 3. WIG files were generated with QuEST and used for visualization in the UCSC Genome Browser.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using QuEST

source_name: HeLa cells

growth_protocol: HeLa cells were grown under standard tissue culture conditions

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min and quenched with glycine to a final concentration of 0.125M for another 10 min. Chromatin was sonicated with a Bioruptor (Diagenode), cleared by centrifugation, and incubated overnight at 4°C with 7.5μg of the desired antibodies: anti-DDX21 (Novus Biologicals BP100-1781), anti-TCOF1 (Novus Biologicals NBP1-86909), Immuno-complexes were immobilized with 100μl of protein-G Dynal magnetic beads (Life Technologies) for 4h hours at 4°C, followed by stringent washes and elution. Eluates were reverse cross-linked overnight at 65°C and deproteinated with proteinase K at 56°C for 30min. DNA was extracted with Phenol Chloroform, followed by ethanol precipitation.
ChIP-seq libraries where prepared according to the NEBNext protocol

treatment_protocol: For treatment with iPol I, HeLa cells were treated for 1 hr at the indicated concentrations. For siTCOF1, HeLa cells were transfected with pools of siRNA targeting TCOF1. For ChIP cells were harvested 48 hours after transfection.


title: HeLa Input


title: D17-105048_K_i_S2

source_name: Universal Human Reference RNA_K_i_S2


title: HeLa DDX21 ChIP-seq in siTCOF1


title: HeLa DDX21 ChIP-seq in iPol I treated cells


title: D17-105071_NE_i_S4


title: HeLa TCOF1 ChIP-seq


title: D17-105047_K_i_S2


title: D17-105046_CR_d_S3

source_name: Universal Human Reference RNA_CR_d_S3

value: Takara/Clontech Ribogone (CR)


title: Mll4KO_2i_H3K4me1

source_name: embryonic stem cell

value: embryonic stem cell

value: Mll4 knockout/Mll4KO

value: H3K4me1 (Homemade, #24)


title: D17-105045_CR_d_S3

value: heat degraded


title: HeLa DDX21 ChIP-seq

value: HeLa


title: D17-105044_CR_i_S3

source_name: Universal Human Reference RNA_CR_i_S3


title: D17-105043_CR_i_S3


title: D17-105042_CZ_d_S3

source_name: Universal Human Reference RNA_CZ_d_S3

value: SMARTer Pico (CZ)


title: D17-105041_CZ_d_S3


title: D17-105050_K_d_S2


title: D17-105040_CZ_i_S3

source_name: Universal Human Reference RNA_CZ_i_S3


title: D17-105039_CZ_i_S3


title: D17-105038_RZ_d_S2

source_name: Universal Human Reference RNA_RZ_d_S2


title: D17-105036_RZ_i_S2

source_name: Universal Human Reference RNA_RZ_i_S2


title: D17-105035_RZ_i_S2


title: DHT_100nM_9

city: Illkirch

first: Angélique

last: Quartier

address: 1, rue Laurent Fries

institute: IGBMC

description:
Processed data file(s):
hNSCs_DHT_100nM_24h_Deanalysis

data_processing:
Image analysis and base calling were performed using RTA 1.17.21.3 / 1.18.61 and CASAVA 1.8.2.
Tophat v1.4.1 with bowtie v0.12.7 was used for read mapping.
Gene expression was quantified using HTSeq v0.5.3p5 and gene annotations from Ensembl release 72.
Normalization was performed using the DESeq2 Bioconductor package (v1.0.19).
Genome_build: hg19
Supplementary_files_format_and_content: .csv file(s) with raw read counts and normalized counts

source_name: Neural Stem Cells

growth_protocol: ES cell–derived hNSC cells were routinely maintained on poly-ornithine and laminin-coated dishes in Dulbecco's modified Eagle's medium/F12 Glutamax and Neurobasal medium (1:1) supplemented with N2, B27 and 50µM 2-mercaptoethanol containing brain-derived growth factor (20ng/mL), fibroblast growth factor-2 (10ng/mL) and epidermal growth factor (10ng/mL).

