title: MPP subset 4

first: Fernando

last: Camargo

address: 300 Longwood Ave

department: Stem Cell and Regenerative Biology

institute: Boston Children's Hospital

data_processing:
The barcode read was first filtered based on presence of two sample barcode components separated by the W1 adaptor sequence (GAGTGATTGCTTGTGACGCCTT), as previously described (Klein et al., Cell 2015).
The cDNA read was then trimmed using Trimomatic (version 0.33; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:16).
Barcodes for each read were matched against a list of the pre-determined barcodes, and errors of up to two nucleotides mismatch were corrected. Reads with a barcode separated by more than two nucleotides from the reference list were discarded. The reads were then split into barcode-specific files for mapping and UMI filtering.
The trimmed reads were aligned using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 100 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (GRCm38.81) including all annotations with ""Transcript Support Levels"" of 1, 2, or NA (only accepted for protein coding genes).
A custom Python and PySAM script to process mapped reads into counts of UMI-filtered transcripts per gene, as previously described (Zilionis et al., Nature Protocols in press)
Genome_build: GRCm38.81
Supplementary_files_format_and_content: The raw_umifm_counts files include raw unique molecular identifier (UMI)-filtered counts for all transcriptomes (prior to filtering). Columns = genes (with exception of first 5 columns), rows = cells. Column 1 contains cell identifier. Column 2 contains matching cell barcode. Column 3 contains library ID. Column 4 contains sequencing run ID. Column 5 contains flag for cell pass filtering (0=fail, 1=pass). Columns 6+ contain counts for each gene.

source_name: Bone marrow HSPCs

extract_protocol:
Cells were encapsulated using the inDrops platform, into droplets on ice and lysed in the 4nL microfluidic droplets using a final concentration of 0.4% NP-40. Single cell lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015).
Libraries were prepared as in Zilionis et al., Nature Protocols (in press), with the exception of the first round of libraries, for which the final PCR step was carried out as in Klein et al., Cell 2015.

treatment_protocol: After euthanasia, whole bone marrow (excluding the cranium) was immediately isolated in 2% fetal bovine serum (FBS) in phosphate buffered saline (PBS), and erythrocytes were removed with RBC lysis buffer. Lineage depletion was performed using Magnetic Assisted Cell Sorting (Miltenyi Biotec) with anti-biotin magnetic beads and the following biotin-conjugated lineage markers: CD3e, CD19, Gr1, Mac1, and Ter119. Cell populations from BM were purified through 4-way sorting using FACSAria (Becton Dickinson) and 6-way sorting using MoFlo XDP (Beckman Coulter). The following combinations of cell surface markers were used to define these cell populations: LT-HSC: Lin- cKit+ Sca1+ CD150+ CD48-, ST-HSC: Lin- cKit+ Sca1+ CD150- CD48-, MPP2: Lin- cKit+ Sca1+ Flt3- CD150+ CD48+, MPP3: Lin- cKit+ Sca1+ Flt3- CD150- CD48+, MPP4: Lin- cKit+ Sca1+ Flt3+ CD48+. Flow cytometry data were analyzed with FlowJo (Tree Star).

value: bone marrow

tag: purification


title: Rat_IFE_rep2

status: Public on Jan 03 2018

type: SRA

city: Irvine

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

country: USA

institute: University of California, Irvine

description:
protocol: SMART-seq2
processed data file: Rat_TPM.txt

library_source: transcriptomic

data_processing:
Sequenced reads were mapped to Ensembl v.87 transcriptomes of Mus musculus (mm10) and Rattus norvegicus (Rnor_6.0) using bowtie v1.0.0 with parameters: -S --offrate 1 -a -m 200 --best -p 8 -v 2
Transcripts per million (TPM) measurements for rat and mouse samples were obtained using read alignments to Ensembl v87 transcriptomes and rsem v1.2.31
Genome_build: mm10 or Rnor_6.0
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for mouse samples and rat samples separately.

molecule: total RNA

organism: Rattus norvegicus

source_name: Rat inter-follicular epidermis

extract_protocol:
Whole tissue was homogenized using Precellys in RLT buffer supplemented with beta-mercapto ethanol to preserve RNA integrity. Total RNA was isolated using Rneasy micro kit as per manufacturer's suggestions (Qiagen), including DNAse treatment. Total RNA was eluted in molecular grade water. RNAs with optimal RIN scores were considered for library preparation.
SMART-seq2 was performed on total RNA as described by Picelli et al. Briefly, 10 ng and 100 ng total RNA was used for RT. Resulting cDNA was pre-amplified for 12 and 10 cycles, respectively and tagmentation  performed on 18 ng and 20 ng cDNA using the Nextera DNA Sample Preparation Kit (Illumina). Fragments were amplified for 8 continuous cycles. Libraries sequenced as single-end (86bp and 43bp) on a NextSeq 500 Illumina Sequencing Platform (Illumina).

tag: tissue

value: skin

tag: tissue compartment

value: epidermis

tag: skin status

value: Normal skin

tag: Stage

value: Adult


title: Short-term HSCs

city: Boston

state: MA

description: STHSC

molecule: polyA RNA

organism: Mus musculus

tag: strain


title: Rat_epidermis_rep4

source_name: Rat wound epidermis

value: Skin wound

value: Scab detachment day 1


title: MPP subset 2


title: Long-term HSCs

description: LTHSC


title: Rat_epidermis_rep3


title: Rat_IFE_rep1


title: MPP subset 3


title: Rat_dermis_rep3

source_name: Rat wound dermis

value: dermis


title: Rat_epidermis_rep2


title: 3110_Input1

city: Austin

first: Bryan

last: Davies

state: TX

address: 2506 Speedway

institute: University of Texas at Austin

description:
processed data file:
2016_12_3110_medium_full_library_partial_properties.xlsx

library_source: genomic

data_processing:
We used ustacks to consolidate and then trimmed reads that originated from a particular nucleotide sequence.
We translated the nucleotide sequences for each nucleotide sequence into an amino acid sequence with a custom python script using the Biopython library, and then summed the total reads for each unique peptide.
A file containing each peptide sequence and the total number of reads in each library was then used as input for the DESeq2 R/Bioconductor package. We used a standard DESeq2 workflow, which includes read count normalization, peptide dispersion estimates, and Wald tests for significance of differential abundance.  For each peptide, we compared the total abundance (normalized reads) in the induced (IPTG) libraries to the abundance in the input libraries, resulting in a log2 FoldChange (log2FC) and p-value for each peptide.  P-values were adjusted (padj) for multiple testing using Benjamini-Hochberg correction as part of the standard DESeq2 workflow detailed in the package manual  (available here: https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.pdf). Generally, peptides that were selected for further experimental validation had a log2FC < -1 and padj < .05.
Supplementary_files_format_and_content: PeplibV3_Hiseq_properties_cory.csv: Comma-separated text file contains nucleotide and corresponding peptide sequences for the massive random library. We provide the full 20-mer sequence as well as sequences truncated by stop codons. Hydrophobicity, charge, lfcMLE, adjusted p-value, and read counts (input and output) are provided for each sequence.

molecule: genomic DNA

organism: Escherichia coli str. K-12 substr. W3110

growth_protocol: An aliquot of the frozen library was thawed and added to 10ml of LB supplemented with carbenicillin 75mg/ml for growth, shaking at 37°C for about 1 hour. The culture was then back diluted into 5ml LB/carb75 to OD600nm 0.01 supplemented with 0.1mM IPTG. The remaining culture was collected as the “Input” sample. Induced cultures were allowed to grow, shaking at 37°C. Cells were harvested after 2, 3, 4 and 5 hours for the defined peptide library and harvest after 4 hours for the random peptide library.

extract_protocol:
Plasmid DNA was isolated using the Zyppy Miniprep Kit in accordance with the prescribed protocol provided with the kit.
Custom primers were used to ligate adaptors to regions flanking the peptide nucleotide sequence. Products were gel-extracted and cleaned using the Zymoclean Gel DNA Recovery Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: 0.1mM IPTG was used for induction.

tag: induced with

value: none (input)

tag: molecule subtype

value: plasmid DNA


title: Rat_dermis_rep2


title: Rat_epidermis_rep1


title: MEF_Rep3 [RNA-Seq]

city: New York

first: Matthias

last: Stadtfeld

address: 540 First Avenue Skirball Lab 4-1

institute: NYU School of Medicine

data_processing:
Reads were aligned using TopHat 2.0.9 with Bowtie 2.2.6.
SAMtools (0.1.19) was used to select paired, unique reads; those aligning to mitochondrial DNA were excluded.
Reads were quantified using HTSeq (0.5.4p3).
Differential genes were identified using DESeq2 (1.12.4) using a fold change of >2, an adjusted p-value of <0.05, and an FPKM of >=1 (estimated using DESeq2's fpkm function and the longest annotated isoform).
Genome_build: mm10
Supplementary_files_format_and_content: Text files with read counts for genes in mm10, quantified using HTSeq.

source_name: cells

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mixed (C57BL/6 x 129)

tag: marker

value: iPSCs


title: iPSC_Rep1 [RNA-Seq]

value: Stage 2 (day 6 + 4)


title: iPSC_Rep3 [RNA-Seq]


title: iPSC_Rep2 [RNA-Seq]


title: MEF_Rep1 [RNA-Seq]


title: Stage2_Rep1 [RNA-Seq]

value: Stage 1 (day 6)


title: Stage1_Rep3 [RNA-Seq]

value: Unsorted

value: MEF


title: ph rep 2

city: Taipei

first: Jia-Ming

last: Chang

address: NO.64, Sec. 2, ZhiNan Rd., Wenshan District

department: Department of Computer Science

country: Taiwan

institute: National Chengchi University

data_processing:
Paired-end reads were mapped to the Drosophila melanogaster genome (assembly dm3) using the bowtie program with parameters (-t -a -m 1 --best).  Unmapped or non-unique mapped reads were discarded.
We then divided read pairs into four groups: SS (reads mapping to the same restriction fragment, or to two adjacent restriction fragments); S2 (reads in which both ends mapped precisely on the DpnII site); S1 (reads in which one of the ends mapped precisely on the DpnII site); S0 (reads in which both ends did not map precisely to a DpnII site). SS, S2 and S1 pairs were discarded from subsequent analysis.
Mapped reads were then associated with the first restriction fragment end encountered when moving from the mapped position in the appropriate strand.
All subsequent analysis was done in the space of fragment end pairs. The Drosophila genome contains 464,246 restriction fragments. After discarding low mappability fragments 301,687 fragments are left (and each defines two fragment ends).
A model accounting for systematic biases in contact probability was constructed as previously (Yaffe and Tanay; Nature Genetics, 43, p.1059-65). Briefly, we used the local G+C content of up to 200 bp from the restriction site (agc, bgc), and the DpnII restriction fragment lengths (alen, blen), to correct for systematic biases in Hi-C coverage by modeling: P(Xa,b) = Pprior x Flen(alen,blen) x Fgc(agc,bgc).
We estimated maximum likelihood model parameters (the matrices Flen and Fgc) through application of an iterative algorithm as described, using 20 bins for G+C content and 20 bins for fragment length.
Genome_build: dm3
Supplementary_files_format_and_content: *.bins: the real genomic co-ordinates of the involved bins  cbin - the identity of the bin  chr - chromosome  from.coord - start co-ordinate of bin  to.coord - end co-ordinate of the bin  count - the number of fends contained within the bin
Supplementary_files_format_and_content: *.n_contact: give the contact score maps  cbin1 - the identity of the first bin  cbin2 - the identity of the second bin  expected_count - the number of counts expected for this pairwise bin combination, based on the technical normalisation  observed_count - the number of tags counted from the Hi-C dataset for this pairwise bin combination
Supplementary_files_format_and_content: The number in the processed data file name (e.g. 160000 in nm_none_160000.bins.txt) refers to the size of the bin in bp.

