title: HI broth + 25mM aspartate microaerophilic early stat.

city: Albany

first: Craig

middle: T

last: Parker

address: 800 Buchanan St

department: PSM

institute: USDA ARS

data_processing:
Illumina MiSeq Real-time analysis (RTA) used for basecalling.
Sequenced reads were trimmed for low-quality sequence, then mapped to CP000814 using bowtie v1.1.2 within Geneious v9.1 parameters -n 2 -l 28 -q -p 4  --best --strata
Geneious v9 software was used to calculate the normalized transcripts per million (TPM) and to compare expression levels between the control growth condition (microaerophilic) and experimental conditions (oxygen limited+ nitrate, and oxygen limited).
Genome_build: CP000814.1
Supplementary_files_format_and_content: tab-delimited text files include TKM values for each Sample ...

organism: Campylobacter jejuni

source_name: monoculture

growth_protocol: Campylobacter precultures were diluted to an OD550 of 0.05 and grown microaerophilic (5% O2, 8% CO2, 8% H2) in HI medium, or HI medium + 25mM serine, or HI medium + 25mM aspartate to mid-log phase (6hr) or early stationary phase (12hr).

extract_protocol:
Total RNA was extracted from  cultures with the RNA-BeeTM kit (Tel-Test, Inc) according to the manufacturer’s specifications. . Subsequently, RNA was treated with RNAse-free DNAseI (Thermo) according to the instructions of the manufacturer.
Ribozero Magnetic Kit for-gram negative bacteria (Illumina) following manufacturer’s instructions using following the 5ug RNA procedure and option 1 (Ethanol precipitation), except using 1/8th reaction volumes/amounts. Illumina libraries were prepared using the KAPA stranded RNA-seq kit (Kapa Biosystems, Wilmington, MA), following manufacturer’s instructions to produce ~300bp fragments. Standard desalting TruSeq LT primers were ordered from Integrated DNA Technologies (Coralville, IA) and used at 50-100nM final concentration based on starting RNA amount. The PCR step was reduced to 6 cycles. Libraries were quantified using the KAPA Library Quantification Kit (Kapa), except with 10 µl volume and 90 sec annealing/extension PCR. Libraries were pooled and normalized to 4 nM. Pooled libraries were re-quantified by ddPCR on a QX200 system (Bio-Rad), using the Illumina TruSeq ddPCR Library Quantification Kit and following manufacturer’s protocols. The libraries were sequenced in two 2x76bp paired end v3 runs on a MiSeq instrument (Illumina) at 13.5 pM, following manufacturer's protocols.

value: wild type

value: 25mM aspartate


title: G1

status: Public on Oct 01 2017

type: SRA

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

country: China

institute: Chinese Academy of Agricultural Sciences

library_source: transcriptomic

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
Aligning: The reads of each accession were aligned into the referenced transcriptome.
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). The DEseq software was used to identify differentially expressed genes. DESeq analysis was performed by fitting normalized count data with a generalized linear model (GLM) estimating a negative binomial distribution to the calculated mean values of the two biologically independent samples. For each gene, fold changes and P values (pval) as well as P values adjusted (padj) for multiple testing with the Benjamini-Hochberg procedure, were used to control false discovery rate (FDR). The Sequence with a padj of less than 0.05 was deemed to be significantly differentially expressed genes (DEGs)

molecule: total RNA

organism: Allium sativum

source_name: Bulbs

growth_protocol: Field experiments were carried out following a randomized complete block design with two replicates. Fifty garlic cloves for each accession were planted into a five-row plot, with a distance of 10 cm between plants within a row and 20 cm between rows, in Sept 15, 2014,

extract_protocol:
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.  The RNA was stored at -80° for cDNA library preparation
RNA of each sample was separately used to construct the cDNA library with a fragment length range of 250 bp

treatment_protocol: The bulbs of five individuals for each accession were collected, when the bulbs is expanding.  The sampled tissues were immediately frozen in liquid nitrogen and stored at -80° until use.

tag: tissue

value: bulbs

tag: Stage

value: bulb expanding


title: G1 Alfalfa Stems 1

city: Santa Barbara

first: John

last: Henske

state: CA

address: Engineering II Building

department: Department of Chemical Engineering

country: USA

institute: University of California, Santa Barbara

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
AS1

data_processing:
Aligned reads from all conditions to transcriptomes using Trinity utility align_and_estimate_abundance.pl with RSEM estimation method
Genome_build: de novo
Supplementary_files_format_and_content: tab delimited text files containing estimated abundances of each transcript

organism: Neocallimastix californiae

source_name: Whole organism

growth_protocol: Cultures grown in ~ 10 ml Medium C (Davies et. al, J Gen Microbiol. 1993 Jun;139 Pt 6:1395-400.) at 39°C to mid-log phase (P≥5 psi)

extract_protocol:
Qiagen RNEasy Mini Kit (Plant/Fungi Protocol)
Illumina TruSeq Stranded mRNA library standard protocol

treatment_protocol: See characteristics for energy source treatments

tag: energy substrate

value: Alfalfa Stems

tag: growth phase harvested from

value: Exponential growth


title: Salt-stress rep1

city: Tucson

first: Kerry

middle: Kevin

last: Cooper

state: AZ

address: 1117 E. Lowell St.

department: School of Animal and Comparative Biomedical Sciences

institute: University of Arizona

description:
Two replicates were merged:
Salt-stress rep1 (SS2)
Salt-stress rep2 (SS4)

data_processing:
The MiSeq Reporter software (v2.3) demultiplexed the samples based on the barcodes for each sample, then the barcodes and adaptors were removed and a FASTQ file for each sample was generated and used for further analysis
There is no reference genome available for P. elongata, therefore the Trinity software (v2.0.6) generated a de novo transcriptome utilizing the Illumina reads from all the samples pooled together.
The original de novo Trinity transcriptome assembly resulted in 84,136 contigs, these contigs were then examined for potential contamination by BLASTing all of the contigs against the NCBI non-redundant (nr) protein database using the blastx command in the DIAMOND (v0.71) program, and then the output matches were screened for non-plant matches using the MEGAN6 program. In total 44 contigs were identified as contamination (10 bacterial matches, 34 fungal matches), and were removed from the transcriptome prior to analysis.
The transcriptome was employed as a reference for further analysis (Kim et al. 2013). Next, the Tuxedo software suite, Bowtie 2 software (v2.1.0), TopHat2 software (v2.0.9), Cufflinks software (v2.1.1), and Cuffdiff software (v2.2.1) determined sequences with differential expression levels in response to salt stress in comparison to the controls (Trapnell et al. 2012). The Tuxedo suite mapped, quantified and determined the expression differences between these conditions from the generated reads. Sequences with a q-value (<0.05) were considered statistically significantly expressed.

A de novo transcriptome has also been deposited in the TSA project under accession number: GFBN00000000

The data was also analyzed using the RSEM program (v1.3.0) to further determine the differentially expressed genes when the P. elongata was salt stressed compared to the controls. Contigs with a p-value (<0.004), which is equal to the q-value (<0.05) used for the Tuxedo software suite, were considered statistically significant.
Genome_build: There is no reference genome available for P. elongata, therefore the Trinity software (v2.0.6) generated a de novo transcriptome utilizing the Illumina reads from all the samples pooled together.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample; normalized abundance measurements output from Cuffdiff, also output from RSEM

organism: Paulownia elongata

source_name: 125 mM NaCl for 10 days

growth_protocol: Three-year-old P. elongata pots were grown in a greenhouse under 25-30°C, 75% relative humidity and 13 hours of natural sunlight for the experiment.

extract_protocol:
Total RNA was extracted from Paulownia leaves using Quick-RNA MiniPrep Kit (Zymo Research, USA) following the manufacturer’s protocol. Paulownia RNA was treated with DNase I (Life Technologies, USA) and the RNA Clean-Up kit (Zymo Research, USA) eliminated genomic DNA contamination.
Barcoded cDNA libraries were synthesized from 1 µg of total RNA using the TruSeq RNA Sample Prep Kit (v2; Illumina, USA) following the manufacturer’s Low Sample Protocol.

treatment_protocol: Plants were irrigated with 1.5 L of 125 mM NaCl every 24 hours for 10 days in Pro-Mix HP Mycorrhizae potting soil (ingredients: Canadian Sphagnum peat moss (65%-70%), perlite and limestone (Premier Tech Horticulture, Canada). Salt water drained completely through the soil and out of the pots. Control plants were irrigated under the same conditions with 1.5 L of water.

value: leaves

tag: age

value: 3-year old pots

tag: treatment

value: salt stress


title: Co-culture_LB2

city: Malaga

first: Carlos

middle: Molina

last: Santiago

state: Malaga

address: Bulevar Louis Pasteur 49

department: MIcrobiology

country: Spain

institute: UMA

description:
This sample has reads of both bacterial strains as is a co-culture of both strains in the same culture
processed data files: CoT1E_LB.xlsx , CoK12_LB.xlsx

data_processing:
We use Rockhopper for alignment and the complete analysis of data
Genome_build: NC_018220 and NC_000913
Supplementary_files_format_and_content: tab-delimited text files include the average of the expression values obtained in Rockhopper for the replicates of each condition
Supplementary_files_format_and_content: T1E_LB.xlsx: Average of expression values of samples DOT-T1E_LB1 and LB2
Supplementary_files_format_and_content: CoT1E_LB.xlsx: Average expression values of reads related with DOT-T1E strain in samples Co-culture_LB1 and LB2
Supplementary_files_format_and_content: K12_LB.xlsx: Average of expression values of samples MG1655_LB1 and LB2
Supplementary_files_format_and_content: CoK12_LB.xlsx: Average expression values of reads related with MG1655 strain in samples Co-culture_LB1 and LB2

organism:
Pseudomonas putida
Escherichia coli

extract_protocol:
Single colonies of P. putida strain DOT-T1E and E. coli MG1655 were grown overnight in Luria–Bertani (LB) medium at 30°C. Overnight cultures were diluted to a starting OD600 of 0.01 in the same medium and 50 ml aliquots were disposed in separate 250 ml Erlenmeyer flasks and incubated with shaking at 200 rpm. When cultures reached exponential phase (0.5 at OD600), antibiotics were added at sub-lethal concentrations to the culture medium to reach a final concentration of 1 µg/ml kanamycin, 300 µg/ml ampicillin, 150 µg/ml chloramphenicol, 4 µg/ml tetracycline, 0.5 µg/ml ciprofloxacin, 300 µg/ml spectinomycin, 500 µg/ml rifampicin and 2 µg/ml gentamicin. Then cultures were incubated under the same conditions for one hour more. Cells were harvested by centrifugation at 8000 g for 10 min and suspended immediately in stop solution (95% (v/v) ethanol, 5% (v/v) phenol) and pelleted by centrifugation. After that, total RNA was extracted with Trizol (Invitrogen). Removal of DNA was carried out by treatment with DNase I (Fermentas) in combination with the RNase inhibitor RiboLock (Fermentas). The integrity and quality of total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Co-culture MG1655/DOT-T1E


title: HI broth + 25mM serine microaerophilic early stat.

tag: genotype

value: 25mM serine


title: G4


title: Co-culture_LB1


title: G1 Corn Stover 3

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
CS3

value: Corn Stover


title: HI broth microaerophilic early stat.

