title: plateA3.positionB2.single.cell

description:
all.single.cell.gene.counts.txt
A3-B2


title: plateA3.positionA2.single.cell

status: Public on Jan 15 2019

type: SRA

city: Guangzhou

first: Guangdun

last: Peng

address: 190 Kaiyuan Road

department: Guangzhou Institutes of Biomedicine and Health

country: China

institute: Chinese Academy of Sciences

description:
all.single.cell.gene.counts.txt
A3-A2

library_source: transcriptomic

data_processing:
Reads were mapped to the mouse GRCm38 genome assemblies by HISAT2 using default settings
Uniquely aligned reads were counted using the ‘htseq-count’ tool of HTSeq
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes counts values for each single cell

molecule: total RNA

organism: Mus musculus

extract_protocol:
Lungs were digest with Collagenase, Dispase and Elastase sollution, Single epithelial cell was sorted by BD AriaII. Cell was lysed by single cell RNA lysis buffer containing 0.45% (vol/vol) NP40, followed by reverse transcription using SuperScript II reverse transcriptase (Invitrogen) and whole transcription amplification using KAPA HiFi HotStart ReadyMix (2X; KAPA Biosystems). PCR product was purified using AMPure XP beads (Agencourt) and quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher).
Libraries were constructed using illumina Nextera XT DNA sample preparation kit

tag: tissue

value: Lung

tag: cell type

value: epithelial cell

tag: genotype

tag: cell sub-type

value: Club cell


title: RMDB_156

type: RNA

city: Leeds

first: Chulin

last: Sha

address: Woodhouse Lane

department: School of Mole&Cell Biology

country: United Kingdom

institute: University of Leeds

description: REMoDLB trial

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Arrays were scanned on a BeadArray reader

data_processing: The data were normalised using lumi package in R

label: Biotin

organism: Homo sapiens

label_protocol: Standard Illumina label protocol

extract_protocol: Total RNA was extracted from 5mm paraffin sections using the Ambion RecoverAll kit standard protocol, with the exception of a 16-hour protease digestion. These were routinely collected tissue samples and no attempt was made to standardise fixation or processing protocols

tag: clinic diagnosis

value: Diffuse Large B-cell Lymphoma

tag: molecular subtype

value: GCB

tag: molecular coo subtype


title: cowpox virus at 2H, biological rep3

city: Singapore

first: Richard

middle: J

last: Sugrue

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description: Mouse RAW_Cowpox virus_2H-3

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45˚C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing:
The data were analyzed with GeneChip Operating Software 5.0 (GCOS 5.0) using Affymetrix default analysis settings. Further analysis was done in GeneSpring 11.0. The normalization was done using internal and external control genes as assigned by Affymetrix. The target intensity of each array on a given time point was first filtered by the flagging of Present (P) in 3 replicates at one time-point, which then further calculated in fold change up- or downregulation with respect to the signal intensity in MOCK infected cells, after analyzed by ANOVA with p value ≤ 0.05.
Algorithm: ExpressionStat 5.0

label: biotin

source_name: Cowpox virus infected mouse RAW 2 hpi

label_protocol: Biotinylated mRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

growth_protocol: The cells were grown in DMEM L929 (30%) cell condition media (Gibco) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2

extract_protocol: RNA extraction was performed using RNAeasy MiniKit (Qiagen) according to the manufacturer's instruction at 4˚C

treatment_protocol: The cells were infected with cowpox virus at 95% confluence at MOI=10 and incubated for 1 hr in DMEM with 2% Fetal Bovine Serum (FBS) at 37˚C, 5% CO2

tag: cell line

value: RAW 264.7 cells

value: murine macrophage cell line

tag: infection

value: Cowpox virus

tag: time point

value: 2 hpi


title: plateA3.positionH1.single.cell

description:
all.single.cell.gene.counts.txt
A3-H1


title: K2231_2

city: Tianjin

first: Ying

last: Wang

address: 288 Nanjing Road

institute: State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).
PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

growth_protocol: Kasumi-1 cells were routinely maintained in RPMI-1640 medium with supplemented with 20% fetal bovine serum (FBS, Invitrogen).

extract_protocol:
RNA was extracted and digested by DNase I, then quantification and qualification were performed and checked before next step. cDNA libraries were constructed using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated

treatment_protocol: The short hairpin double-stranded oligo targeting the back-splice junction of the F-CircAE was inserted into the pLKO.1-puro or pLKO.1-GFP lentiviral vector.  Scramble was used as control. Then lentivirus generation and infection were conducted to knock down the expression of F-CircAE in Kasumi-1 cells.

value: human acute myeloid leukemia cell line (Kasumi-1) with 8;21 chromosome translocation

value: AML1-ETO related fusion circular RNA knockdown


title: plateA3.positionG1.single.cell

description:
all.single.cell.gene.counts.txt
A3-G1


title: K2231_3


title: K2231_1


title: plateA3.positionE1.single.cell

description:
all.single.cell.gene.counts.txt
A3-E1


title: plateA3.positionD1.single.cell

description:
all.single.cell.gene.counts.txt
A3-D1


title: plateA3.positionF1.single.cell

description:
all.single.cell.gene.counts.txt
A3-F1


title: plateA3.positionC1.single.cell

description:
all.single.cell.gene.counts.txt
A3-C1


title: RMDB_149

description: REMoDLB trial


title: RMDB_148

description: REMoDLB trial


title: Mock infected mouse RAW rep 2

description: Mock infected mouse RAW-2

source_name: Mock infected mouse RAW


title: K2133_3


title: K2133_2


title: RMDB_145

description: REMoDLB trial

value: ABC


title: plateA3.positionB1.single.cell

description:
all.single.cell.gene.counts.txt
A3-B1


title: RMDB_147

description: REMoDLB trial

value: MHG


title: plateA3.positionA1.single.cell

description:
all.single.cell.gene.counts.txt
A3-A1


title: Mock infected mouse RAW rep 1

description: Mock infected mouse RAW-1


title: RMDB_144

description: REMoDLB trial


title: K2133_1


title: RMDB_146

description: REMoDLB trial


title: plateA2.positionH12.single.cell

description:
all.single.cell.gene.counts.txt
A2-H12


title: plateA2.positionG12.single.cell

description:
all.single.cell.gene.counts.txt
A2-G12

value: BASCs


title: plateA2.positionF12.single.cell

description:
all.single.cell.gene.counts.txt
A2-F12


title: plateA2.positionE12.single.cell

description:
all.single.cell.gene.counts.txt
A2-E12


title: plateA2.positionC12.single.cell

description:
all.single.cell.gene.counts.txt
A2-C12


title: KSCR_1

value: wild type


title: KSCR_2


title: plateA2.positionB12.single.cell

description:
all.single.cell.gene.counts.txt
A2-B12


title: plateA2.positionD12.single.cell

description:
all.single.cell.gene.counts.txt
A2-D12

value: Ciliated cell


title: Sample_DM_heart_RRBS-seq

city: Beijing

first: Heng

last: Pan

address: 49 North Garden Rd., Haidian District

institute: Peking University Third Hospital

library_source: genomic

data_processing:
FASTQ files were generated by using the Illumina CASAVA 1.8.2 pipeline.
Raw reads alignment and CpG methylation call were formed by using an in-house pipeline described in Akalin et al., PLoSGenetics, 2012.
Genome_build: danRer10
Supplementary_files_format_and_content: methylcall files are in .txt format

molecule: genomic DNA

organism: Danio rerio

source_name: 2d  tet2/3DM dissected zebrafish heart

growth_protocol: Embryos were raised at 28.5°C and morphologically staged as described (Kimmel et al., 1995); all procedures were carried out as approved by the WCMC IACUC. Wild-type embryos were derived from crosses of the AB and TU lines. 48hpf embryonic hearts were dissected manually unders microscope.

extract_protocol:
For RRBS genomic DNA was isolated from 48hpf WT and tet2/3 DM dissected heart using the DNeasy Blood & Tissue Kit (Qiagen, 69504) following manufacturer’s guidelines.
ERRBS libraries were prepared according to a previously published protocol (Akalin et al., PLoSGenetics, 2012).

treatment_protocol: No treatments were applied prior to genomic DNA extraction

tag: strain background

value: AB

tag: age

value: 2d; 48hpf

tag: genotype/variation

value: Inactivating mutations in  tet2 and tet3

value: dissected hearts


title: Sample_WT_heart_RRBS-seq

source_name: 2d  WT dissected zebrafish heart

value: Wild type sequence


title: plateA2.positionH11.single.cell

description:
all.single.cell.gene.counts.txt
A2-H11

value: Lung

value: epithelial cell

value: Club cell


title: RMDB_141

description: REMoDLB trial

value: Diffuse Large B-cell Lymphoma


title: RMDB_140

description: REMoDLB trial


title: KSCR_3


title: plateA2.positionG11.single.cell

description:
all.single.cell.gene.counts.txt
A2-G11


title: RMDB_143

description: REMoDLB trial

value: GCB


title: RMDB_139

description: REMoDLB trial


title: plateA2.positionE11.single.cell

description:
all.single.cell.gene.counts.txt
A2-E11


title: RMDB_138

description: REMoDLB trial


title: pBabe-U2OS-1

first: Haiying

last: Liu

address: NO.135, Xingang xi Road, Haizhu District

institute: Sun Yat-sen University

description: empty vector

data_processing:
All of the RNA-Seq reads were first checked with FastQC
Using homemade Java and GNUBash scripts, unpaired reads and those containing low PHRED score (< Q20) bases, Ns, or no adaptors were removed from the raw reads.
Reads were then mapped to the UCSC build hg19 human genome with Tophat2
Genome_build: hg19
Supplementary_files_format_and_content: Read Counts for each sample.

molecule: polyA RNA

source_name: U2OS cell line

extract_protocol:
Trizol protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hTR or empty vector pBabe were stably expressed in U2OS cells, respectively.

value: osteosarcoma

tag: transfection

value: empty vector pBabe


title: hTR-U2OS-1

description: hTR overexpression

value: hTR


title: pBabe-U2OS-3

description: empty vector


title: hTR-U2OS-2

description: hTR overexpression


title: pBabe-U2OS-2

description: empty vector


title: hTR-U2OS-3

description: hTR overexpression


title: plateA2.positionA12.single.cell

description:
all.single.cell.gene.counts.txt
A2-A12


title: GLOB2

city: Winnipeg

first: Mark

last: Belmonte

state: Manitoba

address: 50 Sifton Rd

department: Biological Sciences

country: Canada

institute: University of Manitoba

data_processing:
Trimminmg and QC performed using Trimmomatic 0.36
Alignments performed with HISAT2
Normalization and differential expression using Cufflinks suite
Genome_build: Darmor BzH v5
Supplementary_files_format_and_content: text file with FPKM

organism: Brassica napus

source_name: globular seed, whole

growth_protocol: B. napus cv Topas were grown under long day conditoins at 22-24C, 50-70% RH, in Sunshine Mix #1

extract_protocol:
RNA extracted using Ambion PlantLink RNA Reagent
NuGen Ultralow DR Multiplex Kit

tag: cultivar

value: Topas

value: globular seed

tag: tissue compartment

value: whole seed

tag: tissue source

value: maternal


title: RMDB_142

description: REMoDLB trial


title: plateA2.positionD11.single.cell

description:
all.single.cell.gene.counts.txt
A2-D11

tag: tissue

value: BASCs


title: GLOB3


title: plateA2.positionC11.single.cell

description:
all.single.cell.gene.counts.txt
A2-C11

tag: cell type


title: RMDB_137

description: REMoDLB trial

value: UNC


title: RMDB_134

description: REMoDLB trial


title: HCMEC

city: wuhan

first: xudong

last: zhang

address: jiefang avenue 1095

institute: tongji hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Cutadapt (Version 1.2.1) (Martin M, 2011) was used to remove 3' end joints, at least 10 bp Overlap (AGATCGGAAG), and 20% base error rate was allowed.
Reads per kilobase of exon per megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Ensembl 38.85

source_name: human cardiac microvascular endothelial cell

growth_protocol: Human cardiac myocytes (HCMs, ScienCell research laboratories, Carlsbad, CA) were from a single fetal donor, not pooled, and were maintained in cardiac myocyte medium (CMM, ScienCell research laboratories, Cat. #6201), according to the instruction manual. CMM consists of basal medium, foetal bovine serum (FBS), cardiac myocyte growth supplement, and penicillin/streptomycin solution. Human cardiac fibroblasts-adult ventricular (HCF-av, ScienCell research laboratories, Carlsbad, CA) were maintained at fibroblast medium-2 (FM-2, ScienCell research laboratories, Cat. #2331), which contained fibroblast growth supplement-2 (FGS-2, Cat #2382) and FBS. Human cardiac microvascular endothelial cells (HCMECs, ScienCell research laboratories, Carlsbad, CA) were maintained in endothelial cell medium (ECM, Cat. #1001). ECM consists of basal medium, FBS, endothelial cell growth supplement and penicillin/streptomycin solution.

