title: pRB+ AZD1152 rep 1

source_name: NCI-H82 cells

tag: cell line

value: NCI-H82 cells

value: Small cell lung cancer cells

value: YES (pRB+)

value: YES


title: Brain_4

status: Public on Sep 28 2018

type: SRA

city: Stanford

first: Alina

last: Isakova

state: CA

address: 318 Campus drive

department: Bioengineering

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
Illumina BaseSpace software used for demultiplexing
Sequenced reads were trimmed for adaptor sequence, and mapped to mm10 whole genome using STAR v2.5.1 (Dobin et al., 2013) with the following parameters --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0 --alignIntronMax 1 --outMultimapperOrder Random --clip3pAdapterSeq TGGAATTCTC --clip3pAdapterMMp 0.1
Transcript counts were calculated using a FeatureCounts, featureCounts -a Mus_musculus.GRCm38.90.gtf -M –primary -s 0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts Sample

molecule: total RNA

organism: Mus musculus

source_name: Brain_Small non-coding RNA

extract_protocol:
Upon collection, tissue samples were submerged and preserved at -80C in RNAlater stabilization solution (ThermoFisher cat # AM7021) until further processing. Total RNA was isolated from ~ 100 mg of tissue using Qiagen miRNeasy mini kit (cat # 217004) and the Qiagen tissue lyser using 5 mm stainless steel beads. RNA integrity was assesses using Agilent Bioanalyzer using RNA 6000 pico kit (Agilent Technologies cat # 5067-1513). Short RNA libraries were prepared following the Illumina TruSeq Small RNA Library Preparation kit (cat # RS-200-0012, RS-200-0024, RS-200-0036, RS-200-0048) according to the manufacturer’s protocol and size-selected using Pippin Prep 3% Agarose Gel Cassette (Safe Science) in a range 135 bp – 210 bp. Samples were pooled in batches of 48 and sequenced using the Illumina Illumina NextSeq 500 instrument in a single-read, 75-base mode.
Short RNA libraries were prepared following the Illumina TruSeq Small RNA Library Preparation kit (cat # RS-200-0012, RS-200-0024, RS-200-0036, RS-200-0048) according to the manufacturer’s protocol and size-selected using Pippin Prep 3% Agarose Gel Cassette (Safe Science) in a range 135 bp – 210 bp. Samples were pooled in batches of 48 and sequenced using the Illumina Illumina NextSeq 500 instrument in a single-read, 75 -base mode.

tag: strain

tag: genotype

value: WT

tag: age

value: adult, 3 months old

tag: tissue

value: Brain

tag: molecule subtype

value: sRNA


title: Brain_5


title: Brain_2


title: DONOR 1_TSLP 6H

type: RNA

city: Paris

first: Lucia

last: Pattarini

address: 26 rue D' Ulm

country: France

institute: Institut Curie

description: CD40 3

hyb_protocol: After fragmentation, 20 ug of cRNA were hybridized on a U133 plus 2.0 gene  for 16 hours

scan_protocol: Gene ship were analyzed using the GCS3000 from Affyemtrix

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

organism: Homo sapiens

source_name: DC_20 hrs in control medium plus TSLP, washed, and cultured for 6 hrs in new medium

label_protocol: 50 ng of total RNA were amplified using Affymetrix double amplification protocol

growth_protocol: Human primary dendritic cells were facs sorted (CD3, CD14, CD16, CD19)-, CD11c+, CD4+ and cultured at 1x10^6 cells/ml  in RPMI medium plus 10%FBS, 1% pen strep

extract_protocol: Total mRNA was extracted using the Quiagen RNAeasy micro kit #74004 according to manufacturer protocol

treatment_protocol: rhTSLP 50 ng/ml, LPS 1 ug/ml, rhCD40L 1 mg/ml

tag: donor

value: DONOR 1

tag: cell type

value: primary blood Dendritic cells

tag: pre-treated in

value: control medium plus TSLP for 20hrs

tag: treated

value: for 6 hours in new medium


title: DONOR 1_MED 12H

description: CD40 7

source_name: DC_20 hrs in control medium, washed, and cultured for 12 hrs in new medium

value: control medium for 20hrs

value: for 12 hours in new medium


title: DONOR 1_MED 6H

description: CD40 1

source_name: DC_20 hrs in control medium, washed, and cultured for 6 hrs in new medium


title: Brain_3


title: DONOR 1_MED 6H CD40L

description: CD40 2

source_name: DC_20 hrs in control medium, washed, and cultured for 6 hrs with rCD40L

value: for 6 hours with rCD40L


title: Brain_1


title: Brain_14


title: Brain_13


title: Endo IFNg+ aA

city: Nagoya

first: Kenta

last: IWASAKI

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Transplant Immunology

country: Japan

institute: Nagoya University School of Medicine

description: Gene expression data from  endothelial cells

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: We employed ClariomTM S Assay based on affimatrix (Filgen Inc., Nagoya, Japan).

source_name: Endothelial cell  expressed blood antigen A in the presence of IFNɤ

label_protocol: Affymetrix

growth_protocol: Blood group A or B antigen-expressing EA.hy926 cells (HLA-A; *24:02, *25:01, HLA-B; *15:01, *18:01, HLA-Cw; *03:03, *12:03, HLA-DRB1; *11:02, *13:42, HLA-DQB1; n/d, HLA-DPB1; n/d), the human endothelial-like immortalized cell line derived from the fusion of human umbilical vein endothelial cells (HUVEC) with the lung carcinoma cell line A549, were maintained in DMEM supplemented with 10% FBS (Hyclone, Logan, UT).

extract_protocol: Total RNA was purified from cultured cells using the Qiazol and miRNeasy mini kits (Qiagen).

treatment_protocol: EA.hy926/A cells were stimulated IFNγ in the presence or absence of anti-A antibody for 48hrs.


title: Endo IFNg- aA

source_name: Endothelial cell  expressed blood antigen A stimulated with anti-A antibody


title: Endo IFNg+ ctr

source_name: Endothelial cell  expressed blood antigen A stimulated with IFNɤ


title: Endo IFNg- ctr

source_name: Endothelial cell  expressed blood antigen A


title: Brain_11


title: Brain_12


title: Brain_10


title: Treated celiac patient_15

city: Leioa

first: Jose Ramon

last: Bilbao

state: Outside the US or Canada

address: Bº Sarriena

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

institute: University of the Basque Country (UPV/EHU)

data_processing:
Housekeeping gene TBP was simultaneously quantified and used as an endogenous control of input RNA (Life Technologies)
Relative expression in each sample was calculated using the accurate Ct method and normalized to the average expression value of the control samples
Fold Change worksheet reports Active CD/CONTROL and Treated CD/CONTROL ratios

label: Taqman Gene Expression assays

source_name: Duodenum

label_protocol:
RNA was normalized to 8 ng/ul and converted to cDNA using the AffinityScript cDNA Synthesis kit (Agilent Technologies) following manufacturer´s protocol
Specific Target Amplification (STA) was performed
Gene expression analyses were performed using Fluidigm Biomark 48.48 dynamic arrays and commercially available TaqMan Gene Expression assays

growth_protocol: Samples stored in liquid nitrogen untill RNA extraction

extract_protocol: NucleoSpin microRNA kit following manufacturer´s instructions for total RNA

tag: disease state

value: treated celiac disease

value: Inflamed mucosa


title: Active celiac patient_15

value: active celiac disease


title: Active celiac patient_16


title: Control patient_13

value: healthy

value: non-nflamed mucosa


title: Treated celiac patient_16


title: Bone_marrow_8

source_name: Bone_Small non-coding RNA

value: Bone


title: Control patient_15


title: Bone_marrow_9

value: WT


title: Treated celiac patient_14


title: Active celiac patient_14


title: Treated celiac patient_13


title: Active celiac patient_13


title: Control patient_14


title: Bone_marrow_6

value: adult, 3 months old


title: Control patient_12


title: Bone_marrow_7


title: Bone_marrow_4


title: Bone_marrow_5


title: Control patient_11


title: Treated celiac patient_11


title: Treated celiac patient_12


title: 285

city: Houston

first: Valerie

last: LeBleu

state: TX

address: 1881 East Road

institute: MDACC

description: Mouse 9

hyb_protocol: Samples were hybridized with Affymetrix MTA 1.0 Genechip

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed using the Limma package from R Bioconductor

label: Biotin

source_name: pancreas tumor

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent,Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Mice treated with gancyclovir (50 ug/kg) to deplete FAP+ or aSMA+ cells

value: PKT; aSMA-TK control (no depletion)

value: pancreas tumor


title: 250

description: Mouse 7


title: 296

description: Mouse 8


title: 803

description: Mouse 12

value: PKT; aSMA depleted


title: 462Z

description: Mouse 6

value: PKT; FAP depleted


title: Active celiac patient_12


title: E644

description: Mouse 5


title: W198

description: Mouse 4


title: 226

description: Mouse 10


title: MDA-MB-231 Cells TNFɑ+Apigenin Triplicate1

city: Tallahassee

first: Elizabeth

middle: A

last: Mazzio

state: Florida

address: 1515 MLK Blvd

department: College of Pharmacy & Pharmaceutical Science

institute: Florida Agricultural & Mechanical University

hyb_protocol: Hybrization was conducted according to manufacturer's instructions as per the GeneChipTM WT PLUS Reagent Manual for Whole Transcript (WT) Expression Arrays. (Affymetrix, ThermoFisher Scientific), using  GeneChip Human Gene 2.0 ST Array cartridges.

scan_protocol: Arrays were scanned with GeneAtlas Imaging station scanner  (Affymetrix, ThermoFisher Scientific)

data_processing:
The data was processed using Affymetrix expression console and evaluated by Affymetrix transcription console software (Affymetrix, ThermoFisher Scientific)
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: MDA-MB-231_TNFɑ 40 ng/ml + Apigenin 40 μM

label_protocol: cDNA was labeled using according to manufacturer's instructions as per the GeneChipTM WT PLUS Reagent Manual for Whole Transcript (WT) Expression Arrays. (Affymetrix, ThermoFisher Scientific).

growth_protocol: MDA-MB-231 cells were cultured in Dulbecco’s Modified Eagle’s Medium - high glucose with 4500 mg/L glucose, L-glutamine, sodium pyruvate, and sodium bicarbonate, supplemented with 10% FBS and 100 U/ml penicillin G sodium /100 μg/ml streptomycin sulfate. Cells were grown at 37°C with 95% air and 5% CO2 and sub-cultured every three to five days.

extract_protocol: After treatment, cells were washed three times in HBSS, rapidly frozen and stored at -80 C. Total RNA was isolated/ purified using the TRIzol/chloroform method, quality was assessed and concentration was equalized to 82ng/ul in nuclease free water

treatment_protocol: Cells were treated ± TNFɑ [40ng/mL] ± Apigenin [40uM] prepared in HBSS with a pH of 7.4 , both at sub-lethal concentrations.  For whole transcriptome microarray studies,  after a 24 hour treatment, cells were rapidly washed in HBSS 3x, spun and frozen at -80C.

value: MDA-MB-231 ATCC® HTB-26™

value: mammary gland/breast; derived from metastatic site:pleural effusion

tag: treatment

value: TNFɑ 40 ng/ml + Apigenin 40 μM


title: W44

description: Mouse 1

value: PKT; FAP-TK control (no depletion)


title: MDA-MB-231 Cells Apigenin Triplicate3

source_name: MDA-MB-231_apigenin 40 μM

value: apigenin 40 μM


title: 589

description: Mouse 11


title: Bone_marrow_3

value: sRNA


title: Bone_marrow_14


title: 354S

description: Mouse 3


title: Bone_marrow_2


title: Bone_marrow_13


title: Bone_marrow_1


title: Control patient_10


title: Heart_6

source_name: Heart_Small non-coding RNA

value: Heart


title: Control patient_9


title: Active celiac patient_11

value: active celiac disease

value: Inflamed mucosa


title: MDA-MB-231 Cells TNFɑ+Apigenin Triplicate2


title: MDA-MB-231 Cells TNFɑ+Apigenin Triplicate3


title: MDA-MB-231 Cells TNFɑ Triplicate3

source_name: MDA-MB-231_TNFɑ 40 ng/ml

value: TNFɑ 40 ng/ml


title: MDA-MB-231 Cells TNFɑ Triplicate2


title: MDA-MB-231 Cells Untreated Control Triplicate2

source_name: MDA-MB-231_No treatment

value: none (untreated control)


title: 941Y

description: Mouse 2


title: Treated celiac patient_10

value: treated celiac disease


title: MDA-MB-231 Cells Apigenin Triplicate1


title: MDA-MB-231 Cells Apigenin Triplicate2


title: Testis_13

source_name: Testis_Small non-coding RNA

value: WT

value: adult, 3 months old

value: Testis


title: MDA-MB-231 Cells Untreated Control Triplicate1


title: MDA-MB-231 Cells Untreated Control Triplicate3


title: MDA-MB-231 Cells TNFɑ Triplicate1


title: Bone_marrow_11

value: Bone


title: Testis_11


title: Spleen_9

source_name: Spleen_Small non-coding RNA

value: Spleen


title: Testis_12


title: Active celiac patient_10


title: Control patient_8

value: healthy

value: non-nflamed mucosa


title: Active celiac patient_9


title: Spleen_8


title: Spleen_7


title: Control patient_7


title: Treated celiac patient_8


title: Spleen_6


title: Treated celiac patient_9


title: Spleen_5


title: MDDC-cGAMP4-rep3

first: Nicolas

last: Manel

address: 12 rue Lhomond

department: INSERM U932

description: Gene expression data from cGAMP4 in NONO KO cells

hyb_protocol: Following fragmentation, 2,5 ug of cDNA were hybridized for 16 hr at 48°C onto Affymetrix Human Gene ST 1.1 array plate.  Array plate was hybridized,  washed and stained using an an Affymetrix Genetitan 4C device.

