title: shISL1 RNA-seq

city: Beijing

first: Yang

last: Wang

state: Beijing

address: Xueyuan Road 38#

department: Molecular Biology and Biochemistry

institute: Peking University Health Science Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and aligned to the mm9 genome assembly using Tophat version 2.0.13 with the following configurations:  -G --library-type=fr-firststrand --no-novel-juncs.
Transcriptome was assembled using Cufflinks version 2.2.1. Differential gene expression was calculated with Cuffdiff version 2.2.1.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file is generated by Cuffdiff, considering FPKM ≥ 1 in either one of the 2 conditions and |fold-change isl1 knowdown vs. ctrl| ≥ 1.5 fold as a cut-off..

source_name: Cardiac progenitor cells

extract_protocol:
RNA was harvested using Trizol reagent.1 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared according to manufacturer’s instructions (Illumina). Briefly, polyA+ RNA was isolated using Dynabeads Oligo(dT)25 (Invitrogen) and constructed into strand-specific libraries using the dUTP method. Once dUTP-marked doublestranded cDNA was obtained, the remaining library construction steps followed the same protocol as described above for ChIP-seq libraries.

value: E14 mES-derived cardiac progenitor cells

tag: treatment

value: knock-down isl1 shRNA


title: 2C_M6

status: Public on Apr 25 2016

type: SRA

city: Crawley

first: Mohammed

last: Alsaweed

state: WA

address: 35 stirling hwy

department: Biochemistry

country: Australia

institute: UWA

description:
Small RNA-seq
miRNA

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Cleaning reads: included getting rid of low-quality reads, reads with 5' primer contaminants, reads without 3' primer, reads without the insert tag, reads with poly A, and reads shorter than 18nt.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Length distribution of all clean reads.
Analysis of base composition and quality.
Map to human genome.
Reads aligned to miRBase 21.0 database.
Novel miRNA prediction.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text file includes reads for each identified SE50 molecule in each Sample.

molecule: total RNA

organism: Homo sapiens

source_name: Total human milk cells, month 6 of lactation

extract_protocol:
Human milk total cells and lipids were isolated by centrifugation of whole milk, then lipids were purified by further centrifugation. Total cells were washed three times using PBS, total RNA/miRNA was extracted using miRNeasy kit (Qiagen) for cells samples and Exiqon Biofluids kit was used for lipids samples.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: gender

value: female

tag: body fluid

value: breast milk

tag: fraction

value: total cell content

tag: collection time

value: during month 6 of lactation (week 20-24)

tag: individual identifier


title: 1C_M4

description:
Small RNA-seq
miRNA

source_name: Total human milk cells, month 4 of lactation

value: during month 4 of lactation (week 12-16)


title: Control RNA-seq

country: China

organism: Mus musculus

tag: cell type

value: control shRNA

tag: strain


title: JMJD3 ChIP-seq

library_source: genomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and aligned to the mm9 genome assembly using Bowtie version 2.2.4 with the following configurations: -p 5 --sensitive.
reads from two biological replicates at each conditions were merged with samtools: samtools merge rep1.bam rep2.bam merged.bam.
peaks were called using MACS version 1.4.2 with the following setting:--pvalue-1E-05 --diag --wig.
peaks were annotated using PeakAnalyzer version 1.4
Genome_build: mm9
Supplementary_files_format_and_content: Excel file is generated by MACS, representing ISL1 peaks or JMJD3 peaks; Bed file is generated by PeakAnalyzer to annotate peaks associated nearest transcription start sites.

molecule: genomic DNA

extract_protocol:
Lysates were clarified from sonicated nuclei and Protein-DNA complexes were isolated with antibody.
Libraries were prepared according to manufacturer’s instructions (Illumina). Briefly, immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicentre), tailed with deoxyadenine using Klenow exo minus (NEB), and ligated to custom adapters with T4 Rapid DNA Ligase (Enzymatics). Fragments of 350 ± 50 bp were size-selected using Agencourt AMPure XP beads, and subjected to ligation-mediated PCR amplification (LM-PCR), using Q5 DNA polymerase (NEB). Libraries were quantified by qPCR using primers annealing to the adaptor sequence and sequenced at a concentration of 10 pM on an Illumina HiSeq 2000.

value: JMJD3NFH-E14 mES-derived cardiac progenitor cells

tag: chip-antibody

value: HA Abcam ab9110


title: Hobit ChIP

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description: anti-V5 (Sigma V5-10 agarose)

data_processing:
Sequence reads that passed the Illumina quality filtering were considered for alignment. Reads were aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9), using bowtie version 1.0.0
Genome coverage and subsequent data conversion was done with 'bedtools' (version 2.16.2) and 'Kent source utilities' (version 2.79) using 'bedtools genomecov'  and 'bedGraphToBigWig' , respectively.
Genome_build: MM9
Supplementary_files_format_and_content: bigwig = bigWig Track format of read density coverage in reads per million after extension to 150 base pairs

source_name: activated CD8 T cells

growth_protocol: 3-day stimulation with anti-CD3, anti-CD28 and IL-2 followed by 2-day cultivation with IL-2 and IL-12

extract_protocol:
phenol-chloroform extraction
About 1-5 ng of cDNA or ChIP-precipitated DNA were used as starting material for the generation of sequencing libraries with the NEBNext Ultra Ligation Module and NEBNext Ultra End Repair/dA-Tailing module. DNA fragments of 200-500 bp were selected with AMPure XP beads (Beckman Coulter). PCR amplification was performed with the KAPA Real Time Amplification kit (KAPA Biosystems). Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS Library Quantification kit. Cluster generation and sequencing was carried out by using the Illumina HiSeq 2000 system with a read length of 50 nucleotides according to the manufacturer’s guidelines.

value: CD8 T cells

tag: genotype

tag: cell preparation


title: 1C_M2

description:
Small RNA-seq
miRNA

source_name: Total human milk cells, month 2 of lactation

value: during month 2 of lactation (week 4-8)


title: wt/FVB week 12 replicate 3

city: Minneapolis

first: Christine

middle: M.

last: Henzler

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

country: USA

institute: University of Minnesota, Twin Cities (Minneapolis, MN, US)

description:
cuffdiff_week12_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_gene_exp.diff.txt
cuffnorm_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_genes.fpkm_tracking.txt
cuffdiff_week5_vs_week12_vs_week28_FVB_gene_exp.diff.txt

data_processing:
Reads were aligned to the mouse reference genome (mm10) with Tophat2 (v. 2.0.11)  using all default parametersexcept setting mate inner distance and standard deviation to the data and only looking for junctions in the supplied gene annotation model (--no-novel-juncs setting). The annotation file used was the mm10 gtf file from iGenomes.
Gene expression was quantified using Cuffquant (in Cufflinks v. 2.2.1) using the bias correction (-b) and multi-read correction (-u) settings using the igenomes mm10 gtf file (for differential expression analysis). The inclusion of miRNAs and snoRNAs in the gtf file was later found to distort the PCA analysis, since miRNAs and snoRNAs are not captured completely by a total RNA library preparation and their quantification is consequently distorted in Cuffquant. Gene expression was re-quantified for CuffNorm using the same gtf with miRNAs and snoRNAs removed for the PCA analysis.
CuffDiff  (in Cufflinks v. 2.2.1) was used with default setttings to test for differential expression between samples.
CuffNorm (in Cufflinks v.2.2.1) was used to normalize data across all samples using the default settings except that output was in cuffdiff format
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files provide output of gene_exp.diff.txt files output from CuffDiff for each of the comparisons listed
Supplementary_files_format_and_content: tab-delimited text file gene.fpkm_tracking.txt provides normalized expression data for all genes (miRNAs and snoRNAs removed; see Cuffquant step above)

