title: Striatum_A9-4

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B474_STRIATUM

source_name: Striatum_ASD 9

tag: mouse status

tag: age

value: male

value: macro-dissected Striatum


title: Striatum_A17-4

status: Public on Feb 01 2019

type: SRA

city: Pasadena

first: Gil

last: Sharon

state: CA

address: 1200 E California Blvd

country: USA

institute: California Institute of Technology

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B473_STRIATUM

library_source: transcriptomic

data_processing:
Demulitplexed fastq files were mapped to the mouse reference genome assembly (GRCm38/mm11) using STAR with Gencode M11 annotations
Quality control was performed using PicardTools (CollectAlignmnetSummaryMetrics, CollectRnaSeqMetrics, CollectGcBiasMetrics, CollectInsertSizeMetrics, MarkDuplicates)
Gene expression was quantified using featureCounts
Alternative splicing was analyzed using rMATS
Genome_build: GRCm38/mm11

molecule: total RNA

organism: Mus musculus

source_name: Striatum_ASD 17

growth_protocol: Mice were anestetized using 5% isoflurane for 30 seconds and euthanized by cervical dislocation. Brains were dissected and the striatum and prefrontal cortex were collected into RNALater and frozen to -80C

extract_protocol:
Approximately 30 mg of frozen brain tissue was then pulverized and RNA was extracted using Qiagen miRNeasy kits according to the manufacturer’s protocol
For each sample, RNA integrity number (RIN) values were quantified using an Agilent Bioanalyzer. RNA sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep kits using polyA selection (Illumina). Libraries were barcoded and randomly pooled in sets of 24.

tag: strain background

value: colonized with Human feces (ASD)

tag: Sex

tag: tissue


title: atf-7(qd22qd130) OP50 1

city: Cambridge

first: Dennis

last: Kim

state: MA

address: 31 Ames Street

institute: MIT

data_processing:
Base-calling was performed using Illumina's NextSeq control software, RTA 2.4.11
Quality control: Reads were aligned against C. elegans (ws206) using bwa aln/ sampe v. 0.7.16a-r1181 with flags –t 16 –f and mapping rates, fraction of multiply-mapping reads, number of unique 20-mers at the 5’ end of the reads, insert size distributions and fraction of ribosomal RNAs were calculated using dedicated perl scripts and bedtools v. 2.25.0.64.
RNA-Seq mapping and quantitation: Reads were aligned against wbps9/ws258  annotation using STAR v. 2.5.3a with flags -runThreadN 16 --runMode alignReads  --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM with --genomeDir pointing to a 75nt-junction wbps9/ws258 STAR suffix array.
Gene expression was quantitated using RSEM v. 1.3.0 with the following flags for all libraries: rsem-calculate-expression --calc-pme --alignments -p 8  --forward-prob 0 against an annotation matching the STAR SA reference. Posterior mean estimates (pme) of counts and estimated RPKM were retrieved.
Genome_build: ws258(wbps9) annotation
Supplementary_files_format_and_content: txt file with, for each gene and each sample, gene length, effective gene length, and posterior mean estimates of read counts (from RSEM).

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Animals were synchronized by bleach prep. Arrested L1s dropped onto agar plates seeded with OP50 and grown at 20 degrees C until the L4 larval stage.

extract_protocol:
After 3 washes in M9 buffer, TRIzol Reagent (Invitrogen) was added to worm pellets and flash frozen in liquid nitrogen. After an additional round of freeze-thaw, RNA was isolated using the Direct-zol RNA MiniPrep kit (Zymo Research)
Libraries prepped using Kapa mRNA Hyperprep kit. Paired end reads sequenced on Illumina NextSeq500 sequencer, with v2 high-output chemistry.

treatment_protocol: L4 animals were washed to agar plates seeded with non-pathogenic (OP50) or pathogenic (PA14) bacteria for a period of 4 hours at 25 degrees C before RNA was harvested

value: whole animal

tag: genotype

tag: bacterial exposure

tag: exposure length

value: 4 hours


title: pmk-1(km25) OP50 2


title: Developing Seed, 16DAF, intermediateGI (GQ02505)

type: RNA

city: Los Banos

last: Sreenivasulu

address: Metro Manila

country: Philippines

institute: IRRI

description: Gene expression of developing seed at 16 DAF(Days after fertilization)

hyb_protocol: Microarray hybridization was conducted in a SureHyb chamber assembly using the large-volume Hi-RPM Gene Expression Hybridization Kit. Hybridization was done in a hybridization oven set at 60°C rotating at 10 rpm for exactly 17 hours.

scan_protocol: Microarray slides with an ozone barrier slide cover were read by an Agilent SureScan microarray scanner controlled by Scan Control software using a scan resolution of 3 µm double pass. Raw data were generated from the TIFF file using Agilent Feature Extraction software. The quality of the data was judged per batch using the PDF QC report and as a group using QC Validation software.

data_processing:
The data were normalized using GeneSpring GX (Agilent, Santa Clara, CA) following the quantile normalization algorithm.
Differentially expressed genes (DEGs) between high GI vs intermediate GI and Intermediate vs Low GI was done.The Limma R package is used following the empirical Bayes method.The p-values adjustment method used was either Bonferroni.The top-ranked genes were selected having an p-value below 0.05 and fold change above ±1.

organism: Oryza sativa Indica Group

source_name: Developing seed,16(DAF)

label_protocol: Labelling was done using One-Color Microarray-Based Gene Expression Analysis protocol using a custom 8 x 60K microarray slide for rice (Agilent, Germany). cDNA synthesis and cRNA labelling were done using a single-color Low Input Quick Amp Labeling Kit following manufacturer's protocol.

growth_protocol: The rice accessions were grown during the 2015 dry season at IRRI using a phytotron glasshouse maintained with ambient light, 29°C/21°C day/night temperature, and 75-85% relative humidity. Soil preparation, fertilizer regime, pesticide application, and glasshouse maintenance were as previously described (Jagadish et al., 2011).

extract_protocol: Total RNA was extracted in a 2.0-mL RNAse-free tube from 200 mg pulverized seeds using 750 uL RNA extraction buffer (100 mM Tris-HCl pH 8.0, 150 mM LiCl, 50 mM EDTA and 1.5% SDS plus 1.5% β-mercaptoehanol freshly added before use) and 500 uL phenol:chloroform:isoamyl (25:24:1). RNA was precipitated from the supernatant at -20°C overnight using 700 µL isopropanol and 400 µL 1.2 M NaCl in a fresh 2-mL microfuge tube. The RNA pellet was re-suspended in 450 µL RLT buffer (Qiagen) with 10% β-mercaptoethanol and further purified using Qiagen RNeasy Plant Mini Kit based on the manufacturer’s recommendation (Qiagen, Germany). Purified total RNA extract was treated with RNAse-free DNAse (Qiagen, Germany) to ensure that no residual genomic DNA were present in the sample

treatment_protocol: No treatment was done. All rice lines were grown under optimum conditions as described in growth protocol. This is to catch any inherent transcriptomic variation within each accession.

value: Developing Seed

tag: type

value: GQ02505, intermediateGI


title: pmk-1(km25) PA14 2


title: pmk-1(km25) PA14 1


title: pmk-1(km25) OP50 1


title: Striatum_C4-4

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B472_STRIATUM

source_name: Striatum_control 4

value: colonized with Human feces (Control)


title: Striatum_N5-7

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B471_STRIATUM

source_name: Striatum_control 5


title: Developing Seed, 16DAF, intermediateGI (GQ02495)

value: GQ02495, intermediateGI


title: Developing Seed, 16DAF, intermediateGI (GQ01858)

value: GQ01858, intermediateGI


title: Developing Seed, 16DAF, intermediateGI (GQ02511)

value: GQ02511, intermediateGI


title: Developing Seed, 16DAF, highGI (GQ01953)

value: GQ01953, highG


title: Striatum_C1-4

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B475_STRIATUM

source_name: Striatum_control 1


title: N2 PA14 3


title: Striatum_N5-3

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B469_STRIATUM


title: N2 OP50 3


title: Striatum_A3-3

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B468_STRIATUM

source_name: Striatum_ASD 3


title: N2 PA14 2


title: Striatum_A24-3

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B467_STRIATUM

source_name: Striatum_ASD 24


title: pmk-1(km25) PA14 3


title: N2 OP50 2


title: Developing Seed, 16DAF, highGI (GQ01936)

value: GQ01936, highGI


title: N2 PA14 1


title: Striatum_A9-3

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B465_STRIATUM


title: N2 OP50 1


title: Developing Seed, 16DAF, highGI (GQ02076)

value: GQ02076, highGI


title: Striatum_A11-3

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B470_STRIATUM

source_name: Striatum_ASD 11


title: Developing Seed, 16DAF, highGI (GQ01705)

value: GQ01705, highGI


title: Developing Seed, 16DAF, highGI (GQ02506)

value: GQ02506, highGI


title: Striatum_A17-3

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B464_STRIATUM


title: Striatum_N5-6

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B462_STRIATUM


title: Developing Seed, 16DAF, highGI (GQ02508)

value: GQ02508, highGI


title: Striatum_C4-3

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B463_STRIATUM

value: male


title: Developing Seed, 16DAF, highGI (GQ02547)

value: GQ02547, highGI


title: G2 genotype replicate 2 - extreme salt stress

city: Catania

first: Angela Roberta

last: Lo Piero

state: CT

address: Via S. Sofia 98

country: Italy

institute: University of Catania

data_processing:
Base calling, base quality and Phred score relationship performed with the Illumina CASAVA v1.8 software
Raw reads are filtered to remove reads containing adapters or reads of low quality
In the absence of a reference genome clean reads have been assembled using Trinity software (K 25, Kmer coverage 2). Corset software was used for hierarchical clustering
Seven databases have been applied for gene functional annotation: Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG and GO.
CDS preduction using blast and EST-scan
De novo transcriptome filtered by Corset used as a reference for mapping reads back to transcriptome and quantify the expression level using RSEM.
DESeq used for gene expression difference analysis
Genome_build: FASTA assembled sequences
Supplementary_files_format_and_content: Sample_annotation.xls: annotation result of genes expressed in each sample; FASTA assembled sequences: FASTA file containing sequences of assembled reads;

organism: Arundo donax

source_name: Leaf

growth_protocol: Weekly irrigation with water

extract_protocol:
Total RNA extraction with SpectrumTM Plant Total RNA Extraction kit (Sigma – Aldrich, St. Louis, MO).
All samples passed through three steps before library construction: Nanodrop for preliminary quantitation, agarose gel electrophoresis to tests RNA degradation and potential contamination, Agilent 2100 to checks RNA integrity and quantitation. After the QC procedures, mRNA is enriched from total RNA using oligo(dT) beads. The mRNA is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added, with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation and AMPure XP beads is used to purify the cDNA. The final cDNA library was ready after a round of purification, terminal repair, Atailing, ligation of sequencing adapters, size selection and PCR enrichment. Libraries are fed into Illumina machines according standard Illumina protocol.

treatment_protocol: Water with no NaCl for CK samples, 250 mM NaCl for S3 samples, 420 mM NaCl for S4 samples

value: Leaf

tag: treatment

value: Sample weekly irrigated with water with 420 mM NaCl


title: G2 genotype replicate 3 - extreme salt stress


title: Striatum_C1-3

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B466_STRIATUM

value: macro-dissected Striatum


title: Developing Seed, 16DAF, highGI (GQ01861)

value: Developing Seed

value: GQ01861, highGI


title: Striatum_N5-2

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B460_STRIATUM

value: colonized with Human feces (Control)


title: Striatum_A11-2

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B461_STRIATUM

value: colonized with Human feces (ASD)


title: Developing Seed, 16DAF, highGI (GQ01938)

value: GQ01938, highGI


title: G2 genotype replicate 3 - severe salt stress

value: Sample weekly irrigated with water with 250 mM NaCl


title: G2 genotype replicate 1 - extreme salt stress


title: UCD382F_MIBC_PDX

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

description: NanoString reporter probe

hyb_protocol: Total RNA samples (150 ng) were analyzed with an nCounter Analysis System (NanoString Technologies, Seattle, WA), which performs all processing steps, including target and reporter probe hybridization, probe-target tripartite complex purification and immobilization, and counting.