scan_protocol: Array plate was scannned using the Affymetrix Genetitan 4C device.

data_processing: Raw data were treated, normalized and summarized using oligo R package.

source_name: Dendritic cells

label_protocol: Biotinylated cDNA were prepared according to the Nugen WT Ovation protocol using 500pg as starting amount.

growth_protocol: CD14+ cells isolated from human blood followed by differentiation with IL-4 and GM-CSF for 4 days

extract_protocol: RNA was extracted with Machery-Nagel NucleoSpin RNA extraction kit

treatment_protocol: 100 000 cells were left untouched, infected with HIV-1 with Vpx, infected with HIV-2, or treated with cGAMP and lipofectamin, for 24 hours.

value: Dendritic cells

value: NONO-KO

value: cGAMP


title: MDDC-HIV2-rep6

description: Gene expression data from HIV2 infection in NONO KO cells


title: MDDC-cGAMP4-rep2

description: Gene expression data from cGAMP4 in WT cells


title: MDDC-NI-rep5

description: Gene expression data from non-infected controls in WT cells

value: control


title: MDDC-cGAMP4-rep1


title: MDDC-HIV2-rep4

description: Gene expression data from HIV2 infection in WT cells


title: MDDC-NI-rep6

description: Gene expression data from non-infected controls in NONO KO cells


title: MDDC-HIV1-Vpx-rep6

description: Gene expression data from HIV1-Vpx infection in NONO KO cells


title: MDDC-HIV1-Vpx-rep5

description: Gene expression data from HIV1-Vpx infection in WT cells


title: Spleen_4

value: sRNA


title: MDDC-NI-rep4


title: MDDC-HIV2-rep3


title: MDDC-HIV2-rep5


title: MDDC-HIV1-Vpx-rep3


title: MDDC-NI-rep3


title: MDDC-HIV1-Vpx-rep2


title: Spleen_3


title: MDDC-HIV2-rep2


title: Active celiac patient_7

value: active celiac disease


title: Control patient_6


title: Spleen_2


title: Treated celiac patient_7

value: Inflamed mucosa


title: Active celiac patient_8


title: Control patient_5


title: Other-WT-GFP-2

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

description: replicate 2-other-WT-GFP-group

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Mouse FAST DB v2016_1_full were also provide.

source_name: GFPnegative brain cells

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy micro kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser (Pico chips).
Full length double strand cDNA librairies were constructed with the Smarter Ultra Low Input RNA kit v4 (Takara-Clontech, Mountain View, CA) with 11 to 14 LD-PCR cycles. Libraries were normalized to 750 pg in 5µl as starting materiel to Nextera XT sample preparation kit (Illumina Incorporated, San Diego, CA). Ligation products were amplified with 12 PCR cycles.

tag: Sex

value: male

value: 9 month-old

value: brain


title: Other-WT-GFP-3

description: replicate 3-other-WT-GFP-group


title: Other-WT-GFP-1

description: replicate 1-other-WT-GFP-group


title: Treated celiac patient_6

value: treated celiac disease


title: MDDC-HIV1-Vpx-rep4

value: WT


title: Astro-APP-SOCS-5

description: replicate 5-astrocyte-APP-SOCS3-group

source_name: astrocyte


title: MDDC-NI-rep2


title: MDDC-HIV1-Vpx-rep1


title: MDDC-HIV2-rep1


title: Spleen_14

value: adult, 3 months old


title: MDDC-NI-rep1


title: Astro-APP-SOCS-4

description: replicate 4-astrocyte-APP-SOCS3-group


title: Astro-APP-SOCS-3

description: replicate 3-astrocyte-APP-SOCS3-group


title: Treated celiac patient_5


title: Spleen_13


title: Spleen_12


title: Astro-APP-SOCS-1

description: replicate 1-astrocyte-APP-SOCS3-group


title: Spleen_1


title: Spleen_11


title: Astro-APP-GFP-4

description: replicate 4-astrocyte-APP-GFP-group


title: Active celiac patient_6


title: Astro-APP-GFP-3

description: replicate 3-astrocyte-APP-GFP-group


title: Spleen_10


title: Astro-APP-GFP-2

description: replicate 2-astrocyte-APP-GFP-group


title: Control patient_4


title: Control patient_3


title: Astro-APP-SOCS-2

description: replicate 2-astrocyte-APP-SOCS3-group


title: Astro-APP-GFP-1

description: replicate 1-astrocyte-APP-GFP-group


title: Pancreas_9

source_name: Pancreas_Small non-coding RNA

value: Pancreas


title: Pancreas_8


title: Treated celiac patient_4


title: Astro-WT-GFP-7

description: replicate 7-astrocyte-WT-GFP-group


title: Astro-WT-GFP-6

description: replicate 6-astrocyte-WT-GFP-group


title: Pancreas_6


title: Active celiac patient_4


title: Treated celiac patient_3


title: day15

city: los angeles

first: Matteo

last: Pellegrini

address: 675 Charles E Young Drive S

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: reduced-representative bisulfite sequencing

library_source: genomic

data_processing:
RRBS data were aligned to human genome with BSSeeker2 software
Methylation call were also performed through BSSeeker2 software
Genome_build: hg19
Supplementary_files_format_and_content: Cgmap format; include the chromosome, location and methylation call for each C

molecule: genomic DNA

source_name: Cardiomyocyte cells

growth_protocol: hESCs were detached and held in suspension culture using cardiac differentiation medium (DCDM) containing IMDM and DMEM (ThermoFisher) supplemented with 1% MEM nonessential amino acid solution, 2 mM L-glutamine, 1% penicillin-streptomycin (ThermoFisher). The medium was additionally supplemented with chemical compounds: 1 uM CHIR (Abcam) for first two days and switched to KY021111 (a gift from Dr. Minami Itsunari, Osaka University) and XAV939 (Santa Cruz) on day 3 and day 5 of differentiation. DCDM was changed every ten days after differentiation day 10.

extract_protocol:
For each sample, 100 ng of purified genomic DNA was digested with 20 U of MspI (NEB, cat # R0106L) at 37°C o/n in the presence of RNase Cocktail Mix (Ambion, cat # AM2286). End-repair and dA-tailing were performed by the addition of Klenow Fragment 3’->5’ exo- (NEB, cat # M0212L) in the presence of dATP, dGTP, and d5mCTP (Fermentas). Adapter Ligation was performed by the addition of 0.3 µl of Illumina TruSeq methylated Adapters (Illumina, TruSeq Nano cat# FC-121-4001) and 1 µl of Quick DNA Ligase (NEB cat# M2200L). Samples were pooled and purified using an equal volume of SPRI beads (Beckman Coulter, cat # B23318). Size-selection was performed using SPRI beads to enrich for fragments from 200 to 400 bp.
Purified converted DNA was PCR amplified using MyTaq HS Mix (Bioline, cat# BIO-25045) and TruSeq PCR Primer Cocktail (Illumina, TruSeq Nano cat# FC-121-4001) according to the following protocol: initial denaturation at 98°C for 30s; 12 cycles of 98°C for 15s, 60°C for 30s, 72°C for 30s; final extension at 72°C for 5 min. Amplified libraries were purified twice with an equal amount of SPRI beads to remove primer and adapter dimers.
Libraries were sequenced on an Illumina HiSeq 3000 for single-end 100 bp run.

treatment_protocol: Bisulfite treatment was performed using Epitect Bisulfite kit (QIAGEN, cat # 59104) according to manufacturer's protocol, except that two consecutive rounds of conversion are performed, for a total of 10 hr of incubation.

value: Cardiomyocyte cells


title: day2

source_name: Mesodermal precursor cells

value: Mesodermal precursor cells


title: Astro-WT-GFP-5

description: replicate 5-astrocyte-WT-GFP-group


title: Active celiac patient_3


title: Active celiac patient_5


title: Pancreas_5


title: day5

source_name: Cardiac progenitor cells

value: Cardiac progenitor cells


title: Astro-WT-GFP-4

description: replicate 4-astrocyte-WT-GFP-group


title: day0

source_name: Embroynic stem cells

value: Embroynic stem cells


title: Pancreas_4


title: Astro-WT-GFP-3

description: replicate 3-astrocyte-WT-GFP-group


title: Control patient_2

source_name: Duodenum

value: healthy

value: non-nflamed mucosa


title: Pancreas_3


title: Astro-WT-GFP-2

description: replicate 2-astrocyte-WT-GFP-group


title: Pancreas_2


title: Pancreas_7


title: Treated celiac patient_2


title: Pancreas_1


title: Astro-WT-GFP-1

description: replicate 1-astrocyte-WT-GFP-group


title: CL3K+DRUG

city: Wuhan

first: Zihui

last: Xu

address: Jiefang Road 238

country: China

institute: Renmin Hospital of Wuhan University

description: miRNA expression profiling from CL3K with cisplatin cell

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on miRNA microarray using Affymetrix miRNA 4.0 and Affymetrix GeneChip (Affymetrix, USA).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with GC-RMA using Affymetrix default analysis settings and global scaling as normalization method.

source_name: CL3K cell line with cisplatin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: OV2008 and C13K cells were maintained in complete RPMI-1640 medium supplemented with 10% fetal bovine serum at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted by Trizol reagent. The RNA sample was purified with an RNeasy Mini Column and the RNA quality was assessed by 1.0% agarose gel electrophoresis.

treatment_protocol: C13K cells were cultured in medium containing 1 μmol/L cisplatin to maintain resistance.

value: ovarian cancer cell line

tag: cell phenotype

value: cisplatin-resistant

value: 1 μmol/L cisplatin


title: CL3K

description: miRNA expression profiling from CL3K cell

source_name: CL3K cell line


title: Pancreas_13

value: sRNA


title: Pancreas_14


title: Pancreas_12


title: Active celiac patient_2

value: active celiac disease

value: Inflamed mucosa


title: Treated celiac patient_1


title: Active celiac patient_1


title: Control patient_1


title: Treated celiac patient_15


title: OV2008

description: miRNA expression profiling from OV2008 cell

source_name: OV2008 cell line

value: cisplatin-sensitive


title: Control patient_15

value: non-inflamed mucosa


title: Muscle_9

source_name: Muscle_Small non-coding RNA

value: WT

value: Muscle


title: muscle_D65_rep2

city: Beijing

first: Zhonglin

last: Tang

address: No. 2 Yuanmingyuan West Road, Beijing, 100193, P.R.China,

department: Institute of Animal Science

institute: Chinese Academy of Agricultural Sciences

hyb_protocol: The labeled cRNAs were hybridized onto the Mouse LncRNA Array v2.0 (8 x 60K, Arraystar).

scan_protocol: slides were scanned with the Agilent DNA Microarray Scanner. Data was extracted using Agilent Feature Extraction software. Normalization was performed using Agilent GeneSpring GX 11.5.1.

data_processing: Data analysis was performed using Agilent GeneSpring GX 11.5.1 software.

source_name: mouse, skeletal muscle, postnatal 65 days,replicate 2

label_protocol: The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method.

extract_protocol: Total RNA was isolated using the TRIzol Reagent (Invitrogen, Carlsbad, CA, USA).  Genomic DNA was removed by DNase I (Qiagen, Beijing, China).mRNA was purified from total RNA after removal of rRNA. Integrity and concentration of RNA was assessed by the NanoDrop ND-1000.

value: skeletal muscle

tag: ages

value: postnatal 65  days

value: ICR


title: muscle_D65_rep3

source_name: mouse, skeletal muscle, postnatal 65 days,replicate 3


title: Treated celiac patient_14

value: treated celiac disease


title: muscle_D65_rep4

source_name: mouse, skeletal muscle, postnatal 65 days,replicate 4


title: muscle_D65_rep1

source_name: mouse, skeletal muscle, postnatal 65 days,replicate 1


title: muscle_D0_rep3

source_name: mouse, skeletal muscle, postnatal 0 days,replicate 3

value: postnatal 0  days


title: Muscle_8

value: adult, 3 months old


title: Treated celiac patient_13


title: Pythium porphyrae infected P tenera

city: Gongju-si

first: Soo Hyun

last: Im

address: Gongjudaehak-ro

department: Department of Biology

country: South Korea

institute: Kongju National University

description: The Red-rot disease infected P. tenera blade.