source_name: cerebellum

growth_protocol: Not applicable

extract_protocol:
Total RNA was isolated from dissected cerebella using TRIzol Reagent (Life Technologies, Carlsbad, California) following the manufacturer’s protocols. Cerebella were homogenized using an RNase-Free Disposable Pellet Pestles in a motorized chuck. For RNA-sequencing, RNA was further purified to remove any organic carryover using the RNeasy Mini Kit (Qiagen, Venlo, Netherlands) following the manufacturer’s RNA Cleanup protocol.
RNA libraries were constructed using standard Illumina protocols.

treatment_protocol: ATXN1[82Q] (Burright et al., 1995), ATXN1[30Q]-D776, ATXN1[82Q]-D776 (Duvick et al., 2010), conditional ATXN1[30Q]-D776 (Ebner et al., 2013), Pcp2-tTA (Zu et al., 2004) and FVB/NJ mice were housed and managed by Research Animal Resources under SPF conditions in an AAALAC-approved facility. Gene-off mice were given 1.5mg/ml doxycycline (dox) (purchased from the University of Minnesota Boynton Health Service Pharmacy) in a 4% sucrose solution in their drinking water. Gene-on animals were given 2% sucrose (to account for sucrose intake) for the same amount of time gene-off mice were administered dox. Pcp2 tTA/+ control mice were administered dox similar to the gene-on cohort. In all experiments involving the use of mice, animals of either sex were used.

value: FVB

tag: tissue

value: cerebellum

tag: age

value: 12 weeks

value: wt/FVB


title: ChIP-seq NPC-Diff B-2

city: La Jolla

first: Xiang-Dong

last: Fu

state: California

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

institute: University of California, San Diego

data_processing:
Basecalls performed using CASAVA version 1.7
Unmapped ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 version 2.1.0 with the following configurations "--local"
The duplicated mappings and low quality (Q>50) mappings were removed
Mapped regions were trimed to be of length 40 bp and read coverage was based on total read normalization to 30,000,000
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were transformed from bedGraph files calculated from mapped reads using the command "bedtools genomecov -bg -scale"; Scores represent ChIP-seq signals at each base.

source_name: NPS_after 2 wks of differentiation

growth_protocol: Human neural progenitor cells (hNPC) were expanded in neural growth (NG) media containing: DMEM/F12 glutamax, 0.5XN2, 0.5XB27, and 1X Penicillin/streptomycin. Stempro Accutase (Life technologies) was used to detach hNPCs. To differentiate hNPCs into cortex neurons, FGF2 was removed from NG media followed by treatment with ROCK inhibitor Y27632 for 24 hours and then cultured in NG media for additional 2-6 weeks.

extract_protocol:
Cell pellets were suspended in 1 ml of Cyto lysis buffer, mixed briefly, and incubated on ice for 10-15min with occasional inversion every 2min.  Cells were pelletted for 5min at 3500rpm, 40C, Supernatant discarded, and the nuclear pellets were resuspended in 500ul of nuclear lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-Cl, pH8.1, 1Xprotease inhibitor cocktail) and incubated on ice for 10min.  The pellets were sonicated seven times for 10 sec each at the maximum setting (Branson, Sonifer cell disruptor 185). The lystate was cleared by centrifugation at 14000 rpm for 10 min in 4C and the supernatant was collected in 15ml tube. The supernatant was diluted 1:10 with the dilution buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-Cl, pH8.1, 1Xprotease inhibitor cocktail) to yield the soluble chromatin fraction, 100ug-200ug of which was used for each ChIP reaction. Lystate was pre-cleared by adding 20ul of Protein A/G beads followed by rotation for 1 hour at 4C. 5ug of specific antibodies were applied to the supernatant and incubated overnight at 4C. 50ul of Protein A&G magnetic beads were blocked with (1xPBS+5mg/ml BSA-fraction V) and incubated at 4C for another 4 hours. Magnetic beads were harvested on a magnetic stand and beads wished sequentially at 4C, twice in 0.7 ml of TSE I (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH8.1, 150 mM NaCl), twice in TSE II (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH8.1, 500 mM NaCl), twice in Buffer III (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, pH8.0, 10 mM Tris-HCl, pH8.1), and finally, twice with 1ml of TE buffer at 4C.  Eluted beads were twice washed with 150ul of elution buffer (TE buffer, 1%SDS) by votexing at 70C, 1000rpm for 10 min. The eluents were heated at 65C overnight to reverse formaldehyde-induced crosslinks. For input sample, 150-300ul of soluble chromatin was also heated at 65C overnight. DNA fragments were purified with a QIAquick Spin PCR purification Kit (Qiagen, CA).
ChIP-seq libraries were constructed by using the TruSeq ChIP Sample Prep Kit (Illumina).

treatment_protocol: Human neural progenitor cells were cross-linked with 1% formaldehyde and quenched by adding 1/20th volume of 2.5M glycine to a final concentration of 0.125M. After washing three times with ice-cold PBS, cells were scraped off from the plate and collected by centrifugation at 2500rpm.

value: Human neural progenitor cells (hNPC)

tag: passages

tag: time point

value: after 2 wks of differentiation

tag: chip antibody

value: mouse monoclonal anti-Brn2

tag: chip antibody vendor

value: Santa Cruz Biotechnology

tag: chip antibody cat. #


title: ChIP-seq NPC-Diff C-20

value: goat anti-Brn2 (C-20)


title: ChIP-seq NPC B-2

source_name: NPS_before 2 wks of differentiation

value: before 2 wks of differentiation


title: UCE

city: Berkeley

first: Richard

last: Harland

state: CA

address: Life Sciences Addition #3200

institute: University of California, Berkeley

data_processing:
fastq_illumina_filter, with settings -v -N -o
Reads were aligned with TOPHAT2 to Xla.v91 using standard parameters
PCR duplicates were removed using samtools rmdup function.
Read counts were generated with htseq- count using the following parameters: -f bam -s no  -t gene -i ID.
Genome_build: X.laevis v9.1
Supplementary_files_format_and_content: tab-delimited text files with counts values generated by htseq for each sample

molecule: polyA RNA

organism: Xenopus laevis

source_name: whole embryo

extract_protocol:
Samples were placed in Trizol and frozen at -80C overnight. Standard protocols for RNA extraction using Trizol were used. 1ug total RNA was used for library construction
Illumina TruSeq RNA Library Prep Kit protocols

treatment_protocol: For dkk injected embryos, 100pg of dkk mRNA was injected animally into both blastomers of a 2-celled embryo.

