title: IL-22_1

city: Shanghai

first: Shengming

last: Xu

address: No.415, Fengyang Road, Huangpu District

department: Department of Orthopaedics

institute: Changzheng Hospital, Second Military Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
low quality sequences were filtered by NGSQC Toolkit, then mapped to rn5 by tophat2 with parameters -p 4 --no-mixed.
FPKM(expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced)were calculated using Cuffdiff.
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample;
GENE_FPKM_matrix.txt: gene normalized abundance measurements,derived from Cuffdiff
LncRNA_FPKM_matrix.txt: lncRNA normalized abundance measurements,derived from Cuffdiff

source_name: Rat SC line treated with IL-22

growth_protocol: Rat SC line (RSC96; Cell Resource Center of Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences) were cultured in Dulbecco’s modified Eagle Medium (DMEM, Hyclone, USA) plus 10% (v/v) fetal bovine serum (FBS, Gibco, UK), 100 µg/ml streptomycin, and 100 U/ml penicillin at 37°C in 5% CO2 humidified atmosphere.

extract_protocol:
According to the manufacturer’s instructions, total RNA were extracted from fresh cells using Trizol agent (Invitrogen, Carlsbad, CA), and genomic DNA were removed using the TurboDNase kit (Ambion Inc., Austin, TX, USA).
mRNA was seperated according to NEBNext Poly (A) mRNA Magnetic Isolation Module,cDNA library was constructed based on the standard protocol of NEBNext Ultra RNA library Prep Kit (Invitrogen, Carlsbad, CA), and cDNAs were amplified using 12 cycles of polymerase chain reaction (PCR). QIAquick PCR extraction kit (Qiagen, Hilden, Germany) was utilized to purify short double-stranded cDNA fragments, and end repair and the addition of an ‘A’ base were performed. Then, short cDNA fragments were ligated to Illumina sequencing adaptors, and DNA fragments of a selected size were gel-purified and amplified by PCR. Finally, the amplified library was sequenced through Illumina HiSeq™ 2000 sequencer based on standard protocols.

treatment_protocol: RSC96 cells (4th generation) were growth-arrested in medium without serum for overnight before IL-22 treatment. For experiment group (2 samples), cells were treated with recombinant rat IL-22 (R&D Systems Inc., Minneapolis, MN, USA) in a concentration of 100 ng/ml for 48 h, while for control group (2 samples), only 0.1% bovine serum albumin (the solvent of IL-22) was added.

value: Rat Schwann cell line

tag: treated with

value: 100 ng/ml rat IL-22


title: IL-22_2

status: Public on Jun 15 2018

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Rattus norvegicus

tag: cell line

tag: cell type


title: Contrlol_1

source_name: Rat SC line_control

value: control


title: Control_2


title: TGFb 8h b

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

data_processing:
Raw sequence reads were pseudo aligned to the Homo sapiens transcriptome GRCh38 (Ensembl Build 79) using Kallisto (Version 0.43.0, Bray et al. Nat. Biotechnology 2016) running 100 bootstrap rounds.
Transcript expression were summarized to Ensembl gene expression using the R/Bioconductor tximport library.
Genome_build: Homo_sapiens.GRCh38.rel79
Supplementary_files_format_and_content: *_abundance.tsv: Tab-delimited text files per sample include effective read counts and transcript per million (TPM) values for each transcript.

organism: Homo sapiens

source_name: SK-MES-1 cell line, TGF-beta, 8h

extract_protocol:
Total RNA was isolated from cultured cells using an RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. The quantity of RNA was measured with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, MA, USA). The quality of total RNA was assessed with an Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano Kit (Agilent Technologies, Boeblingen, Germany). Total RNA was considered to be sufficient for further analyses if it had an RNA integrity number (RIN) of at least 8.0.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Low-passage freshly thawed SK-MES-1 cells were kept in culture for two weeks and then seeded on 6-cm dishes (TPP, #93060) at a density of 1,000,000 cells/dish. Two days later, cells were serum-starved for 3 hours and stimulated with 2 ng/ml TGFβ1 (R&D Systems, #240-B-010) or left untreated. Total RNA was extracted at the indicated time points and sequenced using HiSeq 4000 (Illumina).

value: Squamous cell lung carcinoma cell line

tag: treatment

value: TGF-beta

tag: time

tag: replicate


title: NA19237

city: New York

first: Andrew

last: Sharp

state: NY

address: 1470 Madison Av

department: Genetics and Genomic Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina Casava1.8 software used for basecalling
RNA-seq reads were aligned to the hg19 genome assembly using STAR 2.3 aligner with parameters --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNoverLmax 0.04  --outFilterMismatchNmax 999  --alignIntronMin 20  --alignIntronMax 1000000
WASP pipeline for reducing mapping bias and removing duplicates
Read Count for genes using HTSeq-count 0.6.0
Genome_build: hg19,gencode.v19
Supplementary_files_format_and_content: Read count data with two columns, gene id and read count

source_name: Lymphoblastoid cell line

growth_protocol: Lymphoblastoid cell lines were grown according to Coriell recommended protocols

extract_protocol:
RNA was extracted using TRIZOL according to manufacturers protocol
NEBNext Ultra Directional RNA Library Prep Kit for Illumina

treatment_protocol: 24 hours after feeding actively growing cultures, cells were pelleted and frozen at -80 degrees until RNA extraction

value: EBV-immortalized B-Lymphocyte

value: Lymphoblastoid cell line NA19237


title: NA19249

value: Lymphoblastoid cell line NA19249


title: NA19240

value: Lymphoblastoid cell line NA19240


title: NA19215

value: Lymphoblastoid cell line NA19215


title: NA19258

value: Lymphoblastoid cell line NA19258


title: NA19199

value: Lymphoblastoid cell line NA19199


title: NA19211

value: Lymphoblastoid cell line NA19211


title: NA19205

value: Lymphoblastoid cell line NA19205


title: NA19208

value: Lymphoblastoid cell line NA19208


title: NA19202

value: Lymphoblastoid cell line NA19202


title: CL3_L10

status: Public on Jun 17 2018

city: Bristol

first: Lulu

last: Jiang

state: State...

address: Academic Renal Unit,Dorothy Hodgkin Building,Whitson Street

department: School of Clinical Sciences

country: United Kingdom

institute: University of Bristol

description: The same library was run on 4 different lanes generating 4 pairs of fastq files per sample (paired-end sequencing)

data_processing:
The raw data was processed using Illumina software, RTA 1.17.21.3 with default filter and quality settings.
The reads were demultiplexed with CASAVA 1.8.2.
Read alignment is performed using Tophat. We use HTSeq to generate read counts, using the ENSEMBL GRCh37  annotations for reference.
Genome_build: GRCh37
Supplementary_files_format_and_content: csv file with abundance measurements. There are four counts per gene in each file because the same library was run on four different flowcell lanes.

source_name: Podocytes derived from human kidneys_10μM levamisole

growth_protocol: Conditionally immortalized human podocytes were established from three healthy kidney transplant donors. Cells were grown to 70%-80% confluence at 33 Celsius degree in 5% CO2 before thermo-switching to 37 Celsius degree in 5% CO2 and allowed to differentiate for 10 days.

extract_protocol:
Total RNA was extracted from levamisole-treated podocytes using the TRIzol method. RNA samples were then subjected to DNase treatment (Ambion TURBO DNase, Life Technologies) and purification (RNeasy Mini Kit, QIAGEN) according to the manufacturer’s instructions.
The cDNA library preparation and the sequencing were performed following manufacturer’s instructions at the Bristol Genomics Facility, University of Bristol. Briefly, approximately 1μg of purified total RNA was prepared for sequencing using the Illumina TruSeq mRNA Seq v2 kit.  Sequencing of 100bp paired-end reads was performed with the Illumina HiSeq 2500 instrument.

treatment_protocol: Differentiated cells were then treated with 1μM or 10μM levamisole (Sigma–Aldrich) for 24 hours, then subsequently used for RNA extraction and sequencing.