scan_protocol: Counting was performed according to stardard protocol for the nCounter Analysis System (NanoString Technologies, Seattle, WA).

data_processing: The raw data for each sample was output as Reporter Code Count (RCC) files that contain the counts for each gene in the sample. Data analysis was performed with nSolver Software (NanoString Technologies) and the following processing steps: quality control (i.e., for imaging, binding density, positive control linearity, and positive control limit of detection), background subtraction (negative control subtraction), normalization (geometric mean), fold change estimation, and agglomeration clustering. Samples that required a normalization factor of >10 were flagged and removed from further analysis.

label: biotin

organism: Homo sapiens

source_name: bladder cancer patient-derived xenograft (P0)

label_protocol: Nanostring Technologies standard protocol

growth_protocol: Not applicable

extract_protocol: RNA was isolated from formalin-fixed, paraffin-embedded (FFPE) samples using the miRNeasy FFPE Kit (Qiagen) according to the manufacturer’s protocols specific for each type of specimen.  Total RNA was eluted from the columns in nuclease-free water and stored at -80°C. RNA concentration and purity were assessed with a NanoDrop 2000 Spectrophotometer (Thermo Scientific) and quality assessments (e.g., RNA integrity) were made using an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Not applicable

tag: disease state

value: urothelial carcinoma

tag: disease subtype

value: muscle-invasive

tag: response to therapy


title: UCD479F_MIBC_Post_Resistant_PDX

description: NanoString reporter probe


title: UCD307F_MIBC_PDX

description: NanoString reporter probe


title: G2 genotype replicate 2 - severe salt stress

value: Sample weekly irigated with water with 250 mM NaCl


title: Developing Seed, 16DAF, highGI (GQ02518)

value: GQ02518, highGI


title: UCD429F_MIBC_PDX

description: NanoString reporter probe


title: NE_of_AA_with_BE#08

city: Ann Arbor

first: Derek

middle: John

last: Nancarrow

state: MI

address: 1500 E. Medical Center Dr.

department: Department of Surgery

institute: University of Michigan

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 20 hr at 48C on GeneChip Human Gene 2.1 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.

data_processing: Data was analyzed with R/Bioconductor software, normalized using RMA and log2-transformed. Analyses were restricted to the 24,909 coding and non-coding genes (probesets) for which both HUGO Gene Nomenclature Committee (HGNC) approved gene symbol and Entrez Gene ID annotation details were available.  We used a one-way analysis of variance (ANOVA) model across the four sample groups, but compared pairs of tissue groups by both  ANOVA and fold change in order to chose genes for further study.

source_name: specimen of normal esophageal squamous mucosa collected from subject diagnosed with Barrett's esophagus without dysplasia

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (WT Expression Kit User Manual, 2010, Affymetrix).

extract_protocol: Total RNAs from primary tissues were isolated using Trizol reagent from Invitrogen and the RNeasy mini kit from QIAGEN following the manufacturers' instructions.

treatment_protocol: Samples were immediately fresh frozen in liquid nitrogen and stored at -80C until use

tag: subject group

value: African American with BE

tag: age (yr)

tag: gender

value: female

tag: racial group

value: African American

tag: smoking status

value: Former smoker

tag: gastroesophageal reflux disease (gerd) status

value: GERD

tag: bmi

tag: barrett's esophagus (be) pathology status

value: BE noted

tag: clinical diagnosis

value: BE-no dysplasia

value: normal esophageal squamous


title: Developing Seed, 16DAF, highGI (GQ02501)

tag: tissue

value: Developing Seed

value: GQ02501, highGI


title: Striatum_A24-2

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B458_STRIATUM

tag: strain background

tag: mouse status

value: colonized with Human feces (ASD)

tag: age

tag: Sex

value: male

value: macro-dissected Striatum


title: UCD515F_MIBC_Post_Resistant_PDX

description: NanoString reporter probe

tag: disease state

value: urothelial carcinoma


title: G2 genotype replicate 1 - severe salt stress

value: Leaf

tag: genotype

tag: treatment

value: Sample weekly irrigated with water with 250 mM NaCl


title: Striatum_C1-2

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B457_STRIATUM

value: colonized with Human feces (Control)


title: UCD293F_MIBC_PDX

description: NanoString reporter probe

tag: disease subtype

value: muscle-invasive

tag: response to therapy


title: Striatum_A9-2

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B456_STRIATUM


title: UCD269F_MIBC_Resistant

description: NanoString reporter probe

source_name: primary bladder cancer

value: Resistant


title: G2 genotype replicate 2 - no salt stress

value: Sample weekly irigated with water with no NaCl


title: Striatum_A3-2

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B459_STRIATUM


title: Striatum_C4-2

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B454_STRIATUM


title: G2 genotype replicate 1 - no salt stress


title: UCD066_MIBC_Responsive

description: NanoString reporter probe

value: Responsive


title: UCD064_MIBC_Responsive

description: NanoString reporter probe


title: UCD063_MIBC_Resistant

description: NanoString reporter probe


title: UCD062_MIBC_Responsive

description: NanoString reporter probe


title: Striatum_A11-1

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B452_STRIATUM


title: Striatum_A3-1

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B450_STRIATUM


title: UCD061_MIBC_Responsive

description: NanoString reporter probe


title: Striatum_A24-1

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B449_STRIATUM


title: Striatum_N5-1

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B451_STRIATUM


title: Striatum_C1-1

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B448_STRIATUM


title: G2 genotype replicate 3 - no salt stress


title: UCD058_MIBC_Resistant

description: NanoString reporter probe


title: UCD060_MIBC_Resistant

description: NanoString reporter probe


title: Striatum_A17-2

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B455_STRIATUM


title: UCD057_MIBC_Resistant

description: NanoString reporter probe


title: UCD059_MIBC_Resistant

description: NanoString reporter probe


title: IELs R38EPAR2 GF mice monocolonized P.aeruginosa PA14  2

city: Hamilton

first: Alberto

last: Caminero

state: ON

address: 1280 Main St W

country: Canada

institute: McMaster University

description: Intraepithelial lymphocyte compartment (IEL) from ex-germ free Protease-resistant PAR-2 mutant  (R38E-PAR2) mouse (10-12 weeks) monocolonized with P.aeruginosa PA14

hyb_protocol: The protocol followed was according to manufacturer's intructions

scan_protocol: Sample Cartridges are placed in the Digital Analyzer for data collection. Color codes on the surface of the cartridge are counted and tabulated for each target molecule

data_processing: After collection, the RCC files that were generated by the digital analyzer and contained the counts of each samples were imported into the nSolver software fo further anlysis. After checking the quality scores for each sample, a Positive Control Normalization and a Reference (Housekeeping) Gene Normalization. was performed for each sample.

label: color-coded barcode technology

source_name: Small intestine_ Intraepithelial lymphocyte compartment

extract_protocol: Total RNA extractions were conducted with the RNeasy Mini Kit (Qiagen, Toronto, Canada) according to the manufacturer’s instructions. DNase digestion during purification was carried out using the RNase-free DNase (Qiagen).

tag: strain

tag: status

value: germ free

tag: colonized

value: monocolonized P.aeruginosa PA14


title: IELs R38EPAR2 GF mice monocolonized P.aeruginosa PA14  4

label_protocol: The protocol followed was according to manufacturer's intructions


title: IELs C57 GF mice monocolonized P.aeruginosa PA14 second exp 4

description: Intraepithelial lymphocyte compartment (IEL) from ex-germ free C57BL/6 mouse (10-12 weeks) monocolonized with P.aeruginosa PA14


title: IELs R38EPAR2 GF mice monocolonized P.aeruginosa PA14  3


title: IELs R38EPAR2 GF mice monocolonized P.aeruginosa PA14  1


title: Striatum_A17-1

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B446_STRIATUM


title: IELs C57 GF mice monocolonized P.aeruginosa PA14 second exp 3


title: PrefrontalCortex_N5-5

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B418_PFC

source_name: PrefrontalCortex_control 5

value: macro-dissected prefrontal cortex


title: UCD055_MIBC_Resistant

description: NanoString reporter probe


title: IELs C57 GF mice monocolonized P.aeruginosa PA14 second exp 2


title: Striatum_C4-1

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B445_STRIATUM


title: Striatum_N5-4

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B444_STRIATUM


title: UCD054_MIBC_Resistant

description: NanoString reporter probe


title: UCD053_MIBC_Resistant

description: NanoString reporter probe


title: Striatum_A9-1

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B447_STRIATUM


title: UCD052_MIBC_Resistant

description: NanoString reporter probe


title: Tissue C57 clean SPF mice colonized P.aeruginosa PA14 gliadin 3

description: Tissue from clean specific pathogen free (SPF- derivated of Altered Schaedler flora) C57BL/6 mouse (10-12 weeks) and colonized with P.aeruginosa PA14. Mice were sensitized with gluten and cholera toxin for 3 weeks (1 time a week) and challenged with gluten 3 times a week for 3 weeks.

source_name: Small intestine_Tissue

value: clean

value: colonized P.aeruginosa PA14


title: Tissue C57 clean SPF mice colonized P.aeruginosa LasB gliadin 3 -repeat

description: Tissue from clean specific pathogen free (SPF- derivated of Altered Schaedler flora) C57BL/6 mouse (10-12 weeks) and colonized with P.aeruginosa PA14 disrulted in LasB gene . Mice were sensitized with gluten and cholera toxin for 3 weeks (1 time a week) and challenged with gluten 3 times a week for 3 weeks.

value: colonized P.aeruginosa LasB


title: UCD051_MIBC_Responsive

description: NanoString reporter probe


title: Tissue NODDQ8 clean SPF colonized P.aeruginosa LasB gliadin 4

description: Tissue from clean specific pathogen free (SPF- derivated of Altered Schaedler flora) Non-obese diabetic mouse expresing human HLA-DQ8 (NOD/DQ8, 10-12 weeks) colonized with P.aeruginosa PA14 disrupted in LasB gene. Mice were sensitized with gluten and cholera toxin for 3 weeks (1 time a week) and challenged with gluten 3 times a week for 3 weeks.


title: J1_serum_3

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh, The Institute of Genetics and Cancer

data_processing:
A sailfsh (version 0.9.2) index was built using kmer length 25 against the Ensembl  mm10 transcript database
RNA transcript abundance was calculated using  Sailfish version 0.9.2, libType": "ISR","numBootstraps": "30".
The R package tximport(tximport_1.8.0) was used to import and summarize transcript-level estimates for gene-level analysis
Genome_build: mm10
Supplementary_files_format_and_content: quant.sf,  tab-delimited text files include Ensembl Transcript ID, Length, EffectiveLength, TPM, NumReads. txisailfishrawcounts.csv , csv file with gene level raw counts.

growth_protocol: Serum culture conditions: Dulbecco's Modified Eagle's medium (DMEM) high-glucose supplemented with 15% FCS, 1x Non-essential amino acids, 1mM Sodium Pyruvate, 50mg/ml Penicillin/Streptomycin, 0.1% beta-mercaptoethanol and 500U/ml ESGRO LIF (Millipore).

extract_protocol:
Snap frozen pellets of mESCs were stored in -80 ̊C prior to extraction of RNA. Qiashredder columns (Qiagen) were used to homogenise the samples according to manufacturers protocol. Total RNA was extracted using an RNeasy kit (Qiagen), following the manufacturer’s protocol. RNA was then treated with Turbo Dnase (Ambion, ThermoFisher) according to manufacturers protocol. Total RNA samples were quantified using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific Inc, #Q32866) and the Qubit RNA HS assay kit (#Q33855). RNA integrity (RIN) was assessed using an Agilent 2100 Bioanlyser System (Agilent Technologies Inc, # GS2938B) and Agilent RNA 6000 Nano kit (#5067-1511), samples used had a RIN score of ≥9.9.
Libraries were prepared from 500ng of each total-RNA sample using the TruSeq Stranded  mRNA Library Kit (Illumina Inc, #20020594) according to the provided protocol. PolyA selection method was used. Libraries were quantified by fluorometry using the Qubit dsDNA HS assay and assessed for  quality and fragment size using the Agilent Bioanalyser with the DNA HS Kit (#5067-4626).
Sequencing was performed using the NextSeq 500/550 High-Output v2 (150 cycle) Kit (#FC-404-2002) on the NextSeq 550 platform (Illumina Inc, #SY-415-1002). 24 libraries were  combined in two equimolar pools of 12 based on the library quantification results and each pool was run across a single High-Output Flow Cell.