value: microaerophilic (5% Oxygen)


title: NH4input

city: Pozuelo de Alarcón

first: joaquín

last: Giner Lamia

state: Madrid

address: Campus de Montegancedo

department: Biotecnologia

institute: CBGP-Universidad Politecnica de Madrid

library_source: genomic

data_processing:
Illumina bcl2fastq v2.17.1.14 software used for basecalling.
Illumina sequencing data were pre-processed with the standard Illumina pipeline version 1.6 and only 20% of sequences were then aligned to the Synechocystis sp. PCC 6803 genome (NCBI Reference sequence: NC_000911.1) using Bowtie2 version 2.2.4 with the parameters -p 4
bam files were normalized unsing bamcoverage from DeepTools version 2.0.1
peaks were called using MACS version 1.4.1 with the following setting: band width (300), p-value cutoff= (1.00e-05), and Bayespeak version 1.22.0 with the paramters: method ="lowerbound"
Genome_build: Synechocystis sp. PCC 6803 genome (NCBI Reference sequence: NC_000911.1)
Supplementary_files_format_and_content: bigWig files were generated using bamcoverage from DeepTools version 2.0.1.

molecule: genomic DNA

organism: Synechocystis sp. PCC 6803

source_name: cells

extract_protocol:
DNA was purified using phenol:chloroform extraction followed by ethanol precipitation with ammonium acetate and glycogen. DNA was dissolved in DNAse-free purified water.
Libraries were prepared according to Dianogenode`s instructions accompanying the Dianogenode Microplex Library preparation Kit for Illumina sequencing platform.

value: growth in BG11C containing NH4

tag: chip antibody


title: G1 Corn Stover 2

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
CS2


title: HI broth + 25mM aspartate microaerophilic log


title: G1 Corn Stover 1

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
CS1


title: G1 Switchgrass 2

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
SG2

value: Switchgrass


title: HI broth microaerophilic log


title: G1 Reed Canary Grass 3

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
RCG3

value: Reed Canary Grass


title: G1 Switchgrass 1

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
SG1


title: HI broth + 25mM serine microaerophilic log


title: G1 Reed Canary Grass 2

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
RCG2


title: G1 Reed Canary Grass 1

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
RCG1


title: SA_0S

city: Shanghai

first: Jiming

last: Gong

address: Fenglin Road 300

department: National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
The sequencing reads were cleaned, including removing bases with low quality score (<20) and irregular GC content based on FastQC, cutting sequencing adaptor followed by filtering short reads.
The cleaned data were assembled with Trinity (version of 20140413p1).
The cleaned Illumina/Solexa reads were mapped to the assembled contigs using bowtie (version of 1.0.0) and normalized to FPKM with rsem (version of 1.2.12).
Genome_build: all_plus_454.Trinity.fasta (assembly contigs for illumina sequencing data and 454 sequencing data)
Supplementary_files_format_and_content: Reads count and FPKM of genes were provided.

organism: Sedum alfredii

source_name: Sedum alfredii shoot with 0 μM CdCl2 treatment

extract_protocol:
Total RNA  was isolated from  roots and shoots of 6 weeks old S. plumbizincicola  and were pooled and subjected to 454 sequencing. For Illumina sequencing, Sedum plants were treated with 0 µM or 10 µM CdCl2 for 3 days before roots and shoots were sampled, respectively.Total RNA of Sedum plants was isolated using CTAB buffer(2% CTAB, 0.1 M Tris, 25 mM EDTA-Na2, 1.4 M NaCl, pH 8.0 and 2% mercaptoethanol).
RNA libraries were prepared for sequencing using standard protocols

value: shoot


title: G1 Avicel 3

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
A3

value: Avicel


title: SA_10R

source_name: Sedum alfredii root with 10 μM CdCl2 treatment

value: root


title: G1 Avicel 1

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
A1


title: G1 Cellobiose 3

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
CB3

value: Cellobiose


title: Control rep7

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: UNIVERSITY OF FLORIDA

data_processing:
Illumina Casava1.7 software used for basecalling.
Several quality measures were performed using the web interface/software program Galaxy’s FastQC command to check the data quality of the reads and detect any potential errors introduced during sequencing or library preparation. The Cutadapt software program was used to remove low quality reads from the final dataset. Reads with a Phred-like score of <40 and bases with a score <20 were excluded. A reference-based approach to alignment was used to compare the sequenced transcripts to the genome on file for the manatee (Trichechus manatu)  using the Bowtie2 mapper.
ICBR scripts along with SAMtools and the DESeq, EdgeR, and Bayseq (DEB) computational applications were applied to generate the gene expression data, including fold changes and p-values, to remove duplicates or artifacts from PCR, and choose uniquely mapped reads for gene expression analysis. Digital gene expression was assessed by counting the number of transcripts that mapped to a gene sequence
Genome_build: manatee_ref_dna-23297, TriManLat1.0
Supplementary_files_format_and_content: tab-delimited text files include the mapped read counts for each Sample

organism: Trichechus manatus latirostris

source_name: Buffy coat

extract_protocol:
Sample preparation included RNA extraction from buffy coats, purification using DNase and column treatments to remove residual DNA contamination, depletion of rRNA and globin using EpiCentre ScriptSeq™ kits, and creation of cDNA libraries following standard protocols (EpiCentre, Madison, WI, USA). RNAlater (Life Technologies™, Carlsbad, CA, USA) was used to preserve the buffy coat samples in a ratio of 1.2 mL RNAlater to <0.5 mL buffy coat according to the manufacturer’s protocol (Life Technologies™). The samples were stored at -20 °C in RNAlater for approximately 9 months. RNA was extracted from manatee buffy coat samples according to the Tel-Test Inc. method for total RNA extraction using Stat-60 in a 1:10 ratio of buffy coat sample to Stat-60 (Tel-Test, Inc., Friendswood, TX)
For RNA processing and sequencing library preparation, the Illumina® EpiCentre ScriptSeq™ Complete Gold (Blood)-Low Input Kit (Illumina® EpiCentre, Madison, WI, USA) was used along with the Illumina® FailSafe™ PCR Enzyme Mix and ScriptSeq™ Index PCR primers (set 1). The kit protocols were followed with minor modifications. This kit’s ‘Globin and Ribo-Zero’ reagents were designed to remove globin and rRNA from RNA samples (EpiCentre ScriptSeq™, Madison, WI). The Zymo Research (Irvine, CA, USA) RNA Clean and Concentrator-5 was used to purify RNAs (>200 nt) and concentrate the depleted samples. Individual libraries were made for each of the samples.

treatment_protocol: Red tide group treated for their red tide illness at Lowry Park Zoo. In control group, 2 animals were sampled during the December 2013 Brevard health assessments, 4 during the December 2013 Crystal River manatee health assessments, and 1 manatee was recovering from pneumonia at Lowry Park Zoo

value: buffy coat

tag: location

value: Crystal River, FL, USA

value: Adult


title: Control rep6


title: G1 Cellobiose 2

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
CB2

value: Exponential growth


title: G1 Avicel 2

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
A2


title: SP_10B2S

organism: Sedum plumbizincicola

source_name: Sedum plumbizincicola shoot with 10 μM CdCl2 treatment


title: Control rep4


title: G1 Cellobiose 1

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
CB1


title: Control rep5


title: SP_10B2R

source_name: Sedum plumbizincicola root with 10 μM CdCl2 treatment


title: Control rep3

value: Lowry Park Zoo, FL, USA


title: G1 Maltose 3

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
M3

value: Maltose


title: SA_10S

source_name: Sedum alfredii shoot with 10 μM CdCl2 treatment


title: G1 Maltose 1

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
M1


title: SP_10A2R


title: SP_0B1S

source_name: Sedum plumbizincicola shoot with 0 μM CdCl2 treatment


title: Red tide rep3


title: Control rep2

value: Indian River Lagoon, FL, USA


title: SA_0R

source_name: Sedum alfredii root with 0 μM CdCl2 treatment


title: G1 Glucose 3

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
G3

value: Glucose


title: SP_0B1R

source_name: Sedum plumbizincicola root with 0 μM CdCl2 treatment


title: Red tide rep2


title: G1 Glucose 2

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
G2


title: SP_454

source_name: Sedum plumbizincicola 6-week-old root and shoot

value: root and shoot


title: Red tide rep4


title: SP_0A1S


title: Red tide rep1


title: SP_0A1R


title: Control rep1


title: G1 Glucose 1

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
G1


title: SP_10A2S


title: G1 Maltose 2

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
M2


title: Satb1-/- Hb9 Rep4

status: Public on Sep 30 2017

city: Los Angeles

first: Yi-Rong

last: Peng

address: 100 Stein Plaza Driveway, B-133

department: Department of Ophthalmology

institute: University of California, Los Angeles

description: single end RNA-seq data

data_processing:
Reads were aligned to a reference genome (mm10 Ensembl) using Tophat v2.0.10
Expression levels were quantified using cufflinks (inferred counts and tpm values)
FPKM was transformed into log10(TPM)
mm10
Genome_build: tab-delimited text files include lgTPM values for each Sample

organism: Mus musculus

source_name: Mus musculus retina, P6

extract_protocol:
Dissociated retinal cells were FACS sorted directly into lysis buffer from PicoPure RNA isolation kit (Invitrogen). RNA was extracted and purified with PicoPure RNA isolation kit (Invitrogen) and RNA Clean & Concentrator™- 5 Kit (Zymo). cDNA was synthesized and amplified with the Ovation RNA-Seq kit (Nugen)
RNA libraries were prepared for sequencing using ultralow system V2 kit (Nugen)

value: retina

tag: genotype/variation

value: Satb1-/- Hb9

tag: development age

value: postnatal day 6


title: WT Hb9 Rep5

description: single end RNA-seq data

value: WT Hb9


title: Satb1-/- Hb9 Rep5

description: single end RNA-seq data


title: Satb1-/- Hb9 Rep1

description: single end RNA-seq data


title: WT Hb9 Rep2

description: single end RNA-seq data


title: Satb1-/- Hb9 Rep3

description: single end RNA-seq data


title: Satb1-/- Hb9 Rep2

description: single end RNA-seq data


title: WT Hb9 Rep3

description: single end RNA-seq data


title: WT Hb9 Rep1

description: single end RNA-seq data


title: WT Hb9 Rep4

description: single end RNA-seq data


title: 489_117

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

country: United Kingdom

institute: University of Stirling

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were aligned to the Bovine genome (UMD 3.1) (Ensembl release 63) using the TopHat aligner (ver 1.2.0) with settings -r 300 --mate-std-dev 100 --solexa1.3-quals -G cow.gtf
Data were filtered to only genes with at least 1 count per million reads
Genome_build: Bovine genome (UMD 3.1) from Ensembl release 63
Supplementary_files_format_and_content: CSV files generated using edgeR. Gene counts were filtered to remove genes with zero counts across all samples and with less than one count per million in line with guidelines published by the edgeR authors. The dataset was then normalised using the trimmed mean normalisation (Robinson and Oshlack 2010).