value: Podocytes

tag: tissue

value: kidney


title: NA19221

value: Lymphoblastoid cell line NA19221


title: NA19224

value: Lymphoblastoid cell line NA19224


title: Control 24h c

source_name: SK-MES-1 cell line, control, 24h

value: Squamous cell lung carcinoma cell line

value: control


title: NA19194

value: EBV-immortalized B-Lymphocyte

value: Lymphoblastoid cell line NA19194


title: NA19191

value: Lymphoblastoid cell line NA19191


title: NA19186

value: Lymphoblastoid cell line NA19186


title: NA19180

value: Lymphoblastoid cell line NA19180


title: NA19183

value: Lymphoblastoid cell line NA19183


title: NA19174

value: Lymphoblastoid cell line NA19174


title: NA19173

value: Lymphoblastoid cell line NA19173


title: NA19161

value: Lymphoblastoid cell line NA19161


title: NA19154

value: Lymphoblastoid cell line NA19154


title: NA19151

value: Lymphoblastoid cell line NA19151


title: NA19177

value: Lymphoblastoid cell line NA19177


title: NA19145

value: Lymphoblastoid cell line NA19145


title: NA19148

value: Lymphoblastoid cell line NA19148


title: NA19139

value: Lymphoblastoid cell line NA19139


title: NA19142

value: Lymphoblastoid cell line NA19142


title: NA19132

value: Lymphoblastoid cell line NA19132


title: NA19129

value: EBV-immortalized B-Lymphocyte

value: Lymphoblastoid cell line NA19129


title: NA19123

value: Lymphoblastoid cell line NA19123


title: NA19109

value: Lymphoblastoid cell line NA19109


title: NA19115

value: Lymphoblastoid cell line NA19115


title: NA19120

value: Lymphoblastoid cell line NA19120


title: NA18935

value: Lymphoblastoid cell line NA18935


title: NA19094

value: Lymphoblastoid cell line NA19094


title: NA19097

value: Lymphoblastoid cell line NA19097


title: NA18925

value: Lymphoblastoid cell line NA18925


title: NA18930

value: Lymphoblastoid cell line NA18930


title: NA18914

value: Lymphoblastoid cell line NA18914


title: NA18875

value: Lymphoblastoid cell line NA18875


title: NA18911

value: Lymphoblastoid cell line NA18911


title: NA18515

value: Lymphoblastoid cell line NA18515


title: NA18857

value: Lymphoblastoid cell line NA18857


title: NA18872

value: Lymphoblastoid cell line NA18872


title: NA18863

value: EBV-immortalized B-Lymphocyte

value: Lymphoblastoid cell line NA18863


title: NA18869

value: Lymphoblastoid cell line NA18869


title: NA18854

value: Lymphoblastoid cell line NA18854


title: NA18506

value: Lymphoblastoid cell line NA18506


title: NA18521

value: Lymphoblastoid cell line NA18521


title: NA18500

value: Lymphoblastoid cell line NA18500


title: NA18485

value: Lymphoblastoid cell line NA18485


title: NA19100

value: Lymphoblastoid cell line NA19100


title: NA18484

value: Lymphoblastoid cell line NA18484


title: NA19103

value: Lymphoblastoid cell line NA19103


title: NA12877

value: Lymphoblastoid cell line NA12877


title: NA12864

value: Lymphoblastoid cell line NA12864


title: NA12865

value: Lymphoblastoid cell line NA12865


title: NA12802

value: Lymphoblastoid cell line NA12802


title: NA12801

value: Lymphoblastoid cell line NA12801


title: NA18518

value: Lymphoblastoid cell line NA18518


title: NA12753

value: EBV-immortalized B-Lymphocyte

value: Lymphoblastoid cell line NA12753


title: NA12767

value: Lymphoblastoid cell line NA12767


title: NA12832

value: Lymphoblastoid cell line NA12832


title: NA12817

value: Lymphoblastoid cell line NA12817


title: NA12752

value: Lymphoblastoid cell line NA12752


title: NA18497

value: Lymphoblastoid cell line NA18497


title: NA18503

value: Lymphoblastoid cell line NA18503


title: NA12740

value: Lymphoblastoid cell line NA12740


title: NA18860

value: Lymphoblastoid cell line NA18860


title: NA12386

value: Lymphoblastoid cell line NA12386


title: NA12344

value: Lymphoblastoid cell line NA12344


title: NA12375

value: Lymphoblastoid cell line NA12375


title: NA12485

value: Lymphoblastoid cell line NA12485


title: NA12336

value: Lymphoblastoid cell line NA12336


title: NA12707

value: Lymphoblastoid cell line NA12707


title: NA12335

value: Lymphoblastoid cell line NA12335


title: NA12739

value: EBV-immortalized B-Lymphocyte

value: Lymphoblastoid cell line NA12739


title: NA10865

value: Lymphoblastoid cell line NA10865


title: NA12376

value: Lymphoblastoid cell line NA12376


title: NA12818

value: Lymphoblastoid cell line NA12818


title: NA10864

value: Lymphoblastoid cell line NA10864


title: NA12766

value: Lymphoblastoid cell line NA12766


title: NA10863

value: Lymphoblastoid cell line NA10863


title: NA10861

value: Lymphoblastoid cell line NA10861


title: NA10859

value: Lymphoblastoid cell line NA10859


title: NA10860

value: Lymphoblastoid cell line NA10860


title: NA12878

value: Lymphoblastoid cell line NA12878


title: NA10856

value: Lymphoblastoid cell line NA10856


title: NA10855

value: Lymphoblastoid cell line NA10855


title: NA10857

value: Lymphoblastoid cell line NA10857


title: NA10845

value: Lymphoblastoid cell line NA10845


title: NA10840

value: Lymphoblastoid cell line NA10840


title: NA10843

value: EBV-immortalized B-Lymphocyte

value: Lymphoblastoid cell line NA10843


title: NA10842

value: Lymphoblastoid cell line NA10842


title: NA10846

value: Lymphoblastoid cell line NA10846


title: NA10839

value: Lymphoblastoid cell line NA10839


title: NA10837

value: Lymphoblastoid cell line NA10837


title: NA10836

value: Lymphoblastoid cell line NA10836


title: NA10835

value: Lymphoblastoid cell line NA10835


title: NA07048

value: Lymphoblastoid cell line NA07048


title: NA10830

value: Lymphoblastoid cell line NA10830


title: NA07348

value: Lymphoblastoid cell line NA07348


title: NA10831

value: Lymphoblastoid cell line NA10831


title: NA07019

value: Lymphoblastoid cell line NA07019


title: NA07029

value: Lymphoblastoid cell line NA07029


title: NA07014

value: Lymphoblastoid cell line NA07014


title: NA10854

value: Lymphoblastoid cell line NA10854


title: NA06997

value: Lymphoblastoid cell line NA06997


title: NA10847

value: EBV-immortalized B-Lymphocyte

value: Lymphoblastoid cell line NA10847


title: NA06995

value: Lymphoblastoid cell line NA06995


title: HG00709

value: Lymphoblastoid cell line HG00709


title: HG00703

value: Lymphoblastoid cell line HG00703


title: HG00694

value: Lymphoblastoid cell line HG00694


title: NA10838

value: Lymphoblastoid cell line NA10838


title: HG00700

value: Lymphoblastoid cell line HG00700


title: HG00691

value: Lymphoblastoid cell line HG00691


title: NA07349

value: Lymphoblastoid cell line NA07349


title: NA10851

value: Lymphoblastoid cell line NA10851


title: NA06991

value: Lymphoblastoid cell line NA06991


title: HG00664

value: Lymphoblastoid cell line HG00664


title: HG00658

value: Lymphoblastoid cell line HG00658


title: HG00685

value: Lymphoblastoid cell line HG00685


title: HG00652

value: Lymphoblastoid cell line HG00652


title: HG00706

value: Lymphoblastoid cell line HG00706


title: HG00630

value: EBV-immortalized B-Lymphocyte

value: Lymphoblastoid cell line HG00630


title: HG00627

value: Lymphoblastoid cell line HG00627


title: HG00621

value: Lymphoblastoid cell line HG00621


title: HG00673

value: Lymphoblastoid cell line HG00673


title: HG00597

value: Lymphoblastoid cell line HG00597


title: HG00609

value: Lymphoblastoid cell line HG00609


title: HG00615

value: Lymphoblastoid cell line HG00615


title: HG00612

value: Lymphoblastoid cell line HG00612


title: HG00655

value: Lymphoblastoid cell line HG00655


title: HG00594

value: Lymphoblastoid cell line HG00594


title: HG00636

value: Lymphoblastoid cell line HG00636


title: HG00591

value: Lymphoblastoid cell line HG00591


title: HG00582

value: Lymphoblastoid cell line HG00582


title: HG00579

value: Lymphoblastoid cell line HG00579


title: HG00567

value: Lymphoblastoid cell line HG00567


title: HG00585

value: Lymphoblastoid cell line HG00585


title: HG00526

value: EBV-immortalized B-Lymphocyte

value: Lymphoblastoid cell line HG00526


title: HG00558

value: Lymphoblastoid cell line HG00558


title: HG00538

value: Lymphoblastoid cell line HG00538


title: HG00561

value: Lymphoblastoid cell line HG00561


title: HG00544

value: Lymphoblastoid cell line HG00544


title: HG00532

value: Lymphoblastoid cell line HG00532


title: HG00465

value: Lymphoblastoid cell line HG00465


title: HG00453

value: Lymphoblastoid cell line HG00453


title: HG00459

value: Lymphoblastoid cell line HG00459


title: HG00535

value: Lymphoblastoid cell line HG00535


title: HG00447

value: Lymphoblastoid cell line HG00447


title: HG00480

value: Lymphoblastoid cell line HG00480


title: HG00474

value: Lymphoblastoid cell line HG00474


title: HG00477

value: Lymphoblastoid cell line HG00477


title: HG00438

value: Lymphoblastoid cell line HG00438


title: HG00444

value: Lymphoblastoid cell line HG00444


title: HG00429

value: EBV-immortalized B-Lymphocyte

value: Lymphoblastoid cell line HG00429


title: HG00423

value: Lymphoblastoid cell line HG00423


title: HG00420

value: Lymphoblastoid cell line HG00420


title: HG00408

value: Lymphoblastoid cell line HG00408


title: HG00405

value: Lymphoblastoid cell line HG00405


title: HG00514

value: Lymphoblastoid cell line HG00514


title: HG00502

value: Lymphoblastoid cell line HG00502


title: 4.2 Smad5 KO - EHF

city: Leuven

first: Stein

last: Aerts

address: Herestraat 49

department: Center for Human Genetics

country: Belgium

institute: KULeuven

data_processing: Sequenced reads were trimmed for adaptor sequence, then mapped to GRCm38.83 (mm10) whole genome using TopHat2 (v2.1.1) with colorspace compatible parameters: Bowtie 1 (v1.1.2.0), --color --quals and coverage-search algorithm. Gene counts were obtained using featureCounts v1.5.3 with parameters '-Q 0 -s 0 -t exon -g gene id’. Genome_build: GRCm38.83, Supplementary_files_format_and_content: gene counts in a .xlsx file. Statistical results in .csv files (Group_KOSetB and Group_KOSetA have been defined in silico after unsupervized sample clustering (PCA) based on the transcriptome data).

molecule: polyA RNA

organism: Mus musculus

source_name: E7.5 amnion tissue

extract_protocol:
RNAseq was prepared from single E7.5 amnions and amplified following an adaptation of a procedure originall designed of single-cells on the SOLiD pltform ("Double stranded cDNA synthesis from a single cell", Applied Biosystems demonstrated protocol).
Reverse transcription and secon-strand cDNA synthesis was performed directly in the sample lysate without RNA isolation using SuperScript III Reverse Transcriptase (Invitrogen) and poly-dT universal primers. This was followed by two rounds of PCR amplification (18 and 12 cycles, respectively) and column purifications (QIAquick, QIAGEN) generationg up to 3Kb coverage at the 3' end of all polyadenylated transcripts.

tag: post-analytic subgroup

value: SetB

tag: gender

value: female

tag: genotype

value: mixed C57BL/6J x CBA background


title: 3.2 Smad5 KO - EHF

value: SetA


title: 6.2 Smad5 KO - EPHF

value: male


title: 5.2 Smad5 KO - LPHF


title: 6.1 Ctrl - EPHF

value: Outlier


title: 2.2 Smad5 KO - LHF


title: 4.1 Ctrl - EHF

value: Control


title: HG00450

value: Lymphoblastoid cell line HG00450


title: 5.1 Ctrl - LHF


title: 1.1 Ctrl - 3S


title: Cbfb+/mDE rep3

city: Bethesda

first: Pu

middle: Paul

last: Liu

state: MD

address: 49 Convent Dr.

department: TFGB

institute: NHGRI/NIH

data_processing:
The raw data was processed using RTA version 1.18.64 and CASAVA 1.8.2 for base calling
RNA sequencing raw reads were aligned to the mouse genome reference (GRCm38) and transcript reference (GRCm38.78) using STAR (version 2.4)
RSEM to obtain RNA-seq count and to estimate relative transcript abundance at the gene level from the aligned reads
DESeq2 was implemented in R to perform differential expression analysis
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text file includes transcript per million read counts for each sample

source_name: Bone Marrow

extract_protocol:
Bone marrow cells were extracted from pIpC treated mice and c-KIT+ cells were selected using Stemcell's EasySep Mouse CD117 positive selection kit.  Total RNA was extracted using Qiagen Allprep kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Bone Marrow

value: C-KIT+

value: Cbfb+/mDE


title: Cbfb+/MYH11 rep3


title: 3.1 Ctrl - EHF


title: WT rep3

value: WT


title: Cbfb+/mDE rep2


title: Cbfb+/MYH11 rep2


title: Cbfb+/MYH11 rep1


title: WT rep1


title: WT rep2


title: WT male 1.

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

data_processing:
Pre-processing of raw reads was carried out using Trimmomatic (version 0.35, options: LEADING:3 TRAILING:3 MAXINFO:80:0.4 MINLEN:36)
The trimmed reads were mapped to the Mus musculus genome (GRCm38) using TopHat2 (version 2.1.0, default options).
The gene-level read counts were created from the aligned reads by HTSeq and differential gene expression analysis was carried out using R/Bioconductor DEseq2 package.
The P-values were first corrected by applying empirical estimation of the null distribution using the R fdrtool (v.1.2.15) package and then were adjusted for multiple testing with the Benjamini–Hochberg correction
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: Brain

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

tag: age

tag: genotype/variation

value: wild type


title: WT male 3.


title: HT male 3.

value: Asn2373LysfsX2 heterozygote


title: WT male 2.


title: HT male 2.


title: HT male 1.


title: WT female 3.


title: 2.1 Ctrl - LHF


title: WT female 1.


title: HT female 3.


title: HT female 2.


title: WT female 2.


title: HT female 1.


title: Cbfb+/mDE rep1


title: WT female 2

data_processing:
Pre-processing of raw reads was carried out using Trimmomatic (version 0.35, options: LEADING:3 TRAILING:3 MAXINFO:80:0.4 MINLEN:36)
The trimmed reads were mapped to the Mus musculus genome (GRCm38) using TopHat2 (version 2.1.0, default options).
The gene-level read counts were created from the aligned reads by HTSeq and differential gene expression analysis was carried out using R/Bioconductor DEseq2 package.
A two-factor design with the factors genotype (Het vs. WT) and sex (male vs. female) was used to analyze the interaction effect between genotype and sex implemented in DESeq2 (design=~sex*genotype).
The P-values were first corrected by applying empirical estimation of the null distribution using the R fdrtool (v.1.2.15) package and then were adjusted for multiple testing with the Benjamini–Hochberg correction
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: WT female_brain

tag: strain background


title: WT male 2

source_name: WT male_brain


title: WT male 3


title: HT female 3

source_name: HT female_brain

value: CHD8 Asn2373LysfsX2 heterozygote mutation


title: WT female 1


title: WT male 1


title: HT female 1


title: HT female 2


title: HT male 2

source_name: HT male_brain


title: HT male 1


title: WT female 3


title: HT male 3


title: S2_CGGBP1 shmiR + bisulfite converted genomic DNA

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

description: Whole genome (bisulfite converted)

