title: Col_ChIP_Rep2


title: Col_ChIP_Rep1

status: Public on Aug 03 2020

type: SRA

city: Riverside

first: Xueqing

middle: Maggie

last: Lu

state: CA

address: 3401 Watkins Drive, Genomics, Room 2126

department: Cell Biology

country: USA

institute: University of California, Riverside

library_source: genomic

data_processing:
For ChIP-seq, raw reads quality was first analyzed using FastQC, and any base with a quality score below 25 or N was trimmed using Sickle.  Trimmed reads were then mapped to the A. thaliana genome (TAIR 10) using BWA 0.7.15-r1140 with mem option default parameters. Uniquely mapped reads were further filtered for calculating H3K9me2 coverage in transcript, while unfiltered reads were used for calculating H3K9me2 coverage in transposable elements.
For both RNA-seq,the quality of raw reads was analyzed using FastQC. The first 10 bases and the last base were trimmed. Contaminating adaptor reads, reads that were unpaired, bases below 25 and Ns, and reads shorter than 18 bases are also filtered using Sickle.All trimmed reads were mapped to A. thaliana genome (TAIR 10) using HISAT2 v2.1.0 with a known splice site file, built from Araport annotation file v11, and strand information parameter, --rna-strandness RF. Coverage values for each transcript was calculated using BEDTools with –split, -D, and -S parameters.
For genome browser tracks, read coverage per nucleotide is calculated using BEDTools. Coverage values were then normalized per million mapped reads.
Genome_build: TAIR 10

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Aerial parts of two-weeks old seedlings

growth_protocol: All Arabidopsis seedlings were grown on soil or half-strength Murashige and Skoog (1/2 MS) solid medium containing 1% (w/v) sucrose in a growth chamber (16-h day, 8-h night, 22 °C; 100 μE m-2s-1)

extract_protocol:
For ChIP-seq, chromatin was sonicated and immunoprecipitated with the respective antibody; For RNA-seq, total RNA were isolated using TRIzol reagent, DNA and ribosomal RNA were removed using the Ribo-Zero rRNA Removal Reagents (Plant Leaf)(Epicentre, USA).
ChIP-seq libraries and RNA-seq were prepared using NEBNext Ultra II DNA library prep kit for Illumina (E7645, New England Biolabs) and NEBNext Ultra Directional RNA library prep kit for Illumina (E7420, New England Biolabs) according to the manufacturer’s instruction respectively.

tag: tissue

value: Aerial parts of two-weeks old seedlings


title: input_ibm1_Rep2


title: Non-cancer 3 [SH4ZQ31_Cell1]

type: RNA

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

country: Japan

institute: Toray industries inc

description:
miRNA
XA0417

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.

molecule: total RNA

organism: Homo sapiens

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: serum

tag: Sex

value: F

tag: age

tag: cstage

tag: child-pugh

tag: afp

value: unknown


title: input_WT_Rep2


title: input_WT_Rep1


title: Non-cancer 3 [SH4ZR06_Cell4]

description:
miRNA
XA0465


title: input_edm2_Rep1


title: Non-cancer 3 [SH4ZQ11_Cell2]

description:
miRNA
XA0366


title: input_ibm1_Rep1


title: Non-cancer 3 [SH4ZQ20_Cell4]

description:
miRNA
XA0384


title: Non-cancer 3 [SH4ZQ17_Cell1]

description:
miRNA
XA0373


title: Non-cancer 3 [SH5XE11_Cell4]

description:
miRNA
XA0209


title: Non-cancer 3 [SH5XD51_Cell2]

description:
miRNA
XA0113


title: Non-cancer 3 [SH5XE06_Cell3]

description:
miRNA
XA0186


title: Col_input_Rep1


title: Liver Cirrhosis [SH74L50_Cell3]

description:
miRNA
SR-168


title: H3C_ibm1_Rep1


title: H3C_ibm1_Rep2


title: H3C_edm2_Rep2


title: Chronic hepatitis [SH74L44_Cell2]

description:
miRNA
SL-48

value: M


title: Non-cancer 3 [SH4ZP55_Cell2]

description:
miRNA
XA0294


title: Non-cancer 3 [SH4ZQ36_Cell4]

description:
miRNA
XA0436


title: input_edm2_Rep2


title: Non-cancer 3 [SH4ZQ36_Cell2]

description:
miRNA
XA0434


title: H3C_edm2_Rep1


title: H3C_WT_Rep2


title: Chronic hepatitis [SH74L50_Cell4]

description:
miRNA
SL-323


title: Non-cancer 3 [SH5XE05_Cell3]

description:
miRNA
XA0182


title: Chronic hepatitis [SH74L50_Cell1]

description:
miRNA
SL-341


title: H3C_WT_Rep1


title: H3K9me2_ibm1_Rep2


title: Chronic hepatitis [SH74L49_Cell4]

description:
miRNA
SL-168


title: H3K9me2_edm2_Rep2


title: Chronic hepatitis [SH74L50_Cell2]

description:
miRNA
SL-301


title: Chronic hepatitis [SH74L49_Cell3]

description:
miRNA
SL-165


title: H3K9me2_ibm1_Rep1


title: Chronic hepatitis [SH74L45_Cell3]

description:
miRNA
SL-163


title: Chronic hepatitis [SH74L45_Cell4]

description:
miRNA
SL-166


title: H3K9me2_WT_Rep2


title: H3K9me2_edm2_Rep1


title: H3K9me2_WT_Rep1


title: Worm_daf18_day10

city: Shanghai

first: Xian

last: Xia

address: Yueyang Street

country: China

institute: PICB, CAS

library_source: transcriptomic

data_processing:
The RNA-seq reads were trimmed and mapped to WS256 genome (from Worm Base) for worm data and mm10 genome (from UCSC genome browser) for mouse data, using STAR (version 2.5).
The read counting was implemented by HTseq using annotations from Worm Base and Gencode, for worm and mouse respectively.
The quantification and normalization of reads are conducted by  the R package, DESeq2.
Genome_build: WS256 for worm and mm10 for mouse
Supplementary_files_format_and_content: First column is Gene ID and second column is rlog value as expression level from DESeq2 for each sample.

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole body

extract_protocol:
For RNA-seq sample preparation, worms were collected in 1.5 ml tubes, washed several times with M9 to remove bacteria, RNA was extracted with Trizol reagent according to the manufacture’s instruction. For mouse samples, equal weight tissues were dissected on ice, collected in 1.5 ml tubes, RNA was extracted with Trizol reagent. All RNA samples passed the quality control of RIN > 8 and 18S/28S >1.0. Sequencing were implemented with Illumina HiSeq 2000 system.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole body

tag: strain

value: daf-18-null-allele (ok480)

tag: treatment

value: control

value: adult day 10


title: Chronic hepatitis [SH74L49_Cell2]

description:
miRNA
SL-160


title: Liver Cirrhosis [SH74L49_Cell1]

description:
miRNA
SL-159


title: Worm_daf18_day10_MI

value: MI


title: Worm_N2_day4

value: adult day 4


title: Worm_N2_day10_MI


title: Chronic hepatitis [SH74L45_Cell2]

description:
miRNA
SL-154


title: Chronic hepatitis [SH74L44_Cell4]

description:
miRNA
SL-155


title: Chronic hepatitis [SH74L44_Cell3]

description:
miRNA
SL-157


title: Worm_N2_day10


title: Chronic hepatitis [SH74L45_Cell1]

description:
miRNA
SL-153


title: Non-cancer 1 [SH51861_Cell3]

description:
miRNA
SA0984


title: Non-cancer 1 [SH51857_Cell1]

description:
miRNA
SA0970


title: Non-cancer 1 [SH51861_Cell2]

description:
miRNA
SA0983


title: Non-cancer 1 [SH51860_Cell3]

description:
miRNA
SA0980


title: Non-cancer 1 [SH51849_Cell3]

description:
miRNA
SA0952


title: Non-cancer 1 [SH51854_Cell1]

description:
miRNA
SA0962


title: Non-cancer 1 [SH51841_Cell1]

description:
miRNA
SA0926


title: Mouse_M12_MI_rep2

organism: Mus musculus

source_name: muscle

value: muscle

value: 12 months


title: Non-cancer 1 [SH51840_Cell4]

description:
miRNA
SA0925


title: Non-cancer 1 [SH4YT45_Cell1]

description:
miRNA
SA0854


title: Non-cancer 1 [SH4YT39_Cell3]

description:
miRNA
SA0837


title: Mouse_M12_MI_rep3


title: Non-cancer 1 [SH4YT58_Cell2]

description:
miRNA
SA0899


title: Mouse_M12_MI_rep1


title: Mouse_M12_rep3


title: BT20_shNONO_1

city: Seoul

first: YUNYONG

last: PARK

address: 84 Heukseok-ro

country: South Korea

institute: ChuangAng University

description:
shNONO in BT20 Cell
NONO gene expression profile in breast cancer cell

hyb_protocol: Hyb was done at 58 degree for 18 hrs

scan_protocol: HighScan was used

data_processing:
GenomeStudio was used for data processing and quantile normalization method was used.
Log2 value ((normalized), Raw signal intensity (non-normalized).

source_name: Breast cancer cell

label_protocol: Extracted RNA was amplified and labeled with Amplificatin kit (AMIL1797; Ambion)

growth_protocol: The cells were grown in RPMI1640 media.

extract_protocol: miRvana kit was used for RNA extraction

treatment_protocol: Cells were treated with indicated lenti-viral vector

tag: cell type

value: cancer cell


title: Non-cancer 1 [SH4YT35_Cell1]

description:
miRNA
SA0827


title: Hs578T_shNONO_3

description:
shNONO in Hs578T Cell
NONO gene expression profile in breast cancer cell


title: Hs578T_shNONO_2


title: Non-cancer 1 [SH4YT46_Cell3]

description:
miRNA
SA0860


title: Non-cancer 1 [SH51P36_Cell4]

description:
miRNA
SA0858


title: Non-cancer 1 [SH4YT63_Cell1]

description:
miRNA
SA0914


title: Non-cancer 1 [SH4YT35_Cell4]

description:
miRNA
SA0830


title: Non-cancer 3 [SH5XD35_Cell2]

description:
miRNA
XA0030


title: Mouse_M3_rep3

value: 3 months


title: Non-cancer 3 [SH5XD58_Cell3]

description:
miRNA
XA0140


title: Non-cancer 1 [SH4YT33_Cell4]

description:
miRNA
SA0822


title: Mouse_M3_rep2


title: Non-cancer 1 [SH51P32_Cell2]

description:
miRNA
SA0818


title: Hs578T_shCon_1

description:
shCon in Hs578T Cell
NONO gene expression profile in breast cancer cell


title: Hs578T_shCon_3


title: Mouse_M12_rep2


title: 166_Tig_rep2

city: North Ryde

first: Liping

last: Li

state: Now South Walse

address: 14 Eastern Road

department: Department of Molecular Sciences

country: Australia

institute: Macquarie University

data_processing:
Basecalling and adaptor sequence trimming were processed by commercial sequencing provider
The sequence reads from the 6 RNA-Seq samples were aligned to the A. baumannii AB0057 reference and counted using EDGE-pro (Estimated Degree of Gene Expression in Prokaryotic Genomes)
gene differential expression between the control and experimental samples were analyzed using the DEseq R package
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Acinetobacter baumannii

source_name: Bacterial planktonic cells grown in Müller Hinton broth supplemented with tigecycline at 1/2 MIC

extract_protocol:
The total RNA of each sample was extracted by miRNeasy Mini Kit (QIAGEN, Germany) following the manufacturer’s instructions. Genomic DNA residue was removed by TURBO DNA-freeTM Kit TURBOTM DNase Treatment and Removal Reagents (Ambion Inc., USA).
The resulting gDNA-free total RNA samples were immediately processed for rRNA depletion. rRNA was depleted by using the Ribo-Zero Magnetic kit (bacteria) (Illumina, Inc., USA), following the manufacturer’s instructions. For each sample, 500 ng of rRNA depleted total RNA was used to generate double stranded cDNA library through TruSeq® Stranded Total RNA Sample Preparation kit (Illumina, Inc., USA). The samples were then sequenced through 100 bp paired end (PE) sequencing on Illumina HiSeq2500 platform. Nearly 75 million unique 101 bp reads were obtained from each of the 6 independent A. baumannii 6772166 cultures, representing more than 310-fold genome average coverage (A. baumannii 6772166 chromosome and plasmid size together is around 4 Mb).

treatment_protocol: Three independent A. baumannii 6772166  colonies were suspended and grown in Muller-Hinton (MH, Oxoid) broth with shaking overnight at 37°C. The overnight cultures were diluted 1:100 in fresh MH broth and grown to OD600=0.6. Each of the cultures was then divided into two equal aliquots, with one supplemented with tigecycline (Sigma-Aldrich, USA) of half MIC (2.5μg/ml) and the other without treatment, resulting 6 independent cultures. These 6 cultures were grown further for 30 minutes with shaking at 37°C.