extract_protocol:
RNA was harvested using Trizol reagent following the instructions.
All of our RNA-seq projects used strand specific kits to construct the libraries.By using next-generation sequencing (NGS) technology, paired-end (PE) sequencing of these libraries was performed based on Illumina HiSeq sequencing platform

tag: passages


title: RMDB_136

description: REMoDLB trial

value: ABC


title: plateA2.positionF11.single.cell

description:
all.single.cell.gene.counts.txt
A2-F11

tag: genotype

tag: cell sub-type


title: HCM

source_name: human cardiac myocyte

value: human cardiac myocyte


title: HCF

source_name: human cardiac fibroblasts-adult ventricular


title: gOSC3

source_name: outer seed coat

value: outer seed coat


title: plateA2.positionB11.single.cell

description:
all.single.cell.gene.counts.txt
A2-B11

value: Lung

value: Ciliated cell


title: plateA2.positionA11.single.cell

description:
all.single.cell.gene.counts.txt
A2-A11

value: epithelial cell


title: gOSC2


title: plateA2.positionH10.single.cell

description:
all.single.cell.gene.counts.txt
A2-H10

value: Club cell


title: TDP43 siRNA rep6

city: Boston

first: Rory

last: Kirchner

state: MA

address: 677 Huntington Ave

department: Department of Biostatistics

country: USA

institute: Harvard T.H. Chan School of Public Health

data_processing:
All FASTQ files were analyzed using the bcbioRNASeq workflow and toolchain91. The FASTQ files were aligned to the GRCh37/hg19 reference genome.
Differential expression testing was performed using DESeq2 suite of bioinformatics tools38. The DEXSeq module of Bioconductor was used to identify differential splicing92. We used salmon to generate the counts and tximport to load them at gene level93,94. All p-values are then corrected for multiple comparisons using the method of Benjamini and Hochberg95.  We used an adjusted p-value cutoff of 0.05 with no log fold-change ratio cutoff for differential gene expression analysis and a 0.1 cutoff with no log fold-change ratio cutoff for differential exon usage.
Genome_build: hg19
Supplementary_files_format_and_content:
[tpm.csv.gz]  gene x sample matrix of TPM for each sample
[raw_counts.csv.gz]  gene x sample matrix of raw counts per sample
[category_als_vs_control_all.csv.gz]  differential expression calls for all genes from DESeq2. (ensgene: Ensembl gene ID, baseMean: mean expression across all samples, log2FoldChange: log2Fold change (knockdown/control), lfcSE: standard error of the log2FoldChange, stat: value of Wald test statistic, pvalue: p-value of differential expression, symbol: gene symbol, description: gene description, biotype: biotype of gene, broadClass: broad biotype class gene belongs to, chr: chromosome gene is on, start: start of gene on chromosome, end: end of gene on chromosome, strand: strand gene is on)
[dexseq-all.csv.gz]  gene fragment differential expression calls from DEXSeq. (fragment: gene fragment ID, groupID: group ID of fragment, featureID: gene ID of fragment, exonBaseMean: expressoin of exon across all samples, dispersion: dispersion of fragment across all samples, stat: value from Wald test, pvalue: p-value from Wald test, padj: BH adjusted p-value, scrambled: expression in scrambled siRNA, als: expression in TDP43 knockdown samples, rest of columns are locations of fragments in the genome, counts of the fragment for each individual sample and gene annotation similar to the above)
[combined.dexseq.gz]  exon part count table

source_name: TDP43 siRNA, differentiated HUES3 into hMNs

growth_protocol: Pluripotent stem cells were grown with mTeSR1 medium (Stem Cell Technologies) on tissue culture dishes coated with MatrigelTM (BD Biosciences), and maintained in 5% CO2 incubators at 37ºC. Stem cells were passaged as small aggregates of cells after 1 mM EDTA treatment. 10 μM ROCK inhibitor (Sigma, Y-27632) was added to the cultures for 16-24 hours after dissociation to prevent cell death. The HUES3 Hb9::GFP cell line has been previously described33,34. MN differentiation was achieved using a modified 14-day strategy. This approach relies on neural induction through small molecule inhibition of SMAD signaling, accelerated neural differentiation through FGF and NOTCH signaling inhibition, and MN patterning through the activation of retinoic acid (RA) and Sonic Hedgehog signaling pathways.  In brief, ES cells were dissociated to single cells using accutaseTM (Stem Cell Technologies) and plated at a density of 80,000 cells/cm2 on matrigel-coated culture plates with mTeSR1 medium (Stem Cell Technologies) supplemented with ROCK inhibitor (10μM Y-27632, Sigma).  When cells reached 100% confluency, medium was changed to differentiation medium (½ Neurobasal (Life TechnologiesTM) ½ DMEM-F12 (Life TechnologiesTM) supplemented with 1x B-27 supplement (Gibco®), 1x N-2 supplement (Gibco®), 1x Gibco® GlutaMAXTM (Life TechnologiesTM) and 100μM non-essential amino-acids (NEAA)).  This time point was defined as day 0 (d0) of motor neuron differentiation. Treatment with small molecules was carried out as follows:  10μM SB431542 (Custom Synthesis), 100nM LDN-193189 (Custom Synthesis), 1μM retinoic acid (Sigma) and 1μM Smoothend agonist (Custom Synthesis) on d0-d5; 5μM DAPT (Custom Synthesis), 4μM SU-5402 (Custom Synthesis), 1μM retinoic acid (Sigma) and 1μM Smoothend agonist (Custom Synthesis) on d6-d14.

extract_protocol:
Total RNA was isolated from d10 MNs for RNA-Seq experiments and validation assays   using Trizol LS (Invitrogen) according to manufacturer’s instructions. 500μL were added per well of the 24-well cultures
After RNA extraction, samples with RNA integrity numbers (RIN) above 7.5, determined by a bioAnalyzer, were used for library preparation. In brief, RNA sequencing libraries were generated from ~250ng of total RNA using the illumina TruSeq RNA kit v2, according to the manufacturer’s directions.

treatment_protocol: RNAi in cultures of purified GFP+ MNs was induced with Silencer® Select siRNAs (Life TechnologiesTM) targeting the TDP-43 mRNA or with a non-targeting siRNA control with scrambled sequence that is not predicted to bind to any human transcripts. Lyophilized siRNAs were resuspended in nuclease-free water and stored at -20oC as 20μM stocks until ready to use. For transfection, siRNAs were diluted in Optimem (Gibco®) and mixed with RNAimax (Invitrogen) according to manufacturer’s instructions. After 30 min incubation, the mix was added drop-wise to the MN cultures, so that the final siRNA concentration in each well was 60nM in 1:1 Optimem:MN medium (Neurobasal (Life TechnologiesTM, N2 supplement (Gibco®), B-27 supplement (Gibco®), GlutaMax and neaa) and 10ng/mL of each gdnf, bdnf and cntf (R&D). 12-16 hours post-transfection media was changed. RNA-Seq experiments and validation assays were carried with material collected 4 days after transfection.