library_source: genomic

data_processing:
Unpairing of paired reads into one file
Alignment against Hg38 (bisulfite conversion efficiency 95% established for this library previously (PMID 25981527)). Bismark version 0.16.1 with embedded Bowtie2 was used.
Bismark MethylExtractor used for extracting methylation status in a context-specific and strand-specific manner
Identification of cytosines that exhibit inter-sample change in cytosine methylation but no intra-sample change upon CGGBP1 depletion (S2 compared to S1).
Identification of cytosines (i) methylated in both S1 and S2 (designated as RoM), (ii) unmethylated in both S1 and S2 (designated as RuN), (iii) methylated in S1 and unmethylated in S2 (designated as LoM), and (iv) unmethylated in S1 and methylated in S2 (designated as GoM).
Genome_build: Hg38
processed data files format and content:
bed file with  RoM, RuN, LoM and GoM locations in Hg38 on series record
*alignment_report.txt: Bismark Methylextractor Report
*Bisulfite_report.txt: Bismark Methylextractor Report
*bt2.txt.gz: Bismark Methylextractor Output

molecule: genomic DNA

source_name: 1064Sk normal human foreskin fibroblasts passage 12 transduced with CGGBP1-targeting lentivirus, genomic DNA extracted and subjected to bisulfite conversion

growth_protocol: 10% FBS (Supplemented with Glutamine) in MEM (SIGMA)

extract_protocol:
DNA extracted using Qiagen Genomic DNA extraction kit.
NEXTflex Bisulfite (cat# 5119-01) Sequencing kit provided by Bioo Scientific for Illumina Seq.  Paired-end library for Illumina (library preparation described previously in PMID 25981527)

treatment_protocol: Lentiviral transduction (MoI = 6)

value: Normal human foreskin fibroblasts

tag: passage

tag: transduced with

value: CGGBP1-targeting lentivirus (shmiR)


title: S1_Control shmiR + bisulfite converted genomic DNA

description: Whole genome (bisulfite converted)

source_name: 1064Sk normal human foreskin fibroblasts passage 12 transduced with non-targeting lentivirus, genomic DNA extracted and subjected to bisulfite conversion

value: non-targeting lentivirus (shmiR)


title: Rex1GFP+_Tsc2KO_rep1

city: Hinxton

first: Meng

last: Li

address: Genome Campus

institute: Sanger Institute

data_processing:
Transcript counts were generated using Kallisto (version 0.42.1)
Differential expression analysis was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each transcript;

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ESCs

value: Rex1GFPd2-Cas9 Tsc2-/-


title: Rex1GFP+_Nprl2KO_rep1

value: Rex1GFPd2-Cas9 Nprl2-/-


title: Rex1GFP+_wt_rep2


title: Rex1GFP+_Nprl2KO_rep2


title: Rex1GFP+_Tsc2KO_rep2


title: Day3_differentiation_rep3


title: Day2_differentiation_rep1


title: Day3_differentiation_rep2


title: Day1_differentiation_rep3


title: Day3_differentiation_rep1


title: Rex1GFP+_wt_rep1


title: Day2_differentiation_rep3


title: Day1_differentiation_rep2


title: NA12329

value: EBV-immortalized B-Lymphocyte

value: Lymphoblastoid cell line NA12329


title: Day0_differentiation_rep2


title: Day1_differentiation_rep1


title: Day0_differentiation_rep1


title: WT_12

city: Kunm,ing

first: Xiaopeng

last: Qi

address: 32 East Jiaochang Rd

institute: Kunming Institute of Zoology, CAS

description: F. novicida infected WT BMDMs for 12 h

data_processing:
Basecalling and read demultiplexing done with bcl2fastq version 2.19
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with ngQC which is an internal software
Mapped to GRCm38 whole genome using HISAT v2.0.4 with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010, and quantiles normalized prior to statistical analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: Bone marrow derived macrophage (BMDM)

growth_protocol: To generate bone marrow derived macrophages (BMDMs), bone marrow cells were cultured in L929 cell-conditioned Dulbecco's Modified Eagle Medium and Nutrient Mixture F-12 (DMEM/F-12) supplemented with 10% FBS, 1% non-essential amino acids and 1% Penicillin-streptomycin for 5 days.

extract_protocol:
Total RNA was isolated from tissues or cells using Trizol (Invitrogen), and purified by RNA extraction Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDMs were seeded in 12-well plates (1 million cells per well) and cultured overnight. Next day, cells were washed and supplied with fresh media without antibiotics. BMDMs were infected with F. novicida (100 MOI) for the indicated times.

value: FVB/NJ

value: Primary macrophage

tag: agent

value: F. novicida

tag: time point


title: Hectd3–/–_12

description: F. novicida infected Hectd3-/- BMDMs for 12 h


title: Hectd3–/–_8

description: F. novicida infected Hectd3-/- BMDMs for 8 h

value: 8 h


title: WT_8

description: F. novicida infected WT BMDMs for 8 h

value: WT


title: WT_0

description: uninfected WT BMDMs

value: uninfected


title: WTUntreated2

city: Ribeirao Preto

first: Geraldo

middle: A

last: Passos

state: SP

address: 3900, Bandeirantes Avenue

department: Genetics

country: Brazil

institute: University of Sao Paulo

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence using the FASTX-Toolkit v 0.0.14 (By Hannon Lab - http://hannonlab.cshl.edu/fastx_toolkit/index.html), then mapped to mm10 whole genome using the splice-aware aligner STAR v.2.5.0a along with the UCSC annotation file (gtf) for GRCm38/mm10 (Dec.2011).
Gene counts were compiled using the HTseq tool. Only genes that had at least 20 reads in any given library were used in subsequent analysis.
Normalization and differential expression was carried out using the DESeq2 Bioconductor package with the R statistical programming environment.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing Gene Name, Number of reads (raw counts by HTSesq-counts)

source_name: Wildtype_mTEc cells_without co-culture

growth_protocol: 1x10^6 mTEC 3.10 cells were cultured in RPMI 1640 medium (37 °C with 5% CO2) for 12h.

extract_protocol:
mirVana miRNA Isolation Kit (Ambion) was used for total RNA extraction from mTEC 3.10 cell line according to the manufacturer's instructions. The RNA samples were eluted in RNAse free water and stored at -80 C. The yield was determined by spectrophotometry (A260) and analyzed for phenol or protein contamination, (A260/A230) and (A260/A280), respectively. The integrity of RNA samples was evaluated by microfluidic electrophoresis using Agilent RNA Nano 6000 chips and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). (Parameters: Extracted product = total_RNA, Amplification = none)
RNA libraries were prepared for sequencing using standard Illumina protocol to the TruSeq Stranded mRNA Library Preparation kit (RS-122-2101).

treatment_protocol: Wild type mTEC 3.10 were cultured in RPMI 1640 medium (37 C with 5% CO2) for 12 h.

tag: cell line

value: mTEC 3.10

value: medullary thymic epithelial (mTEC)

tag: passages

value: wildtype


title: WTTreated1

source_name: Wildtype_mTEc cells_co-culture with thymocytes

growth_protocol: 1x10^6 Aire mTEC 3.10 cells were cultured in RPMI 1640 medium (37 °C with 5% CO2) for 12h.

extract_protocol:
mirVana miRNA Isolation Kit (Ambion) was used for total RNA extraction from mTEC 3.10 cells that were co-cultured with thymocytes according to the manufacturer's instructions. The RNA samples were eluted in RNAse free water and stored at -80 C. The yield was determined by spectrophotometry (A260) and analyzed for phenol or protein contamination, (A260/A230) and (A260/A280), respectively. The integrity of RNA samples was evaluated by microfluidic electrophoresis using Agilent RNA Nano 6000 chips and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). (Parameters: Extracted product = total_RNA, Amplification = none)
RNA libraries were prepared for sequencing using standard Illumina protocol to the TruSeq Stranded mRNA Library Preparation kit (RS-122-2101).

treatment_protocol: Thymus of C57BL/6 mice was surgically removed, minced and fragments filtered through a nylon membrane to separate thymocytes. The thymocytes were co-cultured with Aire KO or WT mTEC cells in a ratio 50:1 (thymocytes:mTEC) for 12h. The adherent thymocytes were separated by washing with PBS. The mTECs cells were trypsinized and collected for further total RNA extraction.

tag: cell type


title: E6Treated2

source_name: Aire KO_mTEc cells_co-culture with thymocytes

growth_protocol: 1x10^6 Aire KO mTEC 3.10 cells (clone E6) were cultured in RPMI 1640 medium (37 °C with 5% CO2) for 12 h.

extract_protocol:
mirVana miRNA Isolation Kit (Ambion) was used for total RNA extraction from Aire KO mTEC 3.10 cells (clone E6) after co-culture with thymocytes according to the manufacturer's instructions. The RNA samples were eluted in RNAse free water and stored in a -80 C freezer. The yield was determined by spectrophotometry (A260) and analyzed for phenol or protein contamination, (A260/A230) and (A260/A280), respectively. The integrity of RNA samples was evaluated by microfluidic electrophoresis using Agilent RNA Nano 6000 chips and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). (Parameters: Extracted product = total_RNA, Amplification = none)
RNA libraries were prepared for sequencing using standard Illumina protocol to the TruSeq Stranded mRNA Library Preparation kit (RS-122-2101).

treatment_protocol: Thymus of C57BL/6 mice was surgically remover, minced and filtered through a nylon membrane to separate the thymocytes. The thymocytes were co-cultured with Aire KO mTEC cells (clone E6) in a ratio 50:1 (thymocyts:mTECs) for 12 h. The adherent thymocytes were separated by washing with PBS. The mTECs cells were trypsinized and collected for further total RNA extraction.

value: Aire +/-


title: WTTreated2

growth_protocol: 1x10^6 mTEC 3.10 cells were cultured in RPMI 1640 medium (37 °C with 5% CO2) for 24h.

treatment_protocol: Thymus of C57BL/6 mice was surgically removed, minced and fragments filtered through a nylon membrane to separate thymocytes. The thymocytes were co-cultured with mTEC 3.10 cells in a ratio 50:1 (thymocytes:mTEC) for 12h. The adherent thymocytes were separated by washing with PBS. The mTECs cells were trypsinized and collected for further total RNA extraction.


title: E6Untreated2

source_name: Aire KO_mTEc cells_without co-culture

growth_protocol: 1x10^6 Aire KO or WT mTEC 3.10 cells were cultured in RPMI 1640 medium (37 °C with 5% CO2) for 12 h.

extract_protocol:
mirVana miRNA Isolation Kit (Ambion) was used for total RNA extraction from Aire KO mTEC 3.10 cells (clone E6) according to the manufacturer's instructions. The RNA samples were eluted in RNAse free water and stored in a -80 C freezer. The yield was determined by spectrophotometry (A260) and analyzed for phenol or protein contamination, (A260/A230) and (A260/A280), respectively. The integrity of RNA samples was evaluated by microfluidic electrophoresis using Agilent RNA Nano 6000 chips and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). (Parameters: Extracted product = total_RNA, Amplification = none)
RNA libraries were prepared for sequencing using standard Illumina protocol to the TruSeq Stranded mRNA Library Preparation kit (RS-122-2101).

treatment_protocol: Thymus of C57BL/6 mice was surgically removed, minced and fragments filtered through a nylon membrane to separate the thymocytes. The thymocytes were co-cultured with Aire KO mTEC cells in a ratio 50:1 (thymocytes:mTECs) for 12h. The adherent thymocytes were separated by washing with PBS. The mTECs cells were trypsinized and collected for further total RNA extraction.


title: WTUntreated1

growth_protocol: 1x10^6 mTEC 3.10 cells were cultured in RPMI 1640 medium (37 °C with 5% CO2) for 12 h.

treatment_protocol: Wild type mTEC 3.10 cells were cultured in RPMI 1640 medium at 37 C with 5% CO2 for 12 h.


title: E6Untreated1

growth_protocol: 1x10^6 Aire KO or WT mTEC 3.10 cells were cultured in RPMI 1640 medium (37 °C with 5% CO2) for 24h.

treatment_protocol: Thymus of C57BL/6 mice was surgically removed, minced and fragments filtered through a nylon membrane to separate the thymocytes. The thymocytes were co-cultured with Aire KO or WT mTEC cells in a ratio 50:1 (thymocytes:mTECs) for 12h. The adherent thymocytes were separated by washing with PBS. The mTECs cells were trypsinized and collected for further total RNA extraction.


title: E6Treated1

extract_protocol: mirVana miRNA Isolation Kit (Ambion) was used for total RNA extraction from Aire KO mTEC 3.10 cells (clone E6) after co-culture with thymocytes according to the manufacturer's instructions. The RNA samples were eluted in RNAse free water and stored in a -80 C freezer. The yield was determined by spectrophotometry (A260) and analyzed for phenol or protein contamination, (A260/A230) and (A260/A280), respectively. The integrity of RNA samples was evaluated by microfluidic electrophoresis using Agilent RNA Nano 6000 chips and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). (Parameters: Extracted product = total_RNA, Amplification = none) RNA libraries were prepared for sequencing using standard Illumina protocol to the TruSeq Stranded mRNA Library Preparation kit (RS-122-2101).

