title: HES-2, Naïve, rep1

data_processing:
Quality control was applied to FASTQ files and included: extracting residual adapters, trimming low quality bases and filtering out short reads. Quality control was performed with FASTQC version V0.11.
Filtered reads were mapped directly to the transcriptome with Salmon Aligner version  V1.4.0. Salmon transcriptome was based on GRCh38 with murine mm10 transcripts set as decoys.
Differentially expressed genes were analyzed with R DESeq2 package,
Assembly: GRCh38
Supplementary files format and content: normalizedCounts_H7_HES1_HES2.txt is a tab delemeted text table of (DESeq2) normalized counts. Rows are ensembl gene IDs and columns are samples.

growth_protocol: LN-hPSCs were cultured on mouse LN111, 3-D Culture Matrix Laminin I (CULTREX, TREVIGEN, a final concentration of ~ 8 microgram/ cm2), in a medium composed of DMEM/F12, B27 supplement, N2 supplement, L-glutamine, penicillin, streptomycin, and supplemented daily with 20 ng/ml FGF2.  Conventional/primed hPSCs were cultured on Mitomycin C-treated mouse embryonic fibroblasts in a medium composed of DMEM/F12, 20% KSR, non-essential amino acids, mM 2-mercaptoethanol, L-glutamine, penicillin, streptomycin, and supplemented daily with 10 ng/ml FGF2. Naïve hPSC cultures were established from hPSCs cultured on mTeSR and maintained following the 5iLFA protocol (Theunissen et al., 2014). All hPSCs were maintained in 5% CO2, 5% O2 incubator.

extract_protocol:
hPSCs were detached from the matrix or MEFs by treatment with Collagenase type IV. Total RNA was extracted using the RNeasy Mini Kit (QIAGEN).
mRNA libraries were prepared from 1 µg RNA using the KAPA Stranded mRNA-Seq Kit, with mRNA Capture Beads, following manufacturer's protocols .

value: 5iLFA naïve culture conditions


title: Tissue chunks, ribo-depleted, bulk sequenced, rep3

status: Public on Nov 13 2022

type: SRA

city: Philadelphia

first: Ariel

middle: A

last: Hippen

state: PA

address: 3400 Civic Center Blvd

country: USA

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
Cell Ranger (cellranger count version 6.1.2) was used to generate single-cell feature counts for each single-cell sample.
STAR (STAR version 2.7.10) was used to generate gene counts for each bulk sample.
Assembly: GRCh38 (refdata-gex-GRCh38-2020-A provided with Cell Ranger)
Supplementary files format and content: gene count matrix (matrix_XXX.mtx.gz), features table (features_XXX.tsv.gz), barcodes table (barcodes_XXX.tsv.gz)
Supplementary files format and content: gene count matrix (XXX_STAR.tsv.gz)

molecule: total RNA

organism: Homo sapiens

source_name: ovarian tumor

extract_protocol:
Tumor samples were cut into 1mm chunks, and a portion were flash frozen. The remaining fresh tissue chunks were dissociated using the Miltenyi Biotech Human Tumor Dissociation Kit and digested overnight. The dissociated tissue was filtered through a 100 micrometer nylon mesh and red blood cells removed using ACK Lysis Buffer. Dissociated cells were suspended in Dulbecco’s Phosphate Buffered Saline and cryopreserved.
Single cell library preparation was performed using the 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Pooled single cell library preparation was performed using the 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 with feature barcode technology for cell surface protein. Bulk sequencing library preparation used either the Illumina TruSeq Stranded Total RNA protocol and the RiboZero Gold kit, or the Illumina TruSeq Stranded mRNA protocol.  All libraries were sequenced on an Illumina NovaSeq 6000.

tag: disease state

value: high-grade serous ovarian cancer (HGSOC)

tag: tissue

value: ovarian tumor


title: w303_1C_ss_GSH_rep1

city: Delft

first: Diederik

last: Laman Trip

address: Van der Maasweg 9

department: Bionanoscience

country: Netherlands

institute: Delft University of Technology

description: mRNA

data_processing:
Salmon tool to quantify relative transcript abundance (see methods in the article for details of our methodology)
Assembly: reference transcripts for S. cerevisiae from Ensembl (assembly R64-1-1)
Supplementary files format and content: Salmon outputs (".sf"), readable as ".csv"

organism: Saccharomyces cerevisiae

source_name: steady-state mRNA levels

extract_protocol:
RiboPure Yeast RNA extraction kit (Thermo Fischer Scientific, cat. No. AM1926) following the kit instructions
TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat

tag: temperature (degrees celcius)

tag: added gsh (um)


title: WT2_12h

city: shanghai

first: kun

last: chen

address: No.800 Xiangyin Road, Yangpu District

country: China

institute: Zhejiang University

data_processing:
cDNA library construction and sequencing were performed by Beijing Genomics Institute using BGISEQ-500 platform.
High-quality reads were aligned to the mouse reference genome (GRCm38) using Bowtie2
The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM) using RNA-Seq by Expectation Maximization (RSEM).

organism: Mus musculus

source_name: bone marrow-derived macrophages

growth_protocol: Bone marrow-derived monocyte are cultured in DMEM medium plus M-CSF for 5 days to generate BMDMs.

extract_protocol:
Total RNA was extracted from treated mDCs using TRIzol reagent (Invitrogen) according to manufacturer’s protocol.
cDNA library construction and sequencing were performed by Beijing Genomics Institute using BGISEQ-500 platform.

treatment_protocol: BMDMs  are treated with LPS (100ng/ml) for 4h, 8h, 12h, 24h.

tag: stain

value: bone marrow

tag: age

tag: time point


title: WT2_24h


title: w303_1C_t5_GSH_rep1

description: 4tU-labelled mRNA

source_name: 96 hrs after adding 4tU


title: HES-2, Naïve, rep00

city: Jerusalem

first: Michal

last: Gropp

address: Hadassah Ein-Kerem

country: Israel

institute: Hadassah Medical Center

tag: cell line

tag: cell type

value: human pluripotent stem cells

tag: genotype

value: WT, 46,XX

tag: treatment

value: 5iLFA naive culture conditions


title: KO_L0_1

description: WT_KO_All expression gene.txt

extract_protocol:
Total RNA was extracted from treated BMDMs using TRIzol reagent (Invitrogen) according to manufacturer’s protocol.
cDNA library construction and sequencing were performed by Beijing Genomics Institute using BGISEQ-500 platform.

treatment_protocol: BMDMs  are treated with LPS (100ng/ml) for 12h, 24h.

tag: genotype/variation


title: HES-2, LN, rep1

value: Culture on LN111 in defined conditions


title: Tissue chunks, ribo-depleted, bulk sequenced, rep2


title: w303_1C_t4_GSH_rep1

description: 4tU-labelled mRNA

source_name: 48 hrs after adding 4tU


title: HES-2, LN, rep0


title: WT2_8h


title: WT_L12_1

description: WT_KO_All expression gene.txt

value: WT


title: WT2_4h


title: w303_1C_t3_GSH_rep1

description: 4tU-labelled mRNA

source_name: 24 hrs after adding 4tU


title: Dissociated cells, pooled, single-cell sequenced, rep2

library_source: transcriptomic single cell

molecule: polyA RNA


title: w303_1C_t2_GSH_rep1

description: 4tU-labelled mRNA

source_name: 12 hrs after adding 4tU


title: w303_1C_t0_GSH_rep2

description: 4tU-labelled mRNA

source_name: reference for 1C and with GSH, right before adding 4tU


title: w303_1C_t1_GSH_rep1

description: 4tU-labelled mRNA

source_name: 6 hrs after adding 4tU


title: female mouse E14.5, DMH,  Tfap2b-/- mutant replicate 3

city: Goettingen

first: Yang

last: Hu

country: Germany

institute: MPIBPC

data_processing:
Following base calling, adaptor clipping was performed using  cutadapt 2.4 (Martin 2011 Cutadapt removes adapter sequences from high-  throughput sequencing reads. 17: 3.). Data were mapped against  the GRCm38.p6 genome using STAR v 2.6.1d (Dobin et al.  2013 https://doi.org/10.1093/bioinformatics/bts635) and differentially expressed genes were analyzed  using EdgeR
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

extract_protocol:
total RNA was isolated from each sample individually according to the manufacture’s protocol (Qiagen RNeasy Mini plus).
After quality control using Agilent’s Bioanalyzer, sequencing libraries were prepared from 500ng of total RNA per sample following Roche’s stranded “KAPA RNA HyperPrep” library preparation protocol for single indexed Illumina libraries: First the polyA-RNA fraction was enriched using oligo-dT-probed paramagnetic beads. Enriched RNA was heat-fragmented and subjected to first strand synthesis using random priming. The second strand was synthesized incorporating dUTP instead of dTTP to preserve strand information. After A-tailing, Illumina sequencing compatible adapters were ligated. Following bead-based clean-up steps the libraries were amplified using 11 cycles of PCR. Library quality and size was checked with qBit, Agilent Bioanalyzer and qPCR. Sequencing was carried out on an Illumina NovaSeq2 system in PE100bp mode yielding around 50 million fragments per sample.

value: DMH

tag: gender

value: female


title: Dissociated cells, pooled, single-cell sequenced, rep1


title: HES-2, Conventional, rep0

value: Convenional  culture conditions


title: HES-1, Naïve, rep1


title: female mouse E14.5, SP,  Tfap2b-/- mutant replicate 3

value: SP


title: w303_1C_t0_GSH_rep1

description: 4tU-labelled mRNA


title: HES-1, Naïve, rep0


title: Dissociated cells, single cell sequenced, rep7


title: female mouse E14.5, DMH,  Tfap2b+/+ control replicate 3


title: HES-1, LN, rep2


title: Dissociated cells, single cell sequenced, rep6


title: w303_1C_t5_noGSH_rep3

description: 4tU-labelled mRNA


title: female mouse E14.5, SP,  Tfap2b+/+ control replicate 3


title: HES-1, LN, rep1


title: w303_1C_ss_noGSH_rep3

description: mRNA


title: Dissociated cells, single cell sequenced, rep5


title: w303_1C_t4_noGSH_rep3

description: 4tU-labelled mRNA


title: Tissue chunks, ribo-depleted, bulk sequenced, rep1


title: male mouse E14.5, DMH,  Tfap2b+/+ control replicate 3

value: male


title: Dissociated cells, single cell sequenced, rep4


title: male mouse E14.5, SP,  Tfap2b+/+ control replicate 3


title: WT2_0h


title: HES-2, Conventional, rep1


title: Dissociated cells, single cell sequenced, rep3


title: male mouse E14.5, DMH,  Tfap2b-/- mutant replicate 3


title: w303_1C_t2_noGSH_rep3

description: 4tU-labelled mRNA


title: Dissociated cells, single cell sequenced, rep2


title: w303_1C_t1_noGSH_rep3

description: 4tU-labelled mRNA


title: w303_1C_t3_noGSH_rep3

description: 4tU-labelled mRNA


title: Dissociated cells, single cell sequenced, rep8


title: HES-1, Conventional, rep1


title: HES-1, LN, rep0


title: HES-1, Conventional, rep0


title: male mouse E14.5, SP,  Tfap2b-/- mutant replicate 3


title: Dissociated cells, single cell sequenced, rep1


title: H7, LN, rep1


title: w303_1C_t0_noGSH_rep3

description: 4tU-labelled mRNA

source_name: reference for 1C and no GSH, right before adding 4tU


title: w303_1C_ss_noGSH_rep2

description: mRNA


title: NCCs-WT-rep3

city: Leiden

first: Jiale

last: Chen

address: Einsteinweg 55

institute: Leiden University

data_processing:
Illumina Casava1.7 software used for basecalling.
The RNA-seq data is applied quality and adapter trimming by Trim Galore and mapped to the human genome (hg38) using STAR.
The reads statistical calculation for genomic features via featureCounts.
The raw read counts normalization and differentially expressed genes (DEGs) were analyzed with by using the DESeq2.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Induced pluripotent stem cells，iPSCs

extract_protocol:
Total RNA was extracted and RNA integrity was evaluated using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, United States).
The library quality was evaluated with the Agilent Bioanalyzer 2100 system. The library preparations were sequenced on an Illumina Novaseq platform, and 150 bp paired-end reads were generated.