value: differentiated HUES3 into hMNs

tag: sirna type

value: TDP43 knockdown

tag: date


title: TDP43 siRNA rep5


title: plateA2.positionG10.single.cell

description:
all.single.cell.gene.counts.txt
A2-G10


title: RMDB_132

description: REMoDLB trial

tag: clinic diagnosis

value: Diffuse Large B-cell Lymphoma

tag: molecular subtype

value: GCB

tag: molecular coo subtype


title: gISC2

source_name: inner seed coat

value: Topas

value: inner seed coat


title: RMDB_135

description: REMoDLB trial


title: RMDB_131

description: REMoDLB trial


title: plateA2.positionF10.single.cell

description:
all.single.cell.gene.counts.txt
A2-F10


title: plateA2.positionE10.single.cell

description:
all.single.cell.gene.counts.txt
A2-E10


title: scramble siRNA rep6

source_name: scramble siRNA, differentiated HUES3 into hMNs

value: scramble

value: control


title: RMDB_133

description: REMoDLB trial


title: scramble siRNA rep5


title: fluorescent siRNA rep3

source_name: fluorescent siRNA, differentiated HUES3 into hMNs

value: fluorescent


title: gCPT3

source_name: chalazal proliferating tissue

value: globular seed

value: chalazal proliferating tissue

value: maternal


title: gCPT2


title: plateA2.positionD10.single.cell

description:
all.single.cell.gene.counts.txt
A2-D10


title: GLOB1

value: whole seed


title: gISC3


title: plateA2.positionC10.single.cell

description:
all.single.cell.gene.counts.txt
A2-C10

value: Lung

value: BASCs


title: gISC1


title: gCPT1


title: TDP43 siRNA rep3


title: TDP43 siRNA rep4


title: scramble siRNA rep4


title: gCZE2

source_name: chalazal endosperm

value: chalazal endosperm

value: filial


title: plateA2.positionA10.single.cell

description:
all.single.cell.gene.counts.txt
A2-A10

value: epithelial cell


title: plateA2.positionH9.single.cell

description:
all.single.cell.gene.counts.txt
A2-H9

value: Club cell


title: plateA2.positionB10.single.cell

description:
all.single.cell.gene.counts.txt
A2-B10


title: no siRNA rep3

source_name: no siRNA, differentiated HUES3 into hMNs

value: differentiated HUES3 into hMNs


title: scramble siRNA rep3


title: gCZE1


title: RMDB_126

description: REMoDLB trial

value: Diffuse Large B-cell Lymphoma

value: ABC


title: gPEN2

source_name: peripheral endosperm

value: Topas

value: peripheral endosperm


title: RMDB_129

description: REMoDLB trial

value: UNC


title: RMDB_130

description: REMoDLB trial

value: MHG

value: GCB


title: RMDB_127

description: REMoDLB trial


title: fluorescent siRNA rep2

value: fluorescent

value: control


title: RMDB_128

description: REMoDLB trial


title: RMDB_125

description: REMoDLB trial


title: RMDB_122

description: REMoDLB trial


title: RMDB_124

description: REMoDLB trial


title: gCZE3

value: globular seed


title: RMDB_121

description: REMoDLB trial


title: RMDB_120

description: REMoDLB trial


title: RMDB_123

description: REMoDLB trial


title: gPEN1


title: no siRNA rep2


title: RMDB_119

description: REMoDLB trial


title: plateA2.positionF9.single.cell

description:
all.single.cell.gene.counts.txt
A2-F9

value: Lung


title: TDP43 siRNA rep2

value: TDP43 knockdown


title: plateA2.positionD9.single.cell

description:
all.single.cell.gene.counts.txt
A2-D9


title: no siRNA rep1


title: gMCE3

source_name: micropylar endosperm

value: micropylar endosperm


title: plateA2.positionB9.single.cell

description:
all.single.cell.gene.counts.txt
A2-B9


title: plateA2.positionC9.single.cell

description:
all.single.cell.gene.counts.txt
A2-C9


title: plateA2.positionG9.single.cell

description:
all.single.cell.gene.counts.txt
A2-G9


title: gMCE2

value: filial


title: TDP43 siRNA rep1


title: gMCE4


title: RMDB_118

description: REMoDLB trial


title: gMCE1


title: scramble siRNA rep2

value: scramble


title: plateA3.positionD2.single.cell

description:
all.single.cell.gene.counts.txt
A3-D2

value: epithelial cell

value: Club cell


title: RMDB_116

description: REMoDLB trial

value: Diffuse Large B-cell Lymphoma


title: plateA2.positionE9.single.cell

description:
all.single.cell.gene.counts.txt
A2-E9


title: scramble siRNA rep1

value: differentiated HUES3 into hMNs


title: RMDB_117

description: REMoDLB trial

value: ABC


title: fluorescent siRNA rep1


title: gEP1

source_name: embryo proper

value: Topas

value: embryo proper


title: gEP2


title: plateA2.positionH8.single.cell

description:
all.single.cell.gene.counts.txt
A2-H8

source_name: BASCs-Tracer

value: BASCs


title: RMDB_115

description: REMoDLB trial

value: UNC


title: RMDB_114

description: REMoDLB trial

value: GCB


title: plateA2.positionG8.single.cell

description:
all.single.cell.gene.counts.txt
A2-G8


title: plateA2.positionF8.single.cell

description:
all.single.cell.gene.counts.txt
A2-F8


title: BMPC 3

city: New York

first: Cem

last: Meydan

state: New York

address: 1305 York

department: Physiology & Biophysics

institute: Weill Cornell Medical College

description: Naive B cells (NB), Centroblast (CB), Centrocyte (CC), Memory (MEM) and plasma cells (TPC) were isolated from human tonsils of healthy donors and bone marrow plasma cells (BMPC) from bone marrow of healthy donors by multiparameter fluorescence-activated cell sorting (FACS) using the expression level of 9 different surface antigens as previously describe (Pascual M. 2017). The following monoclonal antibody (MoAb) combination was used for the cell isolation from tonsils: CD45-OC515 (Clone HI30, Immunostep, Salamanca, Spain); CD20-Pacific Blue (Clone 2H7, Bioloegend, San Diego, California, UnitedStates); CD44-APCH7 (Clone G44-26, Beckton Dickinson, Dur-ham, North Carolina, United States). CD10 PE-Cy7 (Clone HI10a BecktonDickinson, Durham, North Carolina, United States); CD38-FITC (Clone LD38, Cytognos, Salamanca, Spain); CXCR4-PE (Clone 12G5, Beckton Dickinson, Durham, North Carolina, UnitedStates); CD27-APC (Clone L128, Beckton Dickinson, Durham, North Carolina, UnitedStates) and CD3-PerCP-Cy5.5 (Clone SK7, Beckton Dickinson, Durham, North Carolina, United States). BMPC were fluorescence-activated cell sorted (FACS) (FACSAria II, Becton Dickinson Biosciences, Durham, North Carolina, United States) from human bone marrow of healthy donors using CD38-FITC (Clone LD38, Cytognos, Salamanca, Spain); CD138-BV421 (Clone MI15, Beckton Dickinson, Dur-ham, North Carolina, United States) and CD27-BV510 (Clone 0323, Bioloegend, San Diego, California, UnitedStates). Monitoring of instrument performance was performed daily using the Cytometer SetupTracking (CST; BD, Durham, North Carolina, United States) after laser stabilization.

data_processing:
A two-step alignment procedure was performed with STAR v2.4 (Dobin A. 2013) to remove any potential ribosomal RNA leftover from the ribodepletion step. A first pass alignment was done against human ribosomal sequences allowing multi-mapping. Unmapped reads from the first step were then aligned to hg19 human reference using GENCODE v19 (Harrow J. 2012) junction points.
Cufflinks v2.2.1 (Trapnell C. 2010; Roberts A. 2011) was run on the resulting alignment files to create de novo transcriptome assembly specific to each sample using strand-specific settings and GENCODE v19 as a database.  Cufflinks outputs for all of the samples were then merged with themselves and GENCODE database using cuffmerge.
Subread featureCounts (Liao Y. 2014) was used to annotate each sample to the merged transcript annotation.
Genome_build: hg19
Supplementary_files_format_and_content: BAM files for the 2-pass alignment after ribosomal cleaning
Supplementary_files_format_and_content: GTF file of merged cufflinks output
Supplementary_files_format_and_content: counts for GENCODE v19 + cufflinks discovered transcripts

source_name: Bone Marrow plasma cell

extract_protocol:
Total RNA from all B cell subpopulations was isolated using Trizol extraction method (LifeTechnologies), purified by RNeasy MinElute spin column (Qiagen) and treated with DNase I (ThermoFisher) following the manufacturer's instructions. Total RNA was quantified using NanoDrop Specthophotometer (NanoDrop Technologies). High quality purified total RNA (300-600ng) from each sample was used for library preparation.
RNA libraries were prepared for strand specific sequencing using users manual of Truseq Stranded Total ribo-depleted RNA sample preparation kit of Illumina.
Strand specific RNA-Seq

value: Bone Marrow

tag: strain

value: Purified Bone Marrow Plasma cells

tag: cytometry markers

value: Healthy donor


title: RMDB_112

description: REMoDLB trial


title: wt_LPS_3

city: Vari, Athens

first: George

last: Kollias

address: 34 Fleming Street

department: Immunology

country: Greece

institute: BSRC "Alexander Fleming"

description:
processed data file: metaseqr_all_out_CU_vs_CL.txt
processed data file: metaseqr_all_out_CL_vs_ML.txt
GK3R169-CL3

data_processing:
The RNA-Seq FASTQ files obtained after Ion Proton sequencing were mapped using TopHat2 [Kim2013], with default settings and using additional transcript annotation data for the mm10 genome from Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html). According to the Ion Proton manufacturers recommendation, the reads which remained unmapped were submitted to a second round of mapping using Bowtie2 [Langmead2012] against the mm10 genome with the --very-sensitive switch turned on and merged with the initial mappings.
The raw bam files were summarized to read counts table using the Bioconductor package GenomicRanges.
The gene counts table was normalized for inherent systematic or experimental biases using the Bioconductor package DESeq after removing genes that had zero counts over all the RNA-Seq samples.
The resulting gene counts table was subjected to differential expression analysis using the Bioconductor package DESeq.
All the above were performed through the Bioconductor package metaseqr.
Differential expression analysis files were subjected to additional filtering by removing the genes that had a value of log2(normalized read counts) less than 1.60 in more than four samples.
Genes : Ugt1a6a, Ugt1a8, Ugt1a5, Ugt1a1, Ugt1a7c, Ugt1a6b, Ugt1a10, Ugt1a2, Ugt1a9, Pcdha1, Pcdha2, Pcdha3, Pcdha4, Pcdha5, Pcdha7, Pcdha8, Pcdha9, Pcdha11, Pcdha12,  were excluded from further analysis, due to having the same read counts across all isoforms.
Genome_build: mm10
Supplementary_files_format_and_content: txt (tab separated) files containing all the results from metaseqr analysis including expression per replicate, fold change compared to control and p-values.

source_name: wt_LPS, intestinal mesenchymal cells

growth_protocol: Intestinal mesenchymal cells were isolated as previously described (Koliaraki et al., 2015) and cultured until passage 3. Cells were then sorted based on their expression of GFP.

extract_protocol:
Total RNA was extracted using RNAeasy Mini kit (QIAGEN), according to the manufacturer's instructions.
The quantity and quality of RNA samples from sorted cells were analyzed using the bioanalyzer form Agilent in combination with the Agilent RNA 6000 Nano. RNA samples with RNA Integrity Number (RIN) > 7 were further used for library preparation using the 3’ mRNA-Seq Library Prep Kit Protocol for Ion Torrent (QuantSeq-LEXOGEN™) according to manufacturer’s instructions. The quantity and quality of libraries were assessed using the DNA High Sensitivity Kit in the bioanalyzer, according to the manufacturer’s instructions (Agilent Technologies). Libraries were subsequently pooled and templated using the Ion PI IC200 Chef Kit (ThermoFisher Scientific) on an Ion Proton Chef instrument or Ion OneTouch System. Sequencing was performed using the Ion PI™ Sequencing 200 V3 Kit and Ion Proton PI™ V2 chips (ThermoFisher Scientific) on an Ion Proton™ System, according to the manufacturer's instructions.
3’ RNA-Seq (QuantSeq)

treatment_protocol: Cells were serum starved overnight and treated with 2μg/ml LPS from E.coli (Sigma) for 6 hours.

value: Small intestine

value: Intestinal mesenchymal cells

tag: cell isolation

value: Cultured and sorted primary cells

tag: treatment

value: LPS


title: plateA2.positionE8.single.cell

description:
all.single.cell.gene.counts.txt
A2-E8

value: Lung

value: epithelial cell


title: wt_LPS_1

description:
processed data file: metaseqr_all_out_CU_vs_CL.txt
processed data file: metaseqr_all_out_CL_vs_ML.txt
GK3R167-CL1


title: BMPC 1


title: wt_LPS_2

description:
processed data file: metaseqr_all_out_CU_vs_CL.txt
processed data file: metaseqr_all_out_CL_vs_ML.txt
GK3R168-CL2


title: RMDB_113

description: REMoDLB trial

value: Diffuse Large B-cell Lymphoma


title: MyD88ko_LPS_3

description:
processed data file: metaseqr_all_out_MU_vs_ML.txt
processed data file: metaseqr_all_out_CL_vs_ML.txt
GK3R166-ML3

source_name: MyD88ko_LPS, intestinal mesenchymal cells


title: BMPC 2


title: plateA2.positionA9.single.cell

description:
all.single.cell.gene.counts.txt
A2-A9

value: Club cell


title: MyD88ko_LPS_2

description:
processed data file: metaseqr_all_out_MU_vs_ML.txt
processed data file: metaseqr_all_out_CL_vs_ML.txt
GK3R165-ML2


title: plateA2.positionC8.single.cell

description:
all.single.cell.gene.counts.txt
A2-C8


title: TPC 4

source_name: Tonsilar plasma cell

value: Tonsil

value: Purified Tonsilar Plasma cells

value: CD45+; CD20+; CD44high; CD10-; CD38high; CD27high; CD3-


title: TPC 5


title: TPC 3


title: MyD88ko_LPS_1

description:
processed data file: metaseqr_all_out_MU_vs_ML.txt
processed data file: metaseqr_all_out_CL_vs_ML.txt
GK3R164-ML1


title: plateA2.positionA8.single.cell

description:
all.single.cell.gene.counts.txt
A2-A8

value: BASCs


title: Untreated_wt_3

description:
processed data file: metaseqr_all_out_CU_vs_CL.txt
processed data file: metaseqr_all_out_CU_vs_MU.txt
GK3R148-CU3

source_name: Untreated_wt, intestinal mesenchymal cells

value: control


title: TPC 2


title: RMDB_111

description: REMoDLB trial

value: GCB


title: plateA2.positionD8.single.cell

description:
all.single.cell.gene.counts.txt
A2-D8


title: RMDB_108

description: REMoDLB trial

value: ABC


title: RMDB_110

description: REMoDLB trial


title: plateA2.positionH7.single.cell

description:
all.single.cell.gene.counts.txt
A2-H7


title: RMDB_109

description: REMoDLB trial


title: RMDB_107

description: REMoDLB trial


title: plateA2.positionG7.single.cell

description:
all.single.cell.gene.counts.txt
A2-G7


title: Untreated_wt_2

description:
processed data file: metaseqr_all_out_CU_vs_CL.txt
processed data file: metaseqr_all_out_CU_vs_MU.txt
GK3R147-CU2


title: MEM 8

source_name: Memory

value: Purified Memory B cells


title: RMDB_105

description: REMoDLB trial


title: Untreated_wt_1

description:
processed data file: metaseqr_all_out_CU_vs_CL.txt
processed data file: metaseqr_all_out_CU_vs_MU.txt
GK3R146-CU1


title: MEM 7

value: Healthy donor


title: Untreated_MyD88ko_2

description:
processed data file: metaseqr_all_out_MU_vs_ML.txt
processed data file: metaseqr_all_out_CU_vs_MU.txt
GK3R141-MU2

source_name: Untreated_MyD88ko, intestinal mesenchymal cells

value: Small intestine


title: plateA2.positionF7.single.cell

description:
all.single.cell.gene.counts.txt
A2-F7


title: Untreated_MyD88ko_3

description:
processed data file: metaseqr_all_out_MU_vs_ML.txt
processed data file: metaseqr_all_out_CU_vs_MU.txt
GK3R142-MU3