extract_protocol:
Total RNA were extracted from treated cells using TRI reagent, treated with DNase I recombinant (1U/µg of nucleic acids) during 30min at 37°C and then purify by using the RNeasy mini kit.
RNA libraries were prepared for high throughput DNA sequencing using “TruSeq™ RNA Sample Preparation v2 Kit” protocol.

treatment_protocol: Cells were placed in depleted medium (phenol-red free medium without N2 and B27) during 48h hours before androgen treatments and thus treated with DMSO, DHT 100nM , 10nM, Testosterone 100nM, 10nM, R1881 1nM, retinoic acid 1µM during 24h hours.

value: ES-derived neural stem cells

value: DHT 100nM 24 hours


title: DHT_100nM_2


title: D17-105037_RZ_d_S2


title: DHT_100nM_3


title: DHT_100nM_7


title: D17-105034_CR_d_S2

source_name: Universal Human Reference RNA_CR_d_S2


title: D17-105033_CR_d_S2


title: DHT_100nM_5

description:
Processed data file(s):
hNSCs_DHT_100nM_24h_Deanalysis
hNSCs_batch1_androgens_24h_Deanalysis


title: DHT_100nM_8


title: DHT_100nM_6


title: D17-105031_CR_i_S2

source_name: Universal Human Reference RNA_CR_i_S2


title: DMSO_7

value: DMSO 24 hours


title: DMSO_8


title: DHT_100nM_4


title: DHT_100nM_1


title: D17-105032_CR_i_S2

value: intact


title: DMSO_9


title: D17-105030_CZ_d_S2

source_name: Universal Human Reference RNA_CZ_d_S2


title: DMSO_10


title: DMSO_6


title: D17-105028_CZ_i_S2

source_name: Universal Human Reference RNA_CZ_i_S2


title: DMSO_5


title: DMSO_4


title: DMSO_3


title: D17-105029_CZ_d_S2


title: PC3 PBS (Vehicle control), 1


title: D17-105027_CZ_i_S2


title: D17-105026_NE_d_S2

source_name: Universal Human Reference RNA_NE_d_S2

value: New England Biolabs NEBNext rRNA Depletion (NE)


title: D17-105023_NE_i_S2

source_name: Universal Human Reference RNA_NE_i_S2


title: D17-105022_CR_d_S1

source_name: Universal Human Reference RNA_CR_d_S1


title: D17-105014_K_d_S1

source_name: Universal Human Reference RNA_K_d_S1

value: Kapa Biosystems


title: D17-105021_CR_d_S1


title: D17-105024_NE_i_S2


title: D17-105025_NE_d_S2


title: D17-105013_K_d_S1


title: D17-105012_K_i_S1

source_name: Universal Human Reference RNA_K_i_S1


title: D17-105020_CR_i_S1

source_name: Universal Human Reference RNA_CR_i_S1


title: DHT_100nM_IP_AR

data_processing:
ChIP-seq reads were aligned to the human reference genome (hg19) using Bowtie v0.12.8
Peak calling was performed using MACS v1.4.2
Peaks were annotated relative to genomic features using Homer
Peaks were annotated using Homer v4.7.2 with annotation extracted from Ensembl v75
Genome_build: hg19
Supplementary_files_format_and_content: wig

extract_protocol:
Cellular lysates were isolated by incubating cells pellets in SDS lysis buffer, sonicated and AR-DNA complexes were isolated with antibody.
Libraries were prepared using NEXTflex ChIP-Seq Kit (#5143-02, Bioo Scientific) following the manufacturer's protocol (V12.10)

treatment_protocol: Cells were placed in depleted medium (phenol-red free medium without N2 and B27) during 48h hours before androgen treatments and thus treated with DMSO, testosterone, DHT 10nM or 100nM during 4h hours.

value: DHT 100nM 4 hours

tag: antibody

value: AR (N-20 Santa Cruz sc-816)


title: Testo_100nM_IP_AR_1

value: Testosterone 100nM 4 hours


title: Testo_100nM_input

value: none, input


title: LnCap DHT_100nM_input

source_name: LNCaP

growth_protocol: Cells were seeded in CellBind® flasks (Corning, NY, USA) in RPMI 1640 medium with 10mM HEPES, 10% fetal calf serum, 1mM sodium pyruvate and gentamicin (40µg/mL)

extract_protocol:
Cellular lysates were isolated by incubating cells pellets in SDS lysis buffer, sonicated and AR-DNA complexes were isolated with antibodies.
Libraries were prepared using NEXTflex ChIP-Seq Kit (#5143-02, Bioo Scientific) following the manufacturer's protocol (V12.10)

treatment_protocol: Cells were placed in depleted medium (phenol-red free medium with charcoal treated serum) during 48h hours before androgen treatments and thus treated with DMSO or 100nM during 4h hours.

