title: Hi-C 8-cell rep1

value: C57BL/12N x PWK


title: MN single cell 15

status: Public on Jul 12 2017

type: SRA

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

country: USA

institute: UCSD

library_source: transcriptomic

data_processing:
Reads were trimmed of adapter sequences TCGTATGCCGTCTTCTGCTTG, ATCTCGTATGCCGTCTTCTGCTTG, CGACAGGTTCAGAGTTCTACAGTCCGACGATC GATCGGAAGAGCACACGTCTGAACTCCAGTCAC using cutadapt v1.8.1
Trimmed reads were aligned to RepBase v18.05 using STAR v2.4.01
Reads that didn't align to RepBase were aligned to hg19 using STAR v2.4.01 and a splice junction database derived from GENCODE v19
Transcripts per million (TPM) per transcript was calculated from reads that didn't align to RepBase were quasi-aligned to GENCODE v19 protein coding and lincRNA transcripts using Sailfish v0.6.3
TPM per gene was calculated by summing the TPM for all transcripts of a gene
Percent spliced-in (Psi) was calculated from junction read output from STAR aligner (SJ.out.tab) were used to create a de novo splicing index in conjunction with GENCODE v19 gene annotations, using outrigger
Outlier cells were calculated using K-means clustering with k=3 on the expression matrix and omitting cells which clustered into a group consisting of a majority of other cell types
Modality was calculated using anchor on the psi scores for all events detected in at least 10 cells, for each cell type
Waypoints were calculated using bonvoyage on the psi scores for all events detected in at least 10 cells, for each cell type
Splicing events were annotated using poshsplice to annotate corresponding genes, splice site strength using MaxEntScan, intron and exon lengths, conservation of alternative splicing from Merkin et al Science 2012,
Genes were annotated with attributes available in Gencode v19, Phylostrata for the matching ENSEMBL identifiers in Domazet-Loso et al MBE 2008, and TF or RBP category from Gerstberger et al Nat Rev Gen 2014
Genome_build: hg19
Supplementary_files_format_and_content: "metadata.csv.gz" contains sample metadata, "splicing.csv.gz" contains Psi scores, "splicing_feature.csv.gz" contains metadata for splicing events, "expression.csv.gz" contains TPM values for genes, "expression_feature.csv.gz" contains metadata for genes, "mapping_stats.csv.gz" contains the number and percentages of reads mapped for each samples

molecule: polyA RNA

organism: Homo sapiens

source_name: Motor neurons

growth_protocol: iPSCs were cultured on matrigel coated plated using mTeSR(Stem Cell Technologies) media with mTeSR supplement at 37C incubator with 5% CO2.

extract_protocol:
Motor neurons were directly differentiated from iPSCs as previous described (Chambers S, Nature Biotechnology, 2009). Briefly, iPSCs were cultured on matrigel coated plates until fully confluent in mTeSR then switch to knock-out serum replacement media (KSR) containing Dorsomorphin(1uM) and SB431542(10uM). Upon day 4 of differentiation, increasing amounts of N2 media (25%, 50%) was added to the KSR. From day 7 of differentiation, 1.5uM retinoic acid and 200nM Smoothened Agonist (SAG, EMD Millipore) were added to induce patterning. Cells were dissociated on day 17 of differentiation and replated in poly-D-lysine and laminin coated plates. Maturation was performed using BDGF(2ng/ml), GDNF(2ng/ml), CNTF(2ng/ml), ascorbid acid, sonic hedgehog and retinoic acid in N2 and B27 media up until 35 days of differentiation.
Single cells were captured on C1 auto prep platform (Fluidigm, CA) according to manufacturer's instructions. C1 auto prep chips were visually inspected with a light microscopy at 20X to ensure singularity of captured cells. All non-single cells were discarded from analysis. SMARTer Ultra Low RNA cDNA Synthesis Kit (Clontech) was used to reverse transcribe polyA-tailed RNA. cDNA was amplified using Advantage 2 Polumerase Mix by PCR at 95¡C for 1 minutes, followed by 21 cylcles of 15 secondes at 95¡C, 30 seconds at 65¡C and 6 minutes at 68¡C, followed by another 10 minutes at 72¡C as a final extension. cDNAs were inspected using Agilent Bioanalyzer High Sensitivity DNA chips and quantitated by PicoGreen dsDNA Assay kit (ThermoFisher). cDNAs were diluted to 1ng to generate libraries using the Nextera XT DNA kit(Illumina, CA).  Libraries were multiplexed and sequenced on Illumina HiSeq200 to generate 100bp PE reads.

treatment_protocol: Neuron progenitor cells were differentiated from iPSCs. Briefly, iPSCs were cultured in Matrigel coated plates and dislodged by dispase. To form embryonic bodies, the dislodged colonies were cultured in DMEM/F12(invitrogen) with GlutaMax and N2 supplement in non-adhere petri dish. Media were replaced every other day for 7 days. EBs were then placed onto matrigel coated plate to allow rosette formation. Clean rosette were picked manually and maintained in EB media for 7 days and subsequently dissociated with accutase and cultured in NPC media (DMEM/F12, GlutaMax, N2 and B27 with 2ug/ml FGF) to allow neuron progenitor cell differentiation. NPCs were maintained in NPC media.

tag: cell type

value: iPSC-derived motor neurons

tag: gender

value: male

tag: sample type

value: Single Cell


title: GmMM_GmLEC1-input_br2

city: Davis

first: John

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California

description:
processed data file:
LEC1-MM_Gmax275_peak.bed

library_source: genomic

data_processing:
Basecalls performed using RTA version 1.12.4.2
Sequenced reads passing Illumina quality filter were aligned to the Glycine max genome (Wm82.a2.v1) using Bowtie v0.12.7 with parameters -v 2 -5 0 -3 0 -m 1 --best --strata
Reads were filtered to remove PCR duplicates using samtools (v.0.1.19).
Peaks were identified using the PeakSeq algorithm of CisGenome (v2.0), using default parameters except min peak length=50.  Peaks were filtered further by applying an FDR threshold of 0.01.
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: peak coordinates (chr, start, end) are in the standard bed format

molecule: genomic DNA

organism: Glycine max

source_name: embryos

growth_protocol: Soybean cv Williams 82 plants were grown in 2 gallon pots containing Ron’s mix (1 part coarse sand, 1 part compost, 1 part peat moss, 3 pounds/yard Dolomite) in UC Davis greenhouses at temperatures ranging 22-30°C and under 16 hour-days.

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp.  Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 3ug of an an antibody raised against a recombinant GST-GmLEC1 (GmLEC1) or a GmLEC1 peptide (GmLEC1pep).  Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow DR Multiplex System, following the manufaturer's instructions and enriched by PCR using 15 cycles.  Libraries were size-selected by electrophoresis and purified using Qiagen MinElute gel purification kit

treatment_protocol: Cotyledon-stage embryos were dissected out of 2.5 to 3.5 mm long seeds, early maturation embryos from 6 to 7 mm seeds and mid-maturation, from seeds weighing between 200 and 250 mg .  Tissues were crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes.  Tissues were rinsed twice with deionized water and stored at -80C until use.

tag: cultivar

value: Williams 82

tag: tissue

value: embryo

tag: Stage

value: Mid-maturation stage

tag: antibody


title: Liver_E145_EC_Translatome_3

city: Würzburg

first: Mike

last: Hupe

address: Biocenter Am Hubland

department: Department of Developmental Biochemistry

country: Germany

institute: University of Würzburg

description:
ribosome-bound mRNA
deseq_E145_liver_EC_vs_E145_liver_total.txt
deseq_E145_liver_EC_vs_E145_brain_EC.txt
deseq_E145_liver_EC_vs_E145_head_EC.txt
deseq_E145_liver_EC_vs_E145_heart_EC.txt
deseq_E145_liver_EC_vs_E145_kidney_EC.txt
deseq_E145_liver_EC_vs_E145_limb_EC.txt
deseq_E145_liver_EC_vs_E145_lung_EC.txt

data_processing:
TRAP and HUVEC: Sequence reads were mapped against the Mus musculus genome assembly (Genome Reference Consortium GRCm38, UCSC version mm10) using the RUM v. 2.04 pipeline (Grant et al.: Bioinformatics, 2011).
Single cell: The reads were aligned to mouse (mm10) genomes using STAR v2.2.0 (Dobin et al.: Bioinformatics, 2013).
Gene expression (reads per kilobase per million mapped reads, RPKM) calculations were performed using rpkmforgenes.py Ramskold et al.: PLoS Comput Biol, 2009).
The mm10 refGene.txt-file was downloaded from UCSC 20130114.
Differential expression analysis was performed with DESeq (Anderset al.: Genome Biol, 2010).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample generated using DESeq.

molecule: total RNA

organism: Mus musculus

source_name: brain

growth_protocol: HUVEC (PromoCell) were cultured in EBM2 bullet kit media (Lonza) on gelatin-coated flasks according to instructions provided by the supplier.

extract_protocol:
TRAP: Translated and transcribed RNA from brain (forebrain and part of the diencephalon), head (without brain), heart, kidney, limb, liver or lung was purified from one to six mCherryTRAP embryos (age-dependent) as described (Hupe et al.: Nucleic Acids Res, 2014).
HUVEC: RNA was purified using RNeasy® Micro Kit (Qiagen) following the manufacturer’s instructions.
Single cell: Forebrains of mCherryTRAP E14.5 embryos were dissected in ice-cold PBS. The tissue was diced with a scalpel and subsequently enzymatically dissociated in PBS containing 1 mg/ml collagenase typ II (Worthington) and 1 µl/ml DNase I (Roche) at 37°C for 30 min with gentle sequential trituration. The cell suspension was filtered through a 40 µm cell strainer and 20 ml of DMEM containing 10 % FBS was added. After centrifugation at 800 x g for 5 min, the cell pellet was resuspended in 2 ml PBS containing 2 % FBS. Cells were sorted on a BD FACSAria III Cell Sorting system (BD Bioscience) based on mCherry fluorescence utilizing the 488-nm laser. mCherryTRAP-negative embryos were used to define background fluorescence. Forward and side scatter analysis were used as gates to avoid cell debris and doublets. Single cells were collected in a 96 well plate contain 4 µl of a mild hypotonic lysis buffer [0.1% Triton X-100 (Sigma), 1 U/µl recombinant RNase inhibitor (Promega), 2.5 µM anchored oligo-dT primer (5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′, Biomers), and 2.5 mM dNTP mix (Fermentas)] in each well.
TRAP and HUVEC: RNA libraries were prepared for sequencing using standard Illumina protocols
Single cell: Libraries were generated following Smart-seq2 (Picelli et al.: Nat Methods, 2013) and Tn5 transposase tagmentation (Picelli et al.: Genome Res, 2014) protocols.

treatment_protocol: Lentiviral infection was carried out in gelatin-coated 12-well plates containing 5 × 10^4 cells per well in 600 µl RPMI medium with 200 µl viral supernatant for 4 h and cells were cultivated for 7 days in growth medium.

tag: mouse line

value: liver

tag: age


title: MN single cell 14


title: GmMM_GmLEC1-input_br1


title: Liver_E145_Transcriptome_1

description:
total mRNA
deseq_E145_liver_EC_vs_E145_liver_total.txt


title: Liver_E145_EC_Translatome_2


title: MN single cell 13


title: ChIP-seq from ascending aorta (ENCLB084AUH)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR248PES/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR248PES
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007WYC
encode release date: 2016-11-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB084AUH
size range: 200-600