value: Intestinal mesenchymal cells


title: RMDB_106

description: REMoDLB trial

value: UNC


title: MEM 5


title: Untreated_MyD88ko_1

description:
processed data file: metaseqr_all_out_MU_vs_ML.txt
processed data file: metaseqr_all_out_CU_vs_MU.txt
GK3R140-MU1

value: Cultured and sorted primary cells


title: TPC 1


title: RMDB_104

description: REMoDLB trial


title: MEM 6


title: plateA2.positionB8.single.cell

description:
all.single.cell.gene.counts.txt
A2-B8

value: Lung


title: RMDB_103

description: REMoDLB trial

value: MHG


title: plateA2.positionE7.single.cell

description:
all.single.cell.gene.counts.txt
A2-E7

value: epithelial cell


title: RMDB_102

description: REMoDLB trial

value: Diffuse Large B-cell Lymphoma


title: plateA2.positionC7.single.cell

description:
all.single.cell.gene.counts.txt
A2-C7


title: MEM 4

value: Tonsil


title: plateA2.positionB7.single.cell

description:
all.single.cell.gene.counts.txt
A2-B7


title: RMDB_100

description: REMoDLB trial


title: RMDB_101

description: REMoDLB trial


title: plateA2.positionA7.single.cell

description:
all.single.cell.gene.counts.txt
A2-A7


title: RMDB_99

description: REMoDLB trial


title: plateA2.positionH6.single.cell

description:
all.single.cell.gene.counts.txt
A2-H6


title: plateA2.positionG6.single.cell

description:
all.single.cell.gene.counts.txt
A2-G6


title: plateA2.positionF6.single.cell

description:
all.single.cell.gene.counts.txt
A2-F6

value: Club cell


title: MEM 1


title: plateA2.positionE6.single.cell

description:
all.single.cell.gene.counts.txt
A2-E6


title: MEM 3


title: CC 5

source_name: Centrocyte

value: Purified Centrocyte cells


title: CC 7


title: plateA2.positionD6.single.cell

description:
all.single.cell.gene.counts.txt
A2-D6

value: BASCs


title: CC 4


title: MEM 2


title: palsma in HF11

description: LncRNA expression data from human plasma

hyb_protocol: Following instructions of Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242)

scan_protocol: GeneChips were scanned using the Agilent Microarray Scanner (Agilent p/n G2565BA)

data_processing: Extract data were analyzed with Agilent Feature Extraction Software

source_name: plasma in HF patients

label_protocol: Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442)

growth_protocol: Blood samples were collected from dilated cardiomyopathy patients and controls in EDTA test tubes.

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

treatment_protocol: Then, plasma was obtained by centrifugation at 2000g at 4ºC for 10 minutes, and the supernatant was carefully transferred to a new RNAse/DNAse-free 1.5mL microtube and stored at -80ºC until use.

tag: diagnosis

value: dilated cardiomyopathy (DCM)

value: plasma


title: palsma in HF14


title: palsma in HF10


title: RMDB_97

description: REMoDLB trial

value: GCB


title: plateA2.positionC6.single.cell

description:
all.single.cell.gene.counts.txt
A2-C6


title: RMDB_98

description: REMoDLB trial


title: RMDB_94

description: REMoDLB trial


title: palsma in HF9


title: palsma in HF13


title: CC 3


title: RMDB_96

description: REMoDLB trial


title: RMDB_95

description: REMoDLB trial


title: RMDB_93

description: REMoDLB trial


title: palsma in HF7


title: CC 6


title: palsma in HF6


title: plateA2.positionB6.single.cell

description:
all.single.cell.gene.counts.txt
A2-B6


title: CC 2


title: plateA2.positionA6.single.cell

description:
all.single.cell.gene.counts.txt
A2-A6


title: palsma in HF8


title: CC 1


title: CB 7

source_name: Centroblast

value: Purified Centroblast cells


title: plateA2.positionG5.single.cell

description:
all.single.cell.gene.counts.txt
A2-G5


title: plateA2.positionF5.single.cell

description:
all.single.cell.gene.counts.txt
A2-F5


title: RMDB_91

description: REMoDLB trial


title: palsma in HF2


title: palsma in HF4


title: RMDB_89

description: REMoDLB trial

value: ABC


title: CB 4

value: Healthy donor


title: CB 5


title: RMDB_90

description: REMoDLB trial


title: plasma in control 10

source_name: plasma in non-HF control

value: control donor


title: CB 3


title: CB 6


title: plateA2.positionC5.single.cell

description:
all.single.cell.gene.counts.txt
A2-C5


title: RMDB_87

description: REMoDLB trial


title: plasma in control 9


title: RMDB_88

description: REMoDLB trial


title: plateA2.positionE5.single.cell

description:
all.single.cell.gene.counts.txt
A2-E5


title: plateA2.positionD5.single.cell

description:
all.single.cell.gene.counts.txt
A2-D5


title: plasma in control 7


title: plasma in control 8


title: plasma in control 6


title: RMDB_86

description: REMoDLB trial


title: RMDB_85

description: REMoDLB trial


title: plateA2.positionA5.single.cell

description:
all.single.cell.gene.counts.txt
A2-A5


title: RMDB_84

description: REMoDLB trial


title: RMDB_83

description: REMoDLB trial


title: NB 5

source_name: Naive

value: Purified Naive B cells


title: CB 2


title: plasma in control 4


title: plateA2.positionG4.single.cell

description:
all.single.cell.gene.counts.txt
A2-G4


title: plateA2.positionH4.single.cell

description:
all.single.cell.gene.counts.txt
A2-H4


title: NB 4


title: RMDB_82

description: REMoDLB trial


title: plasma in control 2


title: plateA2.positionB5.single.cell

description:
all.single.cell.gene.counts.txt
A2-B5


title: NB 3


title: CB 1


title: plateA2.positionF4.single.cell

description:
all.single.cell.gene.counts.txt
A2-F4


title: plasma in control 3


title: plateA2.positionE4.single.cell

description:
all.single.cell.gene.counts.txt
A2-E4


title: plasma in control 5


title: Ipa1-1_input_rep2

city: Bar Harbor

first: Joel

middle: H

last: Graber

state: ME

address: 159 Old Bar Harbor Rd

department: Bioinformatics Core

institute: MDI Biological Laboratory

data_processing:
Quality control with fastqc
All sequences were then aligned to the S. cerevisiae genome (sacCer3 as provided in Galaxy), using BWA (ID toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.15.1) using default parameters
BAM output files were converted to bigwig coverage using the DeepTools Bam Coverage program (ID toolshed.g2.bx.psu.edu/repos/bgruening/ deeptools_bam_coverage/deeptools_bam_coverage/2.5.0.0), using bin-size = 1 (every base independent) (Ramirez et al., 2016)but with averaging over a window 21 nt wide centered on the current base, but with all other parameters left at default values.  Normalization was set to “constant coverage on the genome” such that the total coverage across all samples is forced to be equal.
The bigwig files for each pair of PolII and matched input data set were compared with the Deep Tools bigwigCompare program (ID toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.5.0.0) (Ramirez et al., 2016), producing a log2ratio of the Pol II to input coverage, again using window size = 1
The four resulting Pol II-enrichment files (representing two replicates for the wild-type (WT) and two replicates for the ipa1-1 mutant) were downloaded and processed with command-line tools to generate a joined file that included calculation of the average value at each genomic position (chromosome-nucleotide-position), as well as the difference between them, represented as ipa1-1 average minus WT average
Genome_build: sacCer3
Supplementary_files_format_and_content: bedgraph files were processed with inhouse written c++ code.  Scores represent the polII enrichment (as a log2 ratio of PolII depth to input DNA) for WT and Ipa1-1 samples, averaged over two replicate samples.  For the Delta_PolII enrichment, the score is the difference in enrichment in Ipa1-1 compared to WT, with positive scores representing an increase compared to WT BY4741

organism: Saccharomyces cerevisiae

source_name: TSA1248 yeast

growth_protocol: Yeast cells (50 ml) were grown to OD600 of 0.5, shifted to 37°C for 1 hour

extract_protocol:
Yeast samples were fixed with 1.035% formaldehyde for 15 minutes and neutralized with 0.135 M glycine for 5 minutes.  Washed cells were lysed in FA-lysis buffer (50 mM HEPES-KOH, pH 7.9; 150 mM NaCl; 1% Triton X-100; 1 mM EDTA; 0.1% sodium deoxycholate; 0.1% SDS) with grinding in liquid nitrogen..The resulting 4 ml chromatin were incubated with 40 l 4H8 antibody and 200 l pre-washed protein G beads for 5 hours at 4°C.  The beads were washed as described above and were then eluted in two steps: 1) in 150 l TE + 1% SDS at 65°C for 15 minutes, and 2) in 150 l TE + 0.67% SDS at 65°C for 10 minutes.  Samples were de-crosslinked overnight at 65°C and then treated with Proteinase K for 2-4 hours at 42°C.  LiCl (to 0.4 M), 20 g glycogen and 1 ml 100% ethanol were added to precipitate the DNA.  The DNA pellets were washed in 70% ethanol and were further purified using MinElute columns (Qiagen).  The eluted DNA was submitted to the Tufts Genomics Core Facility for TruSeq ChIP library preparation and for 50 nt single-end sequencing on the Illumina HiSeq 2500 system.
Illumina TruSeq ChIP library preparation

tag: genotype/variation

value: Ipa1-1 mutation

tag: chip antibody


title: RMDB_81

description: REMoDLB trial


title: plateA2.positionD4.single.cell

description:
all.single.cell.gene.counts.txt
A2-D4

tag: tissue

value: Lung


title: NB 1


title: Ipa1-1_input_rep1


title: plateA2.positionC4.single.cell

description:
all.single.cell.gene.counts.txt
A2-C4

tag: cell type


title: IPa1-1_polII_ChiPSeq_rep2

value: anti-pan CTD mouse monoclonal antibody, 4H8 (Santa Cruz)


title: RMDB_78

description: REMoDLB trial


title: plasma in control 1


title: RMDB_79

description: REMoDLB trial


title: WT_polII_ChIPSeq_rep2

source_name: BY4741 yeast

value: wild type


title: WT_input_rep2


title: RMDB_77

description: REMoDLB trial

value: Diffuse Large B-cell Lymphoma


title: plateA2.positionB4.single.cell

description:
all.single.cell.gene.counts.txt
A2-B4

value: epithelial cell


title: plateA2.positionA4.single.cell

description:
all.single.cell.gene.counts.txt
A2-A4


title: RMDB_80

description: REMoDLB trial


title: RMDB_76

description: REMoDLB trial


title: NB 2

value: Tonsil


title: plateA2.positionH3.single.cell

description:
all.single.cell.gene.counts.txt
A2-H3


title: WT_polII_ChIPSeq_rep1


title: WT_input_rep1


title: plateA2.positionG3.single.cell

description:
all.single.cell.gene.counts.txt
A2-G3


title: IPa1-1_polII_ChiPSeq_rep1


title: RMDB_74

description: REMoDLB trial


title: RMDB_75

description: REMoDLB trial


title: Wounded_leaf

city: Taipei

first: Yun-Wei

last: Kuo

address: No. 1, Sec. 4, Roosevelt Road

department: Plant Biology

country: Taiwan

institute: National Taiwan University

data_processing:
Raw sequences were analysis by Mir pipeline on Linux
Clean up poly ATCG
Qualified reads after filtering the low-quality data
Qualified reads after filtering the size (select 18-25)
Conserved miRNA were match with miRBase
Genome_build: miRBase
Supplementary_files_format_and_content: txt file include read counts for sequences.

organism: Ipomoea batatas

source_name: leaf

growth_protocol: Sweet potato was grown in a controlled environment at 25°C under 16 h light/8 h dark with cool fluorescent light at 20 μmol photons m-2 s-1.

extract_protocol:
Total RNA was extracted by Trizol® Reagent (Invitrogen, USA) according to the instruction manual.
Library construction of all samples were used by  Illumina Genome Analyzer IIx platform and the 50 bp Single-End Reads

treatment_protocol: The third fully expanded sweet potato leaves counted from terminal bud were treated by wounding 30 min.