value: prostate cancer cell line


title: LnCap DMSO_IP_AR_3279.4

value: DMSO 4 hours

value: AR (3279.4 homemade)


title: LnCap DHT_100nM_IP_AR_3279.4


title: LnCap DHT_100nM_IP_AR_N20


title: DHT_10nM_input

value: DHT 10nM 4 hours


title: LnCap DMSO_input


title: LNCaP HS-5 CM, 1

tag: tissue

value: Prostate

value: LNCaP

value: 3 days

value: grown in bone marrow stromal cell conditioned medium (CM) from HS-5 bone marrow stromal cells


title: LnCap DMSO_IP_AR_N20

tag: cell type


title: D17-105011_K_i_S1


title: DMSO_2

value: ES-derived neural stem cells


title: D17-105005_RZ_d_S1

source_name: Universal Human Reference RNA_RZ_d_S1

value: RiboZero Gold (RZ)

value: heat degraded


title: D17-105006_RZ_d_S1


title: DHT_10nM_IP_AR_2


title: DMSO_1

value: DMSO 24 hours


title: D17-105019_CR_i_S1

value: Takara/Clontech Ribogone (CR)

value: intact


title: Testo_100nM_IP_AR_2

value: AR (N-20 Santa Cruz sc-816)


title: DHT_100nM_input

value: DHT 100nM 4 hours


title: DHT_10nM_IP_AR_1


title: KOREP2_REFED

city: Dallas

first: Gokhul

middle: Krishna

last: Kilaru

state: TEXAS

address: 6000 Harry Hines Boulevard

department: Department of Neuroscience

institute: University of Texas Southwestern Medical Center

description: mRNA-seq

data_processing:
mRNA-seq libraries were created according to procedures outlined in (Takahashi et al., 2015) and sequenced on a HiSeq Sequencing System (Illumina) in the UT Southwestern Medical Center McDermett NGS Core.   The sequencing reads (RC Diet samples, 28 million average reads/sample; HFD samples, 30 million average reads) were mapped to the mm10 UCSC annotation using TOPHAT (Trapnell and Salzberg, 2009) with the parameters (-a 8 -m 0 -I 500000 -p 16 -g 20 --library-type fr-firststrand --no-novel-indels --no-novel-juncs --no-coverage-search --segment-mismatches 2) for RNA-Seq.  Uniquely mapped reads were filtered using samtools and the remaining reads were considered for RPKM calculations using HOMER (Heinz et al., 2010).  bigWig tracks for visualizing on UCSC were made using HOMER by normalizing to 10 million reads. Transcripts were filtered by having a RPKM across all timepoints/genotypes of >0.5 RPKM and a transcript length >500 bp. Transcripts meeting these filtering criteria were deemed as “expressed”.  Raw read counts for the 61642 transcripts of UCSC's mm10 annotation were extracted using the uniquely mapped reads and featurecounts programs from subread (Liao et al., 2014) package using parameters (-s 2 -O -T 16 -t exon -g gene_id).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

growth_protocol: Mice were single-housed in light-tight environmental chambers on a 12:12 LD cycle for a minimum of 3 weeks prior to harvesting of liver tissue.  For High Fat Diet (HFD, Research Diets D12492i) treatment, mice were fed ad libitium HFD for 3 weeks prior to tissue collection.  For the regular chow, circadian collection, animals were sacrificed at the indicated Zeitgeber Time (ZT).  For HFD treatement, tissues were harvested at ZT22 in the FED (Ad Libitum) condition, ZT22 in the FAST (12h fast, food removed at ZT12) condition and at ZT2 in the REFED (4h refed, food removed at ZT12 and returned at ZT22) condition.