value: iPSCs, induced neural crest cell

value: wild type


title: H7, LN, rep0


title: H7, Conventional, rep1


title: female mouse E14.5, SP,  Tfap2b+/+ control replicate 2


title: NCCs-WT-rep2


title: NCCs-WT-rep1


title: w303_1C_t4_noGSH_rep2

description: 4tU-labelled mRNA


title: CD34(high)EPCR-negative_rep3

city: 4 Shiroganedai, Minato-ku

first: Masatoshi

last: Sakurai

state: Tokyo

department: Stem Cell Biology and Regenerative Medicine

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

data_processing:
8 FASTQ files (per sample) were concatenated by cat command in Linux into 2 files (Read 1 and Read 2) .
These files were named according to run ID (usually LAB_XXX_XX) and Imported to CLC GW as paired-end reads.
Filenames were changed according to project ID (XXX_XXX_XX).
Reads were mapped to reference with gene and transcript annotation (Human, hg19, 57,773 genes, 173,446 transcript isoform).
Raw quantification output was Total Count for each gene (GE files) or transcript (TE files), for each sample
Genome_build: GRCh37/b37 (Hg19)
Supplementary_files_format_and_content: RNAseq_Quantilenormalized_count

source_name: Human cord blood CD34+ cells

growth_protocol:
2×104 cryopreserved human cord blood CD34+ cells (purchased from StemExpress) were thawed in PCL-PVAc-PEG based 3a medium and cultured for 10-days on CellBind 24 well plate (Corning, #3337).
PCL-PVAc-PEG based 3a medium was consist of IMDM, 1×P/S/G, 1×ITSX, 0.1% (w/v) PCL-PVAc-PEG, 0.1μM Butyzamide, 1μM 740Y-P and 70nM UM171 (details is described in the manuscript).

extract_protocol:
Cultured cells were staind by APC labeled anti-human CD34 (BioLegend, 343510), BV605 labeled anti-human CD201(EPCR) (BD Bioscience, 745335) for 30 minutes at 4℃. Dead cells were labeled by propidium Iodide (BioLegened, 421301).
CD34(high)EPCR-positive and CD34(high)EPCR-negative cells were sorted by MoFlo (Beckman Coulter) and stored in TRIZOL-LS reagent (Invitrogen, 0296010) at -80℃.
rRNA-depletion and library synthesis were performed by Takara SMARTer kit.

value: Hematopoietic stem/progenitor cells

tag: epcr expression

value: negative


title: female mouse E14.5, DMH,  Tfap2b-/- mutant replicate 2


title: female mouse E14.5, SP,  Tfap2b-/- mutant replicate 2


title: H7, Conventional, rep0


title: NCCs-MITF-rep3

value: MITF-/-


title: w303_1C_t3_noGSH_rep2

description: 4tU-labelled mRNA


title: female mouse E14.5, DMH,  Tfap2b-/- mutant replicate 1


title: CD34(high)EPCR-negative_rep2


title: CD34(high)EPCR-negative_rep1


title: w303_1C_t2_noGSH_rep2

description: 4tU-labelled mRNA


title: NCCs-MITF-rep1


title: NCCs-MITF-rep2


title: female mouse E14.5, SP,  Tfap2b-/- mutant replicate 1


title: w303_1C_t1_noGSH_rep2

description: 4tU-labelled mRNA


title: female mouse E14.5, DMH,  Tfap2b+/+ control replicate 1


title: female mouse E14.5, DMH,  Tfap2b+/+ control replicate 2


title: MCs-WT-rep3

value: iPSCs, induced melanocyte


title: female mouse E14.5, SP,  Tfap2b+/+ control replicate 1


title: MCs-WT-rep1


title: w303_1C_t5_noGSH_rep2

description: 4tU-labelled mRNA


title: MCs-WT-rep2


title: w303_1C_t0_noGSH_rep2

description: 4tU-labelled mRNA


title: CD34(high)EPCR-positive_rep2

value: positive


title: w303_1C_ss_noGSH_rep1

description: mRNA


title: male mouse E14.5, DMH,  Tfap2b+/+ control replicate 2


title: CD34(high)EPCR-positive_rep1


title: male mouse E14.5, SP,  Tfap2b+/+ control replicate 2


title: MCs-MITF-rep3


title: w303_1C_t4_noGSH_rep1

description: 4tU-labelled mRNA


title: MCs-MITF-rep2


title: w303_1C_t3_noGSH_rep1

description: 4tU-labelled mRNA


title: male mouse E14.5, DMH,  Tfap2b-/- mutant replicate 2


title: Tbrain

city: Hangzhou

first: li

last: lei

address: xiashas street num 6

data_processing:
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and
Sequence quality was verified using FastQC，including the Q20, Q30 and GC-content of the clean data. All downstream analyses were
All assembled Unigenes were aligned against the non-redundant (Nr) protein database，Gene ontology (GO), SwissProt, Kyoto
Salmon was used to perform expression level for Unigenes by calculating TPM. The differentially expressed Unigenes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR. Next, GO and KEGG enrichment analysis were again performed on the differentially expressed Unigenes by perl scripts in house.
Genome_build: tab-delimited text files includeTPM values for each Sample

organism: Symphysodon aequifasciata

source_name: brain

growth_protocol: One one-year-old male  and one one-year-old female were collected from the ornamental Aquatic Breeding Laboratory of Shanghai Ocean University (Shanghai, China).

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number > 7.0. Poly(A) RNA is purified from total RNA (5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq RNA Sample Preparation v2 (Cat. RS-122-2001,RS-122-2002) (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina NovaseqTM 6000 at the (LC Sceiences,USA) following the vendor’s recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: experimental fishes were sacrificed by anaesthesia in well-aerated water containing a 100 mg/L concentration of Tricaine methanesulphonate (MS-222)，brain were collected and immediately frozen in liquid nitrogen and stored at −80 °C until RNA

value: brain

value: 1 year-old


title: Obrain


title: MCs-MITF-rep1


title: w303_1C_t2_noGSH_rep1

description: 4tU-labelled mRNA


title: CD44+ Th cells negative for ChAT-GFP (rep 2)

city: Toronto

first: Tak

last: Mak

state: ON

address: 610 University Ave

department: The Campbell Family Institute for Breast Cancer Research

country: Canada

institute: Princess Margaret Cancer Centre, University Health Network

data_processing:
Paired-end (75 bp) sequenced reads from a Nextseq 500 instrument (Illumina) were quality-checked using FASTQC v0.11.2 and MultiQC v0.8 and aligned to the Mus musculus genome assembly version GRCm38 (mm10) using Tophat v2.1.0. Aligned transcripts were processed using the Cufflinks suite of packages for abundance estimation and differential expression tests using default settings. The differentially expressed gene lists were further analyzed to produce overlap Venn diagrams and arrive at a statistically significant DE subset. Normalized FPKM values for the top genes were used for expression heatmaps. The FPKM values output by Cufflinks have been made available as processed files.
Assembly: mm10
Supplementary files format and content: Text files listing FPKM values for individual genes

source_name: Spleen

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared Illumina NeoPrep system and protocols.

treatment_protocol: Miltenyi B220 MACS beads were used to separate B cells from T cells using the AutoMACS system. Thereafter, B cells were stained with antibodies to discriminate ChAT-GFP+ and ChAT-GFP- FoBs and MzBs (CD19, CD21, CD23) by flow cytometry. The non-B cell fraction was stained with antibodies to purify CD44+ Th cells that do and do not express ChAT-GFP.

value: Spleen

value: primary T cell

tag: sample group

value: CD44+ Th cells negative for ChAT-GFP

value: ChAT-GFP-transgenic

value: B220-MACS followed by FACS


title: male mouse E14.5, DMH,  Tfap2b+/+ control replicate 1

value: DMH


title: CD34(high)EPCR-positive_rep3


title: CD44+ Th cells negative for ChAT-GFP (rep 1)


title: w303_1C_t1_noGSH_rep1

description: 4tU-labelled mRNA


title: CD44+ Th cells expressing ChAT-GFP (rep 2)

value: CD44+ Th cells expressing ChAT-GFP


title: male mouse E14.5, SP,  Tfap2b+/+ control replicate 1

value: SP

value: male


title: w303_1C_t5_noGSH_rep1

description: 4tU-labelled mRNA


title: w303_1C_t0_noGSH_rep1

description: 4tU-labelled mRNA


title: iPSCs-WT-rep2

value: Induced pluripotent stem cells, iPSCs

value: wild type


title: male mouse E14.5, DMH,  Tfap2b-/- mutant replicate 1


title: male mouse E14.5, SP,  Tfap2b-/- mutant replicate 1


title: iPSCs-WT-rep1


title: CD44+ Th cells expressing ChAT-GFP (rep 1)


title: FoB negative for ChAT-GFP (rep 2)

value: primary B cell

value: FoB negative for ChAT-GFP

value: B220+MACS followed by FACS


title: H460 cells, PKP2

city: Nanchang

first: Yi

last: Sang

state: Jiangxi

address: No.128,Xiangshan North Road

institute: Nanchang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo_sapiens.GRCh37 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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: Alignment was initially to the transcriptome (hg19, GRCh37.72), and then to the genome (hg19, GRCh37).
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: lung cancer cell lines

growth_protocol: 10% FBS in DMEM

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

value: lung cancer cells

tag: passages

value: overexpression of PKP2


title: iPSCs-MITF-rep3

value: MITF-/-


title: iPSCs-MITF-rep2


title: male mouse E14.5, SP,  Tfap2b-/- mutant replicate 2


title: FoB negative for ChAT-GFP (rep 1)

value: Spleen


title: Rep 3, ChAT-GFP-negative [ATAC-seq]

library_source: genomic

data_processing:
The raw 51-base pair paired-end reads were quality-checked and processed using the ATACseq data-processing pipeline standardized by the ENCODE project. A peak list for each replicate was obtained using MACS. The functions “dba.count” and “dba.peakset” from the DiffBind R package v2.12.0 were used to generate consensus peaks. Read counts within a summit-centered 201-basepair window in these consensus peaks were used to compute fold changes between each pair's corresponding ChATgfp+ and ChATgfp- samples. A master list for each pair was assembled that contained fold changes, peak locations, and read count values. A peak overlap analysis was conducted in two steps using ChIPpeakAnno v3.22.4. First, overlapping peaks between the ChATgfp+ and ChATgfp- samples were determined for each pair and excluded from further analysis. Peaks unique to the ChATgfp+ and ChATgfp- samples for each pair were retained. Second, a 3-way overlap analysis of the retained peak sets across the three ChATgfp+ samples was conducted to distill a total of 167 peaks that most strongly represented the ChATgfp+ condition. ChIPpeakAnno was utilized to annotate these 167 peaks. The Integrative Genomics Viewer (IGV) tool was used to illustrate selected peak regions.
The full ENCODE pipeline can be accessed from https://github.com/ENCODE-DCC/atac-seq-pipeline
Supplementary files format and content: narrowPeak Croo output files from the ENCODE ATACseq pipeline
Supplementary files format and content: https://github.com/ENCODE-DCC/atac-seq-pipeline

molecule: genomic DNA

growth_protocol: Conditioned IMDM with recombinant mouse IL-1β (20ng/ml), IL-6 (25ng/ml), IL-23 (20ng/ml). Anti-CD3 and anti-CD28 activation (each 2µg/ml), see detailed sample-specific treatments above.

