title: d/d miR-17~92 + Empty MEF Rep 3

city: Montreal

first: Ariel

middle: Octavio

last: Donayo

state: Quebec

address: 3655 Promenade Sir William Osler Room 707

department: Goodman Cancer Research Centre

country: Canada

institute: McGill University

description:
filtered_MEF_miR290-295_NoSpikein_normCounts_rlog.csv
filtered_MEF_miR290-295_spikein_normCounts_rlog.csv

data_processing:
Reads have adapters removed, aligned and quantified using miRDeep2-v0.0.8 against miRBase-v22
Normalization uses size factors calculated using DESeq2 with spike-in reads for spike-in normalization, or with endogenous reads for internal normalization
B-cells do not have spike-in version, they are internally normalized
Genome_build: miRBase-v22
Supplementary_files_format_and_content: Filtered counts. Each CSV file contains all datasets corresponding to each cell line. Different files for Spike-ins (spikein) and internal normalizations (NoSpikein)

source_name: MEF

growth_protocol: Standard conditions for each cell line

extract_protocol:
Total RNA, followed by gel purification of small RNAs
NEBNext small RNA library prep kit

treatment_protocol: Spike-ins

value: Eu-myc mice


title: d/d miR-17~92 + miR-290~295 MEF Rep 3

status: Public on May 20 2019

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain


title: d/d miR-17~92 + miR-290~295 MEF Rep 2


title: d/d miR-17~92 + miR-290~295 MEF Rep 1


title: HEK293T-N12-KO NAD-Capture 2

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

country: USA

institute: Rutgers University

data_processing:
Illumina bcl2fastq2-v2.17.1.14 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and mapped to hg19 whole genome using TopHat v2.1.1 (with Bowtie 2.2.8.0) using default settings.
All samples were modeled using cuffdiff with options -p 6  --no-update-check and the UCSC hg19 genes.gtf file from the Illumina iGenomes site
Raw cuffdiff output files were loaded into the R package cummeRbund
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by cuffdiff and output by cummeRbund
Genome_build: hg19
Supplementary_files_format_and_content: Gzipped, comma-separated-values (CSV) file containing isoform_ID row labels and sample replicate column labels.  The values are FPKM.

organism: Homo sapiens

source_name: HEK293T-N12-KO NAD-Capture

growth_protocol: HEK293T cells were cultured under standard conditions with no modifications

extract_protocol:
Total RNA was isolated by TRIzol extraction, following the manufacturers recommended protocol
enrichment protocol: RiboMinus enrichment for non-ribosomal RNAs was performed as recommended by the kit manufacturer
NAD-Capture enrichment was performed using the NAD-RNA Capture protocol (Cahova et al., 2015) with minor modification.  NAD-Capture was carried out with 100µg total RNAs treated with 10µl 4-pentyn-1-ol (Sigma-Aldrich) and 1.5U Adenosine diphosphate-ribosylcyclase (ADPRC) in 100µl reaction containing 50mM HEPES, 5mM MgCl2 (pH 7) and 40U RNasin® Ribonuclease Inhibitor (Promega) at 37oC 60 minutes. The reaction minus ADPRC was used as background control. The reaction was stopped with phenol/chloroform extraction and RNAs were precipitated with ethanol. The precipitated RNAs were subjected to copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction by incubating with 250µM biotin-PEG3-azide, freshly mixed 1mM CuSO4, 0.5mM THPTA, 2mM Sodium Ascorbate in 100µl reaction with 50mM HEPES, 5mM MgCl2 (pH7) and 40U RNasin® Ribonuclease Inhibitor (Promega) at 30oC for 30 minutes. Following extraction with phenol/chloroform and RNA precipitation, the NAD clicked RNAs were captures by binding to 20µl streptavidin magnet beads at room temperature with gentle rocking for 1 hour in 100µl binding buffer (1M NaCl, 10mM HEPES (pH7) and 5mM EDTA). The beads were washed three time with wash buffer (8mM Urea, 50mM Tris-HCl (pH7.4), 0.25% Triton-X100) and three washes with nuclease free H2O.
RiboMinus-selected RNAs were reverse transcribed and converted to libraries using the Illumina TruSeq RNA Sample Preparation Kit v2.
For NAD-Capture RNAs, samples were reverse transcribed into cDNA and synthesized into dsDNA with the SMARTer® Universal Low Input RNA Kit for Sequencing (Clontech Laboratories, Inc.) following the manufacturer’s protocol.

treatment_protocol: No treatment

tag: cell line

tag: genotype/variation

value: Nudt12-KO (N12-KO)

tag: enrichment

value: NAD-Capture


title: 2HFD-KO-4a

city: Paris

first: Nicolas

last: VENTECLEF

state: Ile de France

address: 15 rue de l’Ecole de Medecine

department: Physiology and Physiopathology

country: France

institute: Centre de Recherche des Cordeliers

data_processing:
Illumina Bcl2fastq2 2.17 software used for basecalling.
Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the genome using STAR (version 2.4.0k)
Alignments from reads matching more than once on the reference genome were removed using Java version of samtools
To compute gene expression, GRCm38.p4 GFF3 genome annotation version 81 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq-count 0.5.3
The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3
Genome_build: GRCm38.p4 Ensembl version 81
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: Intra abdominal adipose tissue

extract_protocol:
RNA was extracted from tissues or purified cells using the RNeasy RNA Mini Kit (Qiagen). Complementary DNAs were synthesized using M-MLV Reverse Transcriptase kit (Promega). RT–qPCR was performed using the QuantStudio 3 Real-Time PCR Systems (ThermoFisher Scientific). 18S was used for normalization to quantify relative mRNA expression levels.  Illumina TruSeq stranded and purification of RNA kit was used with 30 ug of total RNA for the construction of sequencing libraries. Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Adipose tissue

tag: age

value: 11 weeks


title: Primary keratinocytes (Exosomes) patient 377

city: Brisbane

first: Dominic

last: Guanzon

state: Queensland

address: Building 71/918 RBWH Herston

department: UQCCR

country: Australia

institute: University of Queensland

data_processing:
Remove index and adaptor sequences using TagCleaner (version 0.16)
Trim reads to 28 nucleotides using FASTX-Toolkit (version 0.0.13)
miRNAs were identified using the miRDeep2 program (version 2.0.0.7), using the default parameters with the exception of allowing for 1 mismatch and discarding read less than 16 nucleotides in length.
Raw miRNA counts were normalized and statistically analyzed using the DESeq2 package (version 1.10.1) in R (version 3.2.2)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file containing raw miRNA counts

source_name: Conditioned media

growth_protocol: Epidermal primary keratinocytes (PKCs) were freshly isolated from donor skin and propagated on i3T3 feeder cells using the method of Rheinwald and Green. HaCaT cells were purchased from CLS Cell Lines Service GmbH (Eppenheim, Germany). All keratinocyte cultures were maintained at 37 ºC in a 5% CO2 / 95% air atmosphere, with media changes every 2 days, and subcultured when the cultures became 80% confluent.

extract_protocol:
Total RNA was extracted using the Trizol™ method following the manufacturer’s protocol
Libraries were constructed using the TruSeq® SmallRNA Library Prep Kit, following the manufacturer’s instructions. A total of 1 µg RNA or 100 to 300 ng of exosomal RNA was used as input for library construction.

tag: cell type

value: primary keratinocytes

tag: ev population

value: Exosomes


title: Primary keratinocytes (Microvesicles) patient 377

value: Microvesicles


title: d/d miR-17~92 + Empty MEF Rep 1


title: d/d miR-17~92 + Empty MEF Rep 2


title: Primary keratinocytes (Apoptotic bodies) patient 377

value: Apoptotic bodies


title: OV miR-17~92 MEF Rep 3

description:
filtered_MEF_miR17-92_NoSpikein_normCounts_rlog.csv
filtered_MEF_miR17-92_spikein_normCounts_rlog.csv


title: OV miR-17~92 MEF Rep 1


title: fl/fl miR-17~92 MEF Rep 3


title: fl/fl miR-17~92 MEF Rep 2


title: fl/fl miR-17~92 MEF Rep 1


title: d/d miR-17~92 MEF Rep 3


title: Primary keratinocytes (Apoptotic bodies) patient 325


title: Primary keratinocytes (Exosomes) patient 325


title: Primary keratinocytes (Microvesicles) patient 325


title: d/d miR-17~92 MEF Rep 2


title: Primary keratinocytes (Microvesicles) patient 363


title: GDpol1-4A-5-rep1

city: New York

first: Duncan

last: Smith

state: NY

address: 1009 Silver Center, 100 Washington Sq E

department: Dept. of Biology/Center for Genomics and Systems Biology

institute: New York University

description: Okazaki Fragments

library_source: genomic

data_processing:
Bowtie2 (version 2.2.3) was used to align paired-end fastq files to the S. cerevisiae reference genome.
Sam files were converted to bam files using samtools, then reads were sorted.
Bam files were converted to bed files using bedtools paired end function and PCR duplicates were removed.
Printed columns for the chromosome, position of the start and stop of the read, and the strand information into output bed files.
Genome_build: Yeast S288C, build R64-1-1
Supplementary_files_format_and_content: bed files: chromosome, start and end positions of mapped reads, strand information.
Supplementary_files_format_and_content: OEM_position_timing.xls: Origin location (chromosome and base pair), origin efficiency metric for all replicates and conditions: calculated using methodology from (McGuffee et al. (2013) Quantitative, genome-wide analysis of eukaryotic replication initiation and termination. Mol Cell 50, 123-135), and timing of origin firing during S phase (early or late).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: 30°C, grow overnight in YEP + 3% raffinose + 0.5% galactose until log phase then switched into various galactose concentrations + 3% raffinose for four hours.

extract_protocol:
Okazaki fragments were enriched and purified as described previously (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438).
Libraries were generated as previously described (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438).

treatment_protocol: Add rapamycin for one hour.