extract_protocol:
Total RNA was extracted with TriZol according to the manufacturers instructions.
Libraries were prepared according to the mRNA-seq protocol in Takahashi JS et al. 2015. Methods in Enzymology.

treatment_protocol: Mice were sacrificed via decapitation for blood collection and liver tissue harvest.  Liver tissue was snap-frozen in liquid nitrogen and stored at -80 degrees C.  Tissue was pulverized into powder using a mortar and pestle under liquid nitrogen.  Total RNA was extracted from liver tissue powder using TriZol Reagent according to the manufacturers instructions.

tag: strain

tag: genotype

value: KO

tag: diet

value: High Fat Diet

value: Liver


title: KOREP3_REFED

description: mRNA-seq

value: ZT2 in the REFED (4h refed, food removed at ZT12 and returned at ZT22) condition


title: KOREP1_REFED

description: mRNA-seq


title: alpha7E260A:G Control Female

city: Salt Lake City

first: Robert

middle: B

last: Weiss

state: UT

department: Human Genetics

institute: University of Utah

data_processing:
RNA-Seq reads were aligned to the mouse genome (UCSC Genome; Assembly NCBI37/mm9) using STAR
CDS read counts were then extracted from the bam files using the htseq-count script and CDS annotations from mouse GENCODE reference release M1 (NCBIM37)
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: CDS read counts

source_name: Distal lung

extract_protocol:
Lungs were cleared of BALF content, the trachea removed and the more distal lung lobe tissue enriched by dissection. The interstitial cells were collected and reacted with anti-CD45 antibody coupled to magnetic beads before depletion of the CD45+ cells using an autoMACS cell separator .The purity was (>95% epCAM+, <1% CD31+ endothelial cells) and viability (<5% 7-AAD (viability stain)
Standard methods to prepare poly-adenylated strand-specific RNA-Seq libraries using Illumina TruSeq stranded mRNA preparation kits.

tag: protocol

value: Control

tag: Sex

value: Female

value: lung

value: > 90percent C57BL/6

tag: age

value: Adult


title: KOREP3_FAST

description: mRNA-seq

value: ZT22 in the FAST (12h fast, food removed at ZT12) condition


title: alpha7 Control Female


title: alpha7 Smoked Female

value: exposed to side-stream cigarette smoke


title: alpha7E260A:G Control Male

value: Male


title: alpha7E260A:G Smoked Male


title: DMSO_IP_AR

value: ES-derived neural stem cells

value: DMSO 4 hours


title: alpha7G Smoked Male


title: alpha7G Control Male


title: D17-105004_RZ_i_S1

source_name: Universal Human Reference RNA_RZ_i_S1

tag: kit

value: RiboZero Gold (RZ)

tag: state

value: intact

tag: site


title: alpha7E260A:G Smoked Female


title: Pineal Gland Night

description: Barcode: ACAGTG

data_processing:
Illumina Casava1.9 software used for basecalling.
Reads were aligned with the RNA-STAR aligner (v. 2.3.0e) , using a danRer10 genome build. STAR aligner parameters used: --runThreadN 8  --outFilterMultimapNmax 1 --outSAMunmapped Within --outStd SAM. Quality control metrics were calculated and visualized using FastQC software and in-house written scripts, and no major artifacts or abnormalities were found
Gene read counts were provided by R subreads package, (featureCounts function) with parameters specifying: paired-end reads, and reverse-complement for the second strand (-p, -S2).  Annotation for assigning the reads was derived from native annotation for danRer10 genome build.  Differential expression analysis was performed using DESeq2 software package.
Genome_build: danRer10
Supplementary_files_format_and_content: zebrafish_FPKM.txt file includes FPKM values for all of the Samples

organism: Danio rerio

source_name: Pineal Gland

extract_protocol:
Adult (0.5-1.5 years old) transgenic zebrafish, Tg(aanat2:EGFP), which express enhanced green fluorescent protein (EGFP) in the pineal gland under the control of the aanat2 regulatory regions, were used. Fish were raised under 12-hr light:12-hr dark (LD) cycles in a temperature controlled room. For tissue collection fish were anesthetized in 1.5 mM Tricane (Sigma), and sacrificed by decapitation. Dissections were conducted at mid-day (ZT6) and mid-night (ZT18). Fluorescent pineal glands, whole eyes and other tissues were removed under a dissecting microscope. A pool of 18 pineal glands 6 eyes and 4-8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit (Qiagen) according to the manufacturer's instructions. The mixed tissue samples consisted of equal amounts of total RNA (1mg) from muscle, ovary, kidney, gill, liver, intestines, heart and brain.
Poly-A RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: Pineal Gland