treatment_protocol: 2i culture conditions: N2B27 medium (DMEM F-12:  GIBCO,  Neurobasal: GIBCO, N2: GIBCO, B27: GIBCO,  50ug/ml Penicillin/streptomycin, 3.3% BSA (GIBCO), 0.15 mM monothioglycerol and MEK inhibitor PD0325901 [1uM] and Gsk3 beta inhibitor CHIR99021 (3uM) with 1000U/ml ESGRO LIF (Millipore).

tag: cell line

tag: cell type

value: Mouse ES cells

value: Serum+LIF


title: UCD050_MIBC_Responsive

description: NanoString reporter probe


title: UCD049_MIBC_Resistant

description: NanoString reporter probe


title: ASV Del without DHT

city: Hangzhou

first: Chengliang

last: Zhou

state: Zhejiang

address: No. 866th, Yuhangtang Road

department: School of Medicine

country: China

institute: Zhejiang University

description: SAMPLE 5

data_processing:
Matrix normalized worksheet reports normalized signal (against average of geometric mean of housekeeping genes ACTB, B2M, GAPDH, RPLP0).  portal at http://www.qiagen.com/geneglobe. Samples were assigned to controls and test groups. CT values were  normalized based on a/an Manual Selection of reference genes.
Fold Change worksheet reports test/control

label: SYBR Green

source_name: androgen receptor alternative splicing variants (ASVs) without Dihydrotestosterone (DHT)

label_protocol: RT2 First Strand Kit (Qiagen)

growth_protocol: The isolation hGCs were washed three times with DMEM/F12 (Gibco) supplemented with Antibiotic-Antimycotic (Gibco). Next, hGCs were seeded in 12-well plates with optimal inoculating density and cultured in DMEM/F-12 medium wash buffer (Gibco) supplemented with 10% FBS (Gibco) in a humidified atmosphere of 5% CO2 at 37°C. The culture medium was changed every two days.

extract_protocol: RNA was extracted from hGCs using the miRNeasy mini kit (Qiagen) as manufacture’s instruction.

treatment_protocol: Adenovirus vectors of Wt, Ins, and Del AR were manufactured in Sino Geno Max. Adenovirus were transfected into hGCs with MOI 5. For experiments involving DHT treatment, Cells were serum starved for 4 h, followed by 25 nM of DHT stimulation for 24h.

tag: gender

value: female

tag: transfection

value: Del

value: primary ovarian granulosa cells


title: ASV Del with DHT

description: SAMPLE 6

source_name: androgen receptor alternative splicing variants (ASVs) with Dihydrotestosterone (DHT)


title: J1_serum_2


title: Tissue NODDQ8 clean SPF colonized P.aeruginosa PA14 gliadin 4

description: Tissue from clean specific pathogen free (SPF- derivated of Altered Schaedler flora) Non-obese diabetic mouse expresing human HLA-DQ8 (NOD/DQ8, 10-12 weeks) colonized with P.aeruginosa PA14. Mice were sensitized with gluten and cholera toxin for 3 weeks (1 time a week) and challenged with gluten 3 times a week for 3 weeks.


title: IELs C57 GF mice monocolonized P.aeruginosa PA14 second exp 1


title: UCD048_MIBC_Resistant

description: NanoString reporter probe

value: urothelial carcinoma


title: UCD046_MIBC_Responsive

description: NanoString reporter probe


title: UCD044_MIBC_Responsive

description: NanoString reporter probe


title: ASV Ins without DHT

description: SAMPLE 3

value: Ins


title: Tissue NODDQ8 clean SPF colonized P.aeruginosa LasB gliadin 3


title: Tissue NODDQ8 clean SPF colonized P.aeruginosa PA14 gliadin 3


title: AR WT with DHT

description: SAMPLE 2

value: WT


title: J1_2i_3


title: Tissue NODDQ8 clean SPF colonized P.aeruginosa PA14 gliadin 2


title: Tissue NODDQ8 clean SPF colonized P.aeruginosa LasB gliadin 1


title: Tissue NODDQ8 clean SPF colonized P.aeruginosa PA14 gliadin 1


title: AR WT without DHT

description: SAMPLE 1


title: UCD042_MIBC_Resistant

description: NanoString reporter probe

value: muscle-invasive

value: Resistant


title: UCD043_MIBC_Resistant

description: NanoString reporter probe


title: Tissue NODDQ8 clean SPF colonized P.aeruginosa LasB gliadin 2


title: J1_2i_1


title: Tissue NODDQ8 clean SPF colonized P.aeruginosa PA14 control 4

description: Tissue from clean specific pathogen free (SPF- derivated of Altered Schaedler flora) Non-obese diabetic mouse expresing human HLA-DQ8 (NOD/DQ8, 10-12 weeks), non-sensitized, colonized with P.aeruginosa PA14


title: ASV Ins with DHT

description: SAMPLE 4


title: 3B3-3l_serum_3


title: J1_serum_1


title: UCD001_MIBC_Resistant

description: NanoString reporter probe


title: UCD002_MIBC_Post_Resistant

description: NanoString reporter probe


title: Env Wildtype RNA Fragment C; Reverse-transcribed with Accuscript

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

description: cDNA (reverse transcribed with Accuscript) from cells expressing wildtype DU422 gp140; control for background error rate

