title: A431 CO-CULTURE Rep2

description:
A431 CO-CULTURE 0801
replicate10
gene expression data for A431 cells in direct co-culture with VCAF

source_name: A431 CO-CULTURE

value: A431 direct co-culture


title: Mouse DRG E12.5 Lumbar

status: Public on Mar 31 2020

type: SRA

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

country: Sweden

institute: Karolinska Institute

description:
miRNA profile
17

library_source: transcriptomic

data_processing:
Illlumina software used for base calling
Adaptor removel and barcode extraction was used Mirprof tool by defalt settings.  http://srna-workbench.cmp.uea.ac.uk/mirprof-tutorial/
Data are then loaded to The Small RNA workbench software for aligment, normalisation and comparsion analysis. ( Bioinformatics. 2012 Aug 1; 28(15): 2059–2061.)
Genome_build: mm9, galgal4
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Mouse Lumbar DRG at embryonic day 12.5

extract_protocol:
DRG has dissected and immediately disolved in Extraction buffer and proceed as Thermoscientific miRNA extraction kit (PureLink® miRNA Isolation Kit, K157001)
Using illumina standard protocols

treatment_protocol: Dissociated mouse DRG neurons were obtained after enzymatic digestion of whole DRG using collagenase/dispase (C/D, 1mg/ml; Roche) and DNAse (0.5 mg/ml; Sigma) in N2 medium (DMEM/F12 med- ium with N2 supplement) with B27 supplement (Gibco). Cells were plated at low density (300 cells/well) in 24-well plates on glass coverslips precoated with poly-L-lysine (0.01%; Sigma)/laminin (10mg/ml; R&D Systems) or matrigel when indicated (BD Bioscience). Cells were cultured in N2 medium, treatment of neurotrophins, proteins activators and neurontransmitters from sample  29-36  at 10 ng/ml for 14hrs.

tag: genotype/variation

value: wildtype

tag: tissue

value: lumbar

tag: developmental stage


title: A431 CO-CULTURE Rep1

type: RNA

city: London

first: Erik

last: Sahai

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description:
A431 CO-CULTURE 0712
replicate9
gene expression data for A431 cells in direct co-culture with VCAF

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with the lumi package in R

label: biotin

organism: Homo sapiens

label_protocol: Standard Illumina protocol

growth_protocol: DMEM with 10% FCS

extract_protocol: RNEasy mini kit Qiagen

treatment_protocol: Mono-culture vs Co-culture separated by 0.4micron filter vs direct co-culture followed by flow cytometry to sort GFP-labelled A431 cancer cells from mCherry-labelled CAFs

tag: cell type

value: Epithelial Cancer

tag: sample type


title: m6V

city: Los Angeles

first: Dan

last: Theodorescu

state: CA

address: 8700 Beverly Blvd., Davis Building, Rm 3057

country: USA

institute: Cedars Sinai Medical Center

description: AGL full body KO mouse bladder

data_processing:
Illumina CASAVA used for base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads were mapped to refernce genome using TopHat2 and Fragments Per Kilobases per Million Reads (FPKM) determined
Genome_build: mm9
Supplementary_files_format_and_content: xls files including mapped read counts and FPKM per sample

source_name: BBN induced bladder cancer

extract_protocol:
Bladders were removed and flash frozen with liquid nitrogen.  Tumors were weighed, crushed, and RNA purified by Rneasy Plus Mini-Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with 0.05% BBN carcinogen for 12 weeks

tag: strain

value: Bladder

tag: genotype

value: AGL-FBKO


title: VCAF ONLY Rep2

description:
VCAF ONLY 0801
replicate4
gene expression data for VCAF cells

source_name: VCAF ONLY

value: Stromal Fibroblast

value: VCAF mono-culture


title: A431 SOLUBLE Rep1

description:
A431 SOLUBLE 0712
replicate5
gene expression data for A431 cells in co-culture with exchange of soluble factors with VCAF

source_name: A431 SOLUBLE

value: A431 soluble co-culture


title: m5V

description: AGL full body KO mouse bladder


title: A431 ONLY Rep1

description:
A431 ONLY 0712
replicate1
gene expression data for A431 cells

source_name: A431 ONLY

value: A431 mono-culture


title: m4V

description: AGL full body wild type mouse bladder

value: AGL-FBWT


title: A431 ONLY Rep2

description:
A431 ONLY 0801
replicate2
gene expression data for A431 cells


title: VCAF ONLY Rep1

description:
VCAF ONLY 0712
replicate3
gene expression data for VCAF cells


title: Mouse DRG E12.5 Thoracic

description:
miRNA profile
16

source_name: Mouse Thoracic DRG at embryonic day 12.5

value: thoracic


title: m3V

description: AGL full body wild type mouse bladder


title: m2V

description: AGL full body wild type mouse bladder


title: Mouse DRG E12.5 Brachial

description:
miRNA profile
15

source_name: Mouse Brachial DRG at embryonic day 12.5

value: brachical


title: m1V

description: AGL full body wild type mouse bladder


title: Mouse DRG E11.5 Thoracic

description:
miRNA profile
14

source_name: Mouse Thoracic DRG at embryonic day 11.5


title: Mouse DRG E11.5 Brachial

description:
miRNA profile
13

source_name: Mouse Brachial DRG at embryonic day 11.5


title: BM-derived culture

city: Hangzhou

first: xiao

last: HUANG

state: zhejiang

address: yuhangtang road 588#

department: College of Life Sciences

country: China

institute: zhejiang university

data_processing:
RNA-seq reads were mapped to the mouse reference genome (GRCm38.84) using TopHat2.
Read counts for each gene were determined using htseq -count (python) function.
Gene read counts were normalized and differentially expressed genes were determined based on a negative binomial test using edgeR.
Genome_build: GRCm38.84
Supplementary_files_format_and_content: Microsoft Office Excel 2007 files include gene name, sequence ID, and normalized abundance measurements (fpkm) for each gene in each sample.

source_name: hair cell-like cells

growth_protocol: otic progenitors derived from WT, BM and BEM mESC lines were dissociated with Accutase (Gibco), and seeded on top of mitotically inactivated embryonic chicken utricle stromal cells, in 24-well plates. Co-cultures were grown for 9 days using DMEM/F12 (Gibco) supplemented with N2 and B27 (Invitrogen), EGF (Gibco, 25ng/ml) and retinoic acid (RA) (Sigma, 1 μM). The medium was changed every other day.

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Life Technologies) and the quality was assessed with Agilent 2100 Bioanalyzer picochips. mRNA enrichment with Oligo dT, mRNA fragmentation, reverse transcription, adaptor ligation and PCR were performed using the Illumina TruseqTM RNA Sample Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols with Illumina TruseqTM RNA sample prep Kit.

value: Embryonic Stem Cell

tag: cell line

value: BM

tag: age

value: Culture day 9 during induction of otic progenitors towards hair cell-like cells


title: Mouse DRG E10.5 Brachial

description:
miRNA profile
12

source_name: Mouse Brachial DRG at embryonic day 10.5


title: WT-derived culture

value: wild type (WT)


title: Sheared genomic DNA

city: St. Louis

first: Stephen

last: Beverley

state: MO

address: 660 S. Euclid, Campus Box 8230

department: Molecular Microbiology

institute: Washington University School of Medicine

description:
Sheared genomic DNA
Normalizing control for Mnase samples
library strategy: genomic DNA-seq

library_source: genomic

data_processing:
Basecalls performed using Casava (versions specified in "Characteristics" field).
Quality control on all datasets was initially performed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Paired-end data files were aligned to the L. major FV1 reference genome (TriTrypDB version 4.0) by NovoalignMPI (http://novocraft.com) using the following parameters: -o SAM; -r random; -l 30; -e 100; -H; -a AATGATACGGCGACCACCGAGAT  CTACACTCTTTCCCTACACGACGCTCTTCCGATCT  GATCGGAAGAGCACACGTCTGAACTCC  AGTCACGCTTAGATCTCGTATGCCGTCTTCTGCTTG.
Datasets were processed to BAM format using Samtools import, sort, and index programs.
Depth of coverage parameters were calculated using the BEDTools genomeCoverageBed tool [37]; the output from these calculations is shown in Supplemental Table S1.
PAVED pipeline (Shaik et al., in preparation) was utilized to generate normalized fragment depth ratios of experimental datasets (MNAse-digested chromatin, MNAse-digested purified DNA, MNAse-overdigested chromatin, or FAIRE) to their respective controls (MNAse: Sheared genomic DNA; FAIRE: FAIRE input).  Normalizing dataset is indicated as the second name in the wig file name.  All datasets were normalized to a mean of 1 for comparison between datasets.
Wig file format:  The 'a' is used when the dataset in the denominator position has no coverage at that position, and reflects regions that are difficult or impossible to sequence using this platform.  The 'a' is an essential component to the proper interpretation of these experiments in our manuscript, and a software pipeline in preparation for publication is designed to handle data in this format.
Genome_build: L. major TriTrypDB version 4.0
Supplementary_files_format_and_content: wig files were generated by PAVED

molecule: genomic DNA

organism: Leishmania major

source_name: promastigotes

growth_protocol: All studies used derivatives of Leishmania major Friedlin V1 (MHOM/JL/81/Friedlin), grown at 26°C in M199 medium (US Biologicals) supplemented with 40 mM 4-(2-hydroxyethyl)-1-piperazineethanesuphonic acid (HEPES) pH 7.4 (Fisher Scientific), 100 uM adenine (Sigma), 1 µg mL-1 biotin (Sigma), 10 µg mL-1 hemin (Sigma), 2 µg mL-1 biopterin (Schircks Laboratories), 50 units/mL penicillin (Gibco), 50 µg/mL streptomycin (Gibco), and 10% (v/v) heat inactivated fetal calf serum (HyClone). Cell density was determined by using a model Z1 Coulter counter.

extract_protocol: For sheared DNA and FAIRE samples only, end repair was performed using T4 DNA polymerase (Enyzmatics) and Klenow DNA polymerase (Enzymatics), and ends were phosphorylated using T4 polynucleotide kinase (Enzymatics). For all samples (sheared DNA, FAIRE, and MNAse-seq), fragments were A-tailed using Klenow (3'-5' exo-) (Enzymatics) and purified using AMPure XP beads. Libraries for paired end sequencing were prepared from all samples using T4 DNA ligase (Enzymatics) to add adapters containing the following sequences to the ends of the purified DNA fragments: adapter 1, (5' phosphate)- GATCGGAAGAGCACACGTCTGAACTCCAGTCAC; adapter 2, ACACTCTTTCCCTACACGACGCTCTTCCGATCT. Fragments were purified with AMPure XP beads to remove adapter dimers. Index sequences were added by PCR using the following primers: primer 1.0 AATGATACGGCGACCACCGA  GATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT; primer 2.0 GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT; and indexing primer CAAGCAGAAGACGGCATACGAGATNNNNNNNGTGACTGGAGTTCAGACGTGTGC, where N designates the location of the unique 7-mer index sequence from each library. Libraries were validated using an Agilent 2100 Bioanalyzer, quantified using the Invitrogen Quant-iT HS DNA kit (Life Technologies), pooled in equimolar ratios, and subjected to 2x101 paired end sequencing using an Illumina HiSeq 2000.