organism: Drosophila melanogaster

source_name: 16-18 hr embryo

growth_protocol: Flies were raised in standard cornmeal yeast extract media at 25°C. The ph505 stock is described in Dura et al. 1987, and was balanced over the KrGFP-FM7c balancer for the selection of hemizygous ph505 GFP- null mutant males. We used a Y chromosomal GFP reporter line (Y-GFP line: y[1], w[67c23]; P{w[+mC]=ActGFP} Dp(1;Y), y[+]) for the selection of WT GFP+ males to be compared with the ph mutant males. This line was a gift of Shigeo Hayashi and is described in Hayashi, 2010.

extract_protocol:
~3000 embryos were collected in a saline buffer (0.03% Triton X-100, 0.4% NaCl) 16-18 hr after egg laying, then de-chorionated for 5 min in fresh bleach. Embryos were sorted with a Union Biometra COPAS Large Particle Sorter (Union Biometra Inc, Holliston, MA), and then processed for Hi-C as in Sexton et. al. 2012.
Aliquots of 5 µg 3C DNA were sonicated in a Bioruptor (Diagenode) in 50 µl volumes in sonication buffer (50 mM Tris-HCl, pH 8, 10 mM EDTA, 1% SDS) to obtain a smear between 500-1500 bp. The sonicated 3C DNA was then purified by phenol/chloroform extraction and ethanol precipitation and quantified with the Qubit dsDNA assay (Invitrogen). Libraries for paired-end sequencing were made from 500 ng aliquots of sonicated 3C DNA using Illumina reagents and protocols, with size selection for products of ~800 bp.

tag: developmental stage

value: Embryo

tag: age

tag: genotype


title: Stage2_Rep2 [RNA-Seq]


title: Stage2_Rep3 [RNA-Seq]


title: Skin NN 7

city: Ann Arbor

first: William

middle: R

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

description: RNA extracted from full-thickness skin biopsy

data_processing:
Illumina adaptor sequences were removed using CutAdapt (version 1.6).
Reads were trimmed to remove bases with low PHRED quality scores (CutAdapt and Fast-X toolkit)
Filtered reads were mapped to the UCSC GRCh37/hg19 genome using Tophat2 (version 2.0.12)
Overlap between mapped reads and known human genes was tabulated using the htseq-count function from the HTSeq python library (version 0.5.4p3)
Cufflinks (version 2.2.1) was used to calculate fragments per kilobase of exon per million fragments mapped (FPKM) for each gene feature.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Processed data includes raw read counts and FPKM values for all human genes (GRCh37/hg19) and each sample (.txt files).

organism: Homo sapiens

source_name: Skin biopsy

growth_protocol: To establish KC monolayers, skin biopsies were washed in HBSS containing antibiotics to remove blood, fat was trimmed away, and the remaining tissue was rinsed in 70% ethanol before being incubated in 50U/ml dispase (Gibco) at 37°C for 2 hours to release epidermis from dermis. Epidermal sheets were incubated in 0.05% Trypsin-EDTA (Invitrogen) for 15 min at 37°C, after which a slurry of cells was apparent. Trypsin was neutralized by the addition of complete Medium 154 culture medium containing 1% HKGS, 0.1mM Ca2+ and antibiotics (Invitrogen). Cells were passed through a 100µm cell strainer (BD Biosciences), washed, suspended in fresh culture medium, and seeded into 6-well cell culture plates (BD Biosciences).

extract_protocol:
Total RNA was isolated using the RNeasy plus isolation kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.  An Agilent Bioanalzyer (Agilent Technologies, Santa Clara, CA) was used to assess RNA quality and quantity.
Polyadenylated RNA was purified and used to prepare complementary DNA libraries for high throughput sequencing using the Illumina mRNA-Seq kit according to the manufacturer’s protocol (Illumina, San Diego, CA). Sequencing of fragmented complementary cDNA was performed using the Illumina Genome Analyzer Iix

treatment_protocol: Cells were left undisturbed for 6 days at 37oC with 5% CO2. Thereafter medium was replenished every 2-3 days. Cells were harvested shortly after reaching confluence and further processed for RNA extraction.

value: Skin biopsy

tag: group

value: normal skin from control individuals (NN)

tag: patient


title: Skin NN 8


title: Stage1_Rep1 [RNA-Seq]


title: ph rep 1


title: iPSC_Rep3 [ATAC-Seq]

data_processing:
Reads were aligned using Bowtie 2.2.6 (-X 2000).
Aligned reads were filtered using Picard Tools (2.6.0) and SAMtools (0.1.19) (-F 1804); reads aligning to mitochondrial DNA were excluded.
Peaks were called using PeakDEck (1.1).
Peaks consistent to at least on set of replicates were quantified using HTSeq (0.5.4p3).
Differential peaks were identified using DESeq2 (1.12.4) using a fold change of >1.5 and an adjusted p-value of <0.1.
Genome_build: mm10
Supplementary_files_format_and_content: BED files with peaks common to all replicates in each stage (Peaks_MEF.bed, Peaks_Stage1.bed, Peaks_Stage2.bed, Peaks_iPSC.bed) or at least one stage (Peaks_All.bed)
Supplementary_files_format_and_content: Text files with read counts for peaks found in at least one stage (Peaks_All.bed) in mm10, quantified using HTSeq.

extract_protocol:
Cells were harvested and lysed at various stages of 3c enhanced reprogramming as previously described by Buenrostro et al., 2013.
ATAC-Seq libraries were prepared as previously described by Buenrostro et al., 2013.


title: Stage1_Rep2 [RNA-Seq]


title: male rep 2

tag: Sex

value: male


title: iPSC_Rep2 [ATAC-Seq]


title: Skin NN 6


title: MS2-CyaR

city: SHERBROOKE

first: Eric

last: Massé

state: Québec

address: 3201, Jean Mignault

department: Biochemistry

country: Canada

institute: University of Sherbrooke

data_processing:
Basecalls performed using MCS Version 2.4.1.3
Reads were aligned to the Escherichia coli K12 genome assembly using Bowtie for Illumina (Galaxy Project)
Read counts were normalized by coverage according to Oshlack et al., 2010
Genome_build: Escherichia coli K12
Supplementary_files_format_and_content: tab-delimited text file include normalized reads for each sample and MS2-CyaR/CyaR ratio

organism: Escherichia coli K-12

source_name: Bacterium

growth_protocol: Cells were harvested in exponential (OD600nm=0.5; 100 mL LB medium) and in stationary phase (OD600nm=1; 100 mL LB medium).

extract_protocol:
Cells were resuspended in 3 mL of buffer A and lysed using a French Press (430 psi, four times). Lysate was then cleared by centrifugation. The soluble fraction was subjected to affinity chromatography. The column was prepared by adding 100 µL of amylose resin (New England Biolabs) to Bio-Spin disposable chromatography columns (Bio-Rad). The column was washed with 3 mL of buffer A. Next, 200 pmol of MS2-MPB protein was immobilized on the amylose resin, and the column was washed with 2 mL of buffer A. The cleared lysate was then loaded onto the column, which was washed with 8 mL of buffer A. RNA was eluted from the column with 1 mL of buffer A containing 15 mM maltose. Eluted RNA was extracted with phenol-chloroform, followed by ethanol (3 vol) precipitation of the aqueous phase in the presence of 20 mg of glycogen. RNA samples were treated with TURBO DNA-free (DNase treatment) and precipitated again.
cDNA libraries were prepared with ScriptSeq™ RNA-Seq Library Preparation Kit (Illumina)

treatment_protocol: 0.1% arabinose was added to induce the expression of MS2-CyaR/CyaR during 10 min. Cells were chilled for 10 min on ice. Cells were then centrifuged, resuspended in 1 mL of buffer A (20 mMTris-HCl at pH 8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT), and centrifuged again.

value: MG1655 rne131 delta-cyaR

tag: genotype/variation

tag: growth phase

value: exponential and stationary phases


title: Skin NN 5


title: Skin PP 4

value: lesional skin of psoriasis patients (PP)


title: male rep 1


title: CyaR

value: CyaR


title: Rat_dermis_rep1

value: skin

value: dermis

value: Skin wound

value: Scab detachment day 1


title: Skin PN 4

value: uninvolved skin of psoriasis patients (PN)


title: MEF_Rep2 [RNA-Seq]

value: Mixed (C57BL/6 x 129)

value: iPSCs


title: RprA

data_processing:
Basecalls performed using MCS Version 2.4.1.3
Reads were aligned to the Escherichia coli K12 genome assembly using Bowtie for Illumina (Galaxy Project)
Read counts were normalized by coverage according to Oshlack et al., 2010
Genome_build: Escherichia coli K12
Supplementary_files_format_and_content: tab-delimited text file include normalized reads for each sample and MS2-RprA/RprA ratio

growth_protocol: Cells were harvested in stationary phase (OD600nm=1; 100 mL LB medium).

treatment_protocol: 0.1% arabinose was added to induce the expression of MS2-RprA/RprA during 10 min. Cells were chilled for 10 min on ice. Cells were then centrifuged, resuspended in 1 mL of buffer A (20 mMTris-HCl at pH 8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT), and centrifuged again.

value: MG1655 rne131 delta-rprA

value: Stationary phase


title: Stage2_Rep3 [ATAC-Seq]

value: Stage 2 (day 6 + 4)


title: iPSC_Rep1 [ATAC-Seq]


title: S2R+ rep 2

source_name: S2R+ cells

growth_protocol: 1x10^6 S2R+ cells (Drosophila Genomics Resource Center, stock #150) were incubated with 17.5 µg of EGFP dsRNA in 1 mL of S2 serum free medium (Sigma-Aldrich, S0146) with 1% penicillin-streptomycin (Gibco, 15140122) for 30 minutes before addition of 2 mL of medium with 15% FBS (serum Gibco, 10500064) with 1% penicillin-streptomycin. Cells were then grown for 5 days at 25°C.

extract_protocol:
Hi-C and library preparation was performed using the in-situ method as described previously (Rao et al., 2014) with minor modifications. Briefly, 1x10^6 cells were digested overnight at 37°C using 500 U of DpnII. After biotin filling, proximity ligation was carried out for 4 hr at 18°C with 2000 U T4 DNA Ligase, and after reverse-crosslinking, DNA was purified with ethanol precipitation and sheared to 300-400 bp fragments using a Covaris S220 sonicator.
Ligation fragments with biotin were pulled-down using MyOne Streptavidin T1 beads (ThermoFisher Cat.N: 65602), end-repaired and adenylated as described. Fragments were then ligated with NEXTflex adaptors (Bioo Scientific, Cat.N: 514101) and amplified by PCR using KAPA HiFi Library Ampification Kit (Kapa Biosystems, Cat.N: KK2620) for 8 cycles. DNA size-selection (300-800 bp) was done using AMPure XP beads (Agencourt, Cat.N: A63881).

value: Late embryonic stage

tag: cell line

value: wild type


title: MS2-RprA


title: Stage2_Rep2 [ATAC-Seq]


title: Skin PP 3

tag: tissue

value: Skin biopsy


title: Skin PP 2


title: Skin PN 3


title: NAC-MS-3H-3

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

description:
NAC-MS-3H-3_S25_L001_R1_001
small RNA
No antibiotic cleansing.3 hours post blood feeding, sample 3

data_processing:
Our data processing pipeline employs a full-index reference mapping strategy to identify the map position of the sequence reads in the reference genome (AaegL3) using a seed-and-vote method56. In this method, first we generated an index of the AaegL3 reference assembly by comprehensively extracting 16-mer subreads from every position of the genome. Then short seeds (called subreads) were generated from each sequence read and aligned to the full index of reference genome.
The map information of subreads was used to determine the optimal map location (based on majority of votes) of the subreads
For quantification of tRNA fragments (tRFs), the pipeline generates a GTF (general transfer format) file of genomic positions of tRFs within tRNAs as annotated by tRNAscan
The GTF file was then used to determine the number of reads mapped to each tRF in a genome-wide manner by Stringtie
Significance of differential expression was assessed by edgeR robust.
Genome_build: AaegL3
Supplementary_files_format_and_content: read counts to different regions of tRNAs.