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens ascending aorta tissue female adult (53 years)

value: ascending aorta

value: tissue

tag: description

value: EnTEX:Artery- Aorta

tag: biosample encode accession

tag: dev stage

value: adult

tag: lab

value: Bradley Bernstein, Broad

value: 53 year

tag: Sex

value: female

tag: link

value: ENCBS328HPC at ENCODE; https://www.encodeproject.org/ENCBS328HPC/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: Liver_E145_EC_Translatome_1


title: MN single cell 12


title: GmMM_GmLEC1-ChIP_br2

value: anti-recombinant GmLEC1


title: MN single cell 11

value: iPSC-derived motor neurons


title: Limb_E145_Transcriptome_3

description:
total mRNA
deseq_E145_limb_EC_vs_E145_limb_total.txt

value: limb


title: GmMM_GmLEC1-ChIP_br1


title: Limb_E145_Transcriptome_2


title: MN single cell 10

value: male

value: Single Cell


title: GmEM_GmLEC1-input_br1

description:
processed data file:
LEC1-EM_Gmax275_peak.bed

value: Williams 82

value: embryo

value: Early maturation stage


title: Limb_E145_Transcriptome_1


title: GmEM_GmLEC1-input_br2


title: GmEM_GmLEC1-ChIP_br2


title: Limb_E145_EC_Translatome_3

description:
ribosome-bound mRNA
deseq_E145_limb_EC_vs_E145_limb_total.txt
deseq_E145_limb_EC_vs_E145_brain_EC.txt
deseq_E145_limb_EC_vs_E145_head_EC.txt
deseq_E145_limb_EC_vs_E145_heart_EC.txt
deseq_E145_limb_EC_vs_E145_kidney_EC.txt
deseq_E145_limb_EC_vs_E145_liver_EC.txt
deseq_E145_limb_EC_vs_E145_lung_EC.txt


title: GmEM_GmLEC1-ChIP_br1


title: MN single cell 7


title: MN single cell 8


title: GmCOT_GmLEC1-input_br2

description:
processed data file:
LEC1-COT_Gmax275_peak.bed

value: Cotyledon stage


title: MN single cell 6


title: Limb_E145_EC_Translatome_1


title: GmCOT_GmLEC1-input_br1


title: MN single cell 5


title: GmCOT_GmLEC1-ChIP_br2


title: Heart_E145_Transcriptome_2

description:
total mRNA
deseq_E145_heart_EC_vs_E145_heart_total.txt

value: heart


title: Heart_E145_Transcriptome_3


title: GmCOT_GmLEC1-ChIP_br1


title: Heart_E145_Transcriptome_1


title: MN single cell 3


title: MN single cell 9


title: MN single cell 1


title: Heart_E145_EC_Translatome_2

description:
ribosome-bound mRNA
deseq_E145_heart_EC_vs_E145_heart_total.txt
deseq_E145_heart_EC_vs_E145_brain_EC.txt
deseq_E145_heart_EC_vs_E145_head_EC.txt
deseq_E145_heart_EC_vs_E145_kidney_EC.txt
deseq_E145_heart_EC_vs_E145_limb_EC.txt
deseq_E145_heart_EC_vs_E145_liver_EC.txt
deseq_E145_heart_EC_vs_E145_lung_EC.txt


title: Heart_E145_EC_Translatome_3


title: Limb_E145_EC_Translatome_2


title: NPC single cell 32

source_name: Neural progenitor cells

value: iPSC-derived neural progenitor cells


title: Heart_E145_EC_Translatome_1


title: MN single cell 2


title: Head_E145_Transcriptome_1

description:
total mRNA
deseq_E145_head_EC_vs_E145_head_total.txt

value: head (without brain)


title: Head_E145_Transcriptome_3


title: Soybean Dry Seed-Biological Replicate 2

description: mature, dry seed

data_processing:
Basecalls performed using RTA version 1.12.4.2
Each lane of sequencing for each sample is attached as an individual compressed file.  The sequence data are in the fastq format.
Sequenced reads were quality-filtered, reads corresponding to rDNA sequences were removed and the resulting filtered reads were mapped to Glycine max gene models (Wm82.a2.v1) using bowtie v0.12.7 with parameters -v 2 -5 0 -3 0 -m 1 --best --strata
Read counts for each gene models were computed using a custom script. TMM-normalized counts are obtained using the EdgeR package v3.0.8 (Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140).
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: tab-delimited text file including the normalized counts for each sample.

source_name: Soybean Dry Seed

growth_protocol: Soybean plants were grown at the UC Davis Greenhouses with a 16:8 day:night cycle at 22°C-30°C. Seeds were germinated in Modified UC Mix (equal parts of ground canadian sphagnum, horticultural grade sand, white pumice, redwood compost) for 10 days.  Individual seedlings were transfered to 1 gallon pots where they were grown for an additional 3 weeks before being transplanted to 3 gallon pots.  Plants were watered as needed with water containing 190 ppm Nitrogen, 40 ppm Phosphorus and 140 ppm Potassium and micronutrients.

extract_protocol:
Total RNA was isolated using PureLink® Plant RNA Reagent (ThermoFisher) following the manufacturer's instructions.
Illumina-complatible libraries were made starting with 5 ug of total RNA, using Kumar et al. (Kumar R, Ichihashi Y, Kimura S, Chitwood DH, Headland LR, Peng J, Maloof JN and Sinha NR (2012) A high-throughput method for Illumina RNA-Seq library preparation. Front. Plant Sci. 3:202. doi: 10.3389/fpls.2012.00202) Supplemetary Methods 1 library preparation protocol, at the exception of the RNA and mRNA isolation: the polyA isolation from total RNA described in Supplementary Methods 2 was used and the NEXTflex ChIP-Seq Barcodes (BiooScientific) were used for Illumina-compatible adapters. Libraries were quantified using Quant-iT PicoGreen dsDNA Reagent (Grand Island, NY) and a Nanodrop ND-3300 instrument.  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

treatment_protocol: Cotyledon-stage embryos were dissected out of 2.5 to 3.5 mm long seeds, early maturation embryos from 6 to 7 mm seeds, mid-maturation, from seeds weighing between 200 and 250 mg, late maturation from completely yellow seeds (seed coat and embryo) weighing between 230 and 500 mg, dry seeds from mature, dry seeds and 8 DAI seedlings from whole seedlings 8 days after seed sowing.  Tissues were frozen in liquid nitrogen and stored at -80C until use.

value: seed

tag: developmental stage

value: mature, dry seed


title: Soybean Seedling 8 DAI-Biological Replicate 1

description: seedling, 8 days after seed sowing

source_name: Soybean Seedling 8 DAI

value: seedling

value: 8 day after seed sowing


title: Soybean Late Maturation-stage Embryo-Biological Replicate 3

description: Embryos dissected from seeds weighing 230-500 mg and completely yellow (seed coat and embryo).

source_name: Soybean Late Maturation-stage Embryo

value: late maturation


title: Soybean Dry Seed-Biological Replicate 1

description: mature, dry seed


title: Head_E145_Transcriptome_2


title: MN single cell 4


title: NPC single cell 30


title: NPC single cell 29


title: NPC single cell 28


title: Soybean Seedling 8 DAI-Biological Replicate 3

description: seedling, 8 days after seed sowing


title: Head_E145_EC_Translatome_2

description:
ribosome-bound mRNA
deseq_E145_head_EC_vs_E145_head_total.txt
deseq_E145_head_EC_vs_E145_brain_EC.txt
deseq_E145_head_EC_vs_E145_heart_EC.txt
deseq_E145_head_EC_vs_E145_kidney_EC.txt
deseq_E145_head_EC_vs_E145_limb_EC.txt
deseq_E145_head_EC_vs_E145_liver_EC.txt
deseq_E145_head_EC_vs_E145_lung_EC.txt


title: Soybean Dry Seed-Biological Replicate 3

description: mature, dry seed


title: NPC single cell 27


title: Soybean Late Maturation-stage Embryo-Biological Replicate 2


title: Head_E145_EC_Translatome_1


title: Soybean Late Maturation-stage Embryo-Biological Replicate 1


title: NPC pooled 2

value: Pooled


title: Soybean Mid Maturation-stage Embryo-Biological Replicate 3

description: Embryos dissected from seeds weighing 200-250 mg

source_name: Soybean Mid Maturation-stage Embryo

value: mid-maturation


title: NPC single cell 31


title: Soybean Mid Maturation-stage Embryo-Biological Replicate 2


title: Soybean Seedling 8 DAI-Biological Replicate 2

description: seedling, 8 days after seed sowing


title: NPC single cell 26


title: Soybean Mid Maturation-stage Embryo-Biological Replicate 1


title: Brain_E145_EC_Ctnnb1KO_Translatome_2

description:
ribosome-bound mRNA
deseq_E145_KO_brain_EC_vs_E145_KO_brain_total.txt
deseq_E145_wt_brain_total_vs_E145_KO_brain_total.txt

value: forebrain EC


title: Head_E145_EC_Translatome_3


title: Soybean Early Maturation-stage Embryo-Biological Replicate 3

description: Embryos dissected from seeds 6-7 mm long

source_name: Soybean Early Maturation-stage Embryo

value: early maturation


title: NPC single cell 25

value: male

value: Single Cell


title: NPC single cell 23


title: Soybean Early Maturation-stage Embryo-Biological Replicate 2

value: Williams 82

value: embryo


title: NPC single cell 22


title: Brain_E145_Ctnnb1KO_Transcriptome_2

description:
total mRNA
deseq_E145_KO_brain_EC_vs_E145_KO_brain_total.txt
deseq_E145_wt_brain_EC_vs_E145_KO_ brain_EC.txt

value: forebrain


title: Brain_E145_Ctnnb1KO_Transcriptome_3


title: Nab_HTB_rep2

city: Baltimore

first: Jonathan

last: Merran

state: Maryland

address: 725 N. Wolfe Street

department: Molecular Biology and Genetics

institute: Johns Hopkins University

description: PAR-CLIP

data_processing:
PAR-CLIP reads were trimmed of the adapters using a wrapper provided by Sarah Wheelan.
Raw trimmed reads were condensed, removing duplicate sequences, eliminating any PCR artifacts within the data.
The condensed reads were aligned to the SacCer 3 revision R64 Feb 2011 tRNA and RDN reference genomes curated from the SGD database using bowtie 1.1.1 with arguments (-y --best -v 2) to elminate reads that aligned to tRNA and RDN regions of the genome.
The curated reads were then aligned to the full SacCer 3 genome R64 Feb 2011, using -y --best -v 2 -m 2 as parameters in bowtie 1.1.1.
Resulting Sam files were converted into wigle track format and normalized to 10^7 reads.
Genome_build: SacCer3 (R64)
Supplementary_files_format_and_content: Cassette_AARap_diffexp.txt (Deseq normalized abundance reads)
Supplementary_files_format_and_content: Cassette_NrdRap_diffexp.txt (Deseq normalized abundance reads)
Supplementary_files_format_and_content: NrdvsCassette_4gsea.txt (Deseq normalized abundance reads used for GSEA.  GSEA Enrichment Scores - Genes were ranked using a signal to noise ratio and plotted with a running Enrichment Score calculated using GSEA v2.2.3)
Supplementary_files_format_and_content: Cassette_AA_norm4gsea.txt (Deseq normalized abundance reads used for GSEA.  GSEA Enrichment Scores - Genes were ranked using a signal to noise ratio and plotted with a running Enrichment Score calculated using GSEA v2.2.3)
Supplementary_files_format_and_content: Wiggle track format

molecule: nuclear RNA

organism: Saccharomyces cerevisiae

source_name: NabHTB (2633)

growth_protocol: All Yeast cells were cultured in 500 ml of CSM-Limiting Ura to an OD of 1.

extract_protocol:
Cells were irradiated with UV light to crosslink the HTB tagged protein of interest to RNA. Cells were frozen and cracked to isolate the RNA bound proteins.
Extracted RNA bound proteins were isolated 5' and 3' adapters were ligated before reverse transcribing to cDNA. Resulting cDNA was PCR amplified and multiplexed before submitted for illumina Hi-Seq sequencing and analysis. Resulting Data was demultiplexed for us.

tag: rapamycin

value: no


title: Soybean Early Maturation-stage Embryo-Biological Replicate 1


title: Nab_HTB_rep1

description: PAR-CLIP


title: Soybean Cotyledon-stage Embryo-Biological Replicate 3

description: Embryos dissected from seeds 2.5-3.5 mm long

source_name: Soybean Cotyledon-stage Embryo

value: cotyledon


title: Brain_E145_Ctnnb1KO_Transcriptome_1


title: Nab_AnchorAway_Rap_2

description:
PAR-CLIP
Cassette_AARap_diffexp.txt
Cassette_AA_norm4gsea.txt

source_name: NabFRB (2875)

value: yes


title: Brain_E135_Transcriptome_3

description:
total mRNA
deseq_E135_brain_EC_vs_E135_brain_total.txt


title: NPC single cell 20

tag: cell type

value: iPSC-derived neural progenitor cells


title: NPC single cell 21

tag: gender


title: Soybean Cotyledon-stage Embryo-Biological Replicate 2


title: NPC single cell 19

tag: sample type


title: Brain_E145_EC_Ctnnb1KO_Translatome_3


title: Soybean Cotyledon-stage Embryo-Biological Replicate 1

tag: cultivar


title: Brain_E135_Transcriptome_1

tag: tissue


title: NPC single cell 24


title: Nab_AnchorAway_Rap_1


title: Brain_E135_Transcriptome_2


title: NPC single cell 18


title: Brain_E145_EC_Ctnnb1KO_Translatome_1


title: Nab_AnchorAway_noRap_1

description: PAR-CLIP


title: Soybean Mid-Maturation Seed Coat-Biological Replicate 3

description:
Compartments collected from seeds weighing 200-250 mg
MM-SC-3

data_processing:
Basecalls performed using RTA version 1.12.4.2
Each lane of sequencing for each sample is attached as an individual compressed file.  The sequence data are in the fastq format.
Sequenced reads were quality-filtered, reads corresponding to rDNA sequences were removed and the resulting filtered reads were mapped to Glycine max gene models (v1.1) using bowtie v0.12.7 with parameters -v 2 -5 10 -3 4 -m 1 --best --strata
Read counts for each gene models were computed using a custom script. Normalized counts are obtained using the EdgeR package v3.0.8 (Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene    expression data. Bioinformatics 26, 139-140).
Genome_build: Glyma 1.1
Supplementary_files_format_and_content: tab-delimited text file including the normalized counts for each sample.

