title: RNA_dus2D

value: BY4741 with dus2D::kanMX


title: RNA_trm112D

status: Public on Jun 29 2017

type: SRA

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation Street

department: Biochemistry & Molecular Pharm

country: USA

institute: UMass Medical School

description:
rRNA-depleted RNA
processed data files:
Chou_Table_S1.txt
Chou_Table_S3.txt

library_source: transcriptomic

data_processing:
Raw fastq reads were de-multiplexed and removed of adaptor sequence using homerTools function of HOMER package v4.6, with parameters "barcodes 5 -min 0.01" and "trim -5 2 -3 TGGAATTCTCGGGTGCCAAGG -mis 2 -minMatchLength 5", respectively.
De-multiplexed and adaptor-removed reads for RPF were mapped to S. cerevisiae rDNA and the mapping reads were discarded. The remaining RPF reads and RNA-seq reads were mapped to sacCer3 genome using TopHat v2.0.12 with parameters -p 4 -I 5000 --no-coverage-search
Uniquely mapping reads (filtered by samtools view function and parameter -q 10) in length of 27-34 nt (RPF) or >=27 nt (RNA-seq) were used for gene-level analysis, in which reads were quantified as raw counts or reads per kilobase of transcript per million mapped reads (RPKM) using HOMER package with open reading frame annotations downloaded from SGD.
Translational efficiency (TE) was calculated as relative ribosome footprint density (Ribo-rRPKM) divided by relative RNA abundance (RNA-rRPKM), with rRPKM calculated by normalizing RPKM in each mutant by the average of RPKM in WTs grown in the same batch.
Global codon occupancy analysis was calculated as described in (Nedialkova and Leidel, 2015), with minor modifications. The P-site offset was calculated by examining the cumulative distribution of 28-31 nt reads aligning at start codons. After applying the respective offset to reads of each size, only in-frame reads were used. The first 15 and the last 5 codons of each transcript were removed from the reference. The frequency of each codon in ribosomal A, P, and E sites was calculated for normalization, and divided by the average frequency of the same codon in the three downstream codons from the A site
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample (RPF or RNA-seq reads) and normalized codon frequencies per A/P/E site.
Supplementary_files_format_and_content: Chou_Table_S1.txt: RNA counts/RPKM per gene
Supplementary_files_format_and_content: Chou_Table_S2.txt: RPF counts/RPKM per gene
Supplementary_files_format_and_content: Chou_Table_S3.txt: relative Translational Efficiency values (RPF rRPKM/RNA rRPKM, with rRPKM calculated by normalizing RPKM in each mutant by the average of RPKM in WTs grown in the same batch)
Supplementary_files_format_and_content: Chou_Table_S4.txt: A/P/E site normalized values
Supplementary_files_format_and_content: Chou_Table_S5.txt: RiboMeth-seq data with raw counts of 5' read starts

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: 100 mL of yeast cultures were grown to mid-log phase (OD600=0.5-0.6) in YPD (1% Yeast extract, 2% Peptone, 2% Dextrose) at 30°C

extract_protocol:
For RPF, cells were lysed by glass-bead beating in ice-cold lysis buffer, followed by RNase I treatment. Ribosomes were separated on 10-50% sucrose gradient and 80S monosome fractions were collected and RNA extracted. 27-34 nt ribosome footprints were isolated by denaturing PAGE.    For RNA-Seq, total RNA extracted using TRIZOL was depleted of rRNA using Ribo-Zero, followed by zinc-based fragmentation for 10 min at 70°C.
RPF and rRNA-depleted RNA are constructed into deep-sequencing libraries as described in (Heyer et al., 2015). Briefly, RNA 3’ ends were dephosphorylated, ligated with a preadenylated adaptor, and reverse transcribed. cDNA was precipitated and size selected by denaturing PAGE. The purified cDNA was circularized and PCR amplified prior to sequencing. For RiboMeth-seq, total RNAs were end-repaired with T4 PNK, Antarctic phosphatase, or Shrimp alkaline phosphatase for 3’-end dephosphorylation and with T4 PNK and ATP for 5’-end phosphorylation, followed by library construction using NEB Next Small RNA Library Prep kit. Amplified library was purified and subject to Illumina Nextseq 500 single-end sequencing with 75 cycles.

treatment_protocol: 30 sec of cycloheximide in a final concentration of 100 ug/mL in YPD at 30°C

tag: media

value: YPD

tag: strain

value: BY4741 with trm112D::kanMX

tag: treatment

value: Cycloheximide


title: N708.N502

city: Oxford

first: Emma

last: Harvey

address: John Radcliffe Hospital

country: United Kingdom

institute: University of Oxford

description: Sample 2

data_processing:
Sequence reads were trimmed for adaptor sequences using TrimGalore v0.3.3 with parameters "-q 15 --stringency 3 --length 36 --paired"
Trimmed reads were mapped to the reference human genome using Bowtie v1.0.0 with parameters "-a --best --strata -m 100 -X 500 --chunkmbs 256"
Gene and transcript expression quantifications in log2(FPKM+1) units were obtained using MMSEQ v1.0.7 with default parameters (https://github.com/eturro/mmseq)
Differential gene and transcript expression were obtained using MMDIFF v.1.0.7 with default parameters (https://github.com/eturro/mmseq). Genes or transcripts not expressed in 2/3 samples of each ("Poor" and "Good") condition were discarded.
Genome_build: GRCh37.70/Ensembl v70
Supplementary_files_format_and_content: [.mmseq] Gene and transcript expression values
Supplementary_files_format_and_content: [Transcripts_up_good.txt] List of transcripts higher in samples 4-6 than in samples 1-3
Supplementary_files_format_and_content: [Transcripts_up_poor.txt] List of transcripts higher in samples 1-3 than in samples 4-6
Supplementary_files_format_and_content: [Genes_up_good.txt] List of genes higher in samples 4-6 than in samples 1-3
Supplementary_files_format_and_content: [Genes_up_poor.txt] List of genes higher in samples 1-3 than in samples 4-6

organism: Homo sapiens

source_name: Cardiosphere derived cells, poor supporter of angiogenesis

growth_protocol: Cardiosphere derived cells were isolated from right atrial appendage cardic samples donated by patients undergoing elective coronary surgery. Cardiosphere derived cells were isolated using the Marban protocol and were cultured on fibronectin coated plates in IMDM (Life Technologies), 20% foetal bovine serum (FBS, Hyclone), 2mM L-glutamine, 100U/ml penicillin, 100µg/ml streptomycin and 0.1mM 2-mercaptoethanol.

extract_protocol:
Total RNA from 6 CDC samples was isolated using RNeasy mini kits (QIAgen) according to the manufacturer’s instructions and treated with DNase I (Promega) to remove genomic DNA.
Smarter Clontech

treatment_protocol: Cardiosphere derived cells were tested for their supportive potential using a tubule assay based on co-culture with GFP labelled HUVECs. Cardiosphere derived cells were classifies as good or poor supporters of angiogenesis

tag: tissue

value: Heart (right atrial appendage)

tag: cell type

value: Cardiosphere derived cells

tag: supportive ability

value: Poor

tag: cell isolate number


title: ChIP-seq_H3K27ac_Mutu_Replicate1

status: Public on Jun 30 2017

city: New York

first: JJ

last: Miranda

address: 3009 Broadway

institute: Barnard College, Columbia University

library_source: genomic

data_processing:
50 bp reads were mapped using Bowtie to an index containing both the human hg19 and EBV reference [GenBank ID: NC_007605.1] genomes.
Parameters allowed for up to 2 mismatches and 2 alignments
Peaks were visualized after normalization to the background baseline
Formatted for uploading to Integrative Genomics Viewer (www.broadinstitute.org/igv/)
Genome_build: index contains both the human hg19 and EBV reference [GenBank ID: NC_007605.1] genomes
Supplementary_files_format_and_content: Wigs are formatted for IGV. Genome file chrEBV(B95_8_Raji).fa is available from http://www.flemingtonlab.com/rnaseq.html.  Wig columns are chromosome, start, stop, counts per million mapped reads.

molecule: genomic DNA

organism:
Homo sapiens
human gammaherpesvirus 4

source_name: MutuI (EBV+ Burkitt lymphoma cell line)

growth_protocol: MutuI cells were maintained in RPMI-1640 with 25 mM HEPES and 2 g/L NaHCO3 in 5% CO2 with 10% (v/v) fetal bovine serum (Invitrogen)

extract_protocol:
DNA was prepared and ChIP performed as described in the paper
ChIP-seq libraries were prepared as described in the paper

treatment_protocol: Cells were not treated

tag: cell line

value: MutuI

tag: pathogen

value: Epstein-Barr virus

tag: chip antibody


title: RNA_pus4D

value: BY4741 with pus4D::kanMX


title: RNA_trm8D

value: BY4741 with trm8D::kanMX


title: RNA_ncs6D

value: BY4741 with ncs6D::kanMX


title: RNA_tyw4D

value: BY4741 with tyw4D::kanMX


title: RNA_elp2D

value: BY4741 with elp2D::kanMX


title: RNA_trm13D

value: BY4741 with trm13D::kanMX


title: RNA_pus5D

value: BY4741 with pus5D::kanMX


title: RNA_trm82D

value: BY4741 with trm82D::kanMX


title: RNA_mod5D

value: BY4741 with mod5D::kanMX


title: RNA_tyw3D

value: YPD

value: BY4741 with tyw3D::kanMX


title: RNA_tyw1D

value: BY4741 with tyw1D::kanMX

value: Cycloheximide


title: RNA_dus4D

value: BY4741 with dus4D::kanMX


title: RNA_dus3D

value: BY4741 with dus3D::kanMX


title: RNA_BY4741_8


title: RNA_dus1D

value: BY4741 with dus1D::kanMX


title: RNA_trm140D

value: BY4741 with trm140D::kanMX


title: RNA_tum1D

value: BY4741 with tum1D::kanMX


title: RNA_isu1D

value: BY4741 with isu1D::kanMX


title: RNA_isu2D

value: BY4741 with isu2D::kanMX


title: RNA_elp6D

value: BY4741 with elp6D::kanMX


title: RNA_uba4D

value: BY4741 with uba4D::kanMX


title: RNA_sap185D

value: BY4741 with sap185D::kanMX


title: RNA_sap190D

value: BY4741 with sap190D::kanMX


title: RNA_ncs2D

value: BY4741 with ncs2D::kanMX


title: RNA_sit4D

value: BY4741 with sit4D::kanMX


title: RNA_elp4D

value: YPD

value: BY4741 with elp4D::kanMX


title: RNA_kti12D

value: BY4741 with kti12D::kanMX


title: RNA_pus9D

value: BY4741 with pus9D::kanMX

value: Cycloheximide


title: RNA_pus2D

value: BY4741 with pus2D::kanMX


title: RNA_trm10D

value: BY4741 with trm10D::kanMX


title: RNA_trm11D

value: BY4741 with trm11D::kanMX


title: RNA_tad1D

value: BY4741 with tad1D::kanMX


title: RNA_pus3D

value: BY4741 with pus3D::kanMX


title: RNA_BY4741_6


title: RNA_trm44D

value: BY4741 with trm44D::kanMX


title: RNA_trm3D

value: BY4741 with trm3D::kanMX


title: RNA_trm12D

value: BY4741 with trm12D::kanMX


title: RNA_BY4741_5


title: RNA_BY4741_4


title: RNA_urm1D

value: BY4741 with urm1D::kanMX


title: RNA_rit1D

value: BY4741 with rit1D::kanMX


title: RNA_BY4741_3


title: RNA_BY4741_1


title: RNA_BY4741_2


title: RNA_trm1D

value: BY4741 with trm1D::kanMX


title: RNA_pus1D

value: BY4741 with pus1D::kanMX


title: RNA_kti11D

value: YPD

value: BY4741 with kti11D::kanMX


title: RNA_elp3D

value: BY4741 with elp3D::kanMX


title: RNA_elp1D

value: BY4741 with elp1D::kanMX


title: RNA_rtt10D

value: BY4741 with rtt10D::kanMX

value: Cycloheximide


title: RNA_trm2D

value: BY4741 with trm2D::kanMX


title: RNA_trm7D

value: BY4741 with trm7D::kanMX


title: RNA_pus7D

value: BY4741 with pus7D::kanMX


title: RNA_trm732D

value: BY4741 with trm732D::kanMX


title: RNA_trm4D

value: BY4741 with trm4D::kanMX


title: Ribo_kti13D_1

description:
Ribosome-protected footprint RNA
processed data files:
Chou_Table_S2.txt
Chou_Table_S3.txt
Chou_Table_S4.txt