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Agilent E-array (Teleaulax) (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

organism: Pyropia tenera

source_name: Pyropia tenera, Pythium porphyrae infected, oomycete disease infected blade

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol:
[P. tenera] A Pyropia tenera strain was obtained from the national fisheries research and development institute (NFRDI, Korea), and kept in PES medium with constant aeration at 10ºC and 30 mol m–2 s–1 irradiance (16L: 8D). The medium was replaced in every 2 weeks.
[Olpidiopsis pyropiae] Olpidiopsis pyropiae strain was kept with P. tenera blades until it was used for the infection experiment and non-infected P. tenera blades were put if it's necessary. The medium was replaced in every 2 weeks.
[PyroV1] PyroV1 infected P. tenera thalli were stored at -78ºC with DMSO as a cryopreservant and used as an inoculum to initiate infection for the experiment.
[Pythium porphyrae] The pathogen of red-rot disease, Pythium porphyrae were collected in Jindo (34°46′ N 126°36′ E). Pythium porphyrae was kept on corn-meal agar for stationary culture and transferred to Arasaki B medium before the experiment for suspension culture at 20ºC and 9mol m–2 s–1 irradiance (12L: 12D).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol:
[Olpidiopsis blight infection] The Olpidiopsis blight infected blades were put in PES medium with healthy P. tenera for infection experiment and newly infected P. tenera was collected after 72 hours of inoculation.
[Green spot disease infection] Freshly cultured P. tenera blades were incubated with an infected blade in 1.8 L of culture media for 3 days until cellular lysis occurred all over the thalli. The thalli were removed and the resultant lysate was sequentially passed through 4.3µm, 1.2µm, 0.22 µm and 0.1µm filters to remove cell debris and bacteria in the solution. Finally the lysate was concentrated to 50 mL using 100 kD molecular membrane filter and stored in the deep freezer at -78ºC. A drop of the concentrated solution was smeared on the marine agar plate and incubated in 37ºC chamber for 48 h to check if any bacteria passed through the filter. When no bacterial growth was observed from above assay the concentrated lysate solution was stored at 4ºC chamber and used for infection experiment.   To determine the latent period of the virus a freshly cultured P. tenera thalli was wounded with razor, incubated in a concentrated lysate of the virus for 24 hr and transferred to new media with blades of P. tenera. Two blades were taken from the solution every 6 hr and moved to a fresh media again. The total required time for the successful infection of the newly introduced P. tenera blade was used as the latent period of the virus.
[Red rot disease infection] The Pythium porphyrae was transferred to PES medium with healthy blade of P. tenera for infection experiment and newly infected P. tenera blades were collected after 72 hours of inoculation.

tag: infection

value: Red rot disease-infected blade

tag: pathogen

value: Pythium porphyrae


title: muscle_D0_rep4

source_name: mouse, skeletal muscle, postnatal 0 days,replicate 4


title: Pancreas_11

source_name: Pancreas_Small non-coding RNA

value: Pancreas


title: Active celiac patient_15


title: muscle_D0_rep2

source_name: mouse, skeletal muscle, postnatal 0 days,replicate 2


title: Control

description: The host blade. Non-infected healthy blade.

source_name: Pyropia tenera, Non-infected, healthy blade

value: Non-infected blade

value: control (non pathogen)


title: PyroV1 infected P tenera

description: The Green-spot disease infected P. tenera blade.

source_name: Pyropia tenera, PyroV1 infected, virus disease infected blade

value: Green spot disease-infected blade


title: Olpidiopsis pyropiae infected P tenera

description: The Olpidiopsis infected P. tenera blade.

source_name: Pyropia tenera, Olpidiopsis pyropiae infected, oomycete disease infected blade

value: Olpidiopsis-infected blade

value: Olpidipsis pyropiae


title: muscle_D0_rep1

source_name: mouse, skeletal muscle, postnatal 0 days,replicate 1


title: Treated celiac patient_12

source_name: Duodenum

value: Inflamed mucosa


title: KO_RNAseq_Rep1

city: Worcester

first: Thomas

last: Fazzio

state: MA

address: 364 Plantation street

institute: UMMS

data_processing:
Reads were mapped to the mm10 genome and quantified using RSEM (Li and Dewey, 2011). Identification of differentially expressed genes was performed using a combined RSEM-EBseq pipeline (Leng et al., 2013)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with fold change values and differential expression probabilities. PPEE means “posterior probability of equal expression”, PPDE means “posterior probability of differential expression”, PostFC means “posterior fold change” and RealFC means "Real Fold Change". It was made using the “rsem-run-ebseq” command in RSEM.

source_name: mouse embryo

extract_protocol:
RNA was isolated from E8.5 embryos using a Direct-zol RNA MicroPrep kit (Zymo research).
These libraries are not strand specific. Enrichment of mRNA, library preparation, and sequencing were performed at BGI, using the BGI-seq format.

value: FVB/N

tag: developmental stage

value: embryo

tag: genotype/variation

value: Tip55 knockout


title: KO_RNAseq_Rep3

tag: strain


title: rot3

city: Guangzhou

first: Danyu

last: Lin

address: Yanjiang West Road 107

institute: Sun Yat-sen momerial hospital

description: gene expression from cellular model induced by rotenone

hyb_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/lg cRNA) were measured using a NanoDrop ND-1000 instrument. Each labeled cRNA (1 lg) was fragmented by adding 5 lL 10   Blocking Agent and 1 lL of 25   Fragmentation Buffer, and heated at 60  C for 30 min. Finally 25 lL of 2   GE Hybridization buffer was added to dilute the labeled cRNA. Hybridization solution (50 lL) was dispensed into the gasket slide and assembled into the LncRNA expression microarray slide. The slides were incubated for 17 h at 65  C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed, and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).  The hybridized arrays were washed, fixed, and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).  The hybridized arrays were washed, fixed, and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies).
After quantile normalization of the raw data, lncRNAs and mRNAs were chosen for further data analysis. Differentially expressed lncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/false discovery rate (FDR) filtering. Differentially expressed lncRNAs and mRNAs between the two samples were identified through fold change filtering. It was considered significant once the fold change was higher than 1.5. Hierarchical Clustering and combined analysis were performed using in-house scripts. The predicted relationship among lncRNAs, mRNAs, and microRNAs of interest was performed by competing endogenous RNAs (ceRNA) analysis.

source_name: cellular model induced by rotenone

label_protocol: The microarray analysis was performed using Arraystar Human LncRNA Microarray V4.0 (Rockville, MD, USA). Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expres- sion Analysis protocol (Agilent Technology, Santa Clara, CA, USA). Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLYTM Eukaryotic mRNA Isolation Kit, Epicentre, Madison, WI, USA). Each sample was then amplified and transcribed into flu- orescent cRNA along the entire length of the transcripts, without 30 bias, using a random priming method (Arraystar Flash RNA Label- ing Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen, DUS, DE).

growth_protocol: SY-SH5Y cells at 2 X10^5 cells per well were cultured in a 6-well plate.

extract_protocol: The Trizol reagent was used to extract total RNA from SY-SH5Y cells seeded in 6-well plates (according to the manufacture’s pro- tocol).

treatment_protocol: The cells were treated with  with certain doses of a-synuclein oligomers and rotenone.

tag: cell line

value: cellular model induced by rotenone


title: rot2


title: WT_RNAseq_Rep3

tag: tissue

value: wildtype


title: rot1


title: Active celiac patient_14

value: active celiac disease


title: Muscle_6

source_name: Muscle_Small non-coding RNA

tag: genotype

value: WT

tag: age

value: Muscle

tag: molecule subtype

value: sRNA


title: Muscle_5

value: adult, 3 months old


title: WT_RNAseq_Rep2


title: Active celiac patient_13


title: Muscle_4


title: Muscle_7


title: KO_RNAseq_Rep2


title: Treated celiac patient_11

value: treated celiac disease


title: con3

description: gene expression from normal cells

source_name: normal cellular control

value: normal cellular control


title: Muscle_3


title: Muscle_2


title: WT_RNAseq_Rep1


title: Control patient_15 4

label_protocol:
RNA was normalized to 8 ng/ul and converted to cDNA using the AffinityScript cDNA Synthesis kit (Agilent Technologies) following manufacturer´s protocol
Specific Target Amplification (STA) was performed
Gene expression analyses were performed using Fluidigm Biomark 96.96 dynamic arrays and commercially available TaqMan Gene Expression assays

value: healthy

value: non-inflamed mucosa


title: Muscle_1


title: Control patient_15 part2


title: Muscle_14


title: Treated celiac patient_8


title: Treated celiac patient_10


title: Control patient_13 4


title: con2

description: gene expression from normal cells


title: con1

description: gene expression from normal cells


title: α-syn1

description: gene expression from cellular model induced by a-syn

source_name: cellular model induced by a-syn

value: cellular model induced by a-syn


title: Control patient_14 part2


title: α-syn3


title: Treated celiac patient_9


title: Treated celiac patient_7


title: α-syn2


title: Muscle_13


title: Control patient_13 part2


title: Muscle_12


title: Treated celiac patient_6


title: Control patient_12 4


title: Treated celiac patient_5


title: Active celiac patient_12


title: Control patient_11 part2


title: Muscle_10


title: Control patient_10 4


title: Control patient_11 4


title: Control patient_14 4


title: Control patient_12 part2


title: Control patient_9 4


title: Control patient_10 part2


title: Treated celiac patient_4


title: Control patient_8 4


title: Lung_9

source_name: Lung_Small non-coding RNA

value: Lung


title: Muscle_11


title: Lung_7


title: Active celiac patient_11

value: Inflamed mucosa


title: Control patient_8 part2


title: Control patient_7 4


title: Treated celiac patient_3


title: Lung_6


title: Control patient_9 part2


title: Control patient_5 4


title: Treated celiac patient_2


title: Control patient_6 4


title: Control patient_7 part2


title: Control patient_6 part2


title: Control patient_4 4


title: Active celiac patient_10


title: Lung_5


title: Lung_4


title: Lung_3


title: Active celiac patient_9


title: Active celiac patient_8


title: Control patient_4 part2


title: Control patient_5 part2


title: Control patient_3 part2


title: Lung_8


title: Control patient_2 4


title: Control patient_1 4


title: Control patient_3 4


title: Control patient_2 part2


title: Active celiac patient_6


title: Lung_14


title: Control patient_1 part2


title: Treated celiac patient_15 4


title: Lung_1


title: Treated celiac patient_15 part2


title: Lung_13


title: Treated celiac patient_14 4


title: Active celiac patient_7


title: Lung_12


title: Active celiac patient_5


title: Treated celiac patient_14 part2


title: Treated celiac patient_13 4


title: Lung_11


title: Lung_2


title: Active celiac patient_4


title: Treated celiac patient_13 part2


title: Control patient_13


title: Liver_9

source_name: Liver_Small non-coding RNA

value: Liver


title: Treated celiac patient_12 4


title: Treated celiac patient_12 part2


title: Control patient_14


title: Active celiac patient_3


title: Active celiac patient_2


title: Treated celiac patient_10 4


title: Active celiac patient_1


title: Liver_7


title: Treated celiac patient_9 part2


title: Treated celiac patient_10 part2


title: Treated celiac patient_11 part2


title: Treated celiac patient_8 4


title: Liver_6


title: Control patient_12


title: Liver_5


title: Treated celiac patient_9 4


title: Treated celiac patient_7 4


title: Control patient_11


title: Liver_4


title: Treated celiac patient_11 4


title: Treated celiac patient_8 part2


title: Treated celiac patient_6 4


title: Liver_8


title: Control patient_10


title: Liver_3


title: Treated celiac patient_7 part2


title: Control patient_9


title: Treated celiac patient_5 4


title: Control patient_8


title: Treated celiac patient_6 part2


title: Liver_2


title: Treated celiac patient_5 part2


title: Treated celiac patient_4 4


title: Treated celiac patient_4 part2


title: Control patient_7


title: Treated celiac patient_16 4


title: Liver_14


title: Control patient_6


title: Treated celiac patient_3 4


title: Control patient_5


title: Treated celiac patient_3 part2


title: Treated celiac patient_2 4


title: Liver_12


title: Treated celiac patient_2 part2


title: Treated celiac patient_1 4


title: Active celiac patient_15 part2


title: Liver_11


title: Active celiac patient_15 4


title: Liver_10


title: Treated celiac patient_1


title: Control patient_4


title: Active celiac patient_16 4


title: Active celiac patient_13 part2


title: Liver_1


title: Kidney_9

source_name: Kidney_Small non-coding RNA

value: Kidney


title: Active celiac patient_12 part2


title: Control patient_3


title: Control patient_1


title: Active celiac patient_13 4


title: Kidney_8


title: Active celiac patient_14 4


title: Active celiac patient_12 4


title: Kidney_7


title: Treated celiac patient_1 part2


title: Active celiac patient_11 part2


title: Kidney_6


title: Active celiac patient_11 4


title: Active celiac patient_10 part2


title: Active celiac patient_14 part2


title: Active celiac patient_10 4


title: Kidney_5


title: Active celiac patient_9 part2


title: Liver_13


title: Kidney_4


title: Kidney_3


title: Active celiac patient_8 part2


title: Control patient_2


title: Active celiac patient_6 part2


title: Active celiac patient_7 4


title: Kidney_2


title: Active celiac patient_6 4


title: Active celiac patient_4 part2


title: Active celiac patient_2 part2


title: week 1 LL2 TB mouse, replicate 2

status: Public on Sep 27 2018

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: week 1 LL2 TB mouse, replicate 2

data_processing:
RNA-seq data was aligned using bowtie2 against mm10 version of the human genome and RSEM v1.2.31 software was used to estimate raw read counts and FPKM values using transcriptome information from Ensemble v84 set
DESeq2 was used to estimate significance of differential expression between groups
Genome_build: mm10
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene as estimated by RSEM

source_name: bone marrow derived Ly6G+ cells

extract_protocol:
Neutrophils were isolated using Ly6G beads with purity was >95%.
VAHTS Total RNA-Seq Library Preparation Kit was used for library preparation and ran in a 75bp single end run on Illumina HiSeq 2500

tag: group


title: week 3 LL2 TB mouse, replicate 2

description: week 3 LL2 TB mouse, replicate 2


title: Active celiac patient_4 4


title: Active celiac patient_3 part2


title: week 3 LL2 TB mouse, replicate 1

description: week 3 LL2 TB mouse, replicate 1


title: Active celiac patient_3 4


title: Active celiac patient_2 4


title: Active celiac patient_1 4


title: week 1 LL2 TB mouse, replicate 1

description: week 1 LL2 TB mouse, replicate 1


title: Active celiac patient_1 part2


title: Active celiac patient_7 part2


title: Active celiac patient_9 4


title: naïve mouse, replicate 2

description: naïve mouse, replicate 2

value: naive


title: Active celiac patient_5 part2


title: Active celiac patient_5 4


title: Active celiac patient_8 4


title: naïve mouse, replicate 1

description: naïve mouse, replicate 1


title: Adult female Anopheles sinensis small RNA

city: Shanghai

first: Xinyu

last: Feng

address: No. 207 Rui Jin Er Road

department: malaria

institute: National Institute of Parasitic Diseas，Chinese Center for Disease Control and Prevention.