value: tigecycline 1/2 MIC


title: 166_Tig_rep1

value: Bacterial planktonic cells grown in Müller Hinton broth supplemented with tigecycline at 1/2 MIC


title: 166_Tig_rep3


title: 166_NT_rep3

source_name: Bacterial planktonic cells grown in Müller Hinton broth

value: no treatment


title: Non-cancer 1 [SH4YT33_Cell3]

description:
miRNA
SA0821

value: serum


title: Non-cancer 1 [SH51P32_Cell1]

description:
miRNA
SA0817


title: Mouse_M3_rep1


title: Non-cancer 1 [SH4YT34_Cell1]

description:
miRNA
SA0823


title: 166_NT_rep1

value: Bacterial planktonic cells grown in Müller Hinton broth


title: 166_NT_rep2


title: Non-cancer 1 [SH4YT30_Cell3]

description:
miRNA
SA0812

value: F

value: unknown


title: Non-cancer 1 [SH4YT30_Cell1]

description:
miRNA
SA0810

value: M


title: Non-cancer 1 [SH4YT29_Cell2]

description:
miRNA
SA0807


title: BT20_shCon_2

description:
shCon in BT20 Cell
NONO gene expression profile in breast cancer cell


title: Patient 3, 4 Days, DMSO

city: St Louis

first: Lori

last: Setton

state: MO

address: 1 Brookings Drive, Campus box 1097

department: Department of Biomedical Engineering

institute: Washington University in St. Louis

description: P3_4d_DMSO.AATCTGCAGT-ACCTACCAGG.AATCTGCAGT-ACCTACCAGG_S14

data_processing:
FASTQ files were read into Partek Flow software for analysis
Unaligned reads were trimmed based on quality score (minimum quality score, Phred, = 20, minimum read length = 25) before aligned to the whole human genome (hg19) using STAR 2.6.1d. The output of the alignmentt was quantified to the annotation model (Partek E/M; hg19_ensembl_release75_v2)
Within Partek Flow gene counts were calculated and filtered to exclude features where maximum <= 10.0.
Data were subjected to a normalization step per Partek Flow recommendations: counts per million (CPM) and add 1.0E-4
PCA was performed and GSA was conducted based on the factors of timepoint and treatment. FDR step-up was applied to calculate p-value and fold change values were calculated by comparing VP treated to DMSO (VP divided by DMSO). N.B. the average value for the VP treated group (average of the 3 patients) was divided by the average value for the DMSO treated group (average of 3 patients). Model selection criteria = AICc. Differentially expressed genes (fold change greater than or equal to 2 or less than or equal to -2 and with a FDR-adjusted p value <0.05) were analyzed using gene set enrichment. Hierarchical clustering was conducted as well (Clustter distance metric = average linkage; point distance metric = Euclidean; normalization mode = Standarize).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample
Supplementary_files_format_and_content: tab-deliminated text files showing the output of the GSA analysis for comparison of VP treated samples to DMSO control by time point (Total counts, p-value, FDR-step up, Ratio, Fold Change, LSMean)

source_name: Nucleus Pulposus

growth_protocol: NP cells were enzymatically isolated from surgical waste tissue (exempt from IRB review, Washington University Institutional Review Board) as previously described in Gilchrist+, 2011, PLoS One (volume 6, no. 11). Isolated cells were maintained and expanded in tissue culture using Ham's F-12 media supplemented with 1% penicillin/streptomycin and 10% FBS under 5% CO2, atmospheric oxygen at 37 degrees C.

extract_protocol:
At 24 hours, 48 hours, or 4 days, mRNA was extracted using the Rneasy mini kit with DNase I digestion (Qiagen). RNA quality was ensured to be greater than 8 using a Bioanalyzer (Agilent). Ds-cDNA was consructed using Clontech SMARTer Ultra Low RNA kit for Illumina Sequencing. cDNA was fragmented using a Covaris E220 sonicator. cDNA was blunt ended,  an A base added to 3' ends, and then Illumina sequencing adapters ligated to the ends. Ligated fragments were amplified for 12 cycles and run on an Illumina NovaSeq reading 150 bases from both ends to a depth of 30 million reads per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with VP (1 uM) or DMSO control (0.1%) in Ham's F-12 media. VP or vehicle control-containing media was replenished each day during the duration of the culture period.

value: nucleus pulposus

value: 41 year old

value: DMSO

tag: timepoint

value: 4 Days


title: Patient 3, 4 Days, VP

description: P3_4d_VP.AGGTCCATTC-TCAATGAGGT.AGGTCCATTC-TCAATGAGGT_S30

value: VP


title: Non-cancer 1 [SH51P31_Cell2]

description:
miRNA
SA0808


title: Patient 3, 48 Hours, VP

description: P3_48h_VP.CGCTAATTGC-GAAGCAAGCG.CGCTAATTGC-GAAGCAAGCG_S48

value: 48 Hours


title: Patient 3, 48 Hours, DMSO

description: P3_48h_DMSO.CGGACAGCTA-GCCTTCCTCT.CGGACAGCTA-GCCTTCCTCT_S51


title: Patient 3, 24 Hours, DMSO

description: P3_24h_DMSO.CACCGAATCA-CTTAGTCCAA.CACCGAATCA-CTTAGTCCAA_S33

value: 24 Hours


title: Patient 2, 4 Days, DMSO

description: P2_4d_DMSO.AACTGTACGG-ATAACGACGA.AACTGTACGG-ATAACGACGA_S6

value: 38 year old


title: Non-cancer 1 [SH51P28_Cell4]

description:
miRNA
SA0796


title: Non-cancer 1 [SH51P29_Cell2]

description:
miRNA
SA0800


title: Non-cancer 1 [SH51P29_Cell1]

description:
miRNA
SA0797


title: Non-cancer 1 [SH4YT23_Cell1]

description:
miRNA
SA0786


title: Patient 2, 4 Days, VP

description: P2_4d_VP.AATCATCTGG-GAACCACAGG.AATCATCTGG-GAACCACAGG_S13


title: Non-cancer 1 [SH4YT27_Cell1]

description:
miRNA
SA0798


title: Non-cancer 1 [SH51P25_Cell3]

description:
miRNA
SA0790


title: Patient 2, 48 Hours, DMSO

description: P2_48h_DMSO.CGCTGTTGAC-ACGTCTACGA.CGCTGTTGAC-ACGTCTACGA_S49


title: Patient 2, 48 Hours, VP

description: P2_48h_VP.AATGTTCGGA-ACGATTGGCT.AATGTTCGGA-ACGATTGGCT_S18


title: Patient 2, 24 Hours, DMSO

description: P2_24h_DMSO.CCTCTATCTC-CTCATTCTGC.CCTCTATCTC-CTCATTCTGC_S45


title: Non-cancer 1 [SH51P28_Cell1]

description:
miRNA
SA0792


title: Patient 3, 24 Hours, VP

description: P3_24h_VP.AATGCGATGG-GCACACAGCA.AATGCGATGG-GCACACAGCA_S16


title: Patient 2, 24 Hours, VP

description: P2_24h_VP.TCGGAGACCT-AGTAGCTAGT.TCGGAGACCT-AGTAGCTAGT_S67


title: Non-cancer 1 [SH51P28_Cell3]

description:
miRNA
SA0795


title: Patient 1, 4 Days, DMSO

description: P1_4d_DMSO.AGGCGAATTC-TATGACACGT.AGGCGAATTC-TATGACACGT_S29

value: 20 year old


title: Patient 1, 4 Days, VP

description: P1_4d_VP.GCTGAGTTGG-AGTCTGGACG.GCTGAGTTGG-AGTCTGGACG_S55


title: Patient 1, 48 Hours, DMSO

description: P1_48h_DMSO.GTGAAGACAC-CTTAGGCAAC.GTGAAGACAC-CTTAGGCAAC_S61


title: Non-cancer 1 [SH4YT31_Cell1]

description:
miRNA
SA0814


title: Non-cancer 1 [SH4YT09_Cell4]

description:
miRNA
SA0745


title: Non-cancer 1 [SH4YT14_Cell1]

description:
miRNA
SA0750


title: Non-cancer 1 [SH51P24_Cell3]

description:
miRNA
SA0784


title: Non-cancer 1 [SH4YT15_Cell3]

description:
miRNA
SA0756


title: Non-cancer 1 [SH51P22_Cell2]

description:
miRNA
SA0769


title: Non-cancer 1 [SH4YT21_Cell1]

description:
miRNA
SA0778


title: BT20_shNONO_2

description:
shNONO in BT20 Cell
NONO gene expression profile in breast cancer cell

value: cancer cell


title: BT20_shCon_3

description:
shCon in BT20 Cell
NONO gene expression profile in breast cancer cell


title: Hs578T_shCon_2

description:
shCon in Hs578T Cell
NONO gene expression profile in breast cancer cell


title: Patient 1, 48 Hours, VP

description: P1_48h_VP.GCTAACGGCA-GCAACTCCTG.GCTAACGGCA-GCAACTCCTG_S53


title: Patient 1, 24 Hours, DMSO

description: P1_24h_DMSO.CCTCCAGGTA-ATTCACGTGA.CCTCCAGGTA-ATTCACGTGA_S43


title: BT20_shCon_1


title: BT20_shNONO_3


title: Non-cancer 1 [SH4YT18_Cell2]

description:
miRNA
SA0767


title: Non-cancer 1 [SH51P18_Cell4]

description:
miRNA
SA0742


title: Hs578T_shNONO_1

description:
shNONO in Hs578T Cell
NONO gene expression profile in breast cancer cell


title: Patient 1, 24 Hours, VP

description: P1_24h_VP.AACGCACGAG-ATAACCACAC.AACGCACGAG-ATAACCACAC_S5


title: Non-cancer 1 [SH4YT01_Cell3]

description:
miRNA
SA0716


title: Non-cancer 1 [SH4YT01_Cell1]

description:
miRNA
SA0714


title: Non-cancer 1 [SH4YT03_Cell3]

description:
miRNA
SA0724


title: Non-cancer 1 [SH4YT03_Cell1]

description:
miRNA
SA0722


title: Non-cancer 1 [SH4YT02_Cell3]

description:
miRNA
SA0720


title: HD4

city: Rozzano, Milan

first: Emilia Maria Cristina

last: Mazza

address: Via Alessandro Manzoni, 56

country: Italy

institute: Humanitas Clinical and Research Center

data_processing:
Raw sequencing data (bcl-files) were converted to fastq format using the 10x Genomics pipeline Cell Ranger v2.1.1
The cellranger count was run with --transcriptome=refdata-cellranger-GRCh38-1.2.0 for each sample
The outputs of cellranger count for individual samples were concatenated into one matrix  using the “cellranger aggr” pipeline
The raw digital gene expression matrix (UMI counts per gene per cell) was imported in R (version 3.5.1) using Seurat R package (version Seurat_3.0.1)
Genome_build: GRCh38

source_name: Peripheral blood mononuclear cells

extract_protocol:
100,000 FACS-sorted CD95+CD8+ T cells from four healthy donors were resuspended in 1 ml PBS–/– plus 0.04% BSA and washed two times by centrifugation at 450 rcf for 7 min. After the second wash, cells were resuspended in 100 µL and counted with an automatic cell counter (Countess II, Thermo Fisher) to get a precise estimation of total number of cells recovered. Afterwards, about 20,000 cells of each sample were loaded into one channel of the Single Cell Chip A using the Single Cell 3’ v2 reagent kit (10X Genomics) for Gel bead Emulsion generation into the Chromium system. Following capture and lysis, cDNA was synthesized and amplified for 14 cycles by following the manufacturer’s protocol (10X Genomics).
50 ng of the amplified cDNA for each sample were then used to construct sequencing libraries. Sequencing was performed on the NovaSeq 6000 Illumina system following 10X Genomics instruction for reads generation. An average sequencing depth of at least ~50,000 reads/cell was obtained for each sample.

tag: donor

value: healthy donor 4

value: CD95+ CD8+ T cells


title: Non-cancer 1 [SH4YT02_Cell4]

description:
miRNA
SA0721

value: serum


title: Ex7ATRA-posi

city: Kobe City

first: Michiyo

last: Koyanagi-Aoi

address: Chuo-ku, Kusunoki-cho 7-5-1

institute: Kobe University

data_processing:
Raw sequence files (fastq) were aligned to the human genome build 38 (hg38) and mapped to Refseq transcripts by Strand NGS software using default parameters.
All aligned reads were normalized using Transcripts per million (TPM).
TPM values were log2-transformed with an offset value of 1.0. Baseline transformation was not performed.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol, gene ID and TPM values (log2-transformed with an offset value of 1.0) for each Sample.

source_name: Cells differentiated into esophageal-lineage, with ATRA

extract_protocol:
Total RNA was isolated by Trizol reagent (Life Technologies) according to the manufacture's instruction.
RNA libraries were prepared for TrEuSeq Stranded mRNA Sample Preparation Guide (Part#15031047 Rev.3).

value: differentiated cells from hiPSCs

tag: cell line

value: hiPSC line 3AB4


title: Ex7ATRA-nega

source_name: Cells differentiated into esophageal-lineage, without ATRA


title: HD1

value: healthy donor 1


title: HD3

value: healthy donor 3


title: HD2

value: healthy donor 2


title: Ex6ATRA-posi


title: Non-cancer 1 [SH4YE56_Cell1]

description:
miRNA
SA0688

value: F

value: unknown


title: Non-cancer 1 [SH51P19_Cell1]

description:
miRNA
SA0743


title: Ex6ATRA-nega


title: Non-cancer 1 [SH4YJ47_Cell2]

description:
miRNA
SA0699


title: Non-cancer 1 [SH4YE49_Cell2]

description:
miRNA
SA0685


title: Non-cancer 1 [SH4YE34_Cell4]

description:
miRNA
SA0671

value: M


title: Non-cancer 1 [SH4YT03_Cell2]

description:
miRNA
SA0723


title: Ex3ATRA_Nega


title: Non-cancer 1 [SH4YE33_Cell1]

description:
miRNA
SA0664


title: 96    Yg    D

city: Greenville

first: Michelle

middle: L

last: Ratliff

state: NC

address: 600 Moye Blvd, 132 Biotechnology Building

department: Microbiology and Immunology

institute: East Carolina University

data_processing:
Reads aligned to GrCh38 assembly of the human genome using STAR using default parameters
Partek Genomics Suite was run to align reads to perform differenital expression analyses
Genome_build: GrCh38
Supplementary_files_format_and_content: Abundance measurements

source_name: Yg D_peripheral blood HSC

extract_protocol:
Fluidigm C1 single cell platform
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject id

value: Yg D

value: Male

tag: race

value: Caucasian

value: peripheral blood

value: Hematopoietic Stem Cells (HSCs)


title: 95    Yg    D


title: Non-cancer 1 [SH51P15_Cell3]

description:
miRNA
SA0679


title: 94    Yg    D


title: Non-cancer 1 [SH4YE33_Cell2]

description:
miRNA
SA0665


title: Non-cancer 1 [SH4YE40_Cell1]

description:
miRNA
SA0676


title: 93    Yg    D


title: Non-cancer 1 [SH4YE32_Cell3]

description:
miRNA
SA0662


title: Non-cancer 1 [SH4YE32_Cell1]

description:
miRNA
SA0660


title: Non-cancer 1 [SH4YE17_Cell3]

description:
miRNA
SA0658


title: 91    Yg    D


title: Non-cancer 1 [SH4YE17_Cell1]

description:
miRNA
SA0656


title: Non-cancer 1 [SH4YE40_Cell3]

description:
miRNA
SA0678


title: Non-cancer 1 [SH4YE45_Cell4]

description:
miRNA
SA0683


title: Ex3ATRA_Posi


title: 89    Yg    D


title: 88    Yg    D


title: 87    Yg    D


title: 86    Yg    D


title: Non-cancer 1 [SH52223_Cell4]