source_name: Soybean Mid-Maturation Seed Coat

extract_protocol:
Soybean seeds (Williams 82) were fixed in 3:1 ethanol:acetic acid for 16-20 hours at 4°C, then dehydrated with 75% ethanol, 85% ethanol, 95% ethanol, and three times with 100% ethanol, each wash in one hour intervals. Then they were infiltrated with 3:1 ethanol-xylenes, 1:1 ethanol-xylenes, 1:3 ethanol-xylenes, and three times with 100% xylenes, dilution in two hour intervals. They were then infiltrated with molten paraffin at 60 deg C for 1-4 days, depending on the size of the tissue. Laser capture microdissection was used to isolate specific compartments of the seed after tissues were sectioned in 5-10um sections. Total RNA was isolated with Ambion RNaqueous-Micro kit (Grand Island, NY) and quantified with Quant-iT™ RiboGreen® RNA reagent (Grand Island, NY) on a Nanodrop ND-3300.
Amplification was performed using NuGen Ovation Pico WTA V1 (San Carlos, CA), starting with 15ng total RNA. Double-stranded cDNA was generated using the NuGen WT-Ovation Exon-Module (San Carlos, CA). Illumina-complatible libraries were made starting with 150 ng double-stranded cDNA using Kumar et al. (Kumar R, Ichihashi Y, Kimura S, Chitwood DH, Headland LR, Peng J, Maloof JN and Sinha NR (2012) A high-throughput method for Illumina RNA-Seq library preparation. Front. Plant Sci. 3:202. doi: 10.3389/fpls.2012.00202) Supplemetary Methods 1 library preparation protocol, starting at Day 2.  The following modifications were done: the Illumina TruSeq DNA Sample preparation kit adapters were used (1/25 dilution) and the Agilent Pfu Turbo Cx hotstart DNA polymerase was used for the PCR enrichment step (15 cycles).  Libraries were quantified using Quant-iT PicoGreen dsDNA Reagent (Grand Island, NY) and a Nanodrop ND-3300 instrument.  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

value: seed coat


title: Nrd_Rap_rep1

description:
PAR-CLIP
45min rapamycin
Cassette_NrdRap_diffexp.txt


title: NPC single cell 17


title: Nrd_Rap_rep2


title: Soybean Mid-Maturation Seed Coat-Biological Replicate 2

description:
Compartments collected from seeds weighing 200-250 mg
MM-SC-2


title: NPC single cell 16


title: Brain_E135_EC_Translatome_3

description:
ribosome-bound mRNA
deseq_E135_brain_EC_vs_E135_brain_total.txt
deseq_E135_brain_EC_vs_E115_brain_EC.txt
deseq_E135_brain_EC_vs_E125_brain_EC.txt
deseq_E145_brain_EC_vs_E135_brain_EC.txt
deseq_E175_brain_EC_vs_E135_brain_EC.txt


title: Brain_E135_EC_Translatome_2


title: Nab_WT_1_PARCLIP

description:
PAR-CLIP
Cassette_AARap_diffexp.txt
Cassette_NrdRap_diffexp.txt
Cassette_AA_norm4gsea.txt
NrdvsCassette_4gsea.txt

source_name: NabCassette (2876)


title: Brain_E135_EC_Translatome_1


title: Soybean Mid-Maturation Seed Coat-Biological Replicate 1

description:
Compartments collected from seeds weighing 200-250 mg
MM-SC-1


title: NPC pooled 1


title: Nab_WT_2_PARCLIP


title: NPC single cell 14


title: Soybean Mid-Maturation Embryo Cotyledons-Biological Replicate 1

description:
Compartments collected from seeds weighing 200-250 mg
MM-COT-1

value: embryo cotyledons


title: Soybean Mid-Maturation Embryo Cotyledons-Biological Replicate 2

description:
Compartments collected from seeds weighing 200-250 mg
MM-COT-2


title: Brain_E125_Transcriptome_1

description:
total mRNA
deseq_E125_brain_EC_vs_E125_brain_total.txt


title: Brain_E125_Transcriptome_2


title: NPC single cell 12


title: Soybean Mid-Maturation Embryo Cotyledons-Biological Replicate 3

description:
Compartments collected from seeds weighing 200-250 mg
MM-COT-3


title: Soybean Mid-Maturation Embryo Axis-Biological Replicate 2

description:
Compartments collected from seeds weighing 200-250 mg
MM-AX-2

source_name: Soybean Mid-Maturation Embryo Axis

value: embryo axis


title: Soybean Mid-Maturation Embryo Axis-Biological Replicate 3

description:
Compartments collected from seeds weighing 200-250 mg
MM-AX-3


title: NPC single cell 13


title: Brain_E125_Transcriptome_3


title: Brain_E125_EC_Translatome_3

description:
ribosome-bound mRNA
deseq_E125_brain_EC_vs_E125_brain_total.txt
deseq_E125_brain_EC_vs_E115_brain_EC.txt
deseq_E135_brain_EC_vs_E125_brain_EC.txt
deseq_E145_brain_EC_vs_E125_brain_EC.txt
deseq_E175_brain_EC_vs_E125_brain_EC.txt


title: Brain_E125_EC_Translatome_2


title: Nab_AnchorAway_noRap_2

description: PAR-CLIP


title: Brain_E125_EC_Translatome_1


title: Soybean Mid-Maturation Embryo Axis-Biological Replicate 1

description:
Compartments collected from seeds weighing 200-250 mg
MM-AX-1


title: NPC single cell 10


title: NPC single cell 11


title: Brain_E115_Transcriptome_3

description:
total mRNA
deseq_E115_brain_EC_vs_E115_brain_total.txt


title: Brain_E115_Transcriptome_2


title: NPC single cell 9


title: NPC single cell 7


title: Brain_E115_EC_Translatome_3

description:
ribosome-bound mRNA
deseq_E115_brain_EC_vs_E115_brain_total.txt
deseq_E125_brain_EC_vs_E115_brain_EC.txt
deseq_E135_brain_EC_vs_E115_brain_EC.txt
deseq_E145_brain_EC_vs_E115_brain_EC.txt
deseq_E155_brain_EC_vs_E115_brain_EC.txt
deseq_E165_brain_EC_vs_E115_brain_EC.txt
deseq_E175_brain_EC_vs_E115_brain_EC.txt


title: Brain_E115_EC_Translatome_2


title: NPC single cell 4


title: NPC single cell 5


title: Brain_E115_EC_Translatome_1


title: NPC single cell 2


title: NPC single cell 3


title: NPC single cell 1


title: HUVEC_ZIC3_2

description:
total mRNA
Deseq_ZIC3_vs_Control.txt

source_name: Human umbilical vein endothelial cell

value: umbilical vein


title: FGF2 injected #8

city: New Haven

first: Flora

last: Vaccarino

state: CT

address: 230 South Frontage Road

department: Child Study Center

institute: Yale University

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were QCd, then mapped to mm9 whole genome using Tophat v2.0.9 (running Bowtie v2.1.0.0) with parameters -g 1 -p 4 -r 150 --coverage-search --microexon-search --solexa-quals --b2-very-sensitive
Counts were calculated using BEDtools v2.12.0
RPKM were calculated using RSEQtools v0.6
Genome_build: NCBIM37
Supplementary_files_format_and_content: tab-delimited text files include RPKM and Counts values for each Sample

source_name: dorsal telencephalon

extract_protocol:
Total RNA was isolated from Formalin-fixed coronal cryosections mounted onto slides using RecoverAll Total Nuclei Acid Isolation kit (Ambion) following the manufacturer instructions with the exception of the initial deparaffinization step which was not required, then treated with DNAse I to remove trace amounts of DNA.
Paired-end cDNA libraries were prepared introducing a six-base sequence index into the adapter at the PCR stage of sample preparation for Illumina multiplexed sequencing, according to the manufacturer’s specification. Samples were sequenced using Illumina Hi Seq2000 to an average depth of 30M reads per sample.

treatment_protocol: intraventricular injection of 100ng of FGF2 or vehicle (PBS+0.1% BSA( into E13.5 telecenphalic vesicles of E13.5 mouse embryos

tag: strain

tag: embryonic age

tag: agent


title: HUVEC_ZIC3_3

description:
total mRNA
Deseq_ZIC3_vs_Control.txt


title: vehicle-injected #9

value: vehicle


title: FGF2 injected #7


title: vehicle-injected #7


title: NPC single cell 8


title: FGF2 injected #6


title: vehicle-injected#8


title: HUVEC_Foxf2+Foxq1+ZIC3_3

description:
total mRNA
Deseq_Foxf2+Foxq1+ZIC3_vs_Control.txt


title: Brain_E115_Transcriptome_1

tag: mouse line

tag: age


title: NPC single cell 6


title: HUVEC_Foxq1_3

description:
total mRNA
Deseq_Foxq1_vs_Control.txt


title: HUVEC_ZIC3_1

description:
total mRNA
Deseq_ZIC3_vs_Control.txt


title: HUVEC_Foxf2+Foxq1+ZIC3_2


title: HUVEC_Foxf2+Foxq1+ZIC3_1


title: Crushed_1

city: Columbus

first: Dario

last: Motti

state: Ohio [OH]

address: 700 Childrens Drive

department: Research

institute: Nationwide Children's Hospital

description: Poly-RNA from adult mouse laser microdissected DRG neurons, 7 days post sciatic nerve crush injury

data_processing:
Alignment: Tophat software (v. 1.3.2) with default settings except for the following options:  –G option which supplies Tophat with gene model annotation (combined UCSC, Ensembl, and RefSeq annotations) and –i 50 which sets the minimum intron length to 50
Transcript reconstruction an expression estimation: Cufflinks software (v. 1.1.0). At first Cufflinks uses the aligned reads in the dataset to describe a set of transcripts starting from the reads that span splice-junctions. We ran this step using a non-annotated reference genome because without an annotation the software will assemble novel transcripts and isoforms. After transcript assembly, normalized expression levels are estimated and reported as FPKM (Fragments Per Kilobase of exon per Million fragments mapped) together with confidence intervals. A different part of the software, named Cuffcompare (version 0.8.3) classified the reconstructed RNA-species as novel or known according to how they map back to the provided reference annotation. Cuffcompare was run twice, first with a combined reference GTF generated from crossing annotated transcripts found in the UCSC Genome, the Ensembl, and the RefSeq database.  We combined three genome annotations in an effort to minimize falsely identified novel transcripts. UCSC was used as the base since it contained the highest number of annotated RNA species; all non overlapping annotations found in the other databases were added.  We reran Cuffcompare in order to improve the accuracy of read alignment and therefore transcript expression estimation (personal communications with Cole Trapnell).  The nature of the alignment of the reconstructed RNA-specie and the annotated element is reported according to a code letter. For our purposes we isolated from the output only the “=”, “j” and “u” classes (corresponding to a “perfect match” to a known RNA-molecule, new isoforms of known active locus, and to full transcripts never identified before ). We ran Cuffcompare a 2nd time after adding annotation for unknown and novel transcripts assembled by Cufflinks.
Differential expression test: Cuffdiff (v. 1.2.1). Cuffdiff determined statistical significance based on the square root of the Jensen-Shannon divergence between the relative abundance of transcripts. Significance was reported as an uncorrected p-value, and then classified as significant/not –significant after Benjamini-Hochberg correction of the p-value.
Isoform filtering: Logistic regression analysis was performed to define reliable quantification of isoform expression. All isoform with FPKM < 0.0466 were considered unreliable and filtered out.
Genome_build: mm9
Supplementary_files_format_and_content: All_isoforms.gtf: GTF format file with localization information for each genomic element of each isoforms. Table S3_Isoform_Quantification.txt: text file format with information about expression levels and confidence intervals in FPKM of individual isoforms in each sample, plus results for differential expression test between Crushed and Controls.