data_processing:
Basecalls performed using CASAVA version 1.4
The initial reads obtained from Illumina sequencing were pretreated to remove adaptors, poly A reads, reads without the insert fragment, and reads of less than 10 nt.
The clean reads were mapped to the An. sinensis genome (GenBank assembly accession: GCA_000441895.2) using SOAP with a tolerance of one mismatch to analyze their distribution.
The matched sequences were then queried against GenBank miRBase, Rfam, and repeats database to annotate the sRNA (rRNAs, tRNAs, snRNAs, snoRNA, miRNA) sequences.
The remnant reads were compared to the miRBase database to identify the conserved miRNAs. Filtered unmatched clean reads were used for miRNA prediction to identify novel miRNAs. The novel miRNAs candidates were predicted by MiRDeep [25] only if they met the criteria described by Allen et. al and Friedlander et al.
miRNA read counts were calculated by mirdeep2 and the TPM was calculated by: TPM = (readcount*1000000)/library size
Genome_build: AsinC2
Supplementary_files_format_and_content: tab-delimited text file includes counts and TPM.  A file with miRNA IDs and  genome coordinates is available on the series record.

organism: Anopheles sinensis

source_name: Adult female Anopheles sinensis whole body

growth_protocol: An. sinensis (China strain) mosquitoes were reared under insectary in screened cages at 28 ± 2°C, 70–75% humidity. Adult mosquitoes were provided with constant access to sterile glucose solution and water soaked sponges.

extract_protocol:
Adult female samples were pooled with 250μL of TRIzol® reagent (Invitrogen) immediately following collection and stored at −80°C until further processing. Total RNA was extracted from samples for miRNAs (Takara, Dalian, China) followed manufacturer’s protocol.
Small RNAs (sRNAs) libraries were made as manufacturer's instructions (Illumina Inc).

value: China

value: whole body

value: 2-3 day

value: female


title: RNA-Seq of BA treated roots; replicate 1

city: Chapel Hill

first: Joseph

last: Kieber

state: NC

address: 4144 Genome Sciences Building

department: Biology

institute: University of North Carolina

data_processing:
All datasets were trimmed using the BBDuk tool from the BBMap 37.50 package with the following parameters 'k=13 ktrim=r'.
The trimmed RNA-Seq reads were aligned to the Arabidopsis Col-0 genome assembly (TAIR10) with TopHat and bowtie 1.2.0.
Genome_build: TAIR10
Supplementary_files_format_and_content: Genome browser tracks are in BIGWIG format. Replicates were merged in the processed data files.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Roots treated for 45 minutes with benzyl adenine

extract_protocol:
For RNA-Seq, total RNA was extracted using QIAGEN Rneasy Mini kits.
For RNA-Seq, cDNA libraries were prepeared using KAPA Biosystems Stranded RNA-Seq kit as described by manufacturer's instructions.

treatment_protocol: Tissue were treated for 45 minutes with vehicle control or 5uM BA in MS liquid media.

value: Roots

value: BA

tag: replicate number

value: Rep 1


title: RNA-Seq of control treated shoots; replicate 2

source_name: Shoots treated for 45 minutes with control

value: Shoots

value: Control

value: Rep 2


title: RNA-Seq of BA treated roots; replicate 3

value: Rep 3


title: RNA-Seq of control treated shoots; replicate 1


title: RNA-Seq of control treated roots; replicate 3

source_name: Roots treated for 45 minutes with control


title: RNA-Seq of control treated roots; replicate 2


title: RNA-Seq of BA treated shoots; replicate 1

source_name: Shoots treated for 45 minutes with benzyl adenine


title: RNA-Seq of BA treated roots; replicate 2


title: RNA-Seq of BA treated shoots; replicate 3


title: RNA-Seq of control treated roots; replicate 1


title: RNA-Seq of control treated shoots; replicate 3


title: SUM159-Mir100-Ctrl

first: Lu

last: Deng

address: Dong'an Road

institute: USTC

description: Gene expression data from SUM159 Ctrl cells

hyb_protocol: 5ug of target is hybridizedto HTA 2.0 Array in Affymetrix Hybridization Oven 645 for 16 hr

scan_protocol: Arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G

data_processing: The raw data was normalized and compared using the Expression Console and Transcriptome Analysis Console software provided by Affymetrix Corporation. Differentially expressed genes between miR-100 over-expressing cells and the control cells were identified with fold change > 1.5.

source_name: SUM159 transfected with doxy-induced-Mir100 overexpression plasmid treated without doxy for a week

label_protocol: Biotinylated cDNA is generated from 100ng of total RNA and labeled using the GeneChip WT Terminal Labeling kit from Affymetrix

growth_protocol: SUM159-Mir100 cells were cultured in Ham‘s F12 medium with 5% fatal bovine serum (FBS) (Thermo Fisher)  and 1% streptomycin/penicillin, 1mg/ml hydrocortisone, and 5 mg/ml insulin.  MDA-MB-231-Mir100 cells were cultured in DMEM medium with 5% fatal bovine serum (FBS)and 1% streptomycin/penicillin.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Each cell line was split into two group.One group of the cells was treated with tetracycline for a week to induce mir100 overexpression, the other grew with no treatment.

tag: cell type

value: breast cancer

tag: transfection

value: control


title: SKNMC siRNA YT rep1

city: Seville

first: Juan

last: Diaz-Martin

address: Av Manuel Siurot

institute: IBiS

description: Gene expression data from Ewing Sarcoma cells transfected with a mix of siRNAs targeting both YAP1 and TAZ

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GeneChip Command Console Software (AGCC)

data_processing: CEL files were analyzed by Transcriptome Analysis Console (TAC) 4.0 software (Thermo Fisher Scientific, Inc.) using Affymetrix default analysis settings.

source_name: SKNMC cells transfected with a mix of siRNA targeting both YAP1 and TAZ

label_protocol: Biotinylated cRNA were prepared using the GeneChip® WT PLUS Reagent Kit according to manufacturer's intructions.

growth_protocol: SK-N-MC were grown in standard growth medium: EMEM supplemented with 10% Fetal Bovine Serum and 1% penicillin-streptomycin.

extract_protocol: RNA was isolated by using mirVana miRNA isolation kit (Thermo Fisher Scientific, USA). Quantity and quality of total RNA was estimated using the Nanodrop ND-2000 Spectrophotometer (Thermo Fisher Scientific, USA)

treatment_protocol: SK-N-MC cells were transfected with control or a combination of YAP1/TAZ siRNAs oligonucleotides (final concentration 10nM) by using Viromer Blue, according to the manufacturer´s conditions (Lipocalyx, Germany). After 72h, cells were washed with 1XPBS and harvested for RNA extraction.

value: Ewing Sarcoma cell line


title: MDA-MB-231-Mir100-Ctrl

description: Gene expression data from MDA-MB-231 Ctrl cells

source_name: MDA-MB-231 transfected with doxy-induced-Mir100 overexpression plasmid treated without doxy for a week


title: SKNMC siRNA control rep3

description: Gene expression data from Ewing Sarcoma cells transfected with a non-targeting siRNA

source_name: SKNMC cells transfected with control siRNA


title: RNA-Seq of BA treated shoots; replicate 2

tag: treatment


title: SKNMC siRNA YT rep3


title: SKNMC siRNA control rep4


title: SKNMC siRNA YT rep4


title: SUM159-Mir100-Doxy

description: Gene expression data from SUM159 Mir100 overexpression cells

source_name: SUM159 transfected with doxy-induced-Mir100 overexpression plasmid treated with doxy for a week

value: doxy-induced-Mir100 overexpression


title: MDA-MB-231-Mir100-Doxy

description: Gene expression data from MDA-MB-231 Mir100 overexpression cells

source_name: MDA-MB-231 transfected with doxy-induced-Mir100 overexpression plasmid treated with doxy for a week


title: SKNMC siRNA control rep2


title: SKNMC siRNA YT rep2


title: SKNMC siRNA control rep1


title: EML4-ALK Tumor vs. Normal tissue

city: Saitama

first: Norihiro

last: Kotani

institute: Saitama Medical school

hyb_protocol: Samples were mixed with hybridization buffer of Gene Expression Hybridization kit (Agilen), and were applied to Whole Mouse Genome Microarray Kit, 4x44K (Agilent).

scan_protocol: Fluorescence image was scanned on an Agilent G2505B scanner.

data_processing:
Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction.
Go term analysis was performed using Gene Spring GX (Ver. 11.5).

source_name: Lung tumor

label_protocol: cDNAs from total RNA were labeled using Quick Amp labeling kit, two-color (5190-0444:Agilent) following manufacturer's instructions.

growth_protocol: EML4-ALK transgenic mice (generous gift from Professor Hiroyuki Mano, Graduate School of Medicine, University of Tokyo) were maintained under specific pathogen-free (SPF) conditions at room temperature.

extract_protocol: Total RNAs from each mouse lung tissues were extracted using Rneasy mini Kit (Qiagen), respectively, and then mixed each other at a same ratio.

treatment_protocol: Tumor and normal tissues were separated from lung tissues derived from 3 transgenic mice.

tag: gender

value: male

value: 12 weeks old

source_name: Lung normal tissue


title: BB260_PreBII

city: Aalborg

first: Rasmus

middle: Froberg

last: Brøndum

address: Sdr. Skovvej 15

department: Department of Haematology

country: Denmark

institute: Aalborg University Hospital

hyb_protocol: Included in the label protocol, see above.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G. CEL-files generated using AGCC

data_processing: RMA normalized using R (v3.3.2), the affy-package (v1.48.0) from Bioconductor, and probe set data extracted from custom CDF  [Brainarray, hgu133plus2sensgcdf_20.0.0].

source_name: PreBII B-cells_human Iliac crest bone marrow

label_protocol: Biotinylated cRNA were prepared using the GeneChip Expression 3’ amplification One-cycle Target Labeling (#P/N 900493, Affymetrix) from 5 ug total RNA using manual P/N 702232 Rev.2.

extract_protocol: mRNA was isolated using the μMACS™ technology (Miltenyi Biotech, Bergisch-Gladbach, Germany), using μ Columns and elution with pure water. Amplification was performed using WT Ovation Pico RNA Amplification System (NuGEN Technologies, Inc., San Carlos, CA) following manufactures protocol.

treatment_protocol: Normal bone marrow (BM, n=6) was harvested from healthy volunteers. The normal B-cell subsets were directly phenotyped by multiparametric flow cytometry (MFC) and fluorescence-activated cell sorting (FACS) into six distinct B-cell subsets PreBI, PreBII, immature (Im), naïve (N), memory (M) B-cells, and plasma cells (PC) by a highly selected monoclonal antibody panel.