treatment_protocol: Thymus of C57BL/6 mice was surgically removed, minced and fragments filtered through a nylon membrane to separate the thymocytes. The thymocytes were co-cultured with Aire KO mTEC cells (clone E6) in a ratio 50:1 (thymocytes:mTECs) for 12 h. The adherent thymocytes were separated by washing with PBS. The mTECs cells were trypsinized and collected for further total RNA extraction.


title: Day2_differentiation_rep2


title: H1 S/D NPCs

city: Guangzhou

first: qianyu

last: chen

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

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 mm10 whole genome using bowtie
Transcripts Per Million were  calculated using a protocol from RSEM
Genome_build: hg19
Supplementary_files_format_and_content: TPM

source_name: ES derived neural progenitor cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: H1 S/D NPCs

tag: cell subtype

value: dual SMAD inhibition-derived NPCs


title: H1 S/D/C NPCs

value: H1 S/D/C NPCs

value: triple Inhibition of TGFb/BMP/GSK3 Signaling-derived NPCs


title: Day0_differentiation_rep3

value: ESCs


title: Hectd3–/–_0

description: uninfected Hectd3-/- BMDMs


title: TU0075_CD4_LTBI

status: Public on Jun 14 2018

city: La Jolla

first: Bjoern

last: Peters

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description:
PolyAtail selected messenger RNA
Microscaled (SmartSeq2) cDNA amplification - RNA seq

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The reads were then aligned to UCSC hg19 reference genome using TopHat (v 1.4.1) (Trapnell et al., 2009). DUST scores were calculated with PRINSEQ Lite (v 0.20.3) (Schmieder et al., 2011) and low-complexity reads (DUST > 4) were removed from the BAM files.  The alignment results were parsed via the SAMtools (Li et al., 2009) to generate SAM files. Read counts to each genomic feature were obtained with the htseq-count program (v 0.6.0) (Anders et al., 2014) using the “union” option.
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements as a matrix table

source_name: Cryopreserved PBMC

growth_protocol: Cells were directly isolated post thawing of cryopreserved PBMC samples and lysed, no culture were involved.

extract_protocol:
Cryopreserved PBMC were thawed, stained with antibodies, and 100,000 memory CD4 T cells sorted using BD Aria 3 or BD Aria Fusion cell sorter direclty in Trizol. Memory cells were defined as the combination of CCR7-CD45RA-, CCR7-CD45RA+ and CCR7+CD45RA- populations. Total RNA was purified using a miRNAeasy micro kit (Qiagen, USA) and quantified by qPCR as described previously (Seumois et al., 2012).
Purified total RNA (1 to 5 ng) was amplified following the smart-seq2 protocol (16 cycles of cDNA amplification) (Picelli et al., 2014). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina).
RNA-Seq (HISeq 2500 illumina, Single-end 50bp)

treatment_protocol: No specific treatment involved

tag: disease group

value: Latent tuberculosis infection

tag: cell subset

value: Memory CD3+CD4+ T cells


title: TP0003_CD4_LTBI


title: XT0134_CD4_LTBI


title: TP0004_CD4_LTBI


title: TP0008_CD4_LTBI


title: TU0063_CD4_LTBI


title: TU0070_CD4_LTBI


title: TU0046_CD4_LTBI


title: TU0035_CD4_LTBI


title: TU0022_CD4_LTBI


title: TU0033_CD4_LTBI


title: TU0010_CD4_LTBI


title: TU0085_CD4_HC

value: Healthy


title: TU0005_CD4_LTBI


title: TU0084_CD4_HC


title: TP0005_CD4_LTBI


title: TP0013_CD4_LTBI


title: TP0015_CD4_LTBI


title: TP0007_CD4_LTBI


title: TU0056_CD4_HC


title: TU0059_CD4_HC


title: TU0053_CD4_HC


title: TU0057_CD4_HC


title: TU0052_CD4_HC


title: TU0050_CD4_HC


title: XT0103_CD4_HC


title: 1.2 Smad5 KO - 2S

tag: post-analytic subgroup

value: SetA

value: male

value: mixed C57BL/6J x CBA background


title: NMR_NM_6074_LVR

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

data_processing:
Extraction of read information in FastQ format was done using the tool bcl2astq v1.8.4 (provided by Illumina).
Reads were mapped using STAR (v2.4.1d) with a maximum mismatch of 6% and a minimum aligned length of 90%. Reads mapped to multiple loci were discarded.
Reads per gene were counted using HTSeq framework (0.6.1p1)
Genome_build: genome (hetgla2, GCA_000247695.1) can be download from UCSC (ftp://hgdownload.cse.ucsc.edu/goldenPath/hetGla2/bigZips/)
Supplementary_files_format_and_content: The Excel sheet includes raw counts for all genes and each sample.

organism: Heterocephalus glaber

source_name: liver

extract_protocol:
Extraction was done as described in Bens et al. 2016. (PMID:26763976)
Library preparation was done using Illumina's TruSeq RNA Library Prep Kit v2 kit following the manufacturer's description.

tag: tissue

value: liver

tag: Sex

value: 3.8 years

tag: reproductive status

value: non-breeder


title: NMR_NM_6206_LVR

tag: age

value: 2.8 years


title: TU0146_CD4_HC


title: NMR_NF_4060_LVR

value: female

value: 3.9 years


title: NMR_BM_6656_LVR

value: breeder


title: NMR_NF_3439_LVR

value: 3.1 years


title: NMR_NM_4925_LVR

value: 3.7 years


title: NMR_NM_3295_LVR

value: 4.1 years


title: TU0079_CD4_HC


title: TU0119_CD4_HC


title: TU0071_CD4_HC


title: NMR_BM_3274_LVR


title: TU0013_CD4_LTBI


title: TP0001_CD4_LTBI


title: NMR_BM_1147_LVR


title: NMR_NF_2969_LVR


title: NMR_NF_2411_LVR

value: 4 years


title: NMR_NM_1449_LVR

value: 2.7 years


title: XT0106_CD4_HC

value: Memory CD3+CD4+ T cells


title: XT0101_CD4_HC

value: Healthy


title: NMR_NM_0713_LVR

value: 3.4 years


title: XT0082_CD4_HC


title: NMR_BF_6841_LVR

value: 3.3 years


title: TU0024_CD4_LTBI

value: Latent tuberculosis infection


title: NMR_BF_6382_LVR

value: liver

value: 3.5 years


title: TU0110_CD4_HC


title: NMR_BM_5982_LVR

value: male

value: 2.9 years


title: NMR_BF_4772_LVR

value: female


title: NMR_BF_4121_LVR


title: NMR_BM_1400_LVR


title: TU0094_CD4_HC


title: NMR_BF_1816_LVR

value: 3.6 years


title: NMR_BM_1215_LVR

value: breeder


title: p9_t2

first: Sijung

last: Yun

state: Maryland

address: 8908 Ewing Drive

institute: NIH/JHU

data_processing:
Basecall quality was assessed on fastq files using FASTQC version 0.10.1.
Reads were aligned to hg19 reference genome using BWA version 0.7.8.
Peaks were called using MACS version 2.1.0.20140616, to identify DNA regions that are methylated.
For identification of differentially methylated DNA regions between PTSD and Control group, as well as baseline and follow up, we used DiffBind software package;
A differential binding affinity analysis was employed to identify statistically significant differences in methylated peak intervals between groups with a false discovery rate (FDR)= 0.10.
Genome_build: hg19
Supplementary_files_format_and_content: peaks

source_name: Blood

extract_protocol:
Peripheral blood was collected in EDTA tubes at both the baseline and follow up from non-fasting subjects, and frozen immediately and stored at -80°C until use. Peripheral blood mononuclear cells (PBMCs) were isolated from the collected blood.
Genomic DNA was extracted from PBMCs using QIAamp DNA Blood Maxi Kit (Qiagen; Hilden, Germany) according to the manufacturer’s protocol. In order to obtain the methylated DNA, 2.5μg of isolated genomic DNA was fragmented down to 250 bp using a M220 Focused-ultrasonicator (Covaris; Woburn, MA), then 1μg fragmented DNA was processed with MethylMiner Methylated DNA Enrichment kit (Invitrogen; Carlsbad, CA). Enriched 10ng of methylated-DNA was used for a DNA library preparation with TruSeq Nano DNA kit (Illumina; San Diego, CA).