value: Wild-type

tag: cultivar

value: Tainung 57

value: leaf


title: plateA2.positionE3.single.cell

description:
all.single.cell.gene.counts.txt
A2-E3

tag: genotype

value: BASCs


title: RMDB_72

description: REMoDLB trial

value: UNC


title: Unwounded_leaf


title: plateA2.positionD3.single.cell

description:
all.single.cell.gene.counts.txt
A2-D3

tag: cell sub-type


title: plateA2.positionD7.single.cell

description:
all.single.cell.gene.counts.txt
A2-D7


title: patient rep6 Ribo-seq

first: Pankaj

last: Agrawal

address: 300 Longwood ave

institute: Boston Children's Hospital

description:
patient_vs_healthy_Riboseq.csv
patient_vs_healthy_TE.csv

data_processing:
Library strategy: Ribo-seq
analytical pipeline is available here: https://github.com/germaximus/OConnell_2018
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: "differential gene expression analysis" - contains output of DEseq2 package in R; "read count per gene" - contains count tables obtained from FeatureCount standalone software; "read coverage over transcripts" - sequencing read coverage of individual transripts.

source_name: Skin fibroblasts

growth_protocol: DMEM medium with 15% FBS serum

extract_protocol:
mRNA extracted with trizol and Direct-Zol kit from Zymo; ribosomal footprints isolated by fractionation of ribosomes using ultracentrifuge and then extracting footprints according to the protocol in the manuscript
mRNA-seq samples were prepared with TruSeq kit, Ribo-seq samples were prepared with custom protocol described in the manuscript

tag: passage

tag: rna type

value: Ribosomal profiling


title: patient rep5 Ribo-seq


title: plateA2.positionC3.single.cell

description:
all.single.cell.gene.counts.txt
A2-C3

source_name: BASCs-Tracer


title: patient rep4 Ribo-seq


title: plateA2.positionA3.single.cell

description:
all.single.cell.gene.counts.txt
A2-A3

value: Club cell


title: plateA2.positionF3.single.cell

description:
all.single.cell.gene.counts.txt
A2-F3


title: plateA2.positionB3.single.cell

description:
all.single.cell.gene.counts.txt
A2-B3


title: plateA2.positionH2.single.cell

description:
all.single.cell.gene.counts.txt
A2-H2


title: RMDB_92

description: REMoDLB trial

tag: clinic diagnosis

value: MHG

value: GCB


title: healthy individual-2 rep2 Ribo-seq


title: RMDB_73

description: REMoDLB trial

tag: molecular subtype


title: RMDB_67

description: REMoDLB trial

tag: molecular coo subtype


title: dmso_treatment_control_24hr

city: new delhi

first: binay

last: panda

address: 1649A vasant kunj

country: India

institute: ganit labs foundation

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw gene-wise expression signal intensities from GenomeStudio were transformed, normalized using VST (Variance Stabilizing Transformation) and LOESS methods, respectively, using the R package lumi (Du et al., 2008) and further batch-corrected using ComBat (Johnson et al., 2007).

source_name: dmso 0.04%, treatment control, 24hr

label_protocol: The RNA samples were labeled using Illumina TotalPrep RNA Amplification kit (Ambion, USA) and processed following the manufacturer’s recommendations.

growth_protocol: Cells were maintained in DMEM supplemented with 10% FBS, 1X MEM non-essential amino acids solution and 1X penicillin/streptomycin mixture (Gibco) at 370C with 5% CO2 incubation.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: HSC-4 cells were seeded and treated with neem leaf extract (200μg/ml) at nine pre-defined time points (5min, 10min, 15min, 30min, 1hr, 3hr, 6hr, 10hr, and 24hr) and rescued with fresh complete medium post 48-hour treatment at these time-points. The samples were assayed for gene expression using Illumina whole-genome HumanHT-12 v4 expression BeadChip (Illumina, San Diego, CA), following the manufacturer’s specifications.

tag: cell line

value: HSC-4 (human head and neck cancer cell line)

tag: agent

value: dmso (0.04 percent)

tag: group

tag: time point


title: RMDB_69

description: REMoDLB trial


title: cells_only_control, 2

source_name: cells_only, control

value: control


title: plateA2.positionG2.single.cell

description:
all.single.cell.gene.counts.txt
A2-G2

value: Lung


title: RMDB_71

description: REMoDLB trial


title: RMDB_68

description: REMoDLB trial

value: ABC


title: dmso_rescue_control_24hr

source_name: dmso 0.04%, rescue control, 24hr


title: patient rep3 Ribo-seq


title: leaf_rescue_10hr

source_name: leaf, rescue, 10hr

value: neem leaf

value: rescue

value: 10 hr


title: leaf_rescue_6hr

source_name: leaf, rescue, 6hr

value: 6 hr


title: plateA2.positionF2.single.cell

description:
all.single.cell.gene.counts.txt
A2-F2

value: epithelial cell


title: leaf_rescue_24hr

source_name: leaf, rescue, 24hr

value: 24 hr


title: healthy individual-2 rep3 Ribo-seq


title: patient rep2 Ribo-seq


title: leaf_rescue_3hr

source_name: leaf, rescue, 3hr

value: 3 hr


title: plateA2.positionE2.single.cell

description:
all.single.cell.gene.counts.txt
A2-E2

value: BASCs


title: patient rep1 Ribo-seq

value: Ribosomal profiling


title: RMDB_65

description: REMoDLB trial

value: Diffuse Large B-cell Lymphoma


title: plateA2.positionD2.single.cell

description:
all.single.cell.gene.counts.txt
A2-D2


title: leaf_rescue_1hr

source_name: leaf, rescue, 1hr

value: 1 hr


title: RMDB_63

description: REMoDLB trial

value: UNC


title: RMDB_62

description: REMoDLB trial

value: GCB


title: healthy individual-1 rep3 Ribo-seq


title: plateA2.positionC2.single.cell

description:
all.single.cell.gene.counts.txt
A2-C2


title: healthy individual-1 rep2 Ribo-seq

description:
patient_vs_healthy_mRNAseq.csv
patient_vs_healthy_TE.csv


title: plateA2.positionB2.single.cell

description:
all.single.cell.gene.counts.txt
A2-B2

value: Club cell


title: leaf_rescue_15min

source_name: leaf, rescue, 15min

value: HSC-4 (human head and neck cancer cell line)

value: 15 min


title: RMDB_64

description: REMoDLB trial


title: healthy individual-2 rep3 mRNA-seq

data_processing:
analytical pipeline is available here: https://github.com/germaximus/OConnell_2018
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: "differential gene expression analysis" - contains output of DEseq2 package in R; "read count per gene" - contains count tables obtained from FeatureCount standalone software; "read coverage over transcripts" - sequencing read coverage of individual transripts.

value: polyA enriched mRNA-seq


title: leaf_rescue_30min

source_name: leaf, rescue, 30min

value: neem leaf

value: 30 min


title: plateA2.positionA2.single.cell

description:
all.single.cell.gene.counts.txt
A2-A2

data_processing:
Reads were mapped to the mouse GRCm38 genome assemblies by HISAT2 using default settings
Uniquely aligned reads were counted using the ‘htseq-count’ tool of HTSeq
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes counts values for each single cell

value: Lung


title: plateA2.positionH1.single.cell

description:
all.single.cell.gene.counts.txt
A2-H1


title: healthy individual-2 rep1 mRNA-seq


title: leaf_rescue_5min

source_name: leaf, rescue, 5min

value: rescue

value: 5 min


title: leaf_rescue_10min

source_name: leaf, rescue, 10min

value: 10 min


title: RMDB_59

description: REMoDLB trial

data_processing: The data were normalised using lumi package in R


title: cells_only_control, 1

value: control


title: RMDB_60

description: REMoDLB trial


title: dmso_treatment_control_3hr

source_name: dmso 0.125%, treatment control, 3hr

value: dmso (0.125 percent)


title: plateA2.positionH5.single.cell

description:
all.single.cell.gene.counts.txt
A2-H5

value: epithelial cell

value: Ciliated cell


title: healthy individual-2 rep2 mRNA-seq


title: dmso_treatment_control_10hr

source_name: dmso 0.125%, treatment control, 10hr


title: plateA2.positionG1.single.cell

description:
all.single.cell.gene.counts.txt
A2-G1

value: BASCs


title: plateA2.positionF1.single.cell

description:
all.single.cell.gene.counts.txt
A2-F1


title: healthy individual-1 rep3 mRNA-seq


title: plateA2.positionE1.single.cell

description:
all.single.cell.gene.counts.txt
A2-E1


title: healthy individual-1 rep2 mRNA-seq


title: healthy individual-1 rep1 mRNA-seq


title: RMDB_58

description: REMoDLB trial

value: Diffuse Large B-cell Lymphoma


title: leaf_treatment_10hr

source_name: leaf, treatment, 10hr

value: treatment

value: 10 hr


title: RMDB_57

description: REMoDLB trial

value: MHG

value: GCB


title: RMDB_56

description: REMoDLB trial


title: RMDB_54

description: REMoDLB trial

value: ABC


title: plateA2.positionB1.single.cell

description:
all.single.cell.gene.counts.txt
A2-B1


title: leaf_treatment_3hr

source_name: leaf, treatment, 3hr

value: HSC-4 (human head and neck cancer cell line)

value: neem leaf

value: 3 hr


title: plateA2.positionC1.single.cell

description:
all.single.cell.gene.counts.txt
A2-C1

source_name: BASCs-Tracer

value: Lung


title: leaf_treatment_6hr

source_name: leaf, treatment, 6hr

value: 6 hr


title: RMDB_55

description: REMoDLB trial

value: UNC


title: RMDB_53

description: REMoDLB trial


title: patient rep4 mRNA-seq

source_name: Skin fibroblasts

value: polyA enriched mRNA-seq


title: plateA2.positionA1.single.cell

description:
all.single.cell.gene.counts.txt
A2-A1


title: patient rep3 mRNA-seq


title: plateA1.positionH12.single.cell

description:
all.single.cell.gene.counts.txt
A1-H12


title: leaf_treatment_1hr

source_name: leaf, treatment, 1hr

value: 1 hr


title: patient rep5 mRNA-seq


title: leaf_treatment_24hr

source_name: leaf, treatment, 24hr

value: 24 hr


title: patient rep2 mRNA-seq


title: patient rep6 mRNA-seq


title: leaf_treatment_30min

source_name: leaf, treatment, 30min

value: 30 min


title: RMDB_51

description: REMoDLB trial


title: RMDB_52

description: REMoDLB trial


title: plateA1.positionG12.single.cell

description:
all.single.cell.gene.counts.txt
A1-G12

value: epithelial cell

value: BASCs


title: RMDB_70

description: REMoDLB trial

value: Diffuse Large B-cell Lymphoma


title: leaf_treatment_10min

source_name: leaf, treatment, 10min

value: treatment

value: 10 min


title: leaf_treatment_15min

source_name: leaf, treatment, 15min

value: 15 min


title: RMDB_50

description: REMoDLB trial

value: ABC


title: plateA2.positionD1.single.cell

description:
all.single.cell.gene.counts.txt
A2-D1


title: RMDB_49

description: REMoDLB trial


title: plateA1.positionF12.single.cell

description:
all.single.cell.gene.counts.txt
A1-F12


title: plateA1.positionE12.single.cell

description:
all.single.cell.gene.counts.txt
A1-E12


title: RMDB_61

description: REMoDLB trial

value: GCB


title: KR106_miRNA

city: Tartu

first: Tõnis

last: Tasa

address: Liivi 2

country: Estonia

institute: University of Tartu

description: FACS isolated CD10+ stromal cells

data_processing:
Quality of the input reads before and after the read trimming was assessed with FastQC v0.9.5
Read trimming and filtering was performed with Cutadapt v1.8.1. Parameters: "-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -q 15 -m 15 -M 35"
Read mapping tool STAR aligner v2.4.0j was used to align quality controlled sequences to human reference genome (GRCh38). Parameters: "--outSAMtype BAM SortedByCoordinate --outFilterMatchNmin 17 --outFilterMultimapNmax 5  --outFilterType BySJout  --outFilterMismatchNoverLmax 0.05 --outFilterScoreMinOverLread 0  --outFilterMatchNminOverLread 0 --alignIntronMax 1"
Successfully aligned reads were quantified against miRNA regions from miRBase (v.21)  using featureCounts (v1.5.2). Parameters: "-t  miRNA -g Name -s 1 -O"
Genome_build: GRCh38
Supplementary_files_format_and_content: rawcounts_mature_miRNA.tab; Tab separated table of mature miRNA raw counts for 8 study samples. Columns are named as specified in "title" of metadata Samples section.