description:
miRNA
SA0647


title: Non-cancer 1 [SH52224_Cell3]

description:
miRNA
SA0650


title: 85    Yg    D


title: Non-cancer 1 [SH52218_Cell3]

description:
miRNA
SA0638


title: Non-cancer 1 [SH52217_Cell4]

description:
miRNA
SA0635


title: Non-cancer 1 [SH52219_Cell3]

description:
miRNA
SA0642


title: Non-cancer 1 [SH52219_Cell2]

description:
miRNA
SA0641


title: 84    Yg    D


title: Non-cancer 1 [SH52217_Cell1]

description:
miRNA
SA0632


title: 92    Yg    D


title: Non-cancer 1 [SH52167_Cell4]

description:
miRNA
SA0627


title: 80    Yg    D


title: 82    Yg    D


title: Non-cancer 1 [SH52213_Cell2]

description:
miRNA
SA0629


title: Non-cancer 1 [SH52165_Cell4]

description:
miRNA
SA0619


title: Non-cancer 1 [SH52164_Cell2]

description:
miRNA
SA0613


title: 90    Yg    D


title: Non-cancer 1 [SH51P15_Cell2]

description:
miRNA
SA0655


title: 78    Yg    D


title: 77    Yg    D


title: Non-cancer 1 [SH52160_Cell1]

description:
miRNA
SA0608


title: Non-cancer 1 [SH52157_Cell2]

description:
miRNA
SA0605


title: 76    Yg    D


title: Non-cancer 1 [SH52156_Cell1]

description:
miRNA
SA0600


title: 75    Yg    D


title: Non-cancer 1 [SH52152_Cell3]

description:
miRNA
SA0598


title: 83    Yg    D


title: Non-cancer 1 [SH52152_Cell4]

description:
miRNA
SA0599


title: 81    Yg    D


title: Non-cancer 1 [SH52145_Cell3]

description:
miRNA
SA0594


title: Non-cancer 1 [SH52145_Cell2]

description:
miRNA
SA0593


title: 73    Yg    D


title: 71    Yg    D


title: 70    Yg    D


title: 69    Yg    D


title: Non-cancer 1 [SH52134_Cell4]

description:
miRNA
SA0583


title: 79    Yg    D


title: Non-cancer 1 [SH52126_Cell2]

description:
miRNA
SA0565


title: 72    Yg    D


title: Non-cancer 1 [SH52125_Cell3]

description:
miRNA
SA0562


title: 67    Yg    D


title: Non-cancer 1 [SH52123_Cell4]

description:
miRNA
SA0559


title: Mouse_M12_rep1

value: muscle

value: control

value: 12 months


title: 68    Yg    D


title: 66    Yg    D


title: 64    Yg    D


title: 65    Yg    D


title: Non-cancer 1 [SH52118_Cell2]

description:
miRNA
SA0545

value: serum


title: 63    Yg    D


title: Non-cancer 1 [SH52117_Cell4]

description:
miRNA
SA0543


title: 74    Yg    D


title: Non-cancer 1 [SH52121_Cell2]

description:
miRNA
SA0549


title: Non-cancer 1 [SH52113_Cell3]

description:
miRNA
SA0538


title: Non-cancer 1 [SH52127_Cell2]

description:
miRNA
SA0569


title: 60    Yg    D


title: 62    Yg    D


title: 58    Yg    D


title: 61    Yg    D


title: Non-cancer 1 [SH52113_Cell2]

description:
miRNA
SA0537


title: Non-cancer 1 [SH52108_Cell2]

description:
miRNA
SA0533


title: 59    Yg    D


title: 57    Yg    D


title: 56    Yg    D


title: Non-cancer 1 [SH52107_Cell4]

description:
miRNA
SA0531


title: Non-cancer 1 [SH52105_Cell3]

description:
miRNA
SA0526


title: Non-cancer 1 [SH51Z58_Cell4]

description:
miRNA
SA0515


title: Non-cancer 1 [SH52102_Cell3]

description:
miRNA
SA0522


title: 55    Yg    D


title: Non-cancer 1 [SH51Z58_Cell3]

description:
miRNA
SA0514


title: Non-cancer 1 [SH51Z57_Cell4]

description:
miRNA
SA0511


title: 54    Yg    D


title: 53    Yg    D


title: Non-cancer 1 [SH51Z48_Cell4]

description:
miRNA
SA0507


title: Non-cancer 1 [SH51Z47_Cell1]

description:
miRNA
SA0500


title: 52    Yg    D


title: 51    Yg    D


title: 50    Yg    D


title: Non-cancer 1 [SH51Z39_Cell4]

description:
miRNA
SA0495


title: 49    Yg    D


title: Non-cancer 1 [SH51Z27_Cell3]

description:
miRNA
SA0490


title: Non-cancer 1 [SH51Z27_Cell1]

description:
miRNA
SA0488


title: 47    Yg    D


title: 48    Yg    D


title: Non-cancer 1 [SH51Z23_Cell3]

description:
miRNA
SA0486


title: 46    Yg    D


title: 45    Yg    D


title: Non-cancer 1 [SH51Z21_Cell4]

description:
miRNA
SA0483


title: Non-cancer 1 [SH51Z21_Cell3]

description:
miRNA
SA0482


title: 42    Yg    D


title: 43    Yg    D


title: Non-cancer 1 [SH51Z19_Cell2]

description:
miRNA
SA0473


title: 41    Yg    D


title: 40    Yg    D


title: 39    Yg    D


title: Non-cancer 1 [SH51Z19_Cell1]

description:
miRNA
SA0472


title: Non-cancer 1 [SH78726_Cell2]

description:
miRNA
PR1284


title: 38    Yg    D


title: 37    Yg    D


title: Non-cancer 1 [SH51Z27_Cell4]

description:
miRNA
SA0491


title: Non-cancer 1 [SH78726_Cell3]

description:
miRNA
PR1285


title: Non-cancer 1 [SH78724_Cell3]

description:
miRNA
PR1281


title: Non-cancer 1 [SH78726_Cell1]

description:
miRNA
PR1283


title: 36    Yg    D


title: Non-cancer 1 [SH78724_Cell4]

description:
miRNA
PR1282


title: 35    Yg    D


title: 34    Yg    D


title: 33    Yg    D


title: 32    Yg    D


title: Non-cancer 1 [SH78724_Cell1]

description:
miRNA
PR1279


title: Non-cancer 1 [SH78724_Cell2]

description:
miRNA
PR1280


title: Non-cancer 1 [SH51Z19_Cell3]

description:
miRNA
SA0474


title: 31    Yg    D


title: Non-cancer 1 [SH78721_Cell2]

description:
miRNA
PR1276


title: Non-cancer 1 [SH78721_Cell1]

description:
miRNA
PR1275


title: Non-cancer 1 [SH78720_Cell3]

description:
miRNA
PR1273


title: Non-cancer 1 [SH78720_Cell2]

description:
miRNA
PR1272


title: Non-cancer 1 [SH78720_Cell1]

description:
miRNA
PR1271


title: 29    Yg    D


title: 28    Yg    D


title: Non-cancer 1 [SH78719_Cell4]

description:
miRNA
PR1270


title: 26    Yg    D


title: 24    Yg    D


title: Non-cancer 1 [SH78719_Cell1]

description:
miRNA
PR1267


title: Non-cancer 1 [SH78719_Cell2]

description:
miRNA
PR1268


title: 23    Yg    D


title: 30    Yg    D


title: Non-cancer 1 [SH78718_Cell4]

description:
miRNA
PR1266


title: 22    Yg    D


title: Non-cancer 1 [SH78718_Cell3]

description:
miRNA
PR1265


title: 21    Yg    D


title: Non-cancer 1 [SH78718_Cell2]

description:
miRNA
PR1264


title: 20    Yg    D


title: Non-cancer 1 [SH78718_Cell1]

description:
miRNA
PR1263


title: 19    Yg    D


title: Non-cancer 1 [SH78717_Cell4]

description:
miRNA
PR1262


title: 17    Yg    D


title: Non-cancer 1 [SH78717_Cell3]

description:
miRNA
PR1261


title: 15    Yg    D


title: 18    Yg    D


title: Non-cancer 1 [SH78716_Cell2]

description:
miRNA
PR1256


title: Non-cancer 1 [SH78715_Cell4]

description:
miRNA
PR1254


title: Non-cancer 1 [SH78717_Cell1]

description:
miRNA
PR1259


title: Non-cancer 1 [SH78717_Cell2]

description:
miRNA
PR1260


title: Non-cancer 1 [SH78716_Cell3]

description:
miRNA
PR1257


title: 10    Yg    D


title: 27    Yg    D


title: 9    Yg    D


title: Non-cancer 1 [SH78715_Cell2]

description:
miRNA
PR1252


title: Non-cancer 1 [SH78714_Cell4]

description:
miRNA
PR1250


title: 16    Yg    D


title: 5    Yg    D


title: 14    Yg    D


title: 13    Yg    D


title: Non-cancer 1 [SH78713_Cell4]

description:
miRNA
PR1246


title: Non-cancer 1 [SH78713_Cell3]

description:
miRNA
PR1245


title: Non-cancer 1 [SH78713_Cell2]

description:
miRNA
PR1244


title: 3    Yg    D


title: 12    Yg    D


title: Non-cancer 1 [SH52125_Cell2]

description:
miRNA
SA0561


title: Non-cancer 1 [SH78715_Cell1]

description:
miRNA
PR1251


title: 2    Yg    D


title: Non-cancer 1 [SH78713_Cell1]

description:
miRNA
PR1243


title: Non-cancer 1 [SH78P59_Cell2]

description:
miRNA
PR1240


title: Non-cancer 1 [SH78P59_Cell3]

description:
miRNA
PR1241


title: 11    Yg    D


title: 1    Yg    D


title: 7    Yg    D


title: Non-cancer 1 [SH78P59_Cell1]

description:
miRNA
PR1239


title: Non-cancer 1 [SH78P59_Cell4]

description:
miRNA
PR1248


title: 6    Yg    D


title: Non-cancer 1 [SH78721_Cell3]

description:
miRNA
PR1277


title: 4    Yg    D


title: Non-cancer 1 [SH78711_Cell4]

description:
miRNA
PR1238


title: Non-cancer 1 [SH78711_Cell3]

description:
miRNA
PR1237


title: Non-cancer 1 [SH78711_Cell2]

description:
miRNA
PR1236


title: Non-cancer 1 [SH78P58_Cell4]

description:
miRNA
PR1235


title: Non-cancer 1 [SH78715_Cell3]

description:
miRNA
PR1253


title: Non-cancer 1 [SH78714_Cell3]

description:
miRNA
PR1249


title: 91    Yg    C

source_name: Yg C_peripheral blood HSC

value: Yg C


title: 96    Yg    C


title: 95    Yg    C


title: Non-cancer 1 [SH78709_Cell4]

description:
miRNA
PR1234


title: 89    Yg    C


title: 88    Yg    C


title: Non-cancer 1 [SH78709_Cell1]

description:
miRNA
PR1231


title: 87    Yg    C


title: Non-cancer 1 [SH78P58_Cell3]

description:
miRNA
PR1233


title: Non-cancer 1 [SH78708_Cell3]

description:
miRNA
PR1229


title: Non-cancer 1 [SH78708_Cell4]

description:
miRNA
PR1230


title: Non-cancer 1 [SH78708_Cell1]

description:
miRNA
PR1227


title: 84    Yg    C


title: 86    Yg    C


title: 94    Yg    C


title: Non-cancer 1 [SH78P58_Cell2]

description:
miRNA
PR1228


title: 93    Yg    C


title: 90    Yg    C


title: Non-cancer 1 [SH78707_Cell1]

description:
miRNA
PR1223


title: 83    Yg    C


title: 92    Yg    C


title: Non-cancer 1 [SH78707_Cell3]

description:
miRNA
PR1225


title: Non-cancer 1 [SH78707_Cell2]

description:
miRNA
PR1224


title: 80    Yg    C


title: 82    Yg    C


title: 81    Yg    C


title: 79    Yg    C


title: Non-cancer 1 [SH78706_Cell4]

description:
miRNA
PR1222


title: 78    Yg    C


title: Non-cancer 1 [SH78P57_Cell4]

description:
miRNA
PR1221


title: Non-cancer 1 [SH78706_Cell2]

description:
miRNA
PR1220


title: 85    Yg    C


title: Non-cancer 1 [SH78706_Cell1]

description:
miRNA
PR1219


title: 75    Yg    C


title: Non-cancer 1 [SH78P57_Cell3]

description:
miRNA
PR1218


title: 76    Yg    C


title: Non-cancer 1 [SH78719_Cell3]

description:
miRNA
PR1269


title: Non-cancer 1 [SH78P57_Cell2]

description:
miRNA
PR1217


title: 74    Yg    C


title: 73    Yg    C


title: Non-cancer 1 [SH78701_Cell3]

description:
miRNA
PR1214


title: Non-cancer 1 [SH78701_Cell4]

description:
miRNA
PR1215


title: Non-cancer 1 [SH78701_Cell2]

description:
miRNA
PR1213


title: 72    Yg    C


title: 71    Yg    C


title: 70    Yg    C


title: 69    Yg    C


title: Non-cancer 1 [SH78352_Cell4]

description:
miRNA
PR1211


title: 67    Yg    C


title: 66    Yg    C


title: Non-cancer 1 [SH78352_Cell3]

description:
miRNA
PR1210


title: 65    Yg    C


title: Non-cancer 1 [SH78352_Cell2]

description:
miRNA
PR1209


title: 77    Yg    C


title: 64    Yg    C


title: Non-cancer 1 [SH78351_Cell1]

description:
miRNA
PR1204


title: 63    Yg    C


title: Non-cancer 1 [SH78351_Cell4]

description:
miRNA
PR1207


title: Non-cancer 1 [SH78351_Cell2]

description:
miRNA
PR1205


title: Non-cancer 1 [SH78351_Cell3]

description:
miRNA
PR1206


title: 62    Yg    C


title: Non-cancer 1 [SH78350_Cell4]

description:
miRNA
PR1202


title: 61    Yg    C


title: Non-cancer 1 [SH78701_Cell1]

description:
miRNA
PR1212


title: Non-cancer 1 [SH78730_Cell3]

description:
miRNA
PR1203


title: 59    Yg    C


title: 60    Yg    C


title: Non-cancer 1 [SH78350_Cell1]

description:
miRNA
PR1199


title: 58    Yg    C


title: 68    Yg    C


title: Non-cancer 1 [SH78349_Cell4]