tag: condition

value: persistent PTSD


title: p6_t2


title: p9_t1


title: NMR_BF_1090_LVR

value: 3.7 years


title: XT0123_CD4_HC


title: p6_t1


title: NMR_NF_0525_LVR

value: 2.4 years

value: non-breeder


title: p5_t2


title: p5_t1


title: NMR_BF_6841_PIT

source_name: pituitary

value: pituitary


title: NMR_BF_6841_HYP

source_name: hypothalamus

value: hypothalamus


title: NMR_NF_3439_SKN

source_name: skin

value: skin

value: 3.1 years


title: NMR_BF_6382_HYP


title: NMR_NM_3295_THY

source_name: thyroid

value: thyroid

value: 4.1 years


title: NMR_BM_1215_HRT

source_name: heart

value: heart

value: 3.4 years


title: NMR_BF_1816_HYP


title: NMR_NF_3605_THY

value: 3.3 years


title: NMR_BF_4772_HYP


title: NMR_BF_6841_HRT


title: p1_t2


title: p1_t1


title: i13_t2

value: increased PTSD


title: NMR_BF_6841_SKN

value: female


title: NMR_BM_6656_SKN

value: male

value: 2.8 years


title: NMR_BF_6382_SKN

value: 3.5 years

value: breeder


title: NMR_NM_6206_SKN


title: i12_t2


title: i13_t1


title: NMR_NM_4925_SKN

value: 3.7 years


title: NMR_BM_5982_SKN

value: 2.9 years


title: i12_t1


title: NMR_NM_6074_SKN

value: 3.8 years

value: non-breeder


title: NMR_BF_4772_SKN

value: skin


title: NMR_NM_4925_ADR

source_name: adrenal gland

value: adrenal gland


title: NMR_BF_4121_SKN


title: NMR_NF_3605_SKN


title: NMR_NF_4060_SKN

value: 3.9 years


title: NMR_NM_3295_SKN

value: 4.1 years


title: i5_t2


title: NMR_BM_3274_SKN


title: i3_t1


title: c12_t2

value: control


title: i5_t1


title: NMR_NF_2969_SKN


title: NMR_BF_1816_SKN

value: 3.6 years


title: NMR_BM_1400_SKN

value: 4 years


title: NMR_BM_1147_SKN


title: NMR_BM_1215_SKN

value: 3.4 years


title: NMR_NF_2411_SKN

value: female


title: NMR_NM_1449_SKN

value: male

value: 2.7 years


title: c12_t1


title: NMR_BF_1090_SKN


title: NMR_NM_0713_SKN


title: c11_t2


title: NMR_NF_0525_SKN

value: 2.4 years


title: c11_t1


title: NMR_BF_6841_CER

source_name: cerebellum

value: cerebellum

value: 3.3 years

value: breeder


title: NMR_BM_6656_HYP

value: hypothalamus

value: 2.8 years


title: NMR_BM_6656_CER


title: c10_t1


title: NMR_BM_6656_PIT

value: pituitary


title: i3_t2

value: increased PTSD


title: NMR_BF_6382_PIT

value: 3.5 years


title: c8_t2


title: c8_t1


title: NMR_NM_6206_PIT

value: non-breeder


title: NMR_NM_6074_CER

value: 3.8 years


title: NMR_NM_6074_PIT


title: c3_t2

value: control


title: NMR_BM_5982_CER

value: 2.9 years


title: c3_t1


title: NMR_NM_6074_HYP


title: NMR_NM_4925_CER

value: 3.7 years


title: NMR_BM_5982_PIT


title: c1_t2


title: c1_t1


title: NMR_BM_5982_HYP


title: NMR_NM_4925_PIT


title: NMR_BF_6382_CER

value: female


title: NMR_BF_4772_CER


title: NMR_BF_4772_PIT


title: c10_t2


title: NMR_NF_4060_HYP

value: 3.9 years


title: NMR_NF_4060_CER


title: NMR_NM_6206_CER

value: male


title: NMR_NM_6206_HYP


title: NMR_BF_4121_PIT


title: NMR_BF_4121_CER


title: NMR_NF_4060_PIT


title: NMR_NF_3605_CER


title: NMR_NF_3605_HYP


title: NMR_NF_3439_CER

value: 3.1 years


title: NMR_NF_3439_PIT


title: NMR_NF_3439_HYP


title: NMR_NM_3295_CER

value: cerebellum

value: 4.1 years


title: NMR_BM_3274_PIT

value: breeder


title: NMR_BM_3274_HYP

value: hypothalamus


title: NMR_NM_3295_HYP


title: NMR_NM_3295_PIT


title: NMR_NM_4925_HYP


title: NMR_NF_2969_HYP


title: NMR_NF_2969_PIT


title: NMR_NF_2969_CER


title: NMR_NF_2411_HYP

value: 4 years


title: NMR_NF_2411_PIT

value: pituitary


title: NMR_NF_2411_CER


title: NMR_BF_1816_CER

value: 3.6 years


title: NMR_BF_4121_HYP

value: 3.3 years


title: NMR_NM_1449_CER

value: 2.7 years

value: non-breeder


title: NMR_NM_1449_HYP


title: NMR_BM_1400_PIT


title: NMR_BM_1147_CER


title: NMR_BM_1400_CER


title: NMR_BM_1400_HYP


title: NMR_NM_1449_PIT


title: NMR_BM_1147_HYP


title: NMR_BM_1215_PIT

value: 3.4 years


title: NMR_BM_1147_PIT


title: NMR_BF_1090_HYP


title: NMR_BF_1090_CER


title: NMR_BF_1090_PIT


title: NMR_BF_1816_PIT


title: NMR_BM_1215_HYP


title: NMR_BM_1215_CER


title: NMR_NF_3605_PIT


title: NMR_NF_0525_HYP

value: 2.4 years


title: NMR_BF_6382_HRT

value: heart

value: 3.5 years


title: NMR_NM_6206_HRT

value: 2.8 years


title: NMR_BF_4121_HRT

value: female


title: NMR_BM_6656_HRT

value: male


title: NMR_NF_0525_CER

value: cerebellum


title: NMR_NM_0713_CER


title: NMR_NF_4060_HRT

value: 3.9 years


title: NMR_NM_3295_HRT

value: 4.1 years


title: NMR_NF_3605_HRT


title: Elav_RNASeq

city: Paris

first: NIKOLAOS

last: KONSTANTINIDES

address: 15 rue Helene Brion

country: France

institute: Institut Jacques Monod

data_processing:
RNA-Seq reads were trimmed using Trimmomatic version 0.32
RNA-Seq reads were aligned using STAR version 2.5.2
RNA-Seq reads were counted using htseq version 0.6.1
Genome_build: ENSEMBL-release-81-BDGP6
Supplementary_files_format_and_content: RNA-Seq text file includes htseq counts for each sample.

organism: Drosophila melanogaster

source_name: Optic lobe neurons

extract_protocol:
We identified lines for individual cell types and crossed each Gal4 line to UAS-Red Stinger to label the nuclei of the specific neuronal type. Dissected brains were dissociated and cells expressing the transgene were sorted on the basis of their fluorescent signal using FACS (FACS Aria III). Cells were sorted directly into extraction buffer and we extracted total RNA using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems). We assessed RNA quality by Bioanalyzer using RNA 6000 Pico chips (Agilent). Smart-Seq v4 Ultra Low Input RNA Kit was used to generate full-length double stranded cDNA with 300 to 500 pg of total RNA input.
Libraries were prepared using Illumina Nextera XT DNA Library Prep Kit and sequenced on the Illumina HiSeq 2500 System. Three barcoded libraries were pooled per sequencing lane and paired-end 100 bp reads were generated.

value: neurons

tag: developmental stage

value: 3-day to 6-day old adults


title: Tm1_T1_RNASeq

value: T1 and Tm1


title: NMR_BM_5982_HRT

value: 2.9 years

value: breeder


title: NMR_NM_6074_HRT

value: 3.8 years


title: NMR_NM_4925_HRT

value: 3.7 years

value: non-breeder


title: NMR_BF_4772_HRT


title: Stat3 ChIP-exo

city: Berkeley

first: Robert

last: Tjian

state: CA

address: LKS

institute: UC Berkeley/HHMI

description: Stat3 ChIP-exo

data_processing:
Illumina Casava1.7 software used for basecalling
ATAC-seq pair-end reads were adapter removed by Cutadapt . ChIP-exo data processing was followed by Rhee and Pugh, Cell, 2011.
ATAC-seq reads were  mapped to mm9 genome build using Bowtie2 with the following parameters: --no-discordant --no-mixed --phred33 -X2000. For ChIP-exo, after trimming the 3′ most 14 bp error-prone regions, we aligned ChIP-exo reads to the mouse genome using BOWTIE (v 0.12.7; options -S-t -m 1), accepting only uniquely aligning read
ATAC-seq reads mapped to mitochondria and PCR duplicates were removed by samtools
Genome_build: mm9 (ATAC), mm10(ChIP-exo)

source_name: embryonic stem cells

growth_protocol: Mouse  ES cells  were cultured on 0.1% gelatin coated plates without feeders. The ES cell medium was prepared by supplementing knockout DMEM (Invitrogen) with 15% FBS (HyClone), 1 mM GlutaMAX, 0.1 mM nonessential amino acids, 0.1 mM 2-mercaptoethanol, and 1000 units of LIF (Millipore).

extract_protocol: ChIP-exo seq was performed following

treatment_protocol: We employed CRISPR/Cas9 genome editing to biallelically delete the composite Oct4/Sox2 motif in Klf4 E2. Genome editing were validated by Sanger sequencing.

tag: strain

value: embryonic stem cells


title: NMR_NF_3439_HRT

value: heart

value: 3.1 years


title: NMR_BM_3274_HRT


title: NMR_NM_0713_PIT

value: pituitary

value: 3.4 years


title: WT ESC ATAC-seq

description: WT ESC ATAC-seq


title: E2 delOS ESC ATAC-seq

description: E2 delOS ESC ATAC-seq


title: NMR_NM_0713_HYP

value: hypothalamus

value: male


title: Tm9_RNASeq


title: NMR_NF_2411_HRT

value: female

value: 4 years


title: NMR_NF_0525_PIT

value: 2.4 years


title: Tm5c_RNASeq

value: 3-day to 6-day old adults


title: NMR_NM_1449_HRT

value: 2.7 years


title: NMR_BM_1400_HRT


title: Esrrb ChIP-exo

description: Esrrb ChIP-exo


title: NMR_NF_2969_HRT


title: Tm2_RNASeq


title: Tm3_RNASeq


title: NMR_BF_1090_HRT


title: T3_RNASeq


title: NMR_NM_0713_HRT


title: SATB1+ HSCs

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: SATB1+ LSK CD150+ Flt3- cells

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a  101-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks ver.2.2.1.
Genome_build: mm10

source_name: HSC Satb1-Tomato (+)

extract_protocol:
Total RNA samples were prepared by miRNeasy-Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s instructions.
Library preparation was performed using the Clontech SMARTer Stranded RNA-Seq kit according to the manufacturer’s instructions.

value: Hematopoietic stem cells


title: T5_RNASeq


title: NMR_BM_6656_TES

source_name: testis

value: testis

value: 2.8 years

value: breeder


title: NMR_NF_0525_HRT

value: non-breeder


title: T2_RNASeq


title: NMR_BF_6841_OVR

source_name: ovary

value: ovary

value: 3.3 years


title: NMR_BM_1147_HRT

value: heart

value: 3.9 years


title: Mi1_RNASeq


title: NMR_BF_6841_THY

value: thyroid


title: SATB1- HSCs

description: SATB1- LSK CD150+ Flt3- cells

source_name: HSC Satb1-Tomato (-)


title: T1_RNASeq


title: NMR_NM_6074_TES

value: 3.8 years


title: NMR_NM_6206_THY

value: male


title: NMR_BF_6382_OVR

value: female

value: 3.5 years


title: NMR_NM_6074_THY


title: NMR_BM_6656_THY


title: NMR_BM_5982_THY

value: 2.9 years


title: Tm5ab_RNASeq

value: 3-day to 6-day old adults


title: NMR_BM_5982_TES


title: Lawf1_RNASeq


title: NMR_NM_4925_THY

value: 3.7 years


title: NMR_BF_6382_THY


title: NMR_NM_6206_TES


title: Dm8_RNASeq


title: Lawf2_RNASeq


title: NMR_BF_4121_THY


title: NMR_BF_4772_THY


title: NMR_NM_4925_TES


title: NMR_NF_4060_OVR


title: NMR_BF_4772_OVR


title: Dm12_RNASeq


title: NMR_BF_4121_OVR


title: FL-AML3_S3

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

country: Australia

institute: Australian Institute for Bioengineering and Nanotechnology

data_processing:
Reads were mapped to GRCm38 (ENSEMBL 86) whole genome using R version 3.2.2 with package Rsubread version 1.20.6 with default parameters.
Genome_build: GRCm38, ENSEMBL version 86.
Supplementary_files_format_and_content: tab delimited text file containing raw counts, tab delimited text files containing TMM-RPKM log2 abundance measurements.

source_name: AML generated from fetal liver LSKs transformed by NUP98HOXA9

extract_protocol:
RNeasy Mini kit (Qiagen) or Arcturus PicoPure kit (Fisher Scientific)
Total RNA converted to cDNA using the High Capacity cDNA Reverse Transcription Kit (Invitrogen)

tag: disease state

value: Acute Myeloid Leukaemia (AML)

value: bone marrow

tag: donor age

value: Fetal Liver


title: FL-AML2_S2


title: NMR_NF_4060_THY


title: FL-AML1_S1


title: C2_RNASeq


title: NMR_NF_3605_OVR


title: NMR_NF_3439_THY

value: 3.1 years


title: NMR_NF_3439_OVR

value: non-breeder


title: NMR_BM_3274_TES

value: testis

value: 4.1 years

value: breeder


title: NMR_BM_3274_THY


title: NMR_NF_2969_OVR

value: ovary


title: C3_RNASeq


title: 52w_and_above-AML3_S12

source_name: AML generated from 52w and above BM LSKs transformed by NUP98HOXA9

value: 52 week old and above


title: NMR_NF_2411_THY

value: thyroid

value: 4 years


title: NMR_NF_2969_THY

value: female


title: NMR_NF_2411_OVR


title: 52w_and_above-AML2_S11


title: NMR_BF_1816_HRT

value: heart

value: 3.6 years


title: Dm2_RNASeq

value: 3-day to 6-day old adults


title: NMR_BF_1816_OVR


title: 3w-AML3_S6

source_name: AML generated from 3w BM LSKs transformed by NUP98HOXA9

value: 3 week old


title: 52w_and_above-AML1_S10

value: Acute Myeloid Leukaemia (AML)


title: NMR_NM_3295_TES

value: male


title: NMR_NM_1449_THY

value: 2.7 years


title: 3w-AML2_S5

value: bone marrow


title: 3w-AML1_S4


title: NMR_BM_1400_THY


title: NMR_BM_1400_TES


title: NMR_NM_1449_TES

value: non-breeder


title: NMR_BM_1215_TES

value: testis

value: 3.4 years


title: 10w-AML2_S8

source_name: AML generated from 10w BM LSKs transformed by NUP98HOXA9

value: 10 week old


title: Optic_lobe_Dropseq

description: R1 read is the barcode

data_processing:
Drop-seq reads were aligned and counted using the Drop-seq alignment cookbook available from the McCarroll lab website: (http://mccarrolllab.com/wp-content/uploads/2016/03/Drop-seqAlignmentCookbookv1.2Jan2016.pdf)
Genome_build: ENSEMBL-release-81-BDGP6
Supplementary_files_format_and_content: The processed data file includes UMI counts generated according to the Drop-seq alignment cookbook available from the McCarroll lab website: (http://mccarrolllab.com/wp-content/uploads/2016/03/Drop-seqAlignmentCookbookv1.2Jan2016.pdf)

extract_protocol:
\Drop-seq was performed as previously described and following the protocol of the McCarroll lab (http://mccarrolllab.com/dropseq/). Drosophila optic lobes were dissected from Canton-S 3-day old females in PBS and were dissociated into single cell suspension by incubating in 2mg/mL collagenase and 2mg/mL dispase in PBS for 1,5 hours at 25oC. The enzymes were then carefully removed and replaced with PBS + 0.1% BSA. The brains are soft but remain intact if pipetted slowly. The brains were pipetted up and down many times (>200-300) until most large chunks of tissue are dissociated. The cells/tissue were kept cold by putting the tubes in ice. The cells were then filtered using 40um cell strainers. The cells were counted immediately before generating the droplets. The concentration of cells loaded on the microfluidic device was 250 cells/ul.  The lysis buffer was slightly modified to contain 0.2mg/ml Proteinase K. The lysis buffer contained: 0.2M Tris pH 7.5, 20mM EDTA, 50mM DTT, 0.2mg/mL Proteinase K, 6% Ficoll PM-400, and 0.2% Sarkosyl.  The droplets (diameter=125um) were then generated as specified in the Drop-seq protocol and collected in a 50ml falcon tube for a run time of 30 minutes. The emulsions were visualized microscopically in a hemocytometer. 5-10% of the droplets contained a bead and we could observe less than 5% bead-occupied droplets with two beads. After droplet formation, the droplets were incubated in a metal bead bath system at 55oC for 10 min. After incubation, the droplets were broken and the samples were processed as described in the Drop-seq protocol.
Libraries were prepared using Illumina Nextera XT DNA Library Prep Kit and sequenced on the Illumina HiSeq 2500 System.