extract_protocol:
Naive CD4+ T Cell Isolation Kit (Miltenyi Biotech, 130-104-453)
Buenrostro protocol

treatment_protocol: Illumina Nextera kit, 15028252

value: plate-bound anti-CD3 & -CD28; harvested in the presence of sodium butyrate (0.25mM)


title: FoB expressing ChAT-GFP (rep 2)

value: FoB expressing ChAT-GFP


title: iPSCs-WT-rep3


title: HE2

first: Guangyi

state: China

address: Wujin Road 85

institute: Shanghaijaiotong University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: BV2 cell

growth_protocol: The BV2 microglia cell line were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
The hypoxia groups were incubated in a hypoxic workstation (Whitley H35 Hypoxystation; Don Whitley Scientific, Bingley, UK) with 1% O2
BV2 cells were  supplemented with  100uM ethanolamine (Sigma), when they were induced under hypoxia conditions.

value: BV2 cell

value: microglia cells

value: WT

value: hypoxia treatment with 100uM ethanolamine supplementation

tag: time


title: HE3


title: H460 cells, vector

description: vector

value: control


title: Rep 2, ChAT-GFP-negative [ATAC-seq]

value: ChAT-GFP-transgenic

value: plate-bound anti-CD3 & soluble anti-CD28


title: iPSCs-MITF-rep1

value: Induced pluripotent stem cells, iPSCs


title: Rep 1, ChAT-GFP-negative [ATAC-seq]

value: plate-bound anti-CD3 & -CD28


title: Hypoxia3

value: hypoxia treatment


title: MzB negative for ChAT-GFP (rep 2)

value: primary B cell

value: MzB negative for ChAT-GFP

value: B220+MACS followed by FACS


title: HEK293- Y1-KO -3- TT(Nascent)-RNAseq

city: Changsha

first: Jiong

last: Li

address: No.138, Tongzipo Road

department: Department of Radiology

institute: The Third Xiangya Hospital, Central South University

data_processing:
Raw reads of 4su-TT-seq were mapped to genome reference (hg38) via hisat2
htseq-count was used to count reads that mapped to gene annotation (UCSC hg38)
Genome_build: hg38
Supplementary_files_format_and_content: gene.counts.txt

source_name: Human embryonic kidney cells

growth_protocol: The Human Embryonic Kidney 293 cell line was maintained in DMEM medium supplemented with 10% FBS, and 1% penicillin–streptomycin.

extract_protocol: to be updated

treatment_protocol: 4-thiouridine was added to medium for 200 mM final concentration and must be prewarmed. Add the prepared medium into culture dishes label for 1h


title: Hypoxia2


title: MzB negative for ChAT-GFP (rep 1)


title: Rep 3, ChAT-GFP-positive [ATAC-seq]


title: HEK293- Y1-KO -1- TT(Nascent)-RNAseq


title: Rep 2, ChAT-GFP-positive [ATAC-seq]


title: MzB expressing ChAT-GFP (rep 2)

value: MzB expressing ChAT-GFP


title: HEK293- Y1-KO -3-Total-RNAseq


title: Rep 1, ChAT-GFP-positive [ATAC-seq]

value: Spleen


title: MzB expressing ChAT-GFP (rep1)


title: con 3

value: adipogenic differentiation


title: HEK293- Y1-KO -2-Total-RNAseq


title: con 2


title: Perturb-seq in vivo treated

city: Houston

first: Weiyi

last: Peng

state: Tx

address: 4800 Calhoun Rd

department: Department of Biology and Biochemistry

institute: University of Houston

data_processing:
All raw sequence data generated from scRNA-seq were firstly processed by the 10× Genomics Cell Ranger pipeline.
the sequencing output data (BCL files) were demultiplexed, converted into FASTQ files and then aligned to mm10-3.0.0 reference genome to produce count matrices for mRNA and gRNAs.
The count matrices were imported into Seurat (4.0.0) in R (4.0.4) for further filtering, normalization, log-transform, scaling, dimensional reduction by Principal Component Analysis (PCA), and Uniform Manifold Approximation and Projection (UMAP) for clustering.
Assembly: mm10
Supplementary files format and content: mRNA and gRNA counts in h5 formats are provided as processed data files for each sample.

source_name: Colon

growth_protocol: MC38 cells were cultured in RPMI-1640 medium with 10% heated-inactivated fetal bovine serum (FBS; #S11150, R&D System, Minneapolis, MN) and 100μg/ml of Normocin (ant-nr-1, InvivoGen, San Diego, CA). Gp100 and Cas9-expressing MC38 cells (MC38/GC) generated in our previous study were cultured under the treatment of 10g/ml of blasticidin (#A1113903, Gibco, Carlsbad, CA) with the culture media described above. When necessary, culture medium were  supplemented with 1 mM sodium pyruvate (#11360-070), 2 mM glutamax (#35050-061), 1x non-essential amino acids (#11400-050) from Gibco.

extract_protocol:
The single cell partitioning method provided by 10X Genomics was used for both the Perturb-seq and CROP-seq platforms. Single cell suspensions at a concentration of 1000 live cells/ml were prepared. Around 3000-10,000 cells were captured per lane of a 10X Chromium device by using Single Cell 3’ Solution reagents (10X Genomics). In Brief, single cells, RT reagents, single-cell gel beads and oil were loaded on a Chromium controller (10x Genomics) to generate single cell Gel Beads-In-Emulsions (GEMs) where full length cDNAs were synthesized and barcoded for each single cell. Subsequently the GEMs were broken and cDNAs from each single cell were pooled for further process.
For the Perturb-Seq platform, 3’ GEX and gRNA libraries were prepared by using the Chromium Next GEM Single Cell 3’ Reagent Kits V3.1 with Feature Barcoding technology for CRISPR Screening (#PN-1000128,10X Genomics). The construction of 3’GEX library and gRNA library was performed as described in the Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry) with Feature Barcoding technology for CRISPR Screening (Rev_D). The constructed libraries were sequenced by NextSeq 500 (Illumina) in the Seq-N-Edit Core at University of Houston. For the CROP-Seq platform, 3’ GEX library was constructed by using the Chromium Next GEM Single Cell 3' Kit v3.1 (#PN-1000147, 10X Genomics), according to the instructions provided in the Chromium Single Cell 3' Reagent Kits User Guide (v2 Chemistry) (Rev_F). To enrich polyA-tailed gRNA transcripts in 3’GEX libraries, a three-round hemi-nested PCR reaction was performed to enrich gRNA fragment as previously described {Gasperini, 2019 #2}. Briefly, in the first round of nested PCR reactions, 20ng of full-length cDNAs were amplified by KAPA HiFi system(#07958935001, Roche, Pleasanton, CA) at 65°C for annealing temperature. In the second round of PCR reactions, 1/25 of the purified first-round PCR products were used for amplification (65°C for annealing temperature). In the final round of PCR reactions, 1/25th of the purified second-round PCR products were used for amplification at 72°C for annealing temperature. The PCR products from the final round were purified and performed a dual size selection by using 0.6-1x Ampure beads (#A63880, Beckman Coulter, Brea, CA). All primers to enrich gRNA transcripts were listed into the supplementary table 3. The constructed libraries were sequenced by using Novaseq 6000 (Illumina) in the Single Cell Genomics Core at Baylor College of Medicine.

treatment_protocol:
Designated titers of lentivirus were used to infect MC38/GC cells in the presenceof 8μg/ml hexadimethrine bromide (#107689, Sigma-Aldrich, St Louis, MO). 48 hours after transduction, cells were selected with completed growth medium in the presence of 2μg/ml of puromycin (#A1113803, Gibco) to establish stable cell lines. For each scCRISPR screen platform, five different types of modified MC38/GC lines including gNC1, gNC2, gPrmt1, gRipk1 and gAxl cell lines were generated.
For in vitro samples, equal number of gRNA-expressing MC38/GC cells were pooled together. Total 10 × 10^6 pooled MC38/GC cells were pre-seeded into T150 cell culture dishes for 8 hours, then co-incubated with 10 × 10^6 cultured Pmel T cells in present of 300 IU/ml IL-2 for additional 16 hours. Tumor cells in medium with 300 IU/ml IL-2 were served as the control group. After T cell co-culture, non-adhesive cells were removed by repeatedly washing with pre-warmed PBS. Adherent cells were trypsinized, resuspended into PBS supplied with 2% FBS and filtered with 70M cell strainer. In the Perturb-seq screen, single cell suspensions were directly applied for scRNA-seq preparation. In the CROP-seq screen, single cell suspensions were stained with mCD45-PE (#553081, BD bioscience) for 30 mins and followed by sorting CD45- tumor cells using the BD FACS Melody™ Cell Sorter. Sorted tumor cells were used for scRNA-seq sample preparation.
For in vivo samples, equal numbers of five types of modified MC38/GC cell lines were pooled together before tumor inoculation. 5 × 10^5 of pooled gRNA-expressing MC38/gp100 tumor cells were subcutaneously injected into each C57/BL6 mouse. Seven days after tumor inoculation, tumor-bearing mice were intraperitoneally administrated with either anti-PD-1 (#135247, BioLegend, San Diego, CA) or control antibody (#BE0085, Bioxcell, Lebanin, NH) at the dose of 100 g/dose every two days. Five mice for each treatment group were included. Tumor samples were collected on day 7 or day 14 after antibody treatment in the Perturb-seq and CROP-seq screens, respectively. Tumor sizes in all experimental mice were monitored by measuring the perpendicular diameters of the tumors. 100g of tumor tissue sample from each mouse was harvested, cut into small pieces, and incubated in RPMI medium containing 1 mg/ml collagenase (#C0130, Sigma-Aldrich) and 100 μg/ml hyaluronidase (H6254, Sigma-Aldrich) at 37°C for 60 min. After enzymatic digestion, tumor tissues were manually dissociated to generate single cell suspensions. Equal amounts of single cell suspensions from individual tumor tissues in the same group were pooled together. Tumor cells were sorted based on the expression of CD45 as described previously. All experiments were carried out in a blinded, randomized fashion.

value: Colon

value: Colon Cancer


title: HEK293-Y1-KO-1-Total-RNAseq


title: HE1

value: BV2 cell

value: microglia cells


title: con 1

value: WT


title: total RNA polyA purified rep 4

city: Uppsala

first: Erik

last: Holmqvist

state: Uppland

address: Husargatan 3, Box 596, Uppsala University, Dept. of Cell and Molecular Biology

country: Sweden

institute: Uppsala University

data_processing:
Adapter trimming performed with SeqPurge
Read mapping performed with star with --alignIntronMax set to 1
Mapped reads were converted to strand separated bedgraph files with samtools and bedtools genomecov.
Bedgraph files converted to bigWig file format (www.encodeproject.org/software/bedgraphtobigwig/)
Assembly: NC_000913.3
Supplementary files format and content: Strand separated bigWig files for viewing mapping coverage in genome browsers.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: cultered cells

growth_protocol:
E. coli cultured in M9 minimal media supplemented with 100 µg/ml ampicilin, 0,4 % glycerol and 0,1 % cas amino acids, 0,2 % arabinose
E. coli MG1655 cells harboring plasmid pPAPI (for PAPI overexpression) was grown in M9 media until an OD600 of 0.35, where expression of PAPI was induced by addition of arabinose to a final concentration of 0.2% (w/v). After 30 min of induction cultures were UV-light treated (1 J/cm2) and harvested by centrifugation.

extract_protocol:
Cell lysis was done using a FastPrep24 homogenizer for 20 sec at 4.0 M/s and RNA and was extracted using hot phenol/choloform
Performed at Vertis AG using in-house protocols: Depletion of rRNA molecules, Preparation of strand specific cDNA for bacterial whole  transcriptome sequencing, Removal of long poly(A) tails with CRISPR-Cas9

treatment_protocol: For Sample 5-8 the polyadenylated RNA was pulled-down using oligo d(T)25 magnetic beads (New England Biolabs).