tag: developmental stage

tag: treatment

value: Uninjected control

tag: mating pair


title: DKKF

value: DKK


title: ChIP-seq NPC C-20


title: wt/FVB week 5 replicate 3

description:
cuffdiff_week5_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_gene_exp.diff.txt
cuffnorm_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_genes.fpkm_tracking.txt
cuffdiff_week5_vs_week12_vs_week28_FVB_gene_exp.diff.txt

value: 5 weeks


title: DKKD


title: wt/FVB week 5 replicate 2


title: wt/FVB week 5 replicate 1


title: UCC


title: ATXN1[30Q]-D776 week 5 replicate 3

description:
cuffdiff_week5_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_gene_exp.diff.txt
cuffnorm_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_genes.fpkm_tracking.txt
cuffdiff_week5_vs_week12_vs_week28_ATXN1.30Q.D776_gene_exp.diff.txt


title: op416

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

data_processing:
DNA from the RRBS libraries were sequenced in Illumina HiSeq Machines, Base-calling was perfromed using RTA software and demultiplexed to obtain individual Fastq files.
DNA methylation analysis was perfromed using a fragment based approach with our own in house developed pipeline called DMAP (Stockwell et al Bioinformatics, 2014).
Unix scripts and Epiexplorer ( for overlapping analysis with ENCODE data) was used for further processing of data.
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel file contains methylation information of MspI fragments (excel) where enough information ( at least 2 CpG covered by 10 reads) was obtained from atleast 6 placenta samples for a fragment

source_name: Placenta

extract_protocol:
DNA from placental tissue was extracted using QIAamp DNA mini kit (Qiagen) following the manufacturer’s protocol.
Genomic DNA was digested with MspI (New England Biolabs, Ipswich, MA) followed by end repair and addition of 30 A overhangs. Methylated adaptors (Illumina, San Diego, CA) with a 30 T overhang were then ligated with the generated fragments. Following adaptor ligation, DNA fragments ranging from 40 to 220 bp (preligation size) were cut from a 3% (w/v) NuSieve GTG agarose gel (Lonza, Basel, Switzerland) and subsequently bisulphite modified using the EZ DNA methylation kit (Zymo Research, Irvine, CA). The final library was amplified by PCR. The resulting library was sequenced on an Illumina platform with a single-ended, 100bp run.

tag: sample type

value: Placental DNA


title: op410


title: UCA


title: op478


title: ATXN1[30Q]-D776 week 5 replicate 2


title: op140


title: Input-16

data_processing:
fastq_illumina_filter, with settings -v -N -o
Reads were aligned to Xenopus laevis genome version 9.1 using bowtie2 and default settings.
Samtools was used to remove PCR duplicates
Peaks were called with both MACS peak caller and Homer peak caller using input chromatin libraries as control.
Common-peaks.txt was generated using bedtools intersect.
Genome_build: X.laevis v9.1
Supplementary_files_format_and_content: bed files with peak locations called by either MACS or Homer.

source_name: Whole embryo

extract_protocol:
Chromtin was crosslinked using formaldehyde and embryos were frozen at -80 until processing. Pools of 100 embryos were sonicated and chromatin bound by flag-tagged beta-catenin was immunoprecipitated using FLAG anitbody (Sigma F3165).
Illumina TruSeq ChIP prep kit was used for library preperation

treatment_protocol: Embryos were injectedanimally with 500pg triple FLAG tagged beta-catenin into both blastomeres of a two-cell staged embryo.

tag: Stage

tag: replicate


title: ATXN1[30Q]-D776 week 5 replicate 1

tag: strain


title: op173b


title: op122


title: Blimp1-Bio ChIP

description: Dynabeads M-280 Streptavidin (Invitrogen)

tag: cell type

value: Blimp1(Bio/Bio) Rosa26(BirA/BirA)

value: 3-day stimulation with anti-CD3, anti-CD28 and IL-2 followed by 2-day cultivation with IL-2 and IL-12


title: Input-5


title: ATXN1[82Q] week 5 replicate 3

description:
cuffdiff_week5_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_gene_exp.diff.txt
cuffnorm_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_genes.fpkm_tracking.txt
cuffdiff_week5_vs_week12_vs_week28_ATXN1.82Q_gene_exp.diff.txt

tag: genotype


title: ATXN1[82Q] week 5 replicate 2


title: op121


title: ATXN1[82Q] week 5 replicate 1


title: op88

description: 2 raw files were provided for this sample as sequencing was perfromed twice to recover enough reads from this sample.


title: ChIP-beta-catenin-6


title: ChIP-beta-catenin-19


title: DKKB


title: op47


title: ChIP-beta-catenin-2


title: ATXN1[30Q] week 5 replicate 2

description:
cuffdiff_week5_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_gene_exp.diff.txt
cuffnorm_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_genes.fpkm_tracking.txt


title: ATXN1[30Q] week 5 replicate 3


title: Input DNA

city: Aberdeen

first: Stefan

last: Hoppler

address: Foresterhill

department: Institute of Medical Sciences

country: United Kingdom

institute: University of Aberdeen

data_processing:
ChIP-seq reads were mapped to the X. tropicalis genome assembly JGI 4.2/xenTro3 using bwa (version 0.7.5a).
Aligned ChIP-seq files were used for peak calling with two different software: FDR ≤ 0.1 for SPP (version 1.10.1) and p ≤ 0.01 for MACS2 (version 2.0.10.20120913). Subsequently, called peaks were used to identify reproducible peaks using IDR (Li et al., The Annals of Applied Statistics, 2011) with threshold of 0.01.
Peaks were assigned to closest genes using distanceToNearest function (rtracklayer version 1.2.26 and GenomicRanges v 1.12.5).
ChIP-seq data was used to generate bed files using genomeCoverageBed from bedtools v 2.17.0 and then converted to bigWig format using UCSC bedGraphToBigWig.
Genome_build: xenTro3
Supplementary_files_format_and_content: [ChIP-seq] tab-delimited text for peak calls; bigWig

organism: Xenopus tropicalis

source_name: early gastrula embryos

growth_protocol: Embryos were raised in 0.1xMMR to early gastrula stage (stage 10.25 according to Nieuwkoop and Faber staging criteria)

extract_protocol:
Embryos were fixed at stage 10.25, glycine treated, and frozen. Embryos were then homogenized, and sonicated. DNA-protein complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Preparation Kit.

tag: embryonic stage

value: Stage 10.25


title: op32


title: ATXN1[30Q] week 5 replicate 1

value: FVB

tag: tissue


title: Input-12


title: β-catenin_ChIP-seq

value: β-catenin


title: BJ_d5l_SMAD3

status: Public on Apr 24 2016

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
Fastq files were mapped to hg19 genome using STAR Aligner software34 with –AlignIntronMax parameter set to 1 to make the software compatible with ChIP-Seq libraries. Reads with more than 3 mismatches and/or reads mapped to more than one region were filtered out. Mapped reads were visualized in the UCSC genome browser35. Peaks were called using the findPeaks script of HOMER36 with the option –factor for transcription factors and –histone for histones
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files that include deatails about the significant peaks found in the ChIP-Seq libraries.