organism: Bos taurus

source_name: bovine monocyte-derived macrophage

growth_protocol:
Generation of monocyte-derived macrophages - Peripheral blood was asceptically collected from the jugular vein into anticoagulant and PBMC were separated by density gradient centrifugation using Ficoll-Paque Plus (GE Healthcare Life Sciences).  The resulting PBMC were cultured at 9 x 107 cells per 75 cm3 flask in Mø medium [RPMI-1640 medium (Invitrogen) supplemented with 15% foetal bovine serum (Lonza Biologicals), 20 mM L-Glutamine, non-essential amino acids (Invitrogen), 50 mM HEPES and antibiotics/antimycotics (Invitrogen)].  After 2-3 hours culture at 37ºC and 5% CO2, the non-adherent cells were removed and the adherent cells cultured for 9 days in Mø medium.  The Mø medium was replaced after 24h and then after every 48-72 hours.  The bMDM were detached using cell dissociation solution (Sigma-Aldrich) and replated on day 9, which was found to promote differentiation and improve the homogeneity of the bMDM.  On approximately day 13, the bMDM were harvested as described above and transferred to 25 cm3 flasks, at up to 3 x 105 cells/flask and cultured for a further 24 hours before infection.
Generation of Mycobacteria stocks - The isolates were cloned prior to growth to mid-log phase in liquid Middlebrook 7H9 medium supplemented with 10% albumin-dextrose-catalase (ADC).  The mycobacteria were then harvested and prepared as single cell cultures and frozen at 1 x 107 colony forming units (CFU)/ml.

extract_protocol:
At the desired time point the cells were lysed with 2.5 ml Trizol reagent (Invitrogen) for 20 minutes, to ensure mycobacterial inactivation.  RNA was extracted from the samples following the manufacturer's instructions.
mRNA was purified from the total RNA and fractionated to generate fragments with a medium size of 180-210 nucleotides.  These fragments were reverse transcribed using random primers to generate cDNA libraries.

treatment_protocol: Frozen mycobacteria stocks were thawed and prepared in medium and inoculated at a multiplicity of infection (MOI) of 5.  Medium only was added to the uninfected controls.  Flasks containing bMDM were rocked every 15 minutes for two hours and the medium was replaced six hours post infection.

tag: animal identifier

tag: infection

value: Mycobacterium bovis strain G18

tag: time post infection


title: 489_115

value: Mycobacterium bovis strain AF2122/97


title: 489_119

value: Mycobacterium avium subspecies paratuberculosis strain C


title: 489_114

value: Uninfected control


title: 489_120


title: 489_118


title: 489_116


title: 489_121


title: 489_112


title: 489_110

value: Mycobacterium avium subspecies paratuberculosis strain L1


title: 489_108


title: 489_109


title: 489_106


title: 489_107


title: 489_103


title: 489_102


title: 489_105


title: 489_098


title: 489_100


title: 489_097


title: 489_096


title: 489_101


title: 489_093


title: 489_095


title: 489_092


title: 489_091


title: 489_094


title: 489_113


title: 489_111


title: 489_090


title: 489_088


title: 489_089


title: 489_085


title: 489_084


title: 489_104


title: 489_079


title: 489_080


title: 489_083


title: 489_081


title: 489_078


title: 489_086


title: 489_077


title: 489_076


title: 489_073


title: 489_070


title: 489_071


title: 489_082


title: 489_075


title: 489_072


title: 489_068


title: 489_066


title: 489_074


title: 489_067


title: 489_087


title: 489_062


title: 489_069


title: 489_065


title: 489_063


title: 489_039


title: 489_040


title: 489_041


title: 489_061


title: 489_037


title: 489_038


title: 489_035


title: 489_036


title: 489_033


title: 489_031


title: 489_030


title: 489_034


title: 489_003


title: 489_028


title: 489_018


title: 489_023


title: 489_027


title: 489_017


title: 489_064


title: 489_022


title: Psip1-KO Rep3

city: Leuven

first: Jonas

last: Demeulemeester

state: Belgium

address: ON5 Herestraat 49

department: Center for Cancer Biology

country: Belgium

institute: VIB – KU Leuven

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using STAR 2.5.1b with parameters ---outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --quantMode GeneCounts. GENCODE M8 annotation was used.
The R/Bioconductor package DESeq2 was used for normalization and differential gene expression analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files containing raw read counts for each sample

molecule: polyA RNA

source_name: Bone marrow

growth_protocol: Bone marrow cells were isolated from femurs and tibias of 8-10 weeks old mice. Lineage-depleted (Lin-) progenitors were isolated using an EasySep™ Mouse Hematopoietic Progenitor Cell Isolation Kit (STEMCELL technologies) and plated in methylcellulose containing IL-3, IL-6 and mSCF (M3534, STEMCELL technologies). Colonies were harvested after 6–7 days and washed with RPMI-1640 (10% FCS and 50µg/mL gentamicin). Cells were counted in a Neubauer chamber using trypan blue for dead cell exclusion.

extract_protocol:
RNA was isolated using Aurum Total RNA mini kit (Bio-Rad) and 1ug was used as input for the library prep.
Sequencing libraries were prepared using an Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s instructions.

value: bone marrow

value: postnatal week 8-11


title: Psip1-KO Rep2


title: WT rep3

value: wild type


title: WT rep2


title: Psip1-KO Rep1


title: Tg2-L2

first: Xiaojiang

last: Cui

address: 3884 Fredonia  Dr#F

department: Surgery Dept

institute: Cedars Sinai Medical Center

description: lactation day 2

data_processing:
Tophat2 (2.0.7) [1] was applied to align sequencing reads to the reference mouse genome (GRCm38/mm10).
The relative gene expression RPKM and read counts were estimated using SAMMate (2.7.4) and Ensembl database (Mus Musculus.GRCm38.82).
Protein coding genes with at least 2 RPKM on average in either condition were used to perform the differential gene expression analysis (MMTV-FOXC1 transgenic vs. wildtype mice) using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: epithelial cells

extract_protocol:
RNA was isolated form the mouse mammary tissue slides using the RecoverAll™ Total Nucleic Acid Isolation Kit (ThermoFisher).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: FVB/NJ

value: mammary gland at lactation day 2

value: postnatal week 11


title: Wt1-L2

description: lactation day 2


title: Tg1-L2

description: lactation day 2


title: Wt3-L2

description: lactation day 2


title: Wt2-L2

description: lactation day 2


title: Tg3-L2

description: lactation day 2


title: 3mo_Ret-EGFP_M_L6S1_F

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

data_processing:
Genome build: GRCm38.p2
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
Supplementary file format and content: Text file with raw gene counts

source_name: 3 month male Ret-EGFP mouse L6S1 DRG sample F

extract_protocol:
1) Dissect the appropriate level DRGs from the mice carrying a fluorescence reporter of interest, dissociate according to the age appropriate DRG dissociation procedures described on the GUDMAP website under the Jain Group protocols.
2) Add 7-AAD at 1ug/ml concentration, if needed, 10min before sorting to estimate viability and estimating gating parameters (also use fluorescence negative set to establish compensation controls and settings to recover populations of interest).  We have had good success using MoFlo, Sony or AriaII, at 100um nozzle size, and 30psi.
3) Collect directly in 750ul TRIzol-LS (Life Technologies, cat# 10296-010). Can store at -80°C or continue with RNA isolation. The RNA was extracted according to M Southard-Smith's RNA isolation procedure from flow sorted cells found on the GUDMAP website (Southard-Smith Group protocols). After Trizol extraction the RNA was purified with Qiagen RNeasy micro kit and then stored at -80°C until further processing for QC and library preparation for RNA sequencing.
4) Following QC/QA on the Nanodrop and Bioanalyzer 'pico' chip the RNA concentration was adjusted to use a total of 10ng in 9ul unless indicated otherwise for library preparation and RNA sequencing.
1) 10ng total RNA (in 9Âµl) was reverse transcribed and amplified using the SMARTerÂ® Ultraâ„¢ Low Input RNA for IlluminaÂ® Sequencing - HV (Clontech, cat# 634828) according to the manufacturerâ€™s instructions. 2) The cDNA was sheared for 3 minutes with the Covaris ultra-sonicator. 3) The libraries were prepared using VeraSeqâ„¢ ULtra DNA Polymerase (Enzymatics, cat# P7520L) for 12 cycles. PCR conditions were 98Â°C for 30s; 12 cycles of 98Â°C for 10s, 64Â°C for 30s, 72Â°C for 30s; 72Â°C for 5 minutes and then hold at 4Â°C. The forward primer used was: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT. The reverse primer contains the unique reverse complement of the respective index nucleotides. The sequence of the reverse primer where "N" denotes the reverse complement of 7 nucleotides of the index is CAAGCAGAAGACGGCATACGAGATNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGA.  Refer to the details of the BAM file for the sequence of the index used.

treatment_protocol: Total RNA was extracted from 16 pooled DRGs dissected from 4 Ret-EGFP mice at spinal segment  levels L6 & S1. Following DRG dissection, cells were FACS sorted (Adult mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: Tg(Ret-EGFP)SJ/

tag: component sampled

value: dorsal root ganglion,peripheral nervous system

value: (P90) Adult

tag: Sex

value: male

tag: pooled sample

value: yes

tag: pool size

value: Pooled sample of 16 DRGs from 4 mice


title: GRK-triple knockout replicate 7

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

description:
processed data file column name: GRK-TKO_ID30
rRNA-depleted total RNA

data_processing:
Illumina Casava1.6 and Casava1.8 software was used for basecalling. All 50 nt reads use phred33 quality scores.
Sequence reads were mapped to the transcriptome, defined by annotation based on the UCSC mm10 genes.gtf but with mitochondrial RNAs and human-Mfn2 cDNA added, and associated bowtie2 index provided by Illumina iGenomes (incorporating the additional mitochondrial RNAs and phage P1 Cre), using tophat v2.0.10.
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the supplied gtf, based on UCSC mm10 genes.gtf but with mitochondrial RNAs and human-Mfn2 cDNA added.
htseq-count data allows each user maximum flexibility in performing sample (library) depth normalization and differential gene expression using software such as DESeq or edgeR.
Additionally, we used Cufflinks v2.1 to calculate FPKM for each gene entry in each library.  However, this was merely done for later graph display.  Actual calculations of differential gene expression used htseq-count data as input to DESeq.
Genome_build: mm10
Supplementary_files_format_and_content: single tab-delimited text files include htseq-count values for each gene, or FPKM values for each gene.

source_name: Heart

extract_protocol:
Hearts were removed and flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
rRNA was removed using Illumina RiboZero Gold reagents, and remaining RNA was processed via chemical fragmentation and preparation of non-strand-specific, indexed, single-end RNA-Seq libraries, as per Methods Mol Biol. 2015;1299:27-49, PMID 25836573.