tag: strain/background

value: W303 tor1-1::HIS3, fpr1::NatMX4, RPL13A-2xFKBP12::TRP1, CDC9-FRB


title: GDpol1-4A-5-rep2

description: Okazaki Fragments


title: Primary keratinocytes (Exosomes) patient 363


title: GDpol1-4A-14-rep2

description: Okazaki Fragments


title: Primary keratinocytes (Apoptotic bodies) patient 363


title: Primary keratinocytes (Exosomes) patient 366


title: HACAT (Exosomes) passage 52

value: HACAT

value: immortalized keratinocytes


title: GDpol1-4A-14-rep1

description: Okazaki Fragments


title: Primary keratinocytes (Cells) patient 377

source_name: Cells

value: Keratinocytes


title: Primary keratinocytes (Cells) patient 363


title: GDpol1-4A-23-rep2

description: Okazaki Fragments


title: OV miR-17~92 MEF Rep 2


title: HACAT (Microvesicles) passage 52


title: Primary keratinocytes (Microvesicles) patient 366


title: GDpol1-4A-32-rep2

description: Okazaki Fragments


title: Primary keratinocytes (Cells) patient 366


title: GDpol1-4A-41-rep2

description: Okazaki Fragments


title: d/d miR-17~92 MEF Rep 1


title: Primary keratinocytes (Apoptotic bodies) patient 366


title: Primary keratinocytes (Cells) patient 325


title: HACAT (Exosomes) passage 50


title: GDpol1-4A-41-rep1

description: Okazaki Fragments


title: GDpol1-4A-50-rep2

description: Okazaki Fragments


title: HACAT (Microvesicles) passage 50


title: HACAT (Apoptotic bodies) passage 50


title: HACAT (Cells) passage 50


title: GDpol1-4A-50-rep1

description: Okazaki Fragments


title: HACAT (Apoptotic bodies) passage 52


title: GDpol1-4A-500-rep1

description: Okazaki Fragments


title: GDpol1-4A-500-rep2

description: Okazaki Fragments


title: GDPOL1-5-rep3

description: Okazaki Fragments


title: GDPOL1ctf4KO-14-rep1

description:
Okazaki Fragments
GAL1-DHFR-POL1-13xmyc, ctf4Δ

value: GAL1-DHFR-POL1-13xmyc, ctf4<delta>


title: GDPOL1ctf4KO-32-rep2


title: GDPOL1-23-rep3

description: Okazaki Fragments


title: GDPOL1-14-rep3

description: Okazaki Fragments


title: GDpol1-4A-23-rep1

description: Okazaki Fragments


title: GDPOL1-23-rep1

description: Okazaki Fragments


title: HACAT (Cells) passage 52


title: GDPOL1-32-rep3

description: Okazaki Fragments


title: GDPOL1-41-rep3

description: Okazaki Fragments


title: GDPOL1-32-rep2

description: Okazaki Fragments


title: GDPOL1-50-rep3

description: Okazaki Fragments


title: GDPOL1-500-rep3

description: Okazaki Fragments


title: Sample77_KF047_br2_9

city: Cambridge

first: Kathleen

middle: Elizabeth

last: Fleming

state: MA

address: 52 Oxford Street, NW Labs

department: Molecular and Cellular Biology

institute: Harvard University

description: processed data file: Table_S1.csv

data_processing:
ChIP-seq: Data were analyzed using a modified form of the PeakSeq algorithm (Rozowsky et al., 2009) that narrows the regions identified as peaks by requiring that each 50-bp window within a putative peak be enriched (p < 0.05) relative to mock ChIP (as described by Markson et al. 2013). The fold enrichment for each peak was calculated by finding the maximum ChIP-to-mock ratio within 50 bp of the location of the peak maximum in the raw ChIP-Seq signal.
RNA-seq: Sequencing reads were aligned to the S. elongatus genome using Bowtie (RRID:SCR_005476) as described previously (Markson et al., 2013). We quantified expression of a gene by counting the number of aligned sequencing reads corresponding to the appropriate strand between the start and stop of each gene (gene info obtained from Cyanobase, RRID: SCR_007615), and normalized these values between all samples in this work using median normalization, followed by dividing the median normalized read count value by the length of the open reading frame of the gene, as described previously (Anders and Huber, 2010; Markson et al., 2013). The time course and RNA sequencing was repeated twice for two biological replicates.
Genome_build: NC_007604.1
Supplementary_files_format_and_content: ChIP-seq: Location of peak signal for RNA polymerase locked at initiation sites measured based on time-series ChIP-seq signal in cells treated with rifampicin prior to cross-linking for high-confidence circadian genes (e.g. genes annotated by Markson et al. 2013 that have greater than 1.75 fold peak to trough gene expression).
Supplementary_files_format_and_content: RNA-seq: RNA levels – median normalized to total read count and normalized to length of gene – for high-confidence circadian genes (e.g. genes annotated by Markson et al. 2013 that have greater than 1.75 fold peak to trough gene expression) and that have a transcription start site within 250 bp of start codon (e.g. rifampicin locked RNA polymerase ChIP-seq peak with peak signal located within 250 bp of start codon).

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: S. elongatus PCC 7942 (ATCC 33912) OX-D53E + rpoD5∆

growth_protocol: Cultures were grown in tissue culture flasks (Fischer Scientific) illuminated with 100 mE m-2 s-1 (mmoles photons m-2 s-1) of cool fluorescent light and bubbled continuously with 1-percent CO2 in air. Cell density was maintained near OD750nm near 0.3 by measuring OD750nm every 2 h and making necessary dilutions with fresh BG-11 medium supplemented with 10 mM HEPES-KOH pH 8.0 to maintain pH

extract_protocol:
Cells from 50 ml of culture were harvested by vacuum filtration onto nitrocellulose filters (Whatman). Filters were flash-frozen in liquid nitrogen and stored at -80°C until lysis. To prepare lysates, cells were eluted from the filters using 12 ml of ice-cold AE buffer (50 mM NaOAc pH 5.2, 0.5 M EDTA, DEPC treated water). Cell suspensions were transferred to SS34 tubes and lysed by addition of 800 µl of 25-percent SDS and 12 mL unbuffered acid phenol (pH 4.3). Cells were lysed for 10 min while being incubated in 65°C water bath and intermittently vortexed. Lysates were incubated 5 min on ice. Cell debris were pelleted by centrifugation at 12000 rpm at 4°C for 30 min. Supernatants were transferred to phase lock heavy tubes with 12 ml chloroform and centrifuged for 10 min at 3000 rpm. Nucleic acids in supernatants were precipitated for 1h at -20°C in presence of 1 mL 3 M NaOAc pH 5.2 and 10 mL isopropanol. Precipitated nucleic acids were pelleted by centrifugation at 12000 rpm at 4°C for 30 min. Cell pellets were washed with 5 mL 70-percent EtOH and pelleted by centrifugation at 12000 rpm at 4°C for 10 min. The supernatants were discarded and pellets were air dried at 25°C for 1 h. Pellets were resuspended in 500 µl of TE containing 25 µl of Promega RQ1 RNAse free DNAse (1000 Units/ml) and incubated for 1 h at 37°C to digest DNA. Samples were extracted with equal volume phenol/chloroform/isoamyl alcohol and precipitated at -20°C in presence of 0.3 M NaOAc pH 5.2 and 1 mL ethanol. Precipitated nucleic acids were pelleted by centrifugation at 12000 rpm at 4°C for 30 min, air-dried at 25°C for 1 h, and resuspended in 50 µl of nuclease free water. The quality of the isolated total RNA was estimated by the ratio of absorbance at 260 nm to 280 nm. The presence of contaminating DNA was checked by setting up PCR reactions with a 1000-fold range of resuspended cell pellets and assessing by gel electrophoresis. Samples containing isolated and high-quality total RNA free of contaminating DNA were flash frozen and stored at -80°C.
Ribosomal RNA was depleted from 1.25 μg of purified RNA using the Ribo-Zero bacteria rRNA removal kit (Illumina). Strand-specific RNAseq libraries were prepared from the depleted RNA using the Truseq Stranded mRNA Sample prep kit (Illumina) and sequenced on an Illumina HiSeq 2500 machine by the Bauer Core Facility at the Harvard FAS Center for Systems Biology. Sequencing reads were aligned to the S. elongatus genome using Bowtie (RRID:SCR_005476) as described previously (Markson et al., 2013). We quantified expression of a gene by counting the number of aligned sequencing reads corresponding to the appropriate strand between the start and stop of each gene (gene info obtained from Cyanobase, RRID: SCR_007615), and normalized these values between all samples in this work using median normalization, followed by dividing the median normalized read count value by the length of the open reading frame of the gene, as described previously (Anders and Huber, 2010; Markson et al., 2013). The time course and RNA sequencing was repeated twice for two biological replicates.

treatment_protocol: Cells were exposed to two light/dark cycles (12 hours of dark, followed by 12 h of light, followed by 12 h of dark) for entrainment prior to release into light and 100µM IPTG was added after T=0 hours (time cells are released into light). Cells were collected at designated times by vacuum filtration onto nitrocellulose filters, placed in a 50-ml conical tube, flash frozen in liquid nitrogen, and stored in -80C.

value: OX-D53E rpoD5{delta}

tag: culture medium

value: BG-11M + 100µM IPTG after T=0 hours

tag: time and light condition

value: 9 hours in light

tag: biological replicate

value: biological replicate 2

tag: date experiment was sequenced

value: Fall 2016


title: Sample78_KF047_br2_12

description: processed data file: Table_S1.csv

value: 12 hours in light


title: Sample76_KF047_br2_6

description: processed data file: Table_S1.csv

value: 6 hours in light


title: Sample74_KF047_br2_2

description: processed data file: Table_S1.csv

value: 2 hours in light


title: Sample75_KF047_br2_3

description: processed data file: Table_S1.csv

value: 3 hours in light


title: Sample73_KF047_br2_0_5

description: processed data file: Table_S1.csv

value: 0.5 hours in light


title: Notch2 WT MSCs R1

type: RNA

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip MG-430_2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit.

scan_protocol: Arrays were scanned in a GeneChip 3000 scanner with G7 update.

data_processing: The images were analyzed with RMA as implemented in PartekGS.

label: Biotin

source_name: bone marrow derived MSCs

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix ExpressKit protocol starting from 200 ng total RNA.

growth_protocol: PBMCs from C57B6 Notch2fl/fl mice were generated from the bone marrow. Adherend cells were cultured in MEM Alapha + GlutaMAX medium (Invitrogen) supplemented with 10% fetal calf serum (PAA, Cölbe, Germany), 10% horse Serum.

extract_protocol: Total RNA was extracted by using the RNeasy Mini Kit (Qiagen). Total-RNA concentration and purity of total-RNA samples was measured with the NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific).

treatment_protocol: Cells were incubated overnight in a 1:1 mixture of medium (DMEM w/o FCS) and PBS containing 1 μM Tat-Cre protein (HTNC). BMSCs were then cultured at least 8 days after transduction in DMEM supplemented with PS and 10% FCS before co-culture experiments were performed. Primary CLL cells were cultured on MSCs for 5 days, then washed off and remaining CLL cells removed with anti-CD19 beads.

tag: genotype

value: Notch2 WT

tag: original sample name


title: Notch2 WT MSCs R3


title: testes.H3K36M.1553

city: Boulder

first: Justin

last: Brumbaugh

state: CO

address: 347 UCB

department: Molecular, Cellular, and Developmental Biology

institute: University of Colorado Boulder

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 reference genome mm9 using STAR
Transcript abundance was calculated using Htseq
Genome_build: mm9
Supplementary_files_format_and_content: count

molecule: polyA RNA

source_name: Dissociated testes cells

growth_protocol: Mice used in this study were housed and bred in Specific Pathogen Free (SPF) rooms located in the AAALAC-accredited Center for Comparative Medicine vivarium at Massachusetts General Hospital. Mice were housed in ventilated cages on a standard 12:12 light cycle. All procedures involving mice adhered to the guidelines of the approved Massachusetts General Hospital Institutional Animal Care and Use Committee (IACUC) protocol no. 2006N000104.

extract_protocol:
RNA was purified using the RNeasy plus mini kit (Qiagen) using the provided protocol. RNA-Seq libraries were constructed using the SMARTer v3 kit (Clontech) and sequenced on Illumina HiSeq2500 instrument, resulting in approximately 30 million reads per sample on average.
RNA-Seq libraries were constructed using the SMARTer v3 kit (Clontech)

treatment_protocol: Both male and females were used in this study at 6-8 weeks of age and were induced by adding 2 mg/ml doxycycline to drinking water.

value: C57B6/129 hybrid

value: Testes


title: testes.H3K36M.1485


title: Notch2-/- MSCs + CLL 25


title: Sample71_KF047_br1_12

description: processed data file: Table_S1.csv

value: biological replicate 1


title: Notch2 WT MSCs + CLL 24


title: Notch2-/- MSCs + CLL 24


title: Notch2-/- MSCs + CLL 21


title: Notch2-/- MSCs + CLL 26


title: Notch2-/- MSCs + CLL 22


title: testes.H3K9M.1519


title: Notch2 WT MSCs + CLL 25


title: Notch2 WT MSCs + CLL 26


title: Notch2 WT MSCs + CLL 21


title: Notch2 WT MSCs + CLL 23


title: Notch2-/- MSCs S2


title: Notch2-/- MSCs + CLL 23


title: Notch2-/- MSCs S1


title: testes.H3K9M.1516


title: Sample70_KF047_br1_9

description: processed data file: Table_S1.csv


title: Notch2-/- MSCs S3


title: Sample72_KF047_br2_0

description: processed data file: Table_S1.csv

value: 0 hours in light


title: testes.WT.1477

value: wildtype


title: Notch2 WT MSCs + CLL 22


title: Sample69_KF047_br1_6

description: processed data file: Table_S1.csv


title: Sample68_KF047_br1_3

description: processed data file: Table_S1.csv


title: Notch2 WT MSCs R2


title: Sample65_KF047_br1_0

description: processed data file: Table_S1.csv


title: Sample66_KF047_br1_0_5

description: processed data file: Table_S1.csv


title: intestine.H3K36M.1485

source_name: Dissociated intestinal cells

value: Intestine


title: intestine.H3K9M.1519


title: intestine.H3K9M.1516


title: Sample63_KF048_br2_9

description: processed data file: Table_S1.csv

source_name: S. elongatus PCC 7942 (ATCC 33912) OX-D53E + rpoD6∆

value: OX-D53E rpoD6{delta}


title: intestine.H3K36M.1553


title: intestine.WT.1477


title: BSPC.H3K36M.1312

source_name: hematopoietic stem and progenitor cells (Lin-, cKit+ bone marrow cells)

value: Bone marrow


title: GDpol1-4A-32-rep1

description: Okazaki Fragments

value: W303 tor1-1::HIS3, fpr1::NatMX4, RPL13A-2xFKBP12::TRP1, CDC9-FRB


title: Sample61_KF048_br2_3

description: processed data file: Table_S1.csv

value: BG-11M + 100µM IPTG after T=0 hours

value: biological replicate 2


title: Sample64_KF048_br2_12

description: processed data file: Table_S1.csv

value: 12 hours in light

value: Fall 2016


title: Sample59_KF048_br2_0_5

description: processed data file: Table_S1.csv


title: Sample62_KF048_br2_6

description: processed data file: Table_S1.csv

value: 6 hours in light


title: BSPC.H3K36M.1310


title: BSPC.H3K9M.1363


title: Sample67_KF047_br1_2

description: processed data file: Table_S1.csv

value: OX-D53E rpoD5{delta}

value: 2 hours in light


title: BSPC.WT.1266


title: Sample60_KF048_br2_2

description: processed data file: Table_S1.csv


title: BSPC.H3K9M.1362


title: EB.H3K36M.rep2

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 reference genome hg19 using BWA
Normalized genome coverage bigWig files were generated by Deeptools
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: Embryoid bodies

extract_protocol:
60.000 cells were washed once with 100µl PBS and resuspended in 50µl lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.2% IGEPAL CA-630). The suspension of nuclei was then centrifuged for 10min at 500g at 4°C, followed by the addition of 50µl transposition reaction mix (25µl TD buffer, 2.5µl Tn5 Transposase and 22.5µl Nuclease Free H2O) and incubation at 37°C for 30min. DNA was isolated using MinElute Kit (Qiagen). Libraries were amplified by PCR (13 cycles). After the PCR reaction, the library was selected for fragments between 100 and 1000bp with AmpureXP beads (Beckman Coulter). Libraries were purified with Qiaquick PCR (Qiagen) and integrity checked on a Bioanalyzer before sequencing.
Libraries were amplified by PCR (13 cycles). After the PCR reaction, the library was selected for fragments between 100 and 1000bp with AmpureXP beads (Beckman Coulter). Libraries were purified with Qiaquick PCR (Qiagen) and integrity checked on a Bioanalyzer before sequencing.