data_processing:
Data was analyzed using Enrich: http://depts.washington.edu/sfields/software/enrich/
Fuser script: FragmentA1 read 1: python Paired_read_fuser.py --path fragA1_R1/ --read1 DU422gp140_A_R1.fastq.bz2 --read2 DU422gp140_A_R1.fastq.bz2 --wtseq AATCTCGACCTTTGGGTCACCGTATACTACGGAGTCCCCGTGTGGAAAGAGGCTAAGACGACCCTGTTTTGTGCGTCAGACGCGAAAGCGTATGACAAGGAAGTGCATAACGTGTGGGCAACACACGCATGTGTTCCGACGGACCCTAACCCGCAGGAAATCGTCCTTGAAAACGTGACCGAAAACTTCAACATGTGGAAGAACGACATGGTTGACCAA --read1_overlap_start 19 --read1_overlap_end 238 --mode R1
Fuser script: Fragment A1 read 2: python Paired_read_fuser.py --path fragA1_R2/ --read1 DU422gp140_A_R2.fastq.bz2 --read2 DU422gp140_A_R2.fastq.bz2 --wtseq TCCTTCAACACCACGACAGAACTTAGAGATAAAAAGCAAAAAGTCTACGCCCTTTTCTATAAACCGGATGTCGTGCCACTTAACGGTGGTGAGCACAATGAGACAGGTGAGTACATTCTCATCAACTGCAATTCATCTACAATAACGCAAGCATGTCCGAAAGTTTCCTTCGATCCGATCCCTATTCACTACTGCGCTCCTGCA --read2_overlap_start 25 --read2_overlap_end 229 --mode R2
Fuser script: Fragment A2 read 1: python Paired_read_fuser.py --path fragA2_R1/ --read1 DU422gp140_A_R1.fastq.bz2 --read2 DU422gp140_A_R1.fastq.bz2 --wtseq GACCAAATGCACGAGGACATAATCAGTCTTTGGGATCAATCCTTGAAGCCCTGTGTGAAGCTGACGCCTTTGTGCGTAACTTTGAACTGTAAAAACGTAAATATTTCAGCGAATGCTAACGCGACCGCTACACTTAATTCAAGTATGAACGGCGAAATAAAGAATTGCTCCTTCAACACCACGACAGAACTTAGAGATAAAAAGCAA --read1_overlap_start 22 --read1_overlap_end 229 --mode R1
Fuser script: Fragment A2 read 2: python Paired_read_fuser.py --path fragA2_R2/ --read1 DU422gp140_A_R2.fastq.bz2 --read2 DU422gp140_A_R2.fastq.bz2 --wtseq GCAGGGTACGCCATACTGAAGTGTAACAATAAAACGTTTAACGGAACAGGCCCTTGCAATAATGTAAGTACTGTCCAGTGCACGCATGGCATAAAACCCGTCGTGAGCACACAACTTCTTCTTAACGGATCACTCGCCGAGGAAGAGATCATCGTGCGAAGTGAGAACTTGACGAAT --read2_overlap_start 35 --read2_overlap_end 212 --mode R2
Fuser script: Fragment B1 read 1: python Paired_read_fuser.py --path fragB1_R1/ --read1 DU422gp140_B_R1.fastq.bz2 --read2 DU422gp140_B_R1.fastq.bz2 --wtseq AATATAAAGACGATCATAGTCCATCTCAACAAGTCCGTCGAGATTAAATGCACTAGGCCCAACAACAATACGCGGAAATCCGTACGGATAGGTCCTGGACAAACATTCTATGCTACCGGTGAGATTATAGGTGATATACGCGAAGCTCATTGCAATATCAGTAGGGAGACCTGGAATTCCACTTTGATCCAAGTGAAAGAAAAACTGCGGGAGCATTACAAC --read1_overlap_start 22 --read1_overlap_end 244 --mode R1
Fuser script: Fragment B1 read 2: python Paired_read_fuser.py --path fragB1_R2/ --read1 DU422gp140_B_R2.fastq.bz2 --read2 DU422gp140_B_R2.fastq.bz2 --wtseq CCGCCGATTGAAGGGAATATTACTTGCAAGAGCAACATAACTGGTCTTCTTCTCACATGGGATGGTGGAGAGAACAGTACCGAAGGCGTTTTTAGGCCTGGCGGTGGCAATATGAAGGATAACTGGCGCTCAGAACTCTATAAGTACAAAGTCGTCGAAATAAAGCCCTTGGGCGTTGCGCCTACGAAAAGTAAACGAAAAGTAGTAGGGAGG --read2_overlap_start 18 --read2_overlap_end 231 --mode R2
Fuser script: Fragment B2 read 1: python Paired_read_fuser.py --path fragB2_R1/ --read1 DU422gp140_B_R1.fastq.bz2 --read2 DU422gp140_B_R1.fastq.bz2 --wtseq AAAACGATCAAATTTGAACCTTCTTCTGGAGGTGACCTGGAGGTTACGACGCACAGTTTTAACTGTAGGGGAGAATTCTTCTACTGCGATACGACCAAGCTGTTCAACGAGACTAAGCTGTTTAACGAGTCAGAATACGTTGACAATAAGACTATTATCTTGCCCTGCCGGATAAAGCAAATTATCAATATGTGGCAAGAAGTGGGAAGGGCAATGTACGCG --read1_overlap_start 20 --read1_overlap_end 242 --mode R1
Fuser script: Fragment B2 read 2: python Paired_read_fuser.py --path fragB2_R2/ --read1 DU422gp140_B_R2.fastq.bz2 --read2 DU422gp140_B_R2.fastq.bz2 --wtseq GAAAAGCGAGCGGTTGGCTTGGGTGCAGTGCTTCTCGGGTTCCTGGGAGCTGCGGGGTCAACAATGGGAGCTGCTTCCATAACCTTGACTGTGCAGGCAAGGCAGCTGCTGAGTGGGATAGTGCAGCAACAATCCAATCTGCTTAGGGCAATTGAAGCTCAGCAACATCTTTTGCAGCTCACAGTCTGGGGCATAAAGCAACTGCAA --read2_overlap_start 13 --read2_overlap_end 220 --mode R2
Fuser script: Fragment C read 1: python Paired_read_fuser.py --path fragC_R1/ --read1 DU422gp140_C_R1.fastq.bz2 --read2 DU422gp140_C_R1.fastq.bz2 --wtseq ACCAGAGTCCTCGCGATTGAGCGGTATCTTAAGGACCAGCAACTGCTGGGACTCTGGGGGTGTTCCGGGAAGCTTATTTGTGCCACTGCGGTACCATGGAACTCCTCTTGGTCCAACAAGTCTCTGGGCGATATTTGGGACAATATGACGTGGATGCAGTGGGATCGCGAGATATCCAACTACACCAACACGATCTTCCGGCTT --read1_overlap_start 20 --read1_overlap_end 224 --mode R1
Fuser script: Fragment C read 2: python Paired_read_fuser.py --path fragC_R2/ --read1 DU422gp140_C_R2.fastq.bz2 --read2 DU422gp140_C_R2.fastq.bz2 --wtseq CTGGGCGATATTTGGGACAATATGACGTGGATGCAGTGGGATCGCGAGATATCCAACTACACCAACACGATCTTCCGGCTTCTCGAAGACAGTCAGAATCAACAAGAGAAGAATGAGAAGGATCTGTTGGCCCTTGACAGCTGGAAAAATCTTTGGAATTGGTTTGACATTACTAAC --read2_overlap_start 42 --read2_overlap_end 219 --mode R2
Aligner script: Fragment A1 read 1: python Fused_read_aligner.py --path fragA1_R1/ --infile DU422gp140_A_R1.fast_R1_qc1 --referenceDNA AATCTCGACCTTTGGGTCACCGTATACTACGGAGTCCCCGTGTGGAAAGAGGCTAAGACGACCCTGTTTTGTGCGTCAGACGCGAAAGCGTATGACAAGGAAGTGCATAACGTGTGGGCAACACACGCATGTGTTCCGACGGACCCTAACCCGCAGGAAATCGTCCTTGAAAACGTGACCGAAAACTTCAACATGTGGAAGAACGACATGGTTGACCAA --referenceAA NLDLWVTVYYGVPVWKEAKTTLFCASDAKAYDKEVHNVWATHACVPTDPNPQEIVLENVTENFNMWKNDMVDQ --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: Fragment A1 read 2: python Fused_read_aligner.py --path fragA1_R2/ --infile DU422gp140_A_R2.fast_R2_qc1 --referenceDNA TCCTTCAACACCACGACAGAACTTAGAGATAAAAAGCAAAAAGTCTACGCCCTTTTCTATAAACCGGATGTCGTGCCACTTAACGGTGGTGAGCACAATGAGACAGGTGAGTACATTCTCATCAACTGCAATTCATCTACAATAACGCAAGCATGTCCGAAAGTTTCCTTCGATCCGATCCCTATTCACTACTGCGCTCCTGCA --referenceAA SFNTTTELRDKKQKVYALFYKPDVVPLNGGEHNETGEYILINCNSSTITQACPKVSFDPIPIHYCAPA --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: Fragment A2 read 1: python Fused_read_aligner.py --path fragA2_R1/ --infile DU422gp140_A_R1.fast_R1_qc1 --referenceDNA GACCAAATGCACGAGGACATAATCAGTCTTTGGGATCAATCCTTGAAGCCCTGTGTGAAGCTGACGCCTTTGTGCGTAACTTTGAACTGTAAAAACGTAAATATTTCAGCGAATGCTAACGCGACCGCTACACTTAATTCAAGTATGAACGGCGAAATAAAGAATTGCTCCTTCAACACCACGACAGAACTTAGAGATAAAAAGCAA --referenceAA DQMHEDIISLWDQSLKPCVKLTPLCVTLNCKNVNISANANATATLNSSMNGEIKNCSFNTTTELRDKKQ --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: Fragment A2 read 2: python Fused_read_aligner.py --path fragA2_R2/ --infile DU422gp140_A_R2.fast_R2_qc1 --referenceDNA GCAGGGTACGCCATACTGAAGTGTAACAATAAAACGTTTAACGGAACAGGCCCTTGCAATAATGTAAGTACTGTCCAGTGCACGCATGGCATAAAACCCGTCGTGAGCACACAACTTCTTCTTAACGGATCACTCGCCGAGGAAGAGATCATCGTGCGAAGTGAGAACTTGACGAAT --referenceAA AGYAILKCNNKTFNGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIVRSENLTN --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: Fragment B1 read 1: python Fused_read_aligner.py --path fragB1_R1/ --infile DU422gp140_B_R1.fast_R1_qc1 --referenceDNA AATATAAAGACGATCATAGTCCATCTCAACAAGTCCGTCGAGATTAAATGCACTAGGCCCAACAACAATACGCGGAAATCCGTACGGATAGGTCCTGGACAAACATTCTATGCTACCGGTGAGATTATAGGTGATATACGCGAAGCTCATTGCAATATCAGTAGGGAGACCTGGAATTCCACTTTGATCCAAGTGAAAGAAAAACTGCGGGAGCATTACAAC --referenceAA NIKTIIVHLNKSVEIKCTRPNNNTRKSVRIGPGQTFYATGEIIGDIREAHCNISRETWNSTLIQVKEKLREHYN --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: Fragment B1 read 2: python Fused_read_aligner.py --path fragB1_R2/ --infile DU422gp140_B_R2.fast_R2_qc1 --referenceDNA CCGCCGATTGAAGGGAATATTACTTGCAAGAGCAACATAACTGGTCTTCTTCTCACATGGGATGGTGGAGAGAACAGTACCGAAGGCGTTTTTAGGCCTGGCGGTGGCAATATGAAGGATAACTGGCGCTCAGAACTCTATAAGTACAAAGTCGTCGAAATAAAGCCCTTGGGCGTTGCGCCTACGAAAAGTAAACGAAAAGTAGTAGGGAGG --referenceAA PPIEGNITCKSNITGLLLTWDGGENSTEGVFRPGGGNMKDNWRSELYKYKVVEIKPLGVAPTKSKRKVVGR --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: Fragment B2 read 1: python Fused_read_aligner.py --path fragB2_R1/ --infile DU422gp140_B_R1.fast_R1_qc1 --referenceDNA AAAACGATCAAATTTGAACCTTCTTCTGGAGGTGACCTGGAGGTTACGACGCACAGTTTTAACTGTAGGGGAGAATTCTTCTACTGCGATACGACCAAGCTGTTCAACGAGACTAAGCTGTTTAACGAGTCAGAATACGTTGACAATAAGACTATTATCTTGCCCTGCCGGATAAAGCAAATTATCAATATGTGGCAAGAAGTGGGAAGGGCAATGTACGCG --referenceAA KTIKFEPSSGGDLEVTTHSFNCRGEFFYCDTTKLFNETKLFNESEYVDNKTIILPCRIKQIINMWQEVGRAMYA --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: Fragment B2 read 2: python Fused_read_aligner.py --path fragB2_R2/ --infile DU422gp140_B_R2.fast_R2_qc1 --referenceDNA GAAAAGCGAGCGGTTGGCTTGGGTGCAGTGCTTCTCGGGTTCCTGGGAGCTGCGGGGTCAACAATGGGAGCTGCTTCCATAACCTTGACTGTGCAGGCAAGGCAGCTGCTGAGTGGGATAGTGCAGCAACAATCCAATCTGCTTAGGGCAATTGAAGCTCAGCAACATCTTTTGCAGCTCACAGTCTGGGGCATAAAGCAACTGCAA --referenceAA EKRAVGLGAVLLGFLGAAGSTMGAASITLTVQARQLLSGIVQQQSNLLRAIEAQQHLLQLTVWGIKQLQ --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: Fragment C read 1: python Fused_read_aligner.py --path fragC_R1/ --infile DU422gp140_C_R1.fast_R1_qc1 --referenceDNA ACCAGAGTCCTCGCGATTGAGCGGTATCTTAAGGACCAGCAACTGCTGGGACTCTGGGGGTGTTCCGGGAAGCTTATTTGTGCCACTGCGGTACCATGGAACTCCTCTTGGTCCAACAAGTCTCTGGGCGATATTTGGGACAATATGACGTGGATGCAGTGGGATCGCGAGATATCCAACTACACCAACACGATCTTCCGGCTT --referenceAA TRVLAIERYLKDQQLLGLWGCSGKLICATAVPWNSSWSNKSLGDIWDNMTWMQWDREISNYTNTIFRL --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: Fragment C read 2: python Fused_read_aligner.py --path fragC_R2/ --infile DU422gp140_C_R2.fast_R2_qc1 --referenceDNA CTGGGCGATATTTGGGACAATATGACGTGGATGCAGTGGGATCGCGAGATATCCAACTACACCAACACGATCTTCCGGCTTCTCGAAGACAGTCAGAATCAACAAGAGAAGAATGAGAAGGATCTGTTGGCCCTTGACAGCTGGAAAAATCTTTGGAATTGGTTTGACATTACTAAC --referenceAA LGDIWDNMTWMQWDREISNYTNTIFRLLEDSQNQQEKNEKDLLALDSWKNLWNWFDITN --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
MapCounts script: Example: python mapCounts.py --path directory_fragA1_R1/ --infile DU422gp140_A_R1.fast_R1_qc1_PRO_qc2
MapRatios script: Example: python mapRatios.py --path ratios_directory/ --templatepath /deepseq_scripts/r_deepseq_scripts/ --infile2 mapcounts_library --infile1 mapcounts_sorted
MapParts script: Example: python mapParts.py --path ratios_directory/ --infile mapratios_sorted_library --mode mutations:1
Unlink script: Example: python mapUnlink.py --path ratios/ --infile mapratios_sorted_library.m1 --type protein --mode ratios --size ##
In Excel, the log(base2) enrichment ratio of the wildtype sequence was subtracted from the log(2) enrichment ratios for all single mutations.
Data was then assembled from the different fragments/reads to span the full sequence in Excel.  Where there was overlap, real enrichment ratios were averaged and converted back to log(base2). Maximum depletion was set to log(base2) enrichment ratio = -4.
Genome_build: Not applicable
Supplementary_files_format_and_content: Excel spreadsheet of log(base2) enrichment ratios for each single amino acid substitution.  Also includes the frequency of each mutation in the naïve plasmid library and various controls.

organism: Human immunodeficiency virus 1

source_name: Synthetic coding sequences

growth_protocol: Expi293F cells cultured in Expi293 Expression Medium (Life Technologies)

extract_protocol:
Total RNA was harvested from sorted cells using GeneJet RNA Purification Kit (Thermo Scientific) and cDNA prepared using Accuscript Hi-Fi (Agilent Genomics, Libraries A, B and C) or SuperScript IV VILO (Invitrogen, Library A) primed with: random hexamers and oligo-dT (Library A, SuperScript), DU422gp160_libA_RT_rev2 (GGCCTAGTGCATTTAATCTC, Library A, Accuscript), DU422gp160_libB_RT_rev2 (GTTGCTGGTCCTTAAGATAC, Library B), and EBV_reverse (GTGGTTTGTCCAAACTCATC, Library C).
In the first round of PCR, the gp140 coding sequences were amplified as overlapping fragments of ~800 bp each.
Primer pair (Library A Fragment 1): HiSeq_DU422gp160_52_F (TCTTTCCCTACACGACGCTCTTCCGATCTTGTAGCGTCAGTGCTTGC) and HiSeq_DU422gp160_624_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTACACTTCAGTATGGCGTACC)
Primer pair (Library A Fragment 2): HiSeq_DU422gp160_279_F (TCTTTCCCTACACGACGCTCTTCCGATCTCATGTGGAAGAACGACATGG) and HiSeq_DU422gp160_850_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTACGGACTTGTTGAGATGGAC)
Primer pair (Library B Fragment 1): HiSeq_DU422gp160_808_F (TCTTTCCCTACACGACGCTCTTCCGATCTGCGAAGTGAGAACTTGACGA) and HiSeq_DU422gp160_1489_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAGCCAACCGCTCGCTTTTC)
Primer pair (Library B Fragment 2): HiSeq_DU422gp160_1035_F (TCTTTCCCTACACGACGCTCTTCCGATCTAACTGCGGGAGCATTACAAC) and HiSeq_DU422gp160_1713_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAAGATACCGCTCAATCGCGA)
Primer pair (Library C): HiSeq_DU422gp160_1671_F (TCTTTCCCTACACGACGCTCTTCCGATCTGGGGCATAAAGCAACTG) and HiSeq_6His-Linker_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGGTGATGGTGATGATGTCC)
In a second round of PCR, Illumina adaptors and experiment-specific barcodes were added.
Primer pair for adding I5 and I7 Illumina adaptors: MiSeq_Start_Adaptamer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and MiSeq_Index_Adaptamer (CAAGCAGAAGACGGCATACGAGAT-6nt-barcode-GTGACTGGAGTTCAGACGTGTGCTCTTC)
Amplicons were deep sequenced on a HiSeq 2500 using a 2x250 nt paired end protocol, though data is analyzed as single reads.