value: embryonic day 13.5

value: GRK2 fl/fl GRK5 fl/fl GRK6 KO/KO Nkx2.5Cre


title: GRK-triple knockout replicate 5

description:
processed data file column name: GRK-TKO_ID28
rRNA-depleted total RNA


title: GRK-triple knockout replicate 3

description:
processed data file column name: GRK-TKO_ID12
rRNA-depleted total RNA


title: GRK-triple knockout replicate 1

description:
processed data file column name: GRK-TKO_ID10
rRNA-depleted total RNA


title: GRK-triple knockout replicate 2

description:
processed data file column name: GRK-TKO_ID11
rRNA-depleted total RNA


title: GRK-haploinsufficient replicate 7

description:
processed data file column name: haploinsufficient_ID25
rRNA-depleted total RNA

value: GRK2 fl/wt GRK5 fl/fl GRK6 KO/KO Nkx2.5Cre


title: GRK-haploinsufficient replicate 8

description:
processed data file column name: haploinsufficient_ID26
rRNA-depleted total RNA


title: GRK-haploinsufficient replicate 2

description:
processed data file column name: haploinsufficient_ID6
rRNA-depleted total RNA


title: GRK-haploinsufficient replicate 6

description:
processed data file column name: haploinsufficient_ID24
rRNA-depleted total RNA


title: GRK-haploinsufficient replicate 5

description:
processed data file column name: haploinsufficient_ID23
rRNA-depleted total RNA


title: GRK-triple knockout replicate 4

description:
processed data file column name: GRK-TKO_ID27
rRNA-depleted total RNA


title: 489_029

value: Mycobacterium avium subspecies paratuberculosis strain C


title: 489_032

value: Uninfected control


title: GRK-haploinsufficient replicate 3

description:
processed data file column name: haploinsufficient_ID7
rRNA-depleted total RNA


title: GRK-haploinsufficient replicate 1

description:
processed data file column name: haploinsufficient_ID5
rRNA-depleted total RNA


title: WT rep1

tag: tissue

value: bone marrow


title: ntg replicate 7

description:
processed data file column name: ntg_ID21
rRNA-depleted total RNA

value: GRK2 wt/wt GRK5 wt/wt GRK6 wt/wt no Cre


title: ntg replicate 5

description:
processed data file column name: ntg_ID19
rRNA-depleted total RNA


title: ntg replicate 4

description:
processed data file column name: ntg_ID4
rRNA-depleted total RNA


title: ntg replicate 8

description:
processed data file column name: ntg_ID22
rRNA-depleted total RNA


title: GRK-triple knockout replicate 6

description:
processed data file column name: GRK-TKO_ID29
rRNA-depleted total RNA


title: ntg replicate 3

description:
processed data file column name: ntg_ID3
rRNA-depleted total RNA


title: ntg replicate 2

description:
processed data file column name: ntg_ID2
rRNA-depleted total RNA


title: GRK-haploinsufficient replicate 4

description:
processed data file column name: haploinsufficient_ID8
rRNA-depleted total RNA


title: ntg replicate 1

description:
processed data file column name: ntg_ID1
rRNA-depleted total RNA


title: F77_Basal cells from K5CreERT2mTmG adult wild type mouse 24h Post infection with E.coli

data_processing:
genome build: mm10
Cufflinks was called on the resulting bam file from Tophat 2 using -u and -G Mus_musculus.GRCm38.84.gtf.
supplementary file content: Tab-delimited text file including FPKM values. Gene-level results were reported.

source_name: Infected basal cells (UTI 24h)

extract_protocol:
Total RNA was isolated from cells using the RNeasy Micro Kit (Qiagen). Briefly, FACS isolated cells were collected in 200ul of RLT buffer (provided by manufacturer). The cells were quickly frozen on dry-ice and allowed to thaw on ice. After the cells were thawed, 50ul of SDS-lysis buffer (50mMTric-HCL pH 7.4/0.05%SDS) was added, the cells were vortexed and an equal volume of 70% ETOH was added. The cells were voxtexed, placed on a Qiagen column and centrifuged for 1min at 10,000rpm. The column was washed by adding 350ul of RW1 and centrifuged for 1min at 10,000rpm. The extracted RNA was then subject to a 15min on-column DNAse digest following the manufacturer's protocol. After DNase digestion, the column was rinsed with a series of washes including: 350ul of RW1, 500ul RPE and 500ul of 80% ETOH. After the washes, the column was centrifuged at 10,000rpm for 5min to ensure the removal of residual ETOH. The RNA was eluted by adding 16ul of RNAse-free H20 and incubated at room temperature for 2min. The Qiagen column was placed into a 1.5ml eppendorf tube and centrifuged at 10,000rpm for 1min to collect the RNA.
Total RNA was amplified using the Ovation RNA-Seq System v2 (NuGEN) according to the manufacturer’s protocol. The libraries were prepared with the Nextera XT DNA Sample Preparation kit (Illumina Technologies). 1ng of cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Amplicon Tagment Mix), incubating at 55C for 10min. NT Buffer was then added to neutralize the samples. Libraries were prepared by PCR with the Nextera PCR Master Mix, and 2 Nextera Indexes (N7XX, and N5XX) according to the following program: one cycle of 72C for 3min, one cycle of 98C for 30s, 12 cycles of 95C for 10s, 55C for 30s, and 72C for 1min, and one cycle of 72C for 5min.  The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocol.

treatment_protocol: UTI infection set up: Mice were anesthetized using isofluorane. The external genitalia were sterilized using Dermachlor 2% Medical Scrub. Mice were then transuretherally catheterized with a 26 ½ gauge needle coated in sterile plastic tubing. Following catherterization, mice were inoculated with 100uL of uropathogenic E.coli (UTI89) suspended in sterile PBS. Mice were kept anesthetized for 7 minutes following administration of the inoculum to allow ample time for seeding of the infection. Dissection & FACS: Adult female transgenic mice Tg(KRT5-cre/ERT2)2Ipc x Gt(ROSA)26Sor<tm2.1(mix1b-mCherry)Mgn>) were euthanised and the bladder was removed at the bladder neck. The bladder was cut in half and incubated in 20mM EDTA/PBS for 20 mins at 37oC. It was transferred to fresh DMEM/F12 medium in a petri dish and the urothelium was peeled off the basal lamina, torn and placed in 500ul of 0.25% trypsin, with vigorous vortexing and trituration at 37oC for no more than 25 mins. After incubation, all samples were kept on ice. One volume of ice-cold DMEM/F12 plus 10% FBS was added to the sample and spun down at 4oC for 5 mins at 3000rpm. The media was removed and the pellet resuspended in fresh ice-cold DMEM/F12 medium. It was passed through a 35um nylon mesh filter and then FACS sorted to separate RFP+ cells from mCherry+ cells. RNA isolation: Total RNA was isolated from cells using the RNeasy Micro Kit (Qiagen). Briefly, FACS isolated cells were collected in 200ul of RLT buffer (provided by manufacturer) and the RNA extracted according to the manufacturer’s instructions.

value: Gt(ROSA)26Sortm2.1(mix1b-mCherry)Mgn (MGI:5476468) / Tg(KRT5-cre/ERT2)2Ipc (MGI:2177429)

tag: cell type

value: basal cell layer of bladder urothelium

value: Adult

value: unspecified

value: female

value: no


title: F60_Basal cells from K5CreERT2mTmG adult wild type mouse

source_name: Basal cells expressing Gfp were sorted from wild type adult mice

treatment_protocol: Dissection & FACS: Adult female transgenic mice Tg(KRT5-cre/ERT2)2Ipc x Gt(ROSA)26Sor<tm2.1(mix1b-mCherry)Mgn>) were euthanised and the bladder was removed at the bladder neck. The bladder was cut in half and incubated in 20mM EDTA/PBS for 20 mins at 37oC.  It was transferred to fresh DMEM/F12 medium in a petri dish and the urothelium was peeled off the basal lamina, torn and placed in 500ul of 0.25% trypsin, with vigorous vortexing and trituration at 37oC for no more than 25 mins. After incubation, all samples were kept on ice.  One volume of ice-cold DMEM/F12 plus 10% FBS was added to the sample and spun down at 4oC for 5 mins at 3000rpm.  The media was removed and the pellet resuspended in fresh ice-cold DMEM/F12 medium.  It was passed through a 35um nylon mesh filter and then FACS sorted to separate RFP+ cells from mCherry+ cells.  RNA isolation: Total RNA was isolated from cells using the RNeasy Micro Kit (Qiagen).  Briefly, FACS isolated cells were collected in 200ul of RLT buffer (provided by manufacturer) and the RNA extracted according to the manufacturer’s instructions.

tag: age


title: F76_Basal cells from K5CreERT2mTmG adult wild type mouse 24h Post infection with E.coli


title: F49_Basal cells from K5CreERT2mTmG adult wild type mouse


title: F74_Basal cells from K5CreERT2mTmG adult wild type mouse 24h Post infection with E.coli


title: Sample_AnleAPPPS1wtPlaA77_mm_rna_sr_Ana_A_4_S22_L004_R1_001

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

country: Germany

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Reads were mapped to mouse genome mm10
In RNA-Seq reads were counted using FeaturesCount
Genome_build: mm10
Supplementary_files_format_and_content: htseq_counts

source_name: Hippocampus

extract_protocol:
RNA was isolated using TRIZOL from whole tissue
Library preparation and cluster generation for mRNA sequencing was performed according to Illumina standard protocols (TruSeq, Illumina)

value: 6  month of age

tag: agent

value: placebo


title: Sample_AnleAPPPS1wtPlaA37_mm_rna_sr_Ana_A_3_S21_L004_R1_001

tag: strain


title: F47_Basal cells from K5CreERT2mTmG adult wild type mouse

tag: genotype


title: F37_Up3aGCE;Cherry+ cells from Adult female 24h post UTI

data_processing:
genome build: mm10
Cufflinks was called on the resulting bam file from Tophat 2 using -u and -G Mus_musculus.GRCm38.84.gtf.
supplementary file content: Tab-delimited text file including FPKM values. Gene-level results were reported.
supplementary file content: Tab-delimited text file including FPKM values. Transcript-level results were reported.

source_name: Superficial and intermediate cells from Upk3aGCE;mcherry mouse 24h after infection with E. coli

treatment_protocol: UTI infection set up: Mice were anesthetized using isofluorane. The external genitalia were sterilized using Dermachlor 2% Medical Scrub. Mice were then transuretherally catheterized with a 26 ½ gauge needle coated in sterile plastic tubing. Following catherterization, mice were inoculated with 100uL of uropathogenic E.coli (UTI89) suspended in sterile PBS. Mice were kept anesthetized for 7 minutes following administration of the inoculum to allow ample time for seeding of the infection. Dissection & FACS: Adult female transgenic mice (Tg(Upk3a-GFP/cre/ERT2)26Amc x Gt(ROSA)26Sor<tm2.1(mix1b-mCherry)Mgn>) were euthanised and the bladder was removed at the bladder neck. The bladder was cut in half and incubated in 20mM EDTA/PBS for 20 mins at 37oC. It was transferred to fresh DMEM/F12 medium in a petri dish and the urothelium was peeled off the basal lamina, torn and placed in 500ul of 0.25% trypsin, with vigorous vortexing and trituration at 37oC for no more than 25 mins. After incubation, all samples were kept on ice. One volume of ice-cold DMEM/F12 plus 10% FBS was added to the sample and spun down at 4oC for 5 mins at 3000rpm. The media was removed and the pellet resuspended in fresh ice-cold DMEM/F12 medium. It was passed through a 35um nylon mesh filter and then FACS sorted to separate RFP+ cells from mCherry+ cells. RNA isolation: Total RNA was isolated from cells using the RNeasy Micro Kit (Qiagen). Briefly, FACS isolated cells were collected in 200ul of RLT buffer (provided by manufacturer) and the RNA extracted according to the manufacturer’s instructions.