source_name: L3-4-5 DRG neurons

extract_protocol:
RNA was extracted with the Arcturus ® PicoPure® RNA Isolation Kit, following manufacturer instructions
Poly-A selection. 500 ng of RNA was prepared for Next Generation Sequencing following the Illumina mRNA Sample Preparation Guidelines (Illumina, Cat # RS-930-1001).  Reads were barcoded, mixed together and run on three lanes.

treatment_protocol: Adult C57Bl/6 male mice were subjected to sciatic nerve crush (10 seconds) or sham surgery (10 seconds nerve exposure). 7 days post surgery ganglia located at the Lumbar 3, 4 and 5 level on the same side of the surgery were isolated and freshly frozen. Neurons were microdissected from the ganglia

value: 4-6 weeks

tag: treatment

value: sciatic nerve crush


title: Crushed_2


title: Control_2

description: Poly-RNA from adult mouse laser microdissected DRG neurons, 7 days post sham surgery

value: sham surgery


title: Control_3


title: Crushed_3


title: Control_1


title: HUVEC_Foxf2_3

description:
total mRNA
Deseq_Foxf2_vs_Control.txt


title: WT 18h

city: Norwich

middle: Tyson

last: Munnoch

address: Norwich Research Park

department: Schol of Biological Sciences

country: United Kingdom

institute: University of East Anglia

data_processing:
Alignment of reads to reference genome (NC_018750.1) using bowtie2 (bowtie2-2.2.3) options [bowtie2 -x reference_genome -S output.sam -U read_file]
conversion to .bam format and sorting using samtools (version 1.2).  Commands: samtools view -bS [input.sam] > [output.bam].  Samtools sort [input.bam] [output.sortedbam]
Conversion of sorted bam file to a bedgraph format using bedtools.  Command: genomeCoverageBed -ibam sorted.bam -g reference_genome.fna -scale -bga file.bedgraph.  Number of reads per raw data file 10h = 21,207,760 reads.  12h = 22,670,523 reads.  14h = 21,661,901 reads.  16h = 19,397,387 reads.  18h = 13,963,280 reads.  20h = 40,005,264 reads.  Each file was scaled to 13,963,280 reads (based on the 18h time point with the lowest number of reads) during the sorted bam to bedgraph conversion (using the -scale function with a value of 0-1 with 1 being no scaling.  the number of the reads for the 18h time point was divided by the number of reads of the sample to define the division factor used).
production of a wig file suitable for visualisation in IGB using personal unpublished script file contains header (track   type=wiggle_0   name=WT_16h       graphType=points        visibility=full color=168,130,88  fixedStep       chrom=Sven      start=1 step=1  span=1) with each subsequent line corresponding to the number of times a single base was sequenced with each base represented by a seperate line.
Additional visual inspection was carried out using the wig files and IGB to validate target peaks.
Genome_build: NC_018750.1
Supplementary_files_format_and_content: wig files were generated using the below perl (v5.8.8) script: =for comment  ---------------------------------------------------------------------------------------------  this is an example of a bedfile format output from the tools "genomeCoverageBed" in bedtools-  ---------------------------------------------------------------------------------------------        -some weird reference       base     base                               postion  position  frequency                                from     to  i|408675720|ref|NC_018750.1|   0       1       7  gi|408675720|ref|NC_018750.1|   1       2       11  gi|408675720|ref|NC_018750.1|   2       3       12  gi|408675720|ref|NC_018750.1|   3       5       13  gi|408675720|ref|NC_018750.1|   5       7       14  gi|408675720|ref|NC_018750.1|   7       13      15  gi|408675720|ref|NC_018750.1|   13      14      16  gi|408675720|ref|NC_018750.1|   14      15      18  =cut        use strict;  use warnings;  my $file = <STDIN>;  my @array;  my $from;  my $to;  my $cc=1;  open (BED, "$file");    while (<BED>){  chomp $_;  @array = split (/\t/, $_);    $from = $array[1];  $to = $array[2];  my $freq= $array[3];  my $count = 0;  my $dif = $to-$from;  while ($dif-$count>0){  $count++;  my $tt = $from + $count;  print "$freq\n";    }    }  close (BED);  exit;  )

organism: Streptomyces venezuelae ATCC 10712

source_name: Streptomyces venezuelae ATCC 10712'

growth_protocol: 5-7 ul of current spore stock (OD600 ~0.35 after 8h) was innoculated into 35 ml of MYM-tap growth media, and grown for 10h, 12h, 14h, 16h, 18h or 20h.

extract_protocol:
A spore inoculum (~5-10 ul of 1x10^8 spores) sufficient to reach an OD600 of 0.35 after 8 hours of growth was added to 35ml of MYM tap media in 250 ml flasks containing springs.  Following growth to the chosen time point, the entire content of the flask was transferred to a 50 ml falcon tube for crosslinking, which was carried out by incubation at 30oC for 30 mins with 1% final concentration of formaldehyde (v/v).  Crosslinking was quenched by incubation at room temperature with glycine (final concentration of 125 mM).  Mycelium was harvested by centrifugation 4000 rpm at 4oC for 10 min and washed twice with ice cold PBS before transfer to a 2 ml centrifuge tube.  Pellets were resuspended in 0.75 ml lysis buffer (10 mM Tris-HCl pH 8.0, 50 mM NaCl, 10 mg/ml lysozyme, 1x protease inhibitor-Roche1186170001) and incubate at 37C for 10-25 min.  Then 0.75 ml 1x IP buffer (100mM tris-HCl pH 8.0, 250 mM NaCl, 0.5% Triton x-100, 0.1% SDS, 1x protease inhibitor (Roche)) was added and samples mixed by pipetting up and down.  Samples were sonicated 7x at 50Hz, 10 sec/cycle with a 1 min incubation on ice after each cycle.  DNA fragmentation was checked by agarose gel electrophoresis following phenol extraction of 25 µl of the crude lysate mixed with 75 µl of TE buffer with 100-200 µl of phenol/chloroform.   Contaminating RNA was removed with 2 µl RNase (1mg/ml) added to extracted DNA followed by an incubation for 30 min at 37°C. A smear of DNA from 200 to 1000 bp with the majority of DNA 200-400 bp should be visible. Crude lysate was centrifuged at 13,000 rpm for 15 minutes at 4°C to clear the sample of cell debris.  M2 affinity beads (Sigma-Aldrich #A2220) were prepared by washing in ½IP buffer following manufacturers instructions.  The cleared lysate was incubated with 40 µl of washed M2 beads and incubated for 4 h at 4C in a vertical rotor.  The lysate was removed and the beads pooled into one 1.5 microfuge tube and washed in 0.5 IP buffer.  The beads were transferred to a fresh microfuge. tube and washed a further 3 times removing as much buffer as possible without disturbing the beads.  The DNA-protein complex was eluted from the beads with 100 µl elution buffer (50 mM Tris-HCl pH7.6, 10mM EDTA, 1% SDS) by incubating at 65°C overnight.  Removing the ~100µl elution buffer, an extra 50 µl of elution buffer was added and further incubated at 65oC for 5 min.   To extract the DNA 150 µl eluate, 2 µl proteinase K (10 mg/ml) was added and incubated 1.5 hrs at 55oC.   To the reaction 150 µl phenol-chloroform was added.  Samples were vortexed and centrifuged at full speed for 10 min.  The aqueous layer was extracted and purified using the Qiaquick column from Qiagen with a final elution using 50 µl EB buffer (Qiagen).   The concentration of samples were determined using Quant-iT™ PicoGreen ® dsDNA Reagent (Invitrogen) or equivalent kit or by nanodrop measurement.
Cells were treated with formaldehyde to crosslink DNA and protein, lysed, sonicated and the tagged protein/DNA complexes were immunoprecipitated using anti-flag antibody bound M2 beads.
DNA libraries were prepared for sequencing using standard Illumina protocols.

tag: growth time point

tag: chip-antibody

value: ANTI-FLAG M2 Affinity Gel (cat number A2220)

tag: genotype/variation

value: WT


title: Lactobacillus plantarum ATCC14917 rep2

city: Bari

first: Maria

last: De Angelis

state: Italy

address: Via G. Amendola, 165/a

department: Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari Italy

country: Italy

institute: University of Bari

description:
replicate 2
B6_CTTGTA

data_processing:
DNAStar Lasergene Genomics Suite.  Sequenced reads generated for each of the two experimental con-  ditions were mapped against the reference genome of Lactobacillus plantarum JDM1 using the QSeq (DNAStar package) application in order to quantify gene expression levels of the bacterium for each experimental condition. Mapped  read count normalization was applied to the data based on the  number of reads per kilobase of coding sequence per million  mapped reads (RPKM) (Mortazavietal.,2008).
Genome_build: ASM2308v1
Supplementary_files_format_and_content: Tab-delimited text files include expression values (RPKMs) for each RNA molecule. RNA-Seq analysis of sequence data generated was undertaken  using the Array star QSeq application of the DNA Star Lasergene Genomics Suite (DNASTAR,Inc.,Madison,USA).

organism: Lactiplantibacillus plantarum

source_name: bacteria isolated from cheese

growth_protocol: strains were growth in MRS broth until the stationary phase was achieved.

extract_protocol:
Total extraction was carried put using the RiboPure-bacteria Ambion RNA extraction kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Stationary-phase cell were harvested from MRS broth, washed in phosphate buffer and centrifuged. Cell pellets from the same amounts of cells were used for RNA extraction.

tag: cheese type

value: type strain


title: HUVEC_Foxq1_2

description:
total mRNA
Deseq_Foxq1_vs_Control.txt


title: HUVEC_Foxq1_1

description:
total mRNA
Deseq_Foxq1_vs_Control.txt


title: HUVEC_Foxf2_2

description:
total mRNA
Deseq_Foxf2_vs_Control.txt


title: Western_diet_Replicate 2

city: East Lansing

first: James

last: Luyendyk

state: MI

address: 1129 Farm Lane

department: Pathobiology and Diagnostic Investigation

institute: Michigan State University

data_processing:
Raw BCL files are converted to fastQ files using the Illumina Casava software
The RNA sequence reads were mapped to the mouse reference transcriptome sequence (mm10) using TopHat version 2.0.4.
Parameters for TopHat included the --b2-fast, --transcriptome-only, and passing the refFlat.txt file through the –G parameter.
Differential expression was performed using the CuffDiff algorithm.
CummeRBund was used to visualize and categorize the data from CuffDiff into tables of differentially expressed genes using R (version 2.15.1).
Significant results are represented as fold change of HFD with dabigatran relative to HFD alone, with a q-value less than 0.05, where q-value is the false discovery rate (FDR) version of a p-value, such that a q-value <0.05 is equivalent to controlling the FDR at the 5% rate.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: FPKM files output from CuffDiff

source_name: Liver, High fat diet 3 months

extract_protocol:
Total RNA was isolated from approximately 50 mg of snap frozen liver using TRI Reagent (Molecular Research Center) per the manufacturers instructions
The RNA-seq library preparation was performed using the TruSeq RNA Sample Preparation Kit (illumina FC-122-1001).