treatment_protocol: Cells expressing DNA libraries of HIV-1(DU422) gp140 mutants (cloned into pCEP4, Invitrogen) were FACS sorted for binding to soluble CD4 (domains D1-D2) or broadly-neutralizing antibody PG16.  The extracellular region of Env (gp140) was fused at its C-terminus vi a gly/ser-rich linker and 6H-tag to a canonical transmembrane helix for surface display.  Three single site-saturation mutagenesis libraries were created, spanning residues 31-279 (Library A; numbering based on the HXB2 reference strain), 280-577 (Library B), and 578-677 (Library C).

tag: protein

value: Env (gp140)

tag: sort gate

tag: # collected cells


title: Env Wildtype RNA Fragment A; Reverse-transcribed with SuperScript IV VILO

description: cDNA (reverse transcribed with SuperScript IV VILO) from cells expressing wildtype DU422 gp140; control for background error rate


title: Env Wildtype RNA Fragment B; Reverse-transcribed with Accuscript


title: J1_2i_2


title: Tissue NODDQ8 clean SPF colonized P.aeruginosa PA14 control 3


title: 3B3-3l_serum_2


title: UCD037B_MIBC_Responsive

description: NanoString reporter probe

value: Responsive


title: BPS2-IP_Cy5 vs. Input_BPS2_Cy3

type: genomic

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Hsf1 binding profile in iron deprived cells of Candida albicans

hyb_protocol: 5 micrograms of cy3 and cy5 labeled samples were hybridized. Hybridizations were done using the Agilent Hybridization kit of (Part Number: 5188-6420) Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 24 hours. The hybridized slides were washed using Agilent aCGH wash buffers

scan_protocol: Agilent Microarray Scanner

data_processing: Data extraction from Images was done using Feature Extraction software v 10.7 of Agilent. Data analysis was done using Agilent Genomic Workbench Lite Edition 6.5 (Chip-on-Chip Application) and Microsoft Excel.Normalization of the data was done using Lowess normalization

molecule: genomic DNA

organism: Candida albicans

source_name: HSF1 ChIP in iron-deprived Candida cells

label_protocol: The DNA samples were blunted at 12°C for 20 minutes using T4 DNA polymerase as per the Chip on Chip Protocol of Agilent Technologies. The blunted DNA was cleaned, precipitated and resuspended in 25 microlitres of water. The entire DNA was then ligated to linkers. The linker-ligated DNA was subjected to two rounds of LMPCR and resuspended in water. Two micrograms of each sample was labeled using Agilent Genomic DNA Labeling Kit PLUS with Cy3 or Cy5 dUTP( 5190-0453). DNA yield and incorporation of label (specific activity) was measured using NanoDrop spectrophotometer.

growth_protocol: 30 degree YEPD medium

extract_protocol: ChIP experiments were carried out as described earlier (Shukla S et al. 2011). In brief, 15 ml of cultures in YEPD medium wildtype(WT) and iron deprived (BPS) cells were cross-linked with 1% formaldehyde for 20 min at RT with intermittent mixing in between. The cross-linking reaction was quenched with 125 mM glycine and cells were collected by centrifugation at 4K for 5 min. Cells were washed twice with ice cold TBS (Tris Buffered Saline: 20 mM Tris-Cl, pH 7.5, containing 150 mM NaCl) and resuspended in Zymolase buffer (50 mM Tris, pH 7.4, 10 mM MgCl2, 1 M sorbitol, and 30 mM DTT) containing Zymolase 20µg/ml and incubated for 2 hr at 30ºC for the formation of spheroplast. Spheroplasts were washed twice with cold TBS containing 1M sorbitol, resuspended in ChIP lysis buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 1% Triton X-100, 0.1% sodium deoxycholate, and 1 mM PMSF), and incubated on ice for 30 min. SDS was added at a final concentration of 0.5% in each sample. Cells were sonicated for 25 sec at amplitude of 6 for seven cycles with 2 min cooling interval. After sonication cell suspensions were centrifuged at 4ºC for 30 min at 13K rpm and termed soluble total chromatin (STC). 15 µl samples were run on 1% agarose gel to check the size of the fragmented chromatin (approximate size ~250bp to ~500 bp). 50 µl of STC was stored at -20ºC for further use. STC was diluted 5 times with ChIP lysis buffer and pre-cleared by incubating pre-immune serum and 20 µl packed volume of protein-A agarose beads for 2 hrs at 4ºC on rotating rocker. After pre-clearing the samples pre-immune serum (negative control) and antibody was added at a final concentration of 2-5µg and incubated O/N for binding. Next morning 20 µl packed volume of protein-A agarose beads were added and put on rocker for binding, next bead bound immune complexes were precipitated by centrifuging at 3K for 1 min and washed twice with ChIP lysis buffer, TSE 150 (Tris-Cl, pH 8.0, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 1 mM EDTA, pH 8.0, and 1 mM PMSF), TSE 500 (Tris-Cl, pH 8.0, 500 mM NaCl, 1% Triton X-100, 0.1% SDS, 1 mM EDTA, pH 8.0, and 1 mM PMSF), buffer III (10 mM Tris-Cl, pH 8.0, 1 mM EDTA, pH 8.0, 250 mM LiCl, 1% NP-40, and 1% sodium deoxycholate), and finally with TE (10 mM Tris-Cl, pH 8, and 1 mM EDTA, pH 8.0). After washing, immunoprecipitated complexes were eluted in buffer containing (50 mM Tris-Cl, pH 7.5, 10 mM EDTA, pH 8.0, and 1% SDS) at 65ºC O/N. The immunoprecipitated complexes and input DNA were treated with proteinase-K and incubated for 2 hr at 65ºC. The precipitated DNA was purified by using Qiagen PCR purification kit as instructed by the manufacturer.

treatment_protocol: Iron deprived by adding chelator BPS

tag: genotype/variation

value: iron-deprived

tag: antibody

value: Polyclonal anti-Hsf1 antibody (Nair R et al, 2017)

source_name: Input DNA from iron deprived cells of Candida albicans

value: none, input DNA


title: Env Wildtype RNA Fragment A; Reverse-transcribed with Accuscript


title: Tissue NODDQ8 clean SPF colonized P.aeruginosa PA14 control 2

value: clean

value: colonized P.aeruginosa PA14


title: UCD037A_MIBC_Responsive

description: NanoString reporter probe

tag: disease state


title: 3B3-3l_serum_1

value: Mouse ES cells


title: BPS1-IP_Cy5 vs. Input_BPS1_Cy3

treatment_protocol: Input DNA from iron deprived cells of Candida albicans


title: Env Wildtype Plasmid DNA Fragment C

description:
plasmid DNA
Wildtype plasmid DNA of DU422 gp140; control for background error rate


title: 3B3-3l_2i_2


title: Env Wildtype Plasmid DNA Fragment B


title: 3B3-3l_2i_3


title: Env Wildtype Plasmid DNA Fragment A


title: UCD036B_MIBC_Responsive

description: NanoString reporter probe


title: WT4-IP_Cy5 vs. Input_WT4_Cy3

description: Hsf1 binding profile in Wt cells of Candida albicans

source_name: HSF1 ChIP in WT Candida cells

treatment_protocol: Untreated

value: wild type

source_name: Input DNA from WT cells of Candida albicans


title: UCD036A_MIBC_Responsive

description: NanoString reporter probe


title: UCD035_MIBC_Responsive

description: NanoString reporter probe


title: 3B3-3l_2i_1


title: Tissue C57 clean SPF mice colonized P.aeruginosa LasB control 1

description: Tissue from clean specific pathogen free (SPF- derivated of Altered Schaedler flora) C57BL/6 mouse (10-12 weeks), non-sensitized, colonized with P.aeruginosa PA14 disrupted in LasB gene

value: colonized P.aeruginosa LasB


title: Tissue C57 clean SPF mice colonized P.aeruginosa LasB control 3


title: WT3-IP_Cy5 vs. Input_WT3_Cy3

treatment_protocol: Input DNA from WT cells of Candida albicans


title: Tissue C57 clean SPF mice colonized P.aeruginosa LasB control 2


title: Tissue C57 clean SPF mice colonized P.aeruginosa PA14 gliadin 2


title: Tissue C57 clean SPF mice colonized P.aeruginosa PA14 gliadin 1


title: Env PG16 Sorted Library C; Replicate 2

description: Deep mutational scan of DU422 gp140 for binding to broadly-neutralizing antibody PG16

value: Top 0.6% of population for binding signal (3 nM PG16)


title: Env PG16 Sorted Library B; Replicate 2


title: UCD269_MIBC_Resistant

description: NanoString reporter probe


title: UCD032_MIBC_Resistant

description: NanoString reporter probe


title: Tissue NODDQ8 clean SPF colonized P.aeruginosa PA14 control 1


title: Env PG16 Sorted Library A; Replicate 2


title: Tissue C57 clean SPF mice colonized P.aeruginosa PA14 control 3

description: Tissue from clean specific pathogen free (SPF- derivated of Altered Schaedler flora) C57BL/6 mouse (10-12 weeks), non-sensitized, colonized with P.aeruginosa PA14


title: UCD031_MIBC_Responsive

description: NanoString reporter probe


title: Env PG16 Sorted Library C; Replicate 1


title: Tissue C57 clean SPF mice colonized P.aeruginosa PA14 control 2


title: UCD030_MIBC_Responsive

description: NanoString reporter probe


title: Tissue C57 clean SPF mice colonized P.aeruginosa LasB gliadin 3


title: Tissue C57 clean SPF mice colonized P.aeruginosa LasB gliadin 2


title: Env PG16 Sorted Library A; Replicate 1


title: Env PG16 Sorted Library B; Replicate 1


title: UCD029_MIBC_Resistant

description: NanoString reporter probe


title: UCD028_MIBC_Resistant

description: NanoString reporter probe


title: Env sCD4 Sorted Library C; Replicate 2

description: Deep mutational scan of DU422 gp140 for binding to soluble CD4

value: Top 0.4% of population for binding signal (10 nM sCD4(D1-D2))


title: UCD027_MIBC_Resistant

description: NanoString reporter probe

value: urothelial carcinoma


title: Tissue C57 clean SPF mice colonized P.aeruginosa LasB gliadin 1


title: Tissue C57 clean SPF mice colonized P.aeruginosa PA14 control 1


title: Env sCD4 Sorted Library B; Replicate 2


title: UCD071_MIBC_Resistant

description: NanoString reporter probe


title: UCD070_MIBC_Responsive

description: NanoString reporter probe


title: Env sCD4 Sorted Library A; Replicate 2

value: Top 0.3% of population for binding signal (10 nM sCD4(D1-D2))


title: IELs C57 GF mice monocolonized P.aeruginosa LasB 3

description: Intraepithelial lymphocyte compartment (IEL) from ex-germ free C57BL/6 mouse (10-12 weeks) monocolonized with P.aeruginosa PA14 disrupted in LasB

value: germ free

value: monocolonized P.aeruginosa LasB


title: Env sCD4 Sorted Library C; Replicate 1


title: IELs C57 GF mice monocolonized P.aeruginosa LasB 2


title: UCD069_MIBC_Resistant

description: NanoString reporter probe

value: muscle-invasive

value: Resistant


title: LNCaP_GSK126_2

city: Nagoya

first: AKIHIRO

last: MURASHIMA

address: 65 Tsurumai-cho, Showa-ku

department: Division of Cancer Biology

country: Japan

institute: Nagoya University Graduate School of Medicine

description: Gene expression in GSK126 treated Prostate cancer cell LNCaP

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8×60K array slides (G4851B, Agilent Technologies) at 65 °C with rotation at 10 rpm for 17 hours in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA, Agilent Technologies) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Prostate cancer cell, LNCaP, GSK126, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop 2000 Spectrophotometer.