value: Gt(ROSA)26Sortm2.1(mix1b-mCherry)Mgn (MGI:5476468) / Tg(Upk3a-GFP/cre/ERT2)26Amc (MGI:4940379)

value: intermediate cell layer of bladder urothelium,superficial cell layer of bladder urothelium


title: ntg replicate 6

description:
processed data file column name: ntg_ID20
rRNA-depleted total RNA

value: embryonic day 13.5


title: F90_Up3aGCE;Cherry+ cells from Adult female 24h post UTI

value: superficial cell layer of bladder urothelium,intermediate cell layer of bladder urothelium


title: F34_Up3aGCE;Cherry+ cells from Adult female 24h post UTI

treatment_protocol: UTI infection set up: Mice were anesthetized using isofluorane. The external genitalia were sterilized using Dermachlor 2% Medical Scrub. Mice were then transuretherally catheterized with a 26 ½ gauge needle coated in sterile plastic tubing. Following catherterization, mice were inoculated with 100uL of uropathogenic E.coli (UTI89) suspended in sterile PBS. Mice were kept anesthetized for 7 minutes following administration of the inoculum to allow ample time for seeding of the infection. Dissection & FACS: Adult female transgenic mice (Tg(Upk3a-GFP/cre/ERT2)26Amc x Gt(ROSA)26Sor<tm2.1(mix1b-mCherry)Mgn>) were euthanised and the bladder was removed at the bladder neck. The bladder was cut in half and incubated in 20mM EDTA/PBS for 20 mins at 37oC.  It was transferred to fresh DMEM/F12 medium in a petri dish and the urothelium was peeled off the basal lamina, torn and placed in 500ul of 0.25% trypsin, with vigorous vortexing and trituration at 37oC for no more than 25 mins.  After incubation, all samples were kept on ice.  One volume of ice-cold DMEM/F12 plus 10% FBS was added to the sample and spun down at 4oC for 5 mins at 3000rpm.  The media was removed and the pellet resuspended in fresh ice-cold DMEM/F12 medium.  It was passed through a 35um nylon mesh filter and then FACS sorted to separate RFP+ cells from mCherry+ cells.  RNA isolation: Total RNA was isolated from cells using the RNeasy Micro Kit (Qiagen).  Briefly, FACS isolated cells were collected in 200ul of RLT buffer (provided by manufacturer) and the RNA extracted according to the manufacturer’s instructions.


title: Sample_AnleAPPPS1wtPlaA30_mm_rna_sr_Ana_A_1_S19_L004_R1_001


title: F84_Up3aGCE;Cherry+ cells _Adult wild type mouse

source_name: Superficial and intermediate cells from an adult mouse

treatment_protocol: Dissection & FACS: Adult female transgenic mice (Tg(Upk3a-GFP/cre/ERT2)26Amc x Gt(ROSA)26Sor<tm2.1(mix1b-mCherry)Mgn>) were euthanised and the bladder was removed at the bladder neck. The bladder was cut in half and incubated in 20mM EDTA/PBS for 20 mins at 37oC.  It was transferred to fresh DMEM/F12 medium in a petri dish and the urothelium was peeled off the basal lamina, torn and placed in 500ul of 0.25% trypsin, with vigorous vortexing and trituration at 37oC for no more than 25 mins.  After incubation, all samples were kept on ice.  One volume of ice-cold DMEM/F12 plus 10% FBS was added to the sample and spun down at 4oC for 5 mins at 3000rpm.  The media was removed and the pellet resuspended in fresh ice-cold DMEM/F12 medium.  It was passed through a 35um nylon mesh filter and then FACS sorted to separate RFP+ cells from mCherry+ cells.  RNA isolation: Total RNA was isolated from cells using the RNeasy Micro Kit (Qiagen).  Briefly, FACS isolated cells were collected in 200ul of RLT buffer (provided by manufacturer) and the RNA extracted according to the manufacturer’s instructions.


title: Sample_AnleAPPPS1wtMedB41_mm_rna_sr_Ana_B_3_S25_L005_R1_001

value: Wild type


title: Sample_AnleAPPPS1wtMedB83_mm_rna_sr_Ana_B_4_S26_L005_R1_001


title: Sample_AnleAPPPS1TgPlaA71_mm_rna_sr_Ana_C_2_S28_L005_R1_001


title: F38_Up3aGCE;Cherry+ cells from Adult female 24h post UTI


title: F77_Up3aGCE;Cherry+ cells _Adult wild type mouse

value: Gt(ROSA)26Sortm2.1(mix1b-mCherry)Mgm (MGI:5476468) / Tg(Upk3a-GFP/cre/ERT2)26Amc (MGI:4940379)


title: F81_Up3aGCE;Cherry+ cells _Adult wild type mouse


title: Sample_AnleAPPPS1wtMedB39_mm_rna_sr_Ana_B_2_S24_L004_R1_001


title: Sample_AnleAPPPS1TgPlaA74_mm_rna_sr_Ana_C_3_S29_L005_R1_001


title: Sample_AnleAPPPS1TgPlaA75_mm_rna_sr_Ana_C_4_S30_L005_R1_001


title: Sample_AnleAPPPS1wtMedB33_mm_rna_sr_Ana_B_1_S23_L004_R1_001


title: Sample_AnleAPPPS1TgPlaA17_mm_rna_sr_Ana_C_1_S27_L005_R1_001


title: Sample_AnleAPPPS1TgMedB84_mm_rna_sr_Ana_D_4_S34_L006_R1_001


title: 3mo_Ret-EGFP_M_L345_B

data_processing:
assembly: GRCm38.p2
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
supplementary file format and content: Text file with raw gene counts

source_name: 3 month male Ret-EGFP mouse L345 DRG sample B

extract_protocol:
1) Dissect the appropriate level DRGs from the mice carrying a fluorescence reporter of interest, dissociate according to the age appropriate DRG dissociation procedures described on the GUDMAP website under the Jain Group protocols.
2) Add 7-AAD at 1ug/ml concentration, if needed, 10min before sorting to estimate viability and estimating gating parameters (also use fluorescence negative set to establish compensation controls and settings to recover populations of interest). We have had good success using MoFlo, Sony or AriaII, at 100um nozzle size, and 30psi.
3) Collect directly in 750ul TRIzol-LS (Life Technologies, cat# 10296-010). Can store at -80°C or continue with RNA isolation. The RNA was extracted according to M Southard-Smith's RNA isolation procedure from flow sorted cells found on the GUDMAP website (Southard-Smith Group protocols). After Trizol extraction the RNA was purified with Qiagen RNeasy micro kit and then stored at -80°C until further processing for QC and library preparation for RNA sequencing.
4) Following QC/QA on the Nanodrop and Bioanalyzer 'pico' chip the RNA concentration was adjusted to use a total of 10ng in 9ul unless indicated otherwise for library preparation and RNA sequencing.
1) 10ng total RNA (in 9µl) was reverse transcribed and amplified using the SMARTer Ultra Low  Input RNA for Illumina® Sequencing - HV (Clontech, cat# 634828) according to the manufacturer's instructions. 2) The cDNA was sheared for 3 minutes with the Covaris ultra-sonicator. 3) The libraries were prepared using VeraSeq ULtra DNA Polymerase (Enzymatics, cat# P7520L) for 12 cycles. PCR conditions were 98°C for 30s; 12 cycles of 98°C for 10s, 64°C for 30s, 72°C for 30s; 72°C for 5 minutes and then hold at 4°C. The forward primer used was: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT. The reverse primer contains the unique reverse complement of the respective index nucleotides. The sequence of the reverse primer where "N" denotes the reverse complement of 7 nucleotides of the index is CAAGCAGAAGACGGCATACGAGATNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGA. Refer to the details of the BAM file for the sequence of the index used.

treatment_protocol: Total RNA was extracted from 24 pooled DRGs dissected from 4 Ret-EGFP mice at spinal segment levels L3, L4 & L5. Following DRG dissection, cells were FACS sorted (Adult mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: Tg(Ret-EGFP)SJ

value: L345 dorsal root ganglion

value: male

value: yes

value: Pooled sample of 24 DRGs from 4 mice


title: 3mo_Ret-EGFP_M_L345_C

source_name: 3 month male Ret-EGFP mouse L345 DRG sample C

treatment_protocol: Total RNA was extracted from 12 pooled DRGs dissected from 2 Ret-EGFP mice at spinal segment levels L3, L4 & L5. Following DRG dissection, cells were FACS sorted (Adult mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: Adult

value: Pooled sample of 12 DRGs from 2 mice


title: Sample_AnleAPPPS1wtPlaA31_mm_rna_sr_Ana_A_2_S20_L004_R1_001


title: F86_Up3aGCE;Cherry+ cells from Adult female 24h post UTI

value: unspecified

value: female


title: Sample_AnleAPPPS1TgMedB16_mm_rna_sr_Ana_D_2_S32_L006_R1_001

value: 6  month of age


title: Sample_AnleAPPPS1postPlqwtPlaA56_mm_rna_sr_Ana_A_5_S19_L004_R1_001

value: 10 month of age

value: placebo


title: 3mo_Ret-EGFP_M_L345_A

source_name: 3 month male Ret-EGFP mouse L345 DRG sample A

treatment_protocol: Total RNA was extracted from 30 pooled DRGs dissected from 5 Ret-EGFP mice at spinal segment levels L3, L4 & L5. Following DRG dissection, cells were FACS sorted (Adult mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: Pooled sample of 30 DRGs from 5 mice


title: Sample_AnleAPPPS1TgMedB27_mm_rna_sr_Ana_D_3_S33_L006_R1_001


title: 3mo_Ret-EGFP_M_L6S1_A

source_name: 3 month male Ret-EGFP mouse L6S1 DRG sample A

treatment_protocol: Total RNA was extracted from 36 pooled DRGs dissected from 9 Ret-EGFP mice at spinal segment levels L6 & S1. Following DRG dissection, cells were FACS sorted (Adult mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: L6S1 dorsal root ganglion

value: Pooled sample of 36 DRGs from 9 mice


title: Sample_AnleAPPPS1postPlqwtPlaA55_mm_rna_sr_Ana_A_4_S18_L003_R1_001

value: Wild type


title: Sample_AnleAPPPS1TgMedB15_mm_rna_sr_Ana_D_1_S31_L006_R1_001


title: Sample_AnleAPPPS1postPlqwtPlaA53_mm_rna_sr_Ana_A_2_S16_L003_R1_001


title: Sample_AnleAPPPS1postPlqwtPlaA54_mm_rna_sr_Ana_A_3_S17_L003_R1_001


title: E18.5_RetFloxedEGFP-NaV1.8Cre_F_DRG_C

description: URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22806

data_processing:
assembly: GRCm38.p2
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
supplementary file format and content: Text file with raw gene and cpm counts, and rpkm values

source_name: E18.5 Ret-FloxedEGFP:NaV1.8Cre FACSd female mouse DRG sample_C

extract_protocol:
1) Dissect the appropriate level DRGs from the mice carrying a fluorescence reporter of interest, dissociate according to the age appropriate DRG dissociation procedures described on the GUDMAP website under the Jain Group protocols.
2) Add 7-AAD at 1ug/ml concentration, if needed, 10min before sorting to estimate viability and estimating gating parameters (also use fluorescence negative set to establish compensation controls and settings to recover populations of interest). We have had good success using MoFlo, Sony or AriaII, at 100um nozzle size, and 30psi.
3) Collect directly in 750ul TRIzol-LS (Life Technologies, cat# 10296-010). Can store at -80°C or continue with RNA isolation. The RNA was extracted according to M Southard-Smith's RNA isolation procedure from flow sorted cells found on the GUDMAP website (Southard-Smith Group protocols). After Trizol extraction the RNA was purified with Qiagen RNeasy micro kit and then stored at -80°C until further processing for QC and library preparation for RNA sequencing.
4) Following QC/QA on the Nanodrop and Bioanalyzer 'pico' chip the RNA concentration was adjusted to use a total of 10ng in 9ul unless indicated otherwise for library preparation and RNA sequencing.
1) 10ng total RNA (in 9µl) was reverse transcribed and amplified using the SMARTer® Ultra Low Input RNA for Illumina® Sequencing - HV (Clontech, cat# 634828) according to the manufacturer's instructions. 2) The cDNA was sheared for 3 minutes with the Covaris ultra-sonicator. 3) The libraries were prepared using VeraSeq ULtra DNA Polymerase (Enzymatics, cat# P7520L) for 12 cycles. PCR conditions were 98°C for 30s; 12 cycles of 98°C for 10s, 64°C for 30s, 72°C for 30s; 72°C for 5 minutes and then hold at 4°C. The forward primer used was: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT. The reverse primer contains the unique reverse complement of the respective index nucleotides. The sequence of the reverse primer where "N" denotes the reverse complement of 7 nucleotides of the index is CAAGCAGAAGACGGCATACGAGATNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGA. Refer to the details of the BAM file for the sequence of the index used.