value: liver

value: High fat diet 3 months


title: Western_diet_dabigatran_Replicate 2

source_name: Liver, High fat diet+dabigatran 3 months

value: High fat diet+dabigatran 3 months


title: Western_diet_dabigatran_Replicate 1


title: Lactobacillus plantarum CC1 rep2

description:
replicate 2
B5_GGCTAC

value: caciocavallo


title: Lactobacillus plantarum AS52 rep2

description:
replicate 2
B3_GATCAG

value: asiago


title: HUVEC_Control_2

description:
total mRNA
Deseq_Foxf2_vs_Control.txt
Deseq_Foxf2+Foxq1+ZIC3_vs_Control.txt
Deseq_Foxq1_vs_Control.txt
Deseq_ZIC3_vs_Control.txt


title: Western_diet_Replicate 1


title: Lactobacillus plantarum PRME511 rep2

description:
replicate 2
B2_ACTTGA

value: parmigiano reggiano


title: HUVEC_Foxf2_1

description:
total mRNA
Deseq_Foxf2_vs_Control.txt


title: HUVEC_Control_1


title: Lactobacillus plantarum CCG6 rep2

description:
replicate 2
B1_CAGATC

value: caciotta cheese


title: Western_diet_Replicate 0


title: Mutant 20h

source_name: S. venezualae MtrA::apr pMS82 MtrA 3xFlag

tag: flag tag

value: 3x Flag tag

value: MtrA::apr pMS82 MtrA


title: Rnd Hexa

city: Szeged

first: Attila

last: Szűcs

address: Somogyi utca 4

department: Faculty of Medical Research

country: Hungary

institute: University of Szeged

data_processing:
PacBio ReadsofInsert.1 version 2.3.0
Mapping with GMAP version (2015-12-31) with default parameters
Not HSV-1 specific reads were removed from further analysis using samtools
Mapped reads were count by BedTools with the following criterias: 1, Only reads with polyA tail were counted 2, reads mapped to the longest isoforms or transcripts without isoforms were always counted 3, other reads were counted only, where the TSS and the reads 5' prime location were no longer than 10 bp away 4, other reads were sismissed from calculation, because we can not determine exactly to which isoforms belong to reads
We calculate normalised expression values with the following formula (y=a*(bx)^c*e^-(dx), where a=0.001288287,b=0.008581223,c=4.052790325,d=0.003154719,e=2.195216193) to correct the bias of size preferences of PacBio RSII sequencing
Genome_build: X14112.1
Supplementary_files_format_and_content: Expression values in excel format

organism: Human alphaherpesvirus 1

source_name: HSV1 infected Vero cells

extract_protocol:
After total RNA isolation, mRNA were extracted by PolyA primers or Ribodepletion were used
Libraries were prepared using PAcBio default protocol

tag: mrna purification

value: Ribodepletion

tag: cdna preparation

value: Random Hexa

tag: size selection

value: No size selection


title: No size selected polyA

value: Poly(A) selection

value: polyA


title: Lactobacillus plantarum CC1 rep1

description:
replicate 1
A5_ACAGTG


title: Lactobacillus plantarum ATCC14917 rep1

description:
replicate 1
A6_GCCAAT


title: 5+ kb size selected polyA

value: BluePippin prefer mote than 5 kb


title: Mutant 18h

value: ANTI-FLAG M2 Affinity Gel (cat number A2220)


title: Mutant 16h


title: HUVEC_Control_3

value: umbilical vein


title: Mutant 14h


title: Lactobacillus plantarum PER54 rep2

description:
replicate 2
B4_TAGCTT

value: pecorino romano


title: Lactobacillus plantarum AS52 rep1

description:
replicate 1
A3_TTAGGC


title: Lactobacillus plantarum CCG6 rep1

description:
replicate 1
A1_ATCACG


title: 2-3 kb size selected polyA

value: BluePippin prefer 2-3 kb


title: Mutant 12h


title: Lactobacillus plantarum PRME511 rep1

description:
replicate 1
A2_CGATGT


title: 0.8-2 kb size selected polyA

value: BluePippin prefer 0.8-2 kb


title: Mutant 10h


title: HGEPp_cellular

status: Public on Jul 11 2017

city: Cincinnati

first: Scott

middle: M

last: Langevin

state: OH

address: 160 Panzeca Way, ML0056

department: Department of Environmental Health

institute: University of Cincinnati College of Medicine

description: microRNA

data_processing:
Base calling software: Casava 1.8
Preprocessing: Sequence reads were pre-processed to remove adapters and retain only 16-30 base pair- length reads
Alignment: Reads were aligned to the reference human genome (hg19) using the Bowtie aligner
Counts: The reads aligning to each known miRNA were counted using Bioconductor packages for next-generation sequencing data analysis based on miRNA definitions in miRBase database
Normalized abundance measures: RPKM
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file is in .csv format and contains a table of miRNA transcripts (rows) and raw counts and normalized abundance (RPKM) data for each sample (columns)

source_name: primary ginvival epithelial cells: cells

growth_protocol: Cells were cultivated in supplier-recommended media with 10% fetal bovine serum (FBS) that was super-depleted of exosomes via 18 hour ultracentrifugation at 100,000g (verified via nanoparticle tracking analysis) and 1% penicillin/streptomycin at 37°C with 5% CO2 in 150 cm2 flasks with 25mL media. To achieve adequate volume for exosome isolation, cells were cultured in 2-pair sets of flasks in triplicate (6 flasks total per cell-line). Culture media were replaced approximately 48 hours prior to cells reaching 80-90% confluence; media and cells were respectively collected after 48 hours. The media from each 2-flask pair were combined (50mLtotal). After media was harvested, cells were detached from each flask and pooled for each cell-line.

extract_protocol:
Total RNA was extracted from each exosome pellet using the miRNeasy Micro kit (Qiagen, Valencia, CA) according to the manufacturer’s suggested protocol; total RNA was also extracted from the pooled cells for each respective cell-line the miRNeasy Micro Kit (Qiagen), with 7.5 x105 cells in each reaction.
The NEBNext small RNA sample library preparation kit (New England BioLabs, Ipswich, MA) was used with 20 ng to 1 µg of total RNA in a 6-µL solution as input, following the manufacturer’s protocol with modification of library size selection

tag: cell line

value: HGEPp

tag: culture media

value: CnT-Prime

tag: source

value: cellular


title: FaDu_cellular

description: microRNA

source_name: HNSCC cell line: cells

value: FaDu

value: MEM


title: Cal27_cellular

description: microRNA

value: Cal 27

value: DMEM


title: HGEPp_1

description: microRNA

source_name: primary ginvival epithelial cells: small extracellular vesicles

value: small extracellular vesicles


title: Detroit562_cellular

description: microRNA

value: Detroit 562


title: HGEPp_3

description: microRNA


title: Cal27_3

description: microRNA

source_name: HNSCC cell line: small extracellular vesicles


title: HGEPp_2

description: microRNA


title: Lactobacillus plantarum PER54 rep1

description:
replicate 1
A4_TGACCA

tag: strain


title: Cal27_2

description: microRNA


title: Cal27_1

description: microRNA


title: FaDu_3

description: microRNA


title: 3-5 kb size selected polyA

value: Poly(A) selection

value: BluePippin prefer 3-5 kb


title: FaDu_2

description: microRNA


title: Detroit562_3

description: microRNA


title: FaDu_1

description: microRNA


title: Detroit562_2

description: microRNA


title: Detroit562_1

description: microRNA


title: H413_3

description: microRNA


title: H413_2

description: microRNA


title: TS1528B2 RNA-seq_MDBK_tinyLNA-17

city: Copenhagen N

first: Troels

middle: K H

last: Scheel

state: Copenhagen

address: Blegdamsvej 3

department: Institute for Immunology and Microbiology

country: Denmark

institute: University of Copenhagen

description:
mRNA-seq
Processed data file: Table_S5.txt

data_processing:
AGO-CLIP data was processed as described (Moore et al. 2014 Nature Protocols). The deposited CLIP sequences are composed of (i) the index (4 nts), (ii) the RL5 sequence (AGGGAGGACGAUGCGG), (iii) a 5N degenerate linker, (iv) the actual read sequence and, depending on read length (iv) a complete or partial RL3 sequence (GTGTCAGTCACTTCCAGCGGATCTCGTATGCCGTCTTCTGCTTG).
Processed reads were aligned to the bovine genome (BosTau7) using Bowtie. After mapping, reads were collapsed on coordinates such that only those with sufficiently different degenerate linkers were kept; this distinguished unique binding events from PCR duplicates. For AGO-CLIP data, significant peaks were identified using the Homer tool. Clustering of AGO-bound regions, annotation was done essentially as described (Luna et al. 2015 Cell). For annotation on cow, BosTau7 GTF annotation were downloaded from the USCS genome table browser and intersected with CLIP-derived clusters. Quality filtered RNA-seq data were mapped to the cow (BosTau7) genome using Bowtie. The number of reads overlapping each gene (USCS Table Browser and Ensembl annotation) was counted with htseq-count. Expression data was processed essentially as described (Luna et al. 2015 Cell) using the edgeR package in R. RNA-seq derived gene expression data was merged on gene name with AGO-CLIP data to allow CLIP-guided representation of changes to gene expression.
Genome_build: BosTau7 (Btau_4.6.1)
Supplementary_files_format_and_content: Table_S1. AGO-CLIP alignment statistics. Alignment statistics are given with indication of CLIP type (CLIP.type), CLIP- and sequence-experimental ID (CLIP.exp; Seq.pool), sequencing index (Index), small RNA treatment (Small.RNA), the number of unique standard CLIP reads aligned to BosTau7 after collapsing for PCR duplicates (Collapsed.reads), the percentage of viral (BVDV) reads in the sample (Virus.reads.perc), the number of miRfirst and miRlast type chimeras (miRfirst; miRlast), the percentage of chimeras compared to total uniquely mapped reads (perc.miRfirst; perc.miRlast) and the estimated “missing” number of total chimeras and miR-17 chimeras (Estim.perc.missing.chim; Estim.perc.missing.miR-17.chim). In the case of BVDV infected samples, these numbers were calculated from virus-specific chimeras. In the case of miR-17 inhibitor treated samples, it was calculated based on the percentage of miR-17 chimeras of total. Provided as an Excel file.
Supplementary_files_format_and_content: Table_S2. Annotation of significant AGO-CLIP peaks, AGO-CLIP read clusters and overlapping miRNA-target chimeras. Significant AGO-CLIP peaks (FDR<0.001) are listed and annotated with peak ID (PeakID), chromosome (Chr_SignP), start coordinate (Start_SignP), end coordinate (End_SignP), peak height (PH) and strand (Strand_SignP). In addition are given details for the corresponding AGO-CLIP cluster (all overlapping reads clustered) with chromosome (Chr_Cluster), start coordinate (Start_Cluster), end coordinate (End_Cluster), cluster ID (ClusterName), peak height (PH_Cluster), strand (Strand_Cluster), BC (BC_Cluster), overlap with chimeras in nucleotides (Chim_overlap_Cluster_nt) or presences/absence (Chim_overlap_Cluster), gene ID (GeneID), region annotation (Region) and rmsk annotation (rmsk). Overlap with miRNA-chimera clusters is annotated, including information on chromosome (Chr_Chim), start coordinate (Start_Chim), end coordinate (End_Chim), chimera cluster ID (ChimName), peak height (PH_Chim), strand (Strand_Chim), cognate miRNA (miRNA), start distance between individual chimeras within the chimera cluster (Start_dist), BC (BC_Chim), gene ID (GeneID_Chim), region (Region_Chim) and miRNA family (Type.miR). Finally, the following annotation is given for the significant peak: gene ID (GeneID_SignP), region (Region_SignP), unique ID for the combined significant peak/cluster/chimera cluster (UniqueID), chromosome length (Chr.len) and DNA sequence (Seq_SignP). Lastly, presence/absence is indicated for 6mer, 7merA1, 7merM8 and 8mer seed sites of the 50 most abundant miRNAs. Provided as compressed txt file.
Supplementary_files_format_and_content: Table_S3. List and annotation of individual miRNA-target chimeras. All individual miRNA-target chimeras are listed with chromosome (Chr), start coordinate (Start), end coordinate (End), read name (ReadName), collapsing factor (PH), strand (Strand), cognate miRNA (miR1), start coordinate for miRNA within the read (miRstart), start coordinate for target sequence within the read (targetStart), length of target sequence (targetLen), target sequence (targetSeq), chimera sequence (Seq), data set (DataSet), chimera type (Type), gene ID (GeneID), region (Region), miRNA family (Type.miR), rmsk overlap in percentage (rmsk_perc) and rmsk (rmsk). Provided as compressed txt file.
Supplementary_files_format_and_content: Table_S5. Gene expression changes for tinyLNA-17 treated MDBK cells. Alignment statistics are given gene-wise for mRNA-seq data, including gene id (Gene_ID), read numbers for mock 1 (Mock1), mock 2 (Mock2), tinyLNA-17 1 (tinyLNA17.1), and tinyLNA-17 2 (tinyLNA17.2), log2 fold change mock/tinyLNA-17 (logFC), log(CPM) (logCPM), p-value (PValue) and FDR (p.adj). Provided as a txt file.

organism: Bos taurus

source_name: MDBK

extract_protocol:
Total RNA was isolated via Trizol extraction and DNase treated.
RNA libraries were prepared for sequencing using standard Illumina protocols with polyA selection.

tag: sample subseries

value: RNA-seq:tinyLNA-17 vs. Mock

tag: percentage virus (bvdv) reads

value: MDBK

tag: small rna

tag: time point

tag: index

value: GTGAAA


title: TS1528B1 RNA-seq_MDBK_tinyLNA-17

value: CTTGTA


title: TS1524H CLIP-seq_MDBK_LNA

description:
CLIP-seq
Processed data file: Table_S1.xlsx; Table_S2.txt; Table_S3.txt

extract_protocol:
UV crosslinked cells were lysed in 1x PXL buffer, lysates were DNase treated, partially RNaseA digested, clarified by centrifugation, and Argonaute-RNA complexes isolated with pan-Ago 2A8 antibody.
Libraries were prepared as in Moore et al. 2014 Nature Protocols, but with the following modifications: The 2nd PCR step was used to introduce library specific indices that were additionally compatible with MiSeq sequencers using version2 chemistry.