source_name: BJ Fibroblasts

growth_protocol: BJ fibroblast were cultured in 10% Fetal Bovine Serum (Gibco) for expansion and medium was changed every two days. BJ human neonatal fibroblast was routinely tested for Mycoplasma and was negative in all instances. hES cells and iPSCs clones were maintained on irradiated murine embryonic fibroblast (MEFs, Global Stem) and cultured in 20% knockout serum replacement (KSR, Life Technologies), 200mM GlutaMAX (Life Technologies), 1 x minimal essential media (MEM) non-essential amino acids solution (Life Technologies), 8 microgram mL-1 bFGF (Life Technologies), 55 micromolar Beta-mercaptoethanol in DMEM/F12 (Life Technogies). ES and iPSCs clones was passagerd every 4-5 days using L7TM hPSC Passaging Solution (Lonza).

extract_protocol: 10 million cells were cross-linked with 10 mM DTBP (Sigma Aldrich) and 1% formaldehyde for 10 min at room temperature, with the formaldehyde then quenched by the addition of glycine (125mM final concentration) and the cells were then washed twice with ice-cold PBS. Cell lysis was carried out with a buffer containing 10 mM Tris-Cl (pH 8), 100 mM NaCl, 10 mM EDTA, 0.25% Triton X-100 and protease inhibitor cocktail (Roche). Cells were then resuspended in 1% SDS lysis buffer containing 50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1% SDS, 2 mM EDTA, 1% Triton X-100, 0.1% NaDOC and protease inhibitor cocktail. The suspension was nutated for 15 mins at 4°C before spinning down to collect the chromatin pellet. The pellet was then washed twice with 0.1% SDS lysis buffer containing 50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 0.1% SDS, 2 mM EDTA, 1% Triton X-100, 0.1% NaDOC, 1 mM PMSF and protease inhibitor cocktail. Sonication was conducted using the Bioruptor (20 cycles, 30s pulses on with 90s pulses off). The chromatin solution was clarified by centrifugation at 20,000 g at 4°C for 45 mins and then pre-cleared with Dynabeads protein G (Life Technologies) for 2 hrs. The pre-cleared chromatin sample was incubated with 50 μl of Dynabeads protein A loaded with 10 μg antibody overnight. The beads were then washed three times with 0.1% SDS lysis buffer, once with 0.1% SDS lysis buffer/0.35 M NaCl, once with 10 mM Tris-Cl (pH 8), 1 mM EDTA, 0.5% NP40, 0.25 LiCl, 0.5% NaDOC, and once with TE buffer (PH8.0). The immunoprecipitated material was eluted from the beads by heating for 45 min at 68°C in 50 mM Tris-Cl (pH 7.5), 10 mM EDTA, 1% SDS. To reverse the crosslinks, samples were incubated with 1.5 μg/ml Pronase at 42°C for 2 hr followed by 67°C for 6 hr. The samples were then extracted with miniElute DNA purification kit (Qiagen).

tag: cell line

value: BJ Fibroblasts

value: Anti-Smad3 antibody - ChIP Grade (ab28379)- Lot #- GR155884-8

value: BJ fibroblasts 5 days post induced viral expression of OSKM

value: WT


title: BJ_d8l_shSMAD3_H3K4me3

description: Sample 9

value: BJ fibroblasts 8 days post induced viral expression of OSKM and treated with SMAD3 siRNA (SMAD3 Knock-down).

value: SMAD3 Knock-down


title: BJ_d8l_shSMAD3_H3K36me3

description: Sample 10


title: BJ_d8l_shSMAD3_H3K4me1

description: Sample 8


title: BJ_d8l_shENY2_H3K36me3

description: Sample 7

value: BJ fibroblasts 8 days post induced viral expression of OSKM and treated with ENY2 siRNA (ENY2 Knock-down).

value: ENY2 Knock-down


title: BJ_d8l_shNTP_H3K4me1

description: Sample 2

value: BJ fibroblasts 8 days post induced viral expression of OSKM and treated with non-targeting (NTP) siRNA.


title: BJ_d5l_INPUT

value: none (input)


title: BJ_d8l_shENY2_H3K4me3

description: Sample 6


title: BJ_d8l_shNTP_H3K36me3

description: Sample 4


title: BJ_d8l_Input

description: Sample 1

value: BJ fibroblasts 8 days post induced viral expression of OSKM


title: BJ_d8l_shNTP_H3K4me3

description: Sample 3


title: 10F_M4

description:
Small RNA-seq
miRNA

source_name: Human milk lipids, month 4 of lactation

tag: gender

value: female

tag: body fluid

value: breast milk

tag: fraction

value: lipids

tag: collection time

value: during month 4 of lactation (week 12-16)

tag: individual identifier


title: H9

description:
R32
processed data file: Genes_Log2FoldChange_vs_D0.txt

data_processing:
The QC of the generated libraries was performed using FastQC. Reads were mapped to hg19 genome using STAR aligner software. Reads with more than 3 mismatches were filtered out. Reads mapped to more than one region in the human genome were also disregarded. The mapped reads have then undergone geometric normalization and subjected to differential expression analysis using CuffDiff.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files that include FPKM values for all genes in each Sample and Log2 Fold change of all genes in all samples vs Day 0 BJ fibroblasts.

growth_protocol: BJ fibroblast were cultured in 10% Fetal Bovine Serum (Gibco) for expansion and medium was changed every two days. Human Embryonic Stem Cells (hESCs) and induced Pluripotent Stem Cells (iPSCs) clones were maintained on irradiated murine embryonic fibroblast (MEFs, Global Stem) and cultured in 20% knockout serum replacement (KSR, Life Technologies), 200mM GlutaMAX (Life Technologies), 1 x minimal essential media (MEM) non-essential amino acids solution (Life Technologies), 8 microgram mL-1 bFGF (Life Technologies), 55 micromplar Beta-mercaptoethanol in DMEM/F12 (Life Technogies). ES and iPSCs clones was passagerd every 4-5 days using L7TM hPSC Passaging Solution (Lonza).

extract_protocol:
Total RNA was extracted using the Trizol reagent (Invitrogen, 15596-026). Contaminating DNA was removed by DnaseI (Ambion) treatment, and the RNA was further purified using RNeasy column (Qiagen, 74140)
The RNA samples were subject to mRNA selection, fragmentation, cDNA synthesis, and library preparation using a TruSeq RNA Sample Prep Kit (Illumina, RS-122-2001).

value: WT H9 Cells

tag: sorting


title: iPSC

description:
R31
processed data file: Genes_Log2FoldChange_vs_D0.txt

tag: treatment

value: WT iPSCs


title: NHEK-D Input

city: Irvine

first: Bogi

last: Andersen

address: 839 Health Sciences Dr.