treatment_protocol: Total RNA was extracted from 40 pooled DRGs dissected from 2 RetFloxedEGFP:NaV1.8Cre embryos at spinal segment levels T11-S1. Following DRG dissection, cells were FACS sorted (E18.5 mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: RetFloxedEGFP / Scn10a<tm2(cre)Jnw> (MGI:3053096)

value: peripheral nervous system, T11-S1 dorsal root ganglion

tag: developmental stage

value: Pooled sample of 40 DRGs from 2 mice


title: 2-cell_CZ_3

city: Beijing

first: Xiaoying

last: Fan

state: Beijing

address: 5 Yiheyuan Road

department: College of Life Sciences

institute: Peking University

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the mm10 genome assembly using Tophat(version 2.0.12)
the expression level were calculated and normalized by cufflinks(version 2.2.1)
Bisulfite sequencing reads were mapping to the converted mm9 genome using bismark(version 0.7.6)
5mC were called with samtools.
Genome_build: mm9 and mm10

source_name: 2-cell from Cxxc1fl/fl;Zp3-Cre female and wildtype male

extract_protocol:
for transcriptome analysis, oocytes or embryos were extracted from mouse ovary or fallopian tube and put in 350ul RLT buffer（QIAGEN）acutely vortexed for 1min, and RNA was harvested using RNeasy micro kit.NEBNext® Ultra™ RNA Library Prep Kit for Illumina were used for the construction of sequencing libraries.for methylation analysis,200 GV oocytes were extracted from 3week female mouse and put in lysis buffer to release the genomic DNA.
RNA libraries were prepared for sequencing using standard Illumina protocols;then whole genome bisulfite sequencing library was prepared using method published by S.A. smallwood et.al(2014)
RNA-Seq; single cell whole genome bisulfite sequencing


title: 2-cell_CZ_2


title: E18.5_RetFloxedEGFP-NaV1.8Cre_F_DRG_B

description: URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22804

source_name: E18.5 Ret-FloxedEGFP:NaV1.8Cre FACSd female mouse DRG sample_B


title: E18.5_RetFloxedEGFP-NaV1.8Cre_M_DRG_B

description: URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22803

source_name: E18.5 Ret-FloxedEGFP:NaV1.8Cre FACSd male mouse DRG sample_B

treatment_protocol: Total RNA was extracted from 60 pooled DRGs dissected from 3 RetFloxedEGFP:NaV1.8Cre embryos at spinal segment levels T11-S1. Following DRG dissection, cells were FACS sorted (E18.5 mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: male

value: Pooled sample of 60 DRGs from 3 mice


title: E18.5_RetFloxedEGFP-NaV1.8Cre_F_DRG_A

description: URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22805

source_name: E18.5 Ret-FloxedEGFP:NaV1.8Cre FACSd female mouse DRG sample_A

value: yes


title: Sample_AnleAPPPS1postPlqwtMedB64_mm_rna_sr_Ana_B_5_S24_L004_R1_001


title: E18.5_RetFloxedEGFP-NaV1.8Cre_M_DRG_A

description: URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22802

source_name: E18.5 Ret-FloxedEGFP:NaV1.8Cre FACSd male mouse DRG sample_A


title: Sample_AnleAPPPS1postPlqwtMedB63_mm_rna_sr_Ana_B_4_S23_L004_R1_001


title: 2-cell_CZ_1


title: 2-cell_WT_2

source_name: 2-cell from wildtype female and wildtype male


title: Sample_AnleAPPPS1postPlqwtMedB62_mm_rna_sr_Ana_B_3_S22_L004_R1_001


title: 2-cell_WT_1


title: Sample_AnleAPPPS1postPlqwtMedB61_mm_rna_sr_Ana_B_2_S21_L004_R1_001


title: Zygote_CZ_3

source_name: zygote from Cxxc1fl/fl;Zp3-Cre female and wildtype male

value: zygote


title: 3mo_Ret-EGFP_M_L6S1_D

source_name: 3 month male Ret-EGFP mouse L6S1 DRG sample D

treatment_protocol: Total RNA was extracted from 16 pooled DRGs dissected from 4 Ret-EGFP mice at spinal segment levels L6 & S1. Following DRG dissection, cells were FACS sorted (Adult mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: Tg(Ret-EGFP)SJ

value: Adult

value: Pooled sample of 16 DRGs from 4 mice


title: 3mo RetFloxEGFP-NaV1.8Cre_M_L6S1_B

description: URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22801

source_name: 3 month male Ret-FloxedEGFP:NaV1.8Cre FACSd mouse L6S1 DRG sample_B

treatment_protocol: Total RNA was extracted from 20 pooled DRGs dissected from 5 RetFloxedEGFP:NaV1.8Cre mice at spinal segment levels L6 and S1. Following DRG dissection, cells were FACS sorted (Adult mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: peripheral nervous system, L6 & S1 dorsal root ganglion

value: Pooled sample of 20 DRGs from 5 mice


title: Zygote_CZ_2


title: Zygote_WT_3

source_name: zygote from wildtype female and wildtype male


title: Zygote_CZ_1


title: 3mo RetFloxEGFP-NaV1.8Cre_F_L345_B

description: URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22797

source_name: 3 month female Ret-FloxedEGFP:NaV1.8Cre FACSd mouse L345 DRG sample B

treatment_protocol: Total RNA was extracted from 18 pooled DRGs dissected from 3 RetFloxedEGFP:NaV1.8Cre mice at spinal segment levels L3, L4 & L5. Following DRG dissection, cells were FACS sorted (Adult mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: peripheral nervous system,  L3, L4 & L5 dorsal root ganglion

value: female

value: Pooled sample of 18 DRGs from 3 mice


title: 3mo RetFloxEGFP-NaV1.8Cre_F_L6S1_A

description: URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22799

source_name: 3 month female Ret-FloxedEGFP:NaV1.8Cre FACSd mouse L6S1 DRG sample_A

treatment_protocol: Total RNA was extracted from 32 pooled DRGs dissected from 8 RetFloxedEGFP:NaV1.8Cre mice at spinal segment levels L6 and S1. Following DRG dissection, cells were FACS sorted (Adult mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: Pooled sample of 32 DRGs from 8 mice


title: Sample_AnleAPPPS1postPlqwtPlaA52_mm_rna_sr_Ana_A_1_S15_L003_R1_001

source_name: Hippocampus

value: 10 month of age

value: Wild type

value: placebo


title: 3mo RetFloxEGFP-NaV1.8Cre_M_L345_C

description: URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22796

source_name: 3 month male Ret-FloxedEGFP:NaV1.8Cre FACSd mouse L345 DRG sample C

value: peripheral nervous system, L3, L4 & L5 dorsal root ganglion

value: Pooled sample of 18 DRGs from 5 mice


title: Sample_AnleAPPPS1postPlqTgPlaA86_mm_rna_sr_Ana_C_2_S26_L005_R1_001


title: Zygote_WT_1


title: Sample_AnleAPPPS1postPlqTgPlaA57_mm_rna_sr_Ana_C_1_S25_L005_R1_001


title: 3mo RetFloxEGFP-NaV1.8Cre_M_L6S1_A

description: URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22800

source_name: 3 month male Ret-FloxedEGFP:NaV1.8Cre FACSd mouse L6S1 DRG sample_A

value: RetFloxedEGFP / Scn10a<tm2(cre)Jnw> (MGI:3053096)

value: male


title: E14.5_RET-EGFP_FACS-DRG_D

description: URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22791

source_name: E14.5 Ret-EGFP mouse FACSd T11-S1 DRG sample D

treatment_protocol: Total RNA was pooled from 80 DRGs dissected from 4 Ret-EGFP embryos (3 males, 1 female) at spinal segment levels T11-S1. Following DRG dissection, cells were FACS sorted (E14.5 mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: peripheral nervous system, TS11 - S1 dorsal root ganglion

tag: pool gender

value: male and female

value: yes

value: Pooled sample of 80 FACSd DRGs from 4 embryos


title: 3mo RetFloxEGFP-NaV1.8Cre_M_L345_A

description: URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22794

source_name: 3 month male Ret-FloxedEGFP:NaV1.8Cre FACSd mouse L345 DRG sample A

treatment_protocol: Total RNA was extracted from 30 pooled DRGs dissected from 5 RetFloxedEGFP:NaV1.8Cre mice at spinal segment levels L3, L4 & L5. Following DRG dissection, cells were FACS sorted (Adult mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: Adult

value: Pooled sample of 30 DRGs from 5 mice


title: Sample_AnleAPPPS1postPlqTgPlaA100_mm_rna_sr_Ana_C_5_S29_L005_R1_001


title: E14.5_RET-EGFP_FACS-DRG_B

description: URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22790

source_name: E14.5 Ret-EGFP mouse FACSd T11-S1 DRG sample B

treatment_protocol: Total RNA was pooled from 100 DRGs dissected from 6 Ret-EGFP embryos (2 different pregnant mothers, 2 males, 4 females) at spinal segment levels T11-S1. Following DRG dissection, cells were FACS sorted (E14.5 mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: Tg(Ret-EGFP)SJ

value: peripheral nervous system, T11-S1 dorsal root ganglion

value: Pooled sample of 100 FACSd DRGs from 6 embryos


title: Sample_AnleAPPPS1postPlqTgMedB99_mm_rna_sr_Ana_D_5_S34_L006_R1_001


title: GV_CG_3M_2

source_name: GV oocyte from 3month Cxxc1fl/fl;Gdf9-Cre females

value: GV oocyte


title: GV_CG_3M_1


title: Sample_AnleAPPPS1postPlqTgMedB97_mm_rna_sr_Ana_D_4_S33_L006_R1_001

value: 10 month of age


title: Sample_AnleAPPPS1postPlqwtMedB60_mm_rna_sr_Ana_B_1_S20_L004_R1_001

value: Wild type


title: 3mo RetFloxEGFP-NaV1.8Cre_F_L345_C

description: URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22798

source_name: 3 month female Ret-FloxedEGFP:NaV1.8Cre FACSd mouse L345 DRG sample C

extract_protocol:
1) Dissect the appropriate level DRGs from the mice carrying a fluorescence reporter of interest, dissociate according to the age appropriate DRG dissociation procedures described on the GUDMAP website under the Jain Group protocols.
2) Add 7-AAD at 1ug/ml concentration, if needed, 10min before sorting to estimate viability and estimating gating parameters (also use fluorescence negative set to establish compensation controls and settings to recover populations of interest). We have had good success using MoFlo, Sony or AriaII, at 100um nozzle size, and 30psi.
3) Collect directly in 750ul TRIzol-LS (Life Technologies, cat# 10296-010). Can store at -80°C or continue with RNA isolation. The RNA was extracted according to M Southard-Smith's RNA isolation procedure from flow sorted cells found on the GUDMAP website (Southard-Smith Group protocols). After Trizol extraction the RNA was purified with Qiagen RNeasy micro kit and then stored at -80°C until further processing for QC and library preparation for RNA sequencing.
4) Following QC/QA on the Nanodrop and Bioanalyzer 'pico' chip the RNA concentration was adjusted to use a total of 10ng in 9ul unless indicated otherwise for library preparation and RNA sequencing.
1) 10ng total RNA (in 9µl) was reverse transcribed and amplified using the SMARTer® Ultra Low Input RNA for Illumina® Sequencing - HV (Clontech, cat# 634828) according to the manufacturer's instructions. 2) The cDNA was sheared for 3 minutes with the Covaris ultra-sonicator. 3) The libraries were prepared using VeraSeq ULtra DNA Polymerase (Enzymatics, cat# P7520L) for 12 cycles. PCR conditions were 98°C for 30s; 12 cycles of 98°C for 10s, 64°C for 30s, 72°C for 30s; 72°C for 5 minutes and then hold at 4°C. The forward primer used was:
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT. The reverse primer contains the unique reverse complement of the respective index nucleotides. The sequence of the reverse primer where "N" denotes the reverse complement of 7 nucleotides of the index is CAAGCAGAAGACGGCATACGAGATNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGA. Refer to the details of the BAM file for the sequence of the index used.