source_name: endometrioma

extract_protocol:
Total RNA was isolated using miRNeasy Micro kit
Small RNA libraries were prepared using NEBNext Small RNA Library Prep kit (New England Biolabs, Ipswich, MA, USA) and sequencing was performed with 1 × 76 bp NextSeq High Output kit

value: stroma

tag: menstrual cycle phase

value: prolifearative

tag: age


title: plateA1.positionD12.single.cell

description:
all.single.cell.gene.counts.txt
A1-D12

extract_protocol:
Lungs were digest with Collagenase, Dispase and Elastase sollution, Single epithelial cell was sorted by BD AriaII. Cell was lysed by single cell RNA lysis buffer containing 0.45% (vol/vol) NP40, followed by reverse transcription using SuperScript II reverse transcriptase (Invitrogen) and whole transcription amplification using KAPA HiFi HotStart ReadyMix (2X; KAPA Biosystems). PCR product was purified using AMPure XP beads (Agencourt) and quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher).
Libraries were constructed using illumina Nextera XT DNA sample preparation kit

value: Lung


title: RMDB_48

description: REMoDLB trial

extract_protocol: Total RNA was extracted from 5mm paraffin sections using the Ambion RecoverAll kit standard protocol, with the exception of a 16-hour protease digestion. These were routinely collected tissue samples and no attempt was made to standardise fixation or processing protocols


title: leaf_treatment_5min

source_name: leaf, treatment, 5min

value: HSC-4 (human head and neck cancer cell line)

value: neem leaf

value: 5 min


title: KR104_miRNA

description: FACS isolated CD10+ stromal cells


title: RMDB_46

description: REMoDLB trial


title: C_1

data_processing:
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).
PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

value: AML1-ETO related fusion circular RNA overexpression


title: C_3


title: V_3

value: wild type


title: RMDB_47

description: REMoDLB trial

value: UNC


title: patient rep1 mRNA-seq

value: polyA enriched mRNA-seq


title: plateA1.positionC12.single.cell

description:
all.single.cell.gene.counts.txt
A1-C12

value: epithelial cell

value: BASCs


title: KR108_miRNA

description: FACS isolated CD10+ stromal cells


title: V_2


title: KR102_miRNA

description: FACS isolated CD10+ stromal cells


title: C_2


title: plateA1.positionB12.single.cell

description:
all.single.cell.gene.counts.txt
A1-B12


title: KR107_miRNA

description: FACS isolated CD10+ stromal cells

source_name: endometrium


title: V_1


title: RMDB_44

description: REMoDLB trial

value: Diffuse Large B-cell Lymphoma


title: KR105_miRNA

description: FACS isolated CD10+ stromal cells


title: plateA1.positionA12.single.cell

description:
all.single.cell.gene.counts.txt
A1-A12


title: RMDB_45

description: REMoDLB trial


title: plateA1.positionH11.single.cell

description:
all.single.cell.gene.counts.txt
A1-H11

value: Club cell


title: KR103_miRNA

description: FACS isolated CD10+ stromal cells


title: P310.ms4.

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

description: Myelin debris were removed from single-cell suspension by myelin removal beads (#130-096-733, Miltenyi) prior to OPC enrichment.

data_processing:
RNA-seq reads were pre-processed and quality-trimmed using Trim Galore ! https://www.bioinformatics.babraham.ac.uk/projects/trim_galore). Reads were aligned to the mouse reference genome GRCm38/mm10 using Tophat (version 2.1.1, https://ccb.jhu.edu/software/tophat/index.shtml) allowing for one mismatch and selecting uniquely mapping reads only.  Read counts per ENSEMBL (version 92) were obtained by featureCounts (http://bioinf.wehi.edu.au/featureCounts).
Supplementary_files_format_and_content: Read counts per ENSEMBL transcript (version 92) obtained by featureCounts.

source_name: brain

extract_protocol:
OPCs were isolated from wild-type mice using magnetic cell sorting (MACS, Miltenyi Biotec). OPCs were enriched using microbeads conjugated to monoclonal PDGFRα (#130-101-502, Miltenyi). After OPC enrichment RNA was extracted using RNeasy Micro Kit (Qiagen) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using the SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit, according to manufacturer's instructions.

tag: strain

tag: developmental age


title: RMDB_43

description: REMoDLB trial


title: plateA1.positionG11.single.cell

first: Guangdun

last: Peng

address: 190 Kaiyuan Road

institute: Chinese Academy of Sciences

description:
all.single.cell.gene.counts.txt
A1-G11

tag: tissue

tag: cell type


title: KR101_miRNA

description: FACS isolated CD10+ stromal cells


title: plateA1.positionF11.single.cell

description:
all.single.cell.gene.counts.txt
A1-F11

tag: genotype


title: IOX2_3

city: Liverpool

first: Sonia

last: Rocha

address: crown street

department: Biochemistry

institute: University of Liverpool

data_processing:
The raw sequence reads from each replicate were aligned to the Ensembl human genome GRCh37 and ERCC sequence with STAR
The aligned reads were combined and number of read for each gene was counted with subread-featureCounts pipeline
The files were found to contain ribosomal DNA (rDNA) contaminations, majority of which were the following two mitochondrial DNA: ENSG00000211459 and ENSG00000210082 – which were removed manually
Genome_build: GRCh37
Supplementary_files_format_and_content: txt file

growth_protocol: HeLa cells were propagated in DMEM supplemented with 2mM L- glutamine, 10% (v/v) FBS, 50 units/mL penicillin and 50 μg/mL streptomycin

extract_protocol:
Total RNA was extracted using Rneasy Mini Kit from Qiagen according to manufacturer's protocol
Library was prepared using TruSeq stranded total RNA library preparation kit according to manufacturers protocol

treatment_protocol: Cells were treated with 0.05% DMSO, 1% Oxygen, 250 μM VH032 or 250 μM IOX2 for 16 hours

value: HeLa

value: Cervical cancer cells

tag: treatment

value: 1% Oxygen for 16 hours


title: P310.ms1.


title: P310.ms2.


title: VH032_3

value: VH032 250 μM for 16 hours


title: Hpx_3

value: IOX2 250 μM for 16 hours


title: RMDB_41

first: Chulin

last: Sha

address: Woodhouse Lane

institute: University of Leeds

description: REMoDLB trial

value: GCB


title: P80.ms3.


title: plateA1.positionE11.single.cell

description:
all.single.cell.gene.counts.txt
A1-E11

value: Lung

tag: cell sub-type


title: RMDB_40

description: REMoDLB trial


title: P80.ms2.


title: plateA1.positionC11.single.cell

description:
all.single.cell.gene.counts.txt
A1-C11


title: plateA1.positionB11.single.cell

description:
all.single.cell.gene.counts.txt
A1-B11


title: RMDB_66

description: REMoDLB trial


title: P310.ms3.


title: P80.ms1.


title: RMDB_38

description: REMoDLB trial

value: MHG

value: ABC


title: DMSO_3

value: DMSO 0.05% for 16 hours


title: RMDB_42

description: REMoDLB trial


title: IOX2_2


title: VH032_2


title: P12.ms3.


title: P12.ms2.


title: RMDB_35

description: REMoDLB trial


title: plateA1.positionD11.single.cell

description:
all.single.cell.gene.counts.txt
A1-D11


title: P12.ms1.


title: DMSO_2


title: plateA1.positionG10.single.cell

description:
all.single.cell.gene.counts.txt
A1-G10


title: plateA1.positionF10.single.cell

description:
all.single.cell.gene.counts.txt
A1-F10


title: IOX2_1


title: Hpx_2


title: plateA1.positionH10.single.cell

description:
all.single.cell.gene.counts.txt
A1-H10


title: RMDB_37

description: REMoDLB trial


title: plateA1.positionE10.single.cell

description:
all.single.cell.gene.counts.txt
A1-E10


title: E16.ms1.


title: VH032_1


title: E16.ms3.


title: plateA1.positionA11.single.cell

description:
all.single.cell.gene.counts.txt
A1-A11


title: Hpx_1


title: Dicer_KO2

city: Zurich

first: Constance

last: Ciaudo

email: cciaudo@ethz.ch, ciaudobeyer@gmail.com

address: Otto-Stern-Weg 7

department: D-BIOL

country: Switzerland

institute: ETH

data_processing:
Adaptors in the small RNA-seq reads were removed using Cutadapt. Reads ranged from 17-30 nucleotides were taken as input for mapping against mouse genome (mm10) using STAR. No mismatches were allowed for reads shorter than 20nt, and only 1 mismatch for reads longer than 20nt.
Aligned reads were summarized for each miRNA using featureCounts with default settings, using the miRNA annotation file from miRBase V21.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read count

source_name: DicerKO2 cells

growth_protocol: mESCs were cultured in DMEM, 15% serum, 100 U/mL LIF, 01. mM Beta-mercaptoethanol, 1% Pen/Strep on 0.2% gelatine coated plates.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq Small RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina True-seq protocols by the Functional Genomic Center Zurich (Switzerland)

tag: strain background

tag: genotype/variation

value: Dicer knockout

tag: developmental stage

value: Blastocyst; mouse embryonic stem cells


title: DMSO_1


title: plateA1.positionC10.single.cell

city: Guangzhou

description:
all.single.cell.gene.counts.txt
A1-C10


title: RMDB_36

city: Leeds

description: REMoDLB trial

tag: clinic diagnosis

tag: molecular subtype

value: UNC

tag: molecular coo subtype


title: RMDB_32

description: REMoDLB trial


title: RMDB_31

description: REMoDLB trial


title: RMDB_30

description: REMoDLB trial


title: RMDB_28

description: REMoDLB trial


title: E16.ms2.


title: plateA1.positionA10.single.cell

description:
all.single.cell.gene.counts.txt
A1-A10

value: epithelial cell


title: plateA1.positionD10.single.cell

description:
all.single.cell.gene.counts.txt
A1-D10

value: BASCs


title: plateA1.positionH9.single.cell

description:
all.single.cell.gene.counts.txt
A1-H9


title: RMDB_33

description: REMoDLB trial

value: Diffuse Large B-cell Lymphoma


title: RMDB_39

description: REMoDLB trial


title: RMDB_34

description: REMoDLB trial


title: plateA1.positionG9.single.cell

description:
all.single.cell.gene.counts.txt
A1-G9


title: plateA1.positionF9.single.cell

description:
all.single.cell.gene.counts.txt
A1-F9


title: MEG3 TFR2 rep2

city: Aachen

first: Ivan

middle: G.

last: Costa

state: NRW

address: Pauwelsstr. 19

department: RWTH Aachen Medical Faculty

country: Germany

institute: Institute for Computational Genomics

data_processing:
Library strategy: DBD-Capture-Seq
Illumina Nextseq500 Platform was used
Sequenced reads were trimmed for adaptor sequence and their quality was assessed using Fastqc, and the reads were mapped to hg38 whole genome using BWA  (0.7.15-r1140) and filtered by Blacklisted genomic regions of hg38 (ENCODE).
Peakcalling was performed on captured v.s. control (no oligo) signals by RGT-THOR with the p-value cut-off = 10 −2.5.
Genome_build: hg38
Supplementary_files_format_and_content: Differential peak calling was performed by RGT-THOR. Peak coordinates are available in bed files on the series record. BigWig files are included on sample records.

source_name: H1 ES cells

growth_protocol: ES cells were routinely cultured in FTDA media. Please refer PMID:22860038 for more information.

extract_protocol:
RNA-DNA complexes were bound to MyOne Streptavidin C1 Dynabeads (Invitrogen) and washed three times in a buffer containing 10 mM Tris-HCl (pH: 7.4), 50 mM KCl, 5 mM MgCl2, 0.05% Tween-20. RNA-associated DNA was eluted with 25 ng/μl RNase A and 5 mU/μl of Rnase I for 30 min at 37 ° C and recovered by phenol/chloroform extraction.
DNA libraries were prepared from two independent experiments using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) and sequenced on a NexSeq500 Illumina platform.