value: Optic lobe neurons

value: 3-day old adults

value: Canton-S


title: 10w-AML3_S9


title: NMR_BF_1090_OVR

value: ovary

value: 3.7 years

value: breeder


title: NMR_BM_1147_TES

value: 3.9 years


title: NMR_BM_1147_THY

value: thyroid


title: NMR_BM_1215_THY


title: NMR_BF_1090_THY

value: female


title: NMR_NM_0713_THY


title: NMR_NF_0525_THY

value: 2.4 years


title: 10w-AML1_S7

value: Acute Myeloid Leukaemia (AML)


title: NMR_NF_0525_OVR


title: NMR_BF_6841_KID

source_name: kidney

value: kidney

value: 3.3 years


title: NMR_NM_0713_TES

value: male

value: non-breeder


title: CD8 cells timestamped at day 28 rep 1

city: Ithaca

first: Jennifer

middle: K

last: Grenier

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

description:
NaiveCD8_28dayTimestampA
naïve CD8+ T cells made at 28 days
processed data file:
gene_exp.diff: 28D_0
genes.read_group_tracking: 28D_0

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.8 (-m 50 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.0.13 (--no-novel-juncs) was used to map reads to the mouse mm10 reference genome+transcriptome (UCSC).
cuffquant (--no-novel-juncs) was used to quantify transcripts based on the mouse mm10 reference genome+transcriptome (UCSC).
cuffdiff v2.2.1 was used to call differentially expressed genes based on the mouse mm10 reference genome+transcriptome (UCSC).
Genome_build: Mouse mm10 (UCSC)
Supplementary_files_format_and_content: Tab delimited text files including counts, FPKM values, and p-values generated from Cuffdiff2 when corrected for multiple hypothesis testing

source_name: CD8 cells timestamped at day 28

growth_protocol: CD4cre-ERT2 mice were crossed to Ai9 mice bearing a floxed-stop TdTomato element such that when F1 offspring are exposed to tamoxifen, all cells bearing CD4 will begin expressing TdTomato for the duration of tamoxifen exposure.

extract_protocol:
CD8+ cells were magnetically enriched with CD8 microbeads and sorted to > 95% purity with a FACS Aria III on CD4- CD8+ TdTomato+. Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation
RNA-seq libraries were prepared from 50 ng total RNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

treatment_protocol: To mark cell with TdTomato at specific times during development, mice were given tamoxifen at 1 day (through lactation, by administering tamoxifen orally to the Dam) or at 28 days of age (by direct oral administration to the mouse). The mice were then allowed to age to 8 weeks of age.

tag: age of animal

value: 8 weeks

value: spleen

value: CD4- CD8+ TdTomato+ sorted cells


title: CD8 cells timestamped at day 28 rep 2

description:
NaiveCD8_28dayTimestampB
naïve CD8+ T cells made at 28 days
processed data file:
gene_exp.diff: 28D_1
genes.read_group_tracking: 28D_1


title: NMR_BM_6656_ADR

value: adrenal gland

value: 2.8 years


title: NMR_BM_6656_KID


title: NMR_BF_6841_ADR


title: CD8 cells timestamped at day 1, rep 1

description:
NaiveCD8_1dayTimestampA
naïve CD8+ T cells made at 1 day
processed data file:
gene_exp.diff: OneD_0
genes.read_group_tracking: OneD_0

source_name: CD8 cells timestamped at day 1


title: CD8 cells timestamped at day 1, rep 2

description:
NaiveCD8_1dayTimestampB
naïve CD8+ T cells made at 1 day
processed data file:
gene_exp.diff: OneD_1
genes.read_group_tracking: OneD_1


title: NMR_BF_6382_KID

value: 3.5 years


title: NMR_BF_6382_ADR


title: NMR_NM_6206_KID


title: NMR_NM_6074_ADR

value: 3.8 years


title: NMR_BM_5982_ADR

value: 2.9 years

value: breeder


title: NMR_BM_5982_KID


title: NMR_NM_6074_KID


title: NMR_BF_4772_ADR

value: 3.7 years


title: NMR_BF_4121_KID

value: female


title: NMR_NM_4925_KID


title: NMR_BF_4121_ADR


title: NMR_NF_3439_KID

value: 3.1 years


title: NMR_NF_3605_ADR


title: NMR_NF_4060_KID

value: 3.9 years


title: NMR_NF_3605_KID

value: kidney


title: NMR_NM_3295_ADR

value: 4.1 years


title: NMR_NF_3439_ADR


title: NMR_BF_1816_THY

source_name: thyroid

value: thyroid

value: 3.6 years


title: NMR_NM_6206_ADR

value: male

value: non-breeder


title: NMR_NF_2411_ADR

value: 4 years


title: NMR_NF_2411_KID


title: NMR_NM_3295_KID


title: NMR_NF_2969_KID


title: NMR_NF_2969_ADR

value: adrenal gland


title: NMR_BM_3274_ADR


title: NMR_BF_1816_ADR


title: NMR_BM_3274_KID


title: NMR_BF_4772_KID


title: NMR_NM_1449_ADR

value: 2.7 years


title: NMR_BM_1400_ADR


title: NMR_NM_1449_KID


title: NMR_NF_4060_ADR


title: NMR_BM_1400_KID


title: NMR_BM_1147_ADR


title: NMR_BM_1215_ADR

value: 3.4 years


title: NMR_BM_1215_KID


title: NMR_BM_1147_KID


title: NMR_BF_1090_KID


title: NMR_NM_0713_KID


title: GP_NM_28_THY

data_processing:
Extraction of read information in FastQ format was done using the tool bcl2astq v1.8.4 (provided by Illumina).
Reads were mapped using STAR (v2.4.1d) with a maximum mismatch of 6% and a minimum aligned length of 90%. Reads mapped to multiple loci were discarded.
Reads per gene were counted using HTSeq framework (0.6.1p1)
Genome_build: genome (cavpor3) can be download from UCSC (ftp://hgdownload.cse.ucsc.edu/goldenPath/cavPor3/bigZips/)
Supplementary_files_format_and_content: The Excel sheet includes raw counts for all genes and each sample.

organism: Cavia porcellus

value: 0.95 years


title: GP_NM_29_THY

value: 0.96 years


title: GP_NM_23_THY


title: GP_NM_30_THY


title: NMR_NF_0525_KID

value: 2.4 years


title: GP_NM_19_THY

value: 0.74 years


title: NMR_BF_1816_KID

value: female

value: breeder


title: GP_BM_24_THY


title: GP_BM_25_THY


title: NMR_NF_0525_ADR


title: GP_NM_18_THY


title: GP_BM_22_THY


title: GP_BM_20_THY


title: NMR_NM_0713_ADR


title: GP_BM_16_THY

value: 0.97 years


title: GP_BM_21_THY


title: GP_BF_15_THY


title: GP_NF_03_THY


title: GP_NF_08_THY


title: GP_NF_11_THY


title: GP_NF_09_THY


title: NMR_BF_1090_ADR

value: 3.7 years


title: GP_NF_06_THY


title: GP_NF_13_THY


title: GP_BF_05_THY


title: GP_BF_01_THY


title: GP_BF_14_THY


title: GP_NM_29_TES

value: testis


title: GP_NM_28_TES


title: DLD1-siY14-10-exp3-rep2

city: Montpellier

first: Peggy

last: Raynaud

address: 1919 Route de Mende

institute: CRBM

description:
DESeq_table_28-06-17.txt
SOX9_Y14_MATS_output3_results.xlsx

data_processing:
Low quality sequencing reads were trimmed and sequencing adaptor removed with fastq-mcf (Parameters: -D 100 -l 50 for siSOX9-RNAseq experiments and -l 125 for siY14 RNAseq experiments)
High quality sequencing reads were then aligned with tophat2 (bowtie1) and Hisat2 for siSOX9 reads and siY14 reads, respectively
BAM files produced by the aligners were sorted with samtools sort
Differential alternative splicing events were quantified with rMATS (parameters: -t single -len 100 for siSOX9 or -len 125 for siY14).
read counting in gene transcripts were performed with htseq-count
Differential expression analyses were then performed with DESeq
Genome_build: hg19
Supplementary_files_format_and_content: DESeq_table_14-01-14.txt file is tab-delimited text file indicating the differential gene expression analysis (Deseq) between ctrl samples and samples with SOX9 knockdown (Ctrl vs siSOX9)
Supplementary_files_format_and_content: DESeq_table_28-06-17.txt file is tab-delimited text file indicating the differential gene expression analysis (Deseq) between ctrl samples and samples with Y14 knockdown (Ctrl vs siY14)
Supplementary_files_format_and_content: SOX9_Y14_MATS_output3_results.xlsx in en excel files regrouping MATS output for differential splicing analysis of control versus siSOX9 samples and control versus siY14 samples

source_name: DLD-1 colon tumour cell line

growth_protocol: DLD-1 colon tumour cells were maintained in DMEM Glutamax (ThermoFisher Scientific) and supplemented with penicillin/streptomycin (Thermo Fisher Scientific) and 10% FCS (EUROBIO) at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Total RNA extraction was performed using RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions after homogenisation of each samples with a QIAshredder column (Qiagen). A DNase step was additionally performed during RNA isolation as described by the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols.The standard protocol consists of transcripts purification by polyA-tail selection, followed by library construction using illumina TruSeq Stranded mRNA Library Prep kit.

treatment_protocol: For siRNA knockdown, DLD-1 cells were plated in 6 wells plate 24h before transfection and transfected with 50nM of siRNA using INTERFERin® (Polyplus Transfections) according to the manufacturer protocol. Cells were then harvested 72h after transfection for RNA isolation.

tag: cell line

tag: tumour type

value: Dukes' type C, colorectal adenocarcinoma

value: transfection with siRNA against Y14 (siRNA No10)


title: DLD1-siY14-10-exp3-rep1


title: DLD1-siY14-9-exp3-rep1

value: transfection with siRNA against Y14 (siRNA No9)


title: GP_NM_23_TES

value: male

value: non-breeder


title: GP_NM_18_TES


title: GP_NM_19_TES


title: DLD1-siCtrl-exp3-rep1

tag: tranfection

value: siRNAcontrol


title: DLD1-siCtrl-exp3-rep2


title: GP_BM_25_TES


title: DLD1-siSOX9-exp2

description:
DESeq_table_14-01-14.txt
SOX9_Y14_MATS_output3_results.xlsx

value: transfection with siRNA against SOX9


title: GP_BM_24_TES


title: DLD1-siSOX9-exp1-rep3


title: DLD1-siCtrl-exp2


title: GP_BF_02_THY

value: thyroid


title: DLD1-siSOX9-exp1-rep2


title: GP_BM_22_TES


title: GP_NM_30_TES


title: GP_BM_16_TES


title: DLD1-siCtrl-exp1-rep2


title: GP_BM_21_TES


title: WT_Amputated_9hr-3

city: Kansas City

first: Hua

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

description:
MOLNG-373
time.course.fpkm.xlsx

data_processing:
RNAseq reads were aligned to the Schmidtea mediterranea transcriptome smed_20140614 defined in GEO submission GSE72389 using Bowtie2 v2.2.9 default parameters.
Counts were the sum of reads of each transcript. FPKM values were generated using the rpkm function from R package ‘edgeR’.
Genome_build: Schmidtea_mediterranea_3.1
Supplementary_files_format_and_content: FPKM in excel file

organism: Schmidtea mediterranea

source_name: Whole animals

growth_protocol: Asexual S. mediterranea (strain CIW4) and sexual S2F8 animals were maintained at 20 °C as previously described (Newmark and Sanchez Alvarado, 2000). For all experiments, animals were starved for at least 7 days.