description:
miRNA
PR1198


title: 57    Yg    C


title: Non-cancer 1 [SH78352_Cell1]

description:
miRNA
PR1208


title: Non-cancer 1 [SH78349_Cell3]

description:
miRNA
PR1197


title: 56    Yg    C


title: Non-cancer 1 [SH78261_Cell3]

description:
miRNA
PR1195


title: Non-cancer 1 [SH78261_Cell4]

description:
miRNA
PR1196


title: 55    Yg    C


title: Non-cancer 1 [SH78261_Cell2]

description:
miRNA
PR1194


title: Non-cancer 1 [SH78350_Cell2]

description:
miRNA
PR1200


title: Non-cancer 1 [SH78261_Cell1]

description:
miRNA
PR1193


title: 54    Yg    C


title: 53    Yg    C


title: 52    Yg    C


title: Non-cancer 1 [SH78260_Cell4]

description:
miRNA
PR1192


title: 51    Yg    C


title: Non-cancer 1 [SH78260_Cell3]

description:
miRNA
PR1191


title: 50    Yg    C


title: 49    Yg    C


title: 48    Yg    C


title: 47    Yg    C


title: 45    Yg    C


title: Non-cancer 1 [SH78237_Cell4]

description:
miRNA
PR1188


title: 46    Yg    C


title: Non-cancer 1 [SH78260_Cell1]

description:
miRNA
PR1189


title: Non-cancer 1 [SH78260_Cell2]

description:
miRNA
PR1190


title: Non-cancer 1 [SH78237_Cell3]

description:
miRNA
PR1187


title: 43    Yg    C


title: Non-cancer 1 [SH78237_Cell1]

description:
miRNA
PR1185


title: Non-cancer 1 [SH78237_Cell2]

description:
miRNA
PR1186


title: 41    Yg    C


title: Non-cancer 1 [SH78235_Cell4]

description:
miRNA
PR1180


title: Non-cancer 1 [SH78236_Cell2]

description:
miRNA
PR1182


title: Non-cancer 1 [SH78236_Cell1]

description:
miRNA
PR1181


title: Non-cancer 1 [SH78236_Cell3]

description:
miRNA
PR1183


title: 40    Yg    C


title: Non-cancer 1 [SH78235_Cell3]

description:
miRNA
PR1179


title: Non-cancer 1 [SH78235_Cell2]

description:
miRNA
PR1178


title: 37    Yg    C


title: 25    Yg    D


title: 36    Yg    C


title: Non-cancer 1 [SH78234_Cell4]

description:
miRNA
PR1176


title: Non-cancer 1 [SH78234_Cell2]

description:
miRNA
PR1174


title: 34    Yg    C


title: 35    Yg    C


title: 42    Yg    C


title: 33    Yg    C


title: 32    Yg    C


title: 30    Yg    C


title: 29    Yg    C


title: 31    Yg    C


title: Non-cancer 1 [SH78232_Cell2]

description:
miRNA
PR1170


title: Non-cancer 1 [SH78231_Cell2]

description:
miRNA
PR1166


title: 39    Yg    C


title: Non-cancer 1 [SH78232_Cell3]

description:
miRNA
PR1171


title: 28    Yg    C


title: 38    Yg    C


title: Non-cancer 1 [SH78231_Cell4]

description:
miRNA
PR1168


title: Non-cancer 1 [SH78231_Cell3]

description:
miRNA
PR1167


title: 27    Yg    C


title: Non-cancer 1 [SH78232_Cell1]

description:
miRNA
PR1169


title: Non-cancer 1 [SH78235_Cell1]

description:
miRNA
PR1177


title: Non-cancer 1 [SH78231_Cell1]

description:
miRNA
PR1165


title: Non-cancer 1 [SH78230_Cell3]

description:
miRNA
PR1163


title: 25    Yg    C


title: 24    Yg    C


title: Non-cancer 1 [SH78228_Cell4]

description:
miRNA
PR1160


title: 23    Yg    C


title: Non-cancer 1 [SH78234_Cell1]

description:
miRNA
PR1173


title: 22    Yg    C


title: 21    Yg    C


title: 20    Yg    C


title: Non-cancer 1 [SH78P56_Cell3]

description:
miRNA
PR1158


title: Non-cancer 1 [SH78228_Cell1]

description:
miRNA
PR1157


title: 19    Yg    C


title: 26    Yg    C


title: Non-cancer 1 [SH78230_Cell2]

description:
miRNA
PR1162


title: 15    Yg    C


title: 16    Yg    C


title: 14    Yg    C


title: Non-cancer 1 [SH78227_Cell4]

description:
miRNA
PR1156


title: Non-cancer 1 [SH78P56_Cell2]

description:
miRNA
PR1153


title: Non-cancer 1 [SH78225_Cell4]

description:
miRNA
PR1152


title: 13    Yg    C


title: Non-cancer 1 [SH78223_Cell3]

description:
miRNA
PR1147


title: Non-cancer 1 [SH78223_Cell4]

description:
miRNA
PR1148


title: Non-cancer 1 [SH78225_Cell2]

description:
miRNA
PR1150


title: Non-cancer 1 [SH78230_Cell1]

description:
miRNA
PR1161


title: 12    Yg    C


title: Non-cancer 1 [SH78225_Cell3]

description:
miRNA
PR1151


title: Non-cancer 1 [SH78223_Cell2]

description:
miRNA
PR1146


title: 11    Yg    C


title: Non-cancer 1 [SH78228_Cell3]

description:
miRNA
PR1159


title: Non-cancer 1 [SH78223_Cell1]

description:
miRNA
PR1145


title: 10    Yg    C


title: Non-cancer 1 [SH78222_Cell3]

description:
miRNA
PR1143


title: Non-cancer 1 [SH78222_Cell4]

description:
miRNA
PR1144


title: 18    Yg    C


title: 7    Yg    C


title: 17    Yg    C


title: 6    Yg    C


title: Non-cancer 1 [SH78222_Cell1]

description:
miRNA
PR1141


title: Non-cancer 1 [SH78220_Cell4]

description:
miRNA
PR1140


title: 5    Yg    C


title: Non-cancer 1 [SH78220_Cell3]

description:
miRNA
PR1139


title: 4    Yg    C


title: 3    Yg    C


title: Non-cancer 1 [SH78220_Cell2]

description:
miRNA
PR1138


title: 1    Yg    C


title: Non-cancer 1 [SH78220_Cell1]

description:
miRNA
PR1137


title: 94    Yg    B

source_name: Yg B_peripheral blood HSC

value: Yg B

value: Female


title: 92    Yg    B


title: Non-cancer 1 [SH78218_Cell3]

description:
miRNA
PR1135


title: 89    Yg    B


title: 90    Yg    B


title: Non-cancer 1 [SH78218_Cell2]

description:
miRNA
PR1134


title: 86    Yg    B


title: Non-cancer 1 [SH78P56_Cell1]

description:
miRNA
PR1131


title: Non-cancer 1 [SH78218_Cell1]

description:
miRNA
PR1133


title: Non-cancer 1 [SH78217_Cell4]

description:
miRNA
PR1132


title: 9    Yg    C


title: Non-cancer 1 [SH78222_Cell2]

description:
miRNA
PR1142


title: 84    Yg    B


title: Non-cancer 1 [SH78216_Cell3]

description:
miRNA
PR1127


title: Non-cancer 1 [SH78217_Cell2]

description:
miRNA
PR1130


title: Non-cancer 1 [SH78216_Cell4]

description:
miRNA
PR1128


title: 85    Yg    B


title: 83    Yg    B


title: Non-cancer 1 [SH78216_Cell2]

description:
miRNA
PR1126


title: 82    Yg    B


title: 2    Yg    C


title: Non-cancer 1 [SH78216_Cell1]

description:
miRNA
PR1125


title: 81    Yg    B


title: Non-cancer 1 [SH78215_Cell3]

description:
miRNA
PR1123


title: 80    Yg    B


title: Non-cancer 1 [SH78215_Cell2]

description:
miRNA
PR1122


title: Non-cancer 1 [SH78215_Cell1]

description:
miRNA
PR1121


title: 78    Yg    B


title: 79    Yg    B


title: Non-cancer 1 [SH77Q44_Cell4]

description:
miRNA
PR1120


title: 77    Yg    B


title: 74    Yg    B


title: Non-cancer 1 [SH78P55_Cell3]

description:
miRNA
PR1118


title: Non-cancer 1 [SH77Q44_Cell3]

description:
miRNA
PR1119


title: Non-cancer 1 [SH77Q43_Cell2]

description:
miRNA
PR1114


title: Non-cancer 1 [SH77Q43_Cell3]

description:
miRNA
PR1115


title: 72    Yg    B


title: Non-cancer 1 [SH77Q43_Cell1]

description:
miRNA
PR1113


title: 73    Yg    B


title: 71    Yg    B


title: 69    Yg    B


title: Non-cancer 1 [SH77Q40_Cell3]

description:
miRNA
PR1111


title: Non-cancer 1 [SH77Q40_Cell4]

description:
miRNA
PR1112


title: 68    Yg    B


title: 67    Yg    B


title: Non-cancer 1 [SH77Q37_Cell4]

description:
miRNA
PR1108


title: 64    Yg    B


title: Non-cancer 1 [SH77Q37_Cell3]

description:
miRNA
PR1107


title: 66    Yg    B


title: 65    Yg    B


title: Non-cancer 1 [SH77Q40_Cell1]

description:
miRNA
PR1109


title: 62    Yg    B


title: Non-cancer 1 [SH77Q32_Cell4]

description:
miRNA
PR1104


title: Non-cancer 1 [SH77Q37_Cell2]

description:
miRNA
PR1106


title: 60    Yg    B


title: Non-cancer 1 [SH77Q37_Cell1]

description:
miRNA
PR1105


title: 59    Yg    B


title: Non-cancer 1 [SH77Q32_Cell2]

description:
miRNA
PR1102


title: 61    Yg    B


title: Non-cancer 1 [SH77Q31_Cell3]

description:
miRNA
PR1099


title: 56    Yg    B


title: Non-cancer 1 [SH77Q32_Cell1]

description:
miRNA
PR1101


title: Non-cancer 1 [SH77Q32_Cell3]

description:
miRNA
PR1103


title: 63    Yg    B


title: 58    Yg    B


title: Non-cancer 1 [SH77Q30_Cell4]

description:
miRNA
PR1096


title: 55    Yg    B


title: Non-cancer 1 [SH77Q31_Cell2]

description:
miRNA
PR1098


title: Non-cancer 1 [SH77Q31_Cell1]

description:
miRNA
PR1097


title: Non-cancer 1 [SH77Q31_Cell4]

description:
miRNA
PR1100


title: 53    Yg    B


title: 50    Yg    B


title: 49    Yg    B


title: Non-cancer 1 [SH77Q30_Cell3]

description:
miRNA
PR1095


title: 52    Yg    B


title: 47    Yg    B


title: Non-cancer 1 [SH78P55_Cell1]

description:
miRNA
PR1094


title: 51    Yg    B


title: 54    Yg    B


title: Non-cancer 1 [SH77Q22_Cell2]

description:
miRNA
PR1086


title: Non-cancer 1 [SH77Q17_Cell4]

description:
miRNA
PR1084


title: Non-cancer 1 [SH77Q30_Cell1]

description:
miRNA
PR1093


title: Non-cancer 1 [SH77Q29_Cell4]

description:
miRNA
PR1092


title: 43    Yg    B


title: Non-cancer 1 [SH77Q29_Cell3]

description:
miRNA
PR1091


title: 40    Yg    B


title: Non-cancer 1 [SH77Q29_Cell1]

description:
miRNA
PR1089


title: 39    Yg    B


title: Non-cancer 1 [SH77Q17_Cell1]

description:
miRNA
PR1081


title: Non-cancer 1 [SH77Q16_Cell4]

description:
miRNA
PR1080


title: 45    Yg    B


title: 42    Yg    B


title: 36    Yg    B


title: Non-cancer 1 [SH77Q22_Cell1]

description:
miRNA
PR1085


title: 48    Yg    B


title: 46    Yg    B


title: 34    Yg    B


title: Non-cancer 1 [SH77Q13_Cell1]

description:
miRNA
PR1073


title: Non-cancer 1 [SH77Q12_Cell3]

description:
miRNA
PR1071


title: 41    Yg    B


title: 29    Yg    B


title: Non-cancer 1 [SH77Q16_Cell3]

description:
miRNA
PR1079


title: Non-cancer 1 [SH77Q09_Cell4]

description:
miRNA
PR1064


title: Non-cancer 1 [SH77Q16_Cell2]

description:
miRNA
PR1078


title: 25    Yg    B


title: Non-cancer 1 [SH77Q09_Cell3]

description:
miRNA
PR1063


title: 32    Yg    B


title: Non-cancer 1 [SH77Q16_Cell1]

description:
miRNA
PR1077


title: 38    Yg    B


title: 37    Yg    B


title: 24    Yg    B


title: Non-cancer 1 [SH77Q13_Cell4]

description:
miRNA
PR1076


title: Non-cancer 1 [SH77Q13_Cell3]

description:
miRNA
PR1075


title: Non-cancer 1 [SH77Q08_Cell4]

description:
miRNA
PR1060


title: 23    Yg    B


title: Non-cancer 1 [SH78P54_Cell3]

description:
miRNA
PR1074


title: 35    Yg    B


title: 30    Yg    B


title: Non-cancer 1 [SH77Q17_Cell3]

description:
miRNA
PR1083


title: 31    Yg    B


title: Non-cancer 1 [SH77Q12_Cell4]

description:
miRNA
PR1072


title: Non-cancer 1 [SH77Q12_Cell1]

description:
miRNA
PR1069


title: Non-cancer 1 [SH77Q08_Cell2]

description:
miRNA
PR1058


title: Non-cancer 1 [SH77Q08_Cell1]

description:
miRNA
PR1057


title: 18    Yg    B


title: Non-cancer 1 [SH77Q11_Cell1]

description:
miRNA
PR1065


title: 28    Yg    B


title: 27    Yg    B


title: 26    Yg    B


title: Non-cancer 1 [SH77Q05_Cell4]

description:
miRNA
PR1052


title: Non-cancer 1 [SH77Q09_Cell2]

description:
miRNA
PR1062


title: Non-cancer 1 [SH77Q05_Cell3]