tag: strain

value: EHS-2290 (E. coli MG1655 + pPAPI)

value: Poly(A) tailed RNA from Sample 4 was pulled-down using poly(dT) covered beads


title: HEK293-Control-3- TT(Nascent)-RNAseq

value: wild type


title: Perturb-seq in vivo control

tag: tissue

value: control antibody (#BE0085, Bioxcell, Lebanin, NH)


title: FoB expressing ChAT-GFP (rep 1)

value: FoB expressing ChAT-GFP

value: ChAT-GFP-transgenic


title: Perturb-seq in vitro treated

value: Pmel T cells


title: total RNA polyA purified rep 2

value: Poly(A) tailed RNA from Sample 2 was pulled-down using poly(dT) covered beads


title: HEK293- Y1-KO -2- TT(Nascent)-RNAseq


title: HEK293-Control-2- TT(Nascent)-RNAseq


title: Crop-seq in vitro treated v2


title: Crop-seq in vitro control v2


title: HEK293-Control-1-TT(Nascent)-RNAseq


title: Perturb-seq in vitro control


title: total RNA polyA purified rep 1

value: Poly(A) tailed RNA from Sample 1 was pulled-down using poly(dT) covered beads


title: Hypoxia1

value: hypoxia treatment


title: total RNA polyA purified rep 3

value: Poly(A) tailed RNA from Sample 3 was pulled-down using poly(dT) covered beads


title: Crop-seq in vivo treated

value: anti-PD-1 (#135247, BioLegend, San Diego, CA)


title: StemSpan with UM171

data_processing:
Libraries were sequenced on Illumina Hiseq X (Macrogen Inc, Korea).
Sequence data was annotated by the reference genome (GRCh38) using the Cellranger v3.0.1 pipeline.
Genome_build: GRCh38
Supplementary_files_format_and_content: Annotated sequence datas that contain cell barcodes (tsv), features (tsv) and gene expression matrix (mtx).

source_name: Human hematopoietic stem cells

extract_protocol:
PI-negative live cells were sorted from cultured cells by MoFlo (Beckman Coulter) at day 10 and these cells were used for making libraries.
Libraries were prepared according to the manual of NextGEM Single Cell 3' Reagent Kits ver 3.1 (10×genomics).

treatment_protocol: Cord blood derived cryopreserved human CD34-positive cells (purchased from StemExpress) were cultured for 10-days in PCL-PVAc-PEG based 3a medium, StemSpan with SR-1 and StemSpan with UM171 medium (details are described in the manuscript).

value: Hematopoietic stem cells

value: cultured for 10-days in StemSpan with UM171


title: HEK293-Control-3-Total-RNAseq


title: total RNA from lysate rep 4

value: Poly(A) polymerase I (PAPI) overexpression for 30 min and UV light crosslinking was applied before harvest


title: Crop-seq in vivo control

value: Colon

value: Colon Cancer


title: HEK293-Control-2-Total-RNAseq


title: total RNA from lysate rep 2

value: EHS-2290 (E. coli MG1655 + pPAPI)


title: total RNA from lysate rep 3


title: StemSpan with SR-1

value: cultured for 10-days in StemSpan with SR-1


title: PCL-PVAc-PEG based 3a medium

value: cultured for 10-days in PCL-PVAc-PEG based 3a medium


title: HEK293-Control-1-Total-RNAseq

value: wild type


title: total RNA from lysate rep 1


title: Crop-seq in vitro control v1


title: Crop-seq in vitro treated v1


title: female mice fed with STD diet cb rep4

status: Public on Nov 12 2022

type: RNA

city: Monza

first: Valentina

last: Murtaj

state: MI

address: Via Cadore 48

department: School of Medicine and Surgery

country: Italy

institute: University of Milano-Bicocca

description: Gene expression data from female STD fed cerebellum

hyb_protocol: Following fragmentation, 10 ng were hybridized for 16h ad 45°C on Clariom™ S Mouse arrays. The arrays were washed and stained in the genechip system

scan_protocol: GeneChip were scaned using GeneChip® Scanner 3000 7G

data_processing: The data were analysed with Transcriptme Analysis Controls (TAC 4.0 software,Thermo Fisher Scientific, USA) with Robust Multichip Analysis (RMA) algorithm, using a default analysis settings and global scaling as method

label: biotin

source_name: cerebellar

label_protocol: Biotinilated cRNA were prepared according Clariom™ S Mouse arrays, IVT Pico Reagent kit (Thermo Fisher)

growth_protocol: Five weeks old male and female C57Bl/6J mice (Charles River, Italy) were housed in the San Raffaele Institute animal facility, maintained in a 12/12-hour light/dark cycle with access ad libitum to food and water prior to start different diet regimen

extract_protocol: Total RNA was performed according to the manufacturer's instructions from Qiagen RNeasy Plus Micro kit (Qiagen Italia) for anterior cortex and with Direct-zol™ RNA MiniPrep (Zymo Research) for the cerebellum

treatment_protocol: Mice were randomly assigned to one of the following diets: Standard Diet (STD) as controls (D12450B, Research Diets Inc); 45% High Fat Diet (45HFD) (D12451, Research Diets Inc.) and 60% High Fat Diet (60HFD) (D12492, Research Diets Inc.), containing respectively 10%, 45% and 60% of calories derived from fat

value: female

value: cerebellar homogenate

tag: diet

value: control


title: female mice fed with 45HFD cb rep3

description: Gene expression data from female 45HFD fed cerebellum

value: 45% HFD


title: female mice fed with 45HFD cb rep2


title: female mice fed with 60HFD cb rep5

description: Gene expression data from female 60HFD fed cerebellum

value: 60% HFD


title: female mice fed with 45HFD cb rep4


title: female mice fed with STD diet cb rep5


title: female mice fed with STD diet cb rep2


title: female mice fed with STD diet cb rep3


title: male mice fed with 45HFD cb rep4

description: Gene expression data from male 45HFD fed cerebellum

value: male


title: female mice fed with STD diet cb rep1


title: female mice fed with 60HFD cb rep4


title: male mice fed with STD diet cb rep1

description: Gene expression data from male STD fed cerebellum


title: male mice fed with STD diet cb rep2


title: female mice fed with 60HFD cb rep2


title: female mice fed with 60HFD cb rep1


title: male mice fed with 45HFD cb rep2


title: female mice fed with 45HFD cb rep5


title: male mice fed with STD diet cb rep4


title: male mice fed with STD diet cb rep3


title: male mice fed with 45HFD cb rep5


title: female mice fed with 45HFD cb rep1


title: female mice fed with 60HFD cb rep3


title: male mice fed with 60HFD cb rep2

description: Gene expression data from male 60HFD fed cerebellum


title: male mice fed with 45HFD cb rep1


title: male mice fed with 60HFD cb rep4


title: male mice fed with 45HFD cb rep3


title: male mice fed with 60HFD cb rep3


title: male mice fed with 60HFD cb rep1


title: female mice fed with STD diet ant ctx rep5

description: Gene expression data from female STD fed anterior cortex

source_name: anterior cortex

value: anterior cortex homogenate


title: male mice fed with 60HFD cb rep5


title: female mice fed with 45HFD ant ctx rep3

description: Gene expression data from female 45HFD fed anterior cortex


title: female mice fed with STD diet ant ctx rep2


title: male mice fed with STD diet ant ctx rep5

description: Gene expression data from male STD fed anterior cortex


title: female mice fed with 60HFD ant ctx rep1

description: Gene expression data from female 60HFD fed anterior cortex


title: female mice fed with 45HFD ant ctx rep1


title: female mice fed with 60HFD ant ctx rep5


title: female mice fed with 45HFD ant ctx rep4


title: female mice fed with 60HFD ant ctx rep2


title: female mice fed with 60HFD ant ctx rep4


title: female mice fed with 60HFD ant ctx rep3


title: male mice fed with STD diet ant ctx rep2


title: female mice fed with STD diet ant ctx rep4


title: female mice fed with STD diet ant ctx rep1


title: male mice fed with 45HFD ant ctx rep4

description: Gene expression data from male 45HFD fed anterior cortex


title: female mice fed with 45HFD ant ctx rep2


title: male mice fed with 45HFD ant ctx rep2


title: male mice fed with STD diet ant ctx rep1


title: male mice fed with 45HFD ant ctx rep1


title: female mice fed with 45HFD ant ctx rep5


title: female mice fed with STD diet ant ctx rep3


title: Δcfem1-rep 3

city: Shanghai

first: Weihua

last: Tang

address: 300 Fenglin Rd

institute: Shanghai Inst. Plant Phys. & Eco.

description: maize stalk (without epidermis) 24 hours post Δcfem1 infection

data_processing:
Reads were mapped to ribosome RNA (rRNA) database using Bowtie2 (v2.2.8). The rRNA mapped reads were then removed.
Clean reads were mapped to the reference genome using HISAT (v2.2.4)
The mapped reads of each sample were assembled by using StringTie (v1.3.1) in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: Zea mays (Ensembl_release45)
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample

organism: Zea mays

source_name: maize stalk (without epidermis)

growth_protocol: After being mixed with cooked soil, perlite, vermiculite and black soil, it is autoclaved and sub packed into a flower pot of appropriate size. Compound fertilizer, potassium dihydrogen phosphate, calcium superphosphate and urea are added to it. After mixing, it is soaked with tap water. Corn seeds were placed in the shallow soil layer in the artificial climate chamber. After a week, the corn seeds will germinate. During the growth period, it is necessary to properly water and apply green fertilizer to ensure the vigorous growth of corn. The growth conditions of corn in the artificial climate chamber are 14 hours of light / 10 hours of darkness, the relative humidity is about 65%, the temperature is controlled at 26 ℃ in the daytime and 22 ℃ at night. The stem infection experiment of maize can be carried out after planting for about 2 months

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
The RNA sequencing was performed at GENE DENOVO. The libraries for sequencing were prepared using NEBNext Ultra RNA Library Prep Kit

treatment_protocol: When the maize grows for about two months, use alcohol wiped tweezers to make a hole wound on the stalk, and then infiltrate 20 μL water,  20 μL PH-1 conidia suspension (concentration of 106/mL) and 20 μL Δcfem1 conidia suspension (concentration of 106/mL) into the wound of each maize stalk. Then wrap the wound of maize stalk with moist sterile gauze and put it in the light incubator for infection experiment

value: maize stalk (without epidermis)

tag: cultivar

value: two-month-old

value: 24 hours post {delta}cfem1 infected


title: Δcfem1-rep 2


title: male mice fed with 60HFD ant ctx rep3

description: Gene expression data from male 60HFD fed anterior cortex


title: male mice fed with 60HFD ant ctx rep4


title: male mice fed with 60HFD ant ctx rep2


title: male mice fed with 60HFD ant ctx rep5


title: male mice fed with STD diet ant ctx rep4


title: male mice fed with 60HFD ant ctx rep1


title: male mice fed with 45HFD ant ctx rep3


title: Δcfem1-rep 1


title: PH-1-rep 3

description: maize stalk (without epidermis) 24 hours post PH-1 infection

value: 24 hours post PH-1 infected


title: male mice fed with STD diet ant ctx rep3


title: PH-1-rep 2


title: PH-1-rep 1


title: water-rep1

description: maize stalk (without epidermis) 24 hours post water treatment

value: 24 hours post water treated


title: water-rep2


title: water-rep3


title: CC1209

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

institute: Toray Industries, Inc.

description: miRNA

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing:
The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetected) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.
Normalized signal intensity by internal control miRNAs.