treatment_protocol: Total RNA was extracted from 12 pooled DRGs dissected from 2 RetFloxedEGFP:NaV1.8Cre mice at spinal segment levels L3, L4 & L5. Following DRG dissection, cells were FACS sorted (Adult mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: peripheral nervous system,  L3, L4 & L5 dorsal root ganglion

value: female

value: Pooled sample of 12 DRGs from 2 mice


title: Sample_AnleAPPPS1postPlqTgPlaA91_mm_rna_sr_Ana_C_4_S28_L005_R1_001

value: placebo


title: Sample_AnleAPPPS1postPlqTgMedB93_mm_rna_sr_Ana_D_3_S32_L006_R1_001


title: GV_CZ_3

source_name: GV oocyte from 3week Cxxc1fl/fl;Zp3-Cre females


title: Sample_AnleAPPPS1postPlqTgPlaA87_mm_rna_sr_Ana_C_3_S27_L005_R1_001


title: E14.5_RET-EGFP_FACS-DRG_A

description: URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22789

source_name: E14.5 Ret-EGFP mouse FACSd T11-S1 DRG sample A

treatment_protocol: Total RNA was pooled from 100 DRGs dissected from 5 Ret-EGFP embryos (2 different pregnant mothers, 3 males, 2 females) at spinal segment levels T11-S1. Following DRG dissection, cells were FACS sorted (E14.5 mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: Pooled sample of 100 FACSd DRGs from 5 embryos


title: GV_CZ_2


title: E18.5_RET-EGFP_F_FACS-DRG_A

description: URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22788

source_name: E18.5 female Ret-EGFP mouse FACSd T11-S1 DRG sample A

treatment_protocol: Total RNA was extracted from 60 pooled DRGs dissected from 3 Ret-EGFP embryos (2 different pregnant mothers) at spinal segment levels T11-S1. Following DRG dissection, cells were FACS sorted (E18.5 mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: Pooled sample of 60 FACSd DRGs from 3 female embryos


title: CHL1_BRD4q_DMSO_02

city: Berlin

first: Ralf

last: Lesche

address: Muellerstr 178

institute: Bayer Pharma AG

data_processing:
paired-end genome wide sequencing data were aligned to the human reference genome (assembly hg19) using Bowtie2 software and sorted and indexed using SAMtools
Peak calling was done using the Model-bases analysis for ChIP-seq (MACS2) software. Broad peaks from H3K27Ac were called using MACS2 broad mode. MACS2 was used to generate enrichment pileups (log likelihood ratio (logLR)) of treatment vs. input control samples. A pseudocount of 0.00001 was added to avoid log10(0) during logLR calculation.
ChIP-seq tracks were generated using the Integrative Genomics Viewer software (Thorvaldsdottir et al. 2013). Heatmaps and line plots were generated using the seqplots software (http://przemol.github.io/seqplots).
Genome_build: hg19
Supplementary_files_format_and_content: bw (see UCSC file format FAQ http://www.genome.ucsc.edu/FAQ/FAQformat.html) files reporting enrichment pileup as log likelihood ratio

organism: Homo sapiens

source_name: melanoma cancer cell line CHL-1

growth_protocol: CHL-1 melanoma cells were obtained from the American Type Culture Collection (ATCC) and were routinely grown DMEM medium in the presence of 10% (v/v) fetal calf serum (Life Technologies) at 37 °C and in 5% CO2 atmosphere.

extract_protocol:
One 15 cm cell culture dish with 80% confluent cells was used per IP. ChIP DNA preparation for sequencing was carried out as described previously in Nagarajan  et al. (Cell Rep. 2014 Jul 24;8(2):460-9) with the following changes: cross-linked chromatin was sheared to 200-800 base pair fragments using sonication (30 sec on/30 sec off, high power, 2 x 7.5 minutes with a water bath change between the two cycles) in a Biorupter sonicator UCD-200. 1.5 µg antibodies (anti-BRD4 [Bethyl Labs, A301-985A100]; anti-H3K27ac [Diagenode, C15410174]) were used per IP. DNA was purified  using a PCR purification kit (Qiagen)
TrueSeq® ChIP Sample Preparation Guide (Illumina).

treatment_protocol: CHL-1 cells were treated for 4 hr with 500 nM BAY 1238097, OTX-015, or DMSO

tag: cell line

tag: tumor type

value: melanoma

value: skin

tag: chip antibody

value: anti-BRD4 (Bethyl Labs, A301-985A100)


title: Zygote_WT_2

value: zygote


title: CHL1_H3K27Acq_02_DMSO

value: anti-H3K27Ac (Diagenode, C15410174)


title: Sample_AnleAPPPS1postPlqTgMedB59_mm_rna_sr_Ana_D_2_S31_L006_R1_001


title: E18.5_RET-EGFP_M_FACS-DRG_D

description: URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22787

source_name: E18.5 male Ret-EGFP mouse FACSd T11-S1 DRG sample D

treatment_protocol: Total RNA was extracted from 40 pooled DRGs dissected from 2 Ret-EGFP embryos at spinal segment levels T11-S1. Following DRG dissection, cells were FACS sorted (E18.5 mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: Tg(Ret-EGFP)SJ

value: male

value: yes

value: Pooled sample of 40 FACSd DRGs from 2 male embryos


title: GV_CG_3M_3

value: GV oocyte


title: GV_CZ_1


title: 3mo RetFloxEGFP-NaV1.8Cre_M_L345_B

description: URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22795

source_name: 3 month male Ret-FloxedEGFP:NaV1.8Cre FACSd mouse L345 DRG sample B

value: RetFloxedEGFP / Scn10a<tm2(cre)Jnw> (MGI:3053096)

value: Adult


title: E18.5_RET-EGFP_M_FACS-DRG_C

description: URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22786

source_name: E18.5 male Ret-EGFP mouse FACSd T11-S1 DRG sample C

treatment_protocol: Total RNA was extracted from 40 pooled DRGs dissected from 2 Ret-EGFP embryos (2 different pregnant mothers) at spinal segment levels T11-S1. Following DRG dissection, cells were FACS sorted (E18.5 mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: peripheral nervous system, T11-S1 dorsal root ganglion

value: Pooled sample of 40 DRGs from 2 embryos


title: CHL1_input_OTX_02


title: Sample_AnleAPPPS1postPlqTgMedB58_mm_rna_sr_Ana_D_1_S30_L005_R1_001

value: 10 month of age


title: GV_WT_3M_3

source_name: GV oocyte from 3month wildtype females


title: E18.5_RET-EGFP_M_FACS-DRG_A

description: URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22785

source_name: E18.5 male Ret-EGFP mouse FACSd T11-S1 DRG sample A

treatment_protocol: Total RNA was extracted from 60 pooled DRGs dissected from 3 Ret-EGFP embryos at spinal segment levels T11-S1. Following DRG dissection, cells were FACS sorted (E18.5 mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: Pooled sample of 60 DRGs from 3 embryos


title: GV_WT_3M_2


title: CHL1_H3K27Acq_02_OTX


title: Sample_AnleAPPPS1postPlqTgMedB109_mm_rna_sr_Ana_D_7_S36_L006_R1_001

source_name: Hippocampus


title: CHL1_BRD4_OTX_02


title: Sample_AnleAPPPS1postPlqTgMedB108_mm_rna_sr_Ana_D_6_S35_L006_R1_001


title: GV_WT_3M_1


title: CHL1_input_D4_02


title: GV_WT_2

source_name: GV oocyte from 3week wildtype females


title: CHL1_H3K27Acq_02_BAY


title: CHL1_BRD4_D4_02


title: Corticocotical Neurons (Satb2+) B6SJL-Tg(hSOD1*WT)2Gur/J replicate 2

city: Baltimore

first: Loyal

middle: A

last: Goff

state: MD

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

data_processing:
Reads were aligned to the mouse genome (mm9) using TopHat2 (Kim et al., 2013) with the following additional parameters: --no-coverage-search –max-multihits=10 –p 16.
Gene expression was quantified using cuffquant (Trapnell et al., 2013) against a previously-assembled reference transcriptome consisting of UCSC genes supplemented with mouse cortical lncRNAs (Molyneaux et al., 2015).
Differential expression testing was performed using cuffdiff v2.2.1 (RRID:SCRͺ001622), and data were analyzed and visualized using cummeRbund (Trapnell et al., 2013). Additional custom scripts and visualizations were also developed using the cummeRbund framework in R/Bioconductor.
Genome_build: mm9
Supplementary_files_format_and_content: CummeRbund output table containing per-condition gene expression estimates and results of differential tests.

source_name: Satb2+ sorted corticocortical neurons

extract_protocol:
RNA was recovered from the FACS-purified cells as previously described (Molyneaux et al., 2015), quantified by spectral absorbance on the NanoDrop, and qualitatively assessed on the Agilent Bioanalyzer RNA-6000 Pico chip. RNA integrity numbers (RINs) for all samples ranged between 8.3 and 10.
For each enriched sample, 10 ng of total RNA was reverse transcribed to synthesize cDNA using the Smart seq2 V4 kit (Clontech). Amplified cDNA was used as input for high-throughput RNA sequencing library preparation using the Nextera XT library kit (Illumina). Individual libraries were indexed, pooled, and sequenced to a mean depth of 5.466 x 107-125 bp paired-end reads per sample.

treatment_protocol: hSOD1G93A and hSOD1WT P5-7 mice were used for expression profiling. For each biological replicate, the cortex was isolated and dissociated into a single-cell suspension as previously described (Molyneaux et al., 2015). Cells were then immediately fixed in 4% PFA, incubated in RNase free conditions with antibodies against the nuclear markers CTIP2 and SATB2 (Rat anti-CTIP2, 1:100, Abcam, Cat. No. ab18465, RRID:AB_2064130; Mouse anti-SATB2, 1:250, Abcam, Cat. No. ab51502, RRID:AB_882455; Alexa 546 goat anti-rat, 1:1000, Molecular Probes, Cat. No. A11081, RRID:AB_141738; Alexa 488 goat anti-mouse, 1:1000, Molecular Probes, Cat. No. A11011, RRID:AB_2534069), and FACS-sorted as previously described to isolate SATB2-positive and CTIP2-positive neurons (Molyneaux et al., 2015).