description:
miRNA
PR1051


title: Non-cancer 1 [SH77Q09_Cell1]

description:
miRNA
PR1061


title: 22    Yg    B


title: Non-cancer 1 [SH77Q08_Cell3]

description:
miRNA
PR1059


title: 13    Yg    B


title: 20    Yg    B


title: 21    Yg    B


title: 19    Yg    B


title: Non-cancer 1 [SH77Q06_Cell4]

description:
miRNA
PR1056


title: 16    Yg    B


title: Non-cancer 1 [SH77Q03_Cell4]

description:
miRNA
PR1048


title: 12    Yg    B


title: Non-cancer 1 [SH77Q06_Cell2]

description:
miRNA
PR1054


title: 17    Yg    B


title: Non-cancer 1 [SH77Q06_Cell1]

description:
miRNA
PR1053


title: 14    Yg    B


title: Non-cancer 1 [SH67S37_Cell2]

description:
miRNA
OV0428


title: 11    Yg    B


title: 9    Yg    B


title: 10    Yg    B


title: Non-cancer 1 [SH77Q03_Cell2]

description:
miRNA
PR1046


title: Non-cancer 1 [SH77Q05_Cell1]

description:
miRNA
PR1049


title: Non-cancer 1 [SH77Q03_Cell1]

description:
miRNA
PR1045


title: 15    Yg    B


title: 6    Yg    B


title: 2    Yg    B


title: Non-cancer 1 [SH67S34_Cell4]

description:
miRNA
OV0426


title: Non-cancer 1 [SH77Q03_Cell3]

description:
miRNA
PR1047


title: Non-cancer 1 [SH67S34_Cell3]

description:
miRNA
OV0425


title: 3    Yg    B


title: 5    Yg    B


title: 95    Yg    A

source_name: Yg A_peripheral blood HSC

value: Yg A


title: Non-cancer 1 [SH67R61_Cell4]

description:
miRNA
OV0306


title: 96    Yg    A


title: Non-cancer 1 [SH67R56_Cell3]

description:
miRNA
OV0289


title: Non-cancer 1 [SH77Q05_Cell2]

description:
miRNA
PR1050


title: 1    Yg    B


title: Non-cancer 1 [SH67R60_Cell4]

description:
miRNA
OV0302


title: Non-cancer 1 [SH67R55_Cell4]

description:
miRNA
OV0286


title: Non-cancer 1 [SH67S12_Cell2]

description:
miRNA
OV0352


title: 94    Yg    A


title: Non-cancer 1 [SH67R60_Cell3]

description:
miRNA
OV0301


title: 7    Yg    B


title: 93    Yg    A


title: Non-cancer 1 [SH67R53_Cell2]

description:
miRNA
OV0276


title: 4    Yg    B


title: 91    Yg    A


title: 92    Yg    A


title: Non-cancer 1 [SH67R51_Cell1]

description:
miRNA
OV0267


title: 90    Yg    A


title: Non-cancer 1 [SH67R50_Cell1]

description:
miRNA
OV0263


title: Non-cancer 2 [SH6ZC48_Cell2]

description:
miRNA
NB16030302


title: Non-cancer 1 [SH67R50_Cell3]

description:
miRNA
OV0265


title: 88    Yg    A


title: 89    Yg    A


title: 87    Yg    A


title: Non-cancer 2 [SH6YM04_Cell3]

description:
miRNA
NB16022407


title: 86    Yg    A


title: Non-cancer 2 [SH6YM04_Cell2]

description:
miRNA
NB16022406


title: Non-cancer 2 [SH6YH34_Cell1]

description:
miRNA
NB16022302


title: 81    Yg    A


title: 84    Yg    A


title: Non-cancer 2 [SH6YH21_Cell1]

description:
miRNA
NB16021201


title: 80    Yg    A


title: Non-cancer 1 [SH77Q11_Cell4]

description:
miRNA
PR1068


title: 85    Yg    A


title: Non-cancer 2 [SH6YH14_Cell1]

description:
miRNA
NB16020503


title: Non-cancer 2 [SH6YH04_Cell1]

description:
miRNA
NB16012903


title: Non-cancer 2 [SH6YH14_Cell2]

description:
miRNA
NB16020504


title: 78    Yg    A


title: Non-cancer 2 [SH6YH12_Cell3]

description:
miRNA
NB16020309


title: 79    Yg    A


title: Non-cancer 2 [SH6YH02_Cell2]

description:
miRNA
NB16012801


title: Non-cancer 2 [SH6YH02_Cell1]

description:
miRNA
NB16012613


title: 77    Yg    A


title: 75    Yg    A


title: Non-cancer 2 [SH6YH23_Cell3]

description:
miRNA
NB16021207


title: 76    Yg    A


title: Non-cancer 2 [SH6YG59_Cell2]

description:
miRNA
NB16012204


title: Non-cancer 2 [SH6YH01_Cell1]

description:
miRNA
NB16012609


title: Non-cancer 2 [SH6YG53_Cell4]

description:
miRNA
NB16011505


title: 72    Yg    A


title: Non-cancer 2 [SH6YH16_Cell3]

description:
miRNA
NB16020805


title: Non-cancer 2 [SH6YG56_Cell2]

description:
miRNA
NB16011804


title: 74    Yg    A


title: Non-cancer 2 [SH6YG53_Cell3]

description:
miRNA
NB16011504


title: 73    Yg    A


title: 70    Yg    A


title: 66    Yg    A


title: 71    Yg    A


title: 65    Yg    A


title: Non-cancer 2 [SH6YG37_Cell3]

description:
miRNA
NB15122508


title: Non-cancer 2 [SH6YG63_Cell4]

description:
miRNA
NB16012608


title: Non-cancer 2 [SH6YG49_Cell4]

description:
miRNA
NB16011205


title: 64    Yg    A


title: 69    Yg    A


title: Non-cancer 2 [SH6YG52_Cell1]

description:
miRNA
NB16011401


title: 68    Yg    A


title: 63    Yg    A


title: Non-cancer 2 [SH6YH01_Cell3]

description:
miRNA
NB16012611


title: Non-cancer 2 [SH6YG42_Cell2]

description:
miRNA
NB16010502


title: 67    Yg    A


title: Non-cancer 2 [SH6YG31_Cell3]

description:
miRNA
NB15122205


title: Non-cancer 2 [SH6YG20_Cell3]

description:
miRNA
NB15121108


title: 83    Yg    A


title: Non-cancer 2 [SH6YG33_Cell3]

description:
miRNA
NB15122504


title: 62    Yg    A


title: Non-cancer 2 [SH6YG20_Cell2]

description:
miRNA
NB15121107


title: Non-cancer 2 [SH6Y932_Cell4]

description:
miRNA
NB15111006


title: Non-cancer 2 [SH6YG12_Cell2]

description:
miRNA
NB15120703


title: 56    Yg    A


title: Non-cancer 2 [SH6Y952_Cell2]

description:
miRNA
NB15120106


title: Non-cancer 2 [SH6Y930_Cell1]

description:
miRNA
NB15110608


title: 60    Yg    A


title: Non-cancer 2 [SH6Y923_Cell4]

description:
miRNA
NB15110202


title: Non-cancer 2 [SH6Y928_Cell4]

description:
miRNA
NB15110607


title: 55    Yg    A


title: 57    Yg    A


title: Non-cancer 2 [SH6Y946_Cell2]

description:
miRNA
NB15112502


title: 58    Yg    A


title: 59    Yg    A


title: Non-cancer 2 [SH6Y911_Cell2]

description:
miRNA
NB15102003


title: Non-cancer 2 [SH6Y921_Cell1]

description:
miRNA
NB15102803


title: Non-cancer 2 [SH6Y921_Cell4]

description:
miRNA
NB15103001


title: 53    Yg    A


title: 52    Yg    A


title: 51    Yg    A


title: 61    Yg    A


title: Non-cancer 2 [SH6Y903_Cell1]

description:
miRNA
NB15100902


title: Non-cancer 2 [SH6Y858_Cell3]

description:
miRNA
NB15100101


title: 48    Yg    A


title: 46    Yg    A


title: 54    Yg    A


title: Non-cancer 2 [SH6Y855_Cell3]

description:
miRNA
NB15092801


title: 50    Yg    A


title: Non-cancer 2 [SH6Y851_Cell4]

description:
miRNA
NB15091404


title: 42    Yg    A


title: 41    Yg    A


title: 40    Yg    A


title: 49    Yg    A


title: Non-cancer 2 [SH6Y909_Cell2]

description:
miRNA
NB15101906


title: Non-cancer 2 [SH6Y830_Cell4]

description:
miRNA
NB15082106


title: Non-cancer 2 [SH6Y858_Cell1]

description:
miRNA
NB15092902


title: Non-cancer 2 [SH6Y823_Cell1]

description:
miRNA
NB15081302


title: 45    Yg    A


title: Non-cancer 2 [SH6Y848_Cell3]

description:
miRNA
NB15090707


title: Non-cancer 2 [SH6Y839_Cell4]

description:
miRNA
NB15082701


title: 43    Yg    A


title: 36    Yg    A


title: 47    Yg    A


title: Non-cancer 2 [SH6Y832_Cell1]

description:
miRNA
NB15082401


title: Non-cancer 2 [SH6Y828_Cell2]

description:
miRNA
NB15081903


title: Non-cancer 2 [SH6Y814_Cell2]

description:
miRNA
NB15073101


title: Non-cancer 2 [SH6Y814_Cell1]

description:
miRNA
NB15073003


title: 39    Yg    A


title: 38    Yg    A


title: Non-cancer 2 [SH6Y823_Cell3]

description:
miRNA
NB15081402


title: 33    Yg    A


title: 37    Yg    A


title: Non-cancer 2 [SH6Y810_Cell1]

description:
miRNA
NB15072302


title: Non-cancer 2 [SH6Y822_Cell2]

description:
miRNA
NB15081202


title: Non-cancer 2 [SH6Y226_Cell3]

description:
miRNA
NB15070604


title: Non-cancer 2 [SH6Y819_Cell4]

description:
miRNA
NB15081001


title: 31    Yg    A


title: Non-cancer 2 [SH6Y205_Cell3]

description:
miRNA
NB15062907


title: 25    Yg    A


title: Non-cancer 2 [SH6Y827_Cell2]

description:
miRNA
NB15081707


title: Non-cancer 2 [SH6Y812_Cell3]

description:
miRNA
NB15073001


title: Non-cancer 2 [SH6Y810_Cell2]

description:
miRNA
NB15072401


title: Non-cancer 2 [SH6Y809_Cell2]

description:
miRNA
NB15072203


title: Non-cancer 2 [SH6XZ18_Cell3]

description:
miRNA
NB15061901


title: 24    Yg    A


title: 30    Yg    A


title: Non-cancer 2 [SH6XZ14_Cell3]

description:
miRNA
NB15061602


title: Non-cancer 2 [SH6XZ18_Cell1]

description:
miRNA
NB15061801


title: 29    Yg    A


title: 22    Yg    A


title: 20    Yg    A


title: Non-cancer 2 [SH6XZ07_Cell4]

description:
miRNA
NB15060503


title: 28    Yg    A


title: 34    Yg    A


title: 27    Yg    A


title: 35    Yg    A


title: 26    Yg    A


title: Non-cancer 2 [SH6Y216_Cell1]

description:
miRNA
NB15063002


title: Non-cancer 2 [SH6Y218_Cell3]

description:
miRNA
NB15070201


title: 32    Yg    A


title: 82    Yg    A


title: 17    Yg    A


title: 15    Yg    A


title: 23    Yg    A


title: Non-cancer 2 [SH6XS56_Cell2]

description:
miRNA
NB15051201


title: 21    Yg    A


title: Non-cancer 2 [SH6XZ13_Cell3]

description:
miRNA
NB15061503


title: Non-cancer 2 [SH6XZ13_Cell1]

description:
miRNA
NB15061501


title: Non-cancer 2 [SH6XT61_Cell4]

description:
miRNA
NB15052801


title: 19    Yg    A


title: 18    Yg    A


title: 13    Yg    A


title: Non-cancer 2 [SH6XT09_Cell4]

description:
miRNA
NB15052502


title: 10    Yg    A


title: Non-cancer 2 [SH6XS61_Cell2]

description:
miRNA
NB15052001


title: 16    Yg    A


title: Non-cancer 2 [SH6XS32_Cell1]

description:
miRNA
NB15033103


title: 14    Yg    A


title: 6    Yg    A


title: Non-cancer 2 [SH6XS28_Cell2]

description:
miRNA
NB15033005


title: Non-cancer 2 [SH6XS25_Cell4]

description:
miRNA
NB15032701


title: 5    Yg    A


title: Non-cancer 2 [SH6XS49_Cell1]

description:
miRNA
NB15042701


title: 3    Yg    A


title: Non-cancer 2 [SH6XR60_Cell1]

description:
miRNA
NB15021701


title: 11    Yg    A


title: 12    Yg    A


title: Non-cancer 2 [SH6XS45_Cell2]

description:
miRNA
NB15041703


title: 9    Yg    A


title: Non-cancer 2 [SH6XS32_Cell3]

description:
miRNA
NB15040102


title: Non-cancer 2 [SH6XS22_Cell2]

description:
miRNA
NB15032502


title: Non-cancer 2 [SH6XS51_Cell2]

description:
miRNA
NB15043002


title: 4    Yg    A


title: 1    Yg    A


title: 96    Aged    D

source_name: Aged D_peripheral blood HSC

value: Aged D


title: Non-cancer 2 [SH6XS17_Cell1]

description:
miRNA
NB15031603


title: Non-cancer 2 [SH6XS49_Cell3]

description:
miRNA
NB15042801


title: Non-cancer 2 [SH6XS03_Cell4]

description:
miRNA
NB15022601


title: 94    Aged    D


title: Non-cancer 2 [SH6XR59_Cell4]

description:
miRNA
NB15021603


title: Non-cancer 2 [SH6XR35_Cell1]

description:
miRNA
NB15020205


title: 91    Aged    D


title: Non-cancer 2 [SH6XR46_Cell2]

description:
miRNA
NB15011502


title: Non-cancer 2 [SH6XR44_Cell2]

description:
miRNA
NB15010701


title: 93    Aged    D


title: 2    Yg    A


title: 7    Yg    A


title: 87    Aged    D


title: Non-cancer 2 [SH69F49_Cell2]

description:
miRNA
NB14120403


title: Non-cancer 2 [SH69F45_Cell4]