tag: timepoint

value: night


title: Mixed Tissue Day

description: Barcode: GAGTGG

source_name: Mixed Tissue

value: Mixed Tissues (muscle, ovary, kidney, gill, liver, intestines, heart, brain)

value: day


title: Pineal Gland Day

description: Barcode: TGACCA


title: KOREP1_FED

description: mRNA-seq

value: KO

value: High Fat Diet

value: ZT22 in the FED (Ad Libitum) condition

value: Liver


title: KOREP2_FED

description: mRNA-seq


title: KOREP1_FAST

description: mRNA-seq


title: KOREP3_FED

description: mRNA-seq


title: Eye Day

description: Barcode: CAGATC

source_name: Eye

value: Eye


title: WTREP3_REFED

description: mRNA-seq

value: WT

value: ZT2 in the REFED (4h refed, food removed at ZT12 and returned at ZT22) condition


title: sphere cells rep1

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

description: sphere cells rep1

data_processing:
Reads were aligned to theZv9 genome assembly using TopHat v2.0.9
For each sample, RPKM was computed as the number of reads which map per kilobase of exon model per million mapped reads for each gene.
Genome_build: Zv9
Supplementary_files_format_and_content: RPKM for each gene in each development stage

source_name: Danio embryo cells

extract_protocol:
RNA was isolated from Danio cells using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100
Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 50 bp.

tag: developmental stage

value: embryo

value: sphere cells


title: DMSO_input

source_name: Neural Stem Cells

value: ES-derived neural stem cells

value: none, input


title: 1000-cell rep1

description: 1000 cells rep1

value: 1000 cells


title: Mixed Tissue Night

description: Barcode: ATTCCT


title: KOREP2_FAST

description: mRNA-seq

tag: time

value: ZT22 in the FAST (12h fast, food removed at ZT12) condition


title: WTREP2_REFED

description: mRNA-seq


title: WTREP1_REFED

description: mRNA-seq


title: 128-cell rep1

description: 128-cell rep1


title: WTREP3_FAST

description: mRNA-seq


title: S00714 10 week Socs3 cKO rep2

city: Tsurumi-ku, Yokohama City,

first: Archana

last: Bajpai

state: Kanagawa,

address: 1-7-22 Suehiro-cho,

department: IMS

institute: RIKEN Yokohama

data_processing:
Fastq files having nucleotide and quality information were generated using Illumina offline basecaller (OLB) version 1.9.4.
Seqeunces were mapped on mouse genome (mm9) using TopHat2 (version 2.1.0) with parameters “—no-coverage-search -G genes.gtf”, genes.gtf is an annotation file provided Illumina database iGenomes (Trapnell et al., 2009.)
Mapped reads were counted and the fragments per kilobase per million reads (FPKM) of each gene is calculated using Cufflinks with the annotation described above (Mortazavi et al., 2008)
Genome_build: mm9
Supplementary_files_format_and_content: Mapped reads were counted and the fragments per kilobase per million reads (FPKM) of each gene

source_name: keratinocytes

growth_protocol: The generation of keratin 5-specific Socs3 conditional knockout (Socs3 cKO) mice with a C57BL/6 background was described in a previous report [Uto-Konomi et al., 2012].