organism: Aedes aegypti

source_name: Midgut

growth_protocol: The mosquitoes were reared and maintained in environmental chambers following standard conditions55.  Environmental chambers were held at 26°C, 85% relative humidity, with a 16 h light: 8 h dark cycle, which included a 1-h crepuscular period to simulate dawn and dusk. For developmental study, the second, third, fourth instar larvae and adults were sampled from Moyo-S and Moyo-R strains. The adulst were sampled at 3 days post emeregence.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy mini kit according to manufacturer’s protocol. Quality of RNA was assessed using Bioanalyzer (Agilent, Santa Clara, CA, USA) according to manufacturer’s protocol. Quantity of RNA was analyzed using Qubit Fluorometer (Life Technologies, Grand Island, NY, USA) according to manufacturer’s specifications.
Library preparation was conducted by the Notre Dame Genomics & Bioinformatics Core Facility using the Epicentre Scriptminer small RNA kit following the suppliers protocol. All steps of library construction and sequencing were performed at the Genomics Core Facility at University of Notre Dame.
small RNA sequencing libraries. Sequencing of libraries was done by Illumnia MiSeq .

treatment_protocol: In the 1st experiment, we fed Moyo-S and Moyo-R females with either non-infectious blood meal (sheep blood) or blood mixed with dengue virus serotype-2 strain Jam1409 (infectious blood meal) and profiled small RNA expression after 24 hours and 48 hours of feeding. In the 2nd experiment, we performed small RNA sequencing after blood feeding (3 hours) in females that were cleansed for resident bacteria vs control (fed without cleansing). For mosquito feeding, equal volumes of defibrillated sheep blood (Colorado Serum Company, CO, USA) mixed with either uninfected C6/36 cell suspension or DENV-2-infected C6/36 cell suspension were used. The freshly made blood meals were orally fed to 3-day old adult females of the two strains. Blood/cell suspension mixture was warmed to 48°C and aliquoted into glass artificial membrane feeders whose openings were covered in sausage casing. Female mosquitoes were allowed to feed for ~20 minutes. Blood fed females were separated and maintained at 28°C in ~80% RH and provided 5% sucrose solution. Groups of mosquitoes were removed at day1 (after 24 hr of feeding) and day2 (after 48 hr of feeding), and frozen at -80°C until extraction of RNA. Five blood fed mosquitoes from each strain and time point were pooled for RNA isolation. For 2nd experiment, the Moyo-S and Moyo-R pupae were separated into two cages prior to adult emergence. After adult emergence, the two cages were provided with different sugar solution treatments.  One cage was provided a control sterilized 8% sugar solution, while the other cage was provided an 8% sterilized sugar solution containing 2% penicillin-streptomycin and 0.8% gentamicin sulfate for bacterial cleansing. Both sugar treatments were provided ad libitum using saturated sterilized cotton balls.  Mosquitoes were allowed 8 days of sugar feeding to assure optimal clearance of midgut microbial populations among the antibiotic treated samples.  To verify microbial clearance, midguts were dissected from 20 random females for each treatment and homogenized in sterilized PBS57.  Thereafter, 1.5 µl aliquots of the midgut solutions were prepared and spread on blood agar plates under sterile conditions.  After 3 days, plates were examined for microbial growth.  Bacterial clearance was also determined using a culture-independent method utilizing 16s rRNA amplification.  Regions of the 16s rRNA gene from the microflora were amplified with universal primers 16S-27F (5’- CCAGAGTTTGATCMTGGCTCAG -3’) and 16S-343R (5’-ACTGCTGCCTCCCGTA -3’) (GenBank: KF672364.1).  The PCR was run at 95°C for 5 minutes followed by 30 cycles of 1 minute of 94°C, 1 minute at 60°C, and 2 minutes at 72°C, followed by an extension step of 72°C for 10 minutes. Antibiotic cleansed (AC) and control (no antibiotic cleansed, NAC) mosquitoes were identified based on 16s assay where control (untreated) midguts showed substantial bacterial amplification where treated females had minimal or no amplification in their midguts. The AC and NAC females were then starved for 24 hours and then separately provided artificial blood meal prepared using defibrinated sheep blood (Colorado Serum Company, Denver, CO, USA). Blood feeding was performed with the use of an artificial blood feeding apparatus and sausage casing as described above.

value: Moyo-S


title: S2R+ rep 1


title: Stage2_Rep1 [ATAC-Seq]


title: Skin PN 2


title: Stage1_Rep2 [ATAC-Seq]

value: Stage 1 (day 6)


title: NAC-MS-3H-1

description:
NAC-MS-3H-1_S17_L001_R1_001
small RNA
No antibiotic cleansing.3 hours post blood feeding, sample 1


title: KC NN 8

description: RNA extracted from monolayer KC cultures

source_name: Monolayer keratinocytes

value: Monolayer keratinocytes

value: normal skin from control individuals (NN)


title: Skin PN 1


title: Stage1_Rep1 [ATAC-Seq]


title: RN79

city: Guangzhou

first: Lan

last: Tang

state: Guangdong

address: 1838  Guangzhou North Ave,

department: School of Pharmaceutical Science

country: China

institute: Southern Medical University

description:
count_matrix.txt
log2fpkm_matrix_filtered.txt

data_processing:
Illumina Casava1.8 software used for base-calling.
Reads containing adapter, reads containing ploy-N and low quality reads were removed by perl scripts. Bowtie 2 v2.1.0 used for removing rRNA.
TopHat v2.0.13 used for alignment.
Cufflinks-2.2.1 used for assembly.
The counts and Fragments Per Kilobase of exon per Megabase of library size (FPKM) of genes were calculated and normalized by Cufflinks-2.2.1.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include count or log2FPKM values for each Sample …

source_name: Kidney

extract_protocol:
Kidney tissues were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: female

tag: blood type

value: A


title: MEF_Rep3 [ATAC-Seq]

value: Unsorted

tag: Stage

value: MEF


title: RN86

value: male

value: B


title: RN83

value: O


title: MEF_Rep2 [ATAC-Seq]

tag: strain

value: Mixed (C57BL/6 x 129)


title: NAC-MR-3H-3

description:
NAC-MR-3H-3_S26_L001_R1_001
small RNA
No antibiotic cleansing.3 hours post blood feeding, sample 3

value: Moyo-R


title: RN74


title: KN85


title: NAC-MR-3H-2

description:
NAC-MR-3H-2_S22_L001_R1_001
small RNA
No antibiotic cleansing.3 hours post blood feeding, sample 2


title: NAC-MR-3H-1

description:
NAC-MR-3H-1_S18_L001_R1_001
small RNA
No antibiotic cleansing.3 hours post blood feeding, sample 1


title: Stage1_Rep3 [ATAC-Seq]


title: NAC-MS-3H-2

description:
NAC-MS-3H-2_S21_L001_R1_001
small RNA
No antibiotic cleansing.3 hours post blood feeding, sample 2


title: KC NN 7


title: KN84


title: MEF_Rep1 [ATAC-Seq]


title: KN82


title: KC NN 5


title: RN78


title: Skin PP 1

value: lesional skin of psoriasis patients (PP)


title: AC-MS-3H-3

description:
AC-MS-3H-3_S27_L001_R1_001
small RNA
Antibiotic cleansing.3 hours post blood feeding, sample 3


title: KC PP 4


title: KN81


title: M-MDSC from Newborn mice, replicate 77

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description:
M-MDSC from Newborn mice, replicate 77
Gabrilovich_Neo_processed.txt
processed data column header: N.M.77

data_processing:
RNA-Seq data analyzing was done with rsem (ver. 1.2.3) and mm10 genome with ensemble transcriptome information
DESeq2 was used for differentail expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: Prosessed files contains the raw counts estimated by RSEM for each gene

source_name: M-MDSC cells

growth_protocol: After tissue processing and red blood cells lysis, cells were washed in MACS buffer (PBS+1%FBS and 2Mm EDTA), then suspended in MACS Buffer at 108 cells/ml and incubated with mouse FC block (1:200 dilution) 10 min at 4oC

extract_protocol:
PMN-MDSC and M-MDSC from spleens of neonates (7 day old) and adult mice (6-8 weeks old) were enriched by CD11b-beads and then sorted on FACSAria cell sorter (BD Bioscience) using  CD11b+Ly6CintLy6G+ phenotype or PMN-MDSCs and CD11b+Ly6ChighLy6G- for M-MDSCs
VAHTS Total RNA-Seq Library Preparation Kit (Vazyme Biotech Co., Ltd, China) was used for library preparation. Samples were a subject to a 50 bp single-end sequencing run on Illumina HiSeq 2500 following the manufacturer’s instructions.

treatment_protocol: For PMN-MDSC isolation, cells were labelled with biotinylated Ly6G antibody (Miltenyi) followed by Streptavidin Microbeads (Miltenyi) and separation on MACS Columns (Miltenyi) according to manufacturer’s instructions. 2 passages on columns were done to maximize cell purity.  For M-MDSC isolation, CD11b+/Ly6Chigh/Ly6G- cells were sorted on MoFlo®AStrios™ (Becmak Coulter, Brea, CA, USA). All antibodies were obtained from BD Pharmingen. Cell Aqua live dead (LifeTechnologies) was used to exclude dead cells

tag: batch

tag: celltype

value: M-MDSC

value: Newborn

tag: replicatenum

tag: experiment

value: mRNA


title: AC-MS-3H-1

description:
AC-MS-3H-1_S19_L001_R1_001
small RNA
Antibiotic cleansing.3 hours post blood feeding, sample 1

value: Moyo-S


title: AC-MS-3H-2

description:
AC-MS-3H-2_S23_L001_R1_001
small RNA
Antibiotic cleansing.3 hours post blood feeding, sample 2


title: M-MDSC from Newborn mice, replicate 3

description:
M-MDSC from Newborn mice, replicate 3
Gabrilovich_Neo_processed.txt
processed data column header: N.M.3

tag: age


title: KN80


title: AC-MR-3H-3

description:
AC-MR-3H-3_S28_L001_R1_001
small RNA
Antibiotic cleansing.3 hours post blood feeding, sample 3


title: AC-MR-3H-2

description:
AC-MR-3H-2_S24_L001_R1_001
small RNA
Antibiotic cleansing.3 hours post blood feeding, sample 2


title: KC PP 1


title: M-MDSC from Adult mice, replicate 28

description:
M-MDSC from Adult mice, replicate 28
Gabrilovich_Neo_processed.txt
processed data column header: A.M.28

value: Adult


title: KN76


title: KN77


title: M-MDSC from Newborn mice, replicate 1

description:
M-MDSC from Newborn mice, replicate 1
Gabrilovich_Neo_processed.txt
processed data column header: N.M.1


title: AC-MR-3H-1

description:
AC-MR-3H-1_S20_L001_R1_001
small RNA
Antibiotic cleansing.3 hours post blood feeding, sample 1


title: M-MDSC from Newborn mice, replicate 2

description:
M-MDSC from Newborn mice, replicate 2
Gabrilovich_Neo_processed.txt
processed data column header: N.M.2


title: KN75


title: KC PN 4

description: RNA extracted from monolayer KC cultures

value: Monolayer keratinocytes

value: uninvolved skin of psoriasis patients (PN)


title: M-MDSC from Newborn mice, replicate 79

description:
M-MDSC from Newborn mice, replicate 79
Gabrilovich_Neo_processed.txt
processed data column header: N.M.79


title: MS-D2

description:
MS-D2_S8_L001_R1_001
small RNA
Dengu virus mixed blood feeding, 2 days after feeding

source_name: Whole body


title: KC NN 6

value: normal skin from control individuals (NN)


title: MS-D1

description:
MS-D1_S4_L001_R1_001
small RNA
Dengu virus mixed blood feeding, 1 day after feeding


title: M-MDSC from Adult mice, replicate 1

description:
M-MDSC from Adult mice, replicate 1
Gabrilovich_Neo_processed.txt
processed data column header: A.M.1


title: KN71

description:
count_matrix.txt
log2fpkm_matrix_filtered.txt

value: female

value: A


title: KC PN 2


title: KC PN 3


title: KC PP 3


description:
PMN-MDSC from Newborn mice, replicate 39
Gabrilovich_Neo_processed.txt
processed data column header: N.G.39

source_name: PMN-MDSC cells

value: PMN-MDSC


title: KN69

value: male


title: KC PN 1


title: M-MDSC from Adult mice, replicate 3

description:
M-MDSC from Adult mice, replicate 3
Gabrilovich_Neo_processed.txt
processed data column header: A.M.3


title: KC PP 2


title: MS-N1

description:
MS-N1_S3_L001_R1_001
small RNA
Naive blood feeding, 1day after feeding


description:
PMN-MDSC from Newborn mice, replicate 38
Gabrilovich_Neo_processed.txt
processed data column header: N.G.38


title: D shKras.1442 cl1 LT DOX Rep2

city: Cambridge

first: A

last: Bhutkar

address: 77 Massachusetts Avenue

institute: MIT

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_203_21B_011712_DOX

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using rsem v1.2.12 and bowtie v1.0.1 with default options.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file includes estimated read counts (from rsem) per gene for each sample

source_name: Murine pancreatic ductal adenocarcinoma-derived cell line

growth_protocol: Cell lines were cultured in DMEM supplemented with 10% Fetal Bovine Serum (FBS).