description:
miRNA
NB14112803


title: Non-cancer 2 [SH69F43_Cell4]

description:
miRNA
NB14112104


title: 82    Aged    D


title: Non-cancer 2 [SH69F22_Cell4]

description:
miRNA
NB14111802

value: F


title: Non-cancer 2 [SH6XR37_Cell3]

description:
miRNA
NB15020902

value: unknown


title: Non-cancer 2 [SH6XR33_Cell2]

description:
miRNA
NB15020202

value: M


title: 95    Aged    D


title: 80    Aged    D


title: 79    Aged    D


title: Non-cancer 2 [SH6XR47_Cell4]

description:
miRNA
NB15011901


title: Non-cancer 2 [SH69X11_Cell1]

description:
miRNA
NB14122401


title: 90    Aged    D


title: 89    Aged    D


title: 75    Aged    D


title: 88    Aged    D


title: Non-cancer 2 [SH69X06_Cell2]

description:
miRNA
NB14121506


title: Non-cancer 2 [SH69F49_Cell4]

description:
miRNA
NB14120503


title: Non-cancer 2 [SH69F49_Cell3]

description:
miRNA
NB14120502


title: 92    Aged    D


title: 73    Aged    D


title: 86    Aged    D


title: 85    Aged    D


title: Non-cancer 2 [SH69E47_Cell4]

description:
miRNA
NB14091103


title: Non-cancer 2 [SH69F48_Cell3]

description:
miRNA
NB14120204


title: 84    Aged    D


title: 83    Aged    D


title: 81    Aged    D


title: Non-cancer 2 [SH69F44_Cell2]

description:
miRNA
NB14112503


title: Non-cancer 2 [SH69F22_Cell2]

description:
miRNA
NB14111705


title: Non-cancer 2 [SH69F17_Cell1]

description:
miRNA
NB14111104


title: 70    Aged    D


title: 69    Aged    D


title: Non-cancer 2 [SH69E26_Cell4]

description:
miRNA
NB14081902


title: 78    Aged    D


title: Non-cancer 2 [SH69F15_Cell3]

description:
miRNA
NB14111004


title: 67    Aged    D


title: Non-cancer 2 [SH69F07_Cell3]

description:
miRNA
NB14102702


title: Non-cancer 2 [SH69F12_Cell3]

description:
miRNA
NB14103104


title: 66    Aged    D


title: Non-cancer 2 [SH69E24_Cell1]

description:
miRNA
NB14081401


title: Non-cancer 2 [SH69E21_Cell2]

description:
miRNA
NB14080801


title: Non-cancer 2 [SH69E07_Cell3]

description:
miRNA
NB14072504


title: Non-cancer 2 [SH69E41_Cell1]

description:
miRNA
NB14090107


title: 77    Aged    D


title: 76    Aged    D


title: Non-cancer 2 [SH69E63_Cell3]

description:
miRNA
NB14101601


title: 74    Aged    D


title: Non-cancer 2 [SH69826_Cell3]

description:
miRNA
NB14052605


title: Non-cancer 2 [SH69828_Cell4]

description:
miRNA
NB14052901


title: Non-cancer 2 [SH69E55_Cell2]

description:
miRNA
NB14092903


title: 59    Aged    D


title: 58    Aged    D


title: 62    Aged    D


title: Non-cancer 2 [SH69E55_Cell4]

description:
miRNA
NB14093001


title: Non-cancer 2 [SH69E41_Cell3]

description:
miRNA
NB14090203


title: 71    Aged    D


title: 60    Aged    D


title: 56    Aged    D


title: Non-cancer 2 [SH69824_Cell3]

description:
miRNA
NB14051905


title: Non-cancer 2 [SH69E29_Cell4]

description:
miRNA
NB14082701


title: 68    Aged    D


title: 72    Aged    D


title: Non-cancer 2 [SH69E25_Cell4]

description:
miRNA
NB14081802


title: 64    Aged    D


title: 65    Aged    D


title: 63    Aged    D


title: 53    Aged    D


title: Non-cancer 2 [SH69E21_Cell4]

description:
miRNA
NB14080803


title: Non-cancer 2 [SH69E04_Cell1]

description:
miRNA
NB14071804


title: 51    Aged    D


title: Non-cancer 2 [SH69761_Cell2]

description:
miRNA
NB14041501


title: Non-cancer 2 [SH69863_Cell4]

description:
miRNA
NB14071702


title: Non-cancer 2 [SH69760_Cell1]

description:
miRNA
NB14041102


title: 61    Aged    D


title: Non-cancer 2 [SH69862_Cell2]

description:
miRNA
NB14071405


title: 57    Aged    D


title: UV YUMM  1.1-9

city: New Brunswick

first: SAURABH

middle: V

last: LADDHA

state: NEW JERSEY

address: 195 Little Albany Street

department: Center for Systems and Computational Biology

institute: Rutgers Cancer Institute of New Jersey

data_processing:
Library strategy: Exome-seq
Exome sequenced fastq files were probed for quality control using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) followed by alignment to mouse reference genome (mm10 UCSC) using default Burrows-Wheeler Aligner-MEM (bwa-0.7.5a) (http://arxiv.org/abs/1303.3997). Post-alignment processing followed the Genome Analysis ToolKit (GATK) best practices workflow40, including sam to bam file conversion, marking duplicates (Picard), base recalibration and preparing files for calling somatic mutation. Final processed bam files from MB49, YUMM1.1 and UV YUMM1.1-9 samples were used to call somatic single nucleotide variants using Mutect (version 1.1.4) algorithm. In addition to Mutect default filters, we used read depth of 14X (UV YUMM1.1-9) and 8X (YUMM1.1 and MB49) as another filter to remove variants with low sequencing depth. Somatic variants were annotated using online VEP42 to classify/predict consequences of these coding variants and removed known SNPs from the final variants. To identify mutational load for MB49 and YUMM1.1, we used VarScan43 mpileup2snp (with creating mpileup files using Samtools mpileup –q 40 –Q 25) and annotated using VEP online server.
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated mutational file provided as supplementary file

source_name: mouse tumors

growth_protocol: To assess the consequence of acute Atg7 deletion on tumorigenesis of C57Bl/6J isogenic male tumor cells, one week post TAM treatment, MB49 (0.25 x 106 cells) cells were resuspended in 100 ul PBS and injected subcutaneously into the dorsal flanks of mice (2 tumors per mouse). Three weeks post cell injection, mice were sacrificed and tumors were collected.

extract_protocol:
Genomic DNA was extracted from MB49, YUMM 1.1 and UV YUMM 1.1-9 cell lines using the QIAsymphony DSP DNA midi kit (937255, Qiagen). Mouse whole exome libraries were constructed using Agilent SureSelect Mouse All Exon kit according to the manufacturer’s protocol. The resulting sequencing libraries were analyzed using Agilent D1000 screentape and quantified using KAPA qPCR. Libraries were then normalized and pooled into one pool. The library pool was then clustered and sequenced on the Illumina NextSeq550 instrument using 2x151bp paired end reads to a mean death of 80X, following the manufacturer’s protocols.
Genomic DNA was extracted from MB49, YUMM 1.1 and UV YUMM 1.1-9 cell lines using the QIAsymphony DSP DNA midi kit (937255, Qiagen). Mouse whole exome libraries were constructed using Agilent SureSelect Mouse All Exon kit according to the manufacturer’s protocol. The resulting sequencing libraries were analyzed using Agilent D1000 screentape and quantified using KAPA qPCR. Libraries were then normalized and pooled into one pool. The library pool was then clustered and sequenced on the Illumina NextSeq550 instrument using 2x151bp paired end reads to a mean death of 80X, following the manufacturer’s protocols.

treatment_protocol: Mice were treated with TAM everyday for 4 days to induce Atg7 deletion.

value: UV YUMM  1.1-9


title: 49XC-49


title: Non-cancer 2 [SH69743_Cell4]

description:
miRNA
NB14031103


title: Non-cancer 2 [SH69825_Cell4]

description:
miRNA
NB14052203


title: 52    Aged    D

value: Male


title: Non-cancer 2 [SH69824_Cell1]

description:
miRNA
NB14051903


title: 55    Aged    D

value: Caucasian


title: 45    Aged    D

value: peripheral blood


title: Non-cancer 2 [SH69823_Cell2]

description:
miRNA
NB14051605


title: YUMM 1.1

value: YUMM 1.1


title: 54    Aged    D

value: Hematopoietic Stem Cells (HSCs)


title: Non-cancer 2 [SH69743_Cell3]

description:
miRNA
NB14031101


title: Non-cancer 2 [SH69813_Cell2]

description:
miRNA
NB14050801


title: 49    Aged    D


title: 50    Aged    D


title: Non-cancer 2 [SH69809_Cell4]

description:
miRNA
NB14050202


title: 47    Aged    D


title: Non-cancer 2 [SH64703_Cell2]

description:
miRNA
NB14050103


title: Non-cancer 2 [SH69754_Cell4]

description:
miRNA
NB14040203


title: 39    Aged    D


title: M2

city: Houston

first: Haichao

last: Wei

state: TX

address: 1825 Pressler St., SRB 637.C

institute: UTHealth

data_processing:
The 150-bp paired-end reads were aligned to the reference genome (mm10) using TopHat v2.1.0 with default parameters. Cufflinks v2.2.1 was used to analyze FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values for genes and transcripts annotated.Any FPKM < 0.1 was set to 0.1 to avoid ratio inflation.
Read counts for annotated genes and transcripts were acquired using HTSeq-count.
DESeq2 software was used to analyze the FPKM to identify differentially expressed genes (DEGs).The following thresholds were used to classify genes as DEGS: 1) at least one sample's FPKM >1, 2) |log2 (fold-change)| > 1, and 3) FDR < 0.05.
Genome_build: MM10
Supplementary_files_format_and_content: FPKM

source_name: Retinal cone photoreceptor

growth_protocol: Animals were maintained with 12/12 light/dark cycle.

extract_protocol:
Neural retinas were dissected out, retinal cells enzymatically dissociated and sorted by FACS, eGFP+ cells (cones) were collected, lysed and stored in the lysis buffer of Nucleopsin RNA XS kit. 100 ng RNA per sample was used for RNA-seq library was constructed using NEBNext® Ultra™ Directional RNA Library Prep Kit for Ilumina with NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) according to manufacturer’s protocol.
The libraries were quantified using Agilent 2100 Bioanalyzer (Agilent) and Quibit quantification. RNA-seq libraries were sequenced using NextSeq550 PE150 (Illumina).

value: C57BL/6 (with mixed background)

value: retina

value: post natal day 60-80 (2-6 months, or 60-180 days)

tag: genotype


title: 37    Aged    D


title: 42    Aged    D


title: YUMM 1.3

value: YUMM 1.3


title: 46    Aged    D


title: 43    Aged    D


title: Non-cancer 2 [SH69730_Cell3]

description:
miRNA
NB14021704

source_name: Serum

value: serum


title: M3


title: 40    Aged    D


title: 48    Aged    D


title: 33    Aged    D


title: 35    Aged    D


title: 38    Aged    D


title: 36    Aged    D


title: M1


title: Non-cancer 2 [SH69735_Cell3]

description:
miRNA
NB14030301


title: Non-cancer 2 [SH69732_Cell4]

description:
miRNA
NB14022101


title: 32    Aged    D


title: C2


title: 34    Aged    D


title: 31    Aged    D


title: 41    Aged    D


title: C3


title: C1


title: 29    Aged    D


title: 30    Aged    D


title: HS_day4_rep3

city: Wageningen

first: Anneke

last: Horstman

state: Nederland

address: Droevendaalsesteeg,

department: Plant Science Group

country: Netherlands

institute: Wageningen University and Research

data_processing:
Barcoded libraries were pooled and sequenced on a HiSeq2500 platform (125nt paired end reads).
Before mapping of the reads to the Brassica napus genome, raw reads were trimmed by removing adapter sequences.
Reads were mapped to the Brassica napus genome version 4.1 (http://brassicadb.org) with RNA-Seq analysis package CLC Genomics Workbench 11 (www.clcbio.com).
Parameters mapping: min. read length fraction = 0.8, min. read similarity fraction = 0.8. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=10, Count paired reads as two=no.
The R-Bioconductor package Limma-Voom (Law et al., 2014) was used to normalize the reads over the entire experiment. We used the trimmed mean of M-values (TMM) normalization method (Robinson & Oshlack, 2010) to account for small biases in each sample’s overall read library size. Transcripts with less than three counts per million (CPM) in at least 3 library samples were excluded from the analysis.
Genome_build: Brassica napus genome version 4.1 (http://brassicadb.org)
Supplementary_files_format_and_content: csv and xlsx (raw counts, log2CPM values and log2FoldChange values)

organism: Brassica napus

source_name: microspore culture

growth_protocol: Microspore isolation was performed according to the protocol described by (Custers, 2003).

extract_protocol:
Each sample (400,000 - 1,000,000 microspores) was disrupted with stainless steel beads and RNA was using the InviTrap Spin Plant RNA Mini Kit (Stratec).
DNAse-treated RNA was used as template for RNA-seq library preparation (TruSeq RNA Library Prep Kit).

treatment_protocol: LEC1-GFP microspore cultures were sampled at different time points (day 0, day 2, day 4 and day 8). Day 0 microspore cultures were left untreated. To induce microspore embryogenesis, the microspores in culture were treated with heat stress  (at 33 °C) for 24-hrs. To induce callus formation, cultures were treated with  the histone deacetylase inhibitor (HDACi) trichostatin A (TSA) at a concentration of 0.5µM or 0.05µM in combination with heat stress (at 33 °C) for 24-hrs. After 24-hrs, TSA was removed by centrifugation and the cultures were refreshed with new NLN-13 medium. Cultures were then moved to 25 °C for either 1 day, 3 days or 7 days.