department: Medicine

institute: University of California, Irvine

data_processing:
Base-calls were made using RTA  version 1.12.4.2
Reads were aligned to human genome hg19 using Bowtie version 0.12.7, only uniquely aligning reads were retained (-m 1)
Bam file were converted to BED using Bedtools (bamToBed v2.11.2)
Peaks were called using SICER (v1.1),  with  FDR <.05, Input library was used as the control
Galaxy was used for further data analysis (performing intersection/subtraction analysis, extracting features)
Genome_build: Human hg19
Supplementary_files_format_and_content: interval files from galaxy, containing chromosome and coordinates of peak locations

source_name: Primary human epidermal keratinocytes (NHEK)

growth_protocol: NHEK cells were grown in EpiLife medium supplemented with EDGS (Invitrogen) at 37C, 5%CO2

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the respective histone antibodies.
Sequencing libraries were generated for the H3K4me1, H3K27ac, and H3K4me3 samples using the NEB Next reagents and Illumina adaptors and oligos, according to the Illumina protocol for ChIP-Seq library preparation, with some modification. After adaptor ligation, PCR amplification was performed prior to size selection of the library (Schmidt, 2009). Clustering and 50-cycle single end sequencing were performed on the Illumina Hi-Seq 2000 Genome Analyzer.
Libraries were sequenced on the Illumina Hi-Seq 2000, with 50bp single end sequencing

treatment_protocol: To induce differentiation, 1.8mM Calcium Chloride was added to the medium, and cells were collected 24 hours later.

tag: chip antibody

value: Input (Andersen Lab)

tag: chip antibody manufacturer


title: D16 ZMYM2 KD Tra-160-ve

description:
R29
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts

value: BJ Fibroblasts 16 days post induced OSKM viral Expression and treated with ZMYM2 siRNA.

value: Tra-160 negative

value: ZMYM2 Knock-down


title: NHEK-D H3K4me1

value: Primary human epidermal keratinocytes (NHEK)

value: H3K4me1(Andersen Lab)

value: abcam ab8895


title: BJ_d8l_shENY2_H3K4me1

description: Sample 5

value: BJ fibroblasts 8 days post induced viral expression of OSKM and treated with ENY2 siRNA (ENY2 Knock-down).

value: ENY2 Knock-down


title: Emb_MO-Ct_48hpf

city: Pisa

first: Romina

last: D'Aurizio

state: PI

address: via Moruzzi 1

department: IIT

country: Italy

institute: CNR

description:
Sample name: L
smallRNAseq after Mo-Ct injection

data_processing:
Basecalls performed using CASAVA v1.8
Sequenced reads were trimmed for adaptor sequence.
Reads were algned to miRBase v20 using miRExpress v2.1.3
Normalized abundance measurements from DESeq
Genome_build: miRBase v20
Supplementary_files_format_and_content: tab-delimited text file includes normalized read count per sample

organism: Danio rerio

source_name: Embryos, MO-Ct, 48hpf

growth_protocol: Zebrafish was raised and maintained under standard laboratory conditions (Westerfileld M zebrafish book) in Zebrafish Housing Systems (Tecniplast, Varese, Italy).

extract_protocol:
For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol (llumina Inc., San Diego, USA)
cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis (Invitrogen) and eluted into 300 µl elution buffer (Illumina) for at least 2 hours at room temperature, to enrich for molecules containing inserts in the range of 18–33 nt.

treatment_protocol: 1-cell stage zebrafish embryos were microinjected with 1,5 ng of morpholino against dre-Tbx5a (MO-Tbx5a) or with 1,5 ng of control morpholino

value: embryo

value: AB

value: Mo-Ct injection

tag: developmental stage


title: D16 ZMYM2 KD Tra-160+ve

description:
R28
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: Tra-160 positive


title: D16 SFRS11 KD Tra-160-ve

description:
R27
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts 16 days post induced OSKM viral Expression and treated with SFRS11 siRNA.

value: SFRS11 Knock-down


title: op46

tag: sample type

value: Placental DNA


title: D16 SFRS11 KD Tra-160+ve

description:
R26
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt


title: D16 ENY2 KD

description:
R30
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts 16 days post induced OSKM viral Expression and treated with ENY2 siRNA.


title: NHEK-D H3K4me3

value: H3K4me3 (Andersen Lab)

value: millipore 07-473


title: NHEK-D H3K27ac

value: H3K27ac (Andersen Lab)

value: millipore 07-360


title: Emb_MO-Tbx5a_48hpf

description:
Sample name: I
smallRNAseq after Mo-MOTbx5a injection

source_name: Embryos, MO-Tbx5a, 48hpf

tag: strain

value: Mo-MOTbx5a injection


title: Emb_MO-Ct_24hpf_rep2

description:
Sample name: H
smallRNAseq after Mo-Ct injection

source_name: Embryos, MO-Ct, 24hpf, replicate2


title: Emb_MO-Tbx5a_24hpf_rep1

description:
Sample name: E
smallRNAseq after Mo-MOTbx5a injection

source_name: Embryos, MO-Tbx5a, 24hpf, replicate1


title: D16 SMAD3 KD Tra-160+ve

description:
R24
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts

value: BJ Fibroblasts 16 days post induced OSKM viral Expression and treated with SMAD3 siRNA.

value: SMAD3 Knock-down


title: D16 SMAD3 KD Tra-160-ve

description:
R25
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: Tra-160 negative


title: Emb_MO-Ct_24hpf_rep1

description:
Sample name: G
smallRNAseq after Mo-Ct injection

source_name: Embryos, MO-Ct, 24hpf, replicate1

value: embryo


title: D16 SAE1 KD Tra-160-ve

description:
R23
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts 16 days post induced OSKM viral Expression and treated with SAE1 siRNA.

value: SAE1 Knock-down


title: D16 SAE1 KD Tra-160+ve

description:
R22
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: Tra-160 positive


title: asc1-DE YPAD RNA-Seq rep2, pA-tailed

city: Cambridge

first: Wendy

middle: V

last: Gilbert

state: MA

address: 31 Ames St.

department: Biology

institute: Massachusetts Institute of Technology

description:
asc1_DE_T2_pA
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz

data_processing:
Reads were trimmed of adapter sequence: TGGAATTCTCGGGTGCCAAGG
Reads were mapped to the Sigma1278b genome using Tophat and requiring uniquely mapping reads
Mapped reads were assigned to annotated coding sequence features (excluding the first 30 codons for both Ribo-Seq and RNA-Seq) using custom scripts, counts per feature and RPKM values were calculated
Counts per feature were scaled for library size using the DESeq R package
Genome_build: Sigma1278b (SGD, downloaded 6/29/2014)
Supplementary_files_format_and_content: Counts, scaled counts, RPKM values, or log2 fold changes for all coding features

organism: Saccharomyces cerevisiae Sigma1278b

growth_protocol: Yeast were grown to mid log phase (OD 0.6-0.9) in YPAD (2% glucose) or YPAG (3% glycerol) at 30˚C.

extract_protocol:
Cells were lysed by vortexing with glass beads in lysis buffer. Lysates were clarified by centrifugation at 16k xg.
RNAse digestion of lysate and isolation of ribosomal footprints (Ribo-Seq) or random fragmentation and size selection (26-40 nt) of polyA-selected total RNA (RNA-Seq) was followed by 3' adapter ligation, reverse transcription, circularization of the RT product and PCR amplification.