data_processing:
Library strategy: Ribosome profiling
Raw fastq reads were de-multiplexed and removed of adaptor sequence using homerTools function of HOMER package v4.6, with parameters "barcodes 5 -min 0.01" and "trim -5 2 -3 TGGAATTCTCGGGTGCCAAGG -mis 2 -minMatchLength 5", respectively.
De-multiplexed and adaptor-removed reads for RPF were mapped to S. cerevisiae rDNA and the mapping reads were discarded. The remaining RPF reads and RNA-seq reads were mapped to sacCer3 genome using TopHat v2.0.12 with parameters -p 4 -I 5000 --no-coverage-search
Uniquely mapping reads (filtered by samtools view function and parameter -q 10) in length of 27-34 nt (RPF) or >=27 nt (RNA-seq) were used for gene-level analysis, in which reads were quantified as raw counts or reads per kilobase of transcript per million mapped reads (RPKM) using HOMER package with open reading frame annotations downloaded from SGD.
Translational efficiency (TE) was calculated as relative ribosome footprint density (Ribo-rRPKM) divided by relative RNA abundance (RNA-rRPKM), with rRPKM calculated by normalizing RPKM in each mutant by the average of RPKM in WTs grown in the same batch.
Global codon occupancy analysis was calculated as described in (Nedialkova and Leidel, 2015), with minor modifications. The P-site offset was calculated by examining the cumulative distribution of 28-31 nt reads aligning at start codons. After applying the respective offset to reads of each size, only in-frame reads were used. The first 15 and the last 5 codons of each transcript were removed from the reference. The frequency of each codon in ribosomal A, P, and E sites was calculated for normalization, and divided by the average frequency of the same codon in the three downstream codons from the A site
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample (RPF or RNA-seq reads) and normalized codon frequencies per A/P/E site.
Supplementary_files_format_and_content: Chou_Table_S1.txt: RNA counts/RPKM per gene
Supplementary_files_format_and_content: Chou_Table_S2.txt: RPF counts/RPKM per gene
Supplementary_files_format_and_content: Chou_Table_S3.txt: relative Translational Efficiency values (RPF rRPKM/RNA rRPKM, with rRPKM calculated by normalizing RPKM in each mutant by the average of RPKM in WTs grown in the same batch)
Supplementary_files_format_and_content: Chou_Table_S4.txt: A/P/E site normalized values
Supplementary_files_format_and_content: Chou_Table_S5.txt: RiboMeth-seq data with raw counts of 5' read starts

value: BY4741 with kti13D::kanMX


title: RNA_BY4741_7


title: Ribo_gon7D_1

value: BY4741 with gon7D::kanMX


title: Ribo_dus2D_2

value: BY4741 with dus2D::kanMX


title: Ribo_gon7D_2


title: Ribo_dus2D_1


title: Ribo_BY4741_14


title: Cab16: ES d0 Scr KD-BioRep4 RNA-seq

city: Boston

first: Hsueh-Ping

last: Chu

address: 185 Cambridge St

department: molecular biology

institute: MGH, Harvard Medical School

data_processing:
RNA-seq: After removal of adaptor sequences by Trim Galore, reads were aligned to mouse genomes (GRCm38/mm10) using Tophat2. After removal of PCR duplicates, unmapped reads were filtered out, and were divided into unique- and multiple-aligned files. Alignments were divided into positive and negative strands, followed by coverage generation. Scaled wig files were generated by dividing these coverages by number of fragments per million.  Genome_build: mm10  Supplementary_files_format_and_content: RNA-seq: Alignments were divided into positive and negative strands, followed by coverage generation. The processed data are the coverage files (bigwig) files scaled by fragments per million.
Genome_build: mm10

organism: Mus musculus

source_name: ES cell RNA-seq

growth_protocol: Cells were cultured in regular ES mediun (15% FBS) with LIF

extract_protocol:
RNA-seq: Ribosomal depleted total RNA using Ribominus (Invitrogen) that were greater than 200 nt was sheared to a median size of 200 nt.
Library constructions were performed according the NEBNext Ultra Directional RNA library Pre Kit

treatment_protocol: SCR LNA knockdown for 12 hours

value: CAST/Ei x 129/Sv/Jae

value: Embryonic stem cells

tag: molecule subtype

value: rRNA-depleted total RNA


title: Cab16: ES d0 Sense KD-BioRep4 RNA-seq

treatment_protocol: Sense LNA knockdown for 12 hours


title: input_d1

city: Cambridge

first: Suzanne

last: Jacobs

address: 75 Ames Street

institute: The Broad Institute

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 version 2.0.6 with default parameters
PCR duplicates were removed using samtools version 1.3
Peaks were called using Homer version 4.7 with the following steps: makeTagDirectory was used to preprocess input and histone modification tags. findPeaks was used with options -style histone -auto with whole cell extract tags (input) as a control. pos2bed.pl was used to convert resulting peak files to BED format.
To adjust for potential reference-bias introduced during mapping, alignments were post-processed using WASP (Github commit 467651c)
Samtools pileup version 1.3 was used to obtain reference and alternate allele read counts for each sample at each SNP
A binomial test implemented in the binom_test function of the scipy.stats python library was used to test for allelic bias in read counts for each histone modification.  The only relationship to the BED files is that analysis was restricted to regions falling within peaks. Thus only the coordinates of the bed files were used, not any quantitative information about the peaks.
Genome_build: hg19
Supplementary_files_format_and_content: BED files contain peaks output by Homer
Supplementary_files_format_and_content: ChIP_allele_skew_SLC16A11_locus.xlsx (The conclusions in the paper are based on this datafile. d1, d3, d6 are the 3 different hepatocyte lots and the 2 numbers in the counts column refer to counts from each allele. Please see README tab.)

source_name: Commercially available hepatocytes (BioreclamationIVT: lot ACB)

growth_protocol: Cells were thawed and immediately resuspended in CP media (BioreclamationIVT). Cell concentration and viability were assessed prior to use. For ChIP-sequencing, 1×10^6 cells were cross-linked with 1% formaldehyde for 10 min at 37°C prior to freezing in liquid nitrogen.

extract_protocol:
Nuclear lysates were sonicated and histone-DNA complexes were isolated with antibody.
After performing reverse cross linking on sheared chromatin the following steps were performed: end-repair, addition of A base to 3' end of DNA fragments, ligation of adapters to ends of DNA fragments, enrichment by PCR, and gel purification of PCR products.

tag: individual

value: Primary human hepatocytes


title: input_d3

source_name: Commercially available hepatocytes (BioreclamationIVT: lot DSX)


title: d6_wcl_H3K27ac

source_name: Commercially available hepatocytes (BioreclamationIVT: lot QSK)

value: H3K27ac (Active Motif, catalog# 39133, lot# 31814008)


title: Cab16: ES d0 Sense KD-BioRep3 RNA-seq


title: input_d6


title: d6_wcl_H3K4me3

value: H3K4me3 (Cell Signaling Technologies, catalog# 9751BF, lot# 6)


title: Ribo_BY4741_13

value: YPD


title: D15_WT_7_002

city: New Haven

first: Shu

last: Zhu

state: CT

address: 300 Cedar Street

institute: Yale University

data_processing:
Alignment (Tophat v2.0.14)
Generation of normalized abundance measurements (Cufflinks v2.2.1)
Genome_build: mm10

source_name: Ileum epithelial cells

extract_protocol:
Intestinal epithelisal cells were obtained by EDTA isolation of ileum from WT mice followed by facs sorting (EpCAM + CD45 – 7AAD – ).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: wildtype

value: Ileum epithelial cells


title: Ribo_BY4741_12

value: Cycloheximide


title: D15_WT_10_003


title: d3_wcl_H3K27ac


title: Cab16: ES d0 Scr KD-BioRep3 RNA-seq


title: WT tTreg rep3

city: Noda

first: Ei

last: Wakamatsu

state: Chiba

address: 2669 Yamasaki

country: Japan

institute: Tokyo University of Science

description: 50b.p single reads

data_processing:
Illumina HiSeq 2000 reads were trimmed in Trimmomatic v1.
High-quality reads were mapped to GRCm38 by TopHat v2.0.11.
FPKM values were caliculated with Cufflinks.
Genome_build: Mus musculus GRCm38_NCBI
Supplementary_files_format_and_content: tab-delimited text files include FPKM values of each sample

source_name: Spleen

extract_protocol:
Total RNA was extracted with TriReagent
Library was constructed with NEBNext Ultra RNA Library Prep Kit for Illmina

value: Spleen

value: wild type


title: Ribo_BY4741_11


title: WT tTreg rep1

description: 50b.p single reads


title: WT Tconv rep2

description: 50b.p single reads


title: Ribo_cgi121D_2

value: BY4741 with cgi121D::kanMX


title: TS_rep1

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

description:
RNA, 14-38 nt
sRNA

data_processing:
small RNA: cutadapt (adapter sequence removal); fastx toolkit (quality filter; collapse reads to generate read counts); note: 3' tRNA-derived fragments do not align against genomic tRNAs without clipping CCA-tail (use bowtie2-2.2.6 or higher for correct random alignment of multimapping reads)
ChIP-Seq: fastx_trimmer -Q33 -f 6 -l 70; bowtie2 -N 1 -X 250 --no-discordant --no-mixed; samtools view -S -F 4 -b; pairToBed (filtering simple and satellite repeats); samtools rmdup; bedtools genomecov
modified 5' RACE: fastx_clipper -Q 33 -v -a TGGAATTCTCGGGTGCCAAGG; cutadapt -g GCTGATGGCGATGAATGAACACTGCGTTTGCTGGCTTTGATGAAA -O 30 --discard-untrimmed -m 10; fastq_quality_filter -Q33 -v -q 20 -p 90; bowtie-1.1.2 -v0 (alignment against genbank AC126548 and AC124426); samtools view -S -b -F 4; bamToBed; bedtools genomecov (for inserts > 100 bp)
Genome_build: mm9
Supplementary_files_format_and_content: small RNA: readcount.txt are collapsed reads after adapter clipping, before alignment (including 3' tRNA-derived fragments); ChIP: bedGraph are aligned paired end reads without duplicates or low complexity repeats, normalized to total reads per million (RPM); modified 5' RACE: bedGraph are cDNA clones (of 5' RNA ends) that align to AC124426 or AC126548 with 0 mismatches, are longer than 100 bp and normalized to total reads per million (RPM)

source_name: trophoblast stem cell

growth_protocol: grown as previously reported with FGF4 (235-F4-025, R&D systems) and in MEF-conditioned medium (Tanaka et al., 1998).