extract_protocol:
Total RNA was isolated using TRIzol from Life Technologies.
RNA libraries were prepared for sequencing with the Illumina TruSeq kit according to the manufacturer's instructions.
RNA-seq (single end)

treatment_protocol: A, B, and D parental cell lines were transduced with lentiviral vectors permitting expression or rtTA and a doxycycline-inducible mir30-based shRNA targeting Kras or firefly luciferase

tag: genotype


title: KN66


title: D shKras.1442 cl1 LT DOX Rep1

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_203_21A_011712_DOX


description:
PMN-MDSC from Newborn mice, replicate 37
Gabrilovich_Neo_processed.txt
processed data column header: N.G.37


title: MR-D2

description:
MR-D2_S6_L001_R1_001
small RNA
Dengu virus mixed blood feeding, 2 days after feeding


title: KN68


title: MR-D1

description:
MR-D1_S2_L001_R1_001
small RNA
Dengu virus mixed blood feeding, 1 day after feeding


title: D shKras.1442 cl1 No DOX Rep4

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_203_0B_012312_Untr


title: PMN-MDSC from Newborn mice, replicate 2

description:
PMN-MDSC from Newborn mice, replicate 2
Gabrilovich_Neo_processed.txt
processed data column header: N.G.2


title: PMN-MDSC from Newborn mice, replicate 3

description:
PMN-MDSC from Newborn mice, replicate 3
Gabrilovich_Neo_processed.txt
processed data column header: N.G.3


title: MR-N2

description:
MR-N2_S5_L001_R1_001
small RNA
Naive blood feeding, 2 days after feeding


title: KN63

value: B


title: PMN-MDSC from Adult mice, replicate 34

description:
PMN-MDSC from Adult mice, replicate 34
Gabrilovich_Neo_processed.txt
processed data column header: A.G.34


title: MR-N1

description:
MR-N1_S1_L001_R1_001
small RNA
Naive blood feeding, 1day after feeding


title: KN73


title: KN62

value: O


title: D shKras.1442 cl1 No DOX Rep3

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_203_0B_011712_Untr


title: MS-L4-D2

description:
MS-L4-D2_S15_L001_R1_001
small RNA
Larval instar 4.day2


title: MS-N2

description:
MS-N2_S7_L001_R1_001
small RNA
Naive blood feeding, 2 days after feeding


title: D shKras.923 cl1 LT DOX Rep4

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_175_21B_011712_DOX


title: MS-Ad-3DPE

description:
MS-Ad-3DPE_S16_L001_R1_001
small RNA
Adults, 3days post emergence


title: D shKras.1442 cl1 No DOX Rep2

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_203_0A_012312_Untr


title: D shKras.1442 cl1 No DOX Rep1

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_203_0A_011712_Untr


title: KN61

description:
count_matrix.txt
log2fpkm_matrix_filtered.txt


title: KN57


title: PMN-MDSC from Adult mice, replicate 32

description:
PMN-MDSC from Adult mice, replicate 32
Gabrilovich_Neo_processed.txt
processed data column header: A.G.32


title: MS-L3

description:
MS-L3_S13_L001_R1_001
small RNA
Larval instar 3


title: KN58


title: PMN-MDSC from Adult mice, replicate 2

description:
PMN-MDSC from Adult mice, replicate 2
Gabrilovich_Neo_processed.txt
processed data column header: A.G.2


title: D shKras.923 cl1 LT DOX Rep3

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_175_21B_010512_DOX


title: KN60


title: D shKras.923 cl1 LT DOX Rep2

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_175_21A_011712_DOX


title: PMN-MDSC from Adult mice, replicate 3

description:
PMN-MDSC from Adult mice, replicate 3
Gabrilovich_Neo_processed.txt
processed data column header: A.G.3


title: KN56


title: PMN-MDSC from Adult mice, replicate 1

description:
PMN-MDSC from Adult mice, replicate 1
Gabrilovich_Neo_processed.txt
processed data column header: A.G.1


title: D shKras.923 cl1 No DOX Rep4

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_175_0B_011712_Untr


title: PMN-MDSC from Adult mice, replicate 33

description:
PMN-MDSC from Adult mice, replicate 33
Gabrilovich_Neo_processed.txt
processed data column header: A.G.33


title: MS-L2

description:
MS-L2_S12_L001_R1_001
small RNA
Larval instar 2


title: KN65


title: D shKras.923 cl1 LT DOX Rep1

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_175_21A_010512_DOX


title: MR-Ad-3DPE

description:
MR-Ad-3DPE_S11_L001_R1_001
small RNA
Adults, 3days post emergence


title: LSPCT rep3

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

data_processing:
The sequencing quality of RNA-Seq libraries was assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
RNA-Seq libraries were mapped to mouse genome using Tophat (v2.1.0, Trapnell et al., Bioinformatics). UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
Mapped reads were counted using featureCounts.
Reads were normalized using DESeq2 and counts using counts per million (CPM) were outputed to txt files
Genome_build: mm9
Supplementary_files_format_and_content: Text file that has counts per million (CPM)

source_name: Tamoxifen treated Leukemia stem/progenitor cells

extract_protocol:
Leukemia stem/progenitor cells were sort-purified and total RNA was extracted using standard Qiagen RNease columns
RNA libraries were prepared for sequencing using stardard Illumina protocol

tag: cell type

value: leukemia stem cell


title: KN46


title: MS-L4-D1

description:
MS-L4-D1_S14_L001_R1_001
small RNA
Larval instar 4.day1


title: KN45


title: D shKras.923 cl1 No DOX Rep3

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_175_0B_010512_Untr


title: MR-L4-D1

description:
MR-L4-D1_S9_L001_R1_001
small RNA
Larval instar 4.day1

value: Moyo-R


title: LSPCT rep2


title: MR-L4-D2

description:
MR-L4-D2_S10_L001_R1_001
small RNA
Larval instar 4.day2


title: MR-L3

description:
MR-L3_S8_L001_R1_001
small RNA
Larval instar 3


title: D shLuc.1309 cl1 LT DOX Rep4

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_160_21B_012312_shLucDOX


title: D shKras.923 cl1 No DOX Rep1

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_175_0A_010512_Untr


title: D shKras.923 cl1 No DOX Rep2

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_175_0A_011712_Untr


title: KN44

description:
count_matrix.txt
log2fpkm_matrix_filtered.txt


title: KN36


title: MR-L2

description:
MR-L2_S7_L001_R1_001
small RNA
Larval instar 2


title: D shLuc.1309 cl1 LT DOX Rep3

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_160_21B_011712_shLucDOX


title: Trin-male

description:
Trin-male_S10_L001_R1_001
small RNA
Male

value: Trinidad


title: Trin-female

description:
Trin-female_S5_L001_R1_001
small RNA
Female

value: Trinidaa


title: LSPC rep1

source_name: Leukemia stem/progenitor cells


title: KN37


title: KN34


title: Rock-male

description:
Rock-male_S9_L001_R1_001
small RNA
Male

value: Rockefeller


title: D shLuc.1309 cl1 LT DOX Rep2

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_160_21A_012312_shLucDOX


title: siSirt6+TNFa

city: Chicago

first: Fangyi

last: Liu

state: IL

address: 2430 N Halsted St

department: Center for Intestinal and Liver inflammation Research

institute: Stanley Manne Children's Research Institute

data_processing:
Illumina Casava software used for basecalling.
Raw reads were cleaned by removing adaptor sequences, empty reads, and low-quality sequences. The reads that passed filtering were aligned to reference sequences of the mouse transcriptome (Ensembl release 75) using the Bowtie version 1.0.1 alignment tool (bowtie –v –all –best --strata).
Read counts were normalized using edgeR and RPKM values were calculated as the number of counted reads per 1000 mapped and counted bases per geometric mean of normalized read counts per million.
Genome_build: Mouse transcriptome (Ensembl release 75)
Supplementary_files_format_and_content: Excel file containing original reads and RPKM values of each sample

source_name: YAMC cells

growth_protocol: The YAMC cells were maintained in RPMI 1640 medium containing 5% heat-inactivated fetal bovine serum, 5 U/ml mouse interferon-γ, 100 unit/ml penicillin, 100 μg/ml streptomycin 5 μg/ml insulin, 5 μg/ml transferrin, and 5 ng/ml selenous acid at 33 °C as permissive conditions in a water-saturated atmosphere incubator with 5% CO2.

extract_protocol:
Total RNAs were extracted from YAMC cells using RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.  RNA integrity and quantity were assessed using Agilent 2100 Bioanalyzer (Agilent Technologies), RIN≥8. 1 ug of total RNA for the construction of sequencing libraries.
PolyA-enriched RNAs were purified from total RNAs using the paramagnetic oligo-dT beads, fragmented, and used for constructing cDNA libraries using NEBNext Ultra RNA Library Prep Kit for Illuminia (NEB).  Libraries were amplified followed by removing primers prior to sequencing.

treatment_protocol: YAMC cells were seeded onto 6-well plates at a density of 1.5 x 105 cells per well and cultured with complete medium at 33°C overnight.  On the second day, the cells were transfected with nucleic acids of siRNAs (50 nM/well) by using lipofectamine 2000. After 24 h, cells were cultured at 37°C for additional 24 h with interferon-γ-free culture medium as nonpermissive conditions. Forty-eight hours after transfections, the cells were cultured with interferon-γ-free medium containing TNF(100 ng/mL) and interferon-γ-free medium alone respectively for additional 24 h.

value: Young Adult Mouse Colonocytes

tag: passages

tag: treatment

value: Post transfection 48h +TNFa 24h


title: siSirt6

value: Post transfection 48h +Medium 24h


title: D shLuc.1309 cl1 LT DOX Rep1

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_160_21A_011712_shLucDOX


title: LSPC rep3


title: Rock-female

description:
Rock-female_S4_L001_R1_001
small RNA
Female


title: D shLuc.1309 cl1 No DOX Rep4

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_160_0B_012312_shLucUntr


title: MoyoS-male

description:
MoyoS-male_S8_L001_R1_001
small RNA
Male

value: Moyo-S


title: KN21


title: D shLuc.1309 cl1 No DOX Rep3

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_160_0B_011712_shLucUntr


title: D shLuc.1309 cl1 No DOX Rep2

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_160_0A_012312_shLucUntr


title: LSPC rep2


title: KN31


title: MoyoS-female

description:
MoyoS-female_S3_L001_R1_001
small RNA
Female


title: FGOo-BR2

city: Villefranche-sur-mer

first: Evelyn

last: Houliston

address: chemin du Lazaret

country: France

institute: Sorbonne Universités, UPMC Univ. Paris 06, CNRS

data_processing:
Mapping: bowtie2 (version 2,2,0) -a
Counting mapped reads: Perl manual script
Normalization (contig length and number of reads): R script

organism: Clytia hemisphaerica

source_name: Clytia Fully Grown Oocytes Biological Replicate 2

extract_protocol:
Ectoderm, endoderm, growing oocytes and fully grown oocytes samples were manually dissected from about 150 Clytia female gonads. Samples were kept in lysis buffer from RNAqueous micro kit (Ambion Life technologies, CA), frozen in liquid nitrogen and kept at -80ºC until the extraction of total RNA from each sample. For this purpose, we randomly pooled samples taken from different days under the same conditions for each biological replicate of each gonad sample.
RNA libraries were prepared for sequencing by the NGS company.