value: Iliac crest bone marrow aspirate

value: PreBII B-cells


title: BB257_Immature

source_name: Immature B-cells_human Iliac crest bone marrow

value: Immature B-cells


title: BB257_PC_19+56-

source_name: Plasma cell B-cells_human Iliac crest bone marrow

value: Plasma cell B-cells


title: BB251_PreBI

source_name: PreBI B-cells_human Iliac crest bone marrow

value: PreBI B-cells


title: BB248_Memory

source_name: Memory B-cells_human Iliac crest bone marrow

value: Memory B-cells


title: BB248_PreBI


title: BB248_Naive

source_name: Naive B-cells_human Iliac crest bone marrow

value: Naive B-cells


title: BB248_Immature


title: BB236_Naive


title: BB257_PreBII


title: BB236_Immature


title: BB251_Naive


title: BB251_PC_19+56-


title: BB248_PreBII


title: GER007_10x

city: Heidelberg

first: Tobias

last: Gerber

address: Meyerhofstr. 1

department: Developmental Biology

country: Germany

institute: EMBL Heidelberg

data_processing:
"freeIbis" was used for C1 and SmartSeq2 sample data as an efficient basecaller with calibrated quality scores for Illumina sequencers. (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.) Cellranger, version 2.0.0, as part of the 10x Genomics analysis pipeline was used to call bases for 10x experiments.
"leeHom" was used to trim adapters and merge Illumina sequencing reads for C1 and SmartSeq2 sample data. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.) Cellranger, version 2.0.0, of the 10x Genomics analysis pipeline was used to trim adapters for 10x experiments.
"deML" was used for robust demultiplexing of Illumina sequences for C1 and SmartSeq2 sample data using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.) Cellranger, version 2.0.0, of the 10x Genomics analysis pipeline was used to demultiplex reads.
Reads were aligned against the axolotl transcriptome (www.axolotl-omics.org, Download: 2015-07-29) using kallisto (Nat Biotechnol. 2016 May;34(5):525-7. doi: 10.1038/nbt.3519. Epub 2016 Apr 4.) for C1 and SmartSeq 2 sample data or using STAR (Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25.) implemented in 10x' cell ranger software, version 2.0.0, for 10x data.
Transcript Per Million (TPM) values were computed using kallisto for C1 and SmartSeq2 samples. (Nat Biotechnol. 2016 May;34(5):525-7. doi: 10.1038/nbt.3519. Epub 2016 Apr 4.) Cellranger, version 2.0.0, implemented in the 10x Genomics analysis pipeline was used to obtain bam alignment files and gene count (UMI) matrices.
Gene expression values of different isoforms of the same gene were summed using custom Perl scripts.
Genome_build: Axolotl transcriptome (Am_2.2)
Supplementary_files_format_and_content: Master data frame including cell ID, cell type, timepoint, gene ID, and TPM values for each single cell.

organism: Ambystoma mexicanum

source_name: forelimb upper arm uninjured

extract_protocol:
Single cell isolation and cDNA generation was performed using ChromiumTM Single Cell 3’ Reagent Kits v2 according to manufacturer’s protocol (10X Genomics).
Sequencing libraries were generated using ChromiumTM Single Cell 3’ Reagent Kits v2 according to manufacturer’s protocol (10X Genomics).

treatment_protocol: no connective tissue enrichment

tag: cre line

tag: sc-rna-seq method

value: 10X Genomics

value: uninjured upper arm section


title: GER024_10x

source_name: forelimb upper arm blastema 38 dpa

extract_protocol:
CT enrichment was performed through FACS and cDNA generation was performed using ChromiumTM Single Cell 3’ Reagent Kits v2 according to manufacturer’s protocol (10X Genomics).
Sequencing libraries were generated using ChromiumTM Single Cell 3’ Reagent Kits v2 according to manufacturer’s protocol (10X Genomics).

treatment_protocol: FACS enrichment for connective tissue cells


title: GER020_10x

source_name: forelimb upper arm blastema 25 dpa


title: GER014_10x


title: BB251_Immature


title: BB251_Memory


title: BB236_PC_19+56-


title: BB236_PreBI


title: BB239_PreBII


title: BB248_PC_19+56-


title: GER006_10x


title: BB239_Memory


title: bl11_p-axo26p3_5.H9A

source_name: forelimb upper arm blastema 11 dpa

extract_protocol:
Single cell isolation by FACS and cDNA generation following SmartSeq2 protocol. (Nat Protoc. 2014 Jan;9(1):171-81. doi: 10.1038/nprot.2014.006. Epub 2014 Jan 2.)
Libraries were prepared using Illumina Nextera XT kit according to illumina's protocol.