extract_protocol:
Total RNA was isolated with a TRIzol (Thermo Fisher Scientific, Waltham, MA) from ear specimens. cDNA libraries were synthesized with TruSeq RNA Library Preparation Kit v2 (Illumina, San Diego, CA) according to the manufacturer's instruction. Sequencing data were obtained using the HiSeq 1000 system (Illumina)  which could read a 50 bp sequence (single-ended 50–base pair reads).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ear

value: 10 week after birth

value: Socs3 cKO


title: S00715 10 week Socs3 cKO rep3


title: S00479 2 week Socs3 cKO rep4

value: 2 week after birth


title: Eye Night

description: Barcode: GGCTAC

value: night


title: WTREP1_FAST

description: mRNA-seq

value: High Fat Diet


title: WTREP2_FAST

description: mRNA-seq


title: WTREP3_FED

description: mRNA-seq

value: ZT22 in the FED (Ad Libitum) condition


title: S00477 2 week Socs3 cKO rep2


title: S00478 2 week Socs3 cKO rep3


title: S00476 2 week Socs3 cKO rep1


title: S00713 10 week Socs3 cKO rep1


title: oocyte cells rep1

description: oocyte cells rep1

value: oocyte cells


title: 4-cell rep1

description: 4-cell rep1


title: sperm cells rep1

description: sperm cells rep1

value: sperm cells


title: 16-cell rep1

description: 16-cell rep1


title: 1-cell rep1

description: 1-cell rep1


title: S00716 10 week Socs3 cKO rep4


title: WTREP2_FED

description: mRNA-seq

value: WT

value: Liver


title: WTREP1_FED

description: mRNA-seq


title: 256-cell rep1

description: 256-cell rep1

value: embryo


title: KOREP2_ZT21

description: mRNA-seq

value: KO

value: Regular Chow


title: 64-cell rep1

description: 64-cell rep1


title: CO441Fg2d06

city: Ottawa

first: Linda

middle: J

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

country: Canada

institute: Agriculture & Agri-Food Canada (AAFC)

description: Biological replicate 2

data_processing:
basecalls performed using Illumina Casava1.7 software
Sequence reads were trimmed-off of adaptors, low base calls (limit= 0.01), abiguous nucleotides (max = 1) and terminal nucleotides (20 nucleotides from the 5' end)
Trimmed reads were aligned with reference genome B73 Version 2 that was also annotated with 63,074 gene transcripts
Gene transcript expression levels were estimated as Transcripts Per Million (TPM, Li et al, Bioinformatics, 2010) which accounts for variation due to different library size and transcript length
Genome_build: B73 genome version 2
Supplementary_files_format_and_content: Excel file containing differential gene expression analysis output inculding unique and total read counts, TPM expression levels, fold changes, Bonferonni and FDR corrected Probability levels of each gene transcript

organism: Zea mays

source_name: Inbred line CO441

growth_protocol: inbred lines were grown under field condition in 2004 and 2006

extract_protocol:
Inoculated ears were harvested from field at 1 and 2 days after inoculation and stored in -80° C freezer until kernel tissue harvest, RNA was extracted using guanidine isothiocyanate and ultra-centrifugation with CsCL (cesium chloride) cushion (Chirgwin et al, Biochemistry, 1979), Total RNA sequencing libraries were created using Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Inoculation of mock and fungal inoculum were performed 11 days after silk emergence