treatment_protocol: Cells were treated with 0.1 mg/ml cycloheximide at 30˚C for 2 minutes. Cells were then cooled and harvested by centrifugation. Cells were resuspended in cold lysis buffer + cycloheximide.

tag: library type

value: RNA-Seq

tag: media

value: YPAD (2% glucose w/v)

tag: total rna selection method

value: oligo dT beads

tag: 3' capture method

value: polyA tailing

tag: rt enzyme

value: Superscript III

tag: harvest method

value: cool on ice, resuspend cells in cold lysis buffer,  lyse immediately


title: asc1-DE YPAD RNA-Seq rep1, pA-tailed

description:
asc1_DE_T1_pA
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: asc1-DE YPAD Ribo-Seq rep1, pA-tailed

description:
asc1_DE_Fp1_pA
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz

value: Ribo-Seq


title: D16 NTP1 Tra-160+ve

description:
R20
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

tag: cell line

value: BJ Fibroblasts 16 days post induced OSKM viral Expression and treated with non-targeting siRNA.

tag: genotype

value: WT


title: WT YPAD RNA-Seq rep1, pA-tailed

description:
WT_T1_pA
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: D12 ENY2 KD

description:
R19
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts

value: BJ Fibroblasts 12 days post induced OSKM viral Expression and treated with ENY2 siRNA.

value: ENY2 Knock-down


title: WT YPAD RNA-Seq rep2, pA-tailed

description:
WT_T2_pA
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: D12 ZMYM2 KD Tra-160-ve

description:
R18
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts 12 days post induced OSKM viral Expression and treated with ZMYM2 siRNA.

value: Tra-160 negative

value: ZMYM2 Knock-down


title: D12 ZMYM2 KD Tra-160+ve

description:
R17
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt


title: Emb_MO-Tbx5a_24hpf_rep2

description:
Sample name: F
smallRNAseq after Mo-MOTbx5a injection

source_name: Embryos, MO-Tbx5a, 24hpf, replicate2

tag: tissue

value: embryo

value: AB

value: Mo-MOTbx5a injection


title: WT YPAD Ribo-Seq rep1, pA-tailed

description:
WT_Fp1_pA
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz

value: YPAD (2% glucose w/v)


title: D12 SFRS11 KD Tra160-ve

description:
R16
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts 12 days post induced OSKM viral Expression and treated with SFRS11 siRNA.

value: SFRS11 Knock-down


title: rps16b-Null YPAD RNA-Seq rep1, sigma1278b deletion collection background

description:
rps16b_Null_T1_collection
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_rps_rpkms.txt.gz
yeast_rps_counts.txt.gz
yeast_rps_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz

value: RNA-Seq

value: oligo dT cellulose

value: adapter ligation

value: AMV

value: pour over ice, freeze cell pellet in liquid nitrogen, thaw and lyse


title: rps16b-Null YPAD Ribo-Seq rep2, sigma1278b deletion collection background

description:
rps16b_Null_Fp2_collection
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_rps_rpkms.txt.gz
yeast_rps_counts.txt.gz
yeast_rps_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz

value: Ribo-Seq


title: rps16b-Null YPAD RNA-Seq rep2, sigma1278b deletion collection background

description:
rps16b_Null_T2_collection
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_rps_rpkms.txt.gz
yeast_rps_counts.txt.gz
yeast_rps_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: rps16b-Null YPAD Ribo-Seq rep1, sigma1278b deletion collection background

description:
rps16b_Null_Fp1_collection
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_rps_rpkms.txt.gz
yeast_rps_counts.txt.gz
yeast_rps_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: D12 SMAD3 KD Tra-160-ve

description:
R14
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts

value: BJ Fibroblasts 12 days post induced OSKM viral Expression and treated with SMAD3 siRNA.

value: SMAD3 Knock-down


title: rps0b-Null YPAD RNA-Seq rep1, sigma1278b deletion collection background

description:
rps0b_Null_T1_collection
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_rps_rpkms.txt.gz
yeast_rps_counts.txt.gz
yeast_rps_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: rps0b-Null YPAD RNA-Seq rep2, sigma1278b deletion collection background

description:
rps0b_Null_T2_collection
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_rps_rpkms.txt.gz
yeast_rps_counts.txt.gz
yeast_rps_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: D12 SMAD3 KD Tra160+ve

description:
R13
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: Tra-160 positive


title: rps0b-Null YPAD Ribo-Seq rep1, sigma1278b deletion collection background

description:
rps0b_Null_Fp1_collection
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_rps_rpkms.txt.gz
yeast_rps_counts.txt.gz
yeast_rps_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: D12 NTP1 Tra-160+ve

description:
R11
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts 12 days post induced OSKM viral Expression and treated with non-targeting siRNA.

value: WT


title: D8 ENY2 KD

description:
R10
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts 8 days post induced OSKM viral Expression and treated with ENY2 siRNA.

value: ENY2 Knock-down


title: asc1-DE YPAD Ribo-Seq rep2, pA-tailed

description:
asc1_DE_Fp2_pA
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz

value: YPAD (2% glucose w/v)

value: polyA tailing

value: Superscript III

value: cool on ice, resuspend cells in cold lysis buffer,  lyse immediately


title: rps0b-Null YPAD Ribo-Seq rep2, sigma1278b deletion collection background

description:
rps0b_Null_Fp2_collection
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_rps_rpkms.txt.gz
yeast_rps_counts.txt.gz
yeast_rps_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: D8 ZMYM2 KD

description:
R9
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts 8 days post induced OSKM viral Expression and treated with ZMYM2 siRNA.

value: ZMYM2 Knock-down


title: WT YPAD RNA-Seq rep2, sigma1278b deletion collection background

description:
WT_T2_collection
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_rps_rpkms.txt.gz
yeast_rps_counts.txt.gz
yeast_rps_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz

value: RNA-Seq

value: oligo dT cellulose

value: adapter ligation

value: AMV


title: D16 NTP1 Tra-160-ve

description:
R21
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts

value: BJ Fibroblasts 16 days post induced OSKM viral Expression and treated with non-targeting siRNA.

value: Tra-160 negative


title: WT YPAD Ribo-Seq rep2, pA-tailed

description:
WT_Fp2_pA
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz

value: Ribo-Seq


title: WT YPAD RNA-Seq rep1, sigma1278b deletion collection background

description:
WT_T1_collection
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_rps_rpkms.txt.gz
yeast_rps_counts.txt.gz
yeast_rps_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz

value: pour over ice, freeze cell pellet in liquid nitrogen, thaw and lyse


title: D12 SAE1 KD Tra-160+ve

description:
R7
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts 12 days post induced OSKM viral Expression and treated with SAE1 siRNA.

value: Tra-160 positive

value: SAE1 Knock-down


title: D8 SMAD3 KD

description:
R5
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts 8 days post induced OSKM viral Expression and treated with SMAD3 siRNA.