value: Cultured from ES cells


title: Sample56_KF048_br1_9

description: processed data file: Table_S1.csv

value: 9 hours in light


title: Sample58_KF048_br2_0

description: processed data file: Table_S1.csv


title: Sample55_KF048_br1_6

description: processed data file: Table_S1.csv


title: intestine.WT.1476

value: C57B6/129 hybrid


title: Sample54_KF048_br1_3

description: processed data file: Table_S1.csv

value: 3 hours in light

value: biological replicate 1


title: EB.H3K9M.rep2


title: EB.H3K36M.rep1


title: EB.H3K9M.rep1


title: EB.WT.rep2

value: wildtype


title: Sample57_KF048_br1_12

description: processed data file: Table_S1.csv


title: Sample51_KF048_br1_0

description: processed data file: Table_S1.csv

value: 0 hours in light


title: Sample50_KF080_br2_12

description: processed data file: Table_S1.csv

source_name: S. elongatus PCC 7942 (ATCC 33912) OX-D53E + rpoD2∆

value: OX-D53E rpoD2{delta}

value: Spring 2017


title: Sample49_KF080_br2_9

description: processed data file: Table_S1.csv


title: BSPC.H3K36M.rep1

value: Bone marrow


title: EB.WT.rep1


title: Sample52_KF048_br1_0_5

description: processed data file: Table_S1.csv

value: OX-D53E rpoD6{delta}

value: BG-11M + 100µM IPTG after T=0 hours

value: 0.5 hours in light


title: Sample53_KF048_br1_2

description: processed data file: Table_S1.csv

value: Fall 2016


title: BSPC.WT.1262


title: BSPC.H3K9M.rep1


title: BSPC.WT.rep2


title: BSPC.WT.rep1


title: Sample44_KF080_br2_0_5_sa

description: processed data file: Table_S1.csv

value: biological replicate 2


title: Sample47_KF080_br2_3

description: processed data file: Table_S1.csv


title: Sample45_KF080_br2_0_5_sb

description: processed data file: Table_S1.csv


title: Sample43_KF080_br2_0

description: processed data file: Table_S1.csv


title: Sample46_KF080_br2_2

description: processed data file: Table_S1.csv


title: Sample42_KF080_br1_12_sb

description: processed data file: Table_S1.csv

value: 12 hours in light


title: v003_Vglut2CreTom

city: Solna

first: Patrik

last: Ernfors

address: Biomedicum, Solnavägen 9

department: MBB/Molneuro

country: Sweden

institute: Karolinska Institutet

description: FACS Vglut2Cre-Tomato

data_processing:
All individual samples were process with cellranger-2.1.1 with transcriptome refdata-cellranger-mm10-1.2.0.
Genome_build: mm10
Supplementary_files_format_and_content: Aligned output bam files and from CellRanger count output. Processed data includes normalized UMI counts matrix with the assigned celltype clusters, where rows are geneIDs and columns cellIDs, from the clustering performed with Seurat 2 ( explained in Methods).  Corresponding annotation text files, where rows are CellIDs and columns different annotation ( nGene, nUMI,  Sample, percent.mito, Cluster).

source_name: Vagal ganglion complex

extract_protocol:
Isolated ganglia were dissociated using Papain and Collagenase/Dispase. The suspensions were filtered using a cell strainer and cleaned through density gradient centrifugation.
cDNA libraries have been constructed with the kit from 10x Genomics Single Cell 3' v2 and were compatible with standard Illumina sequencing

value: jugular and nodose ganglia

value: 5 weeks


title: Sample48_KF080_br2_6

description: processed data file: Table_S1.csv

value: 6 hours in light


title: BSPC.H3K9M.rep2

value: C57B6/129 hybrid


title: Sample41_KF080_br1_12_sa

description: processed data file: Table_S1.csv


title: v103_WT

description: unbiased cell suspension


title: BSPC.H3K36M.rep2


title: Sample40_KF080_br1_9

description: processed data file: Table_S1.csv

value: 9 hours in light


title: Sample39_KF080_br1_6

description: processed data file: Table_S1.csv

value: biological replicate 1


title: WE-AKT-E17K-Het_9

city: Amsterdam

first: Max

middle: D

last: Wellenstein

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description:
3663_45_45_ATGTCAG
Stranded

data_processing:
The reads were aligned against the mouse transcriptome (mm10) using Tophat2 (Tophat version 2.1.0 / Bowtie version 1.0.0)
Stranded samples were aligned and analysed in a non-stranded way
Genecounts were generated using a custom script but gives the same output as HTSeq-count
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated files with the number of readcounts per gene

source_name: Tumour

extract_protocol:
Total RNA was extracted using TRIzol reagent as per the manufacturer’s protocol
Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit according to the manufacturer’s instructions. Non stranded libraries were generated using the TruSeq V2 mRNA library preparation kit according the manufacturer’s instructions
Libraries were sequenced 50/51 or 65 bp single end

value: FVB/N


title: WE-AKT-E17K-Het_12

description:
3663_48_48_GTGAAAC
Stranded


title: Sample38_KF080_br1_3

description: processed data file: Table_S1.csv

value: 3 hours in light


title: WE-AKT-E17K-Het_8

description:
3663_44_44_AGTTCCG
Stranded


title: WE-AKT-E17K-Het_10

description:
3663_46_46_CCGTCCC
Stranded


title: WE-AKT-E17K-Het_7

description:
3663_43_43_AGTCAAC
Stranded


title: WE-AKT-E17K-Het_11

description:
3663_47_47_GTCCGCA
Stranded


title: Sample36_KF080_br1_0_5

description: processed data file: Table_S1.csv

value: OX-D53E rpoD2{delta}


title: Sample35_KF080_br1_0

description: processed data file: Table_S1.csv

value: 0 hours in light

value: Spring 2017


title: Sample33_OXD53E_br2_9

description: processed data file: Table_S1.csv

source_name: S. elongatus PCC 7942 (ATCC 33912) + kaiBC∆ + rpaA∆ + Ptrc::rpaA(D53E); hereafter OX-D53E strain


title: Sample37_KF080_br1_2

description: processed data file: Table_S1.csv

value: 2 hours in light


title: Sample34_OXD53E_br2_12

description: processed data file: Table_S1.csv

value: BG-11M + 100µM IPTG after T=0 hours


title: Sample32_OXD53E_br2_6

description: processed data file: Table_S1.csv


title: WE-AKT-E17K-Het_5

description:
3663_41_41_CAGATCA
Stranded


title: WE-AKT-E17K-Het_6

description:
3663_42_42_CTTGTAA
Stranded


title: WE-AKT-E17K-Het_4

description:
3663_40_40_GCCAATA
Stranded


title: Sample30_OXD53E_br2_2

description: processed data file: Table_S1.csv


title: Sample31_OXD53E_br2_3

description: processed data file: Table_S1.csv


title: WE-AKT-E17K-Het_3

description:
3663_39_39_ACAGTGA
Stranded


title: Sample29_OXD53E_br2_0_5

description: processed data file: Table_S1.csv

value: 0.5 hours in light


title: v102_WT

description: unbiased cell suspension


title: WE-AKT-E17K-Het_2

description:
3663_38_38_TGACCAA
Stranded


title: WE-AKT-E17K-Het_1

description:
3663_37_37_CGATGTA
Stranded


title: WE-AKT-E17K-Hom_12

description:
3663_36_36_ATTCCTT
Stranded


title: Sample27_OXD53E_br1_12

description: processed data file: Table_S1.csv

value: Fall 2016


title: Sample28_OXD53E_br2_0

description: processed data file: Table_S1.csv

value: biological replicate 2


title: Sample26_OXD53E_br1_9

description: processed data file: Table_S1.csv


title: WE-AKT-E17K-Hom_11

description:
3663_35_35_ACTGATA
Stranded


title: Sample24_OXD53E_br1_3

description: processed data file: Table_S1.csv


title: WE-AKT-E17K-Hom_10

description:
3663_34_34_GAGTGGA
Stranded


title: v005_Vglut2CreTom

description: FACS Vglut2Cre-Tomato


title: Sample23_OXD53E_br1_2

description: processed data file: Table_S1.csv


title: Sample21_OXD53E_br1_0

description: processed data file: Table_S1.csv


title: WE-AKT-E17K-Hom_6

description:
3663_30_30_GGCTACA
Stranded


title: Sample22_OXD53E_br1_0_5

description: processed data file: Table_S1.csv


title: Sample19_KF065_br2_40

description: processed data file: Table_S1.csv

source_name: S. elongatus PCC 7942 (ATCC 33912) + sigF2∆

treatment_protocol: Cells were exposed to two light/dark cycles (12 hours of dark, followed by 12 h of light, followed by 12 h of dark) for entrainment prior to release into continuous light. Cells were collected at designated times by vacuum filtration onto nitrocellulose filters, placed in a 50-ml conical tube, flash frozen in liquid nitrogen, and stored in -80C.

value: 40 hours in constant light


title: WE-AKT-E17K-Hom_5

description:
3663_29_29_TAGCTTA
Stranded


title: WE-AKT-E17K-Hom_7

description:
3663_31_31_GTGGCCT
Stranded


title: Sample18_KF065_br2_36_sc

description: processed data file: Table_S1.csv

value: 36 hours in constant light


title: Sample20_KF065_br2_44

description: processed data file: Table_S1.csv

value: 44 hours in constant light


title: WE-AKT-E17K-Hom_3

description:
3663_27_27_ACTTGAA
Stranded


title: Sample17_KF065_br2_36_sb

description: processed data file: Table_S1.csv


title: WE-AKT-E17K-Hom_4

description:
3663_28_28_GATCAGA
Stranded


title: testes.WT.1476

value: Testes

value: wildtype


title: WE-AKT-E17K-Hom_1

description:
3663_25_25_ATCACGA
Stranded


title: WE-AKT-E17K-Hom_2

description:
3663_26_26_TTAGGCA
Stranded


title: Sample16_KF065_br2_36_sa

description: processed data file: Table_S1.csv


title: Sample15_KF065_br2_32

description: processed data file: Table_S1.csv

value: 32 hours in constant light


title: WE-PIK3CA-E545K_12

description:
3663_24_24_GTGAAAC
Stranded


title: WE-PIK3CA-E545K_11

description:
3663_23_23_GTCCGCA
Stranded


title: Sample14_KF065_br2_28

description: processed data file: Table_S1.csv

value: 28 hours in constant light


title: Sample13_KF065_br2_24

description: processed data file: Table_S1.csv

value: 24 hours in constant light


title: WE-PIK3CA-E545K_10

description:
3663_22_22_CCGTCCC
Stranded

value: FVB/N


title: Sample12_KF065_br1_44

description: processed data file: Table_S1.csv

value: biological replicate 1


title: WE-AKT-E17K-Hom_9

description:
3663_33_33_CGTACGT
Stranded


title: WE-AKT-E17K-Hom_8

description:
3663_32_32_GTTTCGG
Stranded


title: WE-PIK3CA-E545K_8

description:
3663_20_20_AGTTCCG
Stranded


title: Sample11_KF065_br1_40

description: processed data file: Table_S1.csv


title: Sample10_KF065_br1_36

description: processed data file: Table_S1.csv


title: Sample9_KF065_br1_32

description: processed data file: Table_S1.csv


title: WE-PIK3CA-E545K_6

description:
3663_18_18_CTTGTAA
Stranded


title: WE-PIK3CA-E545K_4

description:
3663_16_16_GCCAATA
Stranded


title: WE-PIK3CA-E545K_9

description:
3663_21_21_ATGTCAG
Stranded


title: WE-PIK3CA-E545K_5

description:
3663_17_17_CAGATCA
Stranded


title: Sample6_RNAPrif_br1_44

description: processed data file: Table_S0.csv

source_name: S. elongatus PCC 7942 (ATCC 33912) + Addgene 102337 (Plasmid encoding C-terminal FLAG tag RNA polymerase Beta’ subunit (Synpcc7942_1524) with Kan selection marker, targeted to integrate at native gene locus)