tag: line

value: Kernel

tag: treatment

value: Fusarium graminearum DAOM180378

tag: Stage

value: Days after inoculation 2


title: CO441Fg2d04

description: Biological replicate 1

tag: tissue


title: S01160 10 week WT rep3

tag: strain

value: Ear

value: Wild Type


title: S01159 10 week WT rep2

value: 10 week after birth

tag: genotype


title: CO441Fg1d06

description: Biological replicate 2

value: Days after inoculation 1


title: KOREP2_ZT15

description: mRNA-seq

tag: diet


title: S01158 10 week WT rep1


title: KOREP2_ZT12

description: mRNA-seq


title: CO441B2d04

description: Biological replicate 1

value: Mock


title: CO441B2d06

description: Biological replicate 2


title: S01337 2 week WT rep4

value: 2 week after birth


title: KOREP2_ZT18

description: mRNA-seq


title: CO441B1d06

description: Biological replicate 2


title: S01336 2 week WT rep3


title: CO441B1d04

description: Biological replicate 1


title: KOREP2_ZT6

description: mRNA-seq


title: S01335 2 week WT rep2


title: KOREP2_ZT9

description: mRNA-seq


title: KOREP2_ZT3

description: mRNA-seq


title: B73Fg2d06

description: Biological replicate 2

source_name: Inbred line B73


title: S01369 2 week WT rep1


title: B73Fg1d06

description: Biological replicate 2


title: B73Fg1d04

description: Biological replicate 1


title: KOREP2_ZT0

description: mRNA-seq


title: KOREP1_ZT18

description: mRNA-seq


title: B73Fg2d04

description: Biological replicate 1


title: KOREP1_ZT21

description: mRNA-seq


title: CLAMP RNAi Input Replicate 4

city: Boston

first: Michael

last: Tolstorukov

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
ChIP-Seq reads aligned to fb5_22 release of Drosophila melanogaster genome using bowtie (rel 0.12.9) options -t -p 12 -m 1 -I 50 -X 500 --solexa-quals --best --chunkmbs 256
Peaks were called using MACS2 callpeak (version 2.1.1) and p-value threshold of 0.05. For MSL3 IP, the --broad flag was used.
Genome_build: fb5_22/dm3
Supplementary_files_format_and_content: bedgraph files were generated using MACS2 bdgcmp (version 2.1.1)  with the -m FE flag. Scores represent local fold enrichment.

organism: Drosophila melanogaster

source_name: S2 cells

extract_protocol:
Cells were cross linked in 1% formaldehyde and quenched with glycine prior to incubation in lysis buffer, and sonicated six times with 5 min cycles of 30s on/off o a Bioruptor sonicator. Samples were immunoprecipitated with either GAF, CLAMP, or MSL3 antibodies, and DNA clean-up was performed including RNase and Proteinase-K digestion steps.
Libraries were prepared using the NEBNext Ultra II DNA library prep kit