value: SMAD3 Knock-down


title: WT YPAD Ribo-Seq rep2, sigma1278b deletion collection background

description:
WT_Fp2_collection
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_rps_rpkms.txt.gz
yeast_rps_counts.txt.gz
yeast_rps_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz

value: YPAD (2% glucose w/v)


title: WT YPAD Ribo-Seq rep1, sigma1278b deletion collection background

description:
WT_Fp1_collection
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_rps_rpkms.txt.gz
yeast_rps_counts.txt.gz
yeast_rps_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: D8 SAE1 KD

description:
R4
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts 8 days post induced OSKM viral Expression and treated with SAE1 siRNA.


title: D12 SFRS11 KD Tra-160+ve

description:
R15
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts 12 days post induced OSKM viral Expression and treated with SFRS11 siRNA.

value: SFRS11 Knock-down


title: D8 NTP1

description:
R3
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts 8 days post induced OSKM viral Expression and treated with non-targeting siRNA.

value: WT


title: asc1-Null YPAD RNA-Seq rep1, Ribo-Zero treated

description:
asc1_M1X_rz_T1
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_rz_rpkms.txt.gz
yeast_rz_counts.txt.gz
yeast_rz_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz

value: RNA-Seq

value: Ribo-Zero

value: adapter ligation

value: Superscript III


title: D12 NTP1 Tra-160-ve

description:
R12
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts

value: BJ Fibroblasts 12 days post induced OSKM viral Expression and treated with non-targeting siRNA.

value: Tra-160 negative


title: asc1-Null YPAD RNA-Seq rep2, Ribo-Zero treated

description:
asc1_M1X_rz_T2
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_rz_rpkms.txt.gz
yeast_rz_counts.txt.gz
yeast_rz_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz

value: pour over ice, freeze cell pellet in liquid nitrogen, thaw and lyse


title: D5

description:
R2
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts 5 days post induced OSKM viral Expression.


title: WT YPAD RNA-Seq rep2, Ribo-Zero treated

description:
WT_rz_T2
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_rz_rpkms.txt.gz
yeast_rz_counts.txt.gz
yeast_rz_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: asc1-M1X YPAG RNA-Seq rep1

description:
gly_asc1_M1X_T1
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_glycerol_rpkms.txt.gz
yeast_glycerol_counts.txt.gz
yeast_glycerol_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz

value: YPAG (3% glycerol w/v)

value: oligo dT cellulose


title: D12 SAE1 KD Tra-160-ve

description:
R8
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts 12 days post induced OSKM viral Expression and treated with SAE1 siRNA.

value: SAE1 Knock-down


title: WT YPAD RNA-Seq rep1, Ribo-Zero treated

description:
WT_rz_T1
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_rz_rpkms.txt.gz
yeast_rz_counts.txt.gz
yeast_rz_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz

value: YPAD (2% glucose w/v)


title: ATXN1[82Q] week 12 replicate 3

description:
cuffdiff_week12_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_gene_exp.diff.txt
cuffnorm_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_genes.fpkm_tracking.txt
cuffdiff_week5_vs_week12_vs_week28_ATXN1.82Q_gene_exp.diff.txt

value: FVB

value: cerebellum

tag: age

value: 12 weeks


title: Trans PIC 8 hr

city: Los Angeles

first: Alexander

last: Hoffmann

address: 570 Boyer Hall

department: MIMG

institute: UCLA

data_processing:
Sequencing was performed on Illumina's HiSeq 2000, according to the manufacturer’s recommendations by the University of California, San Diego Biogem facility.
Using cutadapt we removed adapters and using scythe did end trimming based on quality and  discard reads aligning to rRNA (based on sequence)
Reads were aligned to the mouse genome GRCm38  with the STAR RNA-seq aligner
filter out multimappers and reads with quality < 30 and removed rRNA based on coordinates
htseq-count (union mode) from the HTSeq Python package was used to determine raw gene read counts
Genome_build: mouse genome mm10 gencode vM4
Supplementary_files_format_and_content: .txt is text file with two columns first column contains ENSEMBEL gene IDs and read counts for corresponding gene are in second column

source_name: BMDM_Trans PIC 8 hr

growth_protocol: Bone marrow derived macrophages (BMDMs) were isolated from wild type femurs. A total of 7 x 10^6 BM cells were cultured in 15 cm suspension dishes in L929-conditioned media for 7 days at 37°C with 5% CO2. BMDMs were then replated on day 7 at of 2 x 10^6 cells per 6 cm plate in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum and all experiments were performed on day 8.

extract_protocol:
mRNA was extracted from 2 μg total RNA using oligo(dT) magnetic beads and fragmented at high temperature using divalent cations
cDNA library was generated using the Illumina TruSeq kits and quantitation was performed using the Roche Light Cycler 480

treatment_protocol: BMDMs were replated with 5 x 10^6 cells per 10 cm plate on day 7. On day 8, BMDMs were left unstimulated or stimulated with various stimuli.

value: wild type

value: femur bone marrow

tag: cell type

value: macrophage


title: Trans PIC 3 hr

source_name: BMDM_Trans PIC 3 hr


title: WT YPAG RNA-Seq rep2

description:
gly_WT_T2
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_glycerol_rpkms.txt.gz
yeast_glycerol_counts.txt.gz
yeast_glycerol_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz

value: RNA-Seq

value: adapter ligation

value: Superscript III


title: WT YPAG RNA-Seq rep1

description:
gly_WT_T1
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_glycerol_rpkms.txt.gz
yeast_glycerol_counts.txt.gz
yeast_glycerol_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: asc1-M1X YPAG RNA-Seq rep2

description:
gly_asc1_M1X_T2
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_glycerol_rpkms.txt.gz
yeast_glycerol_counts.txt.gz
yeast_glycerol_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: D8 SFRS11 KD

description:
R6
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: BJ Fibroblasts

tag: treatment

value: BJ Fibroblasts 8 days post induced OSKM viral Expression and treated with SFRS11 siRNA.

tag: sorting

value: SFRS11 Knock-down


title: WT YPAG Ribo-Seq rep2

description:
gly_WT_Fp2
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_glycerol_rpkms.txt.gz
yeast_glycerol_counts.txt.gz
yeast_glycerol_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz

value: Ribo-Seq

value: YPAG (3% glycerol w/v)

value: pour over ice, freeze cell pellet in liquid nitrogen, thaw and lyse


title: Trans PIC 1 hr

source_name: BMDM_Trans PIC 1 hr


title: asc1-M1X YPAG Ribo-Seq rep1

description:
gly_asc1_M1X_Fp1
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_glycerol_rpkms.txt.gz
yeast_glycerol_counts.txt.gz
yeast_glycerol_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: LM 1 hr

source_name: BMDM_LM 1 hr


title: WT YPAG Ribo-Seq rep1

description:
gly_WT_Fp1
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_glycerol_rpkms.txt.gz
yeast_glycerol_counts.txt.gz
yeast_glycerol_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: STREP 8 hr

source_name: BMDM_STREP 8 hr


title: rpp1a-Null YPAD Ribo-Seq rep1, reprep

description:
rpp1a_Null_Fp1_r
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: STREP 3 hr

source_name: BMDM_STREP 3 hr


title: LM 3 hr

source_name: BMDM_LM 3 hr


title: D0

description:
R1
processed data file: All Genes_FPKM.txt
processed data file: Genes_Log2FoldChange_vs_D0.txt