extract_protocol:
Samples were thawed on ice and resuspended in 300 µl of ice-cold lysis buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1-percent Triton X-100, 0.1-percent sodium deoxycholate, and 1x Roche Complete EDTA-free Protease Inhibitor Cocktail). Cells were lysed by bead beating at 4°C in 2 ml screw-top tubes with 0.1 mm glass beads for 10 cycles of 30 s each separated by at least 30 s of cooling on ice. Lysate was separated from the beads by piercing the bottom of each tube with a small-diameter needle, placing the tube into a clean 1.5 ml microcentrifuge tube, and centrifuging for several minutes at 1000 x g at 4°C to transfer the lysate to the 1.5-ml tube. Chromatin was then sheared to a length of 250-400 bp by sonication at 4°C in Covaris S220 sonicator with settings: peak incident power 175, duty factor 10, cycles per burst 200, time 160 s. Cell debris was removed by centrifuging twice at 14,000 x g for 15 min each at 4 C. Protein concentration in the lysates was determined by BCA assay using BSA as a standard. For a given ChIP time-course, equal mass quantities (typically 1 mg) of lysate from each time point were prepared in 500 ul of lysis buffer each. For anti-FLAG ChIP, 40 ul (bed volume) of anti-FLAG magnetic beads (Sigma) equilibrated in lysis buffer were added to each tube. Samples were incubated overnight in the dark at 4°C with continuous rotation. Beads were isolated by placement on magnetic stand for 1 min. Beads were then washed twice with 1 ml lysis buffer, once with 1 ml of buffer B (50 mM HEPES pH 7.5, 500 mM NaCl, 1 mM EDTA, 1-percent Triton X-100, 0.1-percent sodium deoxycholate), once with 1 ml of wash buffer (10 mM TrisCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5-percent NP-40, 0.1-percent sodium deoxycholate) and finally with 1 ml of TE pH 7.5 (10 mM TrisCl pH 7.5, 1 mM EDTA); each wash was conducted for 5 min at room temperature on a tube rotator followed by isolation of beads by centrifugation for 1 min at 1000 x g at 25°C. Protein-DNA complexes were then eluted with 250 µl elution buffer (50 mM TrisCl pH 8.0, 10 mM EDTA, 1-percent SDS) for 1h at 65°C.  For both the eluate and a matched sample of lysate not subjected to immunoprecipitation, crosslinks were reversed for 6-18h at 65°C. Next, 250 µl of TE was added to each sample to dilute the SDS, followed by addition of 100 µg of proteinase K and 80 µg of glycogen. Samples were incubated for 2h at 37°C to digest proteins. Samples were then supplemented with 55 µl of 4 M LiCl and extracted with 1 ml of phenol/chloroform/isoamyl alcohol followed by extraction with 1 ml chloroform. DNA in the aqueous phase was precipitated with 0.3 M NaOAc pH 5.2 and 1 ml ethanol at for 1 h at -20°C. Precipitated DNA was pelleted by centrifugation 14000 x g at 4°C for 30 min. Pellets were air-dried and then resuspended in 50 µl of TE containing 20 ng/ml of DNase-free RNase (Fermentas) and incubated for 1h at 37°C to digest RNA. Samples were then supplemented with 150 µl of TE and 22.2 µl of 3 M sodium acetate pH 5.2, extracted with phenol/chloroform/isoamyl alcohol, and precipitated with 0.3 M NaOAc and ethanol for 1h at -20°C. Precipitated DNA was pelleted by centrifugation 14000 x g at 4°C for 30 min. Pellets were air-dried and then resuspended in 50 µl of TE. DNA concentration in ChIP samples was estimated by PicoGreen assay (Invitrogen). Typical immunoprecipitation efficiencies (fraction of flag-tagged sigma factor depleted from the lysate) were greater than 50-percent.
Libraries for Illumina sequencing of ChIP DNA were prepared following a protocol developed by Ethan Ford (http://ethanomics.files.wordpress.com/2012/09/chip_truseq.pdf), with modifications. Specifically, 0.15-3 ng of ChIP DNA was used for each sample. DNA ends were blunted by treatment with 1.4 units of T4 DNA polymerase (NEB), 0.45 units of Klenow fragment (NEB), 4.5 units of T4 polynucleotide kinase (NEB), and 0.4 mM dNTPs (NEB) in 1x T4 DNA ligase buffer (NEB) in a total of 50 µl volume for 30 min at 20°C. DNA was purified using 50 µl of AMPure XP beads (Beckman) and 50 µl of a solution containing 20-percent PEG8000 (Sigma) and 1.25 M NaCl. DNA was eluted in 16.5 µl of TE/10 (10 mM TrisCl pH 8.0, 0.1 mM EDTA). DNA was then A-tailed at the 3’ ends by treating the eluate with 2.5 units of Klenow fragment lacking 3’ to 5’ exonuclease activity (NEB) and 0.2 mM dATP (GE Healthcare) in 1x NEB Buffer 2 (NEB) in a total volume of 20 µl for 30 min at 37°C. TruSeq adapters (Eurofins MWG Operon) were ligated onto the A-tailed DNA by addition of 25 µl of 2X Quick Ligase Buffer (NEB), 0.5 µl of 250 nM TruSeq adaptor, 3 µl of nuclease-free H2O, and 1.5 µl of Quick Ligase (NEB) followed by incubation for 20 min at 21°C. The ligation reaction was stopped by addition of 5 µl of 0.5 M EDTA pH 8.0 (Ambion). Next, DNA was purified using 55 µl of AMPure XP beads without additional PEG or salt. DNA was eluted in 15.5 µl of TE/10. The Y-shaped adapters were then linearized with 5 cycles of PCR (initial denaturation of 30 s at 98 C followed by 5 cycles of [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] followed by 5 min at 72°C) using Phusion polymerase (Life Technologies) and 1 µl of TruSeq primers (25 µM) in a total volume of 31 µL. Linearized DNA was purified using 30 µl of AMPure XP beads without additional PEG or salt. DNA was eluted in 30 µl of TE/10. Fragments between 300 and 500 base pairs in length were size-selected using agarose gel purification and the QIAquick gel extraction kit (QIAGEN). Purified DNA was further amplified with 13-14 cycles of PCR, as described above, in a total volume of 62.5 µl. Following PCR, DNA was purified using 51 µl of AMPure XP beads without additional PEG or salt. DNA was eluted in 12 µl of TE/10. Average fragment sizes for libraries were assessed using a DNA High Sensitivity chip on Agilent 2200 Tapestation. Samples were sequenced at the Harvard FAS Center for Systems Biology. Reads were aligned to the S. elongatus genome (chromosome: NC_007604.1; plasmids: NC_004073.2 and NC_004990.1) using Bowtie (Langmead et al., 2009) counting only those aligned uniquely to one location with up to three mismatches.

treatment_protocol: Cells were exposed to two light/dark cycles (12 hours of dark, followed by 12 h of light, followed by 12 h of dark) for entrainment prior to release into continuous light. For the chromatin immunoprecipitation of epitope-tagged RNA polymerase (gift of A. Puszynska), cells were treated with rifampicin for 20 min at 30°C prior to crosslinking with 1-percent formaldehyde and quenching with 125 mM glycine. Cells were collected by centrifugation for 10 min at 6000 x g at 4°C and then washed twice with 30 ml of ice-cold phosphate-buffered saline (PBS), centrifuging for 10 min at 3000 x g at 4 C after each wash. Samples were then resuspended in 1 ml ice-cold PBS and pelleted in a microcentrifuge tube for 3 min at 3000 x g at 4°C. The supernatant was discarded and the pellet was flash frozen in liquid nitrogen and stored at 80 C.

value: RNAP beta'-(FLAG)c

value: Fall 2014


title: Sample7_KF065_br1_24

description: processed data file: Table_S1.csv

value: Spring 2017


title: Sample8_KF065_br1_28

description: processed data file: Table_S1.csv


title: Sample4_RNAPrif_br1_36

description: processed data file: Table_S0.csv


title: WE-PIK3CA-E545K_3

description:
3663_15_15_ACAGTGA
Stranded


title: Sample3_RNAPrif_br1_32

description: processed data file: Table_S0.csv


title: Sample2_RNAPrif_br1_28

description: processed data file: Table_S0.csv


title: WE-PIK3CA-H1047R_12

description:
3663_12_12_ATTCCTT
Stranded


title: WE-PIK3CA-E545K_1

description:
3663_13_13_CGATGTA
Stranded


title: WE-PIK3CA-E545K_2

description:
3663_14_14_TGACCAA
Stranded


title: WE-PIK3CA-H1047R_10

description:
3663_10_10_GAGTGGA
Stranded


title: WE-PIK3CA-H1047R_11

description:
3663_11_11_ACTGATA
Stranded


title: WE-PIK3CA-H1047R_9

description:
3663_9_9_CGTACGT
Stranded


title: Sample1_RNAPrif_br1_24

description: processed data file: Table_S0.csv


title: IFN 1

city: St Lucia

first: Andrii

last: Slonchak

state: QLD

address: Bldg 76 Cooper Rd

department: School of Chemistry and Molecular Biosciences

institute: The University Of Queensland

data_processing:
Reads were mapped to human genome assembly hg38 using STAR v2.5.2  with default configurations
Reads were counted using HTSeq v0.7.0.1 with default configurations in union mode and counting to “exon” feature. For counting the RNA transcripts and small noncoding RNAs from EVs, gene feature format (GFF) files were obtained from UCSC genome browser (assembly GRCh38/hg38, Dec. 2013). GFF files with coordinates of miRNAs were obtained from miRBase (release 21).
Genome_build: hg38
Supplementary_files_format_and_content: .xls file as produced from HTSeq outputs and contains row counts for miRNA and snoRNAs

source_name: Lung carcinoma cells_IFN alpha 2a

growth_protocol: Human lung carcinoma cells (A549) [ATCC CCL-185] were cultured in F12K medium supplemented with 10% heat-inactivated FBS,100 units penicillin ml−1, 100 µg streptomycin ml−1, 0.29 mg l-glutamine ml−1 (Gibco) and 1 mM sodium pyruvate. Cells were maintained at 37 °C in CO2 incubator.

extract_protocol:
EVs were isolated from conditioned media using ExoQuick-TC (Systems Bioscience, Mountain View, CA) per manufacturer’s protocol. To inactivate and remove contaminating virus particles prior to exosome extraction, 1u/ml RNaseA (Sigma, USA) was added to the conditioned media followed by heating at 56°C for 1 hour and centrifugation for 15 min at 3000 x g, 4oC. RNA was then extracted from pelleted extracellular vesicles using mirVana miRNA isolation Kit (Ambion, USA).
cDNA libraries were prepared using a TruSeq RNA Library Prep Kit (v2) (Illumina Inc., USA)

treatment_protocol: Cells were infected with Kunjin strain of West Nile virus at multiplicity of infection (MOI) = 1 by incubation of cells with 45 μl of inoculum per cm2 of growth area for 2h at 37oC. After inoculum was removed, the cells were washed twice with PBS, and fresh medium was added. Human interferon alpha 2a (Roche, USA) was added to cells at final concentration of 300u/ml for 24h. Infected and IFN-treated cells cells were maintained in exosomes-free F12K medium (Gibgo, USA) supplemented with 2% FBS.