value: AGO-CLIP:tinyLNA-17 vs. Mock

value: TGCA


title: H413_1

description: microRNA


title: TS1524G CLIP-seq_MDBK_LNA

value: CATG


title: TS1524F CLIP-seq_MDBK_LNA

value: ACCG


title: H413_cellular

description: microRNA

value: cellular


title: TS1528A1 RNA-seq_MDBK_Mock

value: Mock

value: ACAGTG


title: TS1486N CLIP-seq_MDBK_NA

value: AGO-CLIP

value: CCGA


title: TS1524B CLIP-seq_MDBK_Mock

value: GATC


title: TS1524E CLIP-seq_MDBK_LNA

value: GTGC


title: TS1524D CLIP-seq_MDBK_Mock

value: GCAT


title: TS1524C CLIP-seq_MDBK_Mock

value: CGTA


title: TS1524A CLIP-seq_MDBK_Mock

value: CTAG


title: TS1528A2 RNA-seq_MDBK_Mock

value: RNA-seq:tinyLNA-17 vs. Mock

value: MDBK

value: GCCAAT


title: TS1486K CLIP-seq_MDBK_NA

value: AGTG


title: TS1486M CLIP-seq_MDBK_NA

value: ATGC


title: TS1486L CLIP-seq_MDBK_NA

value: TACG


title: TS1486J CLIP-seq_MDBK_NA

value: TCAC


title: TS1486D CLIP-seq_MDBK_NA


title: TS1486H CLIP-seq_MDBK_NA

value: CATG


title: TS1486I CLIP-seq_MDBK_NA

value: Mock

value: TGCA


title: TS1486G CLIP-seq_MDBK_NA

value: AGO-CLIP

value: ACCG


title: TS1486E CLIP-seq_MDBK_NA


title: TS1468O CLIP-seq_MDBK_NA


title: TS1486F CLIP-seq_MDBK_NA


title: TS1383H CLIP-seq_MDBK_NA


title: TS1468N CLIP-seq_MDBK_NA


title: TS1383G CLIP-seq_MDBK_NA


title: TS1486O CLIP-seq_MDBK_NA

value: CTCC


title: TS1383E CLIP-seq_MDBK_NA


title: TS1383F CLIP-seq_MDBK_NA


title: TS1383C CLIP-seq_MDBK_NA

value: GTGC


title: TS1468M CLIP-seq_MDBK_NA


title: TS1383A CLIP-seq_MDBK_NA


title: TS1383B CLIP-seq_MDBK_NA

value: GCAT


title: TS1330J CLIP-seq_MDBK_NA


title: TS1330I CLIP-seq_MDBK_NA

value: CCGA


title: TS1330E CLIP-seq_MDBK_NA


title: TS1330D CLIP-seq_MDBK_NA


title: TS1330F CLIP-seq_MDBK_NA


title: TS1330C CLIP-seq_MDBK_NA


title: TS1330G CLIP-seq_MDBK_NA


title: Input DNA

city: Irvine

first: Jiejun

last: Shi

address: 5270 California Ave

department: School of Medicine

institute: University of California Irvine

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie v1.1.0
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS-1.4.2

source_name: HeLa cells

growth_protocol: Cells were maintained in DMEM with 10% FBS, 5% CO2, at 37 degrees

extract_protocol:
Genomic DNA was isolated from crosslinked sheared chromatin subject to immunoprecipitation with the Pol II antibody
ChIP–seq samples were sequenced using the Illumina Solexa Hiseq 2000.

treatment_protocol: Cells were transfected with siRNAs and harvested for ChIP after 72 hours

tag: treatment

tag: antibody

value: HeLa


title: Pol II ChIP-seq siKAT2A/B replicate 2

value: Pol II Active Motif 39097


title: Pol II ChIP-seq siRNA control replicate 1

value: non-targeting control siRNA


title: Pol II ChIP-seq siRNA control replicate 2


title: Pol II ChIP-seq siKAT2A/B replicate 1


title: TTP_CLIP_INPUT

city: Rochester

first: Wenqian

last: Hu

state: Minnesota

address: 200 First St SW, GU16-01A

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

description:
Zfp36_binding_sites.xlsx
CLIP-seq

data_processing:
adapters were removed from the ribosome profiling and CLIP-seq reads
Reads were mapped to mouse genome (mm10) using Tophat
The TE (translation efficiency) was determined by the ratio of ribosome profiling reads to RNA-seq reads in the coding regions of mRNAs
The CLIP-seq peak calling was performed using the Piranha pacakge (v. 1.2.1), the reads from the input RNA was used for normalization in the peak calling process
Genome_build: mm10
Supplementary_files_format_and_content: Files containing: TE (translational efficiency) for each mRNA expressed in BMDMs; the peaks of Zfp36 binding sites determined from the Zfp36 CLIP-seq

source_name: bone marrow derived macrophage

growth_protocol: BMDMs were obtained by culturing bone marrow cells in the L929 supplemented (20%) DMEM medium (10% FBS) for 7 days, with a medium change on Day 4.

extract_protocol:
cell lysate extraction for ribosome profiling analysis and RNA isolation were performed in accordance with the protocols detailed in Ingolia et al., 2012 (PMCID: PMC3535016); The CLIP-seq was performed in accordance with the protocols described in Moore et al., 2014 (PMCID: PMC4156013 ). The anti-V5 antibody in the CLIP-seq was from Bethyl Lab (Cat# A190-120A, note: the vendor did not provide the lot number)
The ribosome profiling libraries were constructed in accordance with the protocol described in Ingolia et al., 2012 (PMCID: PMC3535016); the RNA-seq libraries were constructed on the rRNA-depleted (ribo-zero) total RNAs using the TRUE-seq kit (illumnia); the CLIP-seq libraries were constructed in accordance with the protocols detailed in Moore et al., 2014 (PMCID: PMC4156013 )

treatment_protocol: LPS was added to the BMDM culture at a final concentration of 100ng/ml

tag: agent

value: LPS treatment (100ng/ml)

tag: time

tag: ip antibody

tag: cell type

value: BMDM


title: TTP_CLIP_A

description:
Zfp36_binding_sites.xlsx
CLIP-seq

value: anti-V5 antibody (Bethyl Lab, Cat# A190-120A)


title: TTP_CLIP_B

description:
Zfp36_binding_sites.xlsx
CLIP-seq


title: BMDM_T6A

description:
TE.xlsx
total RNA-seq


title: TS1383D CLIP-seq_MDBK_NA

value: MDBK


title: BMDM_T6B

description:
TE.xlsx
total RNA-seq


title: BMDM_T4B

description:
TE.xlsx
total RNA-seq


title: BMDM_T4A

description:
TE.xlsx
total RNA-seq


title: BMDM_T2B

description:
TE.xlsx
total RNA-seq


title: BMDM_T1B

description:
TE.xlsx
total RNA-seq


title: BMDM_T2A

description:
TE.xlsx
total RNA-seq


title: BMDM_T1A

description:
TE.xlsx
total RNA-seq


title: BMDM_T0B

description:
TE.xlsx
total RNA-seq

value: control


title: BMDM_T0A

description:
TE.xlsx
total RNA-seq


title: TS1330H CLIP-seq_MDBK_NA

value: ATGC


title: MCF10A rna-BS

city: SuZhou

first: Zhen

last: Wei

address: 111 Ren'ai Road Suzhou Dushu Lake Science and Education Innovation District

country: China

institute: Xi'anJiaoTong Liverpool university

data_processing:
Library strategy: RNA Bisulfite-Seq
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using trim_galore with default settings
Bisulfite converted reads are mapped to genome using Bismark aligner, and the Methylation sites are called using Bismark methylation extractor
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file

growth_protocol: MCF10A and MDA-MB-468 (MDA468) cells were obtained from ATCC. Cells were cultured and maintained in DMEM media as per ATCC instructions

extract_protocol:
For BS-Seq total RNA was isolated from MCF10A and MDA_MB-468 cells and was enriched for polyA+ RNA using poly-A selection kits. The purified RNA is subjected to sodium bisulfite treatment at 60 degrees for 8 hours.
Libraries were prepared according to Illumina's instructions

tag: tissue

value: Epithelial


title: MDA468 rna-BS

value: Cancer


title: BMDM_R6B

description:
TE.xlsx
ribosome profiling (Ribo-Seq)


title: BMDM_R2B

description:
TE.xlsx
ribosome profiling (Ribo-Seq)


title: BMDM_R4B

description:
TE.xlsx
ribosome profiling (Ribo-Seq)


title: BMDM_R6A

description:
TE.xlsx
ribosome profiling (Ribo-Seq)


title: BMDM_R1A

description:
TE.xlsx
ribosome profiling (Ribo-Seq)


title: BMDM_R1B

description:
TE.xlsx
ribosome profiling (Ribo-Seq)


title: BMDM_R4A

description:
TE.xlsx
ribosome profiling (Ribo-Seq)


title: BMDM_R0B

description:
TE.xlsx
ribosome profiling (Ribo-Seq)


title: Wild type mouse_3

city: Worcester

first: Rui

last: Li

state: Massachusetts

address: 364 Plantation Street, LRB

department: MCCB

institute: University of Massachusetts Medical School

data_processing:
CLC Genomic Workbench 7.5
Aligned reads to the genome with 0.95 similarity and 0.9 coverage threshold
Quantified gene expression with "uniq exon read count"
Used DESeq2 for differential expression analysis (p value adjusted by FDR method)
Genome_build: Mus_musculus.GRCm38.dna.fa/Mus_musculus.GRCm38.78.gtf
Supplementary_files_format_and_content: [.txt] file contains gene expression values (uniq exon count) and DESeq2 analysis result (KO vs WT)

source_name: Wild type, brain

growth_protocol: Generated from breeding a heterozygous Kdm5c deficient female on the C57BL/6 background with a wild type 129 male.

extract_protocol:
Qiagen Rneasy Mini
Illumina TruSeq RNA library
Illumina protocol for mRNA sequencing

tag: Sex

value: Male

tag: age

value: Adult

tag: genotype/variation

value: Wild type

value: brain


title: Wild type mouse_2


title: Wild type mouse_1


title: Kdm5c deficient mouse_3

source_name: Kdm5c deficient, brain

value: Kdm5c deficient


title: GEK36

city: Porto Alegre

first: Guilherme

last: Cordenonsi da Fonseca

state: RS

address: Av. Bento Gonçalves, 9500

department: Centro de Biotecnologia

country: Brazil

institute: UFRGS

data_processing:
Illumina Casava1.7 software used for basecalling.
low quality reads with 'n' were removed using PrinSeq script (Schmieder and Edwards, 2011)
Unique raw reads counted obtained with perl scripts
Supplementary_files_format_and_content: tab-delimited text files with abundance of unique sequences

source_name: root treatment

growth_protocol: Soybean seeds were germinated in moistened filter paper, 25°C for 2 days. The seedlings were growth in hydroponic system with Hoagland's nutrient solution for 15 days.

extract_protocol: Total RNA was isolated from leaves and roots using Trizol (Invitrogen, CA, USA) according to the manufactures’ protocol, and the RNA quality was evaluated by electrophoresis on a 1% agarose gel. Total RNA (> 10 μg) was sent to Fasteris Life Sciences SA (Plan-les-Ouates, Switzerland) for processing. Eight smallRNAs libraries were constructed. Four libraries from leaves, two for each treatment (salt stress and control), and the same for roots. Briefly, the construction of the small RNA libraries consisted of the following successive steps: acrylamide gel purification of the RNA bands corresponding to the size range 20-30 nt, ligation of the 3p and 5p adapters to the RNA in two separate subsequent steps, each followed by acrylamide gel purification, cDNA synthesis followed by acrylamide gel purification, and a final step of PCR amplification to generate a cDNA colony template library for Illumina sequencing.

treatment_protocol: For the stress treatment 200mM of NaCl were added to the nutrient solution of one group of plantlets and nothing was added to the control group. After 4 hours the the leaves and roots from both groups were harvested to RNA isolation.