source_name: Serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: disease state

value: colorectal cancer

tag: Sex

value: Female

tag: Stage

tag: grade for glioma


title: CC1216

description: miRNA

value: Male

tag: age


title: CC1206

description: miRNA


title: CC1211

description: miRNA


title: CC1207

description: miRNA


title: CC1212

description: miRNA


title: CC1213

description: miRNA


title: CC1214

description: miRNA


title: CC1210

description: miRNA


title: CC1215

description: miRNA


title: CC1218

description: miRNA


title: CC1208

description: miRNA


title: CC1219

description: miRNA


title: CC1204

description: miRNA


title: CC1203

description: miRNA


title: CC1205

description: miRNA


title: CC1202

description: miRNA


title: CC1200

description: miRNA


title: CC1199

description: miRNA


title: CC1198

description: miRNA


title: CC1196

description: miRNA


title: CC1197

description: miRNA


title: CC1195

description: miRNA


title: CC1194

description: miRNA


title: CC1217

description: miRNA


title: CC1193

description: miRNA


title: CC1191

description: miRNA


title: CC1192

description: miRNA


title: CC1187

description: miRNA


title: CC1183

description: miRNA


title: CC1188

description: miRNA


title: CC1184

description: miRNA


title: CC1201

description: miRNA


title: CC1182

description: miRNA


title: CC1186

description: miRNA


title: CC1173

description: miRNA


title: CC1185

description: miRNA


title: CC1189

description: miRNA


title: CC1178

description: miRNA


title: CC1174

description: miRNA


title: CC1180

description: miRNA


title: CC1176

description: miRNA


title: CC1170

description: miRNA


title: CC1181

description: miRNA


title: CC1179

description: miRNA


title: CC1172

description: miRNA


title: CC1166

description: miRNA


title: CC1165

description: miRNA


title: CC1164

description: miRNA


title: CC1168

description: miRNA


title: CC1171

description: miRNA


title: CC1175

description: miRNA


title: CC1167

description: miRNA


title: CC1162

description: miRNA


title: CC1169

description: miRNA


title: CC1163

description: miRNA


title: CC1190

description: miRNA


title: CC1177

description: miRNA


title: CC1160

description: miRNA


title: CC1161

description: miRNA


title: CC1154

description: miRNA


title: CC1158

description: miRNA


title: CC1153

description: miRNA


title: CC1152

description: miRNA


title: CC1156

description: miRNA


title: CC1146

description: miRNA


title: CC1147

description: miRNA


title: CC1155

description: miRNA


title: CC1157

description: miRNA


title: CC1151

description: miRNA


title: CC1139

description: miRNA


title: CC1141

description: miRNA


title: CC1144

description: miRNA


title: CC1159

description: miRNA


title: CC1137

description: miRNA


title: CC1150

description: miRNA


title: CC1142

description: miRNA


title: CC1138

description: miRNA


title: CC1136

description: miRNA


title: CC1135

description: miRNA


title: CC1133

description: miRNA


title: CC1134

description: miRNA


title: CC1143

description: miRNA


title: CC1140

description: miRNA


title: CC1132

description: miRNA


title: CC1148

description: miRNA


title: CC1149

description: miRNA


title: CC1131

description: miRNA


title: CC1145

description: miRNA


title: CC1127

description: miRNA


title: CC1130

description: miRNA


title: CC1129

description: miRNA


title: CC1128

description: miRNA


title: CC1124

description: miRNA


title: CC1119

description: miRNA


title: CC1121

description: miRNA


title: CC1123

description: miRNA


title: CC1118

description: miRNA


title: CC1122

description: miRNA


title: CC1117

description: miRNA


title: CC1114

description: miRNA


title: CC1113

description: miRNA


title: CC1112

description: miRNA


title: CC1109

description: miRNA


title: CC1115

description: miRNA


title: CC1111

description: miRNA


title: CC1107

description: miRNA


title: CC1108

description: miRNA


title: CC1105

description: miRNA


title: CC1103

description: miRNA


title: CC1125

description: miRNA


title: CC1102

description: miRNA


title: CC1126

description: miRNA


title: CC1101

description: miRNA


title: CC1104

description: miRNA


title: CC1120

description: miRNA


title: CC1098

description: miRNA


title: CC1100

description: miRNA


title: CC1099

description: miRNA


title: CC1095

description: miRNA


title: CC1096

description: miRNA


title: CC1091

description: miRNA


title: CC1110

description: miRNA


title: CC1092

description: miRNA


title: CC1089

description: miRNA


title: CC1090

description: miRNA


title: CC1088

description: miRNA


title: CC1116

description: miRNA


title: CC1087

description: miRNA


title: CC1106

description: miRNA


title: CC1083

description: miRNA


title: CC1093

description: miRNA


title: CC1094

description: miRNA


title: CC1086

description: miRNA


title: CC1082

description: miRNA


title: CC1085

description: miRNA


title: CC1084

description: miRNA


title: CC1081

description: miRNA


title: CC1097

description: miRNA


title: CC1079

description: miRNA


title: CC1080

description: miRNA


title: CC1075

description: miRNA


title: CC1076

description: miRNA


title: CC1077

description: miRNA


title: CC1078

description: miRNA


title: CC1074

description: miRNA


title: CC1072

description: miRNA


title: CC1070

description: miRNA


title: CC1068

description: miRNA


title: CC1067

description: miRNA


title: CC1064

description: miRNA


title: CC1071

description: miRNA


title: CC1062

description: miRNA


title: CC1063

description: miRNA


title: CC1061

description: miRNA


title: CC1057

description: miRNA


title: CC1073

description: miRNA


title: CC1058

description: miRNA


title: CC1059

description: miRNA


title: CC1056

description: miRNA


title: CC1060

description: miRNA


title: CC1055

description: miRNA


title: CC1052

description: miRNA


title: CC1053

description: miRNA


title: CC1054

description: miRNA


title: CC1050

description: miRNA


title: CC1051

description: miRNA


title: CC1049

description: miRNA


title: CC1047

description: miRNA


title: CC1048

description: miRNA


title: CC1069

description: miRNA


title: CC1066

description: miRNA


title: CC1046

description: miRNA


title: CC1065

description: miRNA


title: CC1041

description: miRNA


title: CC1040

description: miRNA


title: CC1037

description: miRNA


title: CC1039

description: miRNA


title: CC1036

description: miRNA


title: CC1034

description: miRNA


title: CC1044

description: miRNA


title: CC1043

description: miRNA


title: CC1042

description: miRNA


title: CC1038

description: miRNA


title: CC1031

description: miRNA


title: CC1033

description: miRNA


title: CC1028

description: miRNA


title: CC1032

description: miRNA


title: CC1025

description: miRNA


title: CC1029

description: miRNA


title: CC1027

description: miRNA


title: CC1030

description: miRNA


title: CC1023

description: miRNA


title: CC1024

description: miRNA


title: CC1022

description: miRNA


title: CC1045

description: miRNA


title: CC1019

description: miRNA


title: CC1020

description: miRNA


title: CC1018

description: miRNA


title: CC1017

description: miRNA


title: CC1021

description: miRNA


title: CC1035

description: miRNA


title: CC1016

description: miRNA


title: CC1015

description: miRNA


title: CC1013

description: miRNA


title: CC1012

description: miRNA


title: CC1014

description: miRNA


title: CC1011

description: miRNA


title: CC1008

description: miRNA


title: CC1010

description: miRNA


title: CC1009

description: miRNA


title: CC1026

description: miRNA


title: CC1006

description: miRNA


title: CC1002

description: miRNA


title: CC1004

description: miRNA


title: CC1001

description: miRNA


title: CC0999

description: miRNA


title: CC0998

description: miRNA


title: CC1000

description: miRNA


title: CC0997

description: miRNA


title: CC0996

description: miRNA


title: CC0995

description: miRNA


title: CC0993

description: miRNA


title: CC0994

description: miRNA


title: CC0992

description: miRNA


title: CC0991

description: miRNA


title: CC0990

description: miRNA


title: CC0988

description: miRNA


title: CC0989

description: miRNA


title: CC0987

description: miRNA


title: CC0986

description: miRNA


title: CC0984

description: miRNA


title: CC0985

description: miRNA


title: CC1005

description: miRNA


title: CC1003

description: miRNA


title: CC0983

description: miRNA


title: CC0979

description: miRNA


title: CC0982

description: miRNA


title: CC1007

description: miRNA


title: CC0974

description: miRNA


title: CC0980

description: miRNA


title: CC0981

description: miRNA


title: CC0978

description: miRNA


title: CC0976

description: miRNA


title: CC0975

description: miRNA


title: CC0968

description: miRNA


title: CC0967

description: miRNA


title: CC0973

description: miRNA


title: CC0972

description: miRNA


title: CC0970

description: miRNA


title: CC0966

description: miRNA


title: CC0969

description: miRNA


title: CC0959

description: miRNA


title: CC0958

description: miRNA


title: CC0965

description: miRNA


title: CC0964

description: miRNA


title: CC0961

description: miRNA


title: CC0956

description: miRNA


title: CC0962

description: miRNA


title: CC0977

description: miRNA


title: CC0948

description: miRNA


title: CC0947

description: miRNA


title: CC0952

description: miRNA


title: CC0951

description: miRNA


title: CC0946

description: miRNA


title: CC0960

description: miRNA


title: CC0950

description: miRNA


title: CC0949

description: miRNA


title: CC0945

description: miRNA


title: CC0942

description: miRNA


title: CC0943

description: miRNA


title: CC0944

description: miRNA


title: CC0938

description: miRNA


title: CC0941

description: miRNA


title: CC0937

description: miRNA


title: CC0939

description: miRNA


title: CC0936

description: miRNA


title: CC0935

description: miRNA


title: CC0934

description: miRNA


title: CC0933

description: miRNA


title: CC0932

description: miRNA


title: CC0928

description: miRNA


title: CC0930

description: miRNA


title: CC0957

description: miRNA


title: CC0929

description: miRNA


title: CC0926

description: miRNA


title: CC0925

description: miRNA


title: CC0923

description: miRNA


title: CC0920

description: miRNA


title: CC0919

description: miRNA


title: CC0921

description: miRNA


title: CC0922

description: miRNA


title: CC0918

description: miRNA


title: CC0940

description: miRNA


title: CC0915

description: miRNA


title: CC0913

description: miRNA


title: CC0912

description: miRNA


title: CC0931

description: miRNA


title: CC0907

description: miRNA


title: CC0908

description: miRNA


title: CC0910

description: miRNA


title: CC0909

description: miRNA


title: CC0906

description: miRNA


title: CC0927

description: miRNA


title: CC0903

description: miRNA


title: CC0916

description: miRNA


title: CC0905

description: miRNA


title: CC0904

description: miRNA


title: CC0893

description: miRNA


title: CC0892

description: miRNA


title: CC0901

description: miRNA


title: CC0902

description: miRNA


title: CC0888

description: miRNA


title: CC0899

description: miRNA


title: CC0900

description: miRNA


title: CC0883

description: miRNA


title: CC0898

description: miRNA


title: CC0882

description: miRNA


title: CC0881

description: miRNA


title: CC0894

description: miRNA


title: CC0896

description: miRNA


title: CC0895

description: miRNA


title: CC0914

description: miRNA


title: CC0891

description: miRNA


title: CC0911

description: miRNA


title: CC0879

description: miRNA


title: CC0889

description: miRNA


title: CC0886

description: miRNA


title: CC0884

description: miRNA


title: CC0885

description: miRNA


title: CC0868

description: miRNA


title: CC0869

description: miRNA


title: CC0867

description: miRNA


title: CC0880

description: miRNA


title: CC0897

description: miRNA


title: CC0861

description: miRNA


title: CC0878

description: miRNA


title: CC0877

description: miRNA


title: CC0876

description: miRNA


title: CC0857

description: miRNA


title: CC0875