treatment_protocol:
[Chromatin MNAse digestion] Logarithmic-phase cells were grown to a density of 2-4 x 106 cells/mL. Cells were collected, washed with Dulbecco’s phosphate buffered saline (DPBS), and resuspended in ice-cold cell lysis buffer composed of 10 mM Tris-HCl, pH 7.4 (Sigma), 10 mM sodium chloride (Sigma), 3 mM magnesium chloride (Sigma), 0.5% Igepal-CA630 (Sigma), 0.15 mM spermine (Sigma), and 0.5 mM spermidine (Sigma). Nuclei were pelleted at 4°C and washed with ice-cold micrococcal nuclease digestion buffer composed of 10 mM Tris-HCl, pH 7.4, 15 mM sodium chloride, 60 mM potassium chloride (Sigma), 2 mM calcium chloride (Sigma), 0.15 mM spermine, and 0.5 mM spermidine. Nuclei were pelleted and resuspended at a density of 1.3 x 109 nuclei/mL in digestion buffer. Micrococcal nuclease (Sigma, cat. N3755) was added to a concetration of 1 unit per 3.3 x 107 nuclei and incubated at room temperature for 20 minutes. 1/25 volumes of micrococcal nuclease stop buffer composed of 100 mM EDTA (Sigma) and 10 mM EGTA (Sigma), pH 7.5 was added to stop the reaction. Nuclei were lysed with 1/10 volume of 20% sodium dodecyl sulfate (Sigma) and incubated overnight at 37°C with 750 ug/mL proteinase K (Sigma). The samples were extracted with an equal volume of phenol-chloroform-isoamyl alcohol (25:24:1, Sigma), and the aqueous phase was treated with 200 ug/mL RNAse A (Sigma) for 3 hours at 37°C. DNA was precipitated with 1/10 volumes 3M sodium acetate, pH 5.2 (Sigma) and 3 volumes of 100% ethanol (Pharmco-Aaper). The pellet was washed with 70% ethanol and was resuspended in TE buffer for library preparation or quantitative PCR.
[Control MNAse digestion] MNAse-digested naked DNA was prepared by performing nuclear isolation, DNA extraction, RNAse A treatment, and purification as described above. Purified DNA was resuspended in micrococcal nuclease digestion buffer at a density of 2.2x108 nuclear equivalents/mL.  1 unit of MNAse was added to the reaction, and the reaction was incubated at room temperature. Aliquots of DNA were removed at 0, 15, 30, 60, 90, 120, 300, and 480 seconds and mixed with 1/25 volumes stop buffer. DNA was phenol extracted and precipitated as described previously. Samples were resolved on a 3% agarose gel, and gel fragments for MNAse-treated naked DNA controls were cut out as described in Supplementary Fig. S1. DNA was extracted using a Qiagen Gel Extraction kit according the manufacturer’s instructions.
[Chromatin MNAse overdigestion] Overdigested MNAse samples were prepared identically to the chromatin MNAse digestion, incubating for 25 minutes with MNAse.
[FAIRE protocol] Logarithmic-phase cells were grown to a density of 2-4 x 106 cells/mL. FAIRE was performed according to published protocols with minor modifications [Simon, J; Giresi, P; Davis, I; Lieb, J. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nature Protocols 7:256-267 (2012)].  Cells were crosslinked for 10 minutes in 1% formaldehyde (Fisher), quenched with 125 mM glycine (Sigma), washed three times with ice-cold phosphate-buffered saline, and resuspended in lysis buffer B containing 1X Roche cOmplete protease inhibitor cocktail. Nuclei were pelleted and resuspended in lysis buffer A containing 1X Roche cOmplete protease inhibitor cocktail at a density of 3.3x108 nuclear equivalents/mL. Nuclei were lysed with 10 strokes in a Dounce homogenizer, and 300 uL aliquots were transferred to 1.5 mL TPX tubes (Diagenode). Cells were sonicated at 4°C for 60 cycles of 30 seconds on (high), 30 seconds off, using a Bioruptor (Diagenode) with a circulating water bath. FAIRE and input samples were extracted and prepared as indicated [36].
[Sheared genomic DNA protocol] For preparation of sheared genomic DNA, 3 ug of purified L. major FV1 genomic DNA was diluted in 130 uL nuclease-free water (Ambion) and was sheared using a Covaris focused ultrasonicator using the following parameters: duty cycle 10%, intensity 5, cycles per burst 200, time 240 s, set mode frequency sweeping, and temperature 4°C. Sheared DNA was purified with AMPure XP beads (Beckman Coulter) according to the manufacturer’s protocol.

tag: dna preparation protocol

value: Covaris shearing

tag: casava basecalling version

value: Casava 1.7

tag: index sequence

value: GTATTTG


title: BEM-derived culture

value: BEM


title: FAIRE Input

description:
FAIRE Input
Normalizing control for FAIRE Experimental sample

source_name: logarithmic-phase promastigotes

value: FAIRE Input

value: Casava 1.8

value: TACTCTA


title: CT518_b: genomic DNA of blood from CT518

type: genomic

city: Kumamoto

first: Kazuya

last: Iwamoto

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

department: Faculty of Life Sciences

country: Japan

institute: Kumamoto University

description: blood sample

hyb_protocol: Bisulfite converted DNA was amplified, processed and hybridized to Illumina HumanMethylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: BeadStudio.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol was used.

extract_protocol: Genomic DNA of blood was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions. Genomic DNA of saliva was extracted rom saliva samples using Ora-kit according to standard instructions and purified by precipitation with EtOH.

value: blood

tag: test series

value: test


title: Input DNA

city: Tokyo

first: Shinsuke

last: Ohba

address: 7-3-1 Hongo, Bunkyo-ku

department: Division of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine

institute: The University of Tokyo

data_processing:
DNA-sequence information was aligned to the unmasked mouse genome reference sequence mm9 by bowtie aligner
Peak calling was performed by two-sample analysis on CisGenome software with FDR<0.01 with the input control without antibody immunoprecipitation.
CisGenome software does not give quantitative data.
Genome_build: mm9
Supplementary_files_format_and_content: .bed file reports peaks

source_name: Primary rib chondrocytes

growth_protocol: Neonatal ICR wild-type mice postnatal day 1 rib

extract_protocol:
Rib chondrocytes were manually dissected from ribs of P1 neonatal wild-type ICR mice to include proliferative and prehypertrophic regions and to exclude mature hypertrophic regions.Superficial soft tissue was removed, and ribs were washed in DMEM. Segmented ribs were initially digested in 0.05% Trypsin/EDTA (T4174; Sigma-Aldrich) for 30 minutes at 37 °C, and then in 0.3% Collagenase D (1088858; Roche) for 45 minutes at 37 °C.Rib chondrocytes isolated from newborn wild-type ICR mice were immediately cross-linked with 1% formaldehyde for 10 minutes at room temperature. The crosslinking was quenched by addition of 2.5 M Glycine at the final concentration of 130 mM. Twenty million cells were used for a ChIP reaction. After washing with phosphate buffered saline (PBS) twice, cells were lysed in Lysis buffer (50 mM HEPES-KOH pH 7.5,140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% IGEPAL CA-630, 0.25% Triton-X 100) at 4 ℃ with agitation for 10 minutes, and then washed with Buffer 2 (10 mM Tris-HCl pH8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 10 minutes at room temperature. Chromatin was sonicated in Buffer 3 (10 mM Tris-HCl pH8.0, 1 mM EDTA, 0.5 mM EGTA) by 10 sessions of 30 pulses (1 sec on and 1 sec off) at 50% amplitude using the Branson Advanced-Digital sonifier 250 (Branson Ultrasonics Corporation, Danbury, CT) in order to obtain 100 – 600 bp of DNA fragments. Lysate was cleared by centrifugation and addition of 20% N-Lauroylsarcosine Sodium Salt (L9150; Sigma-Aldrich, St. Louis, MO) at the final concentration of 0.5%. One hundred microlitters of Dynabeads M-280 Sheep anti-Rabbit IgG (112-03D; Life Technologies, Carlsbad, CA) was combined with 10 μg of anti-Sox6 antibodies (ab30455; Abcam, Cambridge, UK). The beads/antibody complex was incubated with the lysate overnight at 4 ℃. Beads were washed 5 times with RIPA buffer (50 mM HEPES-KOH pH 7.5, 500 mM LiCl, 1 mM EDTA, 0.7% Sodium Deoxycolate, 1% IGEPAL CA-630) and once with TE buffer containing 50 mM NaCl. DNA was eluted with Elution buffer (50 mM Tris-HCl pH8.0, 10 mM EDTA, 1% SDS) at 65 ℃ for 15 minutes, and the eluate was incubated overnight at 65 ℃ for reverse crosslinking. After the eluate was treated with RNase (R4642; Sigma-Aldrich) and proteinase K (25530015; Invitrogen), DNA was purified by MinElute PCR Purification kit (28004; Qiagen).
Libraries were constructed with ThruPLEX DNA-seq Kit (R400429; Rubicon Genomics, Ann Arbor, MI) according to manufacturer’s instructions.

treatment_protocol: Wild type, not treated

value: ICR

value: rib

value: Primary rib chondrocytes

tag: chip antibody


title: FAIRE Experimental

description: FAIRE Experimental

value: FAIRE

value: CACCTCC


title: MNase-overdigested chromatin replicate 2

description: MNAse-overdigested chromatin replicate 2

value: Chromatin MNAse overdigestion

value: GCTTAGA


title: Wild type No Asparagine RNA

city: New York

first: Robert

middle: T

last: Williams

state: NY

address: 1230 York Avenue

institute: Rockefeller University

description:
WT_N TPM
processed data file: mergedDF.txt

data_processing:
Reads were aligned using Rsubread's align method and predicted fragment lengths calculated by the ChIPQC package.
Normalised, fragment extended signal bigWigs are created using the rtracklayer package.
Peak calls are made in HOMER software and their peak summits used in MEME-ChIP software for known and de novo motif discovery.
Read counts in peaks are calculated using the featureCounts method in the Rsubread library.
Differential ChIP-seq signal is identified using the binomTest from the edgeR package.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ChIP-Seq and ATAC-Seq: bigWig files
Supplementary_files_format_and_content: RNA-Seq: Tab-delimited text file (mergedDF.txt)  includes RPKM values for each sample.

source_name: Jurkat cells

extract_protocol:
RNA: Cells were harvested and RNA was isolated by Qiagen RNeasy kit. 1ug of total RNA was used for construction of sequencing libraries.
ChIP: Cells were cross-linked with 1% paraformaldehyde for 10 minutes at 37C. Cross-linking was quenched with 125 mM glycine. Cells were pelleted and flash-frozen in liquid nitrogen. Nuclei were isolated and sonicated using a Covaris sonicator. Protein A/G beads were added to 2-4 ug of appropriate antibodies and bound at room temperature for 1.5 hours. Samples were immunoprecipitated with appropriate protein A/G-antibody complexes overnight at 4C. Immunoprecipitates were collected and washed twice each with low salt, high salt, and lithium chloride wash buffers. DNA was eluted, reverse-crosslinked and treated with RNase and proteinase K before being isolated with a PCR purification kit (Zymogen).
ATAC: Cells were treated in the presence or absence of asparagine for 24 hours. Nuclear extracts were prepared from 100,000 cells for each cell line and condition, and incubated with 2.5 μl of transposase (Illumina) in a 50 μl reaction for 30 min at 37 °C. Transposase-fragmented DNA was purified, and the library was amplified by PCR.
RNA, ATAC and ChIP libraries were prepared using standard Illumina protocols.

value: Jurkat

value: Wild type

tag: treatment

value: Asparagine deprivation


title: MNase-digested purified DNA replicate 1

description: MNAse-digested purified DNA replicate 1

value: Control MNAse digestion

value: Casava 1.7

value: GAGTACG


title: MNase-overdigested chromatin replicate 1

description: MNAse-overdigested chromatin replicate 1


title: MNase-digested purified DNA replicate 2

description: MNAse-digested purified DNA replicate 2

value: ACAGATA


title: ZBTB1 KO + ZBTB1 cDNA No Asparagine RNA

description:
Addback_N TPM
processed data file: mergedDF.txt

value: ZBTB1 KO expressing ZBTB1 cDNA


title: MNase-digested chromatin replicate 2

description: MNAse-digested chromatin replicate 2

value: Chromatin MNAse digestion

value: Casava 1.8

value: TGAGGTT


title: CT519_b: genomic DNA of blood from CT519

description: blood sample

value: blood

value: test


title: Wild type Untreated RNA

description:
WT TPM
processed data file: mergedDF.txt

value: Normal media conditions


title: ZBTB1 KO No Asparagine RNA

description:
KO_N TPM
processed data file: mergedDF.txt

value: ZBTB1 KO


title: ZBTB1 KO + ZBTB1 cDNA Untreated RNA

description:
Addback TPM
processed data file: mergedDF.txt


title: MNase-digested chromatin replicate 1

description: MNAse-digested chromatin replicate 1

value: GTATTTG


title: ZBTB1 KO Untreated RNA

description:
KO TPM
processed data file: mergedDF.txt


title: WT_2: Naïve T cells from WT mouse, biological rep2

city: Ann Arbor

first: Nathan

middle: Daniel

last: Mathewson

state: MI

address: 1500 E. Medical Center Dr.

department: Internal Medicine

institute: University of Michigan

description:
WT_2
Gene expression data from naïve SAG WT T cells.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Mouse Gene ST 2.0 cartridge arrays. Samples were processed using the Affymetrix WT-OvationTM Pico System.

scan_protocol: GeneChips were scanned using the Agilent Gene Array Scanner with a 560 nm filter.

data_processing:
The data were analyzed using the R statistical environment provided by Bioconductor and were examined for the quality control by showing the same distribution of the PM probes for each chip and no degradation. The expression values were then calculated for each gene using a robust multi-array average.
GSEA at the Broad Institute.

source_name: WT T cells

label_protocol: Biotinylated RNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Isolated CD90.2+ T cells and immediately extracted RNA using Qiagen RNeasy spin kit.

extract_protocol: Qiagen RNeasy spin kit following the manufacturers protocol and quality of the total RNA was verified by an Agilent 2100 Bioanalyzer.

treatment_protocol: Spleens were isolated and placed in PBS containing 2% FBS and mechanically dissociated to a single cell suspension. Cells were then labelled with CD90.2+ microbeads and magnetically separated. Positive fraction was then immediately used to for RNA isolation following the manufacturers protocol.