tag: sample

value: pool

value: salt stress

value: root


title: BMDM_R0A

description:
TE.xlsx
ribosome profiling (Ribo-Seq)

tag: strain


title: GEK35


title: Kdm5c deficient mouse_1


title: GEK34

source_name: leaves treatment

value: leaves


title: GEK33


title: Kdm5c deficient mouse_2


title: BMDM_R2A

description:
TE.xlsx
ribosome profiling (Ribo-Seq)

value: LPS treatment (100ng/ml)


title: GEK31

source_name: root control


title: GEK32


title: Adult (RNA-seq)

city: Nanjing

first: Bin

address: Wenyuan road NO.1

department: School of Life Science

institute: Nanjing Normal university

data_processing:
Basecalls performed using CASAVA version 1.8.2
BS-seq reads were aligned to theTribolium castaneum genome assembly using BSMAP version 2.73
Aligned reads were sorted and remove duplication reads with samtools version 0.1.19
calculating the methylated and unmethylated reads count in each C sites.
Basecalls performed using CASAVA version 1.8.2
RNA-seq reads were aligned to the Tribolium castaneum reference gene using SOAP2 version 2.21
calculating the reads count on each gene and normalized with RPKM method.
Genome_build: http://beetlebase.org/, Tribolium castaneum v3.0
Supplementary_files_format_and_content: Sample-cout.tar.gz,cout file foramt:1.chromosome number, 2.C site position, 3.plus or minus chain, 4.C type, 5.basic C type, 6.copy number, 7.the number of methylated reads, 8.the number of non-methylated reads, 9.bernoulli distribution e-value. This file contains the depth of all of the cytosines in four life stages of Tribolium castaneum.
Supplementary_files_format_and_content: Sample.Gene.rpkm.txt: the summary of gene expression level in the four life stages of Tribolium castaneum.

organism: Tribolium castaneum

source_name: whole bdoy

growth_protocol: The Tribolium castaneum strain GA-1 were reared in whole wheat flour containing 5% yeast at 30°C

extract_protocol:
Total RNA was extracted from each sample by using the Invitrogen TRIzol® Reagent, and then treated with RNase-free DNase I (Ambion, Guangzhou, China) for 30 minutes. The integrity of total RNA was checked using an Agilent 2100 Bioanalyser.
The mRNA was enriched by using oligo (dT) magnetic beads (Invitrogen), the enriched mRNA was fragmented into short fragments (about 200bp) with fragmentation buffer, and then the first strand cDNA was synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double strand cDNA was purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and dA addition. Finally, sequencing adapters were ligated to the fragments. The fragments were purified by Agarose gel electrophoresis and enriched by PCR amplification. After a series of detection processes, the cDNA library products were sequenced using the Illumina Genome Analyser.

value: whole body

value: 3d adult


title: GEK30

source_name: leaves control


title: abi5-2

city: Beijing

first: chao

last: bi

address: Tsinghua University, Beijing

institute: Tsinghua University

description: Processed data file: genes.fpkm_table.xlsx

data_processing:
The raw reads mapped to the Arabidopsis genome (TAIR10) with TopHat2 and calculate the FPKM of each gene with cuffdiff. All of the parameters set to the default.
Genome_build: TAIR10
Supplementary_files_format_and_content: genes.fpkm_table.xlsx: Excel file includes FPKMs for each sample.

organism: Arabidopsis thaliana

source_name: seed, ABI5-/-

growth_protocol: 16-h light/8-h dark photoperiod for 24 h.

extract_protocol:
Total RNA was isolated using a seed RNA Extraction Kit (BioTeke, China, product No. RP1201), treated with RNase-free DNase I (NEB, USA, product No. M0303) at 37°C for 30 min to degrade genomic DNA, and purified by using an RNA Purification Kit (BioTeke, China, product No. RP1801).
The construction of RNA libraries, RNA sequencing and bioinformatics analysis were performed at Bionova company (Beijing, China).

tag: ecotype/background

value: Col

value: seed


title: abi5-1


title: Col-2

source_name: seed, wild type

value: wild type


title: Larva (RNA-seq)

value: 20d larva


title: Col-1


title: Adult (BS-seq)

extract_protocol:
Genomic DNA was extracted from a pool of 50 individuals for the four life stage samples of Tribolium castaneum: 3d embryo, late larva, 3d pupa and 6d adult, respectively, using the DNeasy Blood & Tissue Kit (Qiagen, CA).
5 ug genomic DNA from each sample spiked with 25ng unmethylated Lambda DNA (Promega, Madison, WI, USA) were fragmented to 100-300bp with Covarias sonication system (Covaris, MA), followed by blunt ending, 3’-end addition of dA. Cytosine-methylated adaptors were ligated to the fragmented DNA according to the manufacture’s introductions using T4 DNA ligase. The bisulfite conversion of sample DNA was carried out using ZYMO EZ DNA Methylation-Gold kit (ZYMO Research, Irvine, CA, USA) according to the manufacture’s introductions. The converted DNA was then amplified by 9 cycles of PCR with the PfuTurboCxHotstart DNA Polymerase (Agilent Technologies, CA).Paired-end sequencing was carried out using Illumina Genome Analyzers at the 90 bp read length.


title: Embryo (RNA-seq)

value: 3d embryo


title: GEK29

value: control


title: GEK40b

extract_protocol: Total RNA was isolated from the seed material using Trizol (Invitrogen, CA, USA) according to the manufactures’ protocol, and the RNA quality was evaluated by electrophoresis on a 1% agarose gel. Total RNA (> 10 μg) was sent to Fasteris Life Sciences SA (Plan-les-Ouates, Switzerland) for processing. Four paired-end mRNAseq libraries were constructed. Two for each treatment (salt stress and control). Briefly, the polyadenylated transcript sequencing (mRNA-seq) was performed using the following successive steps: Poli-A purification, cDNA synthesis using Poli-T primer shotgun to generate inserts of 500 nt, 3p and 5p pair-end adapters ligations, pre-amplification, colony generation and sequencing. The Illumina output data were sequence tags of 50 bases.

treatment_protocol: For the stress treatment 200mM of NaCl were added to the nutrient solution of one group of plantlets and nothing was added to the control group. After 4 hours the the leaves from both groups were harvested to RNA isolation.


title: Pupa (BS-seq)

extract_protocol:
Genomic DNA was extracted from a pool of 50 individuals for the four life stage samples of Tribolium castaneum: 3d embryo, late larva, 3d pupa and 5d adult, respectively, using the DNeasy Blood & Tissue Kit (Qiagen, CA).
5 ug genomic DNA from each sample spiked with 25ng unmethylated Lambda DNA (Promega, Madison, WI, USA) were fragmented to 100-300bp with Covarias sonication system (Covaris, MA), followed by blunt ending, 3’-end addition of dA. Cytosine-methylated adaptors were ligated to the fragmented DNA according to the manufacture’s introductions using T4 DNA ligase. The bisulfite conversion of sample DNA was carried out using ZYMO EZ DNA Methylation-Gold kit (ZYMO Research, Irvine, CA, USA) according to the manufacture’s introductions. The converted DNA was then amplified by 9 cycles of PCR with the PfuTurboCxHotstart DNA Polymerase (Agilent Technologies, CA).Paired-end sequencing was carried out using Illumina Genome Analyzers at the 90 bp read length.

value: 3d pupa


title: Col-3


title: abi5-3


title: Larva (BS-seq)

extract_protocol:
Genomic DNA was extracted from a pool of 50 individuals for the four life stage samples of Tribolium castaneum: 3d embryo, late larva, 3d pupa and 4d adult, respectively, using the DNeasy Blood & Tissue Kit (Qiagen, CA).
5 ug genomic DNA from each sample spiked with 25ng unmethylated Lambda DNA (Promega, Madison, WI, USA) were fragmented to 100-300bp with Covarias sonication system (Covaris, MA), followed by blunt ending, 3’-end addition of dA. Cytosine-methylated adaptors were ligated to the fragmented DNA according to the manufacture’s introductions using T4 DNA ligase. The bisulfite conversion of sample DNA was carried out using ZYMO EZ DNA Methylation-Gold kit (ZYMO Research, Irvine, CA, USA) according to the manufacture’s introductions. The converted DNA was then amplified by 9 cycles of PCR with the PfuTurboCxHotstart DNA Polymerase (Agilent Technologies, CA).Paired-end sequencing was carried out using Illumina Genome Analyzers at the 90 bp read length.


title: Embryo (BS-seq)

extract_protocol:
Genomic DNA was extracted from a pool of 50 individuals for the four life stage samples of Tribolium castaneum: 3d embryo, late larva, 3d pupa and 3d adult, respectively, using the DNeasy Blood & Tissue Kit (Qiagen, CA).
5 ug genomic DNA from each sample spiked with 25ng unmethylated Lambda DNA (Promega, Madison, WI, USA) were fragmented to 100-300bp with Covarias sonication system (Covaris, MA), followed by blunt ending, 3’-end addition of dA. Cytosine-methylated adaptors were ligated to the fragmented DNA according to the manufacture’s introductions using T4 DNA ligase. The bisulfite conversion of sample DNA was carried out using ZYMO EZ DNA Methylation-Gold kit (ZYMO Research, Irvine, CA, USA) according to the manufacture’s introductions. The converted DNA was then amplified by 9 cycles of PCR with the PfuTurboCxHotstart DNA Polymerase (Agilent Technologies, CA).Paired-end sequencing was carried out using Illumina Genome Analyzers at the 90 bp read length.


title: GEK40a


title: Day 7-ZIKV 3

city: Galveston

first: Grant

last: Hughes

state: TX

address: 301 University Boulevard

department: Pathology

institute: University of Texas Medical Branch

data_processing:
The quality of raw data from each library was controlled by CLC Genomic Workbench version 7.5.1.  Raw data were stripped of adapters and reads with quality score above 0.05 and less than 2 ambiguous nucleotides were retained. Reads without 3’ adapters and also reads with less than 16 nt were discarded from the libraries. Clean data considered as mappable reads for further analysis.
Tab separated files with the read sequences and their counts were used as input file for novel and homologous miRNA analysis using sRNAtoolbox. All known Ae. aegypti pre-miRNAs reported in miRBase 21 were used as reference for miRNA annotation.
Genome_build: Ae. aegypti genome (AaegL1)
Supplementary_files_format_and_content: text file, miRNA copy number

organism: Aedes aegypti

source_name: Day 7-ZIKV

extract_protocol:
Total RNA was extracted from infected and non-infected mosquito samples using mirVANA following the manufacturer’s protocol (Life Technologies).
The small RNA libraries were from pools at days 2, 7 and 14 post infection generated from both populations using the  New England Biolabs small RNA library protocol (New England Biolabs) at the UTMB’s Next Generation Sequencing (NGS) Core (Galveston, TX). The purified cDNA libraries were sequenced using the rapid run platform and single end 50 base sequencing by synthesis on an Illumina Hi-Seq 1500 using the TruSeq SBS kit v3.

treatment_protocol: Mosquitoes were provided either a ZIKV infectious blood meal or non-infectious blood meal

value: Galveston

tag: infection

value: ZIKV

value: Day 7

value: Whole mosquito


title: Day 7-ZIKV 2


title: GEK39b

value: pool

value: salt stress


title: Day 7-ZIKV 1


title: Pupa (RNA-seq)

extract_protocol:
Total RNA was extracted from each sample by using the Invitrogen TRIzol® Reagent,and then treated with RNase-free DNase I (Ambion, Guangzhou, China) for 30 minutes. The integrity of total RNA was checked using an Agilent 2100 Bioanalyser.
The mRNA was enriched by using oligo (dT) magnetic beads (Invitrogen), the enriched mRNA was fragmented into short fragments (about 200bp) with fragmentation buffer, and then the first strand cDNA was synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double strand cDNA was purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and dA addition. Finally, sequencing adapters were ligated to the fragments. The fragments were purified by Agarose gel electrophoresis and enriched by PCR amplification. After a series of detection processes, the cDNA library products were sequenced using the Illumina Genome Analyser.


title: 406_IA_3

city: Boston

first: Ramnik

last: Xavier

state: MA

address: 55 Fruit Street

department: Gastroenterology

institute: Massachusetts General Hospital

data_processing:
Whole transcriptome: Alignment with Tophat+Bowtie.
Whole transcriptome: Counting of transcripts with htseq-count.
Whole transcriptome: QC with RSeqC.
Whole transcriptome: Differential expression with EdgeR.
3' DGE: Alignment with BWA.
3' DGE: Counting of transcripts with custom python script.
3' DGE: QC with custom python script.
3' DGE: Differential expression with EdgeR.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.namesorted.htseq.txt: Tab-delimited text files include raw counts for each sample.

source_name: PBMCs, IA, donor 406

growth_protocol: hPBMCs were isolated and plated and stimulated for a total of 21 hours in human serum at 0.5% in Xvivo15 media.

extract_protocol:
RNA extraction using RNeasy Plus Mini kit from Qiagen using gDNA eliminator columns (no on-column DNase digestion needed).
The smart-seq2 protocol (Picelli et al., 2013) was modified for 20 ng total input RNA.