value: Z4B colony-derived jellyfish

value: 4-5 week old medusae

value: Fully Grown Oocytes


title: KN33

value: female


title: KN43


title: B shKras.1442 cl1 LT DOX

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
B_180_21C_043012_DOX


title: B shKras.1442 cl1 No DOX

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
B_180_0C_043012_Untr


title: LVP-female

description:
LVP-female_S1_L001_R1_001
small RNA
Female

value: Liverpool


title: MoyoR-male

description:
MoyoR-male_S7_L001_R1_001
small RNA
Male


title: GrOo-BR1

source_name: Clytia Growing Oocytes Biological Replicate 1

value: Growing Oocytes


title: B shKras.1442 cl1 LT DOX Rep4

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
B_162_21B_011712_DOX


title: B shKras.1442 cl1 LT DOX Rep3

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
B_162_21B_010512_DOX


title: D shLuc.1309 cl1 No DOX Rep1

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
D_160_0A_011712_shLucUntr


title: GEC-BR1

source_name: Clytia Gonad Ectoderm Biological Replicate 1

value: Gonad Ectoderm


title: siControl

value: Post transfection 48h + Medium 24h


title: GrOo-BR2

source_name: Clytia Growing Oocytes Biological Replicate 2


title: HEK293_siFKBP25_KD

city: Toronto

first: Mark

middle: D

last: Minden

state: Ontario

address: 610 University Avenue

department: Medical Oncology & Hematology

institute: Princess Margaret Cancer Centre

description: HEK 293 cell line transfected with FKBP25 targeting siRNA.

data_processing:
Illumina RTA 1.10.36.0 used for base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Processed reads were mapped to UCSC hg19 using  hisat2-2.0.5 (Kim et al. 2015) with the parameters -p4 –dta-cufflinks.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the GFOLD count algorithm V1.1.4 (Feng et al. 2012) for annotated protein coding genes present in UCSC hg19.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample; bigwig files generated from BAM files using DeepTools bamCoverage tool (Ramirez et al. 2016) with the parameters -p 4 -bs 10  --normalizeUsingRPKM .

source_name: HEK 293

growth_protocol: Cells were cultured in DMEM containing 10% (v/v) FBS (ThermoFisher) and antibiotics (10 units/ml penicillin and 10 µg/ml streptomycin, ThermoFisher) at 37℃ and 5% C02.

extract_protocol:
Transfected cells were harvested by trypsinization, pelleted by centrifugation, and flash frozen in liquid nitrogen. mRNA was purified using the µMACs mRNA isolation kit (Miltenyl Biotec, Cat. No . 130-075-102) and analyzed on an Agilent 2100 Bioanalyzer using Agilent 6000 RNA Nano Kit (Agilent Technologies, Cat. No. 5067-1511). cDNA was generated using a Superscript Double-Stranded cDNA Synthesis kit (ThermoFisher, Cat. No. 11917-010) followed by preparation of 75bp paired-end libraries using the Paired-End Sample Prep Kit (Illumina, Version 1.1).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Human embryonic kidney cells (HEK 293) transfected with 10 nM siRNA targeting either FKBP25 or GFP (negative control) using Lipofectamine 2000 following the manufacturer's instructions and incubated for 72 h.

value: embryonic kidney

value: fetus

tag: morphology

value: epithelial


title: B shKras.1442 cl1 LT DOX Rep2

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
B_162_21A_011712_DOX


title: FGOo-BR1

source_name: Clytia Fully Grown Oocytes Biological Replicate 1


title: B shKras.1442 cl1 No DOX Rep4

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
B_162_0B_011712_Untr


title: IPTG2-4

description:
processed data file:
2016_07_11_conditions_normalized_counts_GEO.xlsx

data_processing:
We used flexbar to trim the reads of excess sequence and ustacks to consolidate reads that originated from a particular nucleotide sequence.
We translated the nucleotide sequences for each nucleotide sequence into an amino acid sequence with a custom python script using the Biopython library, and then summed the total reads for each unique peptide.
A file containing each peptide sequence and the total number of reads in each library was then used as input for the DESeq2 R/Bioconductor package. We used a standard DESeq2 workflow, which includes read count normalization, peptide dispersion estimates, and Wald tests for significance of differential abundance.  For each peptide, we compared the total abundance (normalized reads) in the induced (IPTG) libraries to the abundance in the input libraries, resulting in a log2 FoldChange (log2FC) and p-value for each peptide.  P-values were adjusted (padj) for multiple testing using Benjamini-Hochberg correction as part of the standard DESeq2 workflow detailed in the package manual  (available here: https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.pdf). Generally, peptides that were selected for further experimental validation had a log2FC < -1 and padj < .05.
Supplementary_files_format_and_content: xlsx file includes trimmed peptide sequences, input and output normalized read counts for each sample, log2FC MLEunshrunken, log2FC shrunken, adjusted p-value, peptide charge, peptide hydrophobicity, peptide pI value, molecular weight, and nucleotide sequence.

tag: induced with

value: 0.1mM IPTG for 4hrs

tag: molecule subtype

value: plasmid DNA


title: GEN-BR2

source_name: Clytia Gonad Endoderm Biological Replicate 2

tag: tissue

value: Gonad Endoderm


title: B shKras.1442 cl1 No DOX Rep3

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
B_162_0B_010512_Untr


title: HEK293_siGFP_control

description: HEK 293 cell line transfected with GFP targeting siRNA.


title: IPTG2-3

value: 0.1mM IPTG for 3hrs


title: LVP-male

description:
LVP-male_S6_L001_R1_001
small RNA
Male


title: GEC-BR2

source_name: Clytia Gonad Ectoderm Biological Replicate 2


title: GEN-BR1

source_name: Clytia Gonad Endoderm Biological Replicate 1


title: B shKras.1442 cl1 No DOX Rep2

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
B_162_0A_011712_Untr


title: MoyoR-female

description:
MoyoR-female_S2_L001_R1_001
small RNA
Female

value: Moyo-R


title: B shKras.1442 cl1 No DOX Rep1

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
B_162_0A_010512_Untr


title: T47D-sh-Hectd1-2 (n=1)

city: montreal

first: Stephanie

last: Duhamel

state: Quebec

address: 110 avenue des pins ouest

institute: IRCM

description:
shc5a
SD_shC5A

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to the GRCh37 genome with STAR v2.5.0
Raw alignment counts were calculated with featureCounts 1.5.0
Differential expression measurements were performed with Cufflinks 2.2.1
Genome_build: GRCh37
Supplementary_files_format_and_content: Diff files with differential expression

source_name: cancer cell line

extract_protocol:
Total RNAs form confluent T47D cell lines infected with shNT, HectD1-shRNAs (#1 and #2) or transfected with HA-ACF7 for 72 hrs, were extracted using the RNeasy kit (Qiagen). RNA integrity was assessed on a Bioanalyzer RNA pico chip.
The RNA-seq libraries were generated with mRNA enrich Kapa stranded kit and sequencing PE50 was performed on a HiSeq 2500.
Reads were aligned to the GRCh37 genome with Star v2.5.0, and the raw alignment counts were calculated with featureCounts v1.5.0 .

tag: cell line

value: breast cancer

value: HectD1 depletion by shRNA


title: T47D-sh-Hectd1-1 (n=1)

description:
shc4a
SD_shC4A


title: T47D-sh-Hectd1-1 (n=2)

description:
shc4b
SD_shC4B


title: T47D-sh-NT (n=1)

description:
shntb
SD_shNTB

value: Control shRNA


title: IPTG1-2

value: 0.1mM IPTG for 2hrs


title: T47D-GFP-ACF7 (n=2)

description:
acf7c
SD_ACF7C

value: ACF7 overexpression


title: A shKras.1442 cl2 LT DOX

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
A_191_21C_043012_DOX


title: IPTG2-2


title: RNA-Seq EV-2DM

status: Public on Jan 02 2018

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

data_processing:
GERALD within CASAVA version 1.7.0
MACS 1.3.7 peak calling  for Myod1
Cuffllinks expression & cuffdiff fold change analysis
Genome_build: mm9
Supplementary_files_format_and_content: Illumina ELAND format

source_name: Empty vector Myotubes

growth_protocol: Satellite cells were isolated from 4-6 weeks old mice by fluorescent activated cell sorting and cultured under growth condition as described previously (Kuang, S., et al., Asymmetric self-renewal and commitment of satellite stem cells in muscle. Cell, 2007. 129(5): p. 999-1010.) To induce differentiation, fully confluent DNA/protein complexes were cross-linked by 1% formaldehyde in PBS as described previously.primary myoblasts were placed in differentiation media (DMEM supplemented with 5% horse serum) for 48 hours.

extract_protocol: Chromatin immnunoprecipitation sequencing (ChIP-Seq) was performed on 20 mg cell lysate using the following antibodies: anti H3K4me3, Cat # 8580 Abcam; anti H3K27me3, Cat # 07-449, Millipore; anti H3K4me1, Cat # 5326, Cell Signaling; anti histone H3, Cat # 05-499, Millipore. ChIP library was constructed as described previously (Soleimani, V.D., et al., Transcriptional dominance of Pax7 in adult myogenesis is due to high-affinity recognition of homeodomain motifs. Dev Cell, 2012. 22(6): p. 1208-20.). Sequencing was done on Illumina GAIIX Genome Analyzer in duplicates. ChIP-Seq of Sox2 was performed by Chromatin Tandem Affinity Purification Sequencing as described previously (Soleimani, V.D., et al., Transcriptional dominance of Pax7 in adult myogenesis is due to high-affinity recognition of homeodomain motifs. Dev Cell, 2012. 22(6): p. 1208-20. Soleimani, V.D., et al., Chromatin tandem affinity purification sequencing. Nat Protoc, 2013. 8(8): p. 1525-34) . Briefly, to produce the TAP-tagged fusion construct mouse Sox2 gene was fused with a C-terminal TAP tag (6XHIS-TEV-3FLAG) and inserted into Sox2 locus using homologous recombination in G4 ES cell line (G4-129S6B6F1, Samuel Lunenfeld Research Institute, Mount Sinai Hospital). ES cells harboring the recombinant knocked-in allele of Sox2 was grown on Mitomycin C treated MEFs in the presence of LIF.  RNA-Seq: Total RNA was extracted from primary myoblasts or differentiated myotubes over expressing and empty vector retroviral construct (48 hours differentiation) as described previously (Soleimani, V.D., et al., Snail regulates MyoD binding-site occupancy to direct enhancer switching and differentiation-specific transcription in myogenesis. Mol Cell, 2012. 47(3): p. 457-68.).

tag: sample type

value: Myotubes


title: Histone H3 2DM

source_name: Myotubes


title: MyoD-2DM

description: from GSM611279


title: T47D-sh-Hectd1-2 (n=2)

description:
shc5b
SD_shC5B


title: A shKras.1442 cl2 No DOX

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
A_191_0C_043012_Untr


title: A shKras.1442 cl1 LT DOX

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
A_190_21C_043012_DOX


title: LSPCT rep1

value: leukemia stem cell


title: monocytes, from colon tumor, donor V

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

data_processing:
Paired reads mapped using STAR version 2.3
Mapped reads were summaried to gene level using featureCounts version 1.5
filtered out genes with per sample average number of reads less than 10 in all sample groups
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Bioconductor edgeR package with normalized library sizes option and log2 transformation
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text file includes log2 RPKM values for all samples

source_name: Colon tumor

extract_protocol:
Total RNA was extracted using Arcturus PicoPure RNA Isolation Kit (Thermo Fisher Scientific) according to manufacturer's protocol. All mouse RNAs were analyzed on Agilent Bionanlyser for quality assessment; RNA Integrity Number (RIN) range was 6.5-10 and a median of 9.2.
cDNA libraries were prepared starting with 2ng of total RNA and 1ul of a 1:50,000 dilution of ERCC RNA Spike in Controls (Ambion) using SMARTSeq v2 protocol (Picelli et al., 2014) except for the following modifications: 1. Use of 20µM TSO, 2. Use of 250pg of cDNA with 1/5 reaction of Illumina Nextera XT kit. The length distribution of the cDNA libraries was monitored using DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip. All 8 samples were subjected to an indexed PE sequencing run of 2x51 cycles on an Illumina HiSeq 2500 Rapid mode (17 samples/lane).