extract_protocol:
Trizol, TBE urea PAGE size selection 14-38 nt
Illumina sRNA library prep

value: TS6.5, B5/EGFP, Tanaka et al. 1998

tag: illumina platform

tag: read type


title: d3_wcl_H3K4me1

value: H3K4me1 (Cell Signaling Technologies, catalog# 5326BF, lot# 2)


title: d3_wcl_H3K4me3


title: WT pTreg rep3

description: 50b.p single reads


title: d1_wcl_H3K27ac


title: WT Tconv rep1

description: 50b.p single reads


title: WT Tconv rep3

description: 50b.p single reads


title: WT pTreg rep1

description: 50b.p single reads


title: d1_wcl_H3K4me3


title: Ribo_cgi121D_1


title: d6_wcl_H3K4me1


title: d1_wcl_H3K4me1


title: CD28KO tTreg rep3

description: 50b.p single reads


title: CD28KO tTreg rep1

description: 50b.p single reads


title: Ribo_trm9D_2

value: BY4741 with trm9D::kanMX


title: Ribo_bud32D_2

value: BY4741 with bud32D::kanMX


title: WT tTreg rep2

description: 50b.p single reads


title: CD28KO Tconv rep3

description: 50b.p single reads


title: Ribo_trm9D_1


title: CD28KO Tconv rep2

description: 50b.p single reads


title: Ribo_elp5D_2

value: BY4741 with elp5D::kanMX


title: CD28KO pTreg rep2

description: 50b.p single reads


title: CD28KO Tconv rep1

description: 50b.p single reads


title: CD28KO pTreg rep1

description: 50b.p single reads


title: WT pTreg rep2

description: 50b.p single reads


title: Ribo_tan1D_2

value: BY4741 with tan1D::kanMX


title: ES_Dnmt1ko_rep1b

description:
RNA, 14-38 nt
sRNA

data_processing:
small RNA: cutadapt (adapter sequence removal); fastx toolkit (quality filter; collapse reads to generate read counts); note: 3' tRNA-derived fragments do not align against genomic tRNAs without clipping CCA-tail (use bowtie2-2.2.6 or higher for correct random alignment of multimapping reads)
ChIP-Seq: fastx_trimmer -Q33 -f 6 -l 70; bowtie2 -N 1 -X 250 --no-discordant --no-mixed; samtools view -S -F 4 -b; pairToBed (filtering simple and satellite repeats); samtools rmdup; bedtools genomecov
modified 5' RACE: fastx_clipper -Q 33 -v -a TGGAATTCTCGGGTGCCAAGG; cutadapt -g GCTGATGGCGATGAATGAACACTGCGTTTGCTGGCTTTGATGAAA -O 30 --discard-untrimmed -m 10; fastq_quality_filter -Q33 -v -q 20 -p 90; bowtie-1.1.2 -v0 (alignment against genbank AC126548 and AC124426); samtools view -S -b -F 4; bamToBed; bedtools genomecov (for inserts > 100 bp)
Genome_build: mm9
Supplementary_files_format_and_content: small RNA: readcount.txt are collapsed reads before alignment (including 3' tRNA-derived fragments); ChIP: bedGraph are aligned paired end reads without duplicates or low complexity repeats, normalized to total reads per million (RPM); modified 5' RACE: bedGraph are cDNA clones (of 5' RNA ends) that align to AC124426 or AC126548 with 0 mismatches, are longer than 100 bp and normalized to total reads per million (RPM)

source_name: embryonic stem cell, Dnmt1 knockout

growth_protocol: grown in Knockout-DMEM, 1000 U/ml LIF, 0.1 mM 2-mercaptoethanol, 15% FBS, 1 mM MEM non-essential amino acids, 20 mM L-glutamine; weaned off mouse embryonic fibroblast feeder cells 2-24 h before lysis

value: Dnmt1tm1Enl, MGI:1857601, 129S4/SvJae


title: Ribo_bud32D_1


title: Ribo_trm112D_2

value: BY4741 with trm112D::kanMX


title: CD28KO tTreg rep2

description: 50b.p single reads


title: Ribo_mod5D_2

value: BY4741 with mod5D::kanMX


title: Cab8_9: ES d0 Scr KD-BioRep2 RNA-seq

data_processing:
Basecalls performed using Illumina software, version 1.8.
RNA-seq: After removal of adaptor sequences by Trim Galore, reads were aligned to mouse genomes (GRCm38/mm10) using Tophat2. After removal of PCR duplicates, unmapped reads were filtered out, and were divided into unique- and multiple-aligned files. Alignments were divided into positive and negative strands, followed by coverage generation. Scaled wig files were generated by dividing these coverages by number of fragments per million.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: Alignments were divided into positive and negative strands, followed by coverage generation. The processed data are the coverage files (bigwig) files scaled by fragments per million.

growth_protocol: Cells were cultured in regular ES medium (15% FBS) with LIF

extract_protocol:
RNA-seq: Ribosomal depleted total RNA using Ribominus (Invitrogen) that were greater than 200 nt was sheared to a median size of 200 nt.
Library constructions were performed according the NEBNext Ultra Directional RNA library Pre Kit.

treatment_protocol: Scramble LNA knockdown for 12 hours

tag: strain background

value: CAST/Ei x 129/Sv/Jae

value: Embryonic stem cells

value: rRNA-depleted total RNA


title: Cab4_5: ES d0 TERRA KD-BioRep1 RNA-seq

extract_protocol:
RNA-seq: Ribosomal depleted total RNA using Ribominus (Invitrogen) that were greater than 200 nt was sheared to a median size of 200 nt.
RNA-seq: Library constructions were performed according the NEBNext Ultra Directional RNA library Pre Kit.

treatment_protocol: TERRA LNA knockdown for 12 hours


title: Control Biologic Replicate 3

first: Sant-Rayn

middle: Singh

last: Pasricha

state: Oxfordshire

department: MRC Human Immunology UnitC Human Immunology Unit

data_processing:
QC analysis was done with the fastQC package (version 0.11.4)
Reads were aligned using STAR (version 2.4.2a) with a gtf (igenomes mm10) and default parameters.
Gene expression levels were quantified as read counts using the featureCounts function from the Subread package (version 1.5.0-p2) with default parameters.
Differential gene expression between the samples was done using the edgeR package
Genome_build: mm10

source_name: Liver

extract_protocol:
RNA was extracted from liver using the Qiagen RNAeasy Mini kit. RNA was converted to cDNA using Smartseq2 reagents, and libraries were prepared using the Nextera RNA library preparation kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: Vehicle


title: Cab8_9: ES d0 TERRA KD-BioRep2 RNA-seq


title: Cab4_5: ES d0 Scr KD-BioRep1 RNA-seq

data_processing:
RNA-seq: After removal of adaptor sequences by Trim Galore, reads were aligned to mouse genomes (GRCm38/mm10) using Tophat2. After removal of PCR duplicates, unmapped reads were filtered out, and were divided into unique- and multiple-aligned files. Alignments were divided into positive and negative strands, followed by coverage generation. Scaled wig files were generated by dividing these coverages by number of fragments per million.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: Alignments were divided into positive and negative strands, followed by coverage generation. The processed data are the coverage files (bigwig) files scaled by fragments per million.


title: Ribo_elp6D_2

value: YPD

value: BY4741 with elp6D::kanMX

value: Cycloheximide


title: Cab10: ES d0 input CHIRT-seq

data_processing:
library strategy: CHIRT-seq
Basecalls performed using Illumina software, version 1.8. CHIRT-seq: Following the removal of adaptor sequences and PCR duplicates, paired-end 50 bp sequencing data was aligned to mouse reference genome (GRCm38/mm10) using the software Novoalign (v3.00.02) (http://www.novocraft.com/products/novoalign/). The coverage files were generated using R software library SPP software (Kharchenko et al., 2008) with smoothing using 500 bp bins with a 100 bp step size to generate control-subtracted, normalized read densities. Controls include input, sense-CHIRT, and TERRA-CHIRT without RNase H elution (no RNase H).
Genome_build: mm10
Supplementary_files_format_and_content: CHIRT-seq: The processed data are the coverage files (bigwig) generated using R software library SPP software with smoothing using 500 bp bins with a 100 bp step size to generate control-subtracted, normalized read densities.
The input files are wig files generated by MACS software.

source_name: TERRA CHIRT-seq

extract_protocol:
CHIRT-seq: Nuclei were crosslinked in 1% glutaraldehyde and chromatin were sheared to 0.5~3kb. Chromatin was incubated with biotinylated capture oligonucleotides, and the hybridized material was captured by streptavidin beads. Enriched DNA was eluted by RNaseH digestion.
CHIRT-seq: Eluted genomic DNA or input samples were fragmented into a median size of 220 bp, and the sequencing libraries were constructed according to NEB ChIP-Seq library protocol.

tag: capture oligos

value: input DNA


title: CD28KO pTreg rep3

description: 50b.p single reads

value: Spleen


title: Control Biologic Replicate 2


title: Cab10: ES d0 noRNaseH CHIRT-seq

data_processing:
library strategy: CHIRT-seq
Basecalls performed using Illumina software, version 1.8. Following the removal of adaptor sequences and PCR duplicates, paired-end 50 bp sequencing data was aligned to mouse reference genome (GRCm38/mm10) using the software Novoalign (v3.00.02) (http://www.novocraft.com/products/novoalign/). The coverage files were generated using R software library SPP software (Kharchenko et al., 2008) with smoothing using 500 bp bins with a 100 bp step size to generate control-subtracted, normalized read densities. Controls include input, sense-CHIRT, and TERRA-CHIRT without RNase H elution (no RNase H).
Genome_build: mm10
The processed data are the coverage files (bigwig) generated using R software library SPP software with smoothing using 500 bp bins with a 100 bp step size to generate control-subtracted, normalized read densities.The processed data are the coverage files (bigwig) files scaled by fragments per million. All input files are wig files generated by MACS software.

extract_protocol:
CHIRT-seq: Nuclei were crosslinked in 1% glutaraldehyde and chromatin were sheared to 0.5~3kb. Chromatin was incubated with biotinylated capture oligonucleotides, and the hybridized material was captured by streptavidin beads. Enriched DNA was eluted by RNaseH digestion.
Eluted genomic DNA or input samples were fragmented into a median size of 220 bp, and the sequencing libraries were constructed according to NEB ChIP-Seq library protocol.

value: TERRA-AS,noRNaseH

value: no RNaseH control DNA


title: Ribo_trm13D_2

tag: media

value: BY4741 with trm13D::kanMX


title: Cab10: ES d0 Sense CHIRT-seq

data_processing:
library strategy: CHIRT-seq
Basecalls performed using Illumina software, version 1.8. Following the removal of adaptor sequences and PCR duplicates, paired-end 50 bp sequencing data was aligned to mouse reference genome (GRCm38/mm10) using the software Novoalign (v3.00.02) (http://www.novocraft.com/products/novoalign/). The coverage files were generated using R software library SPP software (Kharchenko et al., 2008) with smoothing using 500 bp bins with a 100 bp step size to generate control-subtracted, normalized read densities. Controls include input, sense-CHIRT, and TERRA-CHIRT without RNase H elution (no RNase H).
Genome_build: mm10
Supplementary_files_format_and_content: CHIRT-seq: The processed data are the coverage files (bigwig) generated using R software library SPP software with smoothing using 500 bp bins with a 100 bp step size to generate control-subtracted, normalized read densities.All input files are wig files generated by MACS software.

value: TERRA-sense

value: Sense control DNA


title: Ribo_trm8D_2

tag: strain

value: BY4741 with trm8D::kanMX


title: Cab10: ES d0 TERRA CHIRT-seq

data_processing:
library strategy: CHIRT-seq
Basecalls performed using Illumina software, version 1.8. CHIRT-seq: Following the removal of adaptor sequences and PCR duplicates, paired-end 50 bp sequencing data was aligned to mouse reference genome (GRCm38/mm10) using the software Novoalign (v3.00.02) (http://www.novocraft.com/products/novoalign/). The coverage files were generated using R software library SPP software (Kharchenko et al., 2008) with smoothing using 500 bp bins with a 100 bp step size to generate control-subtracted, normalized read densities. Controls include input, sense-CHIRT, and TERRA-CHIRT without RNase H elution (no RNase H).
Genome_build: mm10
Supplementary_files_format_and_content: CHIRT-seq: The processed data are the coverage files (bigwig) generated using R software library SPP software with smoothing using 500 bp bins with a 100 bp step size to generate control-subtracted, normalized read densities.
All input files are wig files generated by MACS software.

extract_protocol: CHIRT-seq: Nuclei were crosslinked in 1% glutaraldehyde and chromatin were sheared to 0.5~3kb. Chromatin was incubated with biotinylated capture oligonucleotides, and the hybridized material was captured by streptavidin beads. Enriched DNA was eluted by RNaseH digestion. Eluted genomic DNA or input samples were fragmented into a median size of 220 bp, and the sequencing libraries were constructed according to NEB ChIP-Seq library protocol.