tag: development stage

value: blastema 11 dpa


title: GER019_10x


title: GER018_10x

source_name: forelimb upper arm blastema 18 dpa


title: GER025_10x


title: GER017_10x


title: GER015_10x


title: bl11_p-axo26p3_5.H5A


title: bl11_p-axo26p3_5.H3A


title: bl11_p-axo26p3_5.G5A


title: bl11_p-axo26p3_5.G2A


title: bl11_p-axo26p3_5.F8A


title: bl11_p-axo26p3_5.G11A


title: bl11_p-axo26p3_5.F6A


title: bl11_p-axo26p3_5.E6A


title: bl11_p-axo26p3_5.G12A


title: bl11_p-axo26p3_5.C8A


title: bl11_p-axo26p3_5.D9A


title: bl11_p-axo26p3_5.D1A


title: bl11_p-axo26p3_5.F10A


title: bl11_p-axo26p3_5.C9A


title: bl11_p-axo26p3_5.F4A


title: bl11_p-axo26p3_5.C5A


title: bl11_p-axo26p3_5.F12A


title: bl11_p-axo26p3_5.C3A


title: bl11_p-axo26p3_5.C7A


title: bl11_p-axo26p3_5.C2A


title: bl11_p-axo26p3_5.D5A


title: bl11_p-axo26p3_5.C1A


title: bl11_p-axo26p3_5.B6A


title: bl11_p-axo26p3_5.B9A


title: bl11_p-axo26p3_5.B5A


title: bl11_p-axo26p3_5.B4A


title: bl11_p-axo26p3_5.B3A


title: bl11_p-axo26p3_5.B7A


title: bl11_p-axo26p3_5.G3A


title: bl11_p-axo26p3_5.G6A


title: bl11_p-axo26p3_5.C4A


title: bl11_p-axo26p3_5.B1A


title: bl11_p-axo26p3_5.A5A


title: bl11_p-axo26p3_5.B12A


title: bl11_p-axo26p3_5.B10A


title: bl11_p-axo26p3_5.A4A


title: bl11_p-axo26p3_5.A3A


title: bl11_p-axo26p3_5.A12A


title: bl11_p-axo26p2_4.H3A


title: bl11_p-axo26p2_4.H4A


title: bl11_p-axo26p2_4.H8A


title: bl11_p-axo26p2_4.H6A


title: bl11_p-axo26p2_4.H12A


title: bl11_p-axo26p2_4.G8A


title: bl11_p-axo26p2_4.H11A


title: bl11_p-axo26p2_4.G5A


title: bl11_p-axo26p2_4.H2A


title: bl11_p-axo26p2_4.G1A


title: bl11_p-axo26p2_4.G4A


title: bl11_p-axo26p2_4.G3A


title: bl11_p-axo26p2_4.G7A


title: bl11_p-axo26p2_4.G12A


title: bl11_p-axo26p2_4.G11A


title: bl11_p-axo26p2_4.F9A


title: bl11_p-axo26p2_4.F5A


title: bl11_p-axo26p2_4.F10A


title: bl11_p-axo26p2_4.F6A


title: bl11_p-axo26p2_4.E7A


title: bl11_p-axo26p2_4.E6A


title: bl11_p-axo26p2_4.H10A


title: bl11_p-axo26p2_4.H1A


title: bl11_p-axo26p2_4.E11A


title: bl11_p-axo26p2_4.E3A


title: bl11_p-axo26p2_4.E2A


title: bl11_p-axo26p2_4.E5A


title: bl11_p-axo26p2_4.D9A


title: bl11_p-axo26p2_4.D3A


title: bl11_p-axo26p2_4.D2A


title: bl11_p-axo26p2_4.D12A


title: bl11_p-axo26p2_4.D11A


title: bl11_p-axo26p2_4.D1A


title: bl11_p-axo26p2_4.C9A


title: bl11_p-axo26p2_4.C7A


title: bl11_p-axo26p2_4.C3A


title: bl11_p-axo26p2_4.C6A


title: bl11_p-axo26p2_4.D5A


title: bl11_p-axo26p2_4.C11A


title: bl11_p-axo26p2_4.C10A


title: bl11_p-axo26p2_4.B9A


title: bl11_p-axo26p2_4.B5A


title: bl11_p-axo26p3_5.H9B

description:
Single cell transcriptome from blastema 11 dpa
Table_S8.csv


title: bl11_p-axo26p2_4.B1A


title: bl11_p-axo26p3_5.H7B


title: bl11_p-axo26p3_5.H8B


title: bl11_p-axo26p3_5.H6B


title: bl11_p-axo26p3_5.H5B


title: bl11_p-axo26p2_4.D7A


title: bl11_p-axo26p2_4.D6A


title: bl11_p-axo26p3_5.H12B


title: bl11_p-axo26p3_5.H10B


title: bl11_p-axo26p3_5.G7B


title: bl11_p-axo26p3_5.H1B


title: bl11_p-axo26p3_5.H2B


title: bl11_p-axo26p3_5.G4B


title: bl11_p-axo26p3_5.G6B


title: bl11_p-axo26p3_5.G12B


title: bl11_p-axo26p3_5.G3B


title: bl11_p-axo26p3_5.G2B


title: bl11_p-axo26p3_5.F6B


title: bl11_p-axo26p3_5.F5B


title: bl11_p-axo26p3_5.F3B


title: bl11_p-axo26p3_5.F9B


title: bl11_p-axo26p3_5.G11B


title: bl11_p-axo26p3_5.F4B


title: bl11_p-axo26p3_5.F1B


title: bl11_p-axo26p2_4.D4A


title: bl11_p-axo26p3_5.G8B


title: bl11_p-axo26p3_5.E12B


title: bl11_p-axo26p3_5.E10B


title: bl11_p-axo26p3_5.E9B


title: bl11_p-axo26p3_5.F10B


title: bl11_p-axo26p3_5.F12B


title: bl11_p-axo26p3_5.E7B


title: bl11_p-axo26p3_5.G1B


title: bl11_p-axo26p3_5.E8B


title: bl11_p-axo26p3_5.E3B


title: bl11_p-axo26p3_5.D6B


title: bl11_p-axo26p3_5.E5B


title: bl11_p-axo26p3_5.D9B


title: bl11_p-axo26p3_5.D7B


title: bl11_p-axo26p3_5.D4B


title: bl11_p-axo26p3_5.D8B


title: bl11_p-axo26p3_5.E2B


title: bl11_p-axo26p3_5.D5B


title: bl11_p-axo26p3_5.D3B


title: bl11_p-axo26p3_5.D1B


title: bl11_p-axo26p3_5.D11B


title: bl11_p-axo26p3_5.D2B


title: bl11_p-axo26p3_5.D10B


title: bl11_p-axo26p3_5.C9B


title: bl11_p-axo26p3_5.C6B


title: bl11_p-axo26p3_5.C7B


title: bl11_p-axo26p3_5.C8B


title: bl11_p-axo26p3_5.C3B


title: bl11_p-axo26p3_5.C1B


title: bl11_p-axo26p3_5.C2B


title: bl11_p-axo26p3_5.B5B


title: bl11_p-axo26p3_5.A9B


title: bl11_p-axo26p3_5.A6B


title: bl11_p-axo26p3_5.C11B


title: bl11_p-axo26p3_5.A5B


title: bl11_p-axo26p2_4.H8B


title: bl11_p-axo26p3_5.A3B


title: bl11_p-axo26p2_4.H12B


title: bl11_p-axo26p3_5.A2B


title: bl11_p-axo26p3_5.B8B


title: bl11_p-axo26p3_5.A11B


title: bl11_p-axo26p3_5.B12B


title: bl11_p-axo26p2_4.H10B


title: bl11_p-axo26p3_5.C4B


title: bl11_p-axo26p2_4.H11B


title: bl11_p-axo26p3_5.B7B


title: bl11_p-axo26p2_4.G6B


title: bl11_p-axo26p2_4.G2B


title: bl11_p-axo26p2_4.F9B


title: bl11_p-axo26p2_4.G10B


title: bl11_p-axo26p2_4.G11B


title: bl11_p-axo26p2_4.G4B


title: bl11_p-axo26p2_4.G1B


title: bl11_p-axo26p3_5.A4B


title: bl11_p-axo26p2_4.G9B


title: bl11_p-axo26p2_4.F5B


title: bl11_p-axo26p3_5.A7B


title: bl11_p-axo26p2_4.F6B


title: bl11_p-axo26p2_4.G5B


title: bl11_p-axo26p2_4.F12B


title: bl11_p-axo26p2_4.E7B


title: bl11_p-axo26p2_4.E6B


title: bl11_p-axo26p2_4.F4B


title: bl11_p-axo26p2_4.E8B


title: bl11_p-axo26p2_4.F10B


title: bl11_p-axo26p2_4.E5B


title: bl11_p-axo26p2_4.F7B


title: bl11_p-axo26p2_4.F3B


title: bl11_p-axo26p2_4.D5B


title: bl11_p-axo26p2_4.D6B


title: bl11_p-axo26p2_4.D1B


title: bl11_p-axo26p2_4.D7B


title: bl11_p-axo26p2_4.E4B


title: bl11_p-axo26p2_4.E10B


title: bl11_p-axo26p2_4.C9B


title: bl11_p-axo26p2_4.E11B


title: bl11_p-axo26p2_4.C2B


title: bl11_p-axo26p2_4.C1B


title: bl11_p-axo26p2_4.C12B


title: bl11_p-axo26p2_4.C5B


title: bl11_p-axo26p2_4.C6B


title: bl11_p-axo26p2_4.C3B


title: bl11_p-axo26p2_4.B8B


title: bl11_p-axo26p2_4.C10B


title: bl11_p-axo26p2_4.C7B


title: bl11_p-axo26p2_4.B7B


title: bl11_p-axo26p2_4.B3B


title: bl11_p-axo26p2_4.B10B


title: bl11_p-axo26p2_4.A5B


title: bl11_p-axo26p2_4.A3B


title: bl11_p-axo26p2_4.A7B


title: bl11_p-axo26p2_4.A6B


title: bl11_p-axo26p2_4.A9B


title: bl11_p-axo26p2_4.C8B


title: bl11_p-axo26p1.H7B


title: bl11_p-axo26p2_4.C4B


title: bl11_p-axo26p1.H4B


title: bl11_p-axo26p2_4.A10B


title: bl11_p-axo26p2_4.C11B


title: bl11_p-axo26p1.H12B


title: bl11_p-axo26p1.H9B


title: bl11_p-axo26p1.G9B


title: bl11_p-axo26p2_4.A11B


title: bl11_p-axo26p1.H3B


title: bl11_p-axo26p1.H1B


title: bl11_p-axo26p1.G7B


title: bl11_p-axo26p1.G2B


title: bl11_p-axo26p1.F7B


title: bl11_p-axo26p1.G3B


title: bl11_p-axo26p1.G10B


title: bl11_p-axo26p1.F9B


title: bl11_p-axo26p2_4.B12B


title: bl11_p-axo26p1.F6B


title: bl11_p-axo26p1.G5B


title: bl11_p-axo26p1.H2B


title: bl11_p-axo26p1.F5B


title: bl11_p-axo26p1.F4B


title: bl11_p-axo26p1.F1B


title: bl11_p-axo26p1.E3B


title: bl11_p-axo26p1.E8B


title: bl11_p-axo26p1.E2B


title: bl11_p-axo26p1.E9B


title: bl11_p-axo26p1.F10B


title: bl11_p-axo26p1.D4B


title: bl11_p-axo26p1.D2B


title: bl11_p-axo26p1.D5B


title: bl11_p-axo26p1.E1B


title: bl11_p-axo26p1.E4B


title: bl11_p-axo26p1.E7B


title: bl11_p-axo26p1.D1B


title: bl11_p-axo26p1.D12B


title: bl11_p-axo26p1.C9B


title: bl11_p-axo26p1.D9B


title: bl11_p-axo26p1.G12B


title: bl11_p-axo26p1.C8B


title: bl11_p-axo26p1.C3B


title: bl11_p-axo26p1.C6B


title: bl11_p-axo26p1.C4B


title: bl11_p-axo26p1.C2B


title: bl11_p-axo26p1.C12B


title: bl11_p-axo26p1.C10B


title: bl11_p-axo26p1.B9B


title: bl11_p-axo26p1.D11B


title: bl11_p-axo26p1.B5B


title: bl11_p-axo26p1.B4B


title: bl11_p-axo26p1.A9B


title: bl11_p-axo19p3.G9A


title: bl11_p-axo26p1.C5B


title: bl11_p-axo26p1.B3B


title: bl11_p-axo26p1.B12B


title: bl11_p-axo26p1.A7B


title: bl11_p-axo26p1.A5B


title: bl11_p-axo26p1.A11B


title: bl11_p-axo26p1.A2B


title: bl11_p-axo26p1.C7B


title: bl11_p-axo26p1.B7B


title: bl11_p-axo19p3.E9A


title: bl11_p-axo26p1.A6B


title: bl11_p-axo19p3.F3A


title: bl11_p-axo19p3.E4A


title: bl11_p-axo19p3.F5A


title: bl11_p-axo19p3.E5A


title: bl11_p-axo26p1.C1B


title: bl11_p-axo19p3.F6A


title: bl11_p-axo19p3.E8A


title: bl11_p-axo26p1.A1B


title: bl11_p-axo26p1.B6B


title: bl11_p-axo19p3.E2A


title: bl11_p-axo19p3.E11A


title: bl11_p-axo19p3.G8A


title: bl11_p-axo19p3.E12A


title: bl11_p-axo19p3.E7A


title: bl11_p-axo19p3.D9A


title: bl11_p-axo19p3.E10A


title: bl11_p-axo19p3.D8A


title: bl11_p-axo19p3.D12A


title: bl11_p-axo19p3.D4A


title: bl11_p-axo19p3.C9A


title: bl11_p-axo19p3.D11A


title: bl11_p-axo19p3.C6A


title: bl11_p-axo19p3.B5A


title: bl11_p-axo19p3.C11A


title: bl11_p-axo19p3.E3A


title: bl11_p-axo19p3.C8A


title: bl11_p-axo19p3.B10A


title: bl11_p-axo19p3.B4A


title: bl11_p-axo19p3.C4A


title: bl11_p-axo19p3.C5A


title: bl11_p-axo19p3.B7A


title: bl11_p-axo19p3.A3A


title: bl11_p-axo19p3.C12A


title: bl11_p-axo19p3.A10A


title: bl11_p-axo19p2.H9A


title: bl11_p-axo19p3.A7A


title: bl11_p-axo19p3.D6A


title: bl11_p-axo19p2.H2A


title: bl11_p-axo19p2.H12A


title: bl11_p-axo19p2.H4A


title: bl11_p-axo19p2.G4A


title: bl11_p-axo19p2.G8A


title: bl11_p-axo19p2.G12A


title: bl11_p-axo19p2.F9A


title: bl11_p-axo19p2.F6A


title: bl11_p-axo19p2.G10A


title: bl11_p-axo19p2.F5A


title: bl11_p-axo19p2.F1A


title: bl11_p-axo19p2.F10A


title: bl11_p-axo19p2.F3A


title: bl11_p-axo19p2.F4A


title: bl11_p-axo19p2.E4A


title: bl11_p-axo19p2.E8A


title: bl11_p-axo19p2.E6A


title: bl11_p-axo19p2.E9A


title: bl11_p-axo19p2.D9A


title: bl11_p-axo19p2.D5A


title: bl11_p-axo19p2.E2A


title: bl11_p-axo19p2.E1A


title: bl11_p-axo19p2.G2A


title: bl11_p-axo19p2.D7A


title: bl11_p-axo19p2.D2A


title: bl11_p-axo19p2.C7A


title: bl11_p-axo19p2.C8A


title: bl11_p-axo19p2.C4A


title: bl11_p-axo19p2.C3A


title: bl11_p-axo19p2.C12A


title: bl11_p-axo19p2.D11A


title: bl11_p-axo19p2.C10A


title: bl11_p-axo19p2.F12A


title: bl11_p-axo19p2.B7A


title: bl11_p-axo19p2.B5A


title: bl11_p-axo19p2.C6A


title: bl11_p-axo19p2.D4A


title: bl11_p-axo19p2.B12A


title: bl11_p-axo19p2.E12A


title: bl11_p-axo19p2.A7A


title: bl11_p-axo19p2.B10A


title: bl11_p-axo19p2.A4A


title: bl11_p-axo19p2.A6A


title: bl11_p-axo19p2.A12A


title: ad_p-axo17p.H9B

value: uninjured upper arm


title: ad_p-axo17p.H8B


title: ad_p-axo17p.G8B


title: ad_p-axo17p.G3B


title: ad_p-axo17p.F7B


title: ad_p-axo17p.G4B


title: ad_p-axo17p.F6B


title: ad_p-axo17p.F2B


title: ad_p-axo17p.F4B


title: ad_p-axo17p.F12B


title: ad_p-axo17p.F10B


title: ad_p-axo17p.E9B


title: ad_p-axo17p.E5B


title: ad_p-axo17p.E2B


title: ad_p-axo17p.E4B


title: ad_p-axo17p.E12B


title: bl11_p-axo19p2.B3A


title: bl11_p-axo19p2.B9A


title: ad_p-axo17p.D9B


title: ad_p-axo17p.H10B


title: ad_p-axo17p.D8B


title: ad_p-axo17p.E10B


title: ad_p-axo17p.D6B


title: ad_p-axo17p.C5B


title: ad_p-axo17p.D10B


title: ad_p-axo17p.D3B


title: ad_p-axo17p.D5B


title: ad_p-axo17p.C12B


title: ad_p-axo17p.C10B


title: ad_p-axo17p.B7B


title: ad_p-axo17p.B5B


title: ad_p-axo17p.B4B


title: ad_p-axo17p.B6B


title: ad_p-axo17p.B1B


title: ad_p-axo17p.B9B


title: ad_p-axo17p.A3B


title: ad_p-axo17p.B8B


title: axo23.H9B

source_name: Stage 28 forelimb limb field

extract_protocol:
Single cell isolation by pipetting and cDNA generation following SmartSeq2 protocol. (Nat Protoc. 2014 Jan;9(1):171-81. doi: 10.1038/nprot.2014.006. Epub 2014 Jan 2.)
Libraries were prepared using Illumina Nextera XT kit according to illumina's protocol.

value: stage 28 limb field


title: axo23.H8B


title: axo23.H5B


title: axo23.H6B


title: axo23.H7B


title: axo23.H4B


title: ad_p-axo17p.A12B


title: axo23.H2B


title: axo23.H3B


title: axo23.H1B


title: axo23.G9B


title: axo23.G4B


title: axo23.H10B


title: axo23.G3B


title: axo23.G6B


title: axo23.G10B


title: axo23.G11B


title: axo23.F9B


title: axo23.F8B


title: axo23.F4B


title: axo23.F6B


title: axo23.G2B


title: axo23.F3B


title: axo23.F7B


title: axo23.F5B


title: axo23.G1B


title: axo23.F2B


title: axo23.F1B


title: axo23.F12B


title: axo23.F11B


title: axo23.F10B


title: axo23.E7B


title: axo23.E5B


title: axo23.E9B


title: axo23.E4B


title: axo23.E1B


title: axo23.E3B


title: axo23.E2B


title: axo23.D9B


title: axo23.D7B


title: axo23.D1B


title: axo23.D4B


title: axo23.D11B


title: axo23.D10B


title: axo23.E11B


title: axo23.D3B


title: axo23.D8B


title: axo23.E10B


title: axo23.D2B


title: axo23.C6B


title: axo23.D5B


title: axo23.C7B


title: axo23.C5B


title: axo23.C8B


title: axo23.C4B


title: axo23.E8B


title: axo23.C3B


title: axo23.C2B


title: axo23.C11B


title: axo23.B9B


title: axo23.B8B


title: axo23.C1B


title: axo23.C10B


title: bl11_p-axo19p2.B6A


title: axo23.B7B


title: axo23.B6B


title: axo23.C9B


title: axo23.B5B


title: axo23.B4B


title: axo23.B11B


title: axo23.A9B


title: axo23.B3B


title: axo23.B1B


title: axo23.B2B


title: axo23.A7B


title: axo23.B10B


title: axo23.A6B


title: axo23.A2B


title: axo23.A5B


title: axo23.A10B


title: axo23.A4B


title: axo23.A1B


title: axo29.H5A

source_name: forelimb upper arm uninjured 3mpa

extract_protocol:
Single cell isolation and cDNA generation using Fluidigm C1 platform with reagents provided by Fluidigm as well as the SMARTer v2 Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions at a dilution of 1:40,000.
Libraries were prepared using Illumina Nextera XT kit according to illumina's protocol.