description: miRNA


title: CC0873

description: miRNA


title: CC0874

description: miRNA


title: CC0851

description: miRNA


title: CC0850

description: miRNA


title: CC0872

description: miRNA


title: CC0849

description: miRNA


title: CC0870

description: miRNA


title: CC0866

description: miRNA


title: CC0856

description: miRNA


title: CC0864

description: miRNA


title: CC0917

description: miRNA


title: CC0865

description: miRNA


title: CC0845

description: miRNA


title: CC0924

description: miRNA


title: CC0844

description: miRNA


title: CC0843

description: miRNA


title: CC0862

description: miRNA


title: CC0841

description: miRNA


title: CC0860

description: miRNA


title: CC0859

description: miRNA


title: CC0890

description: miRNA


title: CC0838

description: miRNA


title: CC0848

description: miRNA


title: CC0852

description: miRNA


title: CC0837

description: miRNA


title: CC0858

description: miRNA


title: CC0847

description: miRNA


title: CC0863

description: miRNA


title: CC0836

description: miRNA


title: CC0835

description: miRNA


title: CC0854

description: miRNA


title: CC0833

description: miRNA


title: CC0846

description: miRNA


title: CC0855

description: miRNA


title: CC0830

description: miRNA


title: CC0842

description: miRNA


title: CC0840

description: miRNA


title: CC0828

description: miRNA


title: CC0827

description: miRNA


title: CC0823

description: miRNA


title: CC0834

description: miRNA


title: CC0821

description: miRNA


title: CC0832

description: miRNA


title: CC0831

description: miRNA


title: CC0829

description: miRNA


title: CC0839

description: miRNA


title: CC0813

description: miRNA


title: CC0816

description: miRNA


title: CC0825

description: miRNA


title: CC0824

description: miRNA


title: CC0818

description: miRNA


title: CC0826

description: miRNA


title: CC0822

description: miRNA


title: CC0810

description: miRNA


title: CC0809

description: miRNA


title: CC0808

description: miRNA


title: CC0820

description: miRNA


title: CC0815

description: miRNA


title: CC0814

description: miRNA


title: CC0853

description: miRNA


title: CC0803

description: miRNA


title: CC0804

description: miRNA


title: CC0812

description: miRNA


title: CC0811

description: miRNA


title: CC0801

description: miRNA


title: CC0806

description: miRNA


title: CC0807

description: miRNA


title: CC0805

description: miRNA


title: CC0799

description: miRNA


title: CC0871

description: miRNA


title: CC0798

description: miRNA


title: CC0795

description: miRNA


title: CC0796

description: miRNA


title: CC0793

description: miRNA


title: CC0819

description: miRNA


title: CC0802

description: miRNA


title: CC0792

description: miRNA


title: CC0817

description: miRNA


title: CC0791

description: miRNA


title: CC0887

description: miRNA


title: CC0797

description: miRNA


title: CC0789

description: miRNA


title: CC0794

description: miRNA


title: CC0787

description: miRNA


title: CC0790

description: miRNA


title: CC0788

description: miRNA


title: CC0785

description: miRNA


title: CC0781

description: miRNA


title: CC0786

description: miRNA


title: CC0783

description: miRNA


title: CC0782

description: miRNA


title: CC0779

description: miRNA


title: CC0800

description: miRNA


title: CC0773

description: miRNA


title: CC0776

description: miRNA


title: CC0778

description: miRNA


title: CC0777

description: miRNA


title: CC0775

description: miRNA


title: CC0767

description: miRNA


title: CC0774

description: miRNA


title: CC0770

description: miRNA


title: CC0769

description: miRNA


title: CC0766

description: miRNA


title: CC0772

description: miRNA


title: CC0771

description: miRNA


title: CC0765

description: miRNA


title: CC0764

description: miRNA


title: CC0762

description: miRNA


title: CC0756

description: miRNA


title: CC0757

description: miRNA


title: CC0763

description: miRNA


title: CC0755

description: miRNA


title: CC0753

description: miRNA


title: CC0754

description: miRNA


title: CC0750

description: miRNA


title: CC0761

description: miRNA


title: CC0784

description: miRNA


title: CC0751

description: miRNA


title: CC0759

description: miRNA


title: CC0780

description: miRNA


title: CC0749

description: miRNA


title: CC0752

description: miRNA


title: CC0748

description: miRNA


title: CC0758

description: miRNA


title: CC0768

description: miRNA


title: CC0747

description: miRNA


title: CC0743

description: miRNA


title: CC0740

description: miRNA


title: CC0760

description: miRNA


title: CC0738

description: miRNA


title: CC0744

description: miRNA


title: CC0745

description: miRNA


title: CC0746

description: miRNA


title: CC0741

description: miRNA


title: CC0742

description: miRNA


title: CC0739

description: miRNA


title: CC0737

description: miRNA


title: CC0733

description: miRNA


title: CC0732

description: miRNA


title: CC0727

description: miRNA


title: CC0729

description: miRNA


title: CC0723

description: miRNA


title: CC0728

description: miRNA


title: CC0734

description: miRNA


title: CC0731

description: miRNA


title: CC0720

description: miRNA


title: CC0726

description: miRNA


title: CC0725

description: miRNA


title: CC0724

description: miRNA


title: CC0722

description: miRNA


title: CC0716

description: miRNA


title: CC0719

description: miRNA


title: CC0735

description: miRNA


title: CC0713

description: miRNA


title: CC0711

description: miRNA


title: CC0709

description: miRNA


title: CC0714

description: miRNA


title: CC0717

description: miRNA


title: CC0706

description: miRNA


title: CC0736

description: miRNA


title: CC0715

description: miRNA


title: CC0712

description: miRNA


title: CC0710

description: miRNA


title: CC0708

description: miRNA


title: CC0704

description: miRNA


title: CC0707

description: miRNA


title: CC0703

description: miRNA


title: CC0702

description: miRNA


title: CC0705

description: miRNA


title: CC0696

description: miRNA


title: CC0692

description: miRNA


title: CC0701

description: miRNA


title: CC0721

description: miRNA


title: CC0700

description: miRNA


title: CC0691

description: miRNA


title: CC0730

description: miRNA


title: CC0690

description: miRNA


title: CC0699

description: miRNA


title: CC0698

description: miRNA


title: CC0695

description: miRNA


title: CC0697

description: miRNA


title: CC0687

description: miRNA


title: CC0677

description: miRNA


title: CC0694

description: miRNA


title: CC0693

description: miRNA


title: CC0688

description: miRNA


title: CC0675

description: miRNA


title: CC0685

description: miRNA


title: CC0686

description: miRNA


title: CC0684

description: miRNA


title: CC0681

description: miRNA


title: CC0680

description: miRNA


title: CC0682

description: miRNA


title: CC0689

description: miRNA


title: CC0670

description: miRNA


title: CC0671

description: miRNA


title: CC0664

description: miRNA


title: CC0667

description: miRNA


title: CC0662

description: miRNA


title: CC0678

description: miRNA


title: CC0676

description: miRNA


title: CC0674

description: miRNA


title: CC0679

description: miRNA


title: CC0673

description: miRNA


title: CC0654

description: miRNA


title: CC0660

description: miRNA


title: CC0672

description: miRNA


title: CC0653

description: miRNA


title: CC0651

description: miRNA


title: CC0663

description: miRNA


title: CC0669

description: miRNA


title: CC0650

description: miRNA


title: CC0658

description: miRNA


title: CC0668

description: miRNA


title: CC0656

description: miRNA


title: CC0652

description: miRNA


title: CC0657

description: miRNA


title: CC0649

description: miRNA


title: CC0666

description: miRNA


title: CC0648

description: miRNA


title: CC0647

description: miRNA


title: CC0646

description: miRNA


title: CC0665

description: miRNA


title: CC0661

description: miRNA


title: CC0639

description: miRNA


title: CC0659

description: miRNA


title: CC0643

description: miRNA


title: CC0642

description: miRNA


title: CC0644

description: miRNA


title: CC0641

description: miRNA


title: CC0640

description: miRNA


title: CC0655

description: miRNA


title: CC0638

description: miRNA


title: CC0634

description: miRNA


title: CC0631

description: miRNA


title: CC0627

description: miRNA


title: CC0628

description: miRNA


title: CC0636

description: miRNA


title: CC0624

description: miRNA


title: CC0635

description: miRNA


title: CC0633

description: miRNA


title: CC0632

description: miRNA


title: CC0645

description: miRNA


title: CC0629

description: miRNA


title: CC0621

description: miRNA


title: CC0718

description: miRNA


title: CC0619

description: miRNA


title: CC0618

description: miRNA


title: CC0626

description: miRNA


title: CC0615

description: miRNA


title: CC0611

description: miRNA


title: CC0625

description: miRNA


title: CC0623

description: miRNA


title: CC0622

description: miRNA


title: CC0608

description: miRNA


title: CC0617

description: miRNA


title: CC0616

description: miRNA


title: CC0614

description: miRNA


title: CC0610

description: miRNA


title: CC0602

description: miRNA


title: CC0601

description: miRNA


title: CC0613

description: miRNA


title: CC0600

description: miRNA


title: CC0598

description: miRNA


title: CC0637

description: miRNA


title: CC0609

description: miRNA


title: CC0595

description: miRNA


title: CC0596

description: miRNA


title: CC0593

description: miRNA


title: CC0592

description: miRNA


title: CC0607

description: miRNA


title: CC0620

description: miRNA


title: CC0591

description: miRNA


title: CC0605

description: miRNA


title: CC0604

description: miRNA


title: CC0599

description: miRNA


title: CC0603

description: miRNA


title: CC0606

description: miRNA


title: CC0587

description: miRNA


title: CC0585

description: miRNA


title: CC0594

description: miRNA


title: CC0612

description: miRNA


title: CC0582

description: miRNA


title: CC0579

description: miRNA


title: CC0590

description: miRNA


title: CC0589

description: miRNA


title: CC0586

description: miRNA


title: CC0588

description: miRNA


title: CC0581

description: miRNA


title: CC0574

description: miRNA


title: CC0597

description: miRNA


title: CC0572

description: miRNA


title: CC0580

description: miRNA


title: CC0583

description: miRNA


title: CC0567

description: miRNA


title: CC0577

description: miRNA


title: CC0576

description: miRNA


title: CC0564

description: miRNA


title: CC0563

description: miRNA


title: CC0575

description: miRNA


title: CC0573

description: miRNA


title: CC0570

description: miRNA


title: CC0571

description: miRNA


title: CC0569

description: miRNA


title: CC0562

description: miRNA


title: CC0560

description: miRNA


title: CC0568

description: miRNA


title: CC0578

description: miRNA


title: CC0566

description: miRNA


title: CC0565

description: miRNA


title: CC0561

description: miRNA


title: CC0549

description: miRNA


title: CC0559

description: miRNA


title: CC0556

description: miRNA


title: CC0555

description: miRNA


title: CC0557

description: miRNA


title: CC0554

description: miRNA


title: CC0551

description: miRNA


title: CC0547

description: miRNA


title: CC0552

description: miRNA


title: CC0550

description: miRNA


title: CC0543

description: miRNA


title: CC0548

description: miRNA


title: CC0542

description: miRNA


title: CC0544

description: miRNA


title: CC0546

description: miRNA


title: CC0553

description: miRNA


title: CC0541

description: miRNA


title: CC0540

description: miRNA


title: CC0538

description: miRNA


title: CC0558

description: miRNA


title: CC0539

description: miRNA


title: CC0535

description: miRNA


title: CC0537

description: miRNA


title: CC0536

description: miRNA


title: CC0533

description: miRNA


title: CC0531

description: miRNA


title: CC0534

description: miRNA


title: CC0532

description: miRNA


title: CC0525

description: miRNA


title: CC0530

description: miRNA


title: CC0526

description: miRNA


title: CC0529

description: miRNA


title: CC0528

description: miRNA


title: CC0545