treatment_protocol: LP myeloid cells were isolated as described in detail in (Muzaki et al., 2016). Briefly, after CO2 euthanasia of the mice, the colon was opened and rinsed with PBS to remove the luminal contents. To remove the epithelium, the colon was incubated in 25 ml PBS with 1.3 mM EDTA under shaking conditions at 37ºC for 1 h. After incubation, it was washed in IMDM 2% to remove the EDTA solution, and minced. The colon pieces were digested in IMDM 2% and 1 mg/ml Collagenase D (Roche, Switzerland) under shaking conditions at 37ºC for 1 ½ hour. Digested pieces were gently mashed through a cell strainer. The leukocyte population was enriched by a 70/40% Percoll gradient (GE Healthcare Life Science, Chicago, IL, USA). Low-density cells at the interface were harvested and further processed for flow cytometry stainings.

value: APC/Min

tag: tissue origin

value: Colon tumor

value: monocytes

tag: sample group

tag: donorid

value: V


title: monocytes, from colon tumor, donor II

tag: strain

value: II


title: neutrophils, from colon tumor, donor I

value: neutrophils

value: I


title: Input2-0

extract_protocol:
Plasmid DNA was isolated using the Zyppy Miniprep Kit in accordance with the prescribed protocol provided with the kit.
Custom primers were used to ligate adaptors to regions flanking the peptide nucleotide sequence. Products were gel-extracted and cleaned using the Zymoclean Gel DNA Recovery Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: none (input)

value: plasmid DNA


title: T47D-GFP-ACF7 (n=1)

description:
acf7a
SD_ACF7A


title: IPTG1-4

value: 0.1mM IPTG for 4hrs


title: VirTIS05

city: San Francisco

first: Charlie

last: Kim

state: CA

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

data_processing:
Bases were called and reads were demultiplexed with Illumina CASAVA 1.8.2 and read quality assessed using FastQC
Reads were aligned to the transcriptome using STAR version 2.4.2a with default parameters as called by RSEM version 1.2.22
Gene expression per sample was modeled with RSEM version 1.2.22
Genome_build: Release GRCh38 of the human genome
Supplementary_files_format_and_content: RSEM output files with counts, TPM, and FPKM values

source_name: whole biopsy_viremic untreated

extract_protocol:
RNA Isolated using Qiagen AllPrep Kit
RNA libraries were prepared for sequencing following Illumina protocols.  cDNA libraries were diluted to 0.15ng/ul, fragmented with the Nextera XT DNA kit (Illumina PN FC-131-1024), multiplexed, and sequenced on a Hi-Seq4000

tag: subject status

value: viremic untreated

tag: tissue type

value: Intestinal Rectosigmoid Biopsies

value: Mixed

tag: sample storage

value: RNALater Immediately Upon Biopsy


title: VirTIS06


title: macrophages F4/80 high MHCII low, rom colon tumor, donor V

value: macrophages F4/80 high MHCII low


title: A shKras.1442 cl1 No DOX

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
A_190_0C_043012_Untr

source_name: Murine pancreatic ductal adenocarcinoma-derived cell line

tag: genotype


title: Input1-0

city: Austin

first: Bryan

last: Davies

address: 2506 Speedway

institute: University of Texas at Austin


title: macrophages F4/80 high MHCII high, from colon tumor , donor VII

tag: cell type

value: macrophages F4/80 high MHCII high

value: VII


title: H3K27me3-2DM

value: Myotubes


title: H3K4me1-2DM


title: VirTIS02


title: H3K4me3-2DM


title: VirTIS01


title: neutrophils, from colon tumor, donor V

value: APC/Min

value: Colon tumor


title: neutrophils, from healthy lamina propria, donor V

source_name: Healthy lamina propria

value: lamina propria

value: V


title: neutrophils, from healthy lamina propria, donor IV

value: neutrophils

value: IV


title: VirIEC04

source_name: epithelial isolates_viremic untreated

extract_protocol:
Phenol:Chloroform Extraction, Cleanup with Zymo IC Column
RNA libraries were prepared for sequencing following Illumina protocols.  cDNA libraries were diluted to 0.15ng/ul, fragmented with the Nextera XT DNA kit (Illumina PN FC-131-1024), multiplexed, and sequenced on a Hi-Seq4000

value: Intestinal Epithelial Cell

value: EDTA-Isolated, Stored in Trizol


title: VirIEC05


title: neutrophils, from colon tumor, donor II

value: II


title: monocytes, from healthy lamina propria, donor V

value: monocytes


title: monocytes, from healthy lamina propria, donor IV


title: monocytes, from colon tumor, donor I

value: I


title: siControl+TNFa

source_name: YAMC cells

value: Young Adult Mouse Colonocytes

tag: passages

value: Post transfection 48h +TNFa 24h


title: UniTIS04

source_name: whole biopsy_uninfected control

value: uninfected control

value: Intestinal Rectosigmoid Biopsies

value: Mixed

value: RNALater Immediately Upon Biopsy


title: UniTIS05


title: macrophages F4/80 high MHCII low, from healthy lamina propria, donor II

value: macrophages F4/80 high MHCII low


title: VirIEC03

value: viremic untreated


title: macrophages F4/80 high MHCII low, from colon tumor, donor I

value: APC/Min

value: Colon tumor


title: VirTIS04


title: VirTIS03


title: macrophages F4/80 high MHCII high, from colon tumor , donor V

value: macrophages F4/80 high MHCII high

value: V


title: macrophages F4/80 high MHCII high, from colon tumor, donor I


title: VirIEC06

value: Intestinal Epithelial Cell


title: neutrophils, from healthy lamina propria, donor III

value: lamina propria

value: neutrophils

value: III


title: T47D-sh-NT (n=2)

description: shntc

value: breast cancer

value: Control shRNA


title: UniIEC08

source_name: epithelial isolates_uninfected control

value: EDTA-Isolated, Stored in Trizol


title: VirIEC02


title: VirIEC01


title: monocytes, from healthy lamina propria, donor III

value: monocytes


title: macrophages F4/80 high MHCII low, from healthy lamina propria, donor III


title: UniIEC04

value: uninfected control

value: Intestinal Rectosigmoid Biopsies


title: UniTIS03

value: Mixed

value: RNALater Immediately Upon Biopsy


title: UniTIS02


title: macrophages F4/80 high MHCII low, from healthy lamina propria, donor IV

value: macrophages F4/80 high MHCII low

value: IV


title: UniIEC01


title: UniIEC07


title: UniIEC09


title: ArtTIS05

source_name: whole biopsy_HIV-infected ART-treated patient

value: HIV-infected ART-treated patient


title: macrophages F4/80 high MHCII high, from healthy lamina propria, donor V

value: macrophages F4/80 high MHCII high


title: macrophages F4/80 high MHCII high, from healthy lamina propria, donor IV


title: macrophages F4/80 high MHCII high, from healthy lamina propria, donor III


title: UniTIS01


title: IPTG1-3

value: 0.1mM IPTG for 3hrs

value: plasmid DNA


title: UniIEC06

value: Intestinal Epithelial Cell


title: ArtIEC18

source_name: epithelial isolates_HIV-infected ART-treated patient


title: UniIEC03


title: ArtIEC15


title: UniIEC05


title: ArtTIS02


title: ArtIEC11


title: ArtTIS04


title: ArtIEC10


title: ArtTIS03


title: ArtIEC07


title: ArtIEC06


title: B shKras.1442 cl1 LT DOX Rep1

description:
Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor
B_162_21A_010512_DOX


title: ArtIEC17


title: ArtIEC03


title: ArtIEC02


title: ArtIEC14


title: ArtIEC13


title: ArtIEC12


title: UniIEC02


title: ArtIEC08


title: ArtTIS01


title: R436H2_GW4064_2

first: Aimee

last: Deaton

address: 360 Binney St

institute: Amgen Inc

description:
R436H.untrt.vs.WT.untrt.tsv
R436H.untrt.vs.WT.untrt.filter.tsv
R436H.agonist.vs.WT.agonist.tsv
R436H.agonist.vs.WT.agonist.filter.tsv

data_processing:
Adapter sequence and poor quality bases (N or <=Q7) were clipped from the ends of reads using ea-utils. https://github.com/ExpressionAnalysis/ea-utils
Reads were mapped to the human genome (hg38) using tophat and bowtie 2
Differential expression analysis was performed using DESeq2 (Love et al., 2014) using six replicates per condition. The gene model used for DESeq2 was Ensembl GRCh38.
We excluded genes that were not expressed in any condition (FPKM < 1 in all samples) or did not have an Entrez Gene identifier from further analysis; 11,720 genes remained.
We defined differentially expressed genes as those with DESeq2’s adjusted p-value (Benjamini-Hochberg correction) < 10-3 and a log2-fold change > 1
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files for each comparison containing log2-fold change and p-values for each gene calculated using DESeq2. Unfiltered sets containing all genes in Enseml GRCh38 and gene sets filtered for FPKM and NCBI Entrez gene IDs are given.

source_name: iPSC-derived hepatocytes

growth_protocol: iPSCs were grown on matrigel coated plates and maintained in Essential 8 Flex Medium (Invitrogen). Passaging was carried out using Versene (Invitrogen). One day prior to the start of differentiation iPSCs were harvested using Accutase and plated at a density of 5-7.5x104 per cm2 on matrigel-coated plates in mTeSR1 medium (Stem cell technology) and 3μM rock inhibitor (Y-27632). Differentiation to definitive endoderm was performed using STEMdiff Definitive Endoderm Kit (Stem Cell Technologies) according to manufacturer’s instructions [days 1-4]. Hepatic endoderm differentiation was achieved by treating cells with 10ng/ml bFGF (Invitrogen) and 20ng/ml BMP4 (R&D systems) in RPMI-1640 medium (Sigma Aldrich) containing B27 minus vitamin A (Invitrogen 12587010) [days 5-9]. Cells were then differentiated into hepatoblasts in RPMI medium containing B27 (Invitrogen 17504044), 20ng/ml HGF (R&D Systems), 2.5µM Blebbistatin (Invitrogen), 50ng/ml BMP4, 3µM CHIR99021 (Biovision), 60mg/ml FGF10 (R&D Systems), 10ng/ml bFGF and 25µg/ml Gentamicin (Invitrogen) [days 10-14]. Hepatoblasts were treated with RPMI containing B27 minus vitamin A, 20ng/ml Oncostatin M (R&D systems), 0.1µM Dexamethasone (Sigma Aldrich), iCell Hepatocytes 2.0 medium supplement (Cellular Dynamics International) and 25µg/ml Gentamicin for 5 days to achieve differentiation to hepatocyte-like cells [days 15-19]. From day 20 of differentiation onwards cells were maintained in RPMI containing B27 minus vitamin A, 0.1µM Dexamethasone, iCell Hepatocytes 2.0 medium supplement and 25µg/ml Gentamicin . Medium was changed daily throughout the differentiation process.