value: SAG WT

value: CD90.2+ T cells


title: WT_1: Naïve T cells from WT mouse, biological rep1

description:
WT_1
Gene expression data from naïve SAG WT T cells.


title: KO_4: Naïve T cells from KO mouse, biological rep2

description:
KO_2
Gene expression data from naïve SAG KO T cells.

source_name: SAG KO T cells

value: SAG KO


title: PHF19 shRNA-PHF19 RNA-seq [ARP1_sh3]

city: Xi'an

first: Xiaoke

last: Ma

state: Shaanxi

address: No.2 South TaiBai Road

institute: Xidian University

data_processing:
The raw reads are mapped to the  hg19 using Tophat software by allowing maximum 2 mismatch
Only unique mapped reads are used for downstream analysis
The expression of genes are assembled using cufflink
Genome_build: hg19
Supplementary_files_format_and_content: Text file with gene expression in terms of FPKM values

source_name: ARP1_PHF19 shRNA-PHF19 RNA-seq

growth_protocol: ARP1 cells were grown under mycoplasma-free conditions and maintained in complete culture medium (RPMI1640 supplemented with 10% FBS and 100 IU/mL penicillin) in tissue culture flasks, at 37℃ in a 5% CO2 humidified incubator.

extract_protocol:
Total RNA yields were obtained with RNeasy Mini Kit (QIAGEN, Germany) according to manufacturer’s instructions
RNA was extracted using the Qiagen RNeasy Kit. Whole RNA (500ng) was subjected to library preparation, with use of the Beijing Genomics Institute (BGI) Library prep for Illumina kit.

treatment_protocol: PCDH plasmids with PHF19 ORF or empty vector was packaged to lenti-virus in HEK293T cells, ARP1 cells was then infected with those virus.

value: myeloma cells

tag: phenotype

value: Ig A kappa

value: PHF19 overexpressed


title: PHF19 shRNA-PHF19 RNA-seq [ARP1_sh1]


title: PHF19 shRNA-PHF19 RNA-seq [ARP1_sh2]


title: PHF19 scramble RNA-seq [ARP1_Scr3]

source_name: ARP1_PHF19 scramble RNA-seq


title: PHF19 scramble RNA-seq [ARP1_Scr2]


title: KO_3: Naïve T cells from KO mouse, biological rep1

description:
KO_1
Gene expression data from naïve SAG KO T cells.


title: PHF19 OE RNA-seq [ARP1-OE2]

source_name: ARP1_PHF19 OE RNA-seq


title: PHF19 scramble RNA-seq [ARP1_Scr1]


title: WT_ME

first: Jiacheng

last: Deng

state: Not Applicable

address: James Black Centre, 125 Coldharbour Lane

institute: King's College London

data_processing:
Data were processed following standard protocols using Cell Ranger version 2.2.0.
Cellranger mkfastq was used to demultiplex raw base call files into fastq files.
Cellranger count was used to perform alignment, filtering, barcode counting,  UMI counting, and to generate  feature-barcode matices.
Genome_build: mm10
Supplementary_files_format_and_content: H5 files for cells from adventitial and intimal/medial layers of wildtype and ApoE-/- mice.

source_name: Aorta

extract_protocol:
The whole aorta was isolated with perivascular adipose tissues and connective tissues removed. Aortic adventitia was then carefully dissected from the medial and intimal layers. The single cell suspensions were then prepared separately from the aortic adventitia and the remaining medial/intimal layers. The adventitia was cut into fine pieces and digested with 2 mg/ml collagenase I  and 2 mg/ml dispase II in Hank’s balanced salt solution containing calcium and magnesium for a total 40 min. The remaining aortic media and endothelium were cut open longitudinally and digested with 1 mg/ml papain , 0.5 mg/ml 1,4-Dithioerythritol, 0.156 mg/ml Taurine; 0.25 mg/ml bovine serum albumin in PBS. Single nucleated live cells were sorted into PBS with 0.04% BSA using a flow cytometer and were then analyzed on a 10x Chromium instrument using Chromium Single Cell 3' Reagent Kit v2 chemistry (10X Genomics), following a standard protocol.
Library was generated and sequenced on a NovaSeq platform (Illumina) with paired-end 150 bp (PE 150) sequencing strategy.
Single-cell RNA-seq

value: Aorta

value: wildtype


title: APOE_ME

value: ApoE-/-


title: PHF19 OE RNA-seq [ARP1-OE1]


title: PCDH empty vector RNA-seq [EV-5A]

source_name: ARP1_PCDH empty vector RNA-seq

value: PCDH empty vector


title: ERβ scKO rep2

city: Tsukuba

first: Ryo

last: Fujita

state: Ibaraki

department: Transborder Medical Research Center

institute: University of Tsukuba

data_processing:
Sequence data were mapped on the mouse genome (mm10) using Tophat and analyzed by Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: normalized counts

source_name: Primary satellite cells

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen, USA) and an RNeasy spin column kit (Qiagen, USA), followed by treatment with DNase I (Qiagen). RNA samples with RNA integrity number (RIN) greater than 8 were normalized to 100 ng/μl before further analyses.
RNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Prep Kit setA (Illumina, San Diego CA) according to the manufacturer's instructions and subsequently validated for an average size of about 330-340 bp using a 2100 Bioanalyzer and the Agilent DNA1000 kit.for the construction of sequencing libraries.

value: Extensor digitorum longus muscle-derived cells

value: 6-8 weeks old


title: PCDH empty vector RNA-seq [EV-3A]


title: PCDH empty vector RNA-seq [EV-4A]


title: APOE_ADV


title: Nst_4619_Type1_batch2

first: Daochun

last: Sun

state: New York

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

description:
Glioblastoma tumor tissue
9445918035_B

hyb_protocol: Manufactory protocol

scan_protocol: Manufactory protocol

data_processing: The Illumina BeadArray microarray data was summarized using the Illumina Beadstudio software and then processed through Bioconductor in R programming environment by beadarray package. Raw data were normalized by neqc method and the batch effects were removed using inSilicoMerging by DWD method.

source_name: glioma primary tissue

label_protocol: Manufactory protocol

growth_protocol: Mice of Nestin-CreERT2;Nf1f/+;Trp53f/f;Ptenf/+;Rosa-lsl-tdTom or NG2-CreERTM;Nf1f/+;Trp53f/f;Ptenf/+;Rosa-lsl-tdTom were administered with tamoxifen (Sigma) by one dose oral gavage (10mg/20g body weight) at adult ages (6-8 weeks of age) and aged until symptomatic.

extract_protocol: Mouse primary tumor samples were flash frozen in liquid nitrogen and total RNA was extracted using Qiagen Lipid Tissue RNeasy Mini Kit with trizol.

tag: genetic background

value: mixed background


title: Nst_3605_Type1_batch2

description:
Glioblastoma tumor tissue
9445918035_D


title: NG2_2014819_Type2_batch2

description:
Glioblastoma tumor tissue
9445918017_F


title: NG2_2014507_Type2_batch2

description:
Glioblastoma tumor tissue
9445918017_B


title: ERβ scKO rep1


title: NG2_3115_Type2_batch1

description:
Glioblastoma tumor tissue
9445833012_B


title: Nst_3153_Type1_batch1

description:
Glioblastoma tumor tissue
9445833013_A


title: NG2_3349_Type2_batch1

description:
Glioblastoma tumor tissue
9445833012_C


title: Nst_4607_Type1_batch2

description:
Glioblastoma tumor tissue
9445918035_C


title: Nst_2878_Type1_batch1

description:
Glioblastoma tumor tissue
9445918004_A


title: Control rep1


title: M662_KO_input

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
FACS isolated using EMBRACE technique
M662_KO_panH3.filtered.log2ratio.over_M662_KO_input.bw
M662_KO_H4K16ac.filtered.log2ratio.over_M662_KO_input.bw

data_processing:
RNA-seq: Raw sequencing data controlled for quality, trimmed and mapped to the reference mm10 genome using STAR (Dobin et al., 2013).
RNA-seq: The identity of reads was identified through FeatureCount (Liao et al., 2014).
RNA-seq: Differentially expressed genes were identified using DESeq2 (Love et al., 2014).
ChIP seq: Raw sequencing data controlled for quality, trimmed and mapped to the reference mm10 genome using Bowtie2 (Langmead B et al., 2012).
ChIP-seq: PCR duplicates were removed using sambamba (Tarasov et al., 2015)
ChIP-seq: coverage of ChIP and input was calculated and compared using deeptools bamCoverage and bamCompare (Ramirez et al., 2016)
Genome_build: mm10

growth_protocol: pericytes were extracted from the adult brain and maintained in Pericyte medium (ScienCell 1201) with the appropriate growth factors

extract_protocol:
RNA from cultured pericytes, whole E14.5 brains and from neural cells was isolated using the Qiagen mini kit (#74104), while RNA from pericytes, endothelial cells and microglia was extracted using the Qiagen miRNeasy Micro kit (#1071023).
Libraries for RNA-seq of cultured pericytes, whole E14.5 brains and the neural population were prepared using the Illumina TruSeq library preparation kit. For pericytes, endothelial cells and microglia, cDNA was prepared from isolated RNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech 634891). Libraries were prepared using the Nextera XT DNA library preparation kit (Illumina FC-131-1096) and sequenced on the HiSeq Hiseq 3000 or NextSeq 500.
ChIP and library preparation for IP DNA was undertaken using the RELACS protocol (Arrigoni et al. 2018 Communications Biology)

treatment_protocol: FA treatment (FA were conjugated with BSA before application): 200 μM C14:0, 200 μM C16:0, 20 μM C20:0 and 10 μM C24:0. Vehicle: ethanol + BSA.

value: neural cells

tag: genotype/variation

value: Mof nKO

tag: antibody


title: Control rep2


title: 15: DMSO

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

country: Canada

institute: Université de Montréal

data_processing:
Raw Count Matrix was obtained from the standard workflow used at The McGill University and Génome Québec Innovation Centre
Features with at least one count per million (CPM) were kept prior to transformation.
Raw Counts were transformed into log2-CPM values using the voom method from the limma Bioconductor R package.
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with features as rows. First column is the feature ID and each subsequent column represent one sample.

source_name: PBMC

growth_protocol: PBMC sorted CCR6+ T-cells stimulated via the TCR for 3 days and cultured in the presence/absence of T0070907 for additional 18 hours

extract_protocol:
RNA extracted with RNeasy Mini kit plus (QIAGEN).
cDNA libraries and RNA-seq were performed by The McGill University and Génome Québec Innovation Centre, Montreal, QC. 100 bp paired-end sequencing was performed on an Illumina-Hiseq (depth was above 150 million reads).

tag: tissue

value: PBMC sorted CCR6+ T-cells

tag: barcode

tag: lot

tag: stimulation

value: DMSO

tag: randomization code

value: Patient 8


title: Nst_2592_Type1_batch1

description:
Glioblastoma tumor tissue
9445918004_D


title: NG2_3989_Type2_batch2

description:
Glioblastoma tumor tissue
9445918017_E


title: Nst_4827_Type1_batch2

description:
Glioblastoma tumor tissue
9445918035_E


title: 5: DMSO

treatment_protocol: CCR6+ T-cells stimulated via the TCR for 3 days and cultured in the presence/absence of T0070907 for additional 18 hours

value: Patient 3


title: 16: T007


title: 3: DMSO

value: Patient 2


title: M621_KO_input

description:
FACS isolated using EMBRACE technique
M621_KO_panH3.filtered.log2ratio.over_M621_KO_input.bw
M621_KO_H4K16ac.filtered.log2ratio.over_M621_KO_input.bw


title: WT_ADV

tag: strain

tag: genotype


title: 10: T007

value: Patient 5


title: M622_WT_input

description:
FACS isolated using EMBRACE technique
M622_WT_panH3.filtered.log2ratio.over_M622_WT_input.bw
M622_WT_H4K16ac.filtered.log2ratio.over_M622_WT_input.bw

value: wild type


title: M663_KO_input

description:
FACS isolated using EMBRACE technique
M663_KO_panH3.filtered.log2ratio.over_M663_KO_input.bw
M663_KO_H4K16ac.filtered.log2ratio.over_M663_KO_input.bw


title: NG2_2898_Type2_batch1

description:
Glioblastoma tumor tissue
9445833012_D


title: NG2_3112_Type2_batch1

description:
Glioblastoma tumor tissue
9445833012_A


title: 12: T007

value: Patient 6


title: Cre172_WT_input

description:
FACS isolated using EMBRACE technique
Cre172_WT_panH3.filtered.log2ratio.over_Cre172_WT_input.bw
Cre172_WT_H4K16ac.filtered.log2ratio.over_Cre172_WT_input.bw