description: miRNA


title: CC0524

description: miRNA


title: CC0523

description: miRNA


title: CC0521

description: miRNA


title: CC0512

description: miRNA


title: CC0520

description: miRNA


title: CC0510

description: miRNA


title: CC0508

description: miRNA


title: CC0518

description: miRNA


title: CC0517

description: miRNA


title: CC0516

description: miRNA


title: CC0515

description: miRNA


title: CC0519

description: miRNA


title: CC0514

description: miRNA


title: CC0511

description: miRNA


title: CC0509

description: miRNA


title: CC0527

description: miRNA


title: CC0507

description: miRNA


title: CC0501

description: miRNA


title: CC0506

description: miRNA


title: CC0496

description: miRNA


title: CC0503

description: miRNA


title: CC0500

description: miRNA


title: CC0505

description: miRNA


title: CC0499

description: miRNA


title: CC0504

description: miRNA


title: CC0498

description: miRNA


title: CC0497

description: miRNA


title: CC0495

description: miRNA


title: CC0491

description: miRNA


title: CC0488

description: miRNA


title: CC0492

description: miRNA


title: CC0481

description: miRNA


title: CC0487

description: miRNA


title: CC0484

description: miRNA


title: CC0584

description: miRNA


title: CC0480

description: miRNA


title: CC0502

description: miRNA


title: CC0513

description: miRNA


title: CC0479

description: miRNA


title: CC0494

description: miRNA


title: CC0490

description: miRNA


title: CC0477

description: miRNA


title: CC0478

description: miRNA


title: CC0489

description: miRNA


title: CC0493

description: miRNA


title: CC0476

description: miRNA


title: CC0474

description: miRNA


title: CC0486

description: miRNA


title: CC0472

description: miRNA


title: CC0485

description: miRNA


title: CC0482

description: miRNA


title: CC0464

description: miRNA


title: CC0463

description: miRNA


title: CC0462

description: miRNA


title: CC0461

description: miRNA


title: CC0475

description: miRNA


title: CC0459

description: miRNA


title: CC0458

description: miRNA


title: CC0470

description: miRNA


title: CC0469

description: miRNA


title: CC0468

description: miRNA


title: CC0456

description: miRNA


title: CC0453

description: miRNA


title: CC0467

description: miRNA


title: CC0452

description: miRNA


title: CC0447

description: miRNA


title: CC0465

description: miRNA


title: CC0451

description: miRNA


title: CC0466

description: miRNA


title: CC0471

description: miRNA


title: CC0473

description: miRNA


title: CC0449

description: miRNA


title: CC0460

description: miRNA


title: CC0442

description: miRNA


title: CC0444

description: miRNA


title: CC0443

description: miRNA


title: CC0440

description: miRNA


title: CC0457

description: miRNA


title: CC0435

description: miRNA


title: CC0433

description: miRNA


title: CC0455

description: miRNA


title: CC0454

description: miRNA


title: CC0450

description: miRNA


title: CC0431

description: miRNA


title: CC0428

description: miRNA


title: CC0429

description: miRNA


title: CC0448

description: miRNA


title: CC0427

description: miRNA


title: CC0424

description: miRNA


title: CC0425

description: miRNA


title: CC0446

description: miRNA


title: CC0426

description: miRNA


title: CC0423

description: miRNA


title: CC0441

description: miRNA


title: CC0437

description: miRNA


title: CC0445

description: miRNA


title: CC0439

description: miRNA


title: CC0417

description: miRNA


title: CC0436

description: miRNA


title: CC0421

description: miRNA


title: CC0434

description: miRNA


title: CC0415

description: miRNA


title: CC0413

description: miRNA


title: CC0412

description: miRNA


title: CC0408

description: miRNA


title: CC0430

description: miRNA


title: CC0410

description: miRNA


title: CC0438

description: miRNA


title: CC0422

description: miRNA


title: CC0403

description: miRNA


title: CC0432

description: miRNA


title: CC0402

description: miRNA


title: CC0404

description: miRNA


title: CC0419

description: miRNA


title: CC0420

description: miRNA


title: CC0418

description: miRNA


title: CC0405

description: miRNA


title: CC0399

description: miRNA


title: CC0411

description: miRNA


title: CC0409

description: miRNA


title: CC0391

description: miRNA


title: CC0406

description: miRNA


title: CC0390

description: miRNA


title: CC0389

description: miRNA


title: CC0388

description: miRNA


title: CC0382

description: miRNA


title: CC0416

description: miRNA


title: CC0379

description: miRNA


title: CC0401

description: miRNA


title: CC0377

description: miRNA


title: CC0400

description: miRNA


title: CC0398

description: miRNA


title: CC0414

description: miRNA


title: CC0376

description: miRNA


title: CC0397

description: miRNA


title: CC0396

description: miRNA


title: CC0375

description: miRNA


title: CC0374

description: miRNA


title: CC0384

description: miRNA


title: CC0371

description: miRNA


title: CC0394

description: miRNA


title: CC0370

description: miRNA


title: CC0392

description: miRNA


title: CC0393

description: miRNA


title: CC0407

description: miRNA


title: CC0366

description: miRNA


title: CC0364

description: miRNA


title: CC0361

description: miRNA


title: CC0386

description: miRNA


title: CC0387

description: miRNA


title: CC0385

description: miRNA


title: CC0357

description: miRNA


title: CC0383

description: miRNA


title: CC0380

description: miRNA


title: CC0378

description: miRNA


title: CC0352

description: miRNA


title: CC0395

description: miRNA


title: CC0350

description: miRNA


title: CC0351

description: miRNA


title: CC0373

description: miRNA


title: CC0372

description: miRNA


title: CC0368

description: miRNA


title: CC0369

description: miRNA


title: CC0381

description: miRNA


title: CC0347

description: miRNA


title: CC0346

description: miRNA


title: CC0367

description: miRNA


title: CC0365

description: miRNA


title: CC0363

description: miRNA


title: CC0343

description: miRNA


title: CC0341

description: miRNA


title: CC0362

description: miRNA


title: CC0344

description: miRNA


title: CC0360

description: miRNA


title: CC0359

description: miRNA


title: CC0348

description: miRNA


title: CC0336

description: miRNA


title: CC0339

description: miRNA


title: CC0358

description: miRNA


title: CC0356

description: miRNA


title: CC0354

description: miRNA


title: CC0345

description: miRNA


title: CC0333

description: miRNA


title: CC0342

description: miRNA


title: CC0327

description: miRNA


title: CC0355

description: miRNA


title: CC0353

description: miRNA


title: CC0349

description: miRNA


title: CC0340

description: miRNA


title: CC0338

description: miRNA


title: CC0321

description: miRNA


title: CC0320

description: miRNA


title: CC0334

description: miRNA


title: CC0337

description: miRNA


title: CC0335

description: miRNA


title: CC0319

description: miRNA


title: CC0317

description: miRNA


title: CC0332

description: miRNA


title: CC0316

description: miRNA


title: CC0330

description: miRNA


title: CC0331

description: miRNA


title: CC0312

description: miRNA


title: CC0329

description: miRNA


title: CC0311

description: miRNA


title: CC0328

description: miRNA


title: CC0325

description: miRNA


title: CC0326

description: miRNA


title: CC0323

description: miRNA


title: CC0324

description: miRNA


title: CC0322

description: miRNA


title: CC0306

description: miRNA


title: CC0309

description: miRNA


title: CC0307

description: miRNA


title: CC0304

description: miRNA


title: CC0308

description: miRNA


title: CC0302

description: miRNA


title: CC0315

description: miRNA


title: CC0318

description: miRNA


title: CC0313

description: miRNA


title: CC0314

description: miRNA


title: CC0310

description: miRNA


title: CC0305

description: miRNA


title: CC0293

description: miRNA


title: CC0301

description: miRNA


title: CC0287

description: miRNA


title: CC0286

description: miRNA


title: CC0285

description: miRNA


title: CC0284

description: miRNA


title: CC0299

description: miRNA


title: CC0298

description: miRNA


title: CC0283

description: miRNA


title: CC0297

description: miRNA


title: CC0295

description: miRNA


title: CC0278

description: miRNA


title: CC0276

description: miRNA


title: CC0275

description: miRNA


title: CC0273

description: miRNA


title: CC0292

description: miRNA


title: CC0303

description: miRNA


title: CC0288

description: miRNA


title: CC0282

description: miRNA


title: CC0290

description: miRNA


title: CC0296

description: miRNA


title: CC0270

description: miRNA


title: CC0267

description: miRNA


title: CC0265

description: miRNA


title: CC0281

description: miRNA


title: CC0280

description: miRNA


title: CC0279

description: miRNA


title: CC0262

description: miRNA


title: CC0277

description: miRNA


title: CC0260

description: miRNA


title: CC0261

description: miRNA


title: CC0274

description: miRNA


title: CC0294

description: miRNA


title: CC0259

description: miRNA


title: CC0258

description: miRNA


title: CC0268

description: miRNA


title: CC0266

description: miRNA


title: CC0272

description: miRNA


title: CC0269

description: miRNA


title: CC0254

description: miRNA


title: CC0255

description: miRNA


title: CC0263

description: miRNA


title: CC0250

description: miRNA


title: CC0252

description: miRNA


title: CC0249

description: miRNA


title: CC0264

description: miRNA


title: CC0256

description: miRNA


title: CC0248

description: miRNA


title: CC0271

description: miRNA


title: CC0245

description: miRNA


title: CC0251

description: miRNA


title: CC0253

description: miRNA


title: CC0247

description: miRNA


title: CC0236

description: miRNA


title: CC0237

description: miRNA


title: CC0233

description: miRNA


title: CC0234

description: miRNA


title: CC0246

description: miRNA


title: CC0232

description: miRNA


title: CC0229

description: miRNA


title: CC0230

description: miRNA


title: CC0244

description: miRNA


title: CC0243

description: miRNA


title: CC0225

description: miRNA


title: CC0242

description: miRNA


title: CC0224

description: miRNA


title: CC0257

description: miRNA


title: CC0241

description: miRNA


title: CC0221

description: miRNA


title: CC0219

description: miRNA


title: CC0239

description: miRNA


title: CC0240

description: miRNA


title: CC0238

description: miRNA


title: CC0235

description: miRNA


title: CC0217

description: miRNA


title: CC0215

description: miRNA


title: CC0231

description: miRNA


title: CC0228

description: miRNA


title: CC0227

description: miRNA


title: CC0226

description: miRNA


title: CC0220

description: miRNA


title: CC0223

description: miRNA


title: CC0204

description: miRNA


title: CC0218

description: miRNA


title: CC0214

description: miRNA


title: CC0212

description: miRNA


title: CC0201

description: miRNA


title: CC0203

description: miRNA


title: CC0195

description: miRNA


title: CC0199

description: miRNA


title: CC0207

description: miRNA


title: CC0200

description: miRNA


title: CC0198

description: miRNA


title: CC0208

description: miRNA


title: CC0210

description: miRNA


title: CC0209

description: miRNA


title: CC0194

description: miRNA


title: CC0216

description: miRNA


title: CC0211

description: miRNA


title: CC0205

description: miRNA


title: CC0206

description: miRNA


title: CC0197

description: miRNA


title: CC0190

description: miRNA


title: CC0202

description: miRNA


title: CC0193

description: miRNA


title: CC0192

description: miRNA


title: CC0213

description: miRNA


title: CC0188

description: miRNA


title: CC0189

description: miRNA


title: CC0191

description: miRNA


title: CC0187

description: miRNA


title: CC0184

description: miRNA


title: CC0185

description: miRNA


title: CC0196

description: miRNA


title: CC0186

description: miRNA


title: CC0183

description: miRNA


title: CC0182

description: miRNA


title: CC0181

description: miRNA


title: CC0173

description: miRNA


title: CC0174

description: miRNA


title: CC0175

description: miRNA


title: CC0176

description: miRNA


title: CC0172