value: Fluidigm C1

value: uninjured upper arm 3mpa


title: axo29.H4A


title: axo23.A11B


title: axo29.H4B


title: axo29.H2B


title: axo29.H3B


title: axo29.H2A


title: axo29.H12A


title: axo29.H1B


title: axo29.H1A


title: axo29.H11B


title: axo29.H11A


title: axo29.G8A


title: axo23.A8B


title: axo29.G4B


title: axo29.G7B


title: axo29.G3A


title: axo29.G4A


title: axo29.G12B


title: axo29.G11B


title: axo29.G2B


title: axo29.G1A


title: axo29.G10A


title: axo29.F6B


title: axo29.F5A


title: axo29.F12B


title: axo29.F3A


title: axo29.F5B


title: axo29.F10B


title: axo29.F4B


title: axo29.F10A


title: axo29.E8B


title: axo29.F4A


title: axo29.F12A


title: axo29.E5A


title: axo29.E4B


title: axo29.F11A


title: axo29.E6A


title: axo29.G6A


title: axo29.E2B


title: axo29.E2A


title: axo29.E5B


title: axo29.E1A


title: axo29.E12B


title: axo29.E1B


title: axo29.D2B


title: axo29.D4B


title: axo29.D5A


title: axo29.D5B


title: axo29.D3B


title: axo29.D12A


title: axo29.D4A


title: axo29.C8A


title: axo29.C5B


title: axo29.C4B


title: axo29.C2B


title: axo29.C11A


title: axo29.E4A


title: axo29.B7A


title: axo29.B9A


title: axo29.C1A


title: axo29.B6A


title: axo29.B4A


title: axo29.B2B


title: axo29.B5B


title: axo29.B2A


title: axo29.A9A


title: axo29.A6A


title: axo29.A4A


title: axo29.A3B


title: axo29.D10A


title: axo29.C9A


title: axo29.A2A


title: axo29.A12B


title: axo29.A1A


title: axo29.A11B


title: axo20.H6A

source_name: forelimb upper arm uninjured 1apa

value: uninjured upper arm 1apa


title: axo29.C1B


title: axo20.H1A


title: axo20.H12B


title: axo29.C12A


title: axo20.H10B


title: axo20.H6B


title: axo20.G8A


title: axo20.G5A


title: axo20.G6A


title: axo20.F2A


title: axo20.G12B


title: axo20.F4A


title: axo20.F4B


title: axo20.F3A


title: axo20.F10A


title: axo29.A5B


title: axo20.G11A


title: axo20.F7B


title: axo20.E9A


title: axo20.E8A


title: axo20.E6A


title: axo20.E3A


title: axo20.H3B


title: axo20.E5B


title: axo20.D11B


title: axo20.D11A


title: axo20.D7B


title: axo20.C8B


title: axo20.C7B


title: axo20.D6B


title: axo20.F8A


title: axo20.D4B


title: axo20.B9B


title: axo20.B6A


title: axo20.C2B


title: axo20.C1B


title: axo20.B12B


title: axo20.B10B


title: axo20.B5B


title: axo20.B1A


title: axo20.A5B


title: axo20.B11A


title: axo20.A2B


title: axo20.A7B


title: axo21.H8B

value: blastema 18 dpa


title: axo20.C9B


title: axo20.E12A


title: axo20.A2A


title: axo20.A1A


title: axo20.A12B


title: axo20.D8B


title: axo21.H8A


title: axo21.H6B


title: axo21.H5A


title: axo21.H6A


title: axo20.B2B


title: axo21.H4B


title: axo21.H4A


title: axo20.A4A


title: axo21.H3A


title: axo21.H1B


title: axo21.H2A


title: axo21.H12A


title: axo20.A3A


title: axo21.H10A


title: axo21.G9B


title: axo21.G8B


title: axo21.H11B


title: axo21.G8A


title: axo21.G7B


title: axo21.H10B


title: axo21.G6B


title: axo21.H7B


title: axo21.G1B


title: axo21.G1A


title: axo21.G5A


title: axo21.G3B


title: axo21.G2B


title: axo21.G4B


title: axo21.G5B


title: axo21.H3B


title: axo21.G10A


title: axo21.G12B


title: axo21.F9B


title: axo21.F9A


title: axo21.F8B


title: axo21.F8A


title: axo21.F6A


title: axo21.F7B


title: axo21.F6B


title: axo21.F5B


title: axo21.F4B


title: axo21.F5A


title: axo21.F3B


title: axo21.F12B


title: axo21.F4A


title: axo21.F1A


title: axo21.F2B


title: axo21.E9A


title: axo21.E8A


title: axo21.E9B


title: axo21.G11A


title: axo21.F10B


title: axo21.E6B


title: axo21.E6A


title: axo21.E4B


title: axo21.E4A


title: axo21.E7B


title: axo21.E5B


title: axo21.E2A


title: axo21.E12A


title: axo21.E11B


title: axo21.E11A


title: axo21.E10A


title: axo21.D9B


title: axo21.D8A


title: axo21.F1B


title: axo21.D7B


title: axo21.D7A


title: axo21.D8B


title: axo21.D5B


title: axo21.D1B


title: axo21.D1A


title: axo21.D5A


title: axo21.D4B


title: axo21.D2A


title: axo21.D2B


title: axo21.D11A


title: axo21.D12B


title: axo21.D3A


title: axo21.D10B


title: axo21.D11B


title: axo21.E12B


title: axo21.C9A


title: axo21.C8B


title: axo21.C8A


title: axo21.C4B


title: axo21.C6A


title: axo21.D9A


title: axo21.C6B


title: axo21.C7A


title: axo21.D4A


title: axo21.C3B


title: axo21.C2A


title: axo21.C1A


title: axo21.C2B


title: axo21.D12A


title: axo21.C12B


title: axo21.C4A


title: axo21.B5B


title: axo21.B3B


title: axo21.C1B


title: axo21.B5A


title: axo21.C11A


title: axo21.B9B


title: axo21.B1B


title: axo21.B2A


title: axo21.C11B


title: axo21.B7A


title: axo21.B6B


title: axo21.B8B


title: axo21.B9A


title: axo21.B1A


title: axo21.B4A


title: axo21.A5A


title: axo21.A6B


title: axo21.B12B


title: axo21.B12A


title: axo21.A9B


title: axo21.B6A


title: axo21.B11B


title: axo21.B8A


title: axo21.A4A


title: axo21.A8B


title: axo21.A4B


title: axo21.A3B


title: axo21.A1B


title: axo21.A1A


title: axo21.A3A


title: axo21.A2A


title: axo21.A10A


title: axo21.A11B


title: axo16.H7

source_name: forelimb upper arm blastema 8 dpa

value: blastema 8 dpa


title: axo21.A12A


title: axo16.H6B


title: axo21.A12B


title: axo16.H5B


title: axo16.H7B


title: axo16.H6


title: axo21.A11A


title: axo21.A7B


title: axo16.H5


title: axo16.H4B


title: axo16.H4


title: axo16.H2


title: axo16.H1B


title: axo16.H3B


title: axo16.H2B


title: axo21.B4B


title: axo16.H12B


title: axo21.C3A


title: axo16.H12


title: axo16.G9


title: axo16.H10


title: axo16.G8B


title: axo16.G8


title: axo16.G11


title: axo16.G11B


title: axo16.G10B


title: axo16.F6B


title: axo16.F7B


title: axo16.H10B


title: axo16.E9B


title: axo16.E9


title: axo16.E8B


title: axo16.E7


title: axo16.E5B


title: axo16.G6B


title: axo16.F1B


title: axo16.F5B


title: axo16.G3B


title: axo16.F3


title: axo16.G4


title: axo16.F4B


title: axo16.G5


title: axo16.F6


title: axo16.E5


title: axo16.F5


title: axo16.F4


title: axo16.F12


title: axo16.G1B


title: axo16.G6


title: axo16.E4B


title: axo16.G12


title: axo16.G4B


title: axo16.F8B


title: axo16.E2B


title: axo16.E4


title: axo16.E12B


title: axo16.E12


title: axo16.E11


title: axo16.E1


title: axo16.D9


title: axo16.D8B


title: axo16.D7B


title: axo16.D7


title: axo16.D5B


title: axo16.D12B


title: axo16.D1B


title: axo16.D5


title: axo16.D6B


title: axo16.D4B


title: axo16.D3B


title: axo16.D10B


title: axo16.D3


title: axo16.D10


title: axo16.C9


title: axo16.C8


title: axo16.D11


title: axo16.E2


title: axo16.C9B


title: axo16.D1


title: axo16.D6


title: axo16.D11B


title: axo16.D4


title: axo16.C12


title: axo16.C5B


title: axo16.C4


title: axo16.C2


title: axo16.C11B


title: axo16.C3


title: axo16.C6B


title: axo16.C10B


title: axo16.C11


title: axo16.C10


title: axo16.C1


title: axo16.B9B


title: axo16.B7B


title: axo16.B9


title: axo16.B6B


title: axo16.B3


title: axo16.B3B


title: axo16.B2B


title: axo16.B1B


title: axo16.B2


title: axo16.B11B


title: axo16.B10B


title: axo16.B1


title: axo16.A9B


title: axo16.B10


title: axo16.A8


title: axo16.A6B


title: axo16.A6


title: axo16.A7B


title: axo16.A7


title: axo16.A8B


title: axo16.A3


title: axo16.A3B


title: axo16.A4


title: axo16.A4B


title: axo16.A2


title: axo16.A12B


title: axo16.A1B


title: axo16.B12B


title: axo16.A5


title: axo16.A5B


title: axo15.H8B

source_name: forelimb upper arm blastema 3 dpa

value: blastema 3 dpa


title: axo15.H9B


title: axo16.A11B


title: axo15.H4B


title: axo15.H5B


title: axo15.H10B


title: axo15.H12B


title: axo15.G8B


title: axo15.G6B


title: axo15.H6B


title: axo15.G7B


title: axo15.G3B


title: axo16.A1


title: axo15.G5


title: axo15.G1B


title: axo15.G12B


title: axo15.F6


title: axo15.G11B


title: axo15.F9B


title: axo15.F7B


title: axo16.A10


title: axo15.G10B


title: axo15.F4


title: axo15.F3B


title: axo15.F2


title: axo15.F12


title: axo15.F3


title: axo15.G4B


title: axo15.F1B


title: axo15.F10B


title: axo15.G3


title: axo15.E6


title: axo15.E8B


title: axo15.E5B


title: axo15.F10


title: axo15.E1B


title: axo15.E2B


title: axo15.E3B


title: axo15.E10B


title: axo15.E11B


title: axo15.E12B


title: axo15.D8B


title: axo15.D8


title: axo15.D6B


title: axo15.F5


title: axo15.F4B


title: axo15.D2B


title: axo15.D12B


title: axo15.D4B


title: axo15.D5B


title: axo15.D2


title: axo15.D1B


title: axo15.D5


title: axo15.D12


title: axo15.D11


title: axo15.D11B


title: axo15.D10B


title: axo15.E4


title: axo15.C9


title: axo15.C8B


title: axo15.C9B


title: axo15.B9B


title: axo15.C1


title: axo15.B9


title: axo15.B8


title: axo15.B7B


title: axo15.B6


title: axo15.B5B


title: axo15.B6B


title: axo15.C6


title: axo15.C12B


title: axo15.C6B


title: axo15.C2B


title: axo15.C4B


title: axo15.C7B


title: axo15.C2


title: axo15.C4


title: axo15.C5B


title: axo15.C12


title: axo15.C3B


title: axo15.C10B


title: axo15.C11B


title: axo15.B1B


title: axo15.B5


title: axo15.B11B


title: axo15.B3B


title: axo15.B12B


title: axo15.B10B


title: axo15.B4B


title: axo15.B12


title: axo15.A9B


title: axo15.B7


title: axo15.B1


title: axo15.A7B


title: axo15.A8B


title: axo15.A7


title: axo15.A9


title: axo15.A12B


title: axo15.A1B


title: axo15.A12


title: axo15.A11


title: axo15.A4


title: axo15.A6


title: axo15.A5B


title: axo15.A3B


title: axo15.A11B


title: axo15.A5


title: axo15.A10B


title: axo14.H9A

source_name: Stage 40 forelimb limb bud

value: stage 40 limb bud


title: axo14.H8A


title: axo14.H7A


title: axo14.H6A


title: axo14.H4A


title: axo14.H2A


title: axo14.H3A


title: axo14.H12A


title: axo14.G8A


title: axo14.G9A


title: axo14.G7A


title: axo15.A2


title: axo14.G3A


title: axo14.G6A


title: axo15.A6B


title: axo14.G12A


title: axo14.G10A


title: axo14.G1A


title: axo14.G11A


title: axo14.F2A


title: axo14.H5A


title: axo14.F6A


title: axo14.G2A


title: axo14.F4A


title: axo14.F5A


title: axo14.F8A


title: axo14.F10A


title: axo14.E7A


title: axo14.F12A


title: axo14.E5A


title: axo14.E8A


title: axo14.E9A


title: axo14.H1A


title: axo14.F11A


title: axo14.E3A


title: axo14.F1A


title: axo14.E2A


title: axo14.E10A


title: axo14.D9A


title: axo14.E6A


title: axo14.B8A


title: axo14.D1A


title: axo14.B7A


title: axo14.C9A


title: axo14.C8A


title: axo14.D3A


title: axo14.B4A


title: axo14.D2A


title: axo14.C12A


title: axo14.B6A


title: axo14.D7A


title: axo14.D12A


title: axo14.D8A


title: axo14.D11A


title: axo14.B2A


title: axo14.D6A


title: axo14.C5A


title: axo14.C1A


title: axo14.C3A


title: axo14.C11A


title: axo14.C4A


title: axo14.B1A


title: axo14.D5A


title: axo14.B11A


title: axo14.A8A


title: axo7.H7B


title: axo14.A2A


title: axo14.A11A


title: axo14.B3A


title: axo14.A6A


title: axo14.C6A


title: axo14.A12A


title: axo14.G5A


title: axo7.G5B


title: axo7.H3B


title: axo7.G4B


title: axo7.F6B


title: axo14.E11A


title: axo14.B10A


title: axo15.A2B


title: axo14.E4A


title: axo7.E7B


title: axo14.A10A


title: axo7.D6B


title: axo7.E1B


title: axo7.D4B


title: axo7.E4B


title: axo7.C8B


title: axo7.C3B


title: axo14.A3A


title: axo7.B1B


title: axo6.H6B


title: axo6.H5B


title: axo6.H4B


title: axo6.G6B


title: axo6.G10B


title: axo7.C5B


title: axo6.F9B


title: axo6.F11B


title: axo6.E12B


title: axo6.E5B


title: axo6.D7B


title: axo6.D5B


title: axo6.F4B


title: axo6.F2B


title: axo6.E10B


title: axo6.F8B


title: axo6.E3B


title: axo6.F6B


title: axo6.D8B


title: axo6.D4B


title: axo6.C8B


title: axo6.C6B


title: axo6.D12B


title: axo6.C12B


title: axo6.C4B


title: axo6.G9B


title: axo6.C11B


title: axo6.B9B


title: axo6.A7B


title: axo6.B1B


title: axo6.A3B


title: axo6.B8B


title: axo6.B6B


title: axo6.A2B


title: axo6.A12B


title: axo13.H4B


title: axo13.H11B


title: axo13.G11B


title: axo13.G3B


title: axo13.H6B


title: axo13.G5B


title: axo13.H3B


title: axo13.G6B


title: axo14.A4A


title: axo13.G12B


title: axo13.H1B


title: axo13.H12B


title: axo13.F9B


title: axo13.F6B


title: axo13.G8B


title: axo13.F4B


title: axo13.E4B


title: axo13.G9B


title: axo13.E12B


title: axo13.G10B


title: axo13.D10B


title: axo13.C8B


title: axo13.F5B


title: axo13.D8B


title: axo13.D7B


title: axo13.D5B


title: axo13.D2B


title: axo13.D4B


title: axo13.C4B


title: axo13.C7B


title: axo13.A11B


title: axo13.B3B


title: axo12.H7


title: axo13.C1B


title: axo12.E10


title: axo13.B2B


title: axo13.B4B


title: axo12.G10


title: axo12.G7


title: axo12.F5


title: axo12.D6


title: axo12.G9


title: axo12.D9


title: axo12.D2


title: axo12.D7


title: axo12.G1


title: axo12.C4


title: axo12.D3


title: axo13.C2B


title: axo12.C6


title: axo12.C10


title: axo12.A10


title: axo12.A8


title: axo12.C1


title: axo12.B3


title: axo12.B4


title: axo12.B7


title: axo12.A1


title: axo9.H9A


title: axo9.H8A


title: axo9.H7A


title: axo9.H3A


title: axo9.H6A


title: axo12.C3


title: axo9.H4A


title: axo7.G6B


title: axo9.H2A


title: axo9.H1A


title: P.NP-ISCS-B-NA_naive_Female_replicate 2

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn4 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: rn4
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contains the read counts of the gene using htseq-count

organism: Rattus norvegicus

source_name: Nucleus Accumbens

extract_protocol:
RNA was isolated using TRIzol reagent followed by RNeasy mini kit for purification
Total RNA samples about 1-2 ug were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp pair-end (PE) sequencing protocol.