value: Cre control


title: 14: T007

value: Patient 7


title: Cre173_WT_input

description:
FACS isolated using EMBRACE technique
Cre173_WT_panH3.filtered.log2ratio.over_Cre173_WT_input.bw
Cre173_WT_H4K16ac.filtered.log2ratio.over_Cre173_WT_input.bw


title: M662_KO_panH3

description:
FACS isolated using EMBRACE technique
M662_KO_panH3.filtered.log2ratio.over_M662_KO_input.bw

tag: antibody vendor


title: 6: T007


title: M663_KO_panH3

description:
FACS isolated using EMBRACE technique
M663_KO_panH3.filtered.log2ratio.over_M663_KO_input.bw


title: 8: T007

value: Patient 4


title: 2: T007

value: Patient 1


title: 7: DMSO


title: Cre173_WT_panH3

description:
FACS isolated using EMBRACE technique
Cre173_WT_panH3.filtered.log2ratio.over_Cre173_WT_input.bw


title: M622_WT_panH3

description:
FACS isolated using EMBRACE technique
M622_WT_panH3.filtered.log2ratio.over_M622_WT_input.bw


title: Cre172_WT_panH3

description:
FACS isolated using EMBRACE technique
Cre172_WT_panH3.filtered.log2ratio.over_Cre172_WT_input.bw


title: M666_WT_panH3

description:
FACS isolated using EMBRACE technique
M666_WT_panH3.filtered.log2ratio.over_M666_WT_input.bw


title: 11: DMSO


title: M666_WT_input

description:
FACS isolated using EMBRACE technique
M666_WT_panH3.filtered.log2ratio.over_M666_WT_input.bw
M666_WT_H4K16ac.filtered.log2ratio.over_M666_WT_input.bw


title: 1: DMSO


title: 13: DMSO


title: M662_KO_H4K16ac

description:
FACS isolated using EMBRACE technique
M662_KO_H4K16ac.filtered.log2ratio.over_M662_KO_input.bw

value: Millipore #07-329


title: M621_KO_H4K16ac

description:
FACS isolated using EMBRACE technique
M621_KO_H4K16ac.filtered.log2ratio.over_M621_KO_input.bw


title: M663_KO_H4K16ac

description:
FACS isolated using EMBRACE technique
M663_KO_H4K16ac.filtered.log2ratio.over_M663_KO_input.bw


title: FA-treated_3

description:
cultured primary pericytes
FA-treated_gene_counts.tsv
FA-treated_DESeq_results.tsv

source_name: brain

value: pericytes


title: Cre173_WT_H4K16ac

description:
FACS isolated using EMBRACE technique
Cre173_WT_H4K16ac.filtered.log2ratio.over_Cre173_WT_input.bw


title: FA-treated_2


title: M621_KO_panH3

description:
FACS isolated using EMBRACE technique
M621_KO_panH3.filtered.log2ratio.over_M621_KO_input.bw


title: 4: T007


title: FA-treated_1


title: vehicle_3


title: pericytes_K3_335

description:
FACS isolated using EMBRACE technique
pericytes_kansl3_vs_cre_DEseq_basic_counts_DESeq2.normalized.tsv
pericytes_kansl3_vs_cre_DEseq_basic_DEresults.tsv

value: Kansl3 nKO


title: pericytes_K2_330

description:
FACS isolated using EMBRACE technique
pericytes_kansl2_vs_cre_DEseq_basic_counts_DESeq2.normalized.tsv
pericytes_kansl2_vs_cre_DEseq_basic_DEresults.tsv

value: Kansl2 nKO


title: pericytes_K2_338


title: pericytes_M_577

description:
FACS isolated using EMBRACE technique
pericytes_mof_vs_cre_DEseq_basic_counts_DESeq2.normalized.tsv
pericytes_mof_vs_cre_DEseq_basic_DEresults.tsv

value: Mof nKO


title: M666_WT_H4K16ac

description:
FACS isolated using EMBRACE technique
M666_WT_H4K16ac.filtered.log2ratio.over_M666_WT_input.bw

value: neural cells


title: Cre172_WT_H4K16ac

description:
FACS isolated using EMBRACE technique
Cre172_WT_H4K16ac.filtered.log2ratio.over_Cre172_WT_input.bw


title: vehicle_2


title: pericytes_K3_327


title: pericytes_K3_339


title: vehicle_1


title: 9: DMSO

value: PBMC sorted CCR6+ T-cells

value: DMSO


title: pericytes_K2_328


title: M622_WT_H4K16ac

description:
FACS isolated using EMBRACE technique
M622_WT_H4K16ac.filtered.log2ratio.over_M622_WT_input.bw


title: pericytes_Cre_142

description:
FACS isolated using EMBRACE technique
pericytes_mof_vs_cre_DEseq_basic_counts_DESeq2.normalized.tsv


title: S_M mRNA

city: Wuhan

first: Rong

last: Liu

state: Hubei

address: 185 East Lake Road

department: School of Basic Medical Sciences

institute: Wuhan University

description: male worms from SCID mice

data_processing:
Basecalls performed using illumina CASAVA version 1.8
Raw data of RNA-seq reads were separated based on the barcodes, and processed to remove adapters, poly-N contained reads (N%>10%) and low quality reads (quality score ≤ 20) using custom perl scripts. Because the schistosomes were obtained from experimentally infected mice, we aligned the reads to the mouse genome using Bowtie 2 (v0.12.7) and Tophat (v2.0.0). Non-aligned reads were considered to be S. japonicum-specific. Clean reads were matched to the transcriptomes of S. japonicum (PRJEA34885) in WormBase ParaSite (https://parasite.wormbase.org/ftp.html) and assembled using Trinity with default parameters.
The number of clean reads for each transcript was calculated and then normalized to Reads per Kb per Million reads, which associates read numbers with gene expression levels.
Genome_build: S. japonicum (PRJEA34885)
Supplementary_files_format_and_content: tab-delimited .xls file include FPKM values for each Sample ...

organism: Schistosoma japonicum

source_name: Whole body

extract_protocol:
Worms were recovered by hepatic-portal perfusion with PBS solution at five weeks post infection. The worms were transferred into sterile RPMI 1640 and separated by sex under light microscopy, after which the worms were washed three times with sterile RPMI 1640. Schistosomes were homogenized in a glass homogenizer, and total RNA was isolated using TRIzol reagent according to the manufacturer’s instructions (Invitrogen, USA).
A total amount of 3 μg total RNA per sample was used as input material for the subsequent RNA sample preparations. rRNA was depleted using Epicentre® Ribo-zero rRNA Removal Kit, and sequencing libraries were generated and RNA sequencing was performed according to the manufacturer’s protocol using the NEBNext ® Ultra™ Directional RNA Library Prep Kit for Illumina (Illumina®, NEB, USA). Briefly, first strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of the preferred 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA), and the library quality was assessed on the Agilent Bioanalyzer 2100 system. The libraries were quantified with a Qubit 2.0 Fluorometer (Life Technologies, Grand Island, NY) and sequencing was performed on an Illumina HiseqTM 2500/MiSeq platform (Illumina).

tag: host

value: SCID mouse

tag: worm sex

value: male

tag: Stage

value: five weeks post infection


title: pericytes_Cre_139


title: pericytes_K3_333


title: pericytes_Cre_134


title: neural_K3_366

description:
FACS isolated using EMBRACE technique
neural_kansl3_vs_cre_DEseq_basic_counts_DESeq2.normalized.tsv
neural_kansl3_vs_cre_DEseq_basic_DEresults.tsv


title: pericytes_M_586


title: B_M mRNA

description: male worms from BALB/c mice

value: BALB/c mouse


title: pericytes_M_572


title: sciatic nerve_diabetic rats_rep3

city: Ningbo

first: yiji

last: tu

state: Zhejiang

address: 1059 East Zhongshan Road, Yinzhou District

institute: Ningbo 6th hospital

description: Gene expression in the sciatic nerve of diabetic rats

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242). 1.Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing. 2.Equilibrate water bath to 60°C. 3. add 1.65ug cyanine 3-labeled, linearly amplified cRNA, 11ul 10X Blocking Agent, x ul Nuclease-free water, and 2.2ul 25X Fragmentation Buffer to a 1.5 mL nuclease-free microfuge tube for microarray. 4.Mix well but gently on a vortex mixer. 5.Incubate at 60°C for exactly 30 minutes to fragment RNA. Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction. 7.Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles. 8.Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction. 9.Place sample on ice and load onto the array as soon as possible.  10.Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar. 11.Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner. 12.Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned.  13.Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces. 14.Hand-tighten the clamp onto the chamber. 15.Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles. 16.Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm. 17. Hybridize at 65°C for 17 hours.

scan_protocol: Scanning was perfromed using the Agilent Microarray Scanner (Agilent p/n G2565BA). 1.Assemble the slides into an slide holder. 2.Place assembled slide holders into scanner carousel. 3.Verify scan settings for one-color scans. 4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters. 1.Open the Agilent Feature Extraction (FE) software. 2.Add the images (.tif) to be extracted to the FE Project. 3.Set FE Project Properties. 4.Check the Extraction Set Configuration. 5.Save the FE Project (.fep) by selecting File > Save As and browse for desired location. 6.Select Project > Start Extracting and export data to txt.

organism: Rattus norvegicus

source_name: sciatic nerve,diabetic rats,rep3

label_protocol: RNA was labeled with Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442). Then the labeled RNA was purified by RNeasy Mini Kit (Qiagen p/n 74104) and checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Sixty adult male Sprague-Dawley rats (initial weight 250-300g, from the department of laboratory animal science of Fudan University) were randomly assigned into two groups: control rats (n=30) and diabetic rats (n=30). Diabetes was induced with a single intraperitoneal injection of STZ (55mg/kg). Control rats were performed with a single intraperitoneal injection of 0.9% saline solution.

extract_protocol: RNA was prepared using the TRIzol® Reagent (Invitrogen life technologies). Total RNA clean-up was performed using the RNasey Mini Kit(Qiagen p/n 74104). RNA was quantified by NanoDrop ND-1000. RNA Integrity and gDNA contamination were test by Denaturing Agarose Gel Electrophoresis.

treatment_protocol: Six weeks after diabetes induction, nerve tissue samples (about 1cm long) were harvested from the right sciatic nerve of rats in both groups for immediate total RAN isolation.

value: Sprague-Dawley

value: sciatic nerve

tag: gender

tag: disease state

value: diabetic peripheral neuropathy (DPN)


title: sciatic nerve_diabetic rats_rep2

source_name: sciatic nerve,diabetic rats,rep2


title: sciatic nerve_control rats_rep2

description: Gene expression in the sciatic nerve of control rats

source_name: sciatic nerve,control rats,rep2

value: control


title: sciatic nerve_control rats_rep3

source_name: sciatic nerve,control rats,rep3


title: B_F mRNA

description: female worms from BALB/c mice

value: female


title: S_F mRNA

description: female worms from SCID mice


title: neural_K3_356


title: sciatic nerve_control rats_rep1

source_name: sciatic nerve,control rats,rep1


title: 5Y mock

first: Qiangsong

last: Tong

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time (Mortazavi et al., 2008).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: SH-SY5Y stably transfected with empty vector

growth_protocol: Human neuroblastoma cell line SH-SY5Y was grown in RPMI1640 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The HNF4A-AS1 expression or empty vectors were transfected into tumor cells, and stable cell lines were screened by administration of puromycin.