description: miRNA


title: CC0177

description: miRNA


title: CC0169

description: miRNA


title: CC0179

description: miRNA


title: CC0178

description: miRNA


title: CC0164

description: miRNA


title: CC0168

description: miRNA


title: CC0165

description: miRNA


title: CC0163

description: miRNA


title: CC0162

description: miRNA


title: CC0171

description: miRNA


title: CC0160

description: miRNA


title: CC0166

description: miRNA


title: CC0161

description: miRNA


title: CC0159

description: miRNA


title: CC0158

description: miRNA


title: CC0157

description: miRNA


title: CC0154

description: miRNA


title: CC0155

description: miRNA


title: CC0167

description: miRNA


title: CC0156

description: miRNA


title: CC0180

description: miRNA


title: CC0152

description: miRNA


title: CC0170

description: miRNA


title: CC0153

description: miRNA


title: CC0151

description: miRNA


title: CC0148

description: miRNA


title: CC0145

description: miRNA


title: CC0144

description: miRNA


title: CC0141

description: miRNA


title: CC0140

description: miRNA


title: CC0149

description: miRNA


title: CC0137

description: miRNA


title: CC0136

description: miRNA


title: CC0135

description: miRNA


title: CC0134

description: miRNA


title: CC0142

description: miRNA


title: CC0133

description: miRNA


title: CC0147

description: miRNA


title: CC0150

description: miRNA


title: CC0130

description: miRNA


title: CC0138

description: miRNA


title: CC0129

description: miRNA


title: CC0128

description: miRNA


title: CC0127

description: miRNA


title: CC0146

description: miRNA


title: CC0125

description: miRNA


title: CC0139

description: miRNA


title: CC0132

description: miRNA


title: CC0124

description: miRNA


title: CC0123

description: miRNA


title: CC0131

description: miRNA


title: CC0122

description: miRNA


title: CC0121

description: miRNA


title: CC0143

description: miRNA


title: CC0118

description: miRNA


title: CC0120

description: miRNA


title: CC0119

description: miRNA


title: CC0117

description: miRNA


title: CC0115

description: miRNA


title: CC0114

description: miRNA


title: CC0111

description: miRNA


title: CC0112

description: miRNA


title: CC0116

description: miRNA


title: CC0108

description: miRNA


title: CC0126

description: miRNA


title: CC0113

description: miRNA


title: CC0110

description: miRNA


title: CC0109

description: miRNA


title: CC0105

description: miRNA


title: CC0106

description: miRNA


title: CC0107

description: miRNA


title: CC0101

description: miRNA


title: CC0103

description: miRNA


title: CC0102

description: miRNA


title: CC0097

description: miRNA


title: CC0104

description: miRNA


title: CC0099

description: miRNA


title: CC0095

description: miRNA


title: CC0100

description: miRNA


title: CC0096

description: miRNA


title: CC0094

description: miRNA


title: CC0093

description: miRNA


title: CC0092

description: miRNA


title: CC0089

description: miRNA


title: CC0091

description: miRNA


title: CC0088

description: miRNA


title: CC0087

description: miRNA


title: CC0086

description: miRNA


title: CC0084

description: miRNA


title: CC0081

description: miRNA


title: CC0083

description: miRNA


title: CC0080

description: miRNA


title: CC0079

description: miRNA


title: CC0073

description: miRNA


title: CC0074

description: miRNA


title: CC0098

description: miRNA


title: CC0077

description: miRNA


title: CC0078

description: miRNA


title: CC0072

description: miRNA


title: CC0076

description: miRNA


title: CC0070

description: miRNA


title: CC0071

description: miRNA


title: CC0069

description: miRNA


title: CC0067

description: miRNA


title: CC0068

description: miRNA


title: CC0066

description: miRNA


title: CC0063

description: miRNA


title: CC0090

description: miRNA


title: CC0085

description: miRNA


title: CC0082

description: miRNA


title: CC0060

description: miRNA


title: CC0059

description: miRNA


title: CC0061

description: miRNA


title: CC0057

description: miRNA


title: CC0058

description: miRNA


title: CC0075

description: miRNA


title: CC0056

description: miRNA


title: CC0055

description: miRNA


title: CC0054

description: miRNA


title: CC0049

description: miRNA


title: CC0052

description: miRNA


title: CC0051

description: miRNA


title: CC0047

description: miRNA


title: CC0053

description: miRNA


title: CC0050

description: miRNA


title: CC0064

description: miRNA


title: CC0046

description: miRNA


title: CC0044

description: miRNA


title: CC0042

description: miRNA


title: CC0040

description: miRNA


title: CC0043

description: miRNA


title: CC0039

description: miRNA


title: CC0048

description: miRNA


title: CC0062

description: miRNA


title: CC0038

description: miRNA


title: CC0065

description: miRNA


title: CC0037

description: miRNA


title: CC0036

description: miRNA


title: CC0035

description: miRNA


title: CC0034

description: miRNA


title: CC0033

description: miRNA


title: CC0031

description: miRNA


title: CC0032

description: miRNA


title: CC0030

description: miRNA


title: CC0045

description: miRNA


title: CC0028

description: miRNA


title: CC0029

description: miRNA


title: CC0025

description: miRNA


title: CC0024

description: miRNA


title: CC0027

description: miRNA


title: CC0041

description: miRNA


title: CC0023

description: miRNA


title: CC0026

description: miRNA


title: CC0022

description: miRNA


title: CC0021

description: miRNA


title: CC0020

description: miRNA


title: CC0017

description: miRNA


title: CC0019

description: miRNA


title: CC0014

description: miRNA


title: CC0016

description: miRNA


title: CC0015

description: miRNA


title: CC0013

description: miRNA


title: CC0012

description: miRNA


title: CC0010

description: miRNA


title: CC0008

description: miRNA


title: CC0009

description: miRNA


title: CC0006

description: miRNA


title: CC0004

description: miRNA


title: CC0005

description: miRNA


title: CC0011

description: miRNA


title: CC0002

description: miRNA


title: BT0404

description: miRNA

value: biliary tract cancer


title: BT0403

description: miRNA


title: BT0405

description: miRNA


title: CC0003

description: miRNA


title: CC0001

description: miRNA


title: CC0018

description: miRNA


title: BT0397

description: miRNA


title: BT0401

description: miRNA


title: BT0402

description: miRNA


title: BT0399

description: miRNA


title: BT0395

description: miRNA


title: BT0393

description: miRNA


title: BT0394

description: miRNA


title: BT0392

description: miRNA


title: BT0400

description: miRNA


title: BT0391

description: miRNA


title: CC0007

description: miRNA


title: BT0390

description: miRNA


title: BT0389

description: miRNA


title: BT0388

description: miRNA


title: BT0384

description: miRNA


title: BT0406

description: miRNA


title: BT0386

description: miRNA


title: BT0382

description: miRNA


title: BT0385

description: miRNA


title: BT0378

description: miRNA


title: BT0380

description: miRNA


title: BT0381

description: miRNA


title: BT0376

description: miRNA


title: BT0398

description: miRNA


title: BT0396

description: miRNA


title: BT0374

description: miRNA


title: BT0372

description: miRNA


title: BT0375

description: miRNA


title: BT0373

description: miRNA


title: BT0371

description: miRNA


title: BT0370

description: miRNA


title: BT0369

description: miRNA


title: BT0366

description: miRNA


title: BT0364

description: miRNA


title: BT0365

description: miRNA


title: BT0367

description: miRNA


title: BT0383

description: miRNA


title: BT0363

description: miRNA


title: BT0359

description: miRNA


title: BT0361

description: miRNA


title: BT0360

description: miRNA


title: BT0362

description: miRNA


title: BT0387

description: miRNA


title: BT0358

description: miRNA


title: BT0357

description: miRNA


title: BT0377

description: miRNA


title: BT0379

description: miRNA


title: BT0355

description: miRNA


title: BT0354

description: miRNA


title: BT0352

description: miRNA


title: BT0353

description: miRNA


title: BT0351

description: miRNA


title: BT0350

description: miRNA


title: BT0349

description: miRNA


title: BT0368

description: miRNA


title: BT0346

description: miRNA


title: BT0347

description: miRNA


title: BT0344

description: miRNA


title: BT0343

description: miRNA


title: BT0342

description: miRNA


title: BT0340

description: miRNA


title: BT0341

description: miRNA


title: BT0339

description: miRNA


title: BT0338

description: miRNA


title: BT0335

description: miRNA


title: BT0336

description: miRNA


title: BT0334

description: miRNA


title: BT0356

description: miRNA


title: BT0332

description: miRNA


title: BT0329

description: miRNA


title: BT0333

description: miRNA


title: BT0330

description: miRNA


title: BT0328

description: miRNA


title: BT0331

description: miRNA


title: BT0327

description: miRNA


title: BT0326

description: miRNA


title: BT0348

description: miRNA


title: BT0323

description: miRNA


title: BT0322

description: miRNA


title: BT0325

description: miRNA


title: BT0320

description: miRNA


title: BT0317

description: miRNA


title: BT0345

description: miRNA


title: BT0321

description: miRNA


title: BT0318

description: miRNA


title: BT0319

description: miRNA


title: BT0316

description: miRNA


title: BT0312

description: miRNA


title: BT0315

description: miRNA


title: BT0310

description: miRNA


title: BT0337

description: miRNA


title: BT0301

description: miRNA


title: BT0299

description: miRNA


title: BT0311

description: miRNA


title: BT0295

description: miRNA


title: BT0297

description: miRNA


title: BT0294

description: miRNA


title: BT0292

description: miRNA


title: BT0291

description: miRNA


title: BT0309

description: miRNA


title: BT0306

description: miRNA


title: BT0305

description: miRNA


title: BT0304

description: miRNA


title: BT0308

description: miRNA


title: BT0307

description: miRNA


title: BT0285

description: miRNA


title: BT0303

description: miRNA


title: BT0284

description: miRNA


title: BT0302

description: miRNA


title: BT0281

description: miRNA


title: BT0300

description: miRNA


title: BT0293

description: miRNA


title: BT0298

description: miRNA


title: BT0289

description: miRNA


title: BT0314

description: miRNA


title: BT0313

description: miRNA


title: BT0286

description: miRNA


title: BT0288

description: miRNA


title: BT0287

description: miRNA


title: BT0277

description: miRNA


title: BT0275

description: miRNA


title: BT0274

description: miRNA


title: BT0283

description: miRNA


title: BT0282

description: miRNA


title: BT0278

description: miRNA


title: BT0279

description: miRNA


title: BT0280

description: miRNA


title: BT0269

description: miRNA


title: BT0273

description: miRNA


title: BT0272

description: miRNA


title: BT0268

description: miRNA


title: BT0271

description: miRNA


title: BT0270

description: miRNA


title: BT0264

description: miRNA


title: BT0263

description: miRNA


title: BT0265

description: miRNA


title: BT0267

description: miRNA


title: BT0261

description: miRNA


title: BT0259

description: miRNA


title: BT0260

description: miRNA


title: BT0257

description: miRNA


title: BT0258

description: miRNA


title: BT0256

description: miRNA


title: BT0253

description: miRNA


title: BT0262

description: miRNA


title: BT0252

description: miRNA


title: BT0276

description: miRNA


title: BT0250

description: miRNA


title: BT0255

description: miRNA


title: BT0254

description: miRNA


title: BT0251

description: miRNA


title: BT0248

description: miRNA


title: BT0249

description: miRNA


title: BT0244

description: miRNA


title: BT0245

description: miRNA


title: BT0243

description: miRNA


title: BT0246

description: miRNA


title: BT0242

description: miRNA


title: BT0266

description: miRNA


title: BT0240

description: miRNA


title: BT0239

description: miRNA


title: BT0241

description: miRNA


title: BT0238

description: miRNA


title: BT0235

description: miRNA


title: BT0236

description: miRNA


title: BT0237

description: miRNA


title: BT0233

description: miRNA