growth_protocol: Prostate cancer cell lines, PC3 and LNCaP, were cultured in RPMI-1640 medium(Wako) containig 5% fetal bovine serum and 0.5% DMSO at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was isolated using TRIzol (Life Technologies) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000.

treatment_protocol: Cancer cell lines are treated with 5µM GSK126 or NPD13668 for 72hrs. Total RNA was extracted from the cells and the effects was validated.   For blocking of Notch signaling in GSCs, the γ-secretase inhibitor DAPT (N-[N-(3,5-difluorophenacetyl)-l-alanyl]-S-phenylglycine t-butyl ester, Sigma-Aldrich) and RO4929097 (Selleck Chemicals) were added, and the medium was changed every other day.

value: LNCaP

tag: tissue

value: Prostate cancer cell

value: male


title: LNCaP_CONTROL_2

description: Gene expression in DMSO treated Prostate cancer cell LNCaP

source_name: Prostate cancer cell, LNCaP, control, replicate 2


title: LNCaP_NPD13668_2

description: Gene expression in NPD13668 treated Prostate cancer cell LNCaP

source_name: Prostate cancer cell, LNCaP, NPD13668, replicate 2


title: UCD068_MIBC_Responsive

description: NanoString reporter probe

value: Responsive


title: LNCaP_GSK126_1

source_name: Prostate cancer cell, LNCaP, GSK126, replicate 1


title: LNCaP_NPD13668_1

source_name: Prostate cancer cell, LNCaP, NPD13668, replicate 1


title: PC3_GSK126_2

description: Gene expression in GSK126 treated Prostate cancer cell PC3

source_name: Prostate cancer cell, PC3, GSK126, replicate 2


title: PC3_GSK126_1

source_name: Prostate cancer cell, PC3, GSK126, replicate 1


title: Env sCD4 Sorted Library B; Replicate 1

value: Env (gp140)


title: PC3_NPD13668_2

description: Gene expression in NPD13668 treated Prostate cancer cell PC3

source_name: Prostate cancer cell, PC3, NPD13668, replicate 2


title: PC3_NPD13668_1

source_name: Prostate cancer cell, PC3, NPD13668, replicate 1


title: IELs C57 GF mice monocolonized P.aeruginosa LasB 1

source_name: Small intestine_ Intraepithelial lymphocyte compartment


title: UCD307_MIBC_Unknown

description: NanoString reporter probe

source_name: primary bladder cancer

value: Unknown


title: Env sCD4 Sorted Library A; Replicate 1


title: SeV P2-3

city: new york

first: satoshi

last: ikegame

state: new york

address: 1468 madison avenue, Annenbergbuilding 17-24

department: microbiology

institute: Icahn school of medicine at Mount Sinai

description: replicate 3 of passage 2

data_processing:
Illumina Casava software used for basecalling
bowtie2 for alignment
Genome_build: KY295909 (with some modification for technical reason; 'GCG' at the positon of 2630-2632 is replaced by 'TAATAG') for Sendai virus reference sequence, KY295913 (with some modification for tequnical reason; 'TGATGA' insertion at the position of 2768) for mumps virus reference sequence
Supplementary_files_format_and_content: processed data show the coverage of sequenced reads

organism: Respirovirus muris

source_name: african green monkey renal cells

growth_protocol: Viruses were amplified in Bsr-T7 cells (for input) or Vero cells (for passage 1 and passage 2), then virus containing supernatant were collected when infection became confluent in the cells.

extract_protocol:
QIAamp viral RNA extraction kit were used to extract RNA from supernatant.
RNAs were reverse transcribed and amplified by superscript III one-step. Amplified amplicon were processed by TruSeq DNA LT Sample Prep Kit.

tag: host cell type

value: Vero cells

tag: passages

tag: molecule subtype

value: RNA from the virion


title: MuV P2-3

description: replicate 3 of passage 2

organism: Mumps orthorubulavirus


title: MuV P2-2

description: replicate 2 of passage 2


title: Env Naive Plasmid DNA Library B

description:
plasmid DNA
Naïve HIV-1 (DU422 strain) gp140 SSM library B (a.a.N280-Q577)

source_name: Synthetic coding sequences


title: Env Naive Plasmid DNA Library C

description:
plasmid DNA
Naïve HIV-1 (DU422 strain) gp140 SSM library C (a.a. T578-N677)


title: SeV P2-2

description: replicate 2 of passage 2


title: MuV P2-1

description: replicate 1 of passage 2


title: Tissue C57 GF mice monocolonized P.aeruginosa PA14 3

description: Tissue from ex-germ free (GF) C57BL/6 mouse (10-12 weeks) monocolonized with P.aeruginosa PA14

source_name: Small intestine_Tissue

tag: strain

value: monocolonized P.aeruginosa PA14


title: Env Naive Plasmid DNA Library A

description:
plasmid DNA
Naïve HIV-1 (DU422 strain) gp140 SSM library A (a.a. N31-N279 )


title: UCD293_MIBC_Responsive

description: NanoString reporter probe

tag: disease subtype

tag: response to therapy


title: LNCaP_CONTROL_1

source_name: Prostate cancer cell, LNCaP, control, replicate 1

tag: cell line


title: Tissue C57 GF mice monocolonized P.aeruginosa LasB 3

description: Tissue from ex-germ free (GF) C57BL/6 mouse (10-12 weeks) monocolonized with P.aeruginosa PA14 disrupted in LasB gene

tag: status

tag: colonized


title: PC3_CONTROL_2

description: Gene expression in DMSO treated Prostate cancer cell PC3

source_name: Prostate cancer cell, PC3, control, replicate 2

tag: gender


title: Tissue C57 GF mice monocolonized P.aeruginosa PA14 1


title: SeV P2-1

description: replicate 1 of passage 2


title: SeV P1-3

description: replicate 3 of passage 1


title: PC3_CONTROL_1

source_name: Prostate cancer cell, PC3, control, replicate 1


title: Tissue C57 GF mice monocolonized P.aeruginosa PA14 2


title: M. extorquens AM1: La3

city: East Lansing

first: Nathan

middle: M

last: Good

address: 567 Wilson Rd

department: Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Illumina Real Time Analysis (RTA) v1.18.64
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to ASM2268v1 whole genome using bowtie v0.12.2
Trimmed mean of M (TMM) values were counted by Htseq (Robinson and Oshlack, Genome Biology, 2010)
Differential expression analysis was conducted using Bioconductor edgR (https://bioconductor.org/packages/release/bioc/html/edgeR.html)
Genome_build: ASM2268v1
Supplementary_files_format_and_content: a single tab delimited text file including TMM for all samples and differential expression analysis for the two conditions

organism: Methylorubrum extorquens AM1

source_name: culture grown in minimal salts medium with 125 mM methanol and 2 uM lanthanum chloride

growth_protocol: M. extorquens AM1 cells were grown overnight in 2 mL cultures of minimal salts medium with 15 mM succinate. Cells were subcultured into 50 mL of minimal salts medium with 125 mM methanol, with or without 2 uM lanthanum chloride.

extract_protocol:
Cultures were harvested at an optical density (600 nm) of 1.0 and RNA was harvested using the Qiagen RNeasy Kit (Cat#74004). Illumina TruSeq RNA Sample Prep Kit with RiboZero rRNA depletion (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bacterial cells


title: MuV P1-2

description: replicate 2 of passage 1


title: M. extorquens AM1: La2


title: MuV P1-1

description: replicate 1 of passage 1


title: Tissue C57 GF mice monocolonized P.aeruginosa LasB 2


title: SeV P1-1

description: replicate 1 of passage 1


title: SeV P1-2

description: replicate 2 of passage 1


title: M. extorquens AM1: La1


title: IELs C57 GF mice monocolonized P.aeruginosa PA14 3

description: Intraepithelial lymphocyte compartment (IEL) from ex-germ free C57BL/6 mouse (10-12 weeks) monocolonized with P.aeruginosa PA14


title: IELs C57 GF mice monocolonized P.aeruginosa PA14 2


title: M. extorquens AM1: noLa2

source_name: culture grown in minimal salts medium with 125 mM methanol


title: MuV Input_Sheared_DNA

description: MuV Input

library_source: genomic

source_name: plasmid DNA

value: Bsr-T7 cells

value: plasmid DNA


title: vastus laterlis-Inflexible male-rep7

status: Public on Jan 31 2019

city: Baton Rouge

first: Jaycob

middle: D

last: Warfel

state: Louisiana

address: 6400 Perkins Road

department: RNA Homeostasis

institute: PBRC

data_processing:
conversion of SOLiD 5500 XSQ files to csfasta/qual files was performed using perl and bash shell scripts that were developed in-house. These scripts make use of Life Technologies XSQ conversion tools, version 1.5.
alignment of sequence tags back to a mouse reference genome was performed using a modified version of the Applied Biosystems SOLiD™ SAGE™ Analysis Software v1.10 that was developed in-house.
filtering non-unique tags, and establishing counts per RefSeq gene was performed using a modified version of the Applied Biosystems SOLiD™ SAGE™ Analysis Software v1.10 that was developed in-house.
The raw data set was filtered to remove genes where the sum of counts was less than 25  across 16 samples.  The dataset was normalized and differential expression calculated using DESeq2 (Bioconductor.org) version 1.4.5.  JMP Genomics version 6.0 was used for principal components analysis, heatmaps, and Venn diagrams.
Genome_build: hs106/GRCh38
Supplementary_files_format_and_content: processed data file in text format contains DESeq2 normalized counts per gene for 30554 human RefSeq genes

source_name: vastus laterlis

extract_protocol:
Total RNA was prepared using Trizol, RNA concentration was determined usign a nanodrop UV spectrophotometer, and 500ng RNA per sample was used for sequencing library construction.
Libraries were prepared using the Applied Biosystems SOLiDSAGE kit, according to AB's instructions for the SOLiD 4 System (except a 1:100 of Adaptor B dilution was used).
SOLiD SAGE Kit with Barcoding Adaptor Module (#4452811) and SOLiD RNA Barcode Kit (#4427046). Over 551 million mRNA SAGE tags were sequenced corresponding to 4.6 million different mRNA tags present at least  in at least one library.Over 551 million mRNA SAGE tags were sequenced corresponding to 4.6 million different mRNA tags present at least  in at least one library.

treatment_protocol: Vastus lateralis muscles were biopsied from 15 male and 15 female subjects.

tag: Sex

tag: phenotype

value: flexible

value: vastus laterlis


title: vastus laterlis-Inflexible male-rep6


title: IELs C57 GF mice monocolonized P.aeruginosa PA14 1

value: germ free


title: vastus laterlis-Inflexible male-rep5


title: M. extorquens AM1: noLa1


title: SeV Input_Sheared_DNA

description: SeV Input


title: vastus laterlis-Inflexible male-rep2


title: vastus laterlis-Inflexible male-rep1


title: vastus laterlis-Inflexible male-rep3


title: vastus laterlis-Flexible male-rep8


title: Tissue C57 GF mice monocolonized P.aeruginosa LasB 1

value: monocolonized P.aeruginosa LasB


title: vastus laterlis-Flexible male-rep7

value: Inflexibile


title: vastus laterlis-Inflexible male-rep4


title: MuV P1-3

description: replicate 3 of passage 1


title: vastus laterlis-Flexible male-rep5


title: SeV Rescue_P0

description: passage 0

source_name: baby hamster kidney cells

value: passage 0


title: MuV Rescue_P0

description: passage 0


title: vastus laterlis-Flexible male-rep6


title: vastus laterlis-Flexible male-rep2


title: vastus laterlis-Inflexible female-rep6

value: female


title: vastus laterlis-Flexible male-rep3

value: male


title: vastus laterlis-Inflexible female-rep5


title: vastus laterlis-Inflexible female-rep7


title: vastus laterlis-Flexible male-rep4


title: vastus laterlis-Inflexible female-rep4


title: vastus laterlis-Inflexible female-rep3


title: vastus laterlis-Inflexible female-rep1


title: vastus laterlis-Flexible female-rep8


title: vastus laterlis-Inflexible female-rep2


title: vastus laterlis-Flexible female-rep7


title: vastus laterlis-Flexible female-rep5


title: vastus laterlis-Flexible female-rep4


title: vastus laterlis-Flexible female-rep2


title: vastus laterlis-Flexible female-rep3


title: vastus laterlis-Flexible male-rep1


title: vastus laterlis-Flexible female-rep1


title: vastus laterlis-Flexible female-rep6


title: 0138 RBPJ KO Tconv

city: Mainz

first: Michael

last: Delacher

state: Rhineland-Palatinate

address: Langenbeckstrasse 1

department: Institute for Immunology

country: Germany

institute: University Medical Center of the Johannes Gutenberg-University Mainz

hyb_protocol: 1.5 µg of cDNA were hybridized for 17hrs at 55.4 °C on Illumina Mouse WG-6-Microarray

scan_protocol: Illumina iSCAN-Scanner according to Std Illumina Scanning Protocol Part # 11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide). Microarray scanning was done using an iScan array scanner

data_processing: Microarray scanning was done using an iScan array scanner. Data extraction was done for all beads individually, and outliers are removed when the absolute difference to the median is greater than 2.5 times MAD(2.5 Hampelís method). All remaining bead level data points are than quantile normalized [1]. As test for significance the studentís t-test is used on the bead expression values of the two groups of interest. In the case of significance of expression against background we tested for greater than all negative beads for this sample and in the case of comparing separate groups we tested for inequality of the means of the groups. In both cases Benjamini-Hochberg correction [2] was applied to the complete set of p-values of all 48107 ProbeIDs on the chip. The average expression value is calculated as mean of the measured expressions of beads together with the standard deviation of the beads. [1] Probe Level Quantile Normalization of High Density Oligonucleotide Array Data, Ben Bolstad, Division of Biostatistics, University of California, Berkeley December 2001  [2] Y. Benjamini and Y. Hochberg (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society B, Vol. 57, 289ñ300.