value: TERRA-AS

value: TERRA enriched DNA


title: Control Biologic Replicate 1

tag: treatment


title: RGFP966 Biologic Replicate 3

tag: tissue


title: Ribo_elp5D_1

value: BY4741 with elp5D::kanMX


title: Ribo_pus4D_2

value: BY4741 with pus4D::kanMX


title: RGFP966 Biologic Replicate 2

value: Liver


title: Ribo_pus5D_2

value: BY4741 with pus5D::kanMX


title: TS_rep2a

description:
RNA, 14-38 nt
sRNA

value: TS6.5, B5/EGFP, Tanaka et al. 1998


title: RGFP966 Biologic Replicate 1


title: feeder_rep1b

description:
RNA, 14-38 nt
sRNA

source_name: embryonic fibroblast


title: ES_wt_rep1b

description:
RNA, 14-38 nt
sRNA

source_name: embryonic stem cell

value: J1 (ATCC SCRC-1010), 129S4/SvJae


title: Ribo_elp2D_2

value: YPD

value: BY4741 with elp2D::kanMX

value: Cycloheximide


title: ES_Setdb1ko_rep2

description:
RNA, 14-38 nt
sRNA

source_name: embryonic stem cell, Setdb1 induced knockout

treatment_protocol: 800 nM OHT (4-hydroxytamoxifen) as described in Matsui et al. 2010

value: Matsui et al. 2010


title: Ribo_trm82D_2

value: BY4741 with trm82D::kanMX


title: Ribo_tyw1D_2

value: BY4741 with tyw1D::kanMX


title: Ribo_tyw4D_2

value: BY4741 with tyw4D::kanMX


title: ES_Setdb1ko_rep1b

description:
RNA, 14-38 nt
sRNA


title: ES_Setdb1ko_rep1a

description:
RNA, 14-38 nt
sRNA


title: Ribo_tyw3D_2

value: BY4741 with tyw3D::kanMX


title: Ribo_dus4D_2

value: BY4741 with dus4D::kanMX


title: 7N4-WT-sirolimus

city: Bethesda

first: Thomas

last: Darling

state: MD

address: 4301 Jones Bridge Road

department: Dermatology

institute: Uniformed Services University of the Health Sciences

data_processing:
Paired-end sequencing was done using NextSeq 500 (Illumina) at 75bp read length
FASTQ files generated with bcl2fastq v2.17.1.14
Reads were aligned to mouse transcript models using STAR (Dobin et al. Bioinformatics 2013)
FPKM values were produced using RSEM (Li and Dewy, BMC bioinformatics 2011)
FPKM values were adjusted by adding 1 and applying log2 transformation
Differential expression was calculated by two class SAM (Tusher et al. PNAS 2001)
Genome_build: mm10
Supplementary_files_format_and_content: matrix with expression values for each sample

source_name: middle limb dermis

growth_protocol: P0 cells from disociated dermis from a single neonate were plated on one 10 cm dish for 48hr in DMEM + 10% FBS. Cell were trypsinized and 250,000 cells were plated on 6cm dish. After attachment media was changed to 1% FBS.

extract_protocol:
Total RNA was extracted with Qiagen RNeasy colums and on-column Dnase treatment
Truseq Stranded mRNA Library Preparation Kit (Illumina)

treatment_protocol: After 24hr in 1% FBS, cells were treated with 20ng/ML sirolimus (rapamycin, LC Laboratories) or DMSO vehicle.

tag: age

value: postnatal day 1-2

tag: cell type

value: fibroblast

value: 1%FBS 24hr, sirolimus (20ng/mL) 24hr


title: 7N7-KO-vehicle

value: Tsc2flox/flox, prrx1-cre+/-

value: 1% FBS 24hr, vehicle (DMSO) 24hr


title: 7N7-KO-sirolimus


title: 7N4-WT-vehicle


title: 6N2-WT-sirolimus


title: 6N2-WT-vehicle


title: Ribo_tum1D_2

source_name: Yeast

value: BY4741 with tum1D::kanMX


title: Ribo_isu2D_2

value: BY4741 with isu2D::kanMX


title: 6N1-KO-vehicle


title: 5N10-WT-vehicle


title: 6N1-KO-sirolimus


title: 5N6-KO-sirolimus


title: ES_Setdb1ko_rep3

description:
RNA, 14-38 nt
sRNA


title: 5N10-WT-sirolimus


title: Ribo_uba4D_2

value: BY4741 with uba4D::kanMX


title: Ribo_ncs2D_2

value: YPD

value: BY4741 with ncs2D::kanMX


title: Ribo_isu1D_2

value: BY4741 with isu1D::kanMX

value: Cycloheximide


title: 5N6-KO-vehicle


title: Ribo_dus3D_2

value: BY4741 with dus3D::kanMX


title: Ribo_sit4D_2

value: BY4741 with sit4D::kanMX


title: Hela_MusD_rep3

description:
RNA, 14-38 nt
sRNA

source_name: cervix adenocarcinoma, epithelial

growth_protocol: DMEM, 10% FBS

treatment_protocol: lipofectamine2000 transfection with 500 ng ETnIIbeta plasmid (Ribet et al. 2004); harvested 4 days post transfection

value: Hela (ATCC CCL-2), human female

value: MiSeq


title: Ribo_sap185D_2

value: BY4741 with sap185D::kanMX


title: Hela_MusD_rep2

description:
RNA, 14-38 nt
sRNA


title: Ribo_dus1D_2

value: BY4741 with dus1D::kanMX


title: Ribo_trm140D_2

value: BY4741 with trm140D::kanMX


title: Hela_MusD_rep1

description:
RNA, 14-38 nt
sRNA


title: Hela_ETn_rep3

description:
RNA, 14-38 nt
sRNA

treatment_protocol: lipofectamine2000 transfection with 500 ng MusD6 plasmid (Ribet et al. 2004); harvested 4 days post transfection


title: Ribo_kti12D_2

value: BY4741 with kti12D::kanMX


title: K9m3_TS_rep3

description:
DNA, mononucleosomal
H3K9me3-ChIP

extract_protocol:
H3K9me3 native ChIP as described in Karimi et al. 2012
Truseq adapters, https://ethanomics.wordpress.com/chip-seq-library-construction-using-the-illumina-TruSeq-adapters

value: TS6.5, B5/EGFP, Tanaka et al. 1998


title: Hela_ETn_rep1

description:
RNA, 14-38 nt
sRNA


title: Hela_ETn_rep2

description:
RNA, 14-38 nt
sRNA


title: K9m3_TS_rep2

description:
DNA, mononucleosomal
H3K9me3-ChIP


title: Hela_control_rep3

description:
RNA, 14-38 nt
sRNA

treatment_protocol: lipofectamine2000 transfection with 500 ng pCMVbeta plasmid; harvested 4 days post transfection


title: Ribo_elp4D_2

value: BY4741 with elp4D::kanMX


title: Ribo_sap190D_2

value: BY4741 with sap190D::kanMX


title: Hela_control_rep2

description:
RNA, 14-38 nt
sRNA


title: K9m3_TS_rep1

description:
DNA, mononucleosomal
H3K9me3-ChIP


title: RACE_50nM_ETn_tRF_rep2

description:
total RNA, uncapped
5'modRACE

extract_protocol:
Trizol
ligation of 5' RACE adapter (5'-GCUGAUGGCGAUGAAUGAACACUGCGUUUGCUGGCUUUGAUGAAA), RT using SuperScriptII and random hexamers, nested amplification with ERVK-ETn-specific primer (5'-GACTGGAGTTCCTTGGCACCCGAGAATTCCAGCGTTGGGTTAGCACTGATT) and Truseq-linker (5'-TTCAGAGTTCTACAGTCCGACGATCGCTGATGGCGATGAATGAACACT), then Illumina Truseq RNA PCR primers.

treatment_protocol: lipofectamine2000 transfection with RNA oligos (50/100 mM, either ETn- or MusD-specific) and ETn/MusD plasmids (Ribet et al. 2004); harvested 2 days post transfection


title: RACE_50nM_ETn_tRF_rep1

description:
total RNA, uncapped
5'modRACE


title: Ribo_pus9D_2

extract_protocol:
For RPF, cells were lysed by glass-bead beating in ice-cold lysis buffer, followed by RNase I treatment. Ribosomes were separated on 10-50% sucrose gradient and 80S monosome fractions were collected and RNA extracted. 27-34 nt ribosome footprints were isolated by denaturing PAGE.    For RNA-Seq, total RNA extracted using TRIZOL was depleted of rRNA using Ribo-Zero, followed by zinc-based fragmentation for 10 min at 70°C.
RPF and rRNA-depleted RNA are constructed into deep-sequencing libraries as described in (Heyer et al., 2015). Briefly, RNA 3’ ends were dephosphorylated, ligated with a preadenylated adaptor, and reverse transcribed. cDNA was precipitated and size selected by denaturing PAGE. The purified cDNA was circularized and PCR amplified prior to sequencing. For RiboMeth-seq, total RNAs were end-repaired with T4 PNK, Antarctic phosphatase, or Shrimp alkaline phosphatase for 3’-end dephosphorylation and with T4 PNK and ATP for 5’-end phosphorylation, followed by library construction using NEB Next Small RNA Library Prep kit. Amplified library was purified and subject to Illumina Nextseq 500 single-end sequencing with 75 cycles.