tag: developmental stage pollen used

value: microspore + embryogenic cells

value: heat shock

value: late unicellular microspores


title: 28    Aged    D

value: Aged D


title: Non-cancer 2 [SH69718_Cell3]

description:
miRNA
NB14012304

value: unknown


title: 27    Aged    D


title: 26    Aged    D


title: 25    Aged    D


title: Non-cancer 2 [SH69551_Cell3]

description:
miRNA
NB14012803

value: F


title: 24    Aged    D


title: Non-cancer 2 [SH69717_Cell4]

description:
miRNA
NB14012301

value: M


title: Non-cancer 2 [SH69729_Cell2]

description:
miRNA
NB14021401


title: 22    Aged    D

value: Male


title: 23    Aged    D

value: Caucasian


title: 21    Aged    D

value: peripheral blood


title: Non-cancer 2 [SH69715_Cell2]

description:
miRNA
NB14011602


title: 20    Aged    D


title: Non-cancer 2 [SH69719_Cell2]

description:
miRNA
NB14012702


title: HS_day2_rep2


title: Non-cancer 2 [SH69711_Cell1]

description:
miRNA
NB14010901


title: HS_day2_rep3


title: HS_day4_rep1


title: 17    Aged    D


title: 18    Aged    D


title: HS_day2_rep1


title: Non-cancer 2 [SH69716_Cell3]

description:
miRNA
NB14012201


title: HS_day4_rep2


title: 15    Aged    D


title: Non-cancer 2 [SH69705_Cell2]

description:
miRNA
NB13122402


title: Non-cancer 2 [SH69707_Cell3]

description:
miRNA
NB13122702


title: Non-cancer 2 [SH69703_Cell2]

description:
miRNA
NB13121805


title: 14    Aged    D


title: HS+TSA 0.5µM_day4_rep2

value: heat shock + TSA 0.05µM


title: 12    Aged    D

value: Hematopoietic Stem Cells (HSCs)


title: 13    Aged    D


title: 11    Aged    D


title: 10    Aged    D


title: 16    Aged    D


title: 19    Aged    D


title: HS+TSA 0.5µM_day4_rep3


title: Non-cancer 2 [SH69561_Cell2]

description:
miRNA
NB13121201


title: 9    Aged    D


title: Non-cancer 2 [SH69703_Cell1]

description:
miRNA
NB13121804


title: 5    Aged    D


title: HS+TSA 0.5µM_day2_rep3

data_processing:
Barcoded libraries were pooled and sequenced on a HiSeq2500 platform (125nt paired end reads).
Before mapping of the reads to the Brassica napus genome, raw reads were trimmed by removing adapter sequences. Â
Reads were mapped to the Brassica napus genome version 4.1 (http://brassicadb.org) with RNA-Seq analysis package CLC Genomics Workbench 11 (www.clcbio.com).
Parameters mapping: min. read length fraction = 0.8, min. read similarity fraction = 0.8. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=10, Count paired reads as two=no. The R-Bioconductor package Limma-Voom (Law et al., 2014) was used to normalize the reads over the entire experiment. We used the trimmed mean of M-values (TMM) normalization method (Robinson & Oshlack, 2010) to account for small biases in each sample’s overall read library size. Transcripts with less than three counts per million (CPM) in at least 3 library samples were excluded from the analysis.
Genome_build: Brassica napus genome version 4.1 (http://brassicadb.org)
Supplementary_files_format_and_content: csv and xlsx (raw counts, log2CPM values and log2FoldChange values)

source_name: HS+TSA 0.5µM_day2_microspore culture

value: heat shock + TSA 0.5µM


title: Non-cancer 2 [SH69559_Cell3]

description:
miRNA
NB13121002


title: 6    Aged    D


title: 7    Aged    D


title: 4    Aged    D


title: Non-cancer 2 [SH69517_Cell4]

description:
miRNA
NB13120205


title: 3    Aged    D


title: HS+TSA 0.5µM_day4_rep1


title: HS+TSA 0.5µM_day2_rep2


title: 2    Aged    D


title: HS+TSA 0.05µM_day8_rep2

source_name: HS+TSA 0.05µM_day8_microspore culture


title: HS+TSA 0.5µM_day2_rep1


title: Non-cancer 2 [SH69515_Cell4]

description:
miRNA
NB13112701


title: 96    Aged    C

source_name: Aged C_peripheral blood HSC

value: Aged C

value: Female


title: 1    Aged    D


title: Pollen_day0_rep3

source_name: Pollen_day0_microspore culture

value: microspore

value: untreated


title: Non-cancer 2 [SH69511_Cell4]

description:
miRNA
NB13112202

value: serum


title: 94    Aged    C


title: 95    Aged    C


title: Pollen_day0_rep2


title: HS+TSA 0.05µM_day8_rep1

value: microspore + embryogenic cells


title: 93    Aged    C


title: 92    Aged    C


title: Non-cancer 2 [SH69507_Cell4]

description:
miRNA
NB13111905


title: 90    Aged    C


title: 91    Aged    C


title: Pollen_day0_rep1

value: late unicellular microspores


title: 89    Aged    C


title: C59

city: Suwon-si

first: Soah

last: Lee

state: Geonggi-do

address: 2066 Seobu-ro, Jangan-gu, 530502

department: Pharmacy

institute: Sungkyunkwan University

data_processing:
The single cell library was sequenced with illumina hiseq 4000 platform
The data was processed using cellranger v2.0.0 (10x Genomics).  The defaults packages were used.  The default parameters were used with the expected number of cells being 4000.   The reference genome used was refdata-cellranger-hg19-1.2.0 (downloaded from 10x Genomics website).  cellranger calls a local copy of bcl2fastq to generate the fastq files,  bcl2fastq v2.17.1.14 (Illumina) was used.
Genome_build: hg19

source_name: hiPSC-derived cardiomyocytes

growth_protocol: hiPSC-CMs at differentiation day 11 were passaged in 1:6 ratio

extract_protocol:
At day 13 hiPSC-CMs were washed, dissociated and resupended in 1000 cells/uL and stored on ice for direct use after (<30min).
This step was done by following the 10x genomics single cell 3' end ibrary preparation protocol. Briefly, only the 3' end of mRNA fragements were used to make library. One end of the fragements were added P5, read1 illumina sequencing primer, 16 base pairs of 10x barcode, and UMI sequences; The other end ligated with P7, sample index sequences, and illumina read2 sequencing primer sequences.
scRNAseq

treatment_protocol: At day 12 hiPSC-CMs were treated with DMSO (CTR), GSK3 inhibitor CHIR99021 or Wnt inhibitor C59 for 24 hours.

tag: passage

value: Pasaage 1


title: Non-cancer 2 [SH69113_Cell3]

description:
miRNA
NB13100804

tag: tissue

value: unknown


title: CHIR

value: Passage 1


title: Non-cancer 2 [SH69118_Cell1]

description:
miRNA
NB13101701

tag: Sex

value: M


title: 87    Aged    C

tag: age


title: 88    Aged    C


title: 85    Aged    C


title: 86    Aged    C


title: Non-cancer 2 [SH69110_Cell4]

description:
miRNA
NB13100402

value: F

tag: cstage


title: CTR

description: DMSO


title: 83    Aged    C

value: Caucasian


title: 82    Aged    C

value: peripheral blood


title: Hs_H1_BG100_3D_d11_ctrl_RNAseq

city: La Jolla

first: Maike

last: Sander

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

description:
hs_pan_005_bg_mR_S31_L005
processed data file: 3d_pp2_rnaseq_rpkm.txt

data_processing:
Reads were aligned to hg38 using STAR (v2.5.3b) with the following parameters: --twopassMode Basic --outFilterMismatchNmax 6 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 3 --outFilterType BySJout --seedSearchStartLmax 50.
Reads per kilobase of transcript, per million mapped reads (RPKM) were calculated with Cufflinks (v2.2.1)
Count tables for differential gene expression analysis with DESeq2 (v1.10.1) were generated with htseq-count from the HTSeq Python library.
Genome_build: hg38
Supplementary_files_format_and_content: gene expression data table in text format

source_name: Unmodified hESCs were differentiated to the PP2 stage

growth_protocol: Pancreatic differentiation was performed as previously described (Rezania et al., 2012; Rezania et al., 2014), with minor modifications. Cells were grown either as a monolayer (RNA-seq of lncRNA KO hESC-derived tissues and corresponding WT controls) , or in suspension culture (Ribo-seq and matched RNA-seq).

extract_protocol:
Total RNA was extracted using either Trizol or the QIAGEN RNeasy Mini Kit. For cell fractionation experiments, the Paris Kit (Thermo Fisher Scientific) was used.
Libraries were prepared according to Illumina's (TruSeq Stranded Total RNA Library Prep Gold; TruSeq Stranded mRNA Library Prep; TruSeq Ribo Profile (Mammalian) or Roche's (KAPA mRNA HyperPrep Kit) instructions

treatment_protocol: Definitive endoderm and pancreatic progenitor stage cells were collected, and RNA was extracted for RNA-seq library preparation.

value: H1 ES cells

value: ES-derived late pancreatic progenitor cells

value: WT

tag: library

value: polyA, stranded


title: 79    Aged    C

value: Aged C

value: Female

value: Hematopoietic Stem Cells (HSCs)


title: Hs_H1_BG99_3D_d11_ctrl_RNAseq

description:
hs_pan_004_bg_mR_S30_L004
processed data file: 3d_pp2_rnaseq_rpkm.txt


title: Hs_H1_BG101_3D_d11_ctrl_RNAseq

description:
hs_pan_006_bg_mR_S32_L005
processed data file: 3d_pp2_rnaseq_rpkm.txt


title: 80    Aged    C


title: Non-cancer 2 [SH68Z31_Cell1]

description:
miRNA
NB13090602

value: serum

tag: child-pugh

tag: afp


title: 81    Aged    C


title: Non-cancer 2 [SH68Z30_Cell4]

description:
miRNA
NB13090601


title: Non-cancer 2 [SH68Z25_Cell2]

description:
miRNA
NB13082901


title: 77    Aged    C


title: 78    Aged    C


title: Non-cancer 2 [SH68Z23_Cell2]

description:
miRNA
NB13082301


title: Hs_H1_BG98_3D_d11_ctrl_RNAseq

description:
hs_pan_003_bg_mR_S29_L004
processed data file: 3d_pp2_rnaseq_rpkm.txt


title: Non-cancer 2 [SH68Z19_Cell4]

description:
miRNA
NB13081301


title: 76    Aged    C


title: Non-cancer 2 [SH69509_Cell3]

description:
miRNA
NB13112003


title: 84    Aged    C


title: 75    Aged    C


title: Hs_H1_BG97_3D_d11_ctrl_RNAseq

description:
hs_pan_002_bg_mR_S28_L004
processed data file: 3d_pp2_rnaseq_rpkm.txt


title: 72    Aged    C


title: Hs_H1_BG96_3D_d11_ctrl_RNAseq

description:
hs_pan_001_bg_mR_S27_L004
processed data file: 3d_pp2_rnaseq_rpkm.txt


title: Non-cancer 2 [SH68Z17_Cell1]

description:
miRNA
NB13080703


title: Hs_H1_BG101_3D_d11_ctrl_Riboseq_replicate1_5

description:
hs_pan_006_bg_Ri_S15_L008
processed data file: 3d_pp2_riboseq_rpkm.txt

value: ribosome-protected


title: Non-cancer 2 [SH68Z19_Cell1]

description:
miRNA
NB13081204


title: 70    Aged    C


title: 73    Aged    C


title: 71    Aged    C


title: 64    Aged    C


title: 68    Aged    C


title: 67    Aged    C


title: Hs_H1_BG101_3D_d11_ctrl_Riboseq_replicate1_4

description:
hs_pan_006_bg_Ri_S15_L007
processed data file: 3d_pp2_riboseq_rpkm.txt


title: Non-cancer 2 [SH68960_Cell1]

description:
miRNA
NB13072401


title: Non-cancer 2 [SH68Z16_Cell3]

description:
miRNA
NB13080701


title: 74    Aged    C


title: Hs_H1_BG101_3D_d11_ctrl_Riboseq_replicate1_2

description:
hs_pan_006_bg_Ri_S15_L005
processed data file: 3d_pp2_riboseq_rpkm.txt


title: 69    Aged    C


title: Non-cancer 2 [SH68957_Cell1]

description:
miRNA
NB13071803


title: 62    Aged    C


title: Non-cancer 2 [SH68952_Cell3]

description:
miRNA
NB13070902


title: Hs_H1_BG100_3D_d11_ctrl_Riboseq_replicate1_5

description:
hs_pan_005_bg_Ri_S14_L008
processed data file: 3d_pp2_riboseq_rpkm.txt


title: Hs_H1_BG101_3D_d11_ctrl_Riboseq_replicate1_3

description:
hs_pan_006_bg_Ri_S15_L006
processed data file: 3d_pp2_riboseq_rpkm.txt


title: 63    Aged    C


title: Non-cancer 2 [SH68950_Cell4]

description:
miRNA
NB13070802


title: 60    Aged    C


title: 66    Aged    C


title: 65    Aged    C


title: Hs_H1_BG100_3D_d11_ctrl_Riboseq_replicate1_4

description:
hs_pan_005_bg_Ri_S14_L007
processed data file: 3d_pp2_riboseq_rpkm.txt


title: Hs_H1_BG100_3D_d11_ctrl_Riboseq_replicate1_3

description:
hs_pan_005_bg_Ri_S14_L006
processed data file: 3d_pp2_riboseq_rpkm.txt


title: 61    Aged    C


title: Hs_H1_BG101_3D_d11_ctrl_Riboseq_replicate1_1

description:
hs_pan_006_bg_Ri_S15_L004
processed data file: 3d_pp2_riboseq_rpkm.txt


title: 57    Aged    C


title: Non-cancer 2 [SH68947_Cell3]

description:
miRNA
NB13070203


title: Non-cancer 2 [SH67507_Cell3]

description:
miRNA
NB13061903


title: Hs_H1_BG100_3D_d11_ctrl_Riboseq_replicate1_2

description:
hs_pan_005_bg_Ri_S14_L005
processed data file: 3d_pp2_riboseq_rpkm.txt


title: 59    Aged    C


title: 58    Aged    C


title: 53    Aged    C


title: 54    Aged    C


title: 56    Aged    C


title: 55    Aged    C


title: Non-cancer 2 [SH67506_Cell2]

description:
miRNA
NB13061802


title: Hs_H1_BG99_3D_d11_ctrl_Riboseq_replicate1_5

description:
hs_pan_004_bg_Ri_S13_L008
processed data file: 3d_pp2_riboseq_rpkm.txt


title: 51    Aged    C


title: Non-cancer 2 [SH67504_Cell1]

description:
miRNA
NB13061301


title: 50    Aged    C


title: Hs_H1_BG99_3D_d11_ctrl_Riboseq_replicate1_4

description:
hs_pan_004_bg_Ri_S13_L007
processed data file: 3d_pp2_riboseq_rpkm.txt


title: Non-cancer 2 [SH67459_Cell3]