tag: cell compartment

value: Extracellular vesicles


title: IFN 2


title: WE-PIK3CA-H1047R_8

description:
3663_8_8_GTTTCGG
Stranded


title: WNV 2

source_name: Lung carcinoma cells_west nile virus


title: WE-PIK3CA-H1047R_7

description:
3663_7_7_GTGGCCT
Stranded


title: WE-PIK3CA-H1047R_6

description:
3663_6_6_GGCTACA
Stranded


title: WE-PIK3CA-E545K_7

description:
3663_19_19_AGTCAAC
Stranded


title: Mock 2

source_name: Lung carcinoma cells_mock


title: WE-PIK3CA-H1047R_4

description:
3663_4_4_GATCAGA
Stranded


title: WE-PIK3CA-H1047R_3

description:
3663_3_3_ACTTGAA
Stranded


title: CLL-06 COCULTURE

first: Ingo

last: Ringshausen

address: Cambridge biomedical campus

country: United Kingdom

institute: University of Cambridge

data_processing:
Illumina Csava 1.8,2 software used for base-calling
merged fastaq packages of each sample were subject to adapter trimming using Trimmomatic 0.30 software tool. Trimmed sequences were aligned to the human genome 19 using aligner STAR
Sorted alignments were imported into StrandNGS (AvadisNGS)
For quantification of RNAs was used PartekGS
Genome_build: Hg19
Supplementary_files_format_and_content: excel file include raw data and RPKM for each samples, ratio, forld change and p-value

source_name: Primary CLL cells growing for 48h in coculture with EL08-1d1 cells

growth_protocol: Primary CLL cells were isolated from peripheral blood of 6 different patients and cultured with RPMI supplemented with 5% fetal calf serum. Adherend cells were cultured in MEM Alapha + GlutaMAX medium (Invitrogen) supplemented with 10% fetal calf serum (PAA, Cölbe, Germany), 10% horse Serum.

extract_protocol:
Total RNA was extracted by using the RNeasy Mini Kit (Qiagen). Total-RNA concentration and purity of total-RNA samples was measured with the NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific).
Libraries were prepared for sequencing using standard illumina protocols

tag: subject

value: patient 6

tag: diagnosis

value: chronic lymphocytic leukemia (CLL)

value: CD19+CD5+ CLL CELLS


title: CLL-06 MONOCULTURE

source_name: Primary CLL cells cultured for 4h in normal growing medium


title: WE-PIK3CA-H1047R_2

description:
3663_2_2_TTAGGCA
Stranded

tag: strain


title: WE-PIK3CA-H1047R_1

description:
3663_1_1_ATCACGA
Stranded

tag: genotype/variation


title: CLL-05 MONOCULTURE

value: patient 5


title: CLL-04 MONOCULTURE

value: patient 4


title: WNV 1

tag: cell line


title: CLL-04 COCULTURE


title: WB1P_8

description:
3279_28_WB1P-Myc_14TMB176_tumor_3_control_GATCAGA
Stranded


title: CLL-05 COCULTURE


title: WE-PIK3CA-H1047R_5

description:
3663_5_5_TAGCTTA
Stranded


title: WB1P_7

description:
3279_27_WB1P-Myc_14TMB176_tumor_2_control_ACTTGAA
Stranded


title: WB1P_10

description:
3279_30_WB1P-Myc_14TMB196_tumor_1_control_GGCTACA
Stranded


title: CLL-03 COCULTURE

value: patient 3


title: CLL-03 MONOCULTURE


title: Mock 1


title: WB1P_9

description:
3279_29_WB1P-Myc_14TMB195_tumor_1_control_TAGCTTA
Stranded


title: WB1P_6

description:
3279_26_WB1P-Myc_14TMB176_tumor_1_control_TTAGGCA
Stranded


title: CLL-02 COCULTURE

value: patient 2


title: WB1P_5

description:
3279_23_WB1P-Myc_14TMB167_tumor_1_control_GTCCGCA
Stranded


title: MZ dual-κ rep2

city: Aurora

first: Roberta

last: Pelanda

address: 12800 East 19th Avenue

department: Immunology&Microbiology

institute: University of Colorado Anschutz Medical Campus

description:
MZ_dual_sort2_trep1_chip2
MZ_dual_sort2_trep1_chip3

data_processing:
Basecalling, barcode demultiplexing and adapter trimming was performed by Ion Torrent Suite 5.0.2.
Sequence reads of at least 30 nt length were mapped to the mm10 release of the mouse genome using STAR (version 2.4.1d) with splice site data from the Ensembl annotation release 78.
Reads mapping unambiguously to each gene in the Ensembl annotation were quantified using the htseq-count program from the HTSeq package (version 0.6.1) in the “intersection-nonempty” mode.
Statistical comparisons of the gene expression between the cell genotypes were performed with the DESeq2 package version 1.8.1 for the R statistical software version 3.2.0.
Genome_build: mm10
Supplementary_files_format_and_content: read counts assigned to each gene and sample, as tab-separated text table (derived from htseq-count)

source_name: spleen

extract_protocol:
Splenocytes were sorted and total RNA was extracted using the Qiagen RNeasy Micro Kit.
A modified Clontech SMARTer® Ultra™ Low Input RNA Kit for Sequencing - v3 (Mountain View, CA, USA) and modified Kapa Biosystems KAPA Hyper Prep Kit (Wilmington, MA, USA) were used. Briefly, library construction started with 1 ng of RNA, followed by SMARTer 1st strand cDNA synthesis, full length dscDNA amplification by LD-PCR, followed by purification and validation. Afterward, the samples were sheared using a Covaris focused-ultrasonicator, concentrated by vacuum, and then processed through the Kapa protocol. The Kapa protocol consisted of end repair and A-tailing, adapter ligation, library amplification, and a post-amplification cleanup step. Once validated, the libraries were sequenced as barcoded-pooled samples on a P1 Ion Proton chip.

value: MRL/lpr

tag: tissue

value: spleen

tag: cell population

value: Marginal Zone B cells

tag: phenotype

value: CD3- CD22+ CD21high CD1dhigh


title: MZ dual-κ rep1


title: MZ single-κ rep3

description:
MZ_single_sort3_trep1_chip2
MZ_single_sort3_trep1_chip3


title: WB1P_4

description:
3279_22_WB1P-Myc_14TMB153_tumor_2_control_CCGTCCC
Stranded

value: FVB/N


title: CLL-02 MONOCULTURE

tag: cell type


title: CLL-01 COCULTURE

value: patient 1


title: MZ single-κ rep2

description:
MZ_single_sort2_trep1_chip2
MZ_single_sort2_trep1_chip3


title: MZ single-κ rep1


title: FO dual-κ rep3

description:
FO_dual_sort3_trep1_chip2
FO_dual_sort3_trep1_chip3

value: Follicular B cells

value: CD3- CD22+ CD21+ CD1dlow CD24low


title: CLL-01 MONOCULTURE


title: WB1P_3

description:
3279_21_WB1P-Myc_14TMB153_tumor_1_control_ATGTCAG
Stranded


title: FO dual-κ rep2

description:
FO_dual_sort2_trep1_chip2
FO_dual_sort2_trep1_chip3


title: MZ dual-κ rep3

description:
MZ_dual_sort3_trep1_chip2
MZ_dual_sort3_trep1_chip3


title: FO dual-κ rep1


title: WB1P-MYC_20

description:
3279_20_WB1P-Myc_14TMB178_tumor_2A_AGTTCCG
Stranded


title: FO single-κ rep3

description:
FO_single_sort3_trep1_chip2
FO_single_sort3_trep1_chip3


title: FO single-κ rep2

description:
FO_single_sort2_trep1_chip2
FO_single_sort2_trep1_chip3


title: WB1P-MYC_19

description:
3279_19_WB1P-Myc_14TMB178_tumor_1A_AGTCAAC
Stranded


title: DK5955_C RibosomeProfiling

city: Bloomington

first: Daniel

middle: B.

last: Kearns

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University

description: Ribosome protected mRNA fragments

data_processing:
Library strategy: RibosomeProfiling
Basecalls were performed using RTA version 2.4.11
For processed data files, NGSutils verson 0.5.9 was used to remove sequencing adapters and filter out any reads shorter than 25 bp. Fastx version 0.0.13 was subsequently used to remove the first base from each read and resulting reads were aligned to the NCIB 3610 genome (NZ_CP020102.1) using Bowtie version 1.1.2. Reads that uniquely aligned to the genome were assigned to a single position corresponding to the 15th nucleotide from the 3’ end.
Genome_build: Bacillus subtilis NCIB 3610 (NZ_CP020102.1)
Supplementary_files_format_and_content: Wig files with the first column containing the chromosome position and the second column containing the number of reads that mapped to that position.

organism: Bacillus subtilis

source_name: batch culture

growth_protocol: Cells were grown shaking in 300 mL lysogeny broth to an OD600 of 0.3-0.4, isolated by rapid filtration, and flash frozen in liquid nitrogen.

extract_protocol:
Following lysis, 25 A260 units of lysate were digested with 1500 units of S7 micrococcal nuclease (Roche 10107921001) for 1 hr at room temp after which the reaction was quenched by the addition of EGTA to a final concentration of 6 mM. The digested lysate was then applied to a 10%-50% sucrose gradient and centrifuged in a Ti-40 rotor at 35,000 rpm for 2.5 hrs at 4°C. 700 µL of fractions containing 70S ribosomes were denatured in 1% SDS and extracted once with an equal volume of hot acid phenol, once with an equal volume of room temp acid phenol, and RNA was precipitated with isopropanol. The precipitant was resuspended in 12 µL H2O and 25 µg RNA was mixed with 2X loading dye (10 mM EDTA, 30 μg/mL bromophenol blue, and 98% formamide) and resolved on a 15% polyacrylamide TBE Urea gen run at 250 V for 40 min. After staining the gel in SYBR Gold (Sigma S11494) for 3 min, products between ~15 and 40 bp were excised and subsequently gel extracted.
RNA 3' ends were dephosphorylated with T4 poly-nucleotide kinase (Lucigen). Dephosporylated RNA was subsequently ligated to Linker 1 (IDT /5rApp/CTGTAGGCACCATCAAT/3ddC/)  with T4 RNA ligase 2, truncated (NEB) and products between 30-100 bp were gel extracted. Isolated RNA was then reverse transcribed using Superscript III (Invitrogen) with the reverse transcription primer (IDT 5′-(Phos)-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC-(SpC18)-CACTCA-(SpC18)-TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGC CTACAG-3). RNA was subsequently hydrolyzed by the addition of 2.2 µL 1N NaOH and incubation at 98C for 20 min. cDNA products were isolated by gel extraction and circularized using CircLigase (Epicentre). Circularized products were  used as a template for PCR reactions using Phusion Polymerase (NEB M0530S) with forward library primer (IDT 5′-AATGATACGGCGACCACCGAGATCTACAC-3′) and Indexed reverse library primer (IDT 5′-CAAGCAGAAGACGGCATACGAGATNNNNNNNNGACTGGAGTTCAGACGTGTGCTCTTCCG-3′) where NNNNNNNN represents the barcode sequence unique to each library. After 6-10 cycles, two PCR reactions per sample with no apparent duplexed products after resolution of 2 μL on an 8% polyacrylamide TBE urea gel were pooled and DNA was purified with a QIAquick kit (Qiagen) and eluted in 20 µL H2O.

treatment_protocol: Cells were lysed in 650 µL lysis buffer (10 mM MgCl2, 100 mM NH4Cl, 5 mM CaCl2, 20 mM Tris pH 8.0, 0.1% NP-40, 0.4% Triton X-100, 0.1 units/µL RNase free DNase I (Invitrogen AM2222), 0.5 units/μL Superase-In (Invitrogen AM2696)) using a Spex 6875 freezer mill set to 10 cycles of 2 min runs at 15 cps separated by 2 min rests.

value: batch culture

value: comIQ12 <delta>efp nusGN21S

tag: growth medium

value: Lysogeny Broth

tag: growth temperature


title: dyrk1aakrb1 (mutant, -/-) -2_32hpf

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description:
dyrk1aa knock down
D1a-2

data_processing:
Illumina Casava1.7 software used for basecalling.
mapped to danRer10 whole genome using STAR v2.5.1.
Gene expression levels were calculated count-per-million (CPM) values normalized with trimmed mean of M-values (TMM) using a edgeR v.3.12.1. The CPM values are on log2 scale.
Genome_build: danRer10
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

organism: Danio rerio

source_name: Whole embryos

growth_protocol: Zebrafish (Danio rerio) embryos of AB (wild type,+/+) strain and dyrk1aakrb1(-/-) mutant in the Tg(kdrl:egfp) background  were maintained with  E3 Egg water (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4) in a petri dish with a diameter of 95 mm at 28.5℃ until 32 hpf and the embyros were incubated in 1XPTU ( 0.003% 1-phenyl 2-thiourea)-E3 egg water after 6 hpf.

extract_protocol:
Total RNA was isolated from embryos of AB (wild type,+/+) and dyrk1aakrb1(-/-) mutant at 32 hpf using Trizol reagent and RNA quality was validated by Agilent 2100 bioanalyzer using RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands)
The sequencing library was prepared using the Lexogen SENSE mRNA Library Preparation Kit.