source_name: FACS-purified CD4+CD25-Foxp3- Tconv cells from spleen of diseased animal

label_protocol: The NuGEN Ovation Pico WTA System (linear isothermal DNA amplification process) was used to generate single-stranded cDNA from small input amounts of RNA. Labeled cRNA was prepared according to Nugene Encore BiotinIL Module.

extract_protocol: Spleen was isolated and target cells were sorted using FACS

treatment_protocol: Mice were housed at DKFZ central animal facility.

tag: cell type

value: CD4+Foxp3- Tconv

tag: disease

value: Diseased knockout animal

value: Female


title: 0138 RBPJ KO Treg

source_name: FACS-purified CD4+CD25+Foxp3+ Treg cells from spleen of diseased animal

value: CD4+CD25+Foxp3+ Treg


title: 0114 RBPJ WT Treg

source_name: FACS-purified CD4+CD25+Foxp3+ Treg cells from spleen of healthy animal

value: Healthy wildtype animal

value: Male


title: 0098 RBPJ WT Tconv

source_name: FACS-purified CD4+CD25-Foxp3- Tconv cells from spleen of healthy animal


title: 0114 RBPJ WT Tconv


title: 0095 RBPJ KO Treg

value: Healthy animal


title: 0095 RBPJ KO Tconv


title: 0144 RBPJ KO Tconv


title: 0099 RBPJ KO Treg


title: 0105 RBPJ KO Tconv


title: 0105 RBPJ KO Treg


title: 0139 RBPJ KO Tconv


title: 0099 RBPJ KO Tconv


title: LN_KO3_15803_3998574034_F

source_name: Lymph node from diseased Treg Rbpj-deficient animal

extract_protocol: Total lymph nodes were isolated, single-cell suspensions generated and total RNA isolated with the RNEasy Mini Kit according to manufacturers standards.

treatment_protocol: Mice were housed at DKFZ central animal facility and analyzed upon signs of disease

value: lymph node

tag: genotype/variation

value: Treg Rbpj-deficient


title: 0147 RBPJ WT Treg


title: 0147 RBPJ WT Tconv


title: 0145 RBPJ WT Tconv


title: 0139 RBPJ KO Treg

tag: disease state


title: 0137 RBPJ KO Treg


title: 0145 RBPJ WT Treg


title: 0143 RBPJ WT Tconv


title: LN_WT3_976_3998574034_C

source_name: Lymph node from wildtype animal

tag: tissue

value: wild type


title: 0137 RBPJ KO Tconv


title: LN_KO1_15864_3998574034_D


title: 0143 RBPJ WT Treg


title: LN_WT2_980_3998574034_B


title: 0098 RBPJ WT Treg


title: 0144 RBPJ KO Treg


title: LN_KO2_15821_3998574034_E


title: Spleen WT Klrg1-ST- Treg Replicate 3

data_processing:
ATAC-seq read data were processed as described previously (reference see original publication). Reads were trimmed using Skewer and aligned to the mm10 assembly of the murine genome using Bowtie2 with the ‘-very-sensitive’ parameter. Duplicate reads were removed using sambamba markdup, and only properly paired reads with mapping quality >30 were kept. Reads were shifted as previously described to account for the transposition event. Bigwig files were created using bedtools. Preprocessed ATAC-seq data was analyzed with the HOMER package. In brief, mapped sequencing reads were transformed to tag directories using the option ‘-sensitivity 3’. Peaks were called on all reads in all samples using the ‘findPeaks’ command with the options ‘-style factor -size 350 -minDist 300 -L 2’. Peaks from the mitochondrial genome and ENCODE blacklisted regions were removed. Based on this consensus peak set, differential peaks were called using the DEseq2 implementation of HOMER. Specifically, reads form all individual experiments were counted in all individual peaks of consensus peak set using the ‘annotatePeaks.pl’ command with the option ‘-raw’. Based on the read count at each peak, significantly differential peaks were called using the ‘getDiffExpression.pl’ command using the ‘-norm2total’ option. Motifs were then called on differential peaks using the ‘findMotifsGenome.pl’ command using the ‘hypergeometric’ option for p-value calculations. As a background, the non-differential peak set was used. The final motif sets were filtered for motifs with a significance less than 1e-10 and with an occurrence of less than 0.5 % in the background regions set in case the non-differential peaks were used as a background file for motif finding using the ‘compareMotifs.pl’ command. To create heatmaps of differential peaks, sequencing reads were annotated to the differential peaks in 25bp bins in a region of -750 bp to +750p from the peak center. The data matrix was clustered using Cluster 3.066 with the k-means option, and the heatmap was visualized with the TreeView 367 software.
Genome_build: mm10

source_name: Rbpj WT

extract_protocol:
Spleen was isolated and target cells were sorted using FACS; genomic DNA was isolated with the DNEasy Blood and Tissue Kit
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) was performed according to32 with some modifications. In brief, about 50,000 FACS-isolated cells were pelleted on with 10,000xg for 3 min and supernatant removed. Cells were tagmented at 55°C for 8 min in 50 µl 1x tagmentation buffer including 2.5 µl transposome from the Nextera DNA library prep kit and 0.01% digitonin. The transposome was inactivated by addition of 20 µl 5M guanidinium thiocyanate, and the DNA was purified with two volumes, i.e., 140 µl, of DNA-binding beads (HighPrep beads). The DNA was PCR amplified with a LightCycler 480 (Roche) in a 50 µl reaction with the NEBNext High Fidelity mix including 0.5 µl 1x SYBRGreen, forward primer Tn5McP1n (AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTC) and barcoded reverse primers Tn5mCBar (CAAGCAGAAGACGGCATACGAGAT (8-9N barcode) GTCTCGTGGGCTCGG); 72°C, 5 min; 98C, 30 sec (gap repair and initial melting); then cycling with 98°C, 10 sec; 63°C, 30 sec; 72°C, 30sec for 15 cycles when all amplifications turned into saturation. PCR products were purified with 1.4 volumes (70 µl) magnetic beads. Ten µl eluates were sequenced on a HiSeq2000, 125 bp paired-end. ATAC-seq read data were processed as described previously (reference see original publication). Reads were trimmed using Skewer and aligned to the mm10 assembly of the murine genome using Bowtie2 with the ‘-very-sensitive’ parameter. Duplicate reads were removed using sambamba markdup, and only properly paired reads with mapping quality >30 were kept. Bigwig files were created using bedtools.

value: WT animal wo disease


title: Spleen KO Klrg1+ST+ Treg Replicate 3

source_name: Rbpj KO

value: Diseased animal


title: Control_Replicate 2

city: Atlanta

first: Antonio

last: Rampoldi

state: Georgia

address: 2015 Uppergate Dr

department: Pediatrics

institute: Emory University Hospital

description: sample name: AR2

data_processing:
Reads were mapped to GRCh38 genome assembly using HISAT2, followed by using UCSC reference annotation and HTSeq to estimate gene abundance.
Per sample read counts were calculated with htseq-count, mode: union, feature type: exon, id attribute: gene_id, and all other defaults.
Normalized read count abundance was estimated and differential expression was calculated with DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing raw or normalized read counts for each sample (in columns) and each annotated transcript (in rows).

molecule: polyA RNA

source_name: hiPSC-CMs

extract_protocol:
IMR90 iPSCs were induced for cardiac differentiation using a growth factor-guided protocol.  Cardiac spheres were generated from cells at differentiation day 4 with Aggrewell plates. After 24 h cardiac spheres were transferred to a suspension culture, cultured until day 20 and then exposed for 5 days to ethanol (50mM) for subsequent experiments.  RNA samples were prepared using Bio-Rad RNA extraction kit and 1 µg of total RNA/sample was used for the construction of sequencing libraries using Illumina TruSeq RNA Sample Prep Kit.
Libraries were generated using the Illumina standard TruSeq Low-Throughput protocol.  Reads were sequenced on an Illumina HiSeq 2500 in 75bp paired end sequencing reactions.

value: IMR90 iPSC derived cardiomyocytes

tag: developmental stage

value: Day 25 differentiated cells

tag: condition

value: Standard medium


title: Ethanol treated_Replicate 1

description: sample name: AR4

value: Ethanol Treatment


title: Ethanol treated_Replicate 2

description: sample name: AR5


title: Control_Replicate 3

description: sample name: AR3


title: Ethanol treated_Replicate 3

description: sample name: AR6


title: Spleen WT Klrg1-ST- Treg Replicate 1


title: Spleen WT Klrg1-ST- Treg Replicate 2


title: Control_Replicate 1

description: sample name: AR1


title: Spleen KO Klrg1+ST+ Treg Replicate 2


title: Normal14 Rep 2

city: Fayetteville

first: Kevin

last: Roberts

state: AR

address: 700 W Research Ctr Blvd

department: Cell and Molecular Biology Program

institute: University of Arkansas

data_processing:
Base calling performed in Zebra Call
Unstranded RNA-seq reads were aligned to the Rnor_6.0 genome assembly using RNA Star in Galaxy with the two-pass option, readlength=50
Read counts performed using FeatureCounts in Galaxy
Differential gene expression relative to corresponding normal groups (e.g., DSM3 vs Normal3) called using EdgeR, abs(log2(FC))>1, FDR = 0.05, TMM Normalization
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: .XLSX containing log2FC relative to corresponding normal control groups, log2CPM, and FDR

organism: Rattus norvegicus

source_name: Rat Tibialis Anterior

growth_protocol: Food and water given ad libitum

extract_protocol:
~30 mg muscle from middle-third of rat tibialis anterior homogenized, subjected to Trizol-chloroform extraction, and purification via the Purelink RNA Mini Kit by manufacturer's protocol.
cDNA libraries were prepared according to standard BGI-seq500 protocol

treatment_protocol: Middle third of tibialis anterior subjected to biopsy (d = 8 mm, depth = 3 mm), following by repair with autologous minced muscle (MM) prepared from the biopsy, cadaveric rat decellularized skeletal muscle from tibialis anterior (DSM), and a combination of the two (DSM+MM). Uninjured muscle from contralateral limb used as control "Normal."