value: cortex

value: corticospinal neurons

tag: transgene

tag: developmental age

tag: enrichment


title: 3mo_Ret-EGFP_F_L345_B

description:
URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22284
GUDMAP ID: 22284

data_processing:
RNA-seq reads were aligned to the Ensembl release 76 assembly with STAR version 2.0.4b (GRCm38.76 using the GRCm38.p2 assembly). Low base quality reads and adaptors are clipped. The 7 bp index used is GGTGAAT, the reverse complement is in the reverse primers used in library preparation denoted by "N" (CAAGCAGAAGACGGCATACGAGATNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGA). Enumerate all known genes with raw counts to the matching gtf file from the same reference build from Ensembl with Subread:featureCounts (version 1.4.5) using the Ensembl gene ID as the key. Use the Sailfish package to estimate known transcript/isoform expression if needed. Use the counts listed in the output in the Subread:featureCounts files to generate Countsper-Million (CPM) normalized values for heat map generation (Sailfish/Salmon already produces CPM values in it’s output) if needed.
assembly: mm10
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
format and content:  Text file with raw gene counts

source_name: 3 month female Ret-EGFP mouse L345 DRG sample B

extract_protocol:
1) Dissect the appropriate level DRGs from the mice carrying a fluorescence reporter of interest, dissociate according to the age appropriate DRG dissociation procedures described on the GUDMAP website under the Jain Group protocols.
2) Add 7-AAD at 1ug/ml concentration, if needed, 10min before sorting to estimate viability and estimating gating parameters (also use fluorescence negative set to establish compensation controls and settings to recover populations of interest).  We have had good success using MoFlo, Sony or AriaII, at 100um nozzle size, and 30psi.
3) Collect directly in 750ul TRIzol-LS (Life Technologies, cat# 10296-010). Can store at -80°C or continue with RNA isolation. The RNA was extracted according to M Southard-Smith's RNA isolation procedure from flow sorted cells found on the GUDMAP website (Southard-Smith Group protocols). After Trizol extraction the RNA was purified with Qiagen RNeasy micro kit and then stored at -80°C until further processing for QC and library preparation for RNA sequencing.
4) Following QC/QA on the Nanodrop and Bioanalyzer 'pico' chip the RNA concentration was adjusted to use a total of 10ng in 9ul unless indicated otherwise for library preparation and RNA sequencing.
1) 10ng total RNA (in 9uL) was reverse transcribed and amplified using the SMARTer Ultra Low Input RNA for Illumina  Sequencing - HV (Clontech, cat# 634828) according to the manufacturer's instructions. 2) The cDNA was sheared for 3 minutes with the Covaris ultra-sonicator. 3) The libraries were prepared using VeraSeq ULtra DNA Polymerase (Enzymatics, cat# P7520L) for 12 cycles. PCR conditions were 98°C for 30s; 12 cycles of 98°C for 10s, 64°C for 30s, 72°C for 30s; 72°C for 5 minutes and then hold at 4°C. The forward primer used was: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT. The reverse primer contains the unique reverse complement of the respective index nucleotides. The sequence of the reverse primer where "N" denotes the reverse complement of 7 nucleotides of the index is CAAGCAGAAGACGGCATACGAGATNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGA.  Refer to the details of the BAM file for the sequence of the index used.

treatment_protocol: Total RNA was extracted from 24 pooled DRGs dissected from 4 Ret-EGFP mice at spinal segment levels L3, 4 & 5. Following DRG dissection, cells were FACS sorted (Adult mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: L345 dorsal root ganglion

tag: Sex

value: female

value: Pooled sample of  24 DRGs from 4 mice


title: Corticocotical Neurons (Satb2+) B6SJL-Tg(hSOD1*WT)2Gur/J replicate 3


title: 3mo_Ret-EGFP_F_L6S1_C

description:
URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22282
GUDMAP ID: 22282

data_processing:
RNA-seq reads were aligned to the Ensembl release 76 assembly with STAR version 2.0.4b (GRCm38.76 using the GRCm38.p2 assembly). Low base quality reads and adaptors are clipped. The 7 bp index used is GGCAAGA, the reverse complement is in the reverse primers used in library preparation denoted by "N" (CAAGCAGAAGACGGCATACGAGATNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGA). Enumerate all known genes with raw counts to the matching gtf file from the same reference build from Ensembl with Subread:featureCounts (version 1.4.5) using the Ensembl gene ID as the key. Use the Sailfish package to estimate known transcript/isoform expression if needed. Use the counts listed in the output in the Subread:featureCounts files to generate Countsper-Million (CPM) normalized values for heat map generation (Sailfish/Salmon already produces CPM values in it’s output) if needed.
assembly: mm10
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
format and content:  Text file with raw gene counts

source_name: 3 month female Ret-EGFP mouse L6S1 DRG sample C

treatment_protocol: Total RNA was extracted from 20 pooled DRGs dissected from 5 Ret-EGFP mice at spinal segment levels L6 & S1. Following DRG dissection, cells were FACS sorted (Adult mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: L6S1 dorsal root ganglion

tag: pooled sample

value: Pooled sample of 20 DRGs from 5 mice


title: GV_WT_1


title: GV_WT_3


title: 3mo_Ret-EGFP_F_L345_C

description:
URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22285
GUDMAP ID:  22285

data_processing:
RNA-seq reads were aligned to the Ensembl release 76 assembly with STAR version 2.0.4b (GRCm38.76 using the GRCm38.p2 assembly). Low base quality reads and adaptors are clipped. The 7 bp index used is GCCTCCC, the reverse complement is in the reverse primers used in library preparation denoted by "N" (CAAGCAGAAGACGGCATACGAGATNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGA). Enumerate all known genes with raw counts to the matching gtf file from the same reference build from Ensembl with Subread:featureCounts (version 1.4.5) using the Ensembl gene ID as the key. Use the Sailfish package to estimate known transcript/isoform expression if needed. Use the counts listed in the output in the Subread:featureCounts files to generate Countsper-Million (CPM) normalized values for heat map generation (Sailfish/Salmon already produces CPM values in it’s output) if needed.
assembly: mm10
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
format and content:  Text file with raw gene counts

source_name: 3 month female Ret-EGFP mouse L345 DRG sample C

treatment_protocol: Total RNA was extracted from 18 pooled DRGs dissected from 3 Ret-EGFP mice at spinal segment levels L3, 4 & 5. Following DRG dissection, cells were FACS sorted (Adult mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: Tg(Ret-EGFP)SJ

tag: pool size

value: Pooled sample of 18 DRGs from 3 mice


title: 3mo_Ret-EGFP_F_L345_A

description:
URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22283
GUDMAP ID: 22383

data_processing:
RNA-seq reads were aligned to the Ensembl release 76 assembly with STAR version 2.0.4b (GRCm38.76 using the GRCm38.p2 assembly). Low base quality reads and adaptors are clipped. The 7 bp index used is ACCATAC, the reverse complement is in the reverse primers used in library preparation denoted by "N" (CAAGCAGAAGACGGCATACGAGATNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGA). Enumerate all known genes with raw counts to the matching gtf file from the same reference build from Ensembl with Subread:featureCounts (version 1.4.5) using the Ensembl gene ID as the key. Use the Sailfish package to estimate known transcript/isoform expression if needed. Use the counts listed in the output in the Subread:featureCounts files to generate Countsper-Million (CPM) normalized values for heat map generation (Sailfish/Salmon already produces CPM values in it’s output) if needed.
assembly: mm10
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
format and content:  Text file with raw gene counts

source_name: 3 month female Ret-EGFP mouse L345 DRG sample A

treatment_protocol: Total RNA was extracted from 42 pooled DRGs dissected from 7 Ret-EGFP mice at spinal segment levels L3, 4 & 5. Following DRG dissection, cells were FACS sorted (Adult mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

tag: tissue

value: yes

value: Pooled sample of 42 DRGs from 7 mice


title: CHL1_input_DMSO_01

value: melanoma

value: skin


title: Corticocotical Neurons (Satb2+) B6SJL-Tg(hSOD1*WT)2Gur/J replicate 0

tag: cell type


title: 3mo_Ret-EGFP_F_L6S1_B

description:
URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22281
GUDMAP ID: 22281

data_processing:
RNA-seq reads were aligned to the Ensembl release 76 assembly with STAR version 2.0.4b (GRCm38.76 using the GRCm38.p2 assembly).  Low base quality reads and adaptors are clipped.  The 7 bp index used is GTATCCT, the reverse complement is in the reverse primers used in library preparation denoted by "N" (CAAGCAGAAGACGGCATACGAGATNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGA). Enumerate all known genes with raw counts to the matching gtf file from the same reference build from Ensembl with Subread:featureCounts (version 1.4.5) using the Ensembl gene ID as the key. Use the Sailfish package to estimate known transcript/isoform expression if needed. Use the counts listed in the output in the Subread:featureCounts files to generate Countsper-Million (CPM) normalized values for heat map generation (Sailfish/Salmon already produces CPM values in it’s output) if needed.
assembly: mm10
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
format and content:  Text file with raw gene counts

source_name: 3 month female Ret-EGFP mouse L6S1 DRG sample B

treatment_protocol: Total RNA was extracted from 16 pooled DRGs dissected from 4 Ret-EGFP mice at spinal segment levels L6 & S1. Following DRG dissection, cells were FACS sorted (Adult mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

tag: age

value: Adult

value: Pooled sample of 16 DRGs from 4 mice


title: Corticocotical Neurons (Satb2+) B6SJL-Tg(hSOD1*WT)2Gur/J replicate 1


title: Corticocotical Neurons (Satb2+) B6SJL-Tg(hSOD1*G93A)1Gur/J replicate 3


title: M-1

city: Chengdu

first: li

middle: li

last: qin

state: sichuan province

address: wenjiang district huiming 211road

institute: Sichuan Agricultural University

data_processing:
The original image data is transferred into sequence data via base calling, which is defined as raw data or raw reads and saved as FASTQ
We define "dirty" raw reads as reads which contain the sequence of adapter, high content of unknown bases and low quality reads. They need to be removed before data analysis.
Clean reads are mapped to a reference sequences using SOAPaligner/SOAP2. No more than 5 mismatches are allowed in the alignment.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Alternanthera philoxeroides

source_name: alligator weed

growth_protocol: Naturally grown alligatorweed shoots were collected from the test field of the Sichuan Agricultural University

extract_protocol:
Total RNA was isolated from roots of alligator weed using Trizol reagent (Invitrogen, USA) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 10 d hydroponics, the alligator weed plants devide into two groups. Half of the plants were then transferred to a low potassium nutrient solution (lacking K2SO4) as the LK for 7 d. The other half continued to grow under normal solution for 7 d as the CK.

tag: protocol

value: control

value: root


title: K-2

value: low potassium treatment for 7 days


title: CHL1_BRD4q_DMSO_01

value: anti-BRD4 (Bethyl Labs, A301-985A100)


title: CHL1_input_OTX_01


title: Corticocotical Neurons (Satb2+) B6SJL-Tg(hSOD1*G93A)1Gur/J replicate 0

value: cortex

value: corticospinal neurons

tag: strain


title: Corticocotical Neurons (Satb2+) B6SJL-Tg(hSOD1*G93A)1Gur/J replicate 1