treatment_protocol: Alcohol Naïve

value: Experimental

value: Nucleus Accumbens

value: female

value: naive interval-specific congenic strain


title: axo9.H11A


title: P.NP-ISCS-B-NA_naive_Female_replicate 3


title: axo9.G8A


title: axo9.H10A


title: iP-NA_naive_Female_replicate 2

value: Control

value: iP-NA-naive


title: P.NP-ISCS-B-NA_naive_Female_replicate 1


title: axo12.B1


title: axo9.G7A


title: LHM115 under basal condition, biological rep1

city: Tokyo

first: Masumichi

last: Saito

address: Musashimurayama

department: Department of Safety Research on Blood and Biological Products

institute: National Institute of Infectious Diseases

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on Human Genome U133 Plus 2.0 Arraysaccording to the standard Affymetrix protocol ((3’ IVT PLUS Reagent Kit). GeneChips were washed and stained in the GeneChiP Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: HTLV-1/EBV infected B-cell lines (ATLL derived B-cell lines)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from100 ng total RNA (3’ IVT PLUS Reagent Kit ).

growth_protocol: Cell lines were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum, 100 U/ml penicillin, 100 μg/ml streptomycin at 37°C in a 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted using Quick-RNATM Mini Prep kit (Zymo Research) according to the manufacturer's instructions.

value: HTLV-1/EBV infected B-cell lines derived from ATLL

value: Peripheral blood lymphocytes

value: Male


title: axo9.H5A

value: blastema 11 dpa


title: LHM115 under basal condition, biological rep3


title: OATL9 under basal condition, biological rep1


title: OATL9 under basal condition, biological rep3


title: LMY3B under basal condition, biological rep2


title: LHM115 under basal condition, biological rep2


title: iP-NA_naive_Female_replicate 1


title: axo9.G6A

value: Fluidigm C1


title: OATL9 under basal condition, biological rep2


title: LMY3B under basal condition, biological rep1


title: axo9.G5A


title: axo9.G2A


title: LMY3B under basal condition, biological rep3


title: axo9.G4A


title: axo9.G3A


title: axo9.G11A


title: WI38

city: Toronto

first: Donghyun

last: Lee

state: Ontario

address: 686 Bay Street

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

data_processing:
Quality score of bases were determined using Phred score system
Reads underwent filters with unconverted C filter to remove all reads that originated from non bisulfite-converted strands
BS-Seeker2 was used to align the reads and obtain raw methylation values (ranging from 0.0 - 1.0)
Genome_build: hg19
Supplementary_files_format_and_content: .xls file was generated by collecting data from output files of each sample after appropriate processing. Values represent methylation percentage at each CpG site in genomic coordinate Chr5:XXXXXXX (hg19)

source_name: Normal human fibroblast

growth_protocol: Human cancer cell lines were cultured under ATCC-recommended conditions

extract_protocol:
DNA from cultured human cancer cell lines were extracted using QIAGEN Dneasy Blood & Tissue Kit. Tumor and normal DNA samples from human were extracted from other collaborating centers
For NGS using the HiSeq platform, the PCR products were first purified using the QIAquick Gel Purification Kit (Qiagen), followed by sequencing library preparation using Nextera XT DNA Library Preparation Kit (Illumina) according to standard single-end sequencing protocol provided and sequenced following the manufacturer’s instructions for the HiSeq 2500 Rapid Run (Illumina) mode to obtain 126 nucleotide read lengths.
For NGS using the MiSeq platform, the resulting PCR products were prepared in accordance to the 16S Metagenomic Sequencing Library Preparation guide (15044223 B, Illumina) and were sequenced following the manufacturer’s instructions for the MiSeq Reagent Kit v3 (Illumina) to obtain single-end 125 nucleotide read lengths.
Bisulfite-Seq (Targeted)

tag: tissue type

value: Skin


title: SK-N-AS

source_name: Cancer Cell Line

value: Cancer cell line (Brain)

value: SK-N-AS


title: axo9.G1A


title: iP-NA_naive_Female_replicate 3

tag: genotype/variation


title: 148108

source_name: Normal human blood

value: Blood


title: 145370


title: 140364


title: axo9.G10A


title: 1827


title: axo9.F9A


title: 129013


title: 148620


title: 150980


title: 124049


title: axo9.F7A


title: axo9.F5A


title: axo9.F6A


title: 134852


title: 150892


title: axo9.G12A


title: 1754


title: axo9.F1A


title: 127844


title: axo9.F2A


title: 124132


title: axo9.F12A


title: axo9.F10A


title: axo9.F11A


title: 124096


title: axo9.E8A


title: 1505


title: 1644


title: axo9.E7A


title: axo9.F4A


title: axo9.E6A


title: GBP7062


title: axo9.E4A


title: axo9.E3A


title: HeLa

value: Cancer cell line (Cervix)

value: HeLa


title: axo9.E2A


title: A172


title: NF54188


title: T24

value: Cancer cell line (Bladder)


title: Med8a


title: axo9.E1A


title: axo9.E11A


title: axo9.E10A


title: axo9.D9A


title: axo9.D7A


title: 2044


title: GBP7065


title: axo9.D5A


title: axo9.D6A


title: axo9.E5A


title: axo9.D2A


title: axo9.D12A


title: axo9.D3A


title: axo9.D4A


title: T70_GARD_BATCH_2

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

institute: Canadian Centre for Computational Genomics (C3G)

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence.
Read count estimates per gene were obtained using the alignment-free method STAR (2.4.1d).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files include count values for each sample

source_name: Peripheral blood mononuclear cells

growth_protocol: PBMCs were isolated from whole blood by Ficoll-Paque centrifugation and cryopreserved.

extract_protocol:
Total RNA was extracted from the non-stimulated and stimulated cells using the  miRNeasy kit (Qiagen). RNA quantity was evaluated spectrophotometrically, and the  quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies). Only samples with no evidence for RNA degradation (RNA integrity number > 8) were kept for further experiments.
Indexed cDNA libraries were pooled (6 libraries per pool) in  equimolar amounts and sequenced with single-end 100bp reads on an Illumina  HiSeq2500.

treatment_protocol: PBMCs were cultured in RPMI-1640 (Fisher) supplemented with 10% heatinactivated  FBS (FBS premium, US origin, Wisent) and 1% L-glutamine (Fisher). For  each of the tested individuals, PBMCs (2 million per condition) were stimulated for 4  hours at 37° C with 5% CO2 with the immune challenges gardiquimod (GARD, 0.5μg/ml,  TLR7 and TLR8 agonist) or lipopolysaccharide-EB (LPS, 0.25 μg/ml, TLR4 agonist). A  control group of non-stimulated PBMCs were treated the same way but with only  medium.

value: Peripheral blood mononuclear cells

tag: donor id

value: GARD

tag: population

value: Batwa

tag: admixture

tag: fraction assigned

tag: flowcell

tag: Sex

tag: proportion of cd4

tag: proportion of cd8

tag: proportion of cd14

tag: proportion of cd20

tag: proportion of cd56


title: T35_GARD_BATCH_2

tag: cell type

tag: treatment

value: Female


title: T70_CTL_FC5

value: CTL


title: T70_LPS_FC1_4

value: LPS


title: T35_CTL_FC5


title: T32_LPS_FC1_4


title: T32_GARD_BATCH_2


title: axo9.D11A

tag: cre line

tag: sc-rna-seq method


title: axo9.D10A

tag: development stage


title: ONS76

tag: tissue type

tag: cell line


title: T32_CTL_FC1_4

tag: donor id

tag: population


title: Du145

value: Cancer cell line (Prostate)


title: axo9.E12A


title: T35_LPS_FC1_4

tag: admixture

tag: fraction assigned


title: axo9.C5A


title: T121_CTL_FC1_4

tag: flowcell

tag: Sex


title: T120_GARD_BATCH_2

tag: proportion of cd4

tag: proportion of cd8


title: T14_LPS_FC1_4

value: Male

tag: proportion of cd14

tag: proportion of cd20


title: T14_CTL_FC1_4

tag: cell type

tag: proportion of cd56


title: axo9.C8A

tag: cre line

value: blastema 11 dpa


title: axo9.C7A

tag: sc-rna-seq method

value: Fluidigm C1


title: axo9.C6A

tag: development stage


title: axo9.C2A


title: axo9.C1A


title: axo9.C12A


title: T119_LPS_FC1_4

tag: treatment


title: T121_LPS_FC1_4


title: T117_LPS_FC1_4


title: T119_CTL_FC1_4


title: T119_GARD_BATCH_2


title: T14_GARD_BATCH_2


title: T117_CTL_FC1_4


title: axo9.C4A


title: axo9.A6A


title: axo9.A3A


title: T115_GARD_BATCH_2


title: T120_LPS_FC5


title: T120_CTL_FC1_4


title: axo9.C11A


title: axo9.C10A


title: axo9.A2A


title: axo9.C9A


title: axo9.A7A


title: T115_LPS_FC1_4


title: axo9.A8A


title: axo9.A1A


title: T113_LPS_FC5


title: T112_LPS_FC1_4


title: T113_GARD_BATCH_2


title: axo9.A12A


title: axo9.A11A


title: axo9.A10A


title: T112_GARD_BATCH_2


title: T110_GARD_BATCH_2


title: T112_CTL_FC1_4


title: T109_LPS_FC1_4


title: axo8.H5A


title: T109_CTL_FC1_4


title: axo8.H12A


title: axo8.H11B


title: axo8.H4B


title: axo8.H12B


title: T109_GARD_BATCH_2


title: axo8.H1B


title: T107_GARD_BATCH_2


title: T113_CTL_FC1_4


title: axo8.G5A


title: axo8.G7A


title: T106_GARD_BATCH_2


title: T106_LPS_FC1_4


title: T115_CTL_FC5


title: T106_CTL_FC1_4


title: axo8.G4A


title: axo8.H7A


title: T104_CTL_FC1_4


title: T104_LPS_FC1_4


title: T102_LPS_FC1_4


title: axo8.G3A


title: T104_GARD_BATCH_2


title: axo8.G12B


title: T101_LPS_FC1_4


title: T102_CTL_FC1_4


title: axo8.G11A


title: axo8.G10A


title: axo8.F4B


title: axo8.F5A


title: T84_LPS_FC1_4


title: T84_GARD_BATCH_2


title: T101_CTL_FC5


title: T84_CTL_FC5


title: axo8.F4A


title: axo8.F3B


title: T81_CTL_FC1_4


title: axo8.G3B


title: axo8.F3A


title: axo8.F2B


title: axo8.G12A


title: T81_LPS_FC1_4


title: axo8.F2A


title: T81_GARD_BATCH_2


title: T80_CTL_FC1_4


title: T101_GARD_BATCH_2


title: T80_LPS_FC5


title: axo8.F1B


title: axo8.F7A


title: axo8.G11B


title: axo8.F1A


title: T79_CTL_FC1_4


title: axo8.F12A


title: T78_GARD_BATCH_2


title: axo8.F11A


title: T78_LPS_FC1_4


title: axo8.F10A


title: T77_GARD_BATCH_2


title: axo8.E9B


title: axo8.E8B


title: axo8.E6B


title: T76_LPS_FC1_4


title: T77_LPS_FC1_4


title: T76_CTL_FC1_4


title: axo8.E5B


title: axo8.E6A


title: T79_LPS_FC5


title: axo8.E3B


title: axo8.E4A


title: axo8.E3A


title: T75_GARD_BATCH_2


title: axo8.E10B


title: axo8.E12B


title: T75_LPS_FC1_4


title: axo8.E11A


title: axo8.D7B