value: BY4741 with pus9D::kanMX


title: Ribo_pus2D_2

value: BY4741 with pus2D::kanMX


title: RACE_50nM_DJ_tRF_rep2

description:
total RNA, uncapped
5'modRACE


title: Hela_control_rep1

description:
RNA, 14-38 nt
sRNA


title: ES_Setdb1wt_rep3b

description:
RNA, 14-38 nt
sRNA

source_name: embryonic stem cell, Setdb1 wt uninduced

value: Matsui et al. 2010


title: K9m3_TS_rep4

description:
DNA, mononucleosomal
H3K9me3-ChIP


title: RACE_50nM_DJ_tRF_rep1

description:
total RNA, uncapped
5'modRACE


title: Ribo_trm2D_2

value: YPD

value: BY4741 with trm2D::kanMX


title: Ribo_pus3D_2

value: BY4741 with pus3D::kanMX

value: Cycloheximide


title: RACE_100nM_ETn_tRF_rep1

description:
total RNA, uncapped
5'modRACE


title: RACE_100nM_DJ_tRF_rep2

description:
total RNA, uncapped
5'modRACE


title: ES_Setdb1wt_rep2

description:
RNA, 14-38 nt
sRNA


title: RACE_100nM_ETn_tRF_rep2

description:
total RNA, uncapped
5'modRACE


title: ES_Setdb1wt_rep1

description:
RNA, 14-38 nt
sRNA


title: Ribo_trm44D_2

value: BY4741 with trm44D::kanMX


title: Ribo_trm10D_2

value: BY4741 with trm10D::kanMX


title: TS_rep5

description:
RNA, 14-38 nt
sRNA


title: Ribo_trm12D_2

value: BY4741 with trm12D::kanMX


title: TS_rep3b

description:
RNA, 14-38 nt
sRNA


title: Ribo_trm11D_2

value: BY4741 with trm11D::kanMX


title: TS_rep3a

description:
RNA, 14-38 nt
sRNA


title: TS_rep2b

description:
RNA, 14-38 nt
sRNA


title: Ribo_trm1D_2

value: BY4741 with trm1D::kanMX


title: Ribo_trm3D_2

value: BY4741 with trm3D::kanMX


title: ES_Setdb1wt_rep3a

description:
RNA, 14-38 nt
sRNA


title: Ribo_BY4741_10


title: feeder_rep4

description:
RNA, 14-38 nt
sRNA


title: feeder_rep5

description:
RNA, 14-38 nt
sRNA


title: Ribo_trm112D_1

value: BY4741 with trm112D::kanMX


title: ES_Dnmt1ko_rep4

description:
RNA, 14-38 nt
sRNA

value: Dnmt1tm1Enl, MGI:1857601, 129S4/SvJae


title: Ribo_tan1D_1

value: BY4741 with tan1D::kanMX


title: feeder_rep3

description:
RNA, 14-38 nt
sRNA


title: Ribo_BY4741_9


title: ES_wt_rep3

description:
RNA, 14-38 nt
sRNA

value: J1 (ATCC SCRC-1010), 129S4/SvJae


title: ES_wt_rep4

description:
RNA, 14-38 nt
sRNA


title: ES_Dnmt1ko_rep3

description:
RNA, 14-38 nt
sRNA


title: TS_rep4

description:
RNA, 14-38 nt
sRNA

value: TS6.5, B5/EGFP, Tanaka et al. 1998


title: Ribo_trm13D_1

value: BY4741 with trm13D::kanMX


title: Ribo_ncs6D_2

value: BY4741 with ncs6D::kanMX


title: RACE_100nM_DJ_tRF_rep1

description:
total RNA, uncapped
5'modRACE

value: Hela (ATCC CCL-2), human female

value: MiSeq


title: Ribo_mod5D_1

value: YPD

value: BY4741 with mod5D::kanMX


title: ES_Dnmt1ko_rep2b

description:
RNA, 14-38 nt
sRNA


title: ES_wt_rep2b

description:
RNA, 14-38 nt
sRNA


title: Ribo_tyw1D_1

value: BY4741 with tyw1D::kanMX

value: Cycloheximide


title: feeder_rep2

description:
RNA, 14-38 nt
sRNA

value: GAII


title: Ribo_pus5D_1

value: BY4741 with pus5D::kanMX


title: Ribo_trm8D_1

value: BY4741 with trm8D::kanMX


title: Ribo_pus4D_1

value: BY4741 with pus4D::kanMX


title: feeder_rep1a

description:
RNA, 14-38 nt
sRNA


title: Ribo_tad1D_2

value: BY4741 with tad1D::kanMX


title: ES_wt_rep2a

description:
RNA, 14-38 nt
sRNA


title: Ribo_ncs6D_1


title: Ribo_elp2D_1

value: BY4741 with elp2D::kanMX


title: Ribo_trm82D_1

value: BY4741 with trm82D::kanMX


title: ES_wt_rep1a

description:
RNA, 14-38 nt
sRNA

value: J1 (ATCC SCRC-1010), 129S4/SvJae


title: Ribo_elp6D_1

value: BY4741 with elp6D::kanMX


title: SJTALL022664_D1_COG study 0441

city: Albuquerque

first: Ksenia

last: Matlawska

state: NM

address: 915 Camino de Salud

department: Pediatrics

institute: University of New Mexico

description:
209
RNA sequencing data from primary T-ALL samples at diagnosis

data_processing:
Illumina mRNA-seq data (fastq files) were mapped using StrongArm pipeline
genomic rearrangements were identified using CICERO, a novel algorithm identifying fusion transcripts (Illumina data)
Ion Proton data (BAM files) were aligned with STAR (bases calling: IonTorrent Base Caller)
aligned data were analyzed using customized scripts written in R (for Ion Proton data)
Genome_build: hg19
Supplementary_files_format_and_content: txt file containing results of identified fusion transcripts

source_name: COG study 0441

growth_protocol: Derived from bone marrow in newly diagnosed T-ALL patients

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instruction
RNA libraries were prepared for sequencing using standard Illumina protocols (14 samples; Truseq RNA Library Preparation kit ) or standard Ion Proton protocols (3 samples; Xpress Plus Fragment Library kit), respectively.

treatment_protocol: COG study 9404/0434 (diagnostic samples)

tag: diagnosis

value: Newly diagnosed T-ALL patient

value: bone marrow


title: Ribo_tyw4D_1

value: BY4741 with tyw4D::kanMX


title: ES_Dnmt1ko_rep1a

description:
RNA, 14-38 nt
sRNA

value: Dnmt1tm1Enl, MGI:1857601, 129S4/SvJae


title: Ribo_dus1D_1

value: YPD

value: BY4741 with dus1D::kanMX


title: Ribo_dus4D_1

value: BY4741 with dus4D::kanMX


title: Ribo_tyw3D_1

value: BY4741 with tyw3D::kanMX

value: Cycloheximide


title: SJTALL022492_D1_COG study 0442

description:
204
RNA sequencing data from primary T-ALL samples at diagnosis

source_name: COG study 0442


title: SJTALL022444_D1_COG study 0434

description:
181
RNA sequencing data from primary T-ALL samples at diagnosis

source_name: COG study 0434


title: SJTALL022445_D1_COG study 0435

description:
185
RNA sequencing data from primary T-ALL samples at diagnosis

source_name: COG study 0435


title: SJTALL022439_D1_COG study 0434

description:
147
RNA sequencing data from primary T-ALL samples at diagnosis


title: SJTALL022661_D1_COG study 0436

description:
192
RNA sequencing data from primary T-ALL samples at diagnosis

source_name: COG study 0436


title: Ribo_trm140D_1

value: BY4741 with trm140D::kanMX


title: SJTALL022491_D1_COG study 0440

description:
165
RNA sequencing data from primary T-ALL samples at diagnosis

source_name: COG study 0440


title: Ribo_tad1D_1


title: ES_Dnmt1ko_rep2a

description:
RNA, 14-38 nt
sRNA

value: GAII


title: SJTALL022438_D1_COG study 0434

description:
140
RNA sequencing data from primary T-ALL samples at diagnosis


title: Ribo_tum1D_1

value: BY4741 with tum1D::kanMX


title: SJTALL022436_D1_COG study 0438

description:
134
RNA sequencing data from primary T-ALL samples at diagnosis

source_name: COG study 0438


title: Ribo_isu2D_1

value: BY4741 with isu2D::kanMX


title: SJTALL022655_D1_COG study 0444

description:
133
RNA sequencing data from primary T-ALL samples at diagnosis

source_name: COG study 0444


title: SJTALL022654_D1_COG study 0439

description:
131
RNA sequencing data from primary T-ALL samples at diagnosis

source_name: COG study 0439


title: Ribo_uba4D_1

value: BY4741 with uba4D::kanMX


title: Ribo_sap190D_1

value: BY4741 with sap190D::kanMX


title: Ribo_ncs2D_1

value: BY4741 with ncs2D::kanMX


title: SJTALL022433_D1_COG study 0445

description:
114
RNA sequencing data from primary T-ALL samples at diagnosis

source_name: COG study 0445


title: Ribo_sap185D_1

value: BY4741 with sap185D::kanMX


title: Ribo_dus3D_1

value: BY4741 with dus3D::kanMX


title: Ribo_sit4D_1

value: BY4741 with sit4D::kanMX


title: OsNAC6KO

city: Pyeongchang

first: Pil Joong

last: Chung

state: Gangwondo

address: Pyeongchang daero 1447

department: Crop Biotechnology Institute

country: South Korea

institute: Seoul National University

description: Sample 5

data_processing:
Single-end seq were generated and raw seq reads were trimmed to removed adaptor seq, and those with a quality lower than Q20 were removed using the clc quality trim software (CLCBIO).
Duplicate paired short reads were removed using FastUniq.
All reads were assembled with the clc_ref_assmble 6 (version 4.06) program, using annotated gene and noncoding RNA seq from the rapdb (http://rapdb.dna.affrc.go.jp).
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: abundance measurements

organism: Oryza sativa

source_name: OsNAC6-KO (Knockout mutants)

growth_protocol: Rice was germinated on MS (Murashige and Skoog) media at 28C for 4 days, and transplanted into soil pots (4x4x6 cm; 3 plants per pot) and grown in a greenhouse.

extract_protocol:
Total RNA was extracted from the roots of 2-week-old OsNAC6 overexpressors, knockout mutant, and NT rice seedlings grown under normal growth conditions using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.
A modified TruSeq method was used to construct a strand-specific RNA-seq library with different index primers and libraries were sequenced in the Illumina HiSeq 2000 system in the National Instrumentation Center of Environmental Management College of Agriculture and Life Science, Seoul National University (NICEM). Cutoff criteria to eliminate genes that showed no significant difference were more than 2 fold up- and down-regulation in RCc3::OsNAC6 or GOS2::OsNAC6 compared to NT (Nipponbare) and in nac6 compared to NT (Hwayoung).

value: roots

value: 2 weeks

tag: ecotype

value: Hwayoung


title: notransgenic control 2

description: Sample 4

source_name: NT (nontransgenic rice plant)


title: Ribo_kti12D_1

data_processing:
Library strategy: Ribosome profiling
Raw fastq reads were de-multiplexed and removed of adaptor sequence using homerTools function of HOMER package v4.6, with parameters "barcodes 5 -min 0.01" and "trim -5 2 -3 TGGAATTCTCGGGTGCCAAGG -mis 2 -minMatchLength 5", respectively.
De-multiplexed and adaptor-removed reads for RPF were mapped to S. cerevisiae rDNA and the mapping reads were discarded. The remaining RPF reads and RNA-seq reads were mapped to sacCer3 genome using TopHat v2.0.12 with parameters -p 4 -I 5000 --no-coverage-search
Uniquely mapping reads (filtered by samtools view function and parameter -q 10) in length of 27-34 nt (RPF) or >=27 nt (RNA-seq) were used for gene-level analysis, in which reads were quantified as raw counts or reads per kilobase of transcript per million mapped reads (RPKM) using HOMER package with open reading frame annotations downloaded from SGD.
Translational efficiency (TE) was calculated as relative ribosome footprint density (Ribo-rRPKM) divided by relative RNA abundance (RNA-rRPKM), with rRPKM calculated by normalizing RPKM in each mutant by the average of RPKM in WTs grown in the same batch.
Global codon occupancy analysis was calculated as described in (Nedialkova and Leidel, 2015), with minor modifications. The P-site offset was calculated by examining the cumulative distribution of 28-31 nt reads aligning at start codons. After applying the respective offset to reads of each size, only in-frame reads were used. The first 15 and the last 5 codons of each transcript were removed from the reference. The frequency of each codon in ribosomal A, P, and E sites was calculated for normalization, and divided by the average frequency of the same codon in the three downstream codons from the A site
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample (RPF or RNA-seq reads) and normalized codon frequencies per A/P/E site.
Supplementary_files_format_and_content: Chou_Table_S1.txt: RNA counts/RPKM per gene
Supplementary_files_format_and_content: Chou_Table_S2.txt: RPF counts/RPKM per gene
Supplementary_files_format_and_content: Chou_Table_S3.txt: relative Translational Efficiency values (RPF rRPKM/RNA rRPKM, with rRPKM calculated by normalizing RPKM in each mutant by the average of RPKM in WTs grown in the same batch)
Supplementary_files_format_and_content: Chou_Table_S4.txt: A/P/E site normalized values
Supplementary_files_format_and_content: Chou_Table_S5.txt: RiboMeth-seq data with raw counts of 5' read starts

value: YPD

value: BY4741 with kti12D::kanMX


title: RCc3:OsNAC6

description: Sample 2

source_name: RCc3:OsNAC6 (root specific promoter transgenic plants)

value: Nipponbare


title: SJTALL022656_D1_COG study 0443

description:
135
RNA sequencing data from primary T-ALL samples at diagnosis

source_name: COG study 0443

value: Newly diagnosed T-ALL patient

value: bone marrow


title: Ribo_pus2D_1

source_name: Yeast

value: BY4741 with pus2D::kanMX

value: Cycloheximide


title: Ribo_pus3D_1

value: BY4741 with pus3D::kanMX


title: GOS2:OsNAC6

description: Sample 3

source_name: GOS2:OsNAC6 (whole body promoter transgenic plants)


title: Ribo_elp4D_1

value: BY4741 with elp4D::kanMX


title: notransgenic control 1

description: Sample 1


title: Ribo_trm2D_1

value: BY4741 with trm2D::kanMX


title: Ribo_trm44D_1

value: BY4741 with trm44D::kanMX


title: Ribo_isu1D_1

value: BY4741 with isu1D::kanMX


title: Ribo_trm10D_1

value: BY4741 with trm10D::kanMX


title: SJTALL022435_D1_COG study 0437

description:
129
RNA sequencing data from primary T-ALL samples at diagnosis

source_name: COG study 0437


title: C57BL6

first: Alexander

last: Poltorak

state: Massachusetts

address: 150 Harrison avenue

institute: Tufts University

data_processing:
The resulted data were demultiplexed using Illumina CASAVA 1.8 and fastq files for each initial sample were generated
Tophat2 alignment of raw paired reads to UCSC mm10 genome
Cuffdids using the outputs from two previous steps with mm10 annotation
Genome_build: mm10