value: neuroblastoma

tag: cell line

tag: passages

value: stable transfection of empty vector


title: neural_K3_349

tag: genotype/variation

value: Kansl3 nKO


title: neural_K2_351

description:
FACS isolated using EMBRACE technique
neural_kansl2_vs_cre_DEseq_basic_counts_DESeq2.normalized.tsv
neural_kansl2_vs_cre_DEseq_basic_DEresults.tsv

value: Kansl2 nKO


title: neural_K2_345


title: sciatic nerve_diabetic rats_rep1

source_name: sciatic nerve,diabetic rats,rep1


title: neural_M689

description:
FACS isolated using EMBRACE technique
neural_mof_vs_cre_DEseq_basic_counts_DESeq2.normalized.tsv
neural_mof_vs_cre_DEseq_basic_DEresults.tsv

value: Mof nKO


title: neural_K2_348

value: neural cells


title: pericytes_Cre_141

value: pericytes

value: Cre control


title: neural_M646


title: neural_Cre184

description:
FACS isolated using EMBRACE technique
neural_mof_vs_cre_DEseq_basic_counts_DESeq2.normalized.tsv


title: neural_M643


title: EdsRStargocilreplicate2

city: Nashville

first: Clare

last: Laut

state: TN

address: 1161 21st Avenue South  Medical Center North  RM# A5104

institute: Vanderbilt University

description: mid-exponential growth in LB, 10 minute exposure to 10 μg/mL targocil

data_processing:
Quality control checks on raw sequence data from each sample were performed using FastQC (Babraham Bioinformatics, London, UK).
Alignment: Raw reads were imported onto the commercial data analysis platform, Avadis NGS (Strand Scientifics, CA, USA) and mapped to the reference Bacillus anthracis Sterne (NCBI Reference Sequence: NC_005945.1)
Filtering: After quality inspection, the aligned reads were filtered on the basis of read quality metrics where reads with a base quality score less than 30, alignment score less than 95, and mapping quality less than 40 were removed. Remaining reads were then filtered on the basis of their read statistics, where missing mates, translocated, unaligned and flipped reads were removed. The reads list was then filtered to remove duplicates.
Generalization of normalized abundance measurements: Samples were grouped and quantification of transcript abundance was done on this final read list using Trimmed Means of M-values (TMM) (Robinson and Oshlack 2010) as the normalization method. Reference: Robinson MD, Oshlack A. 2010. A scaling normalization method for differential expression analysis of RNA-seq data. Genome biology 11:R25.
Supplementary_files_format_and_content: Comma separate values file containing gene symbol, chromosome, gene start and end, strand, and log2 normalized expression by sample

organism: Bacillus anthracis

source_name: Bacterial culture

growth_protocol: Bacillus anthracis cultures were prepared using colonies streaked to isolation from frozen stocks 2 days prior to the experiment. Overnight cultures in biological triplicate were started from a single colony and grown for sixteen hours in luria broth at 30C with shaking at 180 rpm. Overnight cultures were diluted 1:100 into 3 mL LB in a 15 mL conical tube and grown to mid-exponential phase (6 hr)

extract_protocol:
Cultures were thawed and centrifuged at 7,000 rpm for 10 minutes, supernatants were decanted, RNA was isolated using the RNeasy kit (Qiagen) and DNA was removed using the Turbo DNA-free kit (Invitrogen, Thermo Scientific)
Five hundred ng of total RNA was required for proceeding to downstream RNA-seq applications. First, ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Epidemiology) kit (Illumina, San Diego, CA) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and custom adapter ligation. Post-ligated materials were individually barcoded with unique in-house Genomic Services Lab (GSL) primers and amplified through 12 cycles of PCR. Library quantity was assessed by Qubit 2.0 Fluorometer, and the library quality was estimated by utilizing a DNA High Sense chip on an Caliper Gx (Perkin Elmer). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5nM and pooled equimolar prior to clustering.

treatment_protocol: Cultures were removed from the incubator and treated with 5 microliters of 10 mg/mL targocil (MedChemExpress), for a final concentration of 10 μg/mL, or opened but not treated. After 10 minutes of incubation at 37C with shaking at 180 rpm, cultures were immediately mixed with 10 mL of a 1:1 mixture of ice-cold acetone (JT Baker) and ethanol (Sigma) and frozen at -80C.

value: Sterne

tag: protocol

value: mid-exponential growth in LB, 10 minute exposure to 10 microgram /mL targocil

value: EdsRS -/- strain biological replicate 2


title: EdsRStargocilreplicate3

value: EdsRS -/- strain biological replicate 3


title: EdsRStargocilreplicate1

value: EdsRS -/- strain


title: 5Y HNF4A_AS1

source_name: SH-SY5Y stably transfected with HNF4A-AS1

tag: tissue

value: stable transfection of HNF4A-AS1


title: neural_Cre188


title: EdsRSuntreatedreplicate3

description: mid-exponential growth in LB

value: mid-exponential growth in LB


title: K3-194_endo

description:
FACS isolated using EMBRACE technique
endo_kansl3_vs_cre_DEseq_basic_counts_DESeq2.normalized.tsv
endo_kansl3_vs_cre_DEseq_basic_DEresults.tsv

value: endothelial cells


title: EdsRSuntreatedreplicate1

description: mid-exponential growth in LB


title: WTtargocilreplicate3

value: WT parental strain biological replicate 3


title: K2-206_endo

description:
FACS isolated using EMBRACE technique
endo_kansl2_vs_cre_DEseq_basic_counts_DESeq2.normalized.tsv
endo_kansl2_vs_cre_DEseq_basic_DEresults.tsv


title: neural_Cre183


title: EdsRSuntreatedreplicate2

description: mid-exponential growth in LB


title: K2-188_endo


title: Detection of CNVs

city: Vilnius

first: Živilė

last: Maldžienė

address: Santariškių str. 2

country: Lithuania

institute: Vilnius University

description: Genomic DNA was extracted from the patients’ peripheral blood samples using phenol-chloroform extraction method.

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA extracted from blood was genotyped using HumanCytoSNP-12 BeadChip v2.1 (Illumina).

label: C-Bio and A-DNP

source_name: Blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification reagents (MA1, MA2, MSM). After incubation the amplified DNA was fragmented with fragmentation mix (FMS), precipitated with isopropanol and precipitation mix (PM1) and resuspended in hybridization buffer (RA1).

value: Female

value: Blood

value: syndromic intellectual disability


title: WTuntreatedreplicate2

description: mid-exponential growth in LB

value: WT parental strain biological replicate 2


title: K3-245_endo

value: Kansl3 nKO


title: K3-257_endo


title: WTtargocilreplicate1

value: WT parental strain


title: WTuntreatedreplicate3

description: mid-exponential growth in LB


title: WTuntreatedreplicate1

description: mid-exponential growth in LB


title: K2-196_endo

value: Kansl2 nKO


title: WTtargocilreplicate2


title: M430_endo

description:
FACS isolated using EMBRACE technique
endo_mof_vs_cre_DEseq_basic_counts_DESeq2.normalized.tsv
endo_mof_vs_cre_DEseq_basic_DEresults.tsv

value: Mof nKO


title: Cre91_endo

description:
FACS isolated using EMBRACE technique
endo_mof_vs_cre_DEseq_basic_counts_DESeq2.normalized.tsv

value: Cre control


title: Cre130_endo


title: Cre94_endo


title: Cre89_endo


title: M432_endo


title: Placenta_normal_rep3

city: Shenzhen

first: Jiansheng

last: Xie

address: Medical genetic center, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen 518000, Guangdong province, China

description: Gene expression of normal placenta

hyb_protocol: 1 ug of each labeled cRNA was fragmented by adding 5 ul 10 x Blocking Agent and 1 ul of 25 x Fragmentation Buffer, then heated the mixture at 60 Â°C for 30 min, finally 25 ul 2 x GE Hybridization buffer was added to dilute the labeled cRNA. 50 ul of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65 Â°C in an Agilent Hybridization Oven.

scan_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array V2 (8x15K, Arraystar). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package.

source_name: Placenta,normal,replicate 3

label_protocol: total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: Total RNA was extracted from placenta by using TRIzol Reagent (Invitrogen, USA) according to the manufacture protocol. The purity and concentration of RNA was evaluated with the NanoDrop ND-1000 (Thermo Fisher Scientific, Wilmington, DE).

value: Placenta

tag: phenotype

value: normal


title: Placenta_FGR_rep3

institute: Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University

description: Gene expression of FGR placenta

source_name: Placenta,FGR,replicate 3

value: fetal growth restriction


title: M296_endo


title: Placenta_normal_rep2

description: Gene expression of normal placenta

source_name: Placenta,normal,replicate 2


title: M292_endo


title: Placenta_FGR_rep2

description: Gene expression of FGR placenta

source_name: Placenta,FGR,replicate 2


title: Placenta_normal_rep1

description: Gene expression of normal placenta

source_name: Placenta,normal,replicate 1


title: LK2763

status: Public on Mar 30 2020

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

institute: Toray industries inc

description:
SH83160_Cell2
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 undetEsophageal Cancerted) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

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.).