extract_protocol:
RNA isolation and DNase treatment was performed using the Qiagen RNeasy Mini Kit according to manufacturer’s instructions.
IlluminaTruSeq Stranded mRNA method

treatment_protocol: 5uM GW4064 or DMSO for 24 hours as indicated

value: iPSC-derived hepatocytes

tag: parental cell line

value: Human Episomal iPSC Line (Thermofisher, A18945)

value: NR1H4 homozygous R436H

tag: treatment


title: R436H2_DMSO_2

description:
R436H.untrt.vs.WT.untrt.tsv
R436H.untrt.vs.WT.untrt.filter.tsv
R436H.untrt.vs.WT.untrt.tsv
R436H.untrt.vs.WT.untrt.filter.tsv

value: DMSO


title: ArtIEC04

value: EDTA-Isolated, Stored in Trizol


title: R436H1_GW4064_1


title: human nasal epithelial cells (+SLR14) rep1

city: New Haven

first: Ellen

middle: Flescher

last: Foxman

state: CT

address: 330 Cedar St.

department: Laboratory Medicine

institute: Yale University

description:
Sample 4
mRNA (Total RNA after polyA selection)

data_processing:
The raw reads of RNA-seq experiments were trimmed off sequencing adaptors and low quality reads by btrim
The trimmed reads were mapped to human genome (GRCh37) by tophat2
The counts of reads for each gene were based on Ensembl annotation (release 70)
Differential expression analysis was done by DEseq2[17], which calculated the adjusted p-values.
Genome_build: GRCh37
Supplementary_files_format_and_content: .txt file showing FPKM reads

source_name: human nasal epithelial cells (+SLR14)

growth_protocol: Primary cells were grown in submerged culture on collagen coated 12 well plates using Bronchial Epithelial Growth Medium (Lonza)

extract_protocol:
RNEasy kit by QIAGEN
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected with SLR14 for 1 hr, then incubated at 37C for seven additional hrs prior to RNA isolation.

value: primary nasal epithelial cells

value: 8hr post-stimulation with RIG-I ligand SLR14


title: ArtIEC19

value: Intestinal Rectosigmoid Biopsies


title: ArtIEC05


title: R436H1_DMSO_2


title: human nasal epithelial cells (unstimulated) rep2

description:
Sample 3
mRNA (Total RNA after polyA selection)

value: Unstimulated


title: human nasal epithelial cells (+SLR14) rep2

description:
Sample 5
mRNA (Total RNA after polyA selection)


title: human nasal epithelial cells (unstimulated) rep1

description:
Sample 1n
mRNA (Total RNA after polyA selection)


title: R436H2_GW4064_3


title: KO2_DMSO_3

description:
KO.agonist.vs.untrt.tsv
KO.agonist.vs.untrt.filter.tsv

value: NR1H4 homozygous knockout


title: RNA-Seq EV-GM

source_name: Empty vector Myoblasts

value: Myoblasts


title: ArtIEC16


title: R436H2_GW4064_1


title: R436H2_DMSO_3


title: R436H1_GW4064_3


title: R436H2_DMSO_1


title: ArtIEC09


title: KO2_DMSO_2


title: R436H1_GW4064_2


title: macrophages F4/80 high MHCII low, from colon tumor, donor VII

value: APC/Min

value: Colon tumor

value: macrophages F4/80 high MHCII low

value: VII


title: ArtIEC01

value: HIV-infected ART-treated patient


title: R436H1_DMSO_1


title: KO1_DMSO_3


title: KO1_GW4064_1

description:
KO.agonist.vs.untrt.tsv
KO.agonist.vs.untrt.filter.tsv
KO.agonist.vs.WT.agonist.tsv
KO.agonist.vs.WT.agonist.filter.tsv


title: KO2_DMSO_1


title: KO2_GW4064_2


title: KO1_DMSO_1


title: KO1_DMSO_2


title: KO2_GW4064_1


title: WT2_DMSO_2

description:
WT.agonist.vs.untrt.tsv
WT.agonist.vs.untrt.filter.tsv
R436H.untrt.vs.WT.untrt.tsv
R436H.untrt.vs.WT.untrt.filter.tsv

value: wild-type


title: KO1_GW4064_3

value: iPSC-derived hepatocytes


title: KO2_GW4064_3

value: Human Episomal iPSC Line (Thermofisher, A18945)


title: KO1_GW4064_2


title: R436H1_DMSO_3

value: NR1H4 homozygous R436H


title: WT2_GW4064_1

description:
WT.agonist.vs.untrt.tsv
WT.agonist.vs.untrt.filter.tsv
R436H.agonist.vs.WT.agonist.tsv
R436H.agonist.vs.WT.agonist.filter.tsv


title: WT2_GW4064_3


title: WT2_GW4064_2


title: WT2_DMSO_1

value: DMSO


title: WT2_DMSO_3


title: WT1_GW4064_1


title: WT1_DMSO_2


title: WT1_DMSO_1


title: WT1_DMSO_3


title: WH9 miR-128OE (miR-128 overexpression transgenic mice)

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description: countsTable.xls

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq
fastq seqences were aligned to mm10 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: heart

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

value: hearts

tag: genotype/variation

tag: age

value: postnatal day 7


title: WT1_GW4064_3


title: WH7 Ctrl (Control)

description: countsTable.xls

tag: tissue

value: Ctrl


title: P7 (heart on postnatal day 7)

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq
fastq seqences were aligned to mm10 using Tophat
number of reads was calculated for each Entrez gene
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

extract_protocol: miRNA library was prepared by using NEBnext small RNA library preparation kit

value: wild type


title: P1 (heart on postnatal day 1)

value: postnatal day 1


title: WH8 Ctrl (Control)

description: countsTable.xls


title: exp2_Input_Vehicle

city: Baltimore

first: Hyun Jun

last: Jung

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

institute: Johns Hopkins University School of Medicine

data_processing:
Align and transform the .fastq to .sam files using BWA program and mm10 mouse genome:  bwa samse mm10.fa sample.sai sample.fastq > sample.sam bwa aln -t 8 mm10.fa  sample.fastq > sample.sai.
Convert format from Sam to Bam and index the files using Samtools: Samtools view –bhS sample.sam > sample.bam, samtools sort sample.bam sample.sorted; samtools index sample.sorted.bam.
Create bedgraph files using macs2, macs2 callpeak -t sample_filename.sorted.bam -c input_filename.sorted.bam -f BAM -g mm -n output_filename –B –q 0.01 –SPMR
Create a peak txt file from a macs2 peak file
Create a bedGraph file from pile up file of macs2 output
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph and txt files

source_name: mpkCCD cells

growth_protocol: Cultured mouse mpkCCD (clone 11) cells were grown and maintained in complete medium, DMEM/F12 containing 2% dialyzed serum and supplements (5 μg/mL insulin, 50 nM dexamethasone, 1 nM triiodothyronine, 10 ng/mL epidermal growth factor, 60 nM sodium selenite, 5 μg/mL transferrin), as previously described (Yu MJ, Proc Natl Acad Sci U S A 106:2441-2446, 2009).

extract_protocol:
Shearing of chromatin was carried out by the manufacturer's protocol of truChIP kit (PN 520075, Covaris, Woburn, Massachusetts). All Covaris buffers were provided in kit. Confluent monolayers mpkCCD cells cultured on 100 mm permeable supports of transwell system were treated with dDAVP (0.1 nM) or vehicle for 24 h and then washed in ice-cold PBS followed by cross-linking in 1.11% formaldehyde in Covaris Fixing Buffer (5.5 ml) for 5 min at room temperature with gentle rocking. Cross-linking was terminated by the addition of 0.3 ml of 1X Covaris Quenching Buffer with rocking. The buffer solution was aspirated and ice-cold PBS was added to each plate. Cells were scraped, spun down (200xg, 5 min), and washed twice with ice-cold PBS. Cell pellets were resuspended in 1 ml of 1X Covaris Lysis Buffer for 10 min at 4°C with rocking.  Nuclei were pelleted by spinning at 1,700xg for 5 min at 4°C. Nuclear pellets was resuspended in 1 ml of 1X Covaris Wash Buffer and incubated for 10 min at 4°C with rocking. Samples were spun at 1,700xg for 5 min at 4°C. Nuclear pellets were washed twice with 1 ml of Covaris Non-ionic Shearing Buffer and spun at 1,700xg for 5 min at 4°C. Nuclei were resuspended in 1 ml of Covaris Non-ionic Shearing Buffer. Two 20 ul aliquots of the resuspended pellets were removed prior to shearing to be used as subsequent unsheared controls for immunoblotting and agarose gel electrophoresis. The remaining samples were transferred to AFA tubes (TC12 x 12 mm). Samples were sheared using a Covaris S2 SonoLAB Single system for two minutes (Duty cycle: 5%; Intensity: 4; cycle: 200). Total nuclear protein concentration of each sample in mg/ml was determined with the BCA Protein Assay Kit (Thermo Scientific, Rockford, IL).  To test shearing efficiency, a 20 ul aliquot from each sample was obtained after shearing. The aliquots from the unsheared sample and the sheared sample, were incubated with 100 ul 1X TE buffer, 10 ul 10% SDS, and RNAse A (10 ug/ul, Cell Signaling Technology, Danvers, Massachusetts) for 30 min at 37°C. After adding proteinase K (2 ug), the samples were incubated overnight at 65°C. The DNA was purified using DNA Clean & Concentrator columns (Catalog #: D4013, Zymo Research, Irvine, CA) and ran on an E-gel EX 2% agarose (Invitrogen, Carlsbad, CA). Target fragment sizes for chromatin immunoprecipitation were in the range of 150-700 bp in length with average fragment size of 300 bp.  Immunoprecipitaiton was performed by the manufacturer's instruction (SimpleChIP protocol #9003, Cell Signaling Technology). 'Input' sample (10 ul) was obtained prior to immunoprecipitation.  Chromatin Immunoprecipitation was performed using 30-90 ug of sheared chromatin in 500 uL of 1X Covaris Non-ionic Shearing Buffer with 10 μl anti-H3K27 acetylation antibodies. The mixtures were incubated overnight at 4°C with gentle rotation, followed by incubation with ChIP Grade Protein G Magnet Beads (Catalog #: 9006, Cell Signaling Technology) for 2 h at 4°C with rotation. The beads were washed a total of four times, including three low salt washes followed by one high salt wash for 5 min each at 4°C. Immunoprecipitated chromatin was eluted from the beads with 150 ul of 1X ChIP Elution Buffer for 30 mins at 65°C in a thermomixer. To reverse crosslinks, 6 ul of 5 M NaCl and 2 ul of 20 ug/ul  Proteinase K were added to the chromatin followed by incubation at 65°C overnight. DNA was purified according to the manufacturer's instruction.
Sequencing libraries were prepared according to the manufacturer's instruction (NuGEN Ovation SP Ultralow library system kit). Adaptor-conjugated iibraries were amplified by PCR. The amplified libararies were measured.  A fixed amount of the total measured DNA was used for sequencing in an Illumina Hiseq2000 instrument to obtain single read data.  Libraries were sequenced using an Illumina HiSeq2000, obtaining 1- by 50-bp reads.

treatment_protocol: For dDAVP treatment, cells were transferred to permeable supports (75mm, 0.4um pore, Corning #3419), and grown until confluency as documented transepithelial resistance measurements (Epithelial Volt ohmmeter; WPI). At that point, the complet medium was changed to serum- and hormone-free medium, and cells were maintained for 24 hr. Cells were incubated with the V2 receptor-selective vasopressin analog dDAVP (0.1 nM) or its vehicle (n=2) and harvested after 24 hr.

value: cultured mouse cortical collecting duct cells (mpkCCD)


title: exp1_Input_dDAVP


title: exp2_Input_dDAVP


title: WT1_GW4064_2


title: exp1_H3K27Ac_Vehicle

tag: chip antibody

value: anti-Histone H3 (acetyl K27) antibody (abcam, ab4729)


title: exp2_H3K27Ac_Vehicle


title: exp1_H3K27Ac_dDAVP


title: P28 (heart on postnatal day 28)

value: postnatal day 28


title: Nonspecific Control

city: Louisville

first: Kevin

last: Sokoloski

state: KY

address: 505 S. Hancock St.