source_name: bone marrow derived

growth_protocol: bone marrow was extracted from femurs of mice, counted, and plated at the density of 1 million cells per 10cc plate. The cells were grown for 7 days in the presence of 10% FS, DMEM and M-CSF, rested for two days and subjected to RNA-isolation

extract_protocol:
RNA was prepared according to manufacture's instructions
Library was prepared using Truseq pair-end Illumina kit. Briefly, 10-100 ng of total RNA was reconstituted in water, mixed with Ribosomal removal Buffer containing RNAClean XP beads, and depleted from rRNA. First strand was synthesized using RT, followed by a second strand synthesis, 3' ends were adenylated and ligated to the adaptors, followed by ligateion of the 5' adaptors; the library was purified and measured on DNA-concentration

treatment_protocol: after growth and differentiation, the medium was discarded, the cells were washed twice and lysed in Trisol in a ratio 1 ml of Trisol per 2 million of cells

value: macrophages

tag: genotype/variation


title: MOLF

value: MOLF


title: IFNAR-deficient

value: IFNAR-deficient


title: STING-deficient

value: STING-deficient


title: STING-congenic

value: STING-congenic


title: Ribo_trm11D_1

value: YPD

value: BY4741 with trm11D::kanMX


title: Ribo_trm12D_1

value: BY4741 with trm12D::kanMX


title: Ribo_trm3D_1

value: BY4741 with trm3D::kanMX


title: Ribo_trm1D_1

value: BY4741 with trm1D::kanMX


title: Ribo_BY4741_8

value: Cycloheximide


title: Ribo_BY4741_7


title: Ribo_rit1D_2

value: BY4741 with rit1D::kanMX


title: Ribo_urm1D_2

value: BY4741 with urm1D::kanMX


title: Ribo_pus9D_1

value: BY4741 with pus9D::kanMX


title: Ribo_BY4741_6


title: Ribo_pus7D_2

value: BY4741 with pus7D::kanMX


title: 5693

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

data_processing:
Data processing was performed using partek Flow build version 4.0.15.0702
Bases were trimmied on quality score=20. Adaptors were also trimmed.
Filter BAM files with minimal mapping quality=20.
Alignment usign Bowtie2 version 2.1.0.
Quantification to transcriptome performed using Partek E/M algorithm.
Genome_build: mm9
Supplementary_files_format_and_content: raw expression values

source_name: hippocampus

growth_protocol: Mice were housed in a 12-h light/12-h dark cycle facility, and free access to rodent chow and water was available.

extract_protocol:
Hippocampal RNA was extracted using TRI Reagent (T9242, Sigma-Aldrich, MO,USA) kit followed by mRNA libraries construction.
Customary Illumina TruSeq™ RNA Sample Prep Kit v2 protocol (catalog No. RS-122-2001)

treatment_protocol: Adnp+/- animals were produced according to publications: 1) Activity-dependent neuroprotective protein: a novel gene essential for brain formation, Pinhasov et al., Dev. Brain Res. 144:83-90 (2003); 2) Activity dependent neuriprotective protein snippet NAP reduces Tau hyperphosphorylation and enhances learning in a novel transgenic mouse model. Vulih-Shultzman et al, JPET 323:438-449 (2007); 3) Activity-dependent neuroprotective protein (ADNP) exhibits striking sexual dichotomy impacting on autistic and Alzheimer's pathologies. Transl. Psychiatry 5:e501; doi:10.1038/tp.2014.138 (2015).

value: mixed C57BL and 129/SvJ background

value: wild-type

value: 5 month

tag: gender

value: male


title: 5692


title: Ribo_pus1D_2

value: BY4741 with pus1D::kanMX


title: 5691

value: Adnp+/-


title: 5687

value: female


title: Ribo_elp3D_2

value: YPD

value: BY4741 with elp3D::kanMX


title: 5690


title: Ribo_kti11D_2

value: BY4741 with kti11D::kanMX


title: Ribo_BY4741_5


title: Ribo_elp1D_2

value: BY4741 with elp1D::kanMX


title: 5683


title: 5685


title: Ribo_rtt10D_2

value: BY4741 with rtt10D::kanMX


title: Ribo_trm732D_2

value: BY4741 with trm732D::kanMX

value: Cycloheximide


title: Ribo_trm4D_2

value: BY4741 with trm4D::kanMX


title: Ribo_BY4741_4


title: Ribo_trm7D_2

value: BY4741 with trm7D::kanMX


title: 5681


title: 2211

value: 1 month


title: Ribo_rit1D_1

value: BY4741 with rit1D::kanMX


title: 5631

value: mixed C57BL and 129/SvJ background


title: Ribo_urm1D_1

value: BY4741 with urm1D::kanMX


title: 2208

value: male


title: Yellow-Leaf 1

city: Hangzhou

first: lv

middle: yu

last: song

address: CNRRI

country: China

institute: CNRRI

description: mRNA sequencing

data_processing:
Prior to assembly, we removed the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) in the raw data. And then we aligned reads of sample yl-1 and sample wild-type to the JGI (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Osativa) rice reference genome using Tophat package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. Tophat allows multiple
alignments pe read (up to 20 by default) and a maximum of two mismatchs when mapping the reads to the reference.Tophat build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
Transcript abundance estimation and differentially expressed testing
The aligned read files were processed by Cufflinks, which uses the normalized RNA-seq fragement counts to measure the relative abundances of the tianscripts. The unit of measurement is Fragment Per Kilobase of exon per Million fragments mapped (FPKM).The feference GTF annotation file used in Cufflinks was downloaded from the JGI database. Cufflink was used to de novo assemble the transcripiome at first; The second ,Cuffmerge was used to comerge all transcripts of sample A and B to generate unique transcripts. The downloaded JGI GTF file was passed to Cuffdiff along with the original alinment (SAM) files produced by Tophat. Cuffdiff re-estimates the abundance of the transcripts listed in the GTF file using aligments from the SAM file and concurrently test for different expression. Only the comparisons with “q_value”less than 0.05 and status marked as “OK” in the Cuffdiff output were regarded as showing differential expression.
Genome_build: Oryza sativa v7_JGI (Rice)
Supplementary_files_format_and_content: excel,expression profiles

source_name: plants leaves

growth_protocol: The seedlings were cultivated in 1/2 MS medium

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp).

treatment_protocol: The seedlings were in a growth chamber (12/12h light/dark; light intensity 300 μmol m−2 s−1) at a constant temperature of either 26 ºC

value: yl-1 mutant

tag: background

value: EMS-induced mutant library of indica super early-season rice cv. Zhongjiazao 17

value: plants leaves


title: Ribo_BY4741_3

treatment_protocol: 30 sec of cycloheximide in a final concentration of 100 ug/mL in YPD at 30°C

value: YPD


title: wild-type

description: mRNA sequencing

value: wild type

value: indica super early-season rice cv. Zhongjiazao 17


title: 2193

value: Adnp+/-

value: female


title: 2204


title: Ribo_pus7D_1

value: BY4741 with pus7D::kanMX


title: 2192

value: wild-type


title: Ribo_pus1D_1

value: BY4741 with pus1D::kanMX

value: Cycloheximide


title: 2191

value: 1 month


title: Ribo_kti11D_1

value: BY4741 with kti11D::kanMX


title: Ribo_elp1D_1

value: BY4741 with elp1D::kanMX


title: 5682

value: mixed C57BL and 129/SvJ background

value: 5 month


title: Ribo_elp3D_1

value: BY4741 with elp3D::kanMX


title: Ribo_BY4741_2


title: 5676

value: male


title: 2187


title: Ribo_rtt10D_1

value: BY4741 with rtt10D::kanMX


title: 2188


title: 2184


title: 2185


title: Ribo_trm7D_1

value: YPD

value: BY4741 with trm7D::kanMX


title: Ribo_trm732D_1

value: BY4741 with trm732D::kanMX


title: BLD101_ComX+

city: Louvain-La-Neuve

first: Pascal

last: Hols

address: Croix du Sud, 4-5, box L7.07.06

department: Institute of Life Sciences (ISV) Biochemistry, Biophysics and Genetics of Microorganisms (BBGM)

country: Belgium

institute: Faculty of Sciences Université catholique de Louvain

description: strain carrying the plasmid pGhP32comX

data_processing:
The Illumina raw reads were quality checked using FastQC v2.2
Sequenced reads were mapped onto NC_0022369 reference genome sequence using bowtie2 v2.2.3 with parameters --local and -k 10
The SAM files obtained from Bowtie2 were sorted and converted to BAM format using SAMtools v0.1.19
Reads aligned to genes were counted using HTSeq-count v0.6.1 with default settings
Differential expression between the wild-type and ComX+ strains were performed using DESeq2 v1.8.1, edgeR v3.10.2 and DEXUS v1.8.0 packages
Genome_build: Lactococcus lactis subsp. cremoris KW2 (RefSeq NC_022369.1)
Supplementary_files_format_and_content: Microsoft excel spreadsheet file include output from DESeq2, DEXUS and edgeR

organism: Lactococcus cremoris

source_name: Bacterial culture

growth_protocol: The strains were grown in CDM supplemented with 5% mannitol. Cells were harvested when cultures reached the mid-log phase (OD600 of ~0.3) and washed twice in ice-cold PBS buffer. Pellets were frozen on liquid nitrogen and stored at −80°C.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen). RNA was treated with DNase, purified using the RNA Cleanup protocol from the RNeasy Mini Kit (Qiagen), and stored at −80°C. The integrity of the RNA was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies). Removal of rRNA was performed using the RiboMinus Bacteria Module (Invitrogen).
The transcriptome library for sequencing was constructed according to the NEXTflexRapid Directional RNA-Seq library protocol (Bioo Scientific). The prepared library (insert size of 130-580 bp) was validated for quality by running an aliquot on a High Sensitivity Bioanalyzer Chip (Agilent).

value: BLD101 [pGhP32comX]

value: ComX+


title: Ribo_trm4D_1

value: BY4741 with trm4D::kanMX


title: BLD101_WT

description: control strain with empty vector

value: BLD101 [pGhost9]

value: Wild type


title: blueberry_fruit_sRNA

city: Hefei

first: Junyang

last: Yue

state: Anhui

address: Tunxi Road

institute: Hefei University of Technology

description: small RNA

data_processing:
remove the 5' and 3' adaptor sequences
align to the blueberry genome
align with known miRNA precursors and mature miRNAs present in the miRBase database (Release 21.0)
match to non-coding RNAs (rRNA, tRNA, snRNA, and snoRNA) available in the Rfam database
Genome_build: blueberry genome (https://bitbucket.org/lorainelab/blueberrygenome)
Supplementary_files_format_and_content: read counts and miRNA sequences

organism: Vaccinium ashei

source_name: fruit

growth_protocol: grown under natural conditions

extract_protocol:
use the TRIzol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols
use Illumina Genome Analyzer according to the manufacturer’s protocols

value: fruit

tag: developmental stage

value: ripening


title: Sce RNAi Replicate 3 (rna-seq)

status: Public on Jun 28 2017

city: Saint Louis

first: Dale

last: Dorsett

state: MO

address: 1100 South Grand Boulevard

department: Biochemistry and Molecular Biology

institute: Saint Louis University School of Medicine

data_processing:
Basecalling was performed by Torrent Suite version 4 and 5 software using the default settings
Alignment to Drosophila melanogaster genome sequence was performed using TMAP map4 algorithm with 5' and 3' softclipping and a minimum seed length of 20 nt
The total sequencing base pair coverage in all exons was summed for all annotated genes in each sample and normalized to total coverage using bedtools and custom R as described in Wu et al. 2015 PLoS Genetics Nov 6;11(11):e1005655.
Genome_build: Drosophila melanogaster release 5 (April 2006) with chrU and U_extra sequences removed
Supplementary_files_format_and_content: [Expression.Table.txt, columns B-K, S-U] File with normalized sequencing coverage of all annotated genes and statistical comparison of expression in RNAi treated cells to Mock RNAi control cells.

organism: Drosophila melanogaster

source_name: ML-DmBG3-c2 cultured cells

growth_protocol: BG3 cells were cultured in Schneider's media with 10% FCS and 10 μg per ml insulin.