treatment_protocol: RNA-free genomic DNA from H1 ES cells was fragmented by sonication using Bioruptor Pico (Diagenode) to an average size of 200-300 bp. A total of 6-7 μg of fragmented DNA was incubated with 20 pmoles of biotin labeled-RNA oligonucleotides for 1 h at 37 ° C in 10 mM Tris-HCl (pH: 7.4), 50 mM KCl, 5 mM MgCl 2 , 40U of RNasin (Promega). Control experiments were based on the same protocol without the inclusion of an oligonucleotide.

value: ES cells

tag: cell line


title: GATA6-AS TFR1 rep1

description: GATA6AS_TFR1-diffpeaks_p2.5_captured.bed


title: MEG3 TFR2 rep1


title: GATA6-AS TFR1 rep2


title: plateA1.positionE9.single.cell

description:
all.single.cell.gene.counts.txt
A1-E9


title: Dicer_KO1

source_name: DicerKO1 cells


title: no oligo rep2


title: MEG3 TFR1 rep1


title: plateA1.positionD9.single.cell

description:
all.single.cell.gene.counts.txt
A1-D9

value: Club cell


title: RMDB_26

description: REMoDLB trial


title: RMDB_24

description: REMoDLB trial


title: plateA1.positionC9.single.cell

description:
all.single.cell.gene.counts.txt
A1-C9


title: RMDB_29

description: REMoDLB trial


title: plateA1.positionB9.single.cell

description:
all.single.cell.gene.counts.txt
A1-B9


title: RMDB_23

description: REMoDLB trial


title: RMDB_21

description: REMoDLB trial


title: no oligo rep1


title: RMDB_22

description: REMoDLB trial


title: RMDB_25

description: REMoDLB trial


title: RMDB_20

description: REMoDLB trial


title: induced human podocytes_2

city: Kumamoto

first: Yasuhiro

last: Yoshimura

state: Japan

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

description:
i-Podocyte_2
On day 12 of differentiation from human iPS cell-derived nephron progenitor cells.
Two raw data files per Sample. One file includes the raw read data of the molecular barcodes outputted from the sequencer; 8 bp of index for sample classification with 8 bp of molecular barcode.
processed data file: Processed data file_Podocyte RNA-seq.xlsx

data_processing:
Basecalls performed using bcl2fastq v2.17.
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.32 tool.
The sequence reads were aligned to the human reference genome (hg19) using TopHat 2.1.1 (bowtie2-2.2.3) with the option '-g 1 --no-discordant'.
NuDup ver.2.3 (NuGEN Technologies, San Carlos, CA) analyzing the redundancy of 8 bp molecular barcodes was used to remove PCR duplicate reads.
The read counts allocated for each gene and transcript (RefSeq version 2015.10.5) were quantified using a Trimmed Mean of M-value (TMM) method using StrandNGS 3.1 software (Agilent Technologies, Santa Clara, CA).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Processed data file_Podocyte RNA-seq.xlsx: An Excel format file (XLSX) includes TMM quantification values and gene annotations of all samples.

source_name: human iPS cell-derived podocytes

growth_protocol: Nephron progenitor cells were induced from human iPS cells by the established protocol (A, Taguchi. et al., Cell Stem Cell 2014, 2017). Human iPS cell-derived podocytes were induced from sorted nephron progenitor cells (Itga8+/Pdgfra-) by our newly established protocol (Y, Yoshimura et al., unpublished). The immortalized podocytes were cultured and differentiated as reported previously (M, Saleem. et al., J Am Soc Nephrol 2002).

extract_protocol:
Nephron progenitor cells, human adult podocytes, and human adult non-podocytes were sorted by a FACS SORP Aria (Becton Dickinson) after single cell dissociation. Human iPS cells and the immortalized podocytes were detached from the culture dishes by treatment with accuate and 0.05% Trypsin-EDTA, respectively. Induced human podocytes were detached from the transwell insert by gentle pipetting. Total RNA was extracted using "RNeasy Plus Micro Kit" purchased from QIAGEN following manufacturer's protocol.
Total RNA obtained from each sample was subjected to a sequencing library construction using Ovation Solo RNA-Seq System (NuGEN Technologies, San Carlos, CA) according to the manufacturer's protocol.

value: iPS cell-derived podocytes

tag: clone

tag: passage


title: plateA1.positionA9.single.cell

description:
all.single.cell.gene.counts.txt
A1-A9


title: plateA1.positionH8.single.cell

description:
all.single.cell.gene.counts.txt
A1-H8


title: induced human podocytes_1

description:
i-Podocyte_1
On day 12 of differentiation from human iPS cell-derived nephron progenitor cells.
Two raw data files per Sample. One file includes the raw read data of the molecular barcodes outputted from the sequencer; 8 bp of index for sample classification with 8 bp of molecular barcode.
processed data file: Processed data file_Podocyte RNA-seq.xlsx


title: sorted human non-podocytes from Pt. 3

description:
Pt3_non_Podocyte
Sorted as Nephrin-/Podocalyxin- population from 69-year-old Japanese male.
Two raw data files per Sample. One file includes the raw read data of the molecular barcodes outputted from the sequencer; 8 bp of index for sample classification with 8 bp of molecular barcode.
processed data file: Processed data file_Podocyte RNA-seq.xlsx

source_name: Nephrin-/Podocalyxin- cells of human adult glomeruli

value: kidney

value: Nephrin-/Podocalyxin- cells of adult glomeruli


title: plateA1.positionG8.single.cell

description:
all.single.cell.gene.counts.txt
A1-G8

source_name: BASCs-Tracer


title: sorted human adult podocytes from Pt. 3

description:
Pt3_Podocyte
Sorted as Nephrin+/Podocalyxin+ population from 69-year-old Japanese male.
Two raw data files per Sample. One file includes the raw read data of the molecular barcodes outputted from the sequencer; 8 bp of index for sample classification with 8 bp of molecular barcode.
processed data file: Processed data file_Podocyte RNA-seq.xlsx

source_name: human adult podocytes

value: adult podocytes


title: plateA1.positionF8.single.cell

description:
all.single.cell.gene.counts.txt
A1-F8


title: sorted human adult podocytes from Pt. 2

description:
Pt2_Podocyte
Sorted as Nephrin+/Podocalyxin+ population from 49-year-old Japanese female.
Two raw data files per Sample. One file includes the raw read data of the molecular barcodes outputted from the sequencer; 8 bp of index for sample classification with 8 bp of molecular barcode.
processed data file: Processed data file_Podocyte RNA-seq.xlsx


title: RMDB_19

description: REMoDLB trial

value: GCB


title: plateA1.positionE8.single.cell

description:
all.single.cell.gene.counts.txt
A1-E8

value: Lung


title: RMDB_17

description: REMoDLB trial


title: RMDB_18

description: REMoDLB trial


title: RMDB_16

description: REMoDLB trial


title: plateA1.positionD8.single.cell

description:
all.single.cell.gene.counts.txt
A1-D8


title: nephron progenitor cells_2

description:
NPC_2
On day 13 of differentiation from human iPS cells, sorted as Itga8+/Pdgfra- population.
Two raw data files per Sample. One file includes the raw read data of the molecular barcodes outputted from the sequencer; 8 bp of index for sample classification with 8 bp of molecular barcode.
processed data file: Processed data file_Podocyte RNA-seq.xlsx

source_name: human iPS cell-derived nephron progenitor cells


title: RMDB_14

description: REMoDLB trial


title: Left ventricle_CLP + Lnd_CAL060716

city: Marseille

first: Thom

middle: Thi

last: Tran

address: 163, avenue de Luminy

department: Marseille

country: France

institute: INSERM

hyb_protocol: 0,6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent for 8-pack microarray format following the manufacturers instructions. On completion of the fragmentation reaction, 25 µL of 2x Hi-RPM Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Rat Genome Oligo Microarrays (Feature Number version) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed  at room temperature with GE Wash Buffer 1 (Agilent), then 1 minute at room temperature with GE Wash Buffer 1 (Agilent), and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using AgilentG3_GX_1color setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 074036_D_F_20150914 in male, GE1_107_sep09 and Gid: 074036_D_F_20171118 in female) to obtain background subtracted and spatially detrended Processed Signal intensities. Data  was first log2 transformed then quantile normalization was applied to sample data to correct for global intensity and dispersion . Then, a filtering at 80% was used to keep only genes expressed over the background noise, so 38223 probes in male and 37605 probes in female.

organism: Rattus norvegicus

source_name: left ventricle after 20 hours in CLP+ landiolol infusion in female

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Quick Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification, Rneasy mini kit (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from left ventricle using TRIzol Reagent according to the manufacturer’s procedure (Invitrogen, Life Technologies). The concentration of RNA was determined by reading absorbance at 260 nm on NanoDrop (ND-1000, ThermoScientific). The ratios of A260/280 from all the RNA samples ranged from 1.8 to 2.0. The quality of RNA was confirmed on the Agilent 2100 Bioanalyzer (Agilent technologies, Germany) with the Agilent RNA 6000 Nano chips. The samples with a RIN (RNA Integrity Number) higher than 8 were used for microarray.

tag: Sex

value: female

value: CLP (Cecal ligation and puncture) induction and landiolol administration

tag: heart collection time point

value: left ventricle


title: plateA1.positionB8.single.cell

description:
all.single.cell.gene.counts.txt
A1-B8


title: nephron progenitor cells_1

description:
NPC_1
On day 13 of differentiation from human iPS cells, sorted as Itga8+/Pdgfra- population.
Two raw data files per Sample. One file includes the raw read data of the molecular barcodes outputted from the sequencer; 8 bp of index for sample classification with 8 bp of molecular barcode.
processed data file: Processed data file_Podocyte RNA-seq.xlsx

value: iPS cell-derived nephron progenitor cells


title: plateA1.positionC8.single.cell

description:
all.single.cell.gene.counts.txt
A1-C8


title: RMDB_13

description: REMoDLB trial

value: MHG


title: the immortalized human podocyte cell line_2

description:
Cell_Line_2
On day 14 of differentiation.
Two raw data files per Sample. One file includes the raw read data of the molecular barcodes outputted from the sequencer; 8 bp of index for sample classification with 8 bp of molecular barcode.
processed data file: Processed data file_Podocyte RNA-seq.xlsx

source_name: immortalized human podocytes

value: immortalized podocytes


title: Left ventricle_CLP + Lnd_CAL200516


title: the immortalized human podocyte cell line_1

description:
Cell_Line_1
On day 14 of differentiation.
Two raw data files per Sample. One file includes the raw read data of the molecular barcodes outputted from the sequencer; 8 bp of index for sample classification with 8 bp of molecular barcode.
processed data file: Processed data file_Podocyte RNA-seq.xlsx


title: plateA1.positionH7.single.cell

description:
all.single.cell.gene.counts.txt
A1-H7

value: epithelial cell


title: plateA1.positionG7.single.cell

description:
all.single.cell.gene.counts.txt
A1-G7

value: BASCs


title: plateA1.positionA8.single.cell

description:
all.single.cell.gene.counts.txt
A1-A8


title: human iPS cells_1

description:
201B7_1
Undifferentiated human iPS cells.
Two raw data files per Sample. One file includes the raw read data of the molecular barcodes outputted from the sequencer; 8 bp of index for sample classification with 8 bp of molecular barcode.
processed data file: Processed data file_Podocyte RNA-seq.xlsx

source_name: human iPS cells

value: iPS cells


title: Left ventricle_CLP + Lnd_CAL050716


title: Left ventricle_CLP + Lnd_CAL270416


title: human iPS cells_2

description:
201B7_2
Undifferentiated human iPS cells.
Two raw data files per Sample. One file includes the raw read data of the molecular barcodes outputted from the sequencer; 8 bp of index for sample classification with 8 bp of molecular barcode.
processed data file: Processed data file_Podocyte RNA-seq.xlsx


title: RMDB_15

description: REMoDLB trial

value: Diffuse Large B-cell Lymphoma


title: Left ventricle_CLP + Lnd_CAL270716


title: RMDB_12

description: REMoDLB trial


title: RMDB_9

description: REMoDLB trial


title: Left ventricle_CLP_CAL200716

source_name: left ventricle after 20 hours in CLP induction in female

value: CLP (Cecal ligation and puncture) induction


title: Left ventricle_CLP + Lnd_CAL0290416


title: RMDB_11

description: REMoDLB trial


title: RMDB_10

description: REMoDLB trial

value: ABC


title: plateA1.positionF7.single.cell

description:
all.single.cell.gene.counts.txt
A1-F7


title: plateA1.positionE7.single.cell

description:
all.single.cell.gene.counts.txt
A1-E7


title: plateA1.positionD7.single.cell

description:
all.single.cell.gene.counts.txt
A1-D7

value: Club cell


title: kd_rep2

city: Pieve Emanuele

first: Giulia

last: Cardamone

address: via Rita Levi Montalcini 4

country: Italy

institute: Humanitas University

data_processing:
Reads were mapped to the human genome (hg19) using STAR (version 2.5.2)
Transcript quantification from mapped reads was performed using HTSeq-count (version 0.6.1p1)
Differential expression analysis was carried out using R and the edgeR package
Genome_build: hg19 (GRCh37), transcripts annotations from Ensembl database
Supplementary_files_format_and_content: tab-delimited text files include raw reads counts

source_name: Jurkat E6-1 T cell line

growth_protocol: Jurkat E6-1 cells were cultured in RPMI 1640 supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin, 1% sodium pyruvate,  and 1% nonessential amino acids.