value: dyrk1aakrb1(-/-), Tg(kdrl:egfp)

value: whole embryo

tag: age

value: 32 hpf


title: DK5955_B RibosomeProfiling

description: Ribosome protected mRNA fragments


title: WB1P-MYC_17

description:
3279_17_WB1P-Myc_14TMB130_tumor_1A_CAGATCA
Stranded


title: dyrk1aakrb1 (mutant, -/-) -1_32hpf

description:
dyrk1aa knock down
D1a-1


title: FO single-κ rep1

description:
FO_single_sort1_trep1_chip1
FO_single_sort1_trep2_chip1


title: DK5518_C RibosomeProfiling

description: Ribosome protected mRNA fragments

value: comIQ12 <delta>efp fliYS164A


title: AB (WT, +/+) -1_32hpf

description:
Control sample
AB-1

value: AB (+/+), Tg(kdrl:egfp)


title: AB (WT, +/+) -2_32hpf

description:
Control sample
AB-2


title: DK5955_A RibosomeProfiling

description: Ribosome protected mRNA fragments


title: WB1P-MYC_16

description:
3279_16_WB1P-Myc_14TMB115_tumor_2A_GCCAATA
Stranded


title: OV miR-17~92 B-cells

description: filtered_Bcell_miR17-92_normCounts_rlog.csv

source_name: B-cells / spleen

extract_protocol:
Total RNA, followed by gel purification of small RNAs
NEBNext small RNA library prep kit

value: Eu-myc mice


title: Sample25_OXD53E_br1_6

description: processed data file: Table_S1.csv

tag: culture medium

value: BG-11M + 100µM IPTG after T=0 hours

tag: time and light condition

value: 6 hours in light

tag: biological replicate

value: biological replicate 1

value: Fall 2016


title: fl/fl miR-17~92 B-cells


title: DK5518_A RibosomeProfiling

description: Ribosome protected mRNA fragments

tag: genotype


title: DK5518_B RibosomeProfiling

description: Ribosome protected mRNA fragments


title: WB1P-MYC_18

description:
3279_18_WB1P-Myc_14TMB130_tumor_2_CTTGTAA
Stranded

value: FVB/N


title: WB1P-MYC_15

description:
3279_15_WB1P-Myc_14TMB115_tumor_1A_ACAGTGA
Stranded


title: WB1P-MYC_14

description:
3279_14_WB1P-Myc_14TMB114_tumor_2A_TGACCAA
Stranded


title: DK2050_C RibosomeProfiling

description: Ribosome protected mRNA fragments

value: comIQ12 <delta>efp


title: WB1P-MYC_13

description:
3279_13_WB1P-Myc_14TMB114_tumor_1A_CGATGTA
Stranded


title: WE-PTEN_18

description:
2865_18_11SJK226-04_B
Non Stranded


title: WE-PTEN_16

description:
2865_16_11SJK215-03_B
Non Stranded


title: WB1P-MYC_12

description:
3279_12_WB1P-Myc_14TMB106_tumor_2A_ATTCCTT
Stranded


title: DK2050_B RibosomeProfiling

description: Ribosome protected mRNA fragments


title: WE-PTEN_19

description:
2865_19_11SJK231-04_B
Non Stranded


title: DK2050_A RibosomeProfiling

description: Ribosome protected mRNA fragments


title: WE-PTEN_14

description:
2865_14_11SJK214-04_B
Non Stranded


title: WE-PTEN_13

description:
2865_13_11SJK214-03_B
Non Stranded


title: DK1042_C RibosomeProfiling

description: Ribosome protected mRNA fragments


title: WB1P-MYC_10

description:
3279_10_WB1P-Myc_14TMB95_tumor_4_GAGTGGA
Stranded


title: WB1P-MYC_11

description:
3279_11_WB1P-Myc_14TMB106_tumor_1A_ACTGATA
Stranded


title: WE-PTEN_9

description:
2865_9_11SJK255-03_A
Non Stranded


title: WB1P-MYC_8

description:
3279_8_WB1P-Myc_14TMB93_tumor_4_GTTTCGG
Stranded


title: WE-PTEN_7

description:
2865_7_11SJK253-03_A
Non Stranded


title: WE-PTEN_8

description:
2865_8_11SJK254-03_A
Non Stranded


title: DK5955_C RNA-seq

data_processing:
Basecalls were performed using RTA version 2.4.11
Transcripts per million (TPM) and fragments per kilobase of transcript per million (FPKM) were determined using the default parameters of the calculate expression function of RSEM version 1.3.0 and the NCIB 3610 genome (NZ_CP020102.1) as a reference.
Genome_build: Bacillus subtilis NCIB 3610 (NZ_CP020102.1)
Supplementary_files_format_and_content: Tab delimited text files generated by the RSEM calculate expression function containing TPM and FPKM values for each gene in the NCIB 3610 chromosome.

extract_protocol:
Following lysis, 2.5 A260 units were diluted in 700 µL H2O and denatured in 1% SDS. RNA was extracted once with an equal volume of hot acid phenol, once with an equal volume of room temp acid phenol, and RNA was precipitated with isopropanol. Precipitant was resuspended in H2O and 10 µg RNA was DNAse treated using 4 units of RNase free DNase I (Invitrogen AM2222) at 37°C for 30 min in a 20 μL reaction volume. RNA was precipitated in isopropanol, resuspended in H2O.
Libraries were prepared by the Indiana University Center for Genomics and Bioinformatics using the ScriptSeq RNA-library kit (Illumina SSV21124).


title: DK1042_A RibosomeProfiling

description: Ribosome protected mRNA fragments


title: WB1P-MYC_7

description:
3279_7_WB1P-Myc_14TMB93_tumor_1_GTGGCCT
Stranded


title: WE-PTEN_20

description:
2865_20_11SJK233-04_B
Non Stranded


title: WE-PTEN_10

description:
2865_10_11SJK255-04_A
Non Stranded


title: WE-PTEN_6

description:
2865_6_11SJK252-03_A
Non Stranded


title: WE-PTEN_5

description:
2865_5_11SJK252-04_A
Non Stranded


title: DK1042_B RibosomeProfiling

description: Ribosome protected mRNA fragments


title: DK5955_B RNA-seq


title: WE-PTEN_4

description:
2865_4_11SJK248-03_A
Non Stranded


title: WB1P-MYC_6

description:
3279_6_WB1P-Myc_14TMB87_tumor_2_GGCTACA
Stranded


title: WE-PTEN_3

description:
2865_3_11SJK248-04_A
Non Stranded


title: DK5955_A RNA-seq


title: WE-PTEN_2

description:
2865_2_11SJK247-03_A
Non Stranded


title: WE-PTEN_1

description:
2865_1_11SJK246-04_A
Non Stranded


title: WB1P-MYC_5

description:
3279_5_WB1P-Myc_14TMB87_tumor_1_TAGCTTA
Stranded


title: DK5518_C RNA-seq


title: KB1P_19

description:
2119_10_M888_M888_TGACCAA
Non Stranded


title: WB1P-MYC_4

description:
3279_4_WB1P-Myc_14TMB88_tumor_3_GATCAGA
Stranded


title: KB1P_20

description:
2119_14_M895_M895_CTTGTAA
Non Stranded


title: DK5518_B RNA-seq


title: KB1P_18

description:
2119_1_M605_TAGCTTA
Non Stranded


title: WB1P-MYC_2

description:
3279_2_WB1P-Myc_14MMI31_tumor2_TTAGGCA
Stranded


title: DK5518_A RNA-seq


title: KB1P_17

description:
1866_M924_CTTGTAA
Non Stranded


title: WB1P-MYC_9

description:
3279_9_WB1P-Myc_14TMB95_tumor_1_CGTACGT
Stranded


title: KB1P_15

description:
1866_M922_ACTGATA
Non Stranded


title: DK2050_C RNA-seq


title: KB1P_14

description:
1866_M921_TAGCTTA
Non Stranded


title: d/d miR-17~92 B-cells

data_processing:
Reads have adapters removed, aligned and quantified using miRDeep2-v0.0.8 against miRBase-v22
Normalization uses size factors calculated using DESeq2 with spike-in reads for spike-in normalization, or with endogenous reads for internal normalization
B-cells do not have spike-in version, they are internally normalized
Genome_build: miRBase-v22
Supplementary_files_format_and_content: Filtered counts. Each CSV file contains all datasets corresponding to each cell line. Different files for Spike-ins (spikein) and internal normalizations (NoSpikein)


title: WB1P-MYC_3

description:
3279_3_WB1P-Myc_14TMB88_tumor_1_ACTTGAA
Stranded


title: WE-PTEN_12

description:
2865_12_11SJK260-04_B
Non Stranded


title: day 14 treatment, rep 3

city: University Park

first: Gong

last: Chen

state: PA

address: Old Main

institute: Penn State University

data_processing:
quality check using FastQC v0.11.3
reads were aligned to hg19 using HISAT2 version 2.0.4
counts summarized using featureCounts v1.5.1 (count) or StringTie v1.3.4 (RPKM)
differential analysis by DESeq2 v1.16.1
Genome_build: hg19
Supplementary_files_format_and_content: a txt file containing read count from all samples generated by featureCounts

source_name: HA1800, ScienCell

extract_protocol:
total RNA were extracted according to protocols accompanying with Macherey-Nagel NucleoSpin RNA kit, then sent to sequencing center for polyA enrichment
libraries were constructed using KAPA RNA kit at UCLA Technology Center for Genomics & Bioinformatics

value: human fetal cortical astrocytes

tag: passages

tag: time point

value: day 14


title: KB1P_13

description:
1866_M920_ACTTGAA
Non Stranded


title: DK2050_B RNA-seq

value: batch culture


title: WB1P_2

description:
3716_12_WB1P_15TMB92_tumor_1_ATGTCAG
Stranded


title: Sample5_T1

type: genomic

city: Cologne

first: Alexander

last: Schenk

address: Am Sportpark Müngersdorf 6

institute: German Sports University Cologne

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Illumina iScan system

data_processing: Data was analyzed using Illumina Genome Studio

label: Cy5 und Cy3

source_name: NK-cells

label_protocol: TEM reagent and Xstaining using Illumina chemistry with the standard Illumina protocoll

extract_protocol: genomic DNA was extracted from isolated NK-cells using Norgen Biotek corp. RNA/DNA/Protein Purification Plus Kit

tag: gender

value: female

value: natural killer (NK) cells

tag: measurement time point

value: after exercise


title: Sample2_T1


title: day 14 treatment, rep 2


title: DK2050_A RNA-seq

value: Lysogeny Broth


title: KB1P_12

description:
1866_M919_TTAGGCA
Non Stranded

tag: genotype/variation

tag: strain


title: WE-PTEN_11

description:
2865_11_11SJK260-03_B
Non Stranded


title: DK1042_C RNA-seq

tag: tissue


title: KB1P_11

description:
1866_M917_CAGATCA
Non Stranded


title: day 14 treatment, rep 1


title: WB1P_1

description:
3716_11_WB1P_15TMB53_tumor_1_AGTTCCG
Stranded


title: WB1P-MYB2_10

description:
3716_10_WB1P-Myb_15TMB184_tumor_1_AGTCAAC
Stranded


title: day 5 treatment, rep 3

value: day 5


title: WE-PTEN_15

description:
2865_15_11SJK215-04_B
Non Stranded


title: DK1042_B RNA-seq


title: KB1P_10

description:
1866_M916_GAGTGGA
Non Stranded


title: WB1P-MYB2_9

description:
3716_9_WB1P-Myb_15TMB178_tumor_1_CTTGTAA
Stranded


title: day 5 treatment, rep 2


title: Sample1_T1


title: Sample1_T0

value: before exercise


title: DK1042_A RNA-seq


title: Sample5_T0


title: KB1P_9

description:
1866_M888_ATCACGA
Non Stranded


title: Sample3_T1


title: WB1P-MYB2_8

description:
3716_8_WB1P-Myb_15TMB163_tumor_2_CAGATCA
Stranded


title: WE-PTEN_17

description:
2865_17_11SJK220-04_B
Non Stranded


title: day 5 treatment, rep 1


title: T_cells_3

city: HK

first: Zilong

last: WEN

address: Academic Bld., HKUST, Clearwater Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

description:
2x150 paired-end sequence reads
data_count.csv
data_TPM.csv

data_processing:
Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters.
Read count per gene was then calculated using the FeatureCount program with default parameters.
TPM(transcripts per million) was calculated according to standard formula.
Genome_build: danRer10
Supplementary_files_format_and_content: comma-separated values file including read counts and TPM values for each sample

source_name: specific cells types in zebrafish epidermis

extract_protocol:
Different fluorescence-labeled cell types from Tg(krt4:lyn-GFP), Tg(lck:DsRedx), Tg(lyz:GFP) and Tg(hsp70:mCherry-T2a-CreERT2;mpeg1:loxP-DsRedx-loxP-GFP) fish epidermis were picked into lysis buffer (1% Triton X-100) for direct reverse transcription and cDNA amplification.
cDNA library was generated based on SMART-seq2 protocol. Library construction were done by Novogene using NEBNext kit.