extract_protocol:
Total RNA was extracted using the Zymo Research Quick-RNA MicroPrep Kits with DNaseI treatment following the manufacturer's directions.
Ion Xpress IonXpressRNA barcoded sequencing libraries were constructed using the Eukaryotic Ribominus and Ion Total v2 kits (Life Technologies) according to the manufacturer's directions.

treatment_protocol: For RNAi, media was replaced with 1 ml of Express Five SFM (Invitrogen) with 1% FCS, (and 10 μg per ml insulin for BG3 cells), for 3 hours. For RNAi of all factors, from 0.7 to 40 μg of dsRNA was added per well of a 6-well plate. Media was adjusted to 3 ml and 10% FCS withSchneider's media after 2 hrs of RNAi treatment. Cells were replated as needed. Templates for dsRNA synthesis were made by PCR from cDNA or genomic DNA templates using primers with T7 promoters. In most experiments, equal amounts of two dsRNAs against each target were used. Both individual dsRNAs knocked down the targets, but knockdown was generally more efficient with a mixture. Templates were designed to avoid off-target matches of ≥19 nucleotides using Drosophila RNAi Screening Center (http://www.flyrnai.org/) online tools.

tag: RNAi treatment

value: Sce RNAi treatment


title: Sce RNAi Replicate 1 (rna-seq)


title: Pc RNAi Replicate 1 (rna-seq)

value: Pc RNAi treatment


title: Pc RNAi Replicate 2 (rna-seq)


title: Sce RNAi Replicate 4 (nascent rna-seq)

description:
nascent RNA
iSce.plus.norm.sgr
iSce.minus.norm.sgr

data_processing:
Basecalling was performed by Torrent Suite version 4 and 5 software using the default settings
The fastq files were aligned in two steps. First, they were aligned to a fasta file containing the Drosophila melanogaster release 5.9 pre-rRNA, ncRNA, and miscRNA sequences using TMAP map4 algorithm with 5' and 3' softclipping and a minimum seed length of 20. The reads that did not align were selected using samtols and aligned to the Drosophila melanogaster genome sequence without allowing clipping. The aligned reads were sorted and indexed using samtools and genome coverage was calculated using BEDTools.
The total gene sequence coverage was calculated and used to normalize coverage across all samples. Normalized bedgraph files were generated using BEDTools and converted to sgr files as described in Pherson et al, submitted.
Genome_build: Drosophila melanogaster release 5 (April 2006) with chrU and U_extra sequences removed
Supplementary_files_format_and_content: Normalized plus strand and minus strand sgr files of nascent RNA reads
[Expression.Table.txt, columns L-R, V-W] File with normalized sequencing coverage of all annotated genes and statistical comparison of expression in RNAi treated cells to Mock RNAi control cells.

extract_protocol:
Chromatin was prepared for nascent RNA isolation as described in Weber et al. 2014 Mol Cell 53: 819-30. doi:10.1016/j.molcel.2014.02.014. The chromatin pellet was dissolved in 10 mL Trizol (Invitrogen) and RNA was isolated following the manufacturer's protocol and precipitated by isopropanol with 0.2M NaCl and 20 micrograms of glycogen. Nascent RNA was digested with DNaseI (Epicentre) and uncapped RNAs were degraded in a two step reaction to remove ribosomal RNA, and residual mRNAs were depleted using oligo d(T) dynabeads (Ambion) as decribed in Pherson et al, submitted.
Ion Xpress IonXpressRNA barcoded sequencing libraries were constructed using Ion Total v2 kits (Life Technologies) according to the manufacturer's directions, with modifications to allow for separate 5' and 3' adapter ligation steps. First, the 3' adapter was ligated to capture native 3' ends of the nascent RNA, followed by RNase III treatment, and 5' adapter ligation as described in Pherson et al, submitted. The remaining steps of reverse transcription and PCR amplification were followed as described by the manufacturer.


title: 2189

value: mixed C57BL and 129/SvJ background

tag: genotype

value: wild-type

value: 1 month

value: female


title: Sce RNAi Replicate 3 (nascent rna-seq)


title: Sce RNAi Replicate 2 (nascent rna-seq)


title: Sce RNAi Replicate 1 (nascent rna-seq)


title: Pc iPh Replicate 2 (chip-seq)

data_processing:
Basecalling was performed by Torrent Suite version 4 and 5 software using default settings
Aligmentment to the Drosophila release 5 genome sequence was performed using the TMAP map4 algorithm without soft clipping (-g 3 option)
Genome coverage at each base pair for Input and each ChIP sample was calcluted using BEDtools genomecoveragebed (-d option)
Enrichment in ChIP sample coverage relative to Input coverage in sliding 250 bp windows with 50 bp steps was calculated using custom R scripts as described in Swain et al. submitted. Input file used for each sample is indicated above. Coverage in each window was normalized to total genome coverage prior to normalization to Input.
ChIP enrichment was averaged for all replicates to generate final processed data files
Genome_build: Drosophila melanogaster Release 5 (April 2006) with ChrU and Uextra removed
Supplementary_files_format_and_content: Text graph file (sgr) of log2 enrichment normalized to Input

extract_protocol:
BG3 cells were grown to a concentration of 5E6 per mL, then crosslinked by addition of 36% formaldehyde directly to the cell culture media to a final concentration of 1%, and incubation for 10 minutes at room temperature on a rocking platform. The reaction was stopped by addition of glycine pH 7.0 to a final concentration of 0.125 M. Cells were washed once with 1x PBS and once each with Wash Buffers A (10 mM HEPES pH 7.6; 10 mM EDTA pH 8.0; 0.5 mM EGTA pH 8.0; 0.25% Triton X100) and B (10 mM HEPES pH 7.6; 200 mM NaCl; 1 mM EDTA pH 8.0; 0.5 mM EGTA pH 8.0; 0.01% Triton X-100) for 10 minutes each. Cells were resuspended in sonication buffer to a concentration of 1x10^9/3 mL, and sonicated using a BioRuptor Sonicator for 14-20 cycles of 30 s on, 30 s off. Na-lauroylsarcosine was added to 0.5% and incubated for 10 minutes, rotating. Chromatin was centrifuged at 12,000g for 5 minutes at 4°C to pellet insoluble material, and 200 uL chromatin aliquots, each representing ~50x10^6 cells, were snap frozen on dry ice. For immunoprecipitation, aliquots of chromatin (10 - 20 x 10^6 BG3 cells) were adjusted to RIPA buffer in a final volume of 500 μL. Adjusted chromatin was pre-cleared for 2 hours with Protein A agarose beads, then incubated with primary antibody overnight at 4°C. Antibody-chromatin complexes were pulled down by incubation with Protein A agarose beads for 4 hours at 4°C, and beads were washed consecutively with RIPA, LiCl buffer, and TE. Samples were treated with RNAse A for 30 minutes at 37°C, then DNA crosslinks were reversed by overnight treatment at 65°C with Proteinase K, and DNA was recovered using Qiagen MinElute columns or phenol/choloroform extraction and ethanol precipitation.
Ion Torrent IonXpress barcoded sequencing libraries were constructed using the Ion Xpress Plus Fragment Library Kit (Life Technologies) according to the manufacturer's directions except that size selection was performed using Beckman Agencourt magnetic beads.

treatment_protocol: For RNAi, media was replaced with 1 ml of Express Five SFM (Invitrogen) with 1% FCS, (and 10 μg per ml insulin for BG3 cells), for 3 hours. For RNAi of all factors, from 0.7 to 40 μg of dsRNA was added per well of a 6-well plate. Media was adjusted to 3 ml and 10% FCS with Schneider's media after 2 hrs of RNAi treatment. Cells were replated as needed. Templates for dsRNA synthesis were made by PCR from cDNA or genomic DNA templates using primers with T7 promoters. In most experiments, equal amounts of two dsRNAs against each target were used. Both individual dsRNAs knocked down the targets, but knockdown was generally more efficient with a mixture. Templates were designed to avoid off-target matches of ≥19 nucleotides using Drosophila RNAi Screening Center (http://www.flyrnai.org/) online tools.

value: Ph RNAi treatment

tag: chip antibody source

value: Richard Jones (SMU)

tag: input file for normalization

value: Input_Replicate 1 fastq


title: Pc iPh Replicate 1 (chip-seq)


title: Pc Mock Replicate 2 (chip-seq)

value: Mock RNAi treatment


title: Pc iSce Replicate 1 (chip-seq)


title: Pc Mock Replicate 1 (chip-seq)

value: Input_Replicate 1 and Input_Replicate 2 fastqs


title: Ph iPc Replicate 1 (chip-seq)

value: Jürg Müller (Max Planck Institute of Biochemistry)


title: Ph iPc Replicate 2 (chip-seq)


title: Ribo_BY4741_1

first: Oliver

last: Rando

address: 364 Plantation Street

institute: UMass Medical School

growth_protocol: 100 mL of yeast cultures were grown to mid-log phase (OD600=0.5-0.6) in YPD (1% Yeast extract, 2% Peptone, 2% Dextrose) at 30°C

value: YPD

value: Cycloheximide


title: Spt5 iSce Replicate 1 (chip-seq)

value: John Lis (Cornell)


title: Ph Mock Replicate 1 (chip-seq)


title: Ph Mock Replicate 2 (chip-seq)


title: Spt5 Mock Replicate 2 (chip-seq)


title: Pc iSce Replicate 2 (chip-seq)


title: Spt5 Mock Replicate 3 (chip-seq)


title: Spt5 iSce Replicate 2 (chip-seq)


title: Spt5 Mock Replicate 1 (chip-seq)


title: Thr4P iSce Replicate 2 (chip-seq)

value: Phospho-Rpb1 CTD Thr4P (#26319, Cell Signaling)


title: Ph iSce Replicate 1 (chip-seq)


title: Thr4P iPh Replicate 1 (chip-seq)


title: Thr4P iSce Replicate 1 (chip-seq)


title: Thr4P iPh Replicate 2 (chip-seq)


title: Spt5 iPh Replicate 2 (chip-seq)


title: Spt5 iPh Replicate 1 (chip-seq)


title: Thr4P Mock Replicate 2 (chip-seq)


title: Thr4P Mock Replicate 1 (chip-seq)


title: Ph iSce Replicate 2 (chip-seq)


title: Ser7P iPh Replicate 1 (chip-seq)

value: Phospho-Rpb1 CTD Ser7P (#13780, Cell Signaling)


title: Ser7P iPh Replicate 2 (chip-seq)


title: Ser7P iSce Replicate 1 (chip-seq)

value: Sce RNAi treatment


title: Ser7P iSce Replicate 2 (chip-seq)


title: Ser7P Mock Replicate 1 (chip-seq)


title: Ser2P iPc Replicate 2 (chip-seq)

value: Pc RNAi treatment

value: Phospho-Rpb1 CTD Ser2P (#13499, Cell Signaling)


title: Ser7P Mock Replicate 2 (chip-seq)


title: Ser2P iPh Replicate 2 (chip-seq)


title: Ser2P iPc Replicate 1 (chip-seq)


title: Ser2P iPh Replicate 3 (chip-seq)


title: Ser2P iPh Replicate 1 (chip-seq)


title: Ser2P iSce Replicate 2 (chip-seq)


title: Ser2P iSce Replicate 1 (chip-seq)


title: Ser2P Mock Replicate 2 (chip-seq)


title: Sce RNAi Replicate 2 (rna-seq)


title: Ser5P iPc Replicate 2 (chip-seq)

value: Phospho-Rpb1 CTD Ser5P (#13523, Cell Signaling)


title: Rpb3 iPc Replicate 1 (chip-seq)

value: Karen Adelman (NIEHS)


title: Ser5P iSce Replicate 1 (chip-seq)


title: Ser5P iPh Replicate 3 (chip-seq)


title: Rpb3 Mock Replicate 4 (chip-seq)


title: Ser5P iPh Replicate 2 (chip-seq)


title: Ser5P iPc Replicate 1 (chip-seq)


title: Ser5P iPh Replicate 1 (chip-seq)


title: Ser5P iSce Replicate 2 (chip-seq)


title: Ser5P Mock Replicate 1 (chip-seq)


title: Rpb3 iSce Replicate 1 (chip-seq)


title: Rpb3 Mock Replicate 3 (chip-seq)


title: 2183

value: mixed C57BL and 129/SvJ background

value: wild-type

value: 1 month

value: male


title: Rpb3 iSce Replicate 2 (chip-seq)

value: Input_Replicate 1 fastq


title: N_castellii_G2

city: Norwich

first: Conrad

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

description: PCR duplicates were removed from the uniquely mapped, filtered reads from the replicating (S phase) sample before plotting the read count in 1 kb bins. In the processed data file the values for each chromosome were generated by dividing by 3800. Data points below 0.9 or above 2.1 were excluded.