value: Lung cancer, post-operation

tag: Sex

value: Male

tag: age

value: serum


title: LK2761

description:
SH83159_Cell4
miRNA


title: LK2760

description:
SH83159_Cell3
miRNA


title: LK2766

description:
SH87J13_Cell4
miRNA


title: LK2764

description:
SH83160_Cell3
miRNA


title: LK2758

description:
SH83159_Cell1
miRNA


title: LK2747

description:
SH83155_Cell2
miRNA


title: LK2762

description:
SH83160_Cell1
miRNA


title: Placenta_FGR_rep1

description: Gene expression of FGR placenta

source_name: Placenta,FGR,replicate 1


title: LK2756

description:
SH87J13_Cell3
miRNA


title: LK2759

description:
SH83159_Cell2
miRNA


title: LK2753

description:
SH87J13_Cell2
miRNA


title: LK2765

description:
SH83160_Cell4
miRNA


title: LK2755

description:
SH83157_Cell2
miRNA


title: LK2750

description:
SH83156_Cell1
miRNA


title: LK2749

description:
SH83557_Cell4
miRNA


title: LK2752

description:
SH83156_Cell3
miRNA


title: LK2738

description:
SH83153_Cell1
miRNA


title: LK2740

description:
SH83153_Cell3
miRNA


title: LK2748

description:
SH83557_Cell3
miRNA


title: LK2745

description:
SH83154_Cell4
miRNA


title: LK2731

description:
SH83150_Cell2
miRNA


title: LK2744

description:
SH83154_Cell3
miRNA


title: LK2746

description:
SH83155_Cell1
miRNA


title: LK2720

description:
SH83147_Cell3
miRNA


title: LK2751

description:
SH87J13_Cell1
miRNA


title: LK2732

description:
SH83150_Cell3
miRNA


title: LK2743

description:
SH83557_Cell2
miRNA


title: LK2754

description:
SH83157_Cell1
miRNA


title: LK2741

description:
SH83153_Cell4
miRNA


title: LK2729

description:
SH83149_Cell4
miRNA


title: LK2739

description:
SH83153_Cell2
miRNA


title: LK2736

description:
SH83151_Cell3
miRNA


title: LK2726

description:
SH83149_Cell1
miRNA


title: LK2728

description:
SH83149_Cell3
miRNA


title: LK2734

description:
SH83151_Cell1
miRNA


title: LK2725

description:
SH83148_Cell4
miRNA


title: LK2719

description:
SH83147_Cell2
miRNA


title: LK2723

description:
SH83148_Cell2
miRNA


title: LK2721

description:
SH83147_Cell4
miRNA


title: LK2730

description:
SH83150_Cell1
miRNA


title: LK2737

description:
SH83151_Cell4
miRNA


title: LK2722

description:
SH83148_Cell1
miRNA


title: LK2714

description:
SH83146_Cell1
miRNA


title: LK2727

description:
SH83149_Cell2
miRNA


title: LK2718

description:
SH83147_Cell1
miRNA


title: LK2717

description:
SH83146_Cell4
miRNA


title: LK2735

description:
SH83151_Cell2
miRNA


title: LK2711

description:
SH83145_Cell2
miRNA


title: LK2733

description:
SH83150_Cell4
miRNA


title: LK2713

description:
SH83145_Cell4
miRNA


title: LK2702

description:
SH83142_Cell1
miRNA


title: LK2710

description:
SH83145_Cell1
miRNA


title: LK2716

description:
SH83146_Cell3
miRNA


title: LK2704

description:
SH83142_Cell3
miRNA


title: LK2697

description:
SH83139_Cell4
miRNA


title: LK2693

description:
SH83138_Cell4
miRNA


title: LK2703

description:
SH83142_Cell2
miRNA


title: LK2709

description:
SH83144_Cell4
miRNA


title: LK2701

description:
SH83141_Cell4
miRNA


title: LK2700

description:
SH83141_Cell3
miRNA


title: LK2708

description:
SH83144_Cell3
miRNA


title: LK2705

description:
SH83142_Cell4
miRNA


title: LK2699

description:
SH83141_Cell2
miRNA


title: LK2691

description:
SH83138_Cell2
miRNA


title: LK2698

description:
SH83141_Cell1
miRNA


title: LK2696

description:
SH83139_Cell3
miRNA


title: LK2694

description:
SH83139_Cell1
miRNA


title: LK2689

description:
SH83137_Cell4
miRNA


title: LK2688

description:
SH83137_Cell3
miRNA


title: LK2690

description:
SH83138_Cell1
miRNA


title: LK2715

description:
SH83146_Cell2
miRNA


title: LK2686

description:
SH83137_Cell1
miRNA


title: LK2687

description:
SH83137_Cell2
miRNA


title: LK2692

description:
SH83138_Cell3
miRNA


title: LK2695

description:
SH83139_Cell2
miRNA


title: LK2685

description:
SH83135_Cell4
miRNA


title: LK2681

description:
SH83134_Cell4
miRNA


title: LK2679

description:
SH83134_Cell2
miRNA


title: LK2684

description:
SH83135_Cell3
miRNA


title: LK2682

description:
SH83557_Cell1
miRNA


title: LK2665

description:
SH83130_Cell4
miRNA


title: LK2706

description:
SH83144_Cell1
miRNA


title: LK2671

description:
SH83132_Cell2
miRNA


title: LK2678

description:
SH83134_Cell1
miRNA


title: LK2669

description:
SH83131_Cell4
miRNA


title: LK2680

description:
SH83134_Cell3
miRNA


title: LK2676

description:
SH83133_Cell3
miRNA


title: LK2670

description:
SH83132_Cell1
miRNA


title: LK2662

description:
SH83556_Cell4
miRNA


title: LK2661

description:
SH83128_Cell3
miRNA


title: LK2659

description:
SH83128_Cell1
miRNA


title: LK2657

description:
SH83127_Cell3
miRNA


title: LK2653

description:
SH83126_Cell3
miRNA


title: LK2668

description:
SH83131_Cell3
miRNA


title: LK2651

description:
SH83126_Cell1
miRNA


title: LK2674

description:
SH83133_Cell1
miRNA


title: LK2667

description:
SH83131_Cell2
miRNA


title: LK2663

description:
SH83130_Cell2
miRNA


title: LK2673

description:
SH83132_Cell4
miRNA


title: LK2666

description:
SH83131_Cell1
miRNA


title: LK2646

description:
SH83124_Cell4
miRNA


title: LK2647

description:
SH83125_Cell1
miRNA


title: LK2650

description:
SH83125_Cell4
miRNA


title: LK2658

description:
SH83127_Cell4
miRNA


title: LK2639

description:
SH83123_Cell1
miRNA


title: LK2656

description:
SH83127_Cell2
miRNA


title: LK2660

description:
SH83128_Cell2
miRNA


title: LK2655

description:
SH83127_Cell1
miRNA


title: LK2627

description:
SH83120_Cell1
miRNA


title: LK2629

description:
SH83120_Cell3
miRNA


title: LK2643

description:
SH83124_Cell1
miRNA


title: LK2631

description:
SH83121_Cell1
miRNA


title: LK2622

description:
SH83118_Cell4
miRNA


title: LK2642

description:
SH83123_Cell4
miRNA


title: LK2648

description:
SH83125_Cell2
miRNA


title: LK2652

description:
SH83126_Cell2
miRNA


title: LK2641

description:
SH83123_Cell3
miRNA


title: LK2649

description:
SH83125_Cell3
miRNA


title: LK2654

description:
SH83126_Cell4
miRNA


title: LK2612

description:
SH83115_Cell2
miRNA


title: LK2645

description:
SH83124_Cell3
miRNA


title: LK2637

description:
SH83122_Cell3
miRNA


title: LK2638

description:
SH83122_Cell4
miRNA


title: LK2623

description:
SH83119_Cell1
miRNA


title: LK2613

description:
SH83115_Cell3
miRNA


title: LK2644

description:
SH83124_Cell2
miRNA


title: LK2620

description:
SH83118_Cell2
miRNA


title: LK2640

description:
SH83123_Cell2
miRNA


title: LK2636

description:
SH83122_Cell2
miRNA


title: LK2624

description:
SH83119_Cell2
miRNA


title: LK2617

description:
SH83117_Cell3
miRNA


title: LK2632

description:
SH83121_Cell2
miRNA


title: LK2630

description:
SH83120_Cell4
miRNA


title: LK2618

description:
SH83117_Cell4
miRNA


title: LK2621

description:
SH83118_Cell3
miRNA


title: LK2625

description:
SH83556_Cell3
miRNA


title: LK2609

description:
SH83114_Cell3
miRNA


title: LK2635

description:
SH83122_Cell1
miRNA


title: LK2628

description:
SH83120_Cell2
miRNA


title: LK2633

description:
SH83121_Cell3
miRNA


title: LK2614

description:
SH83115_Cell4
miRNA


title: LK2615

description:
SH83117_Cell1
miRNA


title: LK2602

description:
SH83112_Cell4
miRNA


title: LK2593

description:
SH83108_Cell3
miRNA


title: LK2596

description:
SH83111_Cell2
miRNA


title: LK2611

description:
SH83115_Cell1
miRNA


title: LK2604

description:
SH83113_Cell2
miRNA


title: LK2616

description:
SH83117_Cell2
miRNA


title: LK2683

description:
SH83135_Cell2
miRNA


title: LK2607

description:
SH83114_Cell1
miRNA


title: LK2626

description:
SH83119_Cell4
miRNA


title: LK2757

description:
SH83157_Cell4
miRNA


title: LK2608

description:
SH83114_Cell2
miRNA


title: LK2599

description:
SH83112_Cell1
miRNA


title: LK2610

description:
SH83114_Cell4
miRNA


title: LK2595

description:
SH83111_Cell1
miRNA


title: LK2724

description:
SH83148_Cell3
miRNA


title: LK2600

description:
SH83112_Cell2
miRNA


title: LK2592

description:
SH83108_Cell2
miRNA


title: LK2672

description:
SH83132_Cell3
miRNA


title: LK2677

description:
SH83133_Cell4
miRNA


title: LK2601

description:
SH83112_Cell3
miRNA


title: LK2664

description:
SH83130_Cell3
miRNA


title: LK2619

description:
SH83118_Cell1
miRNA


title: LK2594

description:
SH83108_Cell4
miRNA


title: LK2603

description:
SH83113_Cell1
miRNA


title: LK2742

description:
SH83154_Cell1
miRNA


title: LK2589

description:
SH83107_Cell3
miRNA


title: LK2712

description:
SH83145_Cell3
miRNA


title: LK2606

description:
SH83113_Cell4
miRNA


title: LK2590

description:
SH83107_Cell4
miRNA


title: LK2675

description:
SH83133_Cell2
miRNA


title: LK2605

description:
SH83113_Cell3
miRNA


title: LK2634

description:
SH83121_Cell4
miRNA


title: LK2598

description:
SH83111_Cell4
miRNA


title: LK2588

description:
SH83107_Cell2
miRNA


title: LK2707

description:
SH83144_Cell2
miRNA


title: LK2591

description:
SH83108_Cell1
miRNA


title: XB1000

description:
SH55R11_Cell3
miRNA

value: Non-cancer control


title: LK2587

description:
SH83107_Cell1
miRNA


title: XB0993

description:
SH55R08_Cell4
miRNA


title: XB0990

description:
SH55R08_Cell1
miRNA


title: XB0999

description:
SH55R11_Cell2
miRNA


title: XB0995

description:
SH55R09_Cell2
miRNA


title: XB0989

description:
SH55R06_Cell4
miRNA


title: XB0992

description:
SH55R08_Cell3
miRNA


title: XB0998

description:
SH56N41_Cell1
miRNA


title: XB0994

description:
SH56N41_Cell2
miRNA


title: XB0997

description:
SH55R09_Cell4
miRNA


title: XB0991

description:
SH55R08_Cell2
miRNA


title: XB0983

description:
SH55R05_Cell2
miRNA


title: XB0988

description:
SH55R06_Cell3
miRNA


title: XB0987

description:
SH55R06_Cell2
miRNA


title: XB0986

description:
SH56N41_Cell3
miRNA


title: XB0985

description:
SH55R05_Cell4
miRNA


title: LK2597

description:
SH83111_Cell3
miRNA


title: XB0996

description:
SH55R09_Cell3
miRNA


title: XB0982

description:
SH55R05_Cell1
miRNA


title: XB0977

description:
SH55M67_Cell4
miRNA


title: XB0978

description:
SH55R01_Cell1
miRNA


title: XB0980

description:
SH55R01_Cell3
miRNA


title: XB0979

description:
SH55R01_Cell2
miRNA


title: XB0981

description:
SH55R01_Cell4
miRNA


title: XB0973

description:
SH55M66_Cell4
miRNA


title: XB0972

description:
SH55M66_Cell3
miRNA


title: XB0975

description:
SH55M67_Cell2
miRNA


title: XB0974

description:
SH56N41_Cell4
miRNA


title: XB0971

description:
SH55M66_Cell2
miRNA


title: XB0970

description:
SH55M66_Cell1
miRNA


title: XB0984

description:
SH55R05_Cell3
miRNA


title: XB0967

description:
SH55M65_Cell2
miRNA


title: XB0969

description:
SH55M65_Cell4
miRNA


title: XB0964

description:
SH55M64_Cell3
miRNA


title: XB0963

description:
SH55M64_Cell2
miRNA


title: XB0968

description:
SH55M65_Cell3
miRNA


title: XB0966

description:
SH55M65_Cell1
miRNA


title: XB0965

description:
SH55M64_Cell4
miRNA


title: XB0962

description:
SH56N43_Cell1
miRNA


title: XB0976

description:
SH55M67_Cell3
miRNA


title: XB0956

description:
SH55M62_Cell3
miRNA


title: XB0953

description:
SH55M61_Cell4
miRNA


title: XB0952

description:
SH55M61_Cell3
miRNA


title: XB0960

description:
SH55M63_Cell3
miRNA


title: XB0958

description:
SH55M63_Cell1
miRNA


title: XB0959

description:
SH55M63_Cell2
miRNA


title: XB0954

description:
SH55M62_Cell1
miRNA


title: XB0950

description:
SH55M61_Cell1
miRNA


title: XB0957

description:
SH55M62_Cell4
miRNA


title: XB0955

description:
SH56N43_Cell2
miRNA


title: XB0949

description:
SH55M60_Cell4
miRNA