extract_protocol:
Total RNA was extracted using the Maxwell 16 LEV simplyRNA Cells Kit (Promega).
Libraries were prepared starting from 500 ng of total RNA, using the Illumina TruSeq Stranded Total RNA Library Prep Kit and following the manufacturer’s instructions.  Sequencing was performed on a 2x150 paired end High flow cell on a NextSeq500 platform (Illumina).

treatment_protocol: 50000 Jurkat E6-1 cells were incubated in a 24-well plate with 500 nM GapmeR targeting MALAT1 (kd) or 500 nM GapmeR negative control (mock); the transfection was achieved through a gymnotic delivery. After 24 hours, cells were collected for total RNA extraction.

value: Jurkat E6-1 T cell line

value: T lymphocyte

value: GapmeR targeting MALAT1


title: kd_rep1


title: Left ventricle_CLP_CAL230616


title: kd_rep3


title: mock_rep3

value: GapmeR negative control


title: RMDB_7

description: REMoDLB trial


title: Left ventricle_CLP_CAL150616

value: female


title: plateA1.positionA7.single.cell

description:
all.single.cell.gene.counts.txt
A1-A7

value: Lung


title: Left ventricle_CLP_CAL140616

value: left ventricle


title: RMDB_6

description: REMoDLB trial

value: GCB


title: RMDB_4

description: REMoDLB trial


title: RMDB_5

description: REMoDLB trial

value: MHG


title: mock_rep1


title: plateA1.positionE6.single.cell

description:
all.single.cell.gene.counts.txt
A1-E6


title: plateA1.positionF6.single.cell

description:
all.single.cell.gene.counts.txt
A1-F6


title: plateA1.positionC7.single.cell

description:
all.single.cell.gene.counts.txt
A1-C7


title: plateA1.positionG6.single.cell

description:
all.single.cell.gene.counts.txt
A1-G6


title: mock_rep2


title: Left ventricle_Sham_CAL220716

source_name: left ventricle after 20 hours in Sham female

value: sham


title: Left ventricle_Sham_CAL220616


title: RMDB_8

description: REMoDLB trial


title: Left ventricle_CLP + Lnd_CAL120516

source_name: left ventricle after 20 hours in CLP+ landiolol infusion in male

value: male

value: CLP (Cecal ligation and puncture) induction and landiolol administration


title: Left ventricle_CLP_CAL070416


title: RMDB_2

description: REMoDLB trial


title: Left ventricle_Sham_CAL080416


title: plateA1.positionD6.single.cell

description:
all.single.cell.gene.counts.txt
A1-D6

value: epithelial cell

value: BASCs


title: plateA1.positionC6.single.cell

description:
all.single.cell.gene.counts.txt
A1-C6


title: plateA1.positionB6.single.cell

description:
all.single.cell.gene.counts.txt
A1-B6


title: plateA1.positionH5.single.cell

description:
all.single.cell.gene.counts.txt
A1-H5


title: plateA1.positionA6.single.cell

description:
all.single.cell.gene.counts.txt
A1-A6


title: SRF siRNA R1881 3

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to GRCh38 reference GENCODE annotation (p7) using tophat 2.0.13
TopHat aligned BAMs were merged using MergeSamFiles from Picard v1.97
Reads counts are obtained using HTSeq v0.6.1 using intersect-strict option
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

source_name: LNCaP prostate cancer cells

extract_protocol: RNA Libraries are prepared using the Illumina NextSeq RNA Exome protocol and kit reagents.

value: LNCaP prostate cancer cells

tag: sirna

value: SRF


title: Left ventricle_CLP + Lnd_CAL090616

tag: tissue


title: plateA1.positionG5.single.cell

description:
all.single.cell.gene.counts.txt
A1-G5

tag: cell type


title: Left ventricle_Sham_CAL280716


title: Left ventricle_Sham_CAL080716


title: SRF siRNA R1881 2


title: plateA1.positionF5.single.cell

description:
all.single.cell.gene.counts.txt
A1-F5

tag: genotype


title: RMDB_1

description: REMoDLB trial

value: Diffuse Large B-cell Lymphoma

value: ABC


title: Left ventricle_CLP + Lnd_CAL300616

tag: treatment


title: SRF siRNA R1881 1


title: plateA1.positionE5.single.cell

description:
all.single.cell.gene.counts.txt
A1-E5

tag: cell sub-type


title: Left ventricle_CLP + Lnd_CAL160616


title: Left ventricle_CLP + Lnd_CAL190716


title: Left ventricle_CLP_CAL220316

source_name: left ventricle after 20 hours in CLP induction in male

value: CLP (Cecal ligation and puncture) induction


title: SRF siRNA vehicle 3

value: ETOH


title: plateA1.positionD5.single.cell

description:
all.single.cell.gene.counts.txt
A1-D5


title: Left ventricle_CLP_CAL210616


title: Left ventricle_CLP + Lnd_CAL130716


title: Left ventricle_CLP_CAL040516


title: plateA1.positionB5.single.cell

description:
all.single.cell.gene.counts.txt
A1-B5


title: SRF siRNA vehicle 1


title: plateA1.positionB10.single.cell

description:
all.single.cell.gene.counts.txt
A1-B10


title: MEG3 TFR1 rep2

value: ES cells


title: plateA1.positionA5.single.cell

description:
all.single.cell.gene.counts.txt
A1-A5


title: Nkx2-5 siRNA R1881 3


title: Left ventricle_CLP_CAL130516


title: Left ventricle_CLP_CAL010716


title: RMDB_3

description: REMoDLB trial


title: Nkx2-5 siRNA R1881 2


title: plateA1.positionG4.single.cell

description:
all.single.cell.gene.counts.txt
A1-G4


title: Left ventricle_Sham_CAL010416

source_name: left ventricle after 20 hours in Sham male


title: plateA1.positionF4.single.cell

description:
all.single.cell.gene.counts.txt
A1-F4


title: plateA1.positionH4.single.cell

description:
all.single.cell.gene.counts.txt
A1-H4


title: T-Whiteskin3

city: Wuxi

first: Mingkun

last: Luo

state: Jiangsu

address: East Shanshui Road 9

department: Wuxi Fisheries College

institute: Nanjing Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
The clean reads were first mapped onto the common carp (C. carpio) v3 reference genome (http://www.fishbrowser.org/database/Commoncarp_genome/) independently by TopHat 2.0.10 with 6 mismatches.
We used blat to align assembled transcripts back to reference genome to look up locations of assembled transcripts with at least 90% sequence similarity. Since no lncRNAs information was provided in common carp v3 genome annotations, transcripts which were similar to known lncRNAs of zebrafish (cutoff E-value ≤ 1e-10) were assigned to be putative lncRNAs.In order to detecting novel lncRNAs from the finally assemblies, transcripts locations were compared to reference genome annotation using Gffcompare software (v0.10.1). The unknown transcripts were used to lncRNA identification using CPC, NR and Pfam.
The FPKM value calculated by RSEM program (v1.2.21) was used to estimate the expression levels of lncRNAs and mRNAs in every sample.
Differential expression analyses among different skin color groups were performed using the R package (edgeR 3.22.3), an absolute value of |log2 (fold change)| > 1 and an adjusted P-value of < 0.05 were set as the filter criteria for significant differential expression.
Genome_build: C. carpio v3
Supplementary_files_format_and_content: tab-delimited text files include count, FPKM, TPM number for each Sample

organism: Cyprinus carpio 'koi'

source_name: T-Whiteskin

growth_protocol: Animals (average weight: 200 ± 8 g) were raised at 24 ± 1 ℃ in 256 L tanks in a circulation water system for 1 week before experiments and fed twice daily (in the morning and late afternoon). Aeration was supplied constantly and a 12 h light / 12 h dark photoperiod was employed.

extract_protocol:
Total RNA was isolated using the standard TRIzol (Invitrogen) protocol
The total genomic DNA was removed using DNase I (New England Biolabs) and RNA quality was confirmed with the Agilent 2100 Bioanalyzer (Agilent Technologies). The poly (A) libraries were prepared using Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina). Poly (A) RNA was purified with oligo dT magnetic beads, and the poly (A) RNA was fragmented with divalent cations followed by reverse transcription into cDNA and ligation of Illumina paired-end oligo adapters to the cDNA fragments.
Illumina HiSeq X Ten for 2 × 150 bp pair-end sequencing

treatment_protocol: All of the surviving fishes were tranquilized in 10~15 mg/L MS-222 buffered to pH 7.0-7.5, and three sets of skin tissues including black (BS), white (WS) and red (RS) were collected from three Koi carp (black, white and red spots in one fish synchronous)

tag: strain

value: FFRC

value: skin

tag: skin color

value: white


title: Nkx2-5 siRNA vehicle 3


title: plateA1.positionC5.single.cell

description:
all.single.cell.gene.counts.txt
A1-C5

value: Lung


title: Nkx2-5 siRNA vehicle 2


title: Left ventricle_Sham_CAL170616

value: left ventricle


title: SRF siRNA vehicle 2


title: plateA1.positionE4.single.cell

description:
all.single.cell.gene.counts.txt
A1-E4


title: Left ventricle_Sham_CAL260516

value: sham


title: Left ventricle_Sham_CAL180516

value: male


title: Nkx2-5 siRNA vehicle 1


title: Nkx2-5 siRNA R1881 1


title: T-Whiteskin2


title: plateA1.positionD4.single.cell

description:
all.single.cell.gene.counts.txt
A1-D4


title: T-Whiteskin1


title: plateA1.positionC4.single.cell

description:
all.single.cell.gene.counts.txt
A1-C4


title: control siRNA R1881 3

value: OTPC


title: T-Redskin3

source_name: T-Redskin

value: red


title: Left ventricle_Sham_CAL290616


title: T-Redskin2


title: plateA1.positionA4.single.cell

description:
all.single.cell.gene.counts.txt
A1-A4

value: epithelial cell

value: BASCs


title: T-Redskin1


title: control siRNA R1881 2

value: LNCaP prostate cancer cells


title: control siRNA vehicle 3


title: control siRNA R1881 1


title: plateA1.positionB4.single.cell

description:
all.single.cell.gene.counts.txt
A1-B4


title: plateA1.positionG3.single.cell

description:
all.single.cell.gene.counts.txt
A1-G3


title: plateA1.positionH3.single.cell

description:
all.single.cell.gene.counts.txt
A1-H3


title: plateA1.positionF3.single.cell

description:
all.single.cell.gene.counts.txt
A1-F3


title: control siRNA vehicle 1


title: T-Blackskin2

source_name: T-Blackskin

value: black


title: T-Blackskin1


title: plateA1.positionE3.single.cell

description:
all.single.cell.gene.counts.txt
A1-E3


title: T-Blackskin3


title: plateA1.positionD3.single.cell

description:
all.single.cell.gene.counts.txt
A1-D3