data_processing:
Reads were mapped to the references genome for each organisms (using the Stampy package).
Samtools view was used to filter reads, retaining uniquely mapped reads with each segment properly aligned according to the aligner (-f 2) and with high mapping quality (-q 50).
Replication timing profiles were generated by normalizing the replicating (S phase) sample to the non-replicating (G2) sample in 1 kb windows. The S. castellii profile was generated from the replicating sample only.
Windows where fewer than 250 (500 for T. blattae) reads were mapped in either sample were excluded.
The resulting absolute ratios reflect the read numbers; therefore data was normalized by dividing by an empirically determined factor.
Genome_build: C_glabrata: C_glabrata_CBS138_version_s02-m02-r12_chromosomes.fasta; N_castellii: NCBI assembly ASM251v1; T_blattae: NCBI assembly ASM31591v1; Z_rouxii: NCBI assembly ASM2636v1; K_lactis: NCBI assembly ASM251v1; L_kluyveri: NCBI assembly ASM14922v1; CAY583: sacCer3
Supplementary_files_format_and_content: Processed files (*.wig) are available as Series supplementary files.
Supplementary_files_format_and_content: C_glabrata_CBS138_version_s02-m02-r12_chromosomes.fasta: Genome assembly used for mapping sequencing reads.

organism: Naumovozyma castellii

source_name: genomic DNA from G2 cells enriched by FACS  from asynchronous culture

growth_protocol: Cells were harvested from mid-log phase cultures grown in YPD media.

extract_protocol:
Cells obtained from FACS were resuspended in 500 µL of 1.2 M sorbitol, 200 mM Tris-HCl (pH7.5), 20 mM EDTA, 0.1% b-mercaptoethanol. Cells were spheroplasted with Zymolyase and then treated with SDS, Proteinase K and RNase A. DNA was purified by phenol chloroform extraction.
Library preparation and sequencing was carried out according to Illumina instructions.

treatment_protocol: Cells were sorted by DNA content, selecting S phase and G2 phase cells

tag: relevant genotype

value: wild type

tag: phase


title: Rpb3 Mock Replicate 1 (chip-seq)

value: Mock RNAi treatment


title: Rpb3 iPc Replicate 2 (chip-seq)


title: Ser2P Mock Replicate 3 (chip-seq)


title: Input Replicate 2 (chip-seq)

description: Same raw file as GSM2224493.


title: Passerina_Harv_3

city: Verona

first: Mélanie

last: Massonnet

state: Verona

address: Strada Le Grazie, 15

department: Biotechnology Department

country: Italy

institute: University of Verona

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence
Sequenced reads were aligned onto Vitis vinifera reference genome PN40024 (12x), using the program TopHat v2.0.6, with default parameters.
Mapped reads were used to reconstruct the transcripts using the program Cufflinks v2.0.2 and the V1 version of the 12x draft annotation of the grapevine genome. For each reconstructed transcript, Cufflinks also calculated its normalized expression in FPKM (Fragments Per Kilobase of Mapped reads)
Reconstructed transcripts were merged into a single non-redundant list of 29287 transcripts, using the program Cuffmerge, from the Cufflinks package. Using this novel list of transcripts, the normalized mean expression of each transcript was calculated in FPKM (Fragments Per Kilobase of Mapped reads) for each triplicate using the geometric normalization method.
Genome_build: Vitis vinifera reference genome PN40024
Supplementary_files_format_and_content: tab-delimited text file including mean FPKM values of the biological triplicate for each variety at each stage

organism: Vitis vinifera

source_name: berry pericarp

growth_protocol: Grape berries were collected from five white-skin-coloured Vitis vinifera cultivars, all cultivated in the same experimental vineyard (Conegliano, Veneto region, Italy), during the 2011 season.

extract_protocol:
Total RNA was extracted from approximately 400 mg of berry pericarp tissue (entire berries without seeds) ground in liquid nitrogen, using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich) with some modifications. The sixty non-directional cDNA libraries were prepared from 2,5 µg of total RNA using the Illumina TruSeq RNA Sample preparation protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Passerina

tag: growth stage

value: Berries ripe for harvest

value: berry pericarp


title: Ser2P Mock Replicate 1 (chip-seq)

value: Input_Replicate 1 and Input_Replicate 2 fastqs


title: Passerina_Soft_3

value: Soft berries

tag: tissue


title: Passerina_Harv_1


title: Rpb3 iPh Replicate 1 (chip-seq)

value: Ph RNAi treatment


title: Rpb3 iPh Replicate 2 (chip-seq)


title: Rpb3 iPh Replicate 3 (chip-seq)


title: Rpb3 Mock Replicate 2 (chip-seq)


title: Input Replicate 1 (chip-seq)


title: Passerina_Touch_1

value: Berries beginning to touch


title: Passerina_Touch_3


title: Passerina_Pea_3

value: Pea-sized berries


title: N_castellii_S

source_name: genomic DNA from S phase cells enriched by FACS  from asynchronous culture

tag: strain

value: S


title: Passerina_Soft_1


title: Moscatobianco_Harv_3

value: Moscato bianco


title: Moscatobianco_Harv_1


title: Moscatobianco_Soft_3


title: Moscatobianco_Harv_2


title: Moscatobianco_Touch_3


title: Moscatobianco_Soft_1


title: Passerina_Harv_2


title: Passerina_Pea_2


title: Moscatobianco_Pea_3


title: Moscatobianco_Touch_1


title: Moscatobianco_Touch_2


title: Glera_Harv_3

value: Glera


title: Moscatobianco_Pea_2


title: Glera_Harv_1


title: Glera_Harv_2


title: Passerina_Soft_2


title: Passerina_Touch_2


title: Glera_Soft_3


title: Glera_Soft_2


title: Passerina_Pea_1


title: Glera_Touch_2


title: Glera_Pea_2


title: Glera_Pea_3


title: Glera_Soft_1


title: Glera_Pea_1


title: Garganega_Harv_3

value: Garganega


title: Garganega_Harv_1


title: Moscatobianco_Soft_2


title: Garganega_Touch_2


title: Garganega_Soft_1


title: Garganega_Pea_3


title: Garganega_Touch_1


title: Garganega_Pea_1


title: Garganega_Pea_2


title: Garganega_Soft_3


title: Vermentino_Harv_3

value: Vermentino


title: Vermentino_Soft_3


title: Vermentino_Harv_1


title: Moscatobianco_Pea_1


title: Vermentino_Harv_2


title: Vermentino_Soft_2


title: Vermentino_Soft_1


title: Vermentino_Touch_2


title: Glera_Touch_1


title: Vermentino_Touch_3


title: Glera_Touch_3


title: Vermentino_Touch_1


title: Garganega_Harv_2


title: Vermentino_Pea_3


title: Garganega_Touch_3


title: Garganega_Soft_2


title: E6.75_cell95_Embryo2_Single

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

description: G&T-Seq - (SMARTSEQ2)

data_processing:
Libraries were sequenced with 2x100bp paired-end reads on a HiSeq2500 platform.
Reads were trimmed using Trim Galore v0.4.3 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence. They were mapped to the mouse GRCm38 genome assembly using HISAT2 v2.0.5. BAM files were imported to Seqmonk v1.37.0 (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). Raw read counts per transcript were calculated using the RNA-Seq quantitation pipeline.
Genome_build: GRCm38
Supplementary_files_format_and_content: The Quantitated RNA-Seq report file is tab delimited and contains the following columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (7) mRNA ID (Ensembl) (8) Gene ID (Ensembl) (9) Description (Ensembl); (10) Type; (11) Orientation; (12) Distance; (13-end) raw counts

molecule: polyA RNA

extract_protocol:
E3.5 blastocysts were flushed from the uterus using M2 medium and the zonae removed by short incubation in Acid tyrodes solution. Embryos at E4.5 were dissected from nascent decidua. The trophectoderm was eliminated from E3.5 and E4.5 by immunosurgery (Solter and Knowles, 1975). Embryos were incubated for 15-30 min in 20% anti mouse anti serum in N2B27 (made in house), rinsed 3 times in N2B27 and transferred to 20% freshly thawed rat serum in N2B27 for 15-30 min. Lysed trophectoderm was removed manually by repeated aspiration using a mouth-controlled finely drawn Pasteur pipette just bigger than the ICM. Isolated ICMs were placed individually in 20 µL drops of AccutaseTM in a bacteriological dish for at least 5 min until they assumed a blackberry-like appearance. They were transferred to similar sized drops of M2 and aspirated repeatedly using a very finely drawn Pasteur pipette to separate the cells. Cells were immediately placed individually into wells of lysis buffer and frozen. E5.5 embryos were dissected manually and were observed to be early E5.5 cells lacking distinct thickening of the visceral endoderm (pre-AVE migration). The extra embryonic ectoderm was removed using the tip of a pulled Pasteur pipette. The epiblast was separated from overlying visceral endoderm by aspiration, distal end first, with a pulled Pasteur pipette with diameter just bigger than the epiblast. Both epiblast and visceral endoderm were separately disaggregated and plated into wells as described above for ICMs.  E6.5 embryos were visually staged as early streak (Downs and Davies, 1993) and dissected from decidua in PBS and placed into M2 solution to remove extra embryonic tissues. Differences in dissection may contribute to different proportions of primitive streak and epiblast cells obtained at E6.5. The embryonic ectodermal portion of the early streak embryo was dissociated in drops of AccutaseTM at room temperature and upon partial digestion was fully dissociated by repeated aspiration using a very finely drawn, mouth controlled, siliconised glass needle. Cells were assigned as single, doublets or multiples by visual inspection and placed directly into lysis solution and frozen prior to library generation.
mRNA from isolated single cells was isolated and amplified using the bead based capture and amplification previously described in the G&T-seq protocol which incorporates SMARTSEQ2.
Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol and 100bp paired end sequencing was performed on an Illumina Hiseq2500 instrument.

value: Mouse Embryo

value: Wild Type


title: E6.75_cell94_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell9_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell93_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell96_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell90_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell86_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell85_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell87_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell88_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell92_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell84_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell83_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell8_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell82_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell80_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell79_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell7_Embryo1_Double

description: G&T-Seq - (SMARTSEQ2)


title: Vermentino_Pea_2


title: E6.75_cell78_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell77_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell75_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell72_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell70_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell76_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell74_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell6_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell64_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: Vermentino_Pea_1


title: E6.75_cell71_Embryo2_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell63_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell59_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell58_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell5_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell53_Embryo1_Double

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell56_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell55_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell51_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell4_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell50_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell52_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell49_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell47_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell44_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell48_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell46_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell45_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell62_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell41_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell42_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell43_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell39_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell54_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell35_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell36_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell38_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell60_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell31_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell2_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell33_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell29_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell27_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell28_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell26_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell25_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell23_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell30_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell22_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell21_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell24_Embryo1_Double

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell20_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell1_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell37_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell19_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell18_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell14_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell16_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell15_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell17_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell12_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell13_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell10_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_93_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_84_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_85_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_79_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_68_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_76_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_64_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_63_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_61_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_59_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_67_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_72_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_56_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_62_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_53_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_55_embryo8_double

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_51_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_46_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_50_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_47_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_52_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_44_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_40_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_35_embryo8_double

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_45_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_36_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_37_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_39_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_43_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_60_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_71_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_34_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_33_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_49_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_31_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_29_embryo7_double

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_30_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_23_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_22_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_21_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_14_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_19_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_13_embryo7_single

description: G&T-Seq - (SMARTSEQ2)