treatment_protocol: PBMCs were stimulated with 80uM IA or 0.1% DMSO control for 45 min, followed by 1ng/mL LPS stimulation for 20 hours, at which point supernatant was collected and spun down, pellet and adherent cells used for RNA isolation.

value: peripheral blood mononuclear cells (PBMCs)

value: IA, followed by LPS

tag: donor

tag: number of cells

value: 2 million

tag: rna ng/ul

tag: total volume

tag: collection buffer

value: ultrapure water

tag: plate (index)

tag: well

tag: i7 index 1

value: GTAGAGGA

tag: s

tag: i5 index 1

value: AGAGTAGA

tag: total rna

value: TCTACTCT


title: GEK39a

tag: treatment

tag: tissue

value: leaves


title: 406_IA_1

tag: cell type

value: CGAGGCTG


title: Day 7-Mock 3

source_name: Day 7-Mock

tag: strain

value: Mock

tag: time


title: 406_IA_2

value: AAGAGGCA


title: GEK38b

tag: sample

value: control


title: 406_DMSO_2

source_name: PBMCs, DMSO, donor 406

value: DMSO, followed by LPS

tag: donor

value: CAGAGAGG


title: GEK38a


title: 406_DMSO_3

tag: number of cells

value: GCTACGCT


title: 406_DMSO_1

tag: rna ng/ul

value: CTCTCTAC


title: 1685_IA_3

source_name: PBMCs, IA, donor 1685

tag: total volume

value: TATCCTCT

value: AGAGGATA


title: Day 7-Mock 1

value: Galveston

tag: infection

value: Day 7

value: Whole mosquito


title: Day 2-ZIKV 3

source_name: Day 2-ZIKV

value: ZIKV

value: Day 2


title: GEK37a

value: pool


title: GEK37b

value: leaves


title: Day 2-ZIKV 2


title: Day 7-Mock 2


title: 1685_IA_2

value: peripheral blood mononuclear cells (PBMCs)

value: IA, followed by LPS

value: 2 million

tag: collection buffer

value: ultrapure water

tag: plate (index)


title: Day 2-ZIKV 1


title: 1685_IA_1

tag: well

tag: i7 index 1

value: CGAGGCTG


title: HIF-1b ChIP-seq

city: Erlangen

first: Johannes

last: Schödel

address: Ulmenweg 18

institute: FAU Erlangen-Nürnberg

data_processing:
reads were aligned to the hg19 genome assembly using bowtie with the following configurations: -m1 –best --strata
The read number at one specific position was clamped to 5
Peaks were called using cisGenome
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated, score represent peak height

source_name: Renal tubular cells

growth_protocol: Primary human tubular cell cultures were maintained in Dulbecco’s modified Eagle’s medium/Ham’s F-12 supplemented with 2.5% (day 1) or 0% (day 2 onwards) fetal calf serum, 2 mM L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin, 5 μg/ml insulin, 5 μg/ml transferrin, and 5ng/ml selenium (Sigma), triiodothyronine (T3, Sigma) 10 ng/ml, hydrocortisone 1 mg/ml, epidermal growth factor 100 µg/ml (Peprotech). Epithelial origin was confirmed by immunocytochemistry for N- and E-Cadherin.

extract_protocol:
ChIP samples were prepared according to standard ChIP procedures (Millipore protocol) and D N A was isolated using a phenol/chloroform extraction.
ChIP-seq and FAIRE-seq library preparations were carried out using Illumina protocols and libraries were sequenced on HiSeq 2000/2500 platforms (Illumina)

treatment_protocol: Sub-confluent cell cultures were exposed to 1 mM dimethyloxalylglycine (DMOG, Cayman) to induce HIF.

value: renal tubular cells

tag: passages

tag: antibody

value: Novus HIF-1b (NB100-110)


title: HIF-1a ChIP-seq

value: Cayman HIF-1a (Cay10006421)


title: 1001957_4h_OCT_Contact2

city: Seoul

first: Han Young

last: Chung

address: 1 Gwanak-ro, Gwanak-gu, Seoul 151-742

country: South Korea

institute: Seoul National University

description: Sample 8 (4-2)

data_processing:
The Ribo-Zero rRNA removal kit (Epicentre, USA) was used for ribosomal RNA depletion according to manufacturer instructions.
Libraries for Illumina sequencing were made with the TruSeq Stranded mRNA sample prep kit (Illumina, USA) following the manufacturer’s protocol.
The quality of cDNA libraries was determined by Agilent 2100 Bioanalyzer (Agilent Technologies). Strand-specific paired-ended 100 nucleotide reads from each cDNA library were obtained using HiSeq2500 (Illumina).
For biological replication, two libraries were separately constructed and sequenced from RNAs isolated from two independent filtered culture supernatants of FORC_036.
The reads obtained from RNA-sequencing were mapped to the FORC_036 reference genome using CLC Genomics Workbench ver. 7.5.1 (CLC bio, Aarhus, Denmark). The GenBank (http://www.ncbi.nlm.nih.gov) accession numbers of the reference genome are CP015512 (Chromosome I), CP015513 (Chromosome II), and CP015514 (Plasmid)
Genome_build: ASM211720v1 [CP015512 (Chromosome I), CP015513 (Chromosome II), and CP015514 (Plasmid)]
Supplementary_files_format_and_content: Count calculation by Cuffquant and Cuffdiff

organism: Vibrio vulnificus

source_name: Small Octopus

growth_protocol: FORC_036 was grown to mid-log phase (A600 of 0.8) in VFMG (Vibrio fisheri minimal medium containing glycerol) medium

extract_protocol: Total RNAs were isolated using miRNeasy Mini Kit (Qiagen) according to the manufacturer's procedure. The DNA contaminations were removed by TURBO DNase (AMbion, Austin, TX), and then extracted RNAs were cleaned up using RNeasy MinElute Cleanup kit (Qiagen). The extracted RNA was verified by Agilent 2100 Bioanalyzer with Agilent RNA 6000 Nano reagens (Agilent Technologies, Waldbronn, Germany).

treatment_protocol: We artificially contact the FORC_036 strain to small octopus, and contact to small octopus for 1 h, and 4 h. Non-contact strain to crab in VFGM medium also prepared as negative control.

tag: treatment

value: Contact

value: 4 h


title: FAIRE-seq #3

data_processing:
FAIRE-seq reads were aligned to the hg19 genome assembly using bowtie with the following configurations: -m1 –best --strata
The read number at one specific position was clamped to 5
Peaks were called using cisGenome
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated, score represent peak height

extract_protocol:
Crosslinking was performed for 5 min at room temperature using 1% formaldehyde and DNA isolation was performed using three rounds of phenol chloroform extraction.
ChIP-seq and FAIRE-seq library preparations were carried out using Illumina protocols and libraries were sequenced on HiSeq 2000/2500 platforms (Illumina)


title: FAIRE-seq #2


title: Day 2-Mock 2

source_name: Day 2-Mock

value: Galveston

value: Mock

tag: tissue


title: Day 2-Mock 1

value: Whole mosquito


title: FAIRE-seq #1

tag: cell type


title: 1685_DMSO_1

source_name: PBMCs, DMSO, donor 1685

value: DMSO, followed by LPS

value: CTCTCTAC

tag: s

tag: i5 index 1

value: TATCCTCT

tag: total rna

value: AGAGGATA


title: NPC single cell 15

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Reads were trimmed of adapter sequences TCGTATGCCGTCTTCTGCTTG, ATCTCGTATGCCGTCTTCTGCTTG, CGACAGGTTCAGAGTTCTACAGTCCGACGATC GATCGGAAGAGCACACGTCTGAACTCCAGTCAC using cutadapt v1.8.1
Trimmed reads were aligned to RepBase v18.05 using STAR v2.4.01
Reads that didn't align to RepBase were aligned to hg19 using STAR v2.4.01 and a splice junction database derived from GENCODE v19
Transcripts per million (TPM) per transcript was calculated from reads that didn't align to RepBase were quasi-aligned to GENCODE v19 protein coding and lincRNA transcripts using Sailfish v0.6.3
TPM per gene was calculated by summing the TPM for all transcripts of a gene
Percent spliced-in (Psi) was calculated from junction read output from STAR aligner (SJ.out.tab) were used to create a de novo splicing index in conjunction with GENCODE v19 gene annotations, using outrigger
Outlier cells were calculated using K-means clustering with k=3 on the expression matrix and omitting cells which clustered into a group consisting of a majority of other cell types
Modality was calculated using anchor on the psi scores for all events detected in at least 10 cells, for each cell type
Waypoints were calculated using bonvoyage on the psi scores for all events detected in at least 10 cells, for each cell type
Splicing events were annotated using poshsplice to annotate corresponding genes, splice site strength using MaxEntScan, intron and exon lengths, conservation of alternative splicing from Merkin et al Science 2012,
Genes were annotated with attributes available in Gencode v19, Phylostrata for the matching ENSEMBL identifiers in Domazet-Loso et al MBE 2008, and TF or RBP category from Gerstberger et al Nat Rev Gen 2014
Genome_build: hg19
Supplementary_files_format_and_content: "metadata.csv.gz" contains sample metadata, "splicing.csv.gz" contains Psi scores, "splicing_feature.csv.gz" contains metadata for splicing events, "expression.csv.gz" contains TPM values for genes, "expression_feature.csv.gz" contains metadata for genes, "mapping_stats.csv.gz" contains the number and percentages of reads mapped for each samples

source_name: Neural progenitor cells

growth_protocol: iPSCs were cultured on matrigel coated plated using mTeSR(Stem Cell Technologies) media with mTeSR supplement at 37C incubator with 5% CO2.

extract_protocol:
Motor neurons were directly differentiated from iPSCs as previous described (Chambers S, Nature Biotechnology, 2009). Briefly, iPSCs were cultured on matrigel coated plates until fully confluent in mTeSR then switch to knock-out serum replacement media (KSR) containing Dorsomorphin(1uM) and SB431542(10uM). Upon day 4 of differentiation, increasing amounts of N2 media (25%, 50%) was added to the KSR. From day 7 of differentiation, 1.5uM retinoic acid and 200nM Smoothened Agonist (SAG, EMD Millipore) were added to induce patterning. Cells were dissociated on day 17 of differentiation and replated in poly-D-lysine and laminin coated plates. Maturation was performed using BDGF(2ng/ml), GDNF(2ng/ml), CNTF(2ng/ml), ascorbid acid, sonic hedgehog and retinoic acid in N2 and B27 media up until 35 days of differentiation.
Single cells were captured on C1 auto prep platform (Fluidigm, CA) according to manufacturer's instructions. C1 auto prep chips were visually inspected with a light microscopy at 20X to ensure singularity of captured cells. All non-single cells were discarded from analysis. SMARTer Ultra Low RNA cDNA Synthesis Kit (Clontech) was used to reverse transcribe polyA-tailed RNA. cDNA was amplified using Advantage 2 Polumerase Mix by PCR at 95¡C for 1 minutes, followed by 21 cylcles of 15 secondes at 95¡C, 30 seconds at 65¡C and 6 minutes at 68¡C, followed by another 10 minutes at 72¡C as a final extension. cDNAs were inspected using Agilent Bioanalyzer High Sensitivity DNA chips and quantitated by PicoGreen dsDNA Assay kit (ThermoFisher). cDNAs were diluted to 1ng to generate libraries using the Nextera XT DNA kit(Illumina, CA).  Libraries were multiplexed and sequenced on Illumina HiSeq200 to generate 100bp PE reads.

value: iPSC-derived neural progenitor cells

tag: gender

value: male

tag: sample type

value: Single Cell


title: 1001957_4h_OCT_Contact1

description: Sample 6 (3-2)

tag: strain

tag: time


title: 1001957_4h_OCT_Uncontact1

description: Sample 5 (3-1)

source_name: Vibrio fischeri minimal medium  containing 32.6 mM glycerol (VFMG) media (Non crab)

value: Control (Non-contact)


title: 490_IA_3

source_name: PBMCs, IA, donor 490

value: peripheral blood mononuclear cells (PBMCs)

value: IA, followed by LPS

tag: donor

tag: number of cells

value: 2 million

tag: rna ng/ul

tag: total volume

value: ultrapure water

value: GTAGAGGA

value: CTCTCTAT

value: ATAGAGAG


title: Day 14-ZIKV 3

source_name: Day 14-ZIKV

value: Galveston

tag: infection

value: ZIKV

value: Day 14


title: Day 14-ZIKV 2

value: Whole mosquito


title: 1685_DMSO_3

value: DMSO, followed by LPS

tag: collection buffer

tag: plate (index)

tag: well

tag: i7 index 1

value: GCTACGCT

value: TATCCTCT


title: Day 14-ZIKV 1

tag: tissue