value: epidermis

tag: Stage

value: adult

tag: transgenic line


title: day 3 treatment, rep 3

tag: cell type

value: day 3


title: WB1P-MYB2_7

description:
3716_7_WB1P-Myb_15TMB133_tumor_1_GCCAATA
Stranded


title: T_cells_2


title: KB1P_8

description:
1857_NO.15_GTCCGCA
Non Stranded


title: day 3 treatment, rep 2


title: KB1P_6

description:
1857_NO.11_AGTCAAC
Non Stranded


title: WB1P-MYB2_5

description:
3716_5_WB1P-Myb_14TMB246_tumor_2_TGACCAA
Stranded


title: T_cells_1


title: day 3 treatment, rep 1


title: Neutrophils_3


title: KB1P_5

description:
1857_NO.9_CAGATCA
Non Stranded


title: Sample4_T0


title: WB1P-MYC_1

description:
3279_1_WB1P-Myc_14MMI31_tumor_1_ATCACGA
Stranded


title: WB1P-MYB2_4

description:
3716_4_WB1P-Myb_14TMB240_tumor_3_CGATGTA
Stranded


title: Neutrophils_2


title: KB1P_4

description:
1857_NO.7_ACAGTGA
Non Stranded


title: Sample2_T0


title: WB1P-MYB2_3

description:
3716_3_WB1P-Myb_14TMB240_tumor_1_ATTCCTT
Stranded


title: day 1 treatment, rep 2

value: day 1


title: day 1 treatment, rep 3


title: WB1P-MYB2_6

description:
3716_6_WB1P-Myb_15TMB37_tumor_1_ACAGTGA
Stranded


title: KB1P_7

description:
1857_NO.13_ATGTCAG
Non Stranded


title: KB1P_3

description:
1857_NO.5_CGATGTA
Non Stranded


title: MLCs_4


title: KB1P_2

description:
1857_NO.3_ACTGATA
Non Stranded


title: WB1P-MYB2_1

description:
3716_1_WB1P-Myb_14TMB182_tumor_1_GAGTGGA
Stranded


title: WB1P-MYB2_2

description:
3716_2_WB1P-Myb_14TMB229_tumor_1_ACTGATA
Stranded


title: MLCs_3


title: day 0 treatment, rep 3

value: day 0


title: day 1 treatment, rep 1


title: KB1P_1

description:
1857_NO.1_CGTACGT
Non Stranded


title: KB1P-COL1A1_5

description:
2848_7_KB1P_COLA1_2_1_13TMB036_A_GTCCGCA
Non Stranded


title: day 0 treatment, rep 2


title: KB1P-MET_4

description:
3450_7_7_ATGTCAG
Stranded


title: MLCs_2


title: day 0 treatment, rep 1


title: KB1P-COL1A1_4

description:
2848_6_KB1P_COLA1_2_1_13TMB035_A_CCGTCCC
Non Stranded


title: MLCs_1


title: human astrocyte, rep 3


title: Keratinocytes_3


title: KB1P-COL1A1_3

description:
2848_5_KB1P_COLA1_2_1_13TMB001_A_ATGTCAG
Non Stranded


title: KB1P-MET_5

description:
3450_8_8_CCGTCCC
Stranded


title: human astrocyte, rep 2


title: KB1P-MET_3

description:
3450_6_6_AGTTCCG
Stranded


title: KB1P-COL1A1_2

description:
2848_4_KB1P_COLA1_2_1_12TMB54_A_GGCTACA
Non Stranded


title: Keratinocytes_2


title: Neutrophils_1


title: KB1P-MET_1

description:
3450_1_1_GATCAGA
Stranded


title: KB1P-MET_7

description:
2848_3_KB1P_Met_12TMB055_A_TAGCTTA
Non Stranded


title: human astrocyte, rep 1


title: KB1P-MET_6

description:
2848_2_KB1P_Met_12TMB053_A_ACTTGAA
Non Stranded


title: KEP_5

description:
3457_5_S05_CAGATCA
Stranded


title: cLCs_4


title: KB1P-COL1A1_1

description:
2848_1_KB1P_COLA1_2_1_13TMB43_tumor_1_A_ATCACGA
Non Stranded


title: KEP_3

description:
3457_3_S03_ACAGTGA
Stranded


title: KB1P-MET_2

description:
3450_3_3_GGCTACA
Stranded


title: cLCs_2


title: cLCs_3


title: KEP_1

description:
3457_1_S01_CGATGTA
Stranded


title: AB (WT, +/+) -2

description:
Control sample
cpm_normalized_log2.txt
AB-2

growth_protocol: Zebrafish (Danio rerio) embryos of AB (wild type,+/+) strain and dyrk1aakrb1(-/-) mutant in the Tg(kdrl:egfp) background  were maintained with  E3 Egg water (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4) in a petri dish with a diameter of 95 mm at 28.5℃ until 48 hpf.

extract_protocol:
Total RNA was isolated from embryos of AB (wild type,+/+) and dyrk1aakrb1(-/-) mutant at 48 hpf using Trizol reagent and RNA quality was validated by Agilent 2100 bioanalyzer using RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands)
The sequencing library was prepared using the Lexogen SENSE mRNA Library Preparation Kit.

value: AB (+/+), Tg(kdrl:egfp)

value: whole embryo

value: 48h hpf


title: dyrk1aakrb1 (mutant, -/-) -1

description:
dyrk1aa knock down
cpm_normalized_log2.txt
dlaa2b-1

value: dyrk1aakrb1(-/-), Tg(kdrl:egfp)


title: Keratinocytes_1

description:
2x150 paired-end sequence reads
data_count.csv
data_TPM.csv


title: AB (WT, +/+) -1

description:
Control sample
cpm_normalized_log2.txt
AB-1


title: KEP_2

description:
3457_2_S02_TGACCAA
Stranded

value: FVB/N


title: dyrk1aakrb1 (mutant, -/-) -2

description:
dyrk1aa knock down
cpm_normalized_log2.txt
dlaa2b-2


title: Total RNA from wild type

city: Hefei

first: Yulong

last: Wang

address: 130 West Changjiang Road

country: China

institute: Anhui Agricultural University

data_processing:
quality control on clean data through drawing base composition chart and quality distribution chart.
clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, sequence duplication and GC-content level of the clean data were calculated. Subsequently, the clean reads were mapped to the original Metarhizium robertsii genome sequences using the SOAP.
genome build: GCF_000187425.2

organism: Metarhizium robertsii ARSEF 23

source_name: WT

growth_protocol: Conidia of WT and Δdcl2 were inoculated into SDAY medium at 1×107 conidia/ml at 25°C. Fungal samples were collected after 2.5 days, respectively.

extract_protocol:
Metarhizium robertsii wild type and Δdcl2 were ground into powder in liquid nitrogen,powder was used to isolate total RNAs  using Trizol (Invitrogen, USA).
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000.

value: ARSEF 23

tag: developmental stage

value: asexual developmental stage


title: KEP_4

description:
3457_4_S04_GCCAATA
Stranded

source_name: Tumour


title: Total SEnd-seq rnb ko stationary phase

status: Public on May 19 2019

city: Newyork

first: Xiangwu

last: Ju

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Library strategy: SEnd-seq
Basecalls performed using CASAVA version 1.7
Paired-end reads were merged to single end fasta reads by usin FlASh software v1.2.11
Labled transcript 5' end and 3' end were extracted from merged single end reads and processed to paired-end reads again by custom program scripts
Extracted paired-end reads were mapped to E.coli genome (NC_00913.3) by using Bowtie2 v2.3.4.1, and single end full length sequence was generated by  the paried-end data by custome transcripts and Bowtie2.
rRNA transcripts were removed and TSSs, TTSs and overlap TTSs were extracted from the remaining data.
Genome_build: Escherichia coli str. K-12 substr. MG1655, NC_000913.3
Supplementary_files_format_and_content: wig files

organism: Escherichia coli

source_name: E.coli cell

growth_protocol: Escherichia coli K-12 MG1655 were cultured in LB media (10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl, pH 7.4) under aerobic conditions at 37 °C. The temperature-sensitive RNase E mutant E.coli strain [rne-3071(ts)] was cultured in LB media at 28 °C  for normal culture and shift to 44 °C to deactive RNase E activity.

extract_protocol:
For the RNA-seq samples, the E. coli cells were quenched by adding 0.5 volume of cold Stop Buffer (5% phenol in ethanol) immediately to the culture medium before harvest and stay on the ice for 15 minutes. Cell pellets were collected by centrifugation (6,000 rpm, 5 minutes at 4 °C), thoroughly resuspended in 100 μl of lysozyme solution [2 mg/ml in TE buffer (10 mM Tris-HCl and 1 mM EDTA)], and incubated for 2 minutes. The cells were immediately lysed by adding 1 ml of TRIzol Reagent (Invitrogen, 15596) and the RNA was extracted following manufacture’s instruction. For the ChIP-seq samples, the E. coli cells were fixed with 1% formaldehyde with continued shaking at 37 °C for 10 minutes before quenching with glycine (100 mM final concentration). Cells were then lysed and DNA was sheared by sonication followed by the treatment with micrococcal nuclease and RNase A. Antibody against RNAP β was used for target DNA enrichment.
A new RNA-seq method SEnd-seq was developed and used to prepare the SEnd-seq library, standard RNA-seq library was prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101) following the manufacturer’s instructions, ChIP-seq library was prepared with NEBNext Ultra II DNA Library Prep Kit (New England BioLabs, E7645)after ChIP DNA enrichment. For SEnd_seq, the RNA was ligated to a RNA adaptor (/5Phos/rNrNrN rNrArArCrCrUrGrCrUrArUrCrArArCrUrG/3ddC/ or /5Phos/rNrNrN rNrGrCrUrUrCrCrUrGrCrUrArUrCrArArCrUrG/3ddC/), both adaptors were used if two different samples were mixed together for library preparation(Log phase samples used the first one and stationary phase samples used the second one). The ligated RNA was converted to cDNA with the same Biotinylated RT primer(5GGGCAG T/iBiodT/GATAGCAGG). For RNA-seq , rRNA was depleted with the Ribo-Zero rRNA Removal Kit. The sequencing library was prepared with the TruSeq Stranded mRNA Library Prep Kit following the manufacturer’s instructions. For ChIP-seq, the enriched ChIP DNA and input DNA sequencing libraries were prepared with NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: Wild type E. coli, pnp knoctout, rnb knoctout and rnr knoct out strains were cultured in LB media at 37 °C, RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase.  rne-3071(ts) mutation strain was cultured in LB media at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E. In order to inactive the rho activity, the wild type (WT) Wild type E. coli was cultured in LB media with 50 μg/ml bicyclomycin at 37 °C for 15 min at indicated growth condition.

tag: growth stage

value: Stationary phase

tag: treatment

value: 37°C culture

value: rnb knockout


title: Total RNA from Δdcl2

tag: age


title: Total SEnd-seq pnp ko log phase

value: Log phase

value: pnp knockout


title: Total SEnd-seq rnr ko stationary phase

value: rnr knockout


title: Total SEnd-seq pnp ko stationary phase


title: Total SEnd-seq rnr ko log phase


title: Total SEnd-seq rnb ko log phase


title: Total SEnd-seq WT stationary phase rep4

value: wild type


title: Total SEnd-seq WT log phase rep 6


title: Total SEnd-seq WT log phase rep 5


title: Total SEnd-seq WT log phase rep 4


title: cLCs_1

value: epidermis

value: adult


title: Primary SEnd-seq WT log phase rep 5

description: Primary RNA was enriched from total RNA


title: Primary SEnd-seq WT stationary phase rep2

description: Primary RNA was enriched from total RNA


title: Primary SEnd-seq WT log phase rep 4

description: Primary RNA was enriched from total RNA


title: Total SEnd-seq WT stationary phase BLM treatment rep2

description: Processed data on GSM3307963

extract_protocol:
E. coli cells were quenched by adding 0.5 volume of cold Stop Buffer (5% phenol in ethanol) immediately to the culture medium before harvest and stay on the ice for 15 minutes. Cell pellets were collected by centrifugation (6,000 rpm, 5 minutes at 4 °C), thoroughly resuspended in 100 μl of lysozyme solution [2 mg/ml in TE buffer (10 mM Tris-HCl and 1 mM EDTA)], and incubated for 2 minutes. The cells were immediately lysed by adding 1 ml of TRIzol Reagent (Invitrogen, 15596) and the RNA was extracted following manufacture’s instruction.
A new RNA-seq method SEnd-seq was used to prepare the SEnd-seq library, and  standard RNA-seq was prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101) following the manufacturer’s instructions.