title: XB0951

description:
SH55M61_Cell2
miRNA


title: XB0948

description:
SH55M60_Cell3
miRNA


title: XB0946

description:
SH55M60_Cell1
miRNA


title: XB0945

description:
SH55M58_Cell4
miRNA


title: XB0947

description:
SH55M60_Cell2
miRNA


title: XB0961

description:
SH55M63_Cell4
miRNA


title: XB0943

description:
SH55M58_Cell2
miRNA


title: XB0944

description:
SH55M58_Cell3
miRNA


title: XB0942

description:
SH55M58_Cell1
miRNA


title: XB0941

description:
SH55M49_Cell4
miRNA


title: XB0940

description:
SH55M49_Cell3
miRNA


title: XB0934

description:
SH55M48_Cell1
miRNA


title: XB0938

description:
SH55M49_Cell1
miRNA


title: XB0939

description:
SH55M49_Cell2
miRNA


title: XB0932

description:
SH55M45_Cell3
miRNA


title: XB0933

description:
SH55M45_Cell4
miRNA


title: XB0931

description:
SH55M45_Cell2
miRNA


title: XB0929

description:
SH55M43_Cell4
miRNA


title: XB0928

description:
SH55M43_Cell3
miRNA


title: XB0927

description:
SH55M43_Cell2
miRNA


title: XB0924

description:
SH55M40_Cell3
miRNA


title: XB0925

description:
SH55M40_Cell4
miRNA


title: XB0923

description:
SH55M40_Cell2
miRNA


title: XB0926

description:
SH55M43_Cell1
miRNA


title: XB0922

description:
SH55M40_Cell1
miRNA


title: XB0917

description:
SH55M30_Cell4
miRNA


title: XB0937

description:
SH55M48_Cell4
miRNA


title: XB0914

description:
SH55M30_Cell1
miRNA


title: XB0913

description:
SH55M23_Cell4
miRNA


title: XB0936

description:
SH55M48_Cell3
miRNA


title: XB0921

description:
SH55M35_Cell4
miRNA


title: XB0911

description:
SH56N38_Cell4
miRNA


title: XB0912

description:
SH55M23_Cell3
miRNA


title: XB0915

description:
SH55M30_Cell2
miRNA


title: XB0920

description:
SH55M35_Cell3
miRNA


title: XB0930

description:
SH55M45_Cell1
miRNA


title: XB0910

description:
SH55M23_Cell1
miRNA


title: XB0909

description:
SH55M22_Cell4
miRNA


title: XB0908

description:
SH55M22_Cell3
miRNA


title: XB0907

description:
SH55M22_Cell2
miRNA


title: XB0918

description:
SH55M35_Cell1
miRNA


title: XB0919

description:
SH55M35_Cell2
miRNA


title: XB0906

description:
SH55M22_Cell1
miRNA


title: XB0916

description:
SH55M30_Cell3
miRNA


title: XB0902

description:
SH55M19_Cell1
miRNA


title: XB0904

description:
SH55M19_Cell3
miRNA


title: XB0899

description:
SH56N39_Cell1
miRNA


title: XB0903

description:
SH55M19_Cell2
miRNA


title: XB0900

description:
SH55M18_Cell3
miRNA


title: XB0888

description:
SH55M15_Cell3
miRNA


title: XB0885

description:
SH56827_Cell2
miRNA


title: XB0890

description:
SH56827_Cell1
miRNA


title: XB0892

description:
SH56N40_Cell3
miRNA


title: XB0897

description:
SH56N39_Cell3
miRNA


title: XB0887

description:
SH55M15_Cell2
miRNA


title: XB0886

description:
SH55M15_Cell1
miRNA


title: XB0894

description:
SH56N40_Cell1
miRNA


title: XB0895

description:
SH55M17_Cell2
miRNA


title: XB0889

description:
SH55M15_Cell4
miRNA


title: XB0884

description:
SH56827_Cell3
miRNA


title: XB0896

description:
SH56N39_Cell4
miRNA


title: XB0893

description:
SH56N40_Cell2
miRNA


title: XB0883

description:
SH55M14_Cell2
miRNA


title: XB0905

description:
SH55M19_Cell4
miRNA


title: XB0901

description:
SH55M18_Cell4
miRNA


title: XB0898

description:
SH56N39_Cell2
miRNA


title: XB0882

description:
SH55M14_Cell1
miRNA


title: XB0879

description:
SH55M13_Cell2
miRNA


title: XB0880

description:
SH55M13_Cell3
miRNA


title: XB0876

description:
SH56827_Cell4
miRNA


title: XB0878

description:
SH55M13_Cell1
miRNA


title: XB0877

description:
SH55M09_Cell4
miRNA


title: XB0875

description:
SH56828_Cell1
miRNA


title: XB0871

description:
SH55M08_Cell2
miRNA


title: XB0873

description:
SH55M08_Cell4
miRNA


title: XB0874

description:
SH55M09_Cell1
miRNA


title: XB0881

description:
SH55M13_Cell4
miRNA


title: XB0935

description:
SH55M48_Cell2
miRNA


title: XB0865

description:
SH56828_Cell2
miRNA


title: XB0863

description:
SH55M05_Cell2
miRNA


title: XB0862

description:
SH55M05_Cell1
miRNA


title: XB0864

description:
SH55M05_Cell3
miRNA


title: XB0867

description:
SH55M06_Cell2
miRNA


title: XB0866

description:
SH55M06_Cell1
miRNA


title: XB0872

description:
SH55M08_Cell3
miRNA


title: XB0870

description:
SH55M08_Cell1
miRNA


title: XB0868

description:
SH55M06_Cell3
miRNA


title: XB0860

description:
SH56224_Cell3
miRNA


title: XB0856

description:
SH55M01_Cell3
miRNA


title: XB0859

description:
SH56224_Cell2
miRNA


title: XB0855

description:
SH55M01_Cell2
miRNA


title: XB0848

description:
SH56407_Cell3
miRNA


title: XB0849

description:
SH56407_Cell4
miRNA


title: XB0858

description:
SH56224_Cell1
miRNA


title: XB0853

description:
SH56824_Cell4
miRNA


title: XB0851

description:
SH56824_Cell2
miRNA


title: XB0850

description:
SH56824_Cell1
miRNA


title: XB0854

description:
SH56828_Cell4
miRNA


title: XB0852

description:
SH56824_Cell3
miRNA


title: XB0869

description:
SH55M06_Cell4
miRNA


title: XB0861

description:
SH56224_Cell4
miRNA


title: XB0847

description:
SH56407_Cell2
miRNA


title: XB0846

description:
SH56407_Cell1
miRNA


title: XB0845

description:
SH55L25_Cell4
miRNA


title: XB0844

description:
SH55L25_Cell3
miRNA


title: XB0843

description:
SH55L25_Cell2
miRNA


title: XB0857

description:
SH56828_Cell3
miRNA


title: XB0842

description:
SH55L25_Cell1
miRNA


title: XB0840

description:
SH55R30_Cell3
miRNA


title: XB0838

description:
SH55R30_Cell1
miRNA


title: XB0837

description:
SH56801_Cell4
miRNA


title: XB0834

description:
SH56829_Cell1
miRNA


title: XB0835

description:
SH56801_Cell2
miRNA


title: XB0825

description:
SH55L24_Cell4
miRNA


title: XB0833

description:
SH55M68_Cell4
miRNA


title: XB0831

description:
SH55M68_Cell2
miRNA


title: XB0830

description:
SH55M68_Cell1
miRNA


title: XB0832

description:
SH55M68_Cell3
miRNA


title: XB0827

description:
SH56206_Cell2
miRNA


title: XB0829

description:
SH56206_Cell4
miRNA


title: XB0828

description:
SH56206_Cell3
miRNA


title: XB0822

description:
SH55L24_Cell1
miRNA


title: XB0824

description:
SH55L24_Cell3
miRNA


title: XB0826

description:
SH56206_Cell1
miRNA


title: XB0841

description:
SH55R30_Cell4
miRNA


title: XB0823

description:
SH55L24_Cell2
miRNA


title: XB0821

description:
SH56829_Cell2
miRNA


title: XB0839

description:
SH55R30_Cell2
miRNA


title: XB0836

description:
SH56801_Cell3
miRNA


title: XB0820

description:
SH56829_Cell3
miRNA


title: XB0818

description:
SH56830_Cell1
miRNA


title: XB0819

description:
SH56829_Cell4
miRNA


title: XB0817

description:
SH55L19_Cell4
miRNA


title: XB0811

description:
SH56831_Cell2
miRNA


title: XB0816

description:
SH56830_Cell2
miRNA


title: XB0815

description:
SH56830_Cell3
miRNA


title: XB0813

description:
SH55L18_Cell4
miRNA


title: XB0814

description:
SH56830_Cell4
miRNA


title: XB0810

description:
SH56831_Cell3
miRNA


title: XB0809

description:
SH55L17_Cell4
miRNA


title: XB0808

description:
SH55L17_Cell3
miRNA


title: XB0804

description:
SH56832_Cell2
miRNA


title: XB0805

description:
SH56832_Cell1
miRNA


title: XB0800

description:
SH55L15_Cell3
miRNA


title: XB0802

description:
SH56832_Cell4
miRNA


title: XB0807

description:
SH55L17_Cell2
miRNA


title: XB0803

description:
SH56832_Cell3
miRNA


title: XB0798

description:
SH55L15_Cell1
miRNA


title: XB0801

description:
SH56833_Cell1
miRNA


title: XB0797

description:
SH55L14_Cell4
miRNA


title: XB0795

description:
SH56833_Cell3
miRNA


title: XB0792

description:
SH55L09_Cell3
miRNA


title: XB0793

description:
SH55L09_Cell4
miRNA


title: XB0790

description:
SH56834_Cell1
miRNA


title: XB0791

description:
SH55L09_Cell2
miRNA


title: XB0788

description:
SH56834_Cell3
miRNA


title: XB0789

description:
SH56834_Cell2
miRNA


title: XB0799

description:
SH55L15_Cell2
miRNA


title: XB0785

description:
SH55C64_Cell4
miRNA


title: XB0784

description:
SH55C64_Cell3
miRNA


title: XB0780

description:
SH56834_Cell4
miRNA


title: XB0782

description:
SH55C64_Cell1
miRNA


title: XB0781

description:
SH55C63_Cell4
miRNA


title: XB0783

description:
SH55C64_Cell2
miRNA


title: XB0779

description:
SH55C63_Cell2
miRNA


title: XB0778

description:
SH56835_Cell1
miRNA


title: XB0794

description:
SH56833_Cell4
miRNA


title: XB0777

description:
SH56835_Cell2
miRNA


title: XB0774

description:
SH55C61_Cell1
miRNA


title: XB0787

description:
SH55C65_Cell2
miRNA


title: XB0775

description:
SH56835_Cell4
miRNA


title: XB0776

description:
SH56835_Cell3
miRNA


title: XB0769

description:
SH55C58_Cell4
miRNA


title: XB0806

description:
SH56831_Cell4
miRNA


title: XB0770

description:
SH56836_Cell3
miRNA


title: XB0771

description:
SH56836_Cell2
miRNA


title: XB0768

description:
SH56836_Cell4
miRNA


title: XB0773

description:
SH55C60_Cell4
miRNA


title: XB0767

description:
SH55C58_Cell2
miRNA


title: XB0772

description:
SH56836_Cell1
miRNA


title: XB0766

description:
SH55C58_Cell1
miRNA


title: XB0765

description:
SH55C57_Cell4
miRNA


title: XB0764

description:
SH55C57_Cell3
miRNA


title: XB0763

description:
SH55C57_Cell2
miRNA


title: XB0762

description:
SH55C57_Cell1
miRNA


title: XB0761

description:
SH55C56_Cell4
miRNA


title: XB0760

description:
SH55C56_Cell3
miRNA


title: XB0759

description:
SH55C56_Cell2
miRNA


title: XB0758

description:
SH55C56_Cell1
miRNA


title: XB0757

description:
SH55C55_Cell4
miRNA


title: XB0754

description:
SH55C55_Cell1
miRNA


title: XB0752

description:
SH55C53_Cell3
miRNA


title: XB0753

description:
SH55C53_Cell4
miRNA


title: XB0751

description:
SH55C53_Cell2
miRNA


title: XB0755

description:
SH55C55_Cell2
miRNA


title: XB0749

description:
SH55C52_Cell4
miRNA


title: XB0746

description:
SH55C52_Cell1
miRNA


title: XB0748

description:
SH55C52_Cell3
miRNA


title: XB0737

description:
SH55L28_Cell3
miRNA


title: XB0745

description:
SH55C51_Cell4
miRNA


title: XB0756

description:
SH55C55_Cell3
miRNA


title: XB0736

description:
SH55L28_Cell2
miRNA


title: XB0735

description:
SH55L28_Cell1
miRNA


title: XB0740

description:
SH55L29_Cell2
miRNA


title: XB0744

description:
SH55C51_Cell3
miRNA


title: XB0738

description:
SH55L28_Cell4
miRNA


title: XB0739

description:
SH55L29_Cell1
miRNA


title: XB0743

description:
SH55C51_Cell2
miRNA


title: XB0742

description:
SH55C51_Cell1
miRNA


title: XB0741

description:
SH56N14_Cell1
miRNA


title: XB0786

description:
SH55C65_Cell1
miRNA


title: XB0734

description:
SH55B58_Cell4
miRNA


title: XB0750

description:
SH55C53_Cell1
miRNA


title: XB0747

description:
SH55C52_Cell2
miRNA


title: XB0732

description:
SH55B58_Cell2
miRNA


title: XB0733

description:
SH55B58_Cell3
miRNA


title: XB0728

description:
SH56N14_Cell4
miRNA


title: XB0731

description:
SH55B58_Cell1
miRNA


title: XB0723

description:
SH56N15_Cell4
miRNA


title: XB0725

description:
SH56N15_Cell2
miRNA


title: XB0727

description:
SH56N15_Cell1
miRNA


title: XB0724

description:
SH56N15_Cell3
miRNA


title: XB0726

description:
SH55B56_Cell4
miRNA


title: XB0721

description:
SH55B55_Cell3
miRNA


title: XB0720

description:
SH56N16_Cell1
miRNA


title: XB0722

description:
SH55B55_Cell4
miRNA


title: XB0716

description:
SH54P26_Cell2
miRNA


title: XB0714

description:
SH55B48_Cell4
miRNA


title: XB0719

description:
SH56N16_Cell2
miRNA


title: XB0717

description:
SH54P26_Cell3
miRNA


title: XB0718

description:
SH54P26_Cell4
miRNA


title: XB0710

description:
SH56N16_Cell3
miRNA


title: XB0712

description:
SH55B48_Cell2
miRNA


title: XB0715

description:
SH54P26_Cell1
miRNA


title: XB0730

description:
SH56N14_Cell2
miRNA


title: XB0713

description:
SH55B48_Cell3
miRNA


title: XB0707

description:
SH56N21_Cell2
miRNA


title: XB0708

description:
SH56N21_Cell1
miRNA


title: XB0706

description:
SH55B44_Cell4
miRNA


title: XB0709

description:
SH56N16_Cell4
miRNA


title: XB0704

description:
SH56N21_Cell3
miRNA


title: XB0705

description:
SH55B44_Cell3
miRNA


title: XB0703

description:
SH55B44_Cell1
miRNA


title: XB0729

description:
SH56N14_Cell3
miRNA


title: XB0699

description:
SH56N21_Cell4
miRNA


title: XB0696

description:
SH55B41_Cell2
miRNA


title: XB0695

description:
SH55B41_Cell1
miRNA


title: XB0702

description:
SH55B43_Cell4
miRNA


title: XB0697

description:
SH55B41_Cell3
miRNA


title: XB0701

description:
SH55B43_Cell3
miRNA


title: XB0700

description:
SH55B43_Cell2
miRNA


title: XB0698

description:
SH55B41_Cell4
miRNA


title: XB0694

description:
SH55B40_Cell4
miRNA


title: XB0693

description:
SH55B40_Cell3
miRNA


title: XB0692

description:
SH55B40_Cell2
miRNA


title: XB0711

description:
SH55B48_Cell1
miRNA


title: XB0684

description:
SH55B38_Cell2
miRNA


title: XB0685

description:
SH56N22_Cell2
miRNA


title: XB0686

description:
SH55B38_Cell4
miRNA


title: XB0690

description:
SH55B39_Cell4
miRNA


title: XB0687

description:
SH55B39_Cell1
miRNA


title: XB0689

description:
SH56N22_Cell1
miRNA


title: XB0688

description:
SH55B39_Cell2
miRNA


title: XB0691

description:
SH55B40_Cell1
miRNA


title: XB0683

description:
SH55B38_Cell1
miRNA


title: XB0682

description:
SH55B37_Cell4
miRNA


title: XB0681

description:
SH55B37_Cell3
miRNA


title: XB0677

description:
SH55B36_Cell4
miRNA


title: XB0679

description:
SH55B37_Cell2
miRNA


title: XB0674

description:
SH56N23_Cell1
miRNA


title: XB0680

description:
SH56N43_Cell3
miRNA


title: XB0676

description:
SH55B36_Cell3
miRNA


title: XB0675

description:
SH56N22_Cell4
miRNA


title: XB0673

description:
SH56N23_Cell2
miRNA


title: XB0672

description:
SH55B35_Cell3
miRNA


title: XB0670

description:
SH55B35_Cell1
miRNA


title: XB0671

description:
SH55B35_Cell2
miRNA


title: XB0666

description:
SH55B33_Cell1
miRNA


title: XB0667

description:
SH55B33_Cell2
miRNA


title: XB0669

description:
SH55B33_Cell4
miRNA


title: XB0664

description:
SH55B32_Cell3
miRNA


title: XB0663

description:
SH55B32_Cell2
miRNA


title: XB0662

description:
SH55B32_Cell1
miRNA


title: XB0665

description:
SH55B32_Cell4
miRNA


title: XB0661

description:
SH55B28_Cell4
miRNA


title: XB0660

description:
SH55B28_Cell3
miRNA


title: XB0655

description:
SH55B27_Cell2
miRNA


title: XB0656

description:
SH55B27_Cell3
miRNA


title: XB0654

description:
SH55B27_Cell1
miRNA


title: XB0651

description:
SH55B08_Cell2
miRNA


title: XB0653

description:
SH55B08_Cell4
miRNA


title: XB0668

description:
SH55B33_Cell3
miRNA


title: XB0650

description:
SH55B08_Cell1
miRNA


title: XB0652

description:
SH55B08_Cell3
miRNA


title: XB0649

description:
SH55B07_Cell4
miRNA


title: XB0648

description:
SH55B07_Cell3
miRNA


title: XB0647

description:
SH55B07_Cell2
miRNA


title: XB0640

description:
SH56N23_Cell4
miRNA


title: XB0659

description:
SH55B28_Cell2
miRNA


title: XB0646

description:
SH55B07_Cell1
miRNA


title: XB0645

description:
SH54G09_Cell4
miRNA


title: XB0644

description:
SH54G09_Cell3
miRNA


title: XB0639

description:
SH54G08_Cell2
miRNA


title: XB0638

description:
SH54G08_Cell1
miRNA


title: XB0643

description:
SH54G09_Cell2
miRNA


title: XB0636

description:
SH54G07_Cell3
miRNA


title: XB0637

description:
SH54G07_Cell4
miRNA


title: XB0633

description:
SH54G03_Cell4
miRNA


title: XB0631

description:
SH54G03_Cell2
miRNA


title: XB0634

description:
SH56N24_Cell1
miRNA


title: XB0635

description:
SH54G07_Cell2
miRNA


title: XB0657

description:
SH55B27_Cell4
miRNA


title: XB0658

description:
SH56N23_Cell3
miRNA


title: XB0632

description:
SH54G03_Cell3
miRNA


title: XB0642

description:
SH54G09_Cell1
miRNA


title: XB0630

description:
SH54G03_Cell1
miRNA


title: XB0641

description:
SH54G08_Cell4
miRNA


title: XB0628

description:
SH54E24_Cell3
miRNA


title: XB0629

description:
SH54E24_Cell4
miRNA


title: XB0627

description:
SH54E24_Cell2
miRNA


title: XB0624

description:
SH54E23_Cell3
miRNA


title: XB0625

description:
SH54E23_Cell4
miRNA


title: XB0626

description:
SH54E24_Cell1
miRNA


title: XB0623

description:
SH56N24_Cell2
miRNA


title: XB0620

description:
SH54E22_Cell3
miRNA


title: XB0621

description:
SH54E22_Cell4
miRNA


title: XB0619

description:
SH54E22_Cell2
miRNA


title: XB0618

description:
SH54E22_Cell1
miRNA


title: XB0622

description:
SH54E23_Cell1
miRNA


title: XB0617

description:
SH54E19_Cell4
miRNA


title: XB0616

description:
SH54E19_Cell3
miRNA


title: XB0615

description:
SH54E19_Cell2
miRNA


title: XB0613

description:
SH54E18_Cell4
miRNA


title: XB0614

description:
SH54E19_Cell1
miRNA


title: XB0612

description:
SH54E18_Cell3
miRNA


title: XB0610

description:
SH54E18_Cell1
miRNA


title: XB0605

description:
SH54E16_Cell4
miRNA


title: XB0608

description:
SH54E17_Cell3
miRNA


title: XB0606

description:
SH56N25_Cell1
miRNA


title: XB0602

description:
SH56N25_Cell2
miRNA


title: XB0604

description:
SH54E16_Cell3
miRNA


title: XB0603

description:
SH54E16_Cell2
miRNA


title: XB0597

description:
SH56N26_Cell3
miRNA


title: XB0595

description:
SH56N27_Cell1
miRNA


title: XB0596

description:
SH56N26_Cell4
miRNA


title: XB0600

description:
SH56N25_Cell4
miRNA


title: XB0599

description:
SH56N26_Cell1
miRNA


title: XB0593

description:
SH54E12_Cell4
miRNA


title: XB0592

description:
SH54E12_Cell3
miRNA


title: XB0611

description:
SH54E18_Cell2
miRNA


title: XB0594

description:
SH56N27_Cell2
miRNA


title: XB0607

description:
SH56N24_Cell4
miRNA


title: XB0590

description:
SH56N27_Cell3
miRNA


title: XB0609

description:
SH56N24_Cell3
miRNA


title: XB0585

description:
SH54E09_Cell4
miRNA


title: XB0588

description:
SH54E10_Cell3
miRNA


title: XB0586

description:
SH54E10_Cell1
miRNA


title: XB0584

description:
SH54E09_Cell3
miRNA


title: XB0583

description:
SH54E09_Cell2
miRNA


title: XB0582

description:
SH56N28_Cell1
miRNA


title: XB0589

description:
SH56N27_Cell4
miRNA


title: XB0587

description:
SH54E10_Cell2
miRNA


title: XB0581

description:
SH54E08_Cell4
miRNA


title: XB0601

description:
SH56N25_Cell3
miRNA


title: XB0598

description:
SH56N26_Cell2
miRNA


title: XB0580

description:
SH54E08_Cell3
miRNA


title: XB0591

description:
SH54E12_Cell2
miRNA


title: XB0578

description:
SH54E08_Cell1
miRNA


title: XB0577

description:
SH54E07_Cell4
miRNA


title: XB0576

description:
SH54E07_Cell3
miRNA


title: XB0575

description:
SH54E07_Cell2
miRNA


title: XB0579

description:
SH56N28_Cell2
miRNA


title: XB0574

description:
SH54E07_Cell1
miRNA


title: XB0573

description:
SH54E06_Cell4
miRNA


title: XB0572

description:
SH54E06_Cell3
miRNA


title: XB0571

description:
SH54E06_Cell2
miRNA


title: XB0567

description:
SH54968_Cell2
miRNA


title: XB0570

description:
SH54E06_Cell1
miRNA


title: XB0568

description:
SH54968_Cell3
miRNA


title: XB0566

description:
SH54968_Cell1
miRNA


title: XB0569

description:
SH54968_Cell4
miRNA


title: XB0565

description:
SH54960_Cell4
miRNA


title: XB0563

description:
SH54960_Cell2
miRNA


title: XB0564

description:
SH54960_Cell3
miRNA


title: XB0557

description:
SH54949_Cell4
miRNA


title: XB0560

description:
SH54953_Cell3
miRNA


title: XB0562

description:
SH54960_Cell1
miRNA


title: XB0553

description:
SH54933_Cell4
miRNA


title: XB0554

description:
SH54949_Cell1
miRNA


title: XB0551

description:
SH54933_Cell2
miRNA


title: XB0550

description:
SH54933_Cell1
miRNA


title: XB0549

description:
SH54929_Cell4
miRNA


title: XB0552

description:
SH54933_Cell3
miRNA


title: XB0548

description:
SH54929_Cell3
miRNA


title: XB0547

description:
SH54929_Cell2
miRNA


title: XB0542

description:
SH54928_Cell1
miRNA


title: XB0544

description:
SH54928_Cell3
miRNA


title: XB0543

description:
SH54928_Cell2
miRNA


title: XB0558

description:
SH56N28_Cell3
miRNA


title: XB0561

description:
SH54953_Cell4
miRNA


title: XB0541

description:
SH56N28_Cell4
miRNA


title: XB0545

description:
SH54928_Cell4
miRNA


title: XB0539

description:
SH54927_Cell2
miRNA


title: XB0540

description:
SH54927_Cell3
miRNA


title: XB0538

description:
SH54927_Cell1
miRNA


title: XB0546

description:
SH54929_Cell1
miRNA


title: XB0555

description:
SH54949_Cell2
miRNA


title: XB0537

description:
SH54925_Cell4
miRNA


title: XB0536

description:
SH54925_Cell3
miRNA


title: XB0535

description:
SH54925_Cell2
miRNA


title: XB0534

description:
SH54925_Cell1
miRNA


title: XB0530

description:
SH54921_Cell1
miRNA


title: XB0533

description:
SH56N29_Cell1
miRNA


title: XB0531

description:
SH54921_Cell2
miRNA


title: XB0529

description:
SH54919_Cell4
miRNA


title: XB0527

description:
SH54919_Cell2
miRNA


title: XB0525

description:
SH54917_Cell4
miRNA


title: XB0522

description:
SH54917_Cell1
miRNA


title: XB0521

description:
SH54913_Cell4
miRNA


title: XB0524

description:
SH54917_Cell3
miRNA


title: XB0526

description:
SH54919_Cell1
miRNA


title: XB0514

description:
SH54908_Cell1
miRNA


title: XB0518

description:
SH54913_Cell1
miRNA


title: XB0519

description:
SH54913_Cell2
miRNA


title: XB0517

description:
SH54908_Cell4
miRNA


title: XB0556

description:
SH54949_Cell3
miRNA


title: XB0511

description:
SH54901_Cell2
miRNA


title: XB0513

description:
SH54901_Cell4
miRNA


title: XB0516

description:
SH54908_Cell3
miRNA


title: XB0559

description:
SH54953_Cell2
miRNA


title: XB0510

description:
SH54901_Cell1
miRNA


title: XB0532

description:
SH54921_Cell3
miRNA


title: XB0507

description:
SH54857_Cell2
miRNA


title: XB0528

description:
SH54919_Cell3
miRNA


title: XB0523

description:
SH54917_Cell2
miRNA


title: XB0506

description:
SH54857_Cell1
miRNA


title: XB0520

description:
SH54913_Cell3
miRNA


title: XB0515

description:
SH54908_Cell2
miRNA


title: XB0503

description:
SH54851_Cell2
miRNA


title: XB0504

description:
SH54851_Cell3
miRNA


title: XB0505

description:
SH54851_Cell4
miRNA


title: XB0502

description:
SH54851_Cell1
miRNA


title: XB0501

description:
SH54849_Cell4
miRNA


title: XB0499

description:
SH54849_Cell2
miRNA


title: XB0500

description:
SH54849_Cell3
miRNA


title: XB0512

description:
SH54901_Cell3
miRNA


title: XB0496

description:
SH54847_Cell3
miRNA


title: XB0509

description:
SH54857_Cell4
miRNA


title: XB0497

description:
SH54847_Cell4
miRNA


title: XB0492

description:
SH54845_Cell3
miRNA


title: XB0494

description:
SH54847_Cell1
miRNA


title: XB0493

description:
SH56N29_Cell3
miRNA


title: XB0495

description:
SH54847_Cell2
miRNA


title: XB0485

description:
SH56N29_Cell4
miRNA


title: XB0484

description:
SH54833_Cell3
miRNA


title: XB0481

description:
SH54829_Cell4
miRNA


title: XB0483

description:
SH54833_Cell2
miRNA


title: XB0482

description:
SH54833_Cell1
miRNA


title: XB0491

description:
SH54845_Cell2
miRNA


title: XB0486

description:
SH54837_Cell1
miRNA


title: XB0480

description:
SH56N30_Cell1
miRNA


title: XB0487

description:
SH54837_Cell2
miRNA


title: XB0498

description:
SH56N29_Cell2
miRNA


title: XB0479

description:
SH54829_Cell2
miRNA


title: XB0490

description:
SH54845_Cell1
miRNA


title: XB0489

description:
SH54837_Cell4
miRNA


title: XB0478

description:
SH54829_Cell1
miRNA