extract_protocol:
For untreated and 1-day irradiated animals, total RNA was purified using Trizol as described (Zeng et al., 2013). For sorted X1, X2 and Xins populations based on Hoechst staining, 1x105 cells were sorted into 800 μl Trizol LS, and RNA was extracted according to the manufacturer’s manual. RNA from whole worms was treated with RNase-free DNase on QIAGEN RNAeasy columns and was eluted in nuclease-free water (Ambion). For each replicate, 500ng-1μg RNA from five worms or 100 ng RNA from 1x105 sorted cells were used to generate RNA-Seq libraries using the Illumina TruSeq Stranded kit. For RNA extraction from fixed cells, total RNA was isolated from the pellet using the RecoverAll Total Nucleic Acid Isolation kit (Ambion), starting at the protease digestion stage of manufacturer-recommended protocol. The following modification to the isolation procedure was made: instead of incubating cells in digestion buffer for 15 minutes at 50°C and 15 minutes at 80°C, we carried out the incubation for 1 hours at 50°C. Cell lysates were frozen at −80°C overnight before continuing the RNA isolation by the manufacturer's instructions.
For each replicate, 500ng-1μg RNA per whole worm sample or 100ng of sorted cell RNA was used for generation of RNAseq libraries using the Illumina TruSeq kit. cDNA quality was determined by Agilent high sensitivity DNA kit on Agilent 2100 BioAnalyzer (Agilent Technologies).

treatment_protocol: 1) For RNA-seq of lethal -irradiated animals, GammaCell 40 Exactor irradiator exposed animals to 10,000 rads. 2) For ampuated aniamals, small fragments from one side of planarian were amputated, and whole small regenerating fragments were collected from each time point.

tag: genotype

value: Wild-type

value: Whole animals

tag: treatment


title: DLD1-siSOX9-exp1-rep1

value: siRNA against SOX9


title: WT_Amputated_9hr-5

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_9hr-1

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_BM_20_TES

value: 0.74 years


title: DLD1-siCtrl-exp1-rep1


title: WT_Amputated_9hr-4

description:
MOLNG-373
time.course.fpkm.xlsx


title: DLD1-siY14-9-exp3-rep2


title: GP_NM_30_SKN

source_name: skin

value: skin

value: 0.96 years


title: WT_Amputated_7day-5

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_7day-4

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_NM_29_SKN


title: WT_Amputated_7day-1

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_72hr-5

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_NM_28_SKN

value: 0.95 years


title: GP_NM_23_SKN


title: WT_Amputated_72hr-2

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_72hr-3

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_72hr-1

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_NM_19_SKN


title: WT_Amputated_6hr-1

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_6hr-4

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_NM_18_SKN


title: WT_Amputated_6hr-6

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_6hr-5

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_6day-1

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_60hr-6

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_60hr-2

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_60hr-3

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_6day-2

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_BM_24_SKN

value: breeder


title: GP_BM_22_SKN


title: GP_BM_21_SKN


title: GP_BM_25_SKN


title: GP_BM_20_SKN


title: WT_Amputated_5day-6

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_5day-3

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_5day-2

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_6day-6

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_BM_16_SKN

value: 0.97 years


title: WT_Amputated_5day-1

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_4day-5

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_NF_13_SKN

value: female


title: WT_Amputated_4day-4

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_7day-3

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_4day-6

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_6day-3

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_NF_09_SKN


title: WT_Amputated_4day-3

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_48hr-5

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_NF_08_SKN


title: WT_Amputated_48hr-2

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_48hr-4

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_3hr-6

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_NF_11_SKN


title: GP_NF_03_SKN


title: WT_Amputated_3hr-5

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_3hr-2

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_36hr-6

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_BF_14_SKN


title: WT_Amputated_36hr-4

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_36hr-3

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_24hr-6

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_BF_12_SKN


title: WT_Amputated_24hr-4

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_BF_05_SKN


title: WT_Amputated_24hr-3

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_BF_02_SKN


title: WT_Amputated_24hr-1

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_1hr-6

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_1hr-4

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_48hr-1

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_1hr-3

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_BF_01_SKN


title: WT_Amputated_14day-6

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_1hr-1

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_NM_30_PIT

source_name: pituitary

value: pituitary


title: GP_BF_15_SKN


title: WT_Amputated_3hr-1

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_NF_06_SKN


title: WT_Amputated_14day-3

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_NM_29_PIT


title: WT_Amputated_12hr-5

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_36hr-2

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_14day-1

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_NM_28_PIT


title: WT_Amputated_12hr-6

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_NM_23_PIT


title: WT_Amputated_12hr-1

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_12hr-4

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_10day-5

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_NM_18_PIT


title: WT_Amputated_10day-1

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_0hr-4

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_10day-2

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_10day-3

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_0hr-3

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_BM_25_PIT


title: WT_Amputated_0hr-1

description:
MOLNG-373
time.course.fpkm.xlsx


title: WT_Amputated_0hr-2

description:
MOLNG-373
time.course.fpkm.xlsx


title: GP_BM_21_PIT


title: GP_BM_22_PIT


title: WT_Amputated_14day-4

description:
MOLNG-373
time.course.fpkm.xlsx


title: Replicate4_PIWI-1_low

description:
MOLNG-1555
piwi.sorted.fpkm.xlsx

source_name: Sorted PIWI-1 low cells

value: Sorted PIWI-1 low cells


title: Replicate4_PIWI-1_high

description:
MOLNG-1555
piwi.sorted.fpkm.xlsx

source_name: Sorted PIWI-1 high cells

value: Sorted PIWI-1 high cells


title: GP_NM_19_PIT

value: male

value: non-breeder


title: Replicate3_PIWI-1_high

description:
MOLNG-1555
piwi.sorted.fpkm.xlsx


title: GP_BM_16_PIT


title: Replicate3_PIWI-1_low

description:
MOLNG-1555
piwi.sorted.fpkm.xlsx


title: Replicate3_PIWI-1_neg

description:
MOLNG-1555
piwi.sorted.fpkm.xlsx

source_name: Sorted PIWI-1 negative cells

value: Sorted PIWI-1 negative cells


title: Replicate2_PIWI-1_low

description:
MOLNG-1555
piwi.sorted.fpkm.xlsx


title: Replicate2_PIWI-1_neg

description:
MOLNG-1555
piwi.sorted.fpkm.xlsx


title: GP_NF_11_PIT


title: GP_NF_13_PIT


title: GP_NF_09_PIT


title: GP_BM_24_PIT


title: GP_NF_08_PIT


title: Replicate1_PIWI-1_low

description:
MOLNG-1555
piwi.sorted.fpkm.xlsx


title: 10k24h_Rep_3

description:
MOLNG-1069
x1.sorted.fpkm.xlsx

value: 24hours after 10K irradiation


title: 10k24h_Rep_1

description:
MOLNG-1069
x1.sorted.fpkm.xlsx

value: Wild-type


title: Replicate4_PIWI-1_Neg

description:
MOLNG-1555
piwi.sorted.fpkm.xlsx


title: GP_NF_06_PIT


title: unc_totalRNA

description:
MOLNG-1555
piwi.sorted.fpkm.xlsx

value: Whole animals


title: Xins_Rep_3

description:
MOLNG-1069
x1.sorted.fpkm.xlsx

source_name: Sorted Xins cells

value: Sorted Xins cells


title: 10k24h_Rep_2

description:
MOLNG-1069
x1.sorted.fpkm.xlsx


title: GP_NF_03_PIT


title: Xins_Rep_1

description:
MOLNG-1069
x1.sorted.fpkm.xlsx


title: x2_Rep_2

description:
MOLNG-1069
x1.sorted.fpkm.xlsx

source_name: Sorted X2 cells

value: Sorted X2 cells


title: x2_Rep_3

description:
MOLNG-1069
x1.sorted.fpkm.xlsx


title: Replicate2_PIWI-1_high

description:
MOLNG-1555
piwi.sorted.fpkm.xlsx


title: Xins_Rep_2

description:
MOLNG-1069
x1.sorted.fpkm.xlsx


title: GP_BF_14_PIT


title: GP_BF_05_PIT


title: WT_Amputated_60hr-1

description:
MOLNG-373
time.course.fpkm.xlsx


title: X1_Rep_1

description:
MOLNG-1069
x1.sorted.fpkm.xlsx

source_name: Sorted X1 cells

value: Sorted X1 cells


title: X1_Rep_2

description:
MOLNG-1069
x1.sorted.fpkm.xlsx


title: Replicate1_PIWI-1_high

description:
MOLNG-1555
piwi.sorted.fpkm.xlsx


title: x2_Rep_1

description:
MOLNG-1069
x1.sorted.fpkm.xlsx


title: Replicate1_PIWI-1_Neg

description:
MOLNG-1555
piwi.sorted.fpkm.xlsx


title: GP_BF_02_PIT


title: GP_BF_01_PIT


title: WT_Rep_3

description:
MOLNG-1069
x1.sorted.fpkm.xlsx


title: GP_BF_12_PIT

value: 0.96 years


title: WT_Rep_1

description:
MOLNG-1069
x1.sorted.fpkm.xlsx


title: Mantis_X1-cell-27

description:
L24088
Mantis_read_counts.xlsx

data_processing:
for sample 1 to sample 160: Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
for sample 1 to sample 160: RNA-seq was aligned to smed transcriptome smed_20140614 defined in GEO submission GSE72389 using Bowtie 2 version 2.2.9
for sample 1 to sample 160: Read counts for each transcripts are generated using samtools idxstats (version 1.3.1)
for sample 161 to sample 162: Cell Range pipleine (v1.3), mkfastq and count, was used to generate fastq files, perform alignments, filter and generate UMI counts.
Genome_build: Schmidtea mediterranea transcriptome is available from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72389
Supplementary_files_format_and_content: for sample 1 to sample 160: Read counts in excel files
Supplementary_files_format_and_content: for sample 161 to sample 162: Normalized expression values in csv files

extract_protocol:
For plate based single cell RNA-seq assay, cells were harvested into 96-well plate directly, and cDNA libraries were prepared using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) as per manufacturer’s recommendations using 18 cycles of amplification.  Specifically, reactions were run at  the recommended volume.  Libraries were made using the Nextera XT kit (Illumina). After the PCR step, the libraries were individually cleaned with 0.8x AMPure XP SPRI beads (Beckman Coulter), and eluted in Resuspension Buffer. The libraries were quantified using Quant-IT DNA High-Sensitivity Assay Kit (Invitrogen) and examined using a high sensitivity DNA chip (Agilent). All libraries were then combined to one pool at equimolar concentrations for sequencing.  Finally, samples were sequenced deeply using a HiSeq 2500 sequencer.
cDNA libraries were prepared using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) as per manufacturer’s recommendations using 18 cycles of amplification.

treatment_protocol: 1) For regenerating sample, animals were amputated to produce pre-pharyngeal pieces; 2) GammaCell 40 Exactor irradiator exposed animals to 1,250  rad for sublethal irradiations.