treatment_protocol: Wild type E.coli RNA samples were collected once the growth stage  reached to log phase or stationary phase.  rne-3071(ts) mutation strain was cultured in LB media at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E. In order to inactive the rho activity, the wild type (WT) Wild type E.coli was cultured in LB media with 50 μg/ml bicyclomycin at 37 °C for 15 min at indicated growth condition.

value: 37 degrees C 50 microgram/ml bicyclomycin for 15 minutes


title: Sample5_RNAPrif_br1_40

description: processed data file: Table_S0.csv

data_processing:
ChIP-seq: Data were analyzed using a modified form of the PeakSeq algorithm (Rozowsky et al., 2009) that narrows the regions identified as peaks by requiring that each 50-bp window within a putative peak be enriched (p < 0.05) relative to mock ChIP (as described by Markson et al. 2013). The fold enrichment for each peak was calculated by finding the maximum ChIP-to-mock ratio within 50 bp of the location of the peak maximum in the raw ChIP-Seq signal.
RNA-seq: Sequencing reads were aligned to the S. elongatus genome using Bowtie (RRID:SCR_005476) as described previously (Markson et al., 2013). We quantified expression of a gene by counting the number of aligned sequencing reads corresponding to the appropriate strand between the start and stop of each gene (gene info obtained from Cyanobase, RRID: SCR_007615), and normalized these values between all samples in this work using median normalization, followed by dividing the median normalized read count value by the length of the open reading frame of the gene, as described previously (Anders and Huber, 2010; Markson et al., 2013). The time course and RNA sequencing was repeated twice for two biological replicates.
Genome_build: NC_007604.1
Supplementary_files_format_and_content: ChIP-seq: Location of peak signal for RNA polymerase locked at initiation sites measured based on time-series ChIP-seq signal in cells treated with rifampicin prior to cross-linking for high-confidence circadian genes (e.g. genes annotated by Markson et al. 2013 that have greater than 1.75 fold peak to trough gene expression).
Supplementary_files_format_and_content: RNA-seq: RNA levels – median normalized to total read count and normalized to length of gene – for high-confidence circadian genes (e.g. genes annotated by Markson et al. 2013 that have greater than 1.75 fold peak to trough gene expression) and that have a transcription start site within 250 bp of start codon (e.g. rifampicin locked RNA polymerase ChIP-seq peak with peak signal located within 250 bp of start codon).

value: RNAP beta'-(FLAG)c

tag: culture medium

tag: time and light condition

value: 40 hours in constant light

value: biological replicate 1

tag: date experiment was sequenced

value: Fall 2014


title: Primary SEnd-seq WT log phase rep 3

description: Primary RNA was enriched from total RNA


title: Soma_24hpf_RNA-seq_rep2_RUN2

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

institute: Garvan Institute

description: GENE_PGCs_Soma_expected_count_table_RUN2.csv; GENE_PGCs_Soma_effective_length_table_RUN2.csv; GENE_PGCs_Soma_TPM_table_RUN2.csv

data_processing:
Adaptor sequences and low quality bases were removed using TrimGalore (https://github.com/FelixKrueger/TrimGalore/)
Sequencing reads were aligned to zebrafish genome danRer10 using STAR (Dobin et al, 2013; Bioinformatics)
Transcript abundancies were quantified using RSEM tool (Li et al, 2011, BMC Bioinformatics)
Genome_build: danRer10
Supplementary_files_format_and_content: .csv format containing transcripts per million (TPM); expected count and effective length for PGCs and Soma RNA-seq samples at 2 developmental stages in replicates.

source_name: Soma 24hpf RNA-seq replicate 2 RUN2

extract_protocol:
PGCs were FACS-sorted from the kop-EGFP-F-nos3’UTR transgenic zebrafish line
Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 (2x100bp)

value: somatic cells


title: Soma_24hpf_RNA-seq_rep1_RUN2

source_name: Soma 24hpf RNA-seq replicate 1 RUN2


title: Total SEnd-seq WT log phase BLM treatment rep2

description: Processed data on GSM3307961

tag: genotype


title: Total SEnd-seq WT log phase BLM treatment rep1

description: Processed data file includes data from GSM3307962


title: RNA-seq WT log phase related to total SEnd-seq WT stationary phase rep4

description: rRNA removed RNA

data_processing:
Basecalls performed using CASAVA version 1.7
Paired-end reads were merged to single end fasta reads by usin FlASh software v1.2.11
Labled transcript 5' end and 3' end were extracted from merged single end reads and processed to paired-end reads again by custom program scripts
Extracted paired-end reads were mapped to E.coli genome (NC_00913.3) by using Bowtie2 v2.3.4.1, and single end full length sequence was generated by  the paried-end data by custome transcripts and Bowtie2.
rRNA transcripts were removed and TSSs, TTSs and overlap TTSs were extracted from the remaining data.
Genome_build: Escherichia coli str. K-12 substr. MG1655, NC_000913.3
Supplementary_files_format_and_content: wig files


title: RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6

description: rRNA removed RNA


title: KB1P_16

description:
1866_M923_ATTCCTT
Non Stranded

extract_protocol:
Total RNA was extracted using TRIzol reagent as per the manufacturer’s protocol
Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit according to the manufacturer’s instructions. Non stranded libraries were generated using the TruSeq V2 mRNA library preparation kit according the manufacturer’s instructions
Libraries were sequenced 50/51 or 65 bp single end

value: FVB/N


title: Sample4_T1

value: female

value: natural killer (NK) cells

value: after exercise


title: Soma_7hpf_RNA-seq_rep1_RUN2

source_name: Soma 7hpf RNA-seq replicate 1 RUN2


title: Soma_7hpf_RNA-seq_rep2_RUN2

source_name: Soma 7hpf RNA-seq replicate 2 RUN2


title: RNA-seq WT log phase related to total SEnd-seq WT log phase rep 5

description: rRNA removed RNA

value: 37°C culture


title: Total SEnd-seq rents mutation stationary phase rep1

value: Stationary phase

value: 44 degrees C for 30 minutes

value: RNase E mutation


title: Total SEnd-seq rents mutation stationary phase rep2


title: Primary SEnd-seq WT stationary phase rep3

description: Primary RNA was enriched from total RNA

value: wild type


title: RNA-seq WT log phase related to total SEnd-seq WT log phase rep 4

description: rRNA removed RNA

value: Log phase


title: Total SEnd-seq WT stationary phase rep3_part1

description: Processed data file includes data from GSM3307956

value: 37 degrees C


title: Total SEnd-seq WT stationary phase rep3_part2

description: Processed data on GSM3307955

value: 38 degrees C


title: Total SEnd-seq rents mutation log phase rep1


title: Total SEnd-seq WT stationary phase rep2


title: PGC_24hpf_RNA-seq_rep1_RUN2

source_name: PGCs 24hpf RNA-seq replicate 1 RUN2

value: primordial germ cells


title: Bos_taurus_15 (30M)

city: Yangling

first: Hua

last: He

state: Shaanxi

address: Xinong Road NO.22

department: College of Animal Science and Technology

institute: Northwest A&F University

description: Qinchuan beef cattle

data_processing:
Images generated by sequencers are converted by base calling into nucleotide sequences
using clean-fastq_v1.pl to remove adapters and low quality tags as well as contaminants
Fastq files were generated using clean-fastq_v1.pl filter software; Clean reads are stored for each sample after filter dirty raw reads.
clean reads were perfect matched to the bovine reference genome  UMD 3.1 for the assembly using SOAP2 software and not allowed to mismatches in reads.
Data were normalized by calculating the number of reads per kilobase of exon region in a gene per million mapped reads (RPKM) (RPKM= total exon reads/mapped reads in millions × exon length in kb) (Mortazavi et al., Nature Methods, 2008) for each gene and then annotated with the Ensembl bovine genome assembly.
Genome_build: UMD 3.1 reference genome (available at ftp://ftp.ensembl.org/pub/release-67/fasta/bos_taurus/) from the Ensembl database
Supplementary_files_format_and_content: xls table files include GeneID,number of reads which aligned to just one position of gene,length of gene, the coverage of gene and RPKM values for each Sample.

organism: Bos taurus

source_name: Longissimus Muscle

extract_protocol:
longissimus muscle from each individual were harvested for RNA isolation within 10 minutes after slaughter. All fresh tissue samples were collected and divide it into 1.5 mL plastic centrifuge tube (each sample weighing around 100 mg ) and snap frozen in liquid nitrogen for RNA-seq.
two cDNA libraries were constructed from pooled Emb135 (n=3) and 30M (n=3) samples.Messenger RNA was isolated from the total RNA samples using oligo (dT) magnetic beads (Invitrogen). The purified mRNA was first fragmented to approximately 200-700 nt fragments using the RNA fragmentation kit (Ambion). First-strand cDNA synthesis was performed using random hexamer primers and reverse transcriptase. After the first strand was synthesized, a custom second-strand primer and strand synthesis buffer (Illumina) were added, followed by dNTPs, RNase H and DNA polymerase I to nick translate the second-strand. The reaction was then purified using a QiaQuick PCR column (Qiagen) and eluted in EB buffer (Qiagen); the samples were then subjected to end repair, addition of a single A base, adaptor ligation, agarose gel isolation of approximately 200-bp cDNA, and PCR amplification. Finally, the samples were sequenced using the Illumina HiSeq™ 2000 platform.

value: 30 month after birth (30M)

value: Adult

value: thoracis


title: Total SEnd-seq WT stationary phase rep1


title: Bos_taurus_41 (Emb135)

description: Qinchuan beef cattle

value: 135 days after insemination (Emb135)

value: Embryo


title: Total SEnd-seq WT log phase rep3_part2

description: Processed data on GSM3307951


title: PGC_7hpf_RNA-seq_rep2_RUN2

source_name: PGCs 7hpf RNA-seq replicate 2 RUN2


title: Total SEnd-seq WT stationary phase BLM treatment rep1

description: Processed data file includes data from GSM3307964

value: 37 degrees C 50 microgram/ml bicyclomycin for 15 minutes


title: Total SEnd-seq WT log phase rep3_part1

description: Processed data file includes data from GSM3307952


title: PGC_7hpf_RNA-seq_rep1_RUN2

source_name: PGCs 7hpf RNA-seq replicate 1 RUN2


title: Sample3_T0

value: female

value: natural killer (NK) cells

value: before exercise


title: Total SEnd-seq WT log phase rep2


title: Total SEnd-seq WT log phase rep1


title: liver_adult_WGBS

data_processing:
Sequenced reads were trimmed using the Trimmomatic software (Bolger et al, 2014) with the following settings: (ILLUMINACLIP:adapter.fa:2:30:10 SLIDINGWINDOW:5:20 LEADING:5 TRAILING:5 MINLEN:50
Sequencing reads were aligned to in-silico bisulphite-converted reference genome danRer10 using WALT mapping tool using the following settings: -m 10 -t 24 -N 10000000 -L 2000 (Chen et al, 2016)
DNA methylation calling was performed using MethylDackel (https://github.com/dpryan79/MethylDackel)
Genome_build: danRer10
Supplementary_files_format_and_content: bw / The file contains genomic positions of CpG sites with corresponding methylation values on scale from 0 to 1
Supplementary_files_format_and_content: bigtable.tsv / For bigtable.tsv" processed data files the column headers are as follows: column 1 - chromosome. column 2 - position: coordinate for the cytosine position on the chromosome. column 3 (.C) - number of reads depicting a methylated cytosine. column 4 (.cov) - total number of reads at that position.

source_name: Adult liver tissue subject to WGBS

extract_protocol:
DNA from adult zebrafish liver tissue was extracted using DNeasy Blood & Tissue kit (Qiagen, USA).
MethylC-seq library generation was performed as described previously (Ulrich et al, 2015; Nature Protocols). Briefly, the genomic DNA was sonicated to an average size of 300 bp using a Covaris sonicator. Sonicated DNA was then purified and end-repaired followed by the ligation of methylated Illumina TruSeq sequencing adapters. Library amplification was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA).

value: liver


title: Total SEnd-seq rents mutation log phase rep2

value: 44 degrees C for 30 minutes


title: Primary SEnd-seq rents mutation @ 44 °C stationary phase rep1

description: Primary RNA was enriched from total RNA

value: Stationary phase

value: RNase E mutation


title: Primary SEnd-seq rents mutation @ 44 °C log phase rep1

description: Primary RNA was enriched from total RNA

value: Log phase


title: PGC_24hpf_RNA-seq_rep2_RUN2

source_name: PGCs 24hpf RNA-seq replicate 2 RUN2


title: Primary SEnd-seq WTstationary phase rep1

description: Primary RNA was enriched from total RNA

value: 37 degrees C

value: wild type


title: Primary SEnd-seq rents mutation @ 44 °C log phase rep2

description: Primary RNA was enriched from total RNA