department: Microbiology and Immunology

institute: University of Louisville

description: Library generated from total RNA immunoprecipitated with nonspecific polyclonal sera, and fragmented with RNAse T1

data_processing:
Libraries were demultiplex and trimmed to remove adaptors on the MiSeq interface to generate the raw sequence files.
All analyses of data sets were performed using the Galaxy web services found at Usegalaxy.org, where applicable the programs utilized are indicated by "_" and the version is noted by the (_) following immediately after. Deviations from the default settings are noted.
Library quality was assessed using "FastQC"
Fastq files were converted to Fasta via the "fastQ_to_fasta" tool.
The cDNA libraries were aligned to the Hg38 genome via "Bowtie2" (2.3.2.2) with the following parameters- Require 22bp word with matches in 14 specific positions, allow 2 transitions per hit, Gap open penalty= 1000, Gap Extension. Penalty= 1000,
Genome_build: Homo sapiens Hg38
Supplementary_files_format_and_content: .BAM and .BAI files generated from Bowtie2 Analyses

source_name: 293HEK cells

growth_protocol: 293HEK cells were maintained in MEM supplemented with 10% FBS at 37 degrees Celsius in the presence of 5% CO2. Purified SINV particles were obtained from 293HEK cells and purified using a 27% sucrose cushion via ultracentrifugation.

extract_protocol:
Lysates were generated via the addition of RIPA buffer (50mM Tris [pH 7.6] / 150mM NaCl / 1.0% NP-40 / 0.5% Sodium Deoxycholate / 0.1% SDS). The lysates were clarified via centrifugation and immunoprecipitated with either nonspecific control sera, or anti-hnRNP   sera and Protein A agarose beads. Purified RNA:Protein complexes were treated with RNAse T1 for 15 minutes at room temperature, washed several times to remove contaminating sequences and then released from the resin via proteinase K digestion at 37 degrees Celsius for 30 minutes.
The libraries were generated using the NEBNext Small RNA Library Prep Set for Illumina, with the following Index / Sample pairs- (Input, Illumina 13 AGTCAA) (Nonspecific, Illumina 19 GTGAAA) (hnRNP K, Illumina 23 GTGTGG) (hnRNP I, Illumina 22 CGTACG) (hnRNP M, Illumina 24 GGTAGC)

treatment_protocol: Per library, a total of 2E7 293HEK tissue culture cells were infected with SINV Toto1101 at an MOI of 5 PFU/cell. Infection was allowed to proceed for 18 hours prior to UV crosslinking via 5700x100 ujoules per cm2. Purified viral particles, ~1E11 particles in total, were treated similarly.

value: 293HEK cells

tag: virus strain

value: SINV Toto1101

tag: antibody

value: Preimmune IgG

tag: rna treatment

value: RNAse T1


title: WH10 miR-128OE (miR-128 overexpression transgenic mice)

description: countsTable.xls


title: hnRNP K Library

description: Library generated from total RNA immunoprecipitated with anti-SINV Capsid polyclonal sera, and fragmented with RNAse T1

value: anti-hnRNP K


title: PKA dKO clone3

data_processing:
Sequenced reads were mapped to GENCODE mouse gene set (GRCm38.p5) using STAR v2.5.2a
SAM and BAM files were generated using Samtools
Reads in exons of GENCODE gene set were counted using HOMER (v4.8, analyzeRepeats.pl)
Differential expression analysis was carried out using edgeR
Genome_build: GRCm38.p5 (GENCODE)
Supplementary_files_format_and_content: tab-delimited text files include raw counts/FPKM values for each sample and differential expression of each genes

source_name: mouse mpkCCD cell line

growth_protocol: Cells were grown on permeable membrane supports in DMEM/F12 medium containing 2 % serum and other supplements (5 μg/mL insulin, 50 nM dexamethasone, 1 nM triiodothyronine, 10 ng/mL epidermal growth factor, 60 nM sodium selenite, 5 μg/mL transferrin) for 4 days.

extract_protocol:
The mpkCCD cells grown on permeable inserts of 6-well transwell were washed with PBS and lysed with 100 ul Trizol solution. Total RNA was isolated using Direct-zol RNA mini prep plus (ZYMO RESEARCH, R2070) as manufacturer's protocol.
Sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Prep Kit (Cat#RS-122-2201) as manufacturer's instruction. Total RNA (262 ng) of each sample was applied to ribosomal RNA removal beads to deplete ribosomal RNAs. The purified RNA was fragmented and then primed with random hexamers for cDNA synthesis using reverse transcriptase and random primers. First strand cDNA and second strand cDNA were sythesized serially and ligated with indexing adapters. DNA fragments including adapters were amplified by PCR using a PCR primer cocktail. Sample libraries were qualified using Agilent Technologies Bioanalyzer.

treatment_protocol: After 4 days, cells were incubated in serum- and hormone-free medium with 0.1 nM dDAVP for 3 days. Media was changed daily.

value: Kidney

value: Stable


title: PKA dKO clone1


title: Input Control

description: Library generated from total RNA fragmented with RNAse T1

value: Not immunoprecipitated


title: hnRNP M Library

description: Library generated from RNA extracted from purified viral particles, and immunoprecipitated with anti-SINV Capsid polyclonal sera, and fragmented with RNAse T1

value: anti-hnRNP M


title: Control clone2


title: PKA dKO clone2


title: Control clone1


title: Control clone3


title: exp1_Input_Vehicle


title: MC-3

status: Public on Jan 01 2018

city: Zhengzhou

first: zhenglong

last: guo

state: Henan

address: NO.7, Weiwu road

institute: Henan Provincial People's Hospital

description: Processed data file: fpkm.txt

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500 platform and 100 bp/50bp single-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Reference genome and gene model annotation files were downloaded from genome website ftp://ftp.ensembl.org/pub/release-84/fasta/homo_sapiens/dna/. Index of the reference genome was built using Bowtie v2.0.6 and single-end clean reads were aligned to the reference genome using TopHat v2.0.9. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Genome_build: Homo sapiens Ensembl Release 84
Supplementary_files_format_and_content: fpkm.xls: Excel file includes FPKM values for all six Samples.

organism: Callithrix jacchus

source_name: marmoset hepatic progenitor cell line

extract_protocol:
Total RNA of marmoset liver progenitor cell line and adult liver tissue was harvested using Trizol reagent. A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: fetal liver-derived hepatic progenitor cell line


title: ML-3

description: Processed data file: fpkm.txt

source_name: adult marmoset liver tissue

value: adult liver

value: 5-10 years


title: ML-2

description: Processed data file: fpkm.txt


title: ML-1

description: Processed data file: fpkm.txt


title: MC-2

description: Processed data file: fpkm.txt


title: cbp80-3

city: Oldenburg

first: Sascha

last: Laubinger

address: Carl-von-Ossietzky-Str. 9-11

country: Germany

institute: University of Oldenburg

description: cbp80 mutant - replicate 3

data_processing:
ribosomal and tRNA sequence filtering with Bowtie2  (version 2.1.0), using –fr parameter in addition to default parameters and using unaligned forward and reverse reads later.
Aligning to A. thaliana genome to collect expression data: TopHat (version 2.1.1), with -p 10 -i 10 -I 1000 --library-type fr-secondstrand -G Arabidopsis_thaliana.TAIR10.34.gtf parameters.
Collecting unnormalized read counts from alignment with featureCounts (Subead package, version 1.5.0-p3), with default parameters for paired-end analysis.
Differential expression analysis: DESeq2 (version1.14.1), with default parameters, but using “contrast” argument. Control was always wild-type.
Genome_build: Arabidopsis thaliana: Ensembl Plants release 34 (ftp://ftp.ensemblgenomes.org/pub/release-34/plants/) genome fasta and GTF files, for rRNA/tRNA filering:  Arabidopsis thaliana sequences from tRNA collections (http://gtrnadb2009.ucsc.edu/download/tRNAs/GtRNAdb-all-tRNAs.fa.gz),  Arabidopsis thaliana genes for 5.8S rRNA and 25S rRNA with 18S rRNA fragment (geneBank ID: X52320.1);  sequences from arabidopsis.org: AT2G01010.1 – 18SrRNA, AT2G01020 – 5.8sRNA, ATCG00920 – 16SrRNA, ATCG00950 – 23SrRNA, ATCG00960 – 4.5SrRNA, ATCG01160.1 – 5SrRNA, ATMG00020.1 – 26SrRNA
Supplementary_files_format_and_content: “counts_all.txt” output file from featureCounts, ”_all.txt” and  “_005.txt” files for differencial expression data from DESeq2, unfiltered or  filtered values to padj < 0.05.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: Plants material were grown on ½ strength MS for 16 days under constant light conditions. Plant material was collected on ice (for apporximately 30 minutes) before snap freezing in liquid nitrogen.

extract_protocol:
RNA for library preparation has been extracted using the RNeasy Plant RNeasy Plant Mini Kit (Qiagen) according to the manufacture’s protocol.
mRNA was isolated using the NEBnext poly(A) mRNA Magnetic Isolation Module (NEB #7490), this was followed by library preparation using ScriptSeq™ v2 RNA-Seq Library Preparation Kit (epicentre). For library preparation mRNA was used as input starting at the fragmentation step in the protocol (step number 5).

treatment_protocol: no treatment

value: whole seedlings

tag: ecotype

value: cbp80 (CAP-BINDING PROTEIN 80) mutant


title: hnRNP I Library

value: anti-hnRNP I


title: cbp20-2

description: cbp20 mutant - replicate 2

value: cbp20 (CAP-BINDING PROTEIN 20) mutant


title: MC-1

description: Processed data file: fpkm.txt


title: cbp20-1

description: cbp20 mutant - replicate 1


title: se-3

description: se-1 mutant - replicate 3

value: se-1 (SERRATE) mutant


title: cbp80-2

description: cbp80 mutant - replicate 2


title: CC flower and fruit RNA-seq

city: Beijing

first: Xia

last: Cui

address: 12 Zhongguancun Nandajie

institute: Chinese Academy of Agricultural Sciences

data_processing:
The RNA-seq reads were aligned to the tomato genome (ITAG2.4) using tophat-2.0.11 (Trapnell et al., 2009) with anchor length more than 8nt for spliced alignments. Only uniquely mapped reads were retained for subsequent analysis.
Genome_build: ITAG2.4
Supplementary_files_format_and_content: bigWig

organism: Solanum lycopersicum var. cerasiforme

source_name: 5DPA, 20DPA, mature green, break stage and red ripen fruits and -2DPA flower from S. lycopersicum var. cerasiforme LA1310 (CC)

growth_protocol: the tomato plants were grown in greenhouse on soil

extract_protocol:
the flowers and fruits from different stages were collected. The total RNA was extracted using TRIZOL reagent (Invitrogen Cat#15596026).
Strand-specific RNA-Seq libraries generated from samples above were constructed using dUTP method (Parkhomchuk et al., 2009) and sequenced on Illumina Hiseq 2500.

treatment_protocol: No treatment

tag: cultivar

value: fruit/flower

tag: Stage


title: se-2

description: se-1 mutant - replicate 2


title: se-1

description: se-1 mutant - replicate 1


title: WT-3

description: WT - replicate 3

value: wild type


title: WT-2

description: WT - replicate 2


title: WT-1

description: WT - replicate 1


title: MM flower and fruit RNA-seq

organism: Solanum lycopersicum

source_name: 5DPA, 20DPA, mature green, break stage and red ripen fruits and -2DPA flower from S. lycopersicum var. Moneymaker (MM)

value: Moneymaker


title: ow_2DPAe_rep1 RNA-seq

source_name: ovary wall/pericarp of 2DPAe (emasculated) fruit

extract_protocol:
the fruits of different stages were collected and the ovule and ovary wall were dissected under microscope. The total RNA was extracted using TRIZOL reagent (Invitrogen Cat#15596026).
Strand-specific RNA-Seq libraries generated from samples above were constructed using dUTP method (Parkhomchuk et al., 2009) and sequenced on Illumina Hiseq 2500.

value: ovary wall/pericarp

value: 2DPA (emasculated at -2DPA)


title: ov_2DPAe_rep2 RNA-seq

source_name: ovule of 2DPAe (emasculated) fruit

value: ovule


title: ov_2DPAe_rep1 RNA-seq