value: WT BJ Fibroblasts

value: WT


title: rpl23b-Null YPAD Ribo-Seq rep1, reprep

description:
rpl23b_Null_Fp1_r
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz

value: YPAD (2% glucose w/v)


title: asc1-Null YPAD Ribo-Seq rep1, reprep

description:
asc1_Null_Fp1_r
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: VSV 8 hr

source_name: BMDM_VSV 8 hr


title: VSV 3 hr

source_name: BMDM_VSV 3 hr


title: STREP 1 hr

source_name: BMDM_STREP 1 hr


title: asc1-M1X YPAD Ribo-Seq rep1, reprep

description:
asc1_M1X_Fp1_r
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: asc1-D109Y YPAD Ribo-Seq rep1, reprep

description:
asc1_D109Y_Fp1_r
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: asc1-M1X YPAG Ribo-Seq rep2

description:
gly_asc1_M1X_Fp2
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_glycerol_rpkms.txt.gz
yeast_glycerol_counts.txt.gz
yeast_glycerol_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: VSV 1 hr

source_name: BMDM_VSV 1 hr


title: LM 8 hr

source_name: BMDM_LM 8 hr


title: WT YPAD Ribo-Seq rep1, reprep

description:
WT_Fp1_r
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: MCMV 3 hr

source_name: BMDM_MCMV 3 hr


title: MCMV 1 hr

source_name: BMDM_MCMV 1 hr


title: rpp1a-Null YPAD RNA-Seq rep2

description:
rpp1a_Null_T2
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz

value: oligo dT cellulose


title: No Stimulus 4

source_name: BMDM_No Stimulus 4


title: rpp1a-Null YPAD RNA-Seq rep1

description:
rpp1a_Null_T1
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: rpp1a-Null YPAD Ribo-Seq rep2

description:
rpp1a_Null_Fp2
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: rpp1a-Null YPAD Ribo-Seq rep1

description:
rpp1a_Null_Fp1
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: IFNB 3 hr

source_name: BMDM_IFNB 3 hr


title: No Stimulus 3

source_name: BMDM_No Stimulus 3


title: TNF 8 hr

source_name: BMDM_TNF 8 hr


title: IFNB 8 hr

source_name: BMDM_IFNB 8 hr


title: rpl23b-Null YPAD Ribo-Seq rep1

description:
rpl23b_Null_Fp1
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: rpl23b-Null YPAD Ribo-Seq rep2

description:
rpl23b_Null_Fp2
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: rpl23b-Null YPAD RNA-Seq rep1

description:
rpl23b_Null_T1
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: TNF 1 hr

source_name: BMDM_TNF 1 hr


title: IFNB 1 hr

source_name: BMDM_IFNB 1 hr


title: CPG 8 hr

source_name: BMDM_CPG 8 hr


title: MCMV 8 hr

source_name: BMDM_MCMV 8 hr


title: asc1-M1X YPAD RNA-Seq rep2

description:
asc1_M1X_T2
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: asc1-Null YPAD RNA-Seq rep1

description:
asc1_Null_T1
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: asc1-Null YPAD Ribo-Seq rep2

description:
asc1_Null_Fp2
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: CPG 1 hr

source_name: BMDM_CPG 1 hr


title: asc1-Null YPAD RNA-Seq rep2

description:
asc1_Null_T2
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: R848 8 hr

source_name: BMDM_R848 8 hr


title: asc1-M1X YPAD RNA-Seq rep1

description:
asc1_M1X_T1
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: rpl23b-Null YPAD RNA-Seq rep2

description:
rpl23b_Null_T2
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: R848 3 hr

source_name: BMDM_R848 3 hr


title: asc1-Null YPAD Ribo-Seq rep1

description:
asc1_Null_Fp1
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: FSL 8 hr

source_name: BMDM_FSL 8 hr


title: asc1-D109Y YPAD RNA-Seq rep2

description:
asc1_D109Y_T2
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: TNF 3 hr

source_name: BMDM_TNF 3 hr


title: R848 1 hr

source_name: BMDM_R848 1 hr


title: FSL 1hr

source_name: BMDM_FSL 1hr


title: asc1-D109Y YPAD RNA-Seq rep1

description:
asc1_D109Y_T1
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: asc1-M1X YPAD Ribo-Seq rep1

description:
asc1_M1X_Fp1
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: LPS 8 hr

source_name: BMDM_LPS 8 hr


title: CPG 3 hr

source_name: BMDM_CPG 3 hr


title: asc1-D109Y YPAD Ribo-Seq rep1

description:
asc1_D109Y_Fp1
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: FLA 1 hr

source_name: BMDM_FLA 1 hr


title: WT YPAD RNA-Seq rep2

description:
WT_T2
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: LPS 3 hr

source_name: BMDM_LPS 3 hr


title: PIC 8 hr

source_name: BMDM_PIC 8 hr


title: PIC 3 hr

source_name: BMDM_PIC 3 hr


title: WT YPAD RNA-Seq rep1

description:
WT_T1
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: PIC 1 hr

source_name: BMDM_PIC 1 hr


title: PAM 8 hr

source_name: BMDM_PAM 8 hr


title: WT YPAD Ribo-Seq rep2

description:
WT_Fp2
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: PAM 3 hr

source_name: BMDM_PAM 3 hr


title: PAM 1 hr

source_name: BMDM_PAM 1 hr


title: No Stimulus 2

source_name: BMDM_No Stimulus 2


title: FLA 3 hr

source_name: BMDM_FLA 3 hr


title: No Stimulus 1

source_name: BMDM_No Stimulus 1


title: FLA 8 hr

source_name: BMDM_FLA 8 hr


title: WT YPAD Ribo-Seq rep1

description:
WT_Fp1
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: Control 2

status: Public on Apr 23 2016

city: Nanchang

first: chenlong

last: liu

state: Jiangxi province

address: Lushanzhong street NO.888, Nanchang, China

department: Animal science and technology department

institute: Jiangxi Agricultural University

data_processing:
Illumina GA Pipeline v1.5 software used for basecalling.
Bowtie2_build was used to build a  index file of Bos_taurus.UMD3.1.75.dna.chromosome.1-29 and X
SOAPaligner (V2.21) was used to align cleaned RNA-seq reads to reference genome to identify genes. The NOISeq method was applied to identify the differentially expressed genes and transcripts with parameters
Genome_build: Bos_taurus.UMD3.1.75.dna.chromosome 1-29 and X (unmasked reference genomic sequence) [ftp://ftp.ensembl.org/pub/release-75/fasta/bos_taurus/dna/]
Supplementary_files_format_and_content: [.rpkm] Abundances of all gene models

organism: Bos taurus

source_name: Control

extract_protocol:
longissimus muscles were removed from  -80°C freezer , and total RNA isolated with TRIzol reagent. Illumina HiSeq 2000 was used for RNA-Seq.
RNA libraries were prepared for sequencing using standard Illumina protocols
single-end sequencing library

value: 2 years

tag: agent

value: control

value: longissimus muscle


title: NA 2

value: Nicotinic acid