treatment_protocol: S2 cells were treated with 4.5 ug/mL dsRNA

tag: RNAi treatment

value: CLAMP

tag: chip antibody


title: KOREP1_ZT15

description: mRNA-seq


title: KOREP1_ZT12

description: mRNA-seq


title: CO441Fg1d04

description: Biological replicate 1


title: B73B2d06

description: Biological replicate 2


title: B73B2d04

description: Biological replicate 1


title: CLAMP RNAi MSL3 IP Replicate 3

value: goat anti-MSL3


title: B73B1d06

description: Biological replicate 2


title: CLAMP RNAi Input Replicate 3


title: CLAMP RNAi GAF IP Replicate 3

value: rabbit anti-GAF


title: B73B1d04

description: Biological replicate 1


title: KOREP1_ZT3

description: mRNA-seq


title: KOREP1_ZT0

description: mRNA-seq


title: KOREP1_ZT6

description: mRNA-seq


title: CLAMP RNAi CLAMP IP Replicate 2

value: rabbit anti-CLAMP


title: CLAMP RNAi GAF IP Replicate 2


title: CLAMP RNAi Input Replicate 2


title: WTREP2_ZT21

description: mRNA-seq

value: WT

value: Liver


title: CLAMP RNAi MSL3 IP Replicate 1


title: WTREP2_ZT9

description: mRNA-seq


title: KOREP1_ZT9

description: mRNA-seq

value: KO


title: WTREP2_ZT15

description: mRNA-seq

value: Regular Chow


title: WTREP2_ZT18

description: mRNA-seq


title: CLAMP RNAi CLAMP IP Replicate 1


title: CLAMP RNAi GAF IP Replicate 1


title: GAF RNAi Input Replicate 4

value: GAF


title: WTREP1_ZT18

description: mRNA-seq


title: WTREP2_ZT3

description: mRNA-seq


title: GAF RNAi Input Replicate 3


title: GAF RNAi MSL3 IP Replicate 3


title: WTREP1_ZT21

description: mRNA-seq


title: CLAMP RNAi Input Replicate 1


title: WTREP2_ZT0

description: mRNA-seq


title: WTREP1_ZT15

description: mRNA-seq


title: CLAMP RNAi MSL3 IP Replicate 2


title: GAF RNAi GAF IP Replicate 2


title: GAF RNAi CLAMP IP Replicate 2


title: GAF RNAi MSL3 IP Replicate 2


title: WTREP2_ZT12

description: mRNA-seq


title: WTREP1_ZT12

description: mRNA-seq


title: WTREP1_ZT6

description: mRNA-seq


title: GAF RNAi Input Replicate 2


title: GAF RNAi MSL3 IP Replicate 1


title: WTREP1_ZT3

description: mRNA-seq


title: WTREP2_ZT6

description: mRNA-seq


title: GAF RNAi GAF IP Replicate 1


title: GAF RNAi Input Replicate 1


title: IMOK_Rep2

city: Buffalo

first: Rose-Anne

last: Romano

address: 3435 Main Street

department: Oral Biology

institute: State University of New York at Buffalo

data_processing:
Reads were mapped to the Mus musculus genome (mm9 build) with TopHat2 (v2.1.1),using Bowtie2 (v2.2.6) as the underlying aligner.
Reads aligning to the UCSC mm9 build were quantified with featureCounts (v1.5.1) , which disregarded any read/read pair that aligned to more than one location, or more than one gene at a single location.
DESeq2 (v1.12.4) was used to normalize the read counts and derive FPKM values and TPM values were calculated by dividing the FPKM value of each gene by the total FPKM values in the sample.
Genome_build: mm9
Supplementary_files_format_and_content: featureCounts output containing gene-level read count summaries for each RNA-Seq sample

source_name: Immortalised Mouse Oral Keratinocyte

extract_protocol:
RNA was extracted from mouse submandibular salivary gland epithelial cells using the Direct-zol RNA Mini-Prep kit.
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.

value: Immortalised Mouse Oral Keratinocyte

tag: growth condition

value: IMOK media

tag: passage

value: Early


title: IMOK_Rep3


title: IMOK_Rep1


title: mSGc-P25_D

source_name: Mouse submandibular salivary gland epithelial cells

value: Differentiating Media

value: Late


title: mSGc-P25_P

value: Mouse submandibular salivary gland epithelial cells

value: Progenitor Media


title: GFP RNAi CLAMP IP Replicate 4

value: GFP


title: GFP RNAi Input Replicate 4


title: mSGc-P10_D

value: Mid


title: mSGc-P4_P

value: Progenitor media


title: mSGc-P10_P


title: GFP RNAi MSL3 IP Replicate 3

value: goat anti-MSL3


title: GFP RNAi MSL3 IP Replicate 4


title: GFP RNAi Input Replicate 3


title: WTREP1_ZT9

description: mRNA-seq


title: GFP RNAi GAF IP Replicate 3

value: rabbit anti-GAF


title: mSGc-P2_P


title: GFP RNAi MSL3 IP Replicate 2


title: GFP RNAi GAF IP Replicate 2


title: GFP RNAi CLAMP IP Replicate 2

value: rabbit anti-CLAMP


title: HSC_β-glucan inj-5FU-rep2

city: Dresden

first: Triantafyllos

last: Chavakis

address: Fiedlerstraße 42

department: Klinische Pathobiochemie

institute: Medizinische Fakultät der TU Dresden

data_processing:
basecalling: bcl2fastq 1.8.4
alignment of read data against mm10 with gsnap version v2014-12-17,v2016-06-30,v2016-09-23; splice sites were supported by using Ensembl version 81 (gsnap -d mm10 --gunzip --use-sarray=1 -B 4 -t 16 -N 1 -s EnsemblGene-81.ss.mm10.iit -n 1 -A sam)
counting was done with featureCounts version 1.5.0,1.5.1 (-a EnsemblGene-81.mm10.TR.gtf -s 2 -Q 1) and the Ensembl version 81 gtf file
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited files from featureCounts (featureCounts.mm10.e81.first.csv.gz, featureCounts.mm10.e81.second.csv.gz, featureCounts.mm10.e81.third.csv.gz); columns are in the following order: Ensembl Gene ID, Chromosom, Exon Start Coordinates, Exon End Coordinates, Gene Length; Counts from the Conditions and their replicates

source_name: bone marrow

extract_protocol:
RNA was harvested from sorted cells using RNeasy Plus Micro Kit from Qiagen (Cat#74034)
Samples were prepped with the SMARTer Ultra HV v2 protocol (TaKaRa Bio)

tag: cell type

value: long-term hematopoietic stem cells

tag: age

value: 10 weeks


title: HSC_β-glucan inj-5FU-rep3