value: HSD

value: Tibialis Anterior muscle

tag: day post-injury


title: Normal14 Rep 3

tag: strain


title: DSM+MM14 Rep 2


title: Normal14 Rep 1


title: Normal14 Rep 4


title: DSM+MM14 Rep 3


title: DSM+MM14 Rep 1


title: DSM14 Rep 3


title: DSM14 Rep 2


title: RBPJ KO SICK Treg R2 #15325_10006025017

value: Diseased


title: RBPJ KO SICK Tconv R3 #15387_10006025017

value: CD4+Foxp3- Tconv

value: Female


title: LN_WT1_985_3998574034_A

value: CD4+CD25+Foxp3+ Treg


title: RBPJ KO SICK Tconv R2 #15325_10006025017


title: RBPJ KO SICK Treg R3 #15387_10006025017


title: RBPJ KO SICK Treg R1 #182_10006025017


title: Spleen KO Klrg1+ST+ Treg Replicate 1


title: Normal3 Rep 3


title: MM14 Rep 2


title: VML14 Rep 1


title: Normal3 Rep 2


title: RBPJ KO SICK Tconv R1 #182_10006025017


title: MM14 Rep 3


title: Normal3 Rep 4


title: MM14 Rep 1


title: VML14 Rep 2


title: DSM14 Rep 1


title: DSM+MM3 Rep 3


title: WT_Male2

city: Montreal

first: Alexandre

last: Prat

state: Quebec

address: 900 Rue Saint-Denis

department: Neurosciences

institute: CRCHUM

description:
male SJL/J
mRNA

data_processing:
RTA (Real-Time Analysis) version RTA 2.4.11 software used for basecalling and quality scoring.
Bcl2fastq version 2.17 used to demultiplex data.
Alignment to the reference genes (Genome Reference Consortium Mouse Build 38 - Mus Musculus mm10) was done using Bowtie2
Around 200 M single-end PF reads was generated per sample.
Sequenced in single-end (85nt)
Genome_build: mm10
Supplementary_files_format_and_content: Count matrix was generated using HTSEq algorithm

source_name: Secondary lymphoid organs

growth_protocol: Spleens and lymph nodes from pre-symptomatic mice (d35-d55) were harvested and immune cells were isolated. Cells were cultured for 4 days (typically 5-7× 10^6 cells into a T75 flask).

extract_protocol:
Cells were taken and resuspended in Trizol and frozen at -80°C until needed. RNA was isolated using the standard RNeasy mini kit (Qiagen, 74104) . A total of 500 ng RNA was used for library preparation.
Library preparation was done with the KAPA mRNAseq stranded kit for Illumina platforms (KAPA, Cat no. KK8420).

treatment_protocol: Cells were stimulated in RPMI supplemented with 10% foetal bovine serum, non-essential amino acids, HEPES, β- mercaptoethanol in the presence of recombinant mouse IL23 (20 ng/ml), recombinant human TGF-β (4 ng/ml), recombinant mouse IL6 (20 ng/ml), recombinant mouse IL12 (3 ng/ml) and mouse anti-CD3 (1 μg/ml).

value: immune cells

value: WT

tag: in vitro stimulation


title: DSM3 Rep 3


title: DSM+MM3 Rep 2


title: DSM+MM3 Rep 1


title: WT_Fem2

description:
female SJL/j
mRNA


title: WT_Fem1

description:
female SJL/j
mRNA


title: Normal3 Rep 1


title: DSM3 Rep 2


title: DSM3 Rep 1


title: MM3 Rep 3


title: TCR_Fem2

description:
female TCR1640
mRNA


title: TCR_Male2

description:
male TCR1640
mRNA


title: TCR_Male1

description:
male TCR1640
mRNA


title: TCR_Fem1

description:
female TCR1640
mRNA


title: MM3 Rep 1


title: VML3 Rep 3


title: VML14 Rep 3


title: VML3 Rep 1


title: Sample_46

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

data_processing:
RNA-seq: the cDNA library with a fragment length range of 250 bp (±25 bp) was consturcted and the paired-end sequencing was performed by using the Illumina sequencing platform (HiSeqTM 2500).
Filtering: the trimming adapter sequences were removed and low-quality reads (less than 13 bp or reads with unknown nucleotides larger than 5%) were filtered with the software
SNP discovery: The clean reads from the transcriptome of 111 F2 families and two parents were aligned to the ramie genome (genome accession ID: PHNS00000000) using the Burrows-Wheeler Aligner (BWA) software (settings: mem –t − 4 –k 32 –MR). The alignment files were converted to bam files using SAMtools (settings: –bS –t; Li et al., 2009). If multiple read pairs had identical external coordinates, only the pair with the highest mapping quality was retained. Thereafter, SNP identification was performed for the two parents and 111 families using SAMtools.
Gene expression analysis: Gene expression levels were measured in the RNA-Seq analysis as expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM).
Supplementary_files_format_and_content: the excel file contain the gene name, sample name, read count, and FPKM value

organism: Boehmeria nivea

source_name: F2 population

extract_protocol:
The young leaves of 111 F2 families and two parents were individually collected, when the ramie grows 30 days.. The sampled tissues were immediately frozen in liquid nitrogen and stored at -80° until use. Total RNA of each sample was extracted using an E.Z.N.A. Plant RNA Kit (OMEGA Bio-Tek, USA) according to the manufacturer’s protocol.
RNA of four samples were separately used to construct the cDNA library with a fragment length range of 250 bp (±25 bp). Then, the paired-end sequencing was performed by using the Illumina sequencing platform (HiSeqTM 2500) according to the manufacturer’s instructions (Illumina, San Diego, CA).

value: young leaves


title: Sample_43


title: Sample_45


title: MM3 Rep 2


title: Sample_42


title: Sample_39


title: Sample_41


title: Sample_40


title: Sample_37


title: Sample_38


title: Sample_44


title: Sample_30


title: Sample_33


title: Sample_31


title: Sample_32


title: Sample_35


title: Sample_34


title: VML3 Rep 2


title: Sample_36


title: Sample_28


title: Sample_26


title: WT_Male1

description:
male SJL/J
mRNA


title: Sample_22


title: Sample_29


title: Sample_27


title: Sample_24


title: Sample_21


title: Sample_19


title: Sample_17


title: Sample_18


title: Sample_16


title: Sample_13


title: Sample_15


title: Sample_12


title: Sample_11


title: Sample_10


title: Sample_7


title: Sample_9


title: Sample_4


title: Sample_2


title: Sample_3


title: Sample_1


title: Sample_25


title: Sample_8


title: Sample_112


title: Sample_111


title: Sample_108


title: Sample_109


title: QY1

source_name: Qingyezhuma


title: Sample_107


title: Sample_23


title: Sample_20


title: Sample_106


title: Sample_14


title: Sample_105


title: Sample_104


title: Sample_103


title: Sample_102


title: Sample_101


title: Sample_100


title: Sample_99


title: Sample_98


title: Sample_6


title: ZSZ1

source_name: Zhongsizhu 1


title: Sample_97


title: Sample_5


title: Sample_88


title: Sample_94


title: Sample_87


title: Sample_89


title: Sample_96


title: Sample_95


title: Sample_81


title: Sample_82


title: Sample_85


title: Sample_86


title: Sample_84


title: Sample_90


title: Sample_83


title: Sample_79


title: Sample_78


title: Sample_76


title: Sample_74


title: Sample_75


title: Sample_80


title: Sample_77


title: Sample_72


title: Sample_71


title: Sample_70


title: Sample_93


title: Sample_92


title: Sample_91


title: Sample_69


title: Sample_67


title: Sample_68


title: Sample_66


title: Sample_61


title: Sample_64


title: Sample_62


title: Sample_57


title: Sample_63


title: Sample_60


title: Sample_55


title: Sample_56


title: Sample_59


title: Sample_58


title: Sample_54


title: Sample_53


title: Sample_52


title: Sample_73


title: NHJS2_GA [28-2_6dGA2]

city: Daejeon

first: Haemyeong

last: Jung

address: 125 Gwahak-ro, Yuseong-gu

department: Plant Systems Engineering Research Center

country: South Korea

institute: KRIBB

data_processing:
Raw sequencing data were filtered using standard RNA-seq parameters (Illumina pipeline).
Adapter contamination, low-quality regions, and N-base reads were trimmed from the raw reads, and then reads with a Phred quality score of 31 (Q ≥ 20) or 25 base pairs (bp) were filtered out.
The cleaned datasets were pooled and mapped to the radish reference data set. The cleaned data sets were pooled and mapped to the radish reference geneset.To obtain assembly results, reference-guided assembly was performed using 46,512 genes from the coding sequence regions of the reference genome.
Using the TopHat program, 71,188 assembled unigenes were identified and imposed on the radish reference genesets. These data sets were pooled and mapped to the radish reference geneset. Mapping was performed using the Bowtie2(v2.1.0) program(Langmeadand Salzberg,2012) allowing only unique mapping with a maximum of two mismatches; otherwise, the default options were used. The expression levels in each sample were calculated with an in-house script, and read counts for each gene were normalized against library size and rounded to the nearest whole number.
Genome_build: Rs1.0
Supplementary_files_format_and_content: raw, normalized count and log2 FC

organism: Raphanus sativus

extract_protocol:
Total RNA was prepared from radish shoot tissue using Trizol (TaKaRa, Tyoko, Japan).
mRNA collectd from shoot tissues of the two inbred lines was fragmented and used as a template for synthesis of first-strand cDNA using random hexamers and reverse transcriptase. Second-strand cDNA was synthesized using DNA polymerase I (New England BioLabs, Ipswich, MA, USA) amd RNase H (Invitrogen, Carlsbad, CA, USA). The resultant cDNA fragments were purifed, end-reparided, polyA-tailed, and ligated to index adapters following the Illumina protocol.

tag: inbred line

value: Bolting

value: whole shoot

tag: treatment

value: Gibberellin (GA)


title: Sample_50


title: Sample_51


title: NHJS2_no GA [28-2_6d2]

source_name: NHJS2_no GA

value: Vegetative growth


title: Sample_49


title: NHJS1_GA [28-1_6dGA2]


title: NHJS1_GA [28-1_6dGA1]


title: NHJS2_no GA [28-2_6d1]


title: NHJS1_no GA [28-1_6d1]

source_name: NHJS1_no GA


title: Sample_47


title: NHJS1_no GA [28-1_6d2]


title: Sample_65


title: Sample_48


title: NHJS2_GA [28-2_6dGA1]


title: Treat_Replicate 3

status: Public on Jan 30 2019

city: ATLANTA

first: Dong

last: Li

state: GEORGIA

address: 2015 UPPERGATE DR

institute: Emory University

description:
DL_Treat_C_S9
Sample_9_Treat C

data_processing:
Reads were mapped to GRCh38 genome assembly with the HISAT2 followed by using UCSC reference annotation and HTSeq to estimate gene abundance.
Per sample read counts were calculated with htseq-count, mode: union, feature type: exon, id attribute: gene_id, and all other defaults.
Normalized read count abundance was estimated and differential expression was calculated with DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing raw or normalized read counts for each sample (in columns) and each annotated transcript (in rows).

extract_protocol:
IMR90 iPSCs were induced for cardiac differentiation using a growth factor-guided protocol. Cardiac spheres were generated from cells at differentiation day 5 and subjected to maturation factors or DMSO treatment from day 21 to day 28. RNA samples from cells at differentiation day 28 were prepared using Bio-Rad RNA extraction kit and 1 µg of total RNA/sample was used for the construction of sequencing libraries using Illumina TruSeq RNA Sample Prep Kit.
Libraries were generated using the Illumina standard TruSeq protocol and next-generation sequencing was done through an Illumina HiSeq 2500, 75bp paired end sequencing.

value: IMR90 iPSC derived cardiomyocytes

value: Day 28 differentiated cells

value: 3D cardiac spheres


title: DMSO_Replicate 2

description:
DL_DMSO_B_S2
Sample_2_DMSO B


title: DMSO_Replicate 1

description:
DL_DMSO_A_S1
Sample_1_DMSO A


title: Left Ventricle_Replicate 1

description:
DL_LV1_S4
Sample_4_LV1

source_name: cardiomyocytes_Left Ventricle

value: pediatric heart samples

tag: tissue subtype

value: tissue samples of left ventricle

value: tissue


title: Left Ventricle_Replicate 3

description:
DL_LV3_S6
Sample_6_LV3


title: Left Ventricle_Replicate 2

description:
DL_LV2_S5
Sample_5_LV2


title: Treat_Replicate 2

description:
DL_Treat_B_S8
Sample_8_Treat B