value: 3days after amputation from small fragments


title: Mantis_X1-cell-29

description:
L24090
Mantis_read_counts.xlsx


title: GP_NF_13_OVR

source_name: ovary

value: ovary


title: Mantis_X1-cell-25

description:
L24086
Mantis_read_counts.xlsx


title: GP_NF_11_OVR

value: 0.95 years


title: Mantis_X1-cell-26

description:
L24087
Mantis_read_counts.xlsx


title: Mantis_X1-cell-32

description:
L24093
Mantis_read_counts.xlsx


title: Mantis_X1-cell-30

description:
L24091
Mantis_read_counts.xlsx


title: GP_NF_08_OVR

value: female


title: X1_Rep_3

description:
MOLNG-1069
x1.sorted.fpkm.xlsx


title: Mantis_X1-cell-28

description:
L24089
Mantis_read_counts.xlsx


title: Mantis_X1-cell-3

description:
L24064
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-6

description:
L24117
Mantis_read_counts.xlsx


title: GP_BF_15_PIT

value: pituitary

value: breeder


title: Mantis_X1-cell-1

description:
L24062
Mantis_read_counts.xlsx


title: GP_BF_15_OVR


title: Mantis_X1-cell-5

description:
L24066
Mantis_read_counts.xlsx


title: Mantis_X1-cell-2

description:
L24063
Mantis_read_counts.xlsx


title: GP_NF_06_OVR


title: X1_cells_10x

description:
L28489
X1_cells_10x_exprs.csv

value: wild-type


title: Mantis_X1-cell-4

description:
L24065
Mantis_read_counts.xlsx


title: GP_NF_03_OVR

value: 0.97 years


title: Mantis_X1-cell-7

description:
L24068
Mantis_read_counts.xlsx


title: Sublethal_cells_10x

description:
L28490
Sublethal_cells_10x_exprs.csv

source_name: Sorted (X1+X2) cells

value: Sorted (X1+X2) cells

value: 7days after 1250R irradiation treatment


title: Mantis_X1-cell-6

description:
L24067
Mantis_read_counts.xlsx


title: GP_BF_14_OVR


title: GP_BF_12_OVR


title: Mantis_X1-cell-37

description:
L24098
Mantis_read_counts.xlsx


title: Mantis_X1-cell-31

description:
L24092
Mantis_read_counts.xlsx


title: GP_NF_09_OVR

value: non-breeder


title: Mantis_X1-cell-33

description:
L24094
Mantis_read_counts.xlsx

value: Wild-type


title: GP_BF_05_OVR


title: WT_Rep_2

description:
MOLNG-1069
x1.sorted.fpkm.xlsx

value: Whole animals


title: GP_BF_02_OVR


title: Mantis_X1-cell-35

description:
L24096
Mantis_read_counts.xlsx


title: Mantis_X1-cell-38

description:
L24099
Mantis_read_counts.xlsx


title: Mantis_X1-cell-36

description:
L24097
Mantis_read_counts.xlsx


title: Mantis_X1-cell-39

description:
L24100
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-19

description:
L24130
Mantis_read_counts.xlsx


title: GP_NM_30_LVR

source_name: liver

value: male

value: liver


title: Mantis_X1-cell-40

description:
L24101
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-21

description:
L24132
Mantis_read_counts.xlsx


title: GP_NM_29_LVR


title: Mantis_Xins-cell-24

description:
L24135
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-20

description:
L24131
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-18

description:
L24129
Mantis_read_counts.xlsx


title: GP_NM_28_LVR


title: Mantis_Xins-cell-22

description:
L24133
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-23

description:
L24134
Mantis_read_counts.xlsx


title: GP_NM_23_LVR


title: Mantis_Xins-cell-1

description:
L24112
Mantis_read_counts.xlsx


title: GP_NM_19_LVR

value: 0.74 years


title: Mantis_X1-cell-34

description:
L24095
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-4

description:
L24115
Mantis_read_counts.xlsx


title: GP_BM_25_LVR


title: Mantis_Xins-cell-2

description:
L24113
Mantis_read_counts.xlsx


title: Mantis_X1-cell-11

description:
L24072
Mantis_read_counts.xlsx


title: GP_NM_18_LVR


title: Mantis_Xins-cell-3

description:
L24114
Mantis_read_counts.xlsx


title: GP_BM_24_LVR

value: 0.96 years


title: Mantis_X1-cell-13

description:
L24074
Mantis_read_counts.xlsx

value: 3days after amputation from small fragments


title: Mantis_Xins-cell-17

description:
L24128
Mantis_read_counts.xlsx


title: Mantis_X1-cell-10

description:
L24071
Mantis_read_counts.xlsx


title: GP_BM_21_LVR


title: Mantis_X1-cell-16

description:
L24077
Mantis_read_counts.xlsx


title: Mantis_X1-cell-14

description:
L24075
Mantis_read_counts.xlsx


title: Mantis_X1-cell-9

description:
L24070
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-25

description:
L24136
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-27

description:
L24138
Mantis_read_counts.xlsx


title: GP_BM_20_LVR


title: Mantis_X1-cell-15

description:
L24076
Mantis_read_counts.xlsx


title: GP_BM_22_LVR


title: Mantis_X1-cell-12

description:
L24073
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-29

description:
L24140
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-5

description:
L24116
Mantis_read_counts.xlsx


title: GP_NF_11_LVR


title: Mantis_Xins-cell-26

description:
L24137
Mantis_read_counts.xlsx


title: GP_BM_16_LVR


title: Mantis_Xins-cell-31

description:
L24142
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-30

description:
L24141
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-28

description:
L24139
Mantis_read_counts.xlsx


title: GP_NF_13_LVR


title: GP_BF_01_OVR

value: ovary


title: GP_NF_09_LVR


title: GP_NF_08_LVR

value: 0.95 years


title: GP_NF_06_LVR

value: female


title: Mantis_Xins-cell-8

description:
L24119
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-9

description:
L24120
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-32

description:
L24143
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-11

description:
L24122
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-13

description:
L24124
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-16

description:
L24127
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-10

description:
L24121
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-12

description:
L24123
Mantis_read_counts.xlsx


title: Mantis_X1-cell-19

description:
L24080
Mantis_read_counts.xlsx


title: GP_BF_15_LVR


title: GP_NF_03_LVR


title: Mantis_X1-cell-24

description:
L24085
Mantis_read_counts.xlsx


title: Mantis_X1-cell-21

description:
L24082
Mantis_read_counts.xlsx


title: Mantis_X1-cell-18

description:
L24079
Mantis_read_counts.xlsx


title: GP_BF_05_LVR


title: Mantis_X1-cell-22

description:
L24083
Mantis_read_counts.xlsx


title: GP_BF_14_LVR


title: GP_NM_30_KID

source_name: kidney

value: kidney


title: GP_BF_12_LVR

value: breeder


title: Mantis_X1-cell-23

description:
L24084
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-35

description:
L24146
Mantis_read_counts.xlsx


title: GP_BF_02_LVR


title: Mantis_Xins-cell-7

description:
L24118
Mantis_read_counts.xlsx


title: Mantis_X1-cell-17

description:
L24078
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-33

description:
L24144
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-40

description:
L24151
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-37

description:
L24148
Mantis_read_counts.xlsx


title: GP_NM_28_KID


title: Mantis_Xins-cell-14

description:
L24125
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-36

description:
L24147
Mantis_read_counts.xlsx


title: GP_NM_29_KID


title: Mantis_Xins-cell-38

description:
L24149
Mantis_read_counts.xlsx


title: Mantis_Xins-cell-15

description:
L24126
Mantis_read_counts.xlsx


title: Mantis_X1-cell-8

description:
L24069
Mantis_read_counts.xlsx


title: GP_NM_23_KID


title: Mantis_Xins-cell-39

description:
L24150
Mantis_read_counts.xlsx


title: GP_BF_01_LVR


title: GP_NM_19_KID


title: ClonTechv4_X1-cell-29

description:
L23726
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-25

description:
L23722
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-27

description:
L23724
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-26

description:
L23723
ClonTechv4_read_counts.xlsx


title: GP_NM_18_KID


title: GP_BM_25_KID


title: ClonTechv4_X1-cell-28

description:
L23725
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-32

description:
L23729
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-30

description:
L23727
ClonTechv4_read_counts.xlsx


title: Mantis_Xins-cell-34

description:
L24145
Mantis_read_counts.xlsx


title: GP_BM_24_KID


title: GP_BM_22_KID


title: ClonTechv4_X1-cell-1

description:
L23698
ClonTechv4_read_counts.xlsx


title: GP_BM_21_KID


title: ClonTechv4_X1-cell-2

description:
L23699
ClonTechv4_read_counts.xlsx


title: GP_BM_20_KID


title: ClonTechv4_X1-cell-3

description:
L23700
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-6

description:
L23703
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-7

description:
L23704
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-31

description:
L23728
ClonTechv4_read_counts.xlsx


title: GP_BM_16_KID


title: ClonTechv4_X1-cell-35

description:
L23732
ClonTechv4_read_counts.xlsx


title: GP_NF_13_KID


title: ClonTechv4_X1-cell-37

description:
L23734
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-33

description:
L23730
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-38

description:
L23735
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-40

description:
L23737
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-34

description:
L23731
ClonTechv4_read_counts.xlsx


title: GP_NF_09_KID


title: GP_NF_08_KID


title: GP_NF_11_KID


title: ClonTechv4_X1-cell-4

description:
L23701
ClonTechv4_read_counts.xlsx


title: Mantis_X1-cell-20

description:
L24081
Mantis_read_counts.xlsx


title: GP_NF_06_KID


title: ClonTechv4_Xins-cell-21

description:
L23768
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-17

description:
L23764
ClonTechv4_read_counts.xlsx


title: GP_NF_03_KID


title: ClonTechv4_X1-cell-39

description:
L23736
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-18

description:
L23765
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-19

description:
L23766
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-24

description:
L23771
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-20

description:
L23767
ClonTechv4_read_counts.xlsx


title: GP_BF_14_KID


title: GP_BF_15_KID


title: ClonTechv4_Xins-cell-22

description:
L23769
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-2

description:
L23749
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-23

description:
L23770
ClonTechv4_read_counts.xlsx


title: GP_BF_12_KID


title: ClonTechv4_X1-cell-36

description:
L23733
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-5

description:
L23752
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-1

description:
L23748
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-4

description:
L23751
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-3

description:
L23750
ClonTechv4_read_counts.xlsx


title: GP_BF_05_KID


title: GP_BF_02_KID


title: ClonTechv4_X1-cell-11

description:
L23708
ClonTechv4_read_counts.xlsx


title: GP_BF_01_KID


title: GP_NM_30_HYP

source_name: hypothalamus

value: hypothalamus


title: GP_NM_29_HYP


title: GP_NM_28_HYP


title: ClonTechv4_X1-cell-12

description:
L23709
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-6

description:
L23753
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-16

description:
L23713
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-9

description:
L23706
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-27

description:
L23774
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-26

description:
L23773
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-10

description:
L23707
ClonTechv4_read_counts.xlsx


title: GP_NM_19_HYP


title: ClonTechv4_Xins-cell-25

description:
L23772
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-28

description:
L23775
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-32

description:
L23779
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-29

description:
L23776
ClonTechv4_read_counts.xlsx


title: GP_NM_23_HYP


title: GP_NM_18_HYP


title: ClonTechv4_Xins-cell-30

description:
L23777
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-13

description:
L23710
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-31

description:
L23778
ClonTechv4_read_counts.xlsx


title: GP_BM_25_HYP


title: ClonTechv4_Xins-cell-11

description:
L23758
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-8

description:
L23755
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-14

description:
L23711
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-9

description:
L23756
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-15

description:
L23712
ClonTechv4_read_counts.xlsx


title: GP_BM_24_HYP


title: ClonTechv4_Xins-cell-13

description:
L23760
ClonTechv4_read_counts.xlsx


title: GP_BM_22_HYP


title: GP_BM_21_HYP


title: ClonTechv4_Xins-cell-10

description:
L23757
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-15

description:
L23762
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-12

description:
L23759
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-14

description:
L23761
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-16

description:
L23763
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-19

description:
L23716
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-21

description:
L23718
ClonTechv4_read_counts.xlsx


title: GP_BM_20_HYP


title: ClonTechv4_X1-cell-17

description:
L23714
ClonTechv4_read_counts.xlsx


title: GP_NF_13_HYP

value: 0.97 years


title: GP_NF_11_HYP


title: ClonTechv4_X1-cell-24

description:
L23721
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-22

description:
L23719
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-20

description:
L23717
ClonTechv4_read_counts.xlsx


title: GP_BM_16_HYP


title: ClonTechv4_X1-cell-23

description:
L23720
ClonTechv4_read_counts.xlsx


title: GP_NF_09_HYP


title: ClonTechv4_X1-cell-8

description:
L23705
ClonTechv4_read_counts.xlsx