description:
miRNA
NB13060403


title: 49    Aged    C


title: Hs_H1_BG99_3D_d11_ctrl_Riboseq_replicate1_3

description:
hs_pan_004_bg_Ri_S13_L006
processed data file: 3d_pp2_riboseq_rpkm.txt


title: 48    Aged    C


title: 47    Aged    C


title: 45    Aged    C


title: Non-cancer 2 [SH67459_Cell1]

description:
miRNA
NB13060306


title: Hs_H1_BG100_3D_d11_ctrl_Riboseq_replicate1_1

description:
hs_pan_005_bg_Ri_S14_L004
processed data file: 3d_pp2_riboseq_rpkm.txt


title: 43    Aged    C


title: Hs_H1_BG99_3D_d11_ctrl_Riboseq_replicate1_1

description:
hs_pan_004_bg_Ri_S13_L004
processed data file: 3d_pp2_riboseq_rpkm.txt


title: Hs_H1_BG99_3D_d11_ctrl_Riboseq_replicate1_2

description:
hs_pan_004_bg_Ri_S13_L005
processed data file: 3d_pp2_riboseq_rpkm.txt


title: Non-cancer 2 [SH67507_Cell1]

description:
miRNA
NB13061901


title: 42    Aged    C


title: 52    Aged    C


title: Sarcoma [SH59X17_Cell3]

description:
miRNA
SA0422


title: 40    Aged    C


title: 41    Aged    C


title: Sarcoma [SH59X21_Cell2]

description:
miRNA
SA0440


title: 39    Aged    C


title: 38    Aged    C


title: Hs_H1_BG98_3D_d11_ctrl_Riboseq_replicate1_5

description:
hs_pan_003_bg_Ri_S12_L008
processed data file: 3d_pp2_riboseq_rpkm.txt


title: Non-cancer 2 [SH69709_Cell2]

description:
miRNA
NB14010802


title: 37    Aged    C


title: Sarcoma [SH59X03_Cell4]

description:
miRNA
SA0368


title: Hs_H1_BG98_3D_d11_ctrl_Riboseq_replicate1_3

description:
hs_pan_003_bg_Ri_S12_L006
processed data file: 3d_pp2_riboseq_rpkm.txt


title: Sarcoma [SH59X06_Cell1]

description:
miRNA
SA0378


title: 36    Aged    C


title: 35    Aged    C


title: 46    Aged    C


title: 34    Aged    C


title: Hs_H1_BG98_3D_d11_ctrl_Riboseq_replicate1_2

description:
hs_pan_003_bg_Ri_S12_L005
processed data file: 3d_pp2_riboseq_rpkm.txt


title: Sarcoma [SH59W59_Cell4]

description:
miRNA
SA0343


title: 33    Aged    C


title: 32    Aged    C


title: Sarcoma [SH59W55_Cell3]

description:
miRNA
SA0326


title: 31    Aged    C


title: 30    Aged    C


title: 29    Aged    C


title: Hs_H1_BG98_3D_d11_ctrl_Riboseq_replicate1_4

description:
hs_pan_003_bg_Ri_S12_L007
processed data file: 3d_pp2_riboseq_rpkm.txt


title: Hs_H1_BG97_3D_d11_ctrl_Riboseq_replicate1_4

description:
hs_pan_002_bg_Ri_S11_L007
processed data file: 3d_pp2_riboseq_rpkm.txt


title: 27    Aged    C


title: Sarcoma [SH59W53_Cell2]

description:
miRNA
SA0317


title: Hs_H1_BG97_3D_d11_ctrl_Riboseq_replicate1_5

description:
hs_pan_002_bg_Ri_S11_L008
processed data file: 3d_pp2_riboseq_rpkm.txt


title: 28    Aged    C


title: 25    Aged    C


title: 26    Aged    C


title: Hs_H1_BG97_3D_d11_ctrl_Riboseq_replicate1_2

description:
hs_pan_002_bg_Ri_S11_L005
processed data file: 3d_pp2_riboseq_rpkm.txt


title: Sarcoma [SH59W50_Cell1]

description:
miRNA
SA0304


title: Sarcoma [SH59W49_Cell3]

description:
miRNA
SA0302


title: Sarcoma [SH59X07_Cell1]

description:
miRNA
SA0382


title: Sarcoma [SH59W44_Cell2]

description:
miRNA
SA0284


title: 24    Aged    C


title: 23    Aged    C


title: Hs_H1_BG97_3D_d11_ctrl_Riboseq_replicate1_1

description:
hs_pan_002_bg_Ri_S11_L004
processed data file: 3d_pp2_riboseq_rpkm.txt


title: Sarcoma [SH59W41_Cell4]

description:
miRNA
SA0274


title: 21    Aged    C


title: Hs_H1_BG97_3D_d11_ctrl_Riboseq_replicate1_3

description:
hs_pan_002_bg_Ri_S11_L006
processed data file: 3d_pp2_riboseq_rpkm.txt


title: Hs_H1_BG96_3D_d11_ctrl_Riboseq_replicate1_5

description:
hs_pan_001_bg_Ri_S10_L008
processed data file: 3d_pp2_riboseq_rpkm.txt


title: Hs_H1_BG98_3D_d11_ctrl_Riboseq_replicate1_1

description:
hs_pan_003_bg_Ri_S12_L004
processed data file: 3d_pp2_riboseq_rpkm.txt


title: Sarcoma [SH59W27_Cell2]

description:
miRNA
SA0219


title: 19    Aged    C


title: Hs_H1_BG96_3D_d11_ctrl_Riboseq_replicate1_4

description:
hs_pan_001_bg_Ri_S10_L007
processed data file: 3d_pp2_riboseq_rpkm.txt


title: Sarcoma [SH59W14_Cell3]

description:
miRNA
SA0165


title: 22    Aged    C


title: 17    Aged    C


title: 16    Aged    C


title: Hs_H1_BG96_3D_d11_ctrl_Riboseq_replicate1_3

description:
hs_pan_001_bg_Ri_S10_L006
processed data file: 3d_pp2_riboseq_rpkm.txt


title: 20    Aged    C


title: 15    Aged    C


title: Hs_H1_BG96_3D_d11_ctrl_Riboseq_replicate1_2

description:
hs_pan_001_bg_Ri_S10_L005
processed data file: 3d_pp2_riboseq_rpkm.txt


title: 13    Aged    C


title: 14    Aged    C


title: 12    Aged    C


title: Hs_H1_BG96_3D_d11_ctrl_Riboseq_replicate1_1

description:
hs_pan_001_bg_Ri_S10_L004
processed data file: 3d_pp2_riboseq_rpkm.txt


title: 11    Aged    C


title: 10    Aged    C


title: Sarcoma [SH59W12_Cell1]

description:
miRNA
SA0153


description:
Hs_H1_BG149_d13_cytoplasmic_RNA_RNAseq_2_S10_L001
processed data file: pp2_fractionation_rpkm.txt

source_name: Unmodified hESCs were differentiated to the PP2 stage. RNA from nuclear and cytosolic fractions was isolated.

value: ribo-depleted, stranded


title: 9    Aged    C


title: 7    Aged    C


title: Sarcoma [SH59W10_Cell2]

description:
miRNA
SA0141


title: 6    Aged    C


title: Hs_H1_BG149_d13_nuclear_RNA_RNAseq_2

description:
Hs_H1_BG149_d13_nuclear_RNA_RNAseq_2_S9_L001
processed data file: pp2_fractionation_rpkm.txt


description:
Hs_H1_BG080_d13_cytoplasmic_RNA_RNAseq_1_S8_L007
processed data file: pp2_fractionation_rpkm.txt


title: 18    Aged    C


title: 5    Aged    C


title: Sarcoma [SH51904_Cell4]

description:
miRNA
SA1005


title: 4    Aged    C


title: Hs_H1_BG080_d13_nuclear_RNA_RNAseq_1

description:
Hs_H1_BG080_d13_nuclear_RNA_RNAseq_1_S7_L007
processed data file: pp2_fractionation_rpkm.txt


title: Sarcoma [SH59W04_Cell2]

description:
miRNA
SA0114


title: Sarcoma [SH51847_Cell2]

description:
miRNA
SA0943


title: 2    Aged    C


title: Hs_H1_BG130_d13_LINC00261-sORF3-10_RNAseq_1

description:
Hs_H1_BG130_d13_LINC00261_sORF3_10_RNAseq_1_S14_L004
processed data file: lncrna_ko_rpkm.txt

source_name: hESCs with bilallelic frameshifts in LINC00261 sORF1 were differentiated to the PP2 stage

value: LINC00261 sORF1 frameshift


title: 1    Aged    C


title: Sarcoma [SH59Q63_Cell2]

description:
miRNA
SA0091

value: unknown


title: Sarcoma [SH59Q64_Cell2]

description:
miRNA
SA0095


title: Non-cancer 3 [SH55R05_Cell3]

description:
miRNA
XB0984


title: Hs_H1_BG129_d13_LINC00261-sORF3-3_RNAseq_1

description:
Hs_H1_BG129_d13_LINC00261_sORF3_3_RNAseq_1_S18_L004
processed data file: lncrna_ko_rpkm.txt


title: 96    Aged    B

source_name: Aged B_peripheral blood HSC

value: Aged B


title: 94    Aged    B


title: Hs_H1_BG113_d13_LINC00261_6-8_RNAseq_1

description:
Hs_H1_BG113_d13_LINC00261_6-8_RNAseq_1_S8_L001
processed data file: lncrna_ko_rpkm.txt

source_name: LINC00261 KO hESCs were differentiated to the PP2 stage


title: 95    Aged    B


title: 92    Aged    B


title: 91    Aged    B


title: Hs_H1_BG111_d13_LINC00261_7-9_RNAseq_1

description:
Hs_H1_BG111_d13_LINC00261_7-9_RNAseq_1_S6_L001
processed data file: lncrna_ko_rpkm.txt


title: 90    Aged    B


title: 87    Aged    B


title: 89    Aged    B


title: 3    Aged    C


title: 88    Aged    B


title: Hs_H1_BG111_d13_LINC00261_6-8_RNAseq_1

description:
Hs_H1_BG111_d13_LINC00261_6-8_RNAseq_1_S5_L001
processed data file: lncrna_ko_rpkm.txt


title: 86    Aged    B


title: Hs_H1_BG057_d13_Alien_30_RNAseq_1

description:
Hs_H1_BG057_d13_Alien_30_RNAseq_1_merged
processed data file: lncrna_ko_rpkm.txt


title: 84    Aged    B


title: Non-cancer 3 [SH55M62_Cell3]

description:
miRNA
XB0956

value: M


title: 85    Aged    B


title: 83    Aged    B


title: Hs_H1_BG063_d13_Alien_7_RNAseq_1

description:
Hs_H1_BG063_d13_Alien_7_RNAseq_1_merged
processed data file: lncrna_ko_rpkm.txt


title: 82    Aged    B


title: 81    Aged    B


title: Non-cancer 3 [SH55M61_Cell2]

description:
miRNA
XB0951


title: Hs_H1_BG063_d13_834C11.4_6_RNAseq_1

description:
Hs_H1_BG063_d13_834C11_4_6_RNAseq_1_merged
processed data file: lncrna_ko_rpkm.txt

source_name: RP11-834C11.4 KO hESCs were differentiated to the PP2 stage


title: 79    Aged    B


title: 78    Aged    B


title: Non-cancer 3 [SH55M49_Cell3]

description:
miRNA
XB0940


title: Non-cancer 3 [SH55M65_Cell4]

description:
miRNA
XB0969


title: 77    Aged    B


title: Hs_H1_BG158_d13_LINC00261-knockout_RNAseq_1

description:
Hs_H1_BG158_d13_LINC00261-knockout_RNAseq_2_S3_L001
processed data file: lncrna_ko_rpkm.txt


title: 76    Aged    B


title: Hs_H1_BG49_834C11.4_20_d13_RNAseq_1

description:
BG49_834C11-4_20_d13_S9_L001
processed data file: lncrna_ko_rpkm.txt


title: 75    Aged    B


title: 74    Aged    B


title: Hs_H1_BG020_d13_834C11.4_RNAseq_1

description:
Hs_H1_BG020_d13_834C11-4_RNAseq_1_S9_L004
processed data file: lncrna_ko_rpkm.txt


title: Non-cancer 3 [SH55M58_Cell1]

description:
miRNA
XB0942


title: 73    Aged    B


title: Non-cancer 3 [SH55M40_Cell1]

description:
miRNA
XB0922


title: Non-cancer 3 [SH56N38_Cell4]

description:
miRNA
XB0911


title: Non-cancer 3 [SH55M45_Cell2]

description:
miRNA
XB0931


title: Non-cancer 3 [SH56N39_Cell3]

description:
miRNA
XB0897


title: Non-cancer 3 [SH55M49_Cell2]

description:
miRNA
XB0939


title: Non-cancer 3 [SH56N39_Cell2]

description:
miRNA
XB0898


title: 72    Aged    B


title: Hs_H1_BG052_d13_MIR7-3HG_11_RNAseq_1

description:
Hs_H1_BG052_d13_MIR7-3HG_25_RNAseq_1_merged
processed data file: lncrna_ko_rpkm.txt

source_name: MIR7-3HG KO hESCs were differentiated to the PP2 stage


title: Hs_H1_BG063_d13_834C11.4_40_RNAseq_1

description:
Hs_H1_BG063_d13_834C11_4_40_RNAseq_1_merged
processed data file: lncrna_ko_rpkm.txt


title: 71    Aged    B


title: Hs_H1_BG020_d13_MIR7-3HG_32_RNAseq_1

description:
Hs_H1_BG020_d13_MIR7-3HG_32_RNAseq_1_S10_L004
processed data file: lncrna_ko_rpkm.txt


title: 80    Aged    B


title: Non-cancer 3 [SH56N40_Cell2]

description:
miRNA
XB0893


title: Non-cancer 3 [SH56N40_Cell3]

description:
miRNA
XB0892


title: 69    Aged    B


title: Hs_H1_BG80_d13_SOX9-AS1_RNAseq_2

description:
Hs_H1_BG80_d13_SOX9-AS1_RNAseq_2_S12_L003
processed data file: lncrna_ko_rpkm.txt

source_name: SOX9-AS1 KO hESCs were differentiated to the PP2 stage


title: 67    Aged    B


title: 66    Aged    B


title: Non-cancer 3 [SH55M15_Cell4]

description:
miRNA
XB0889


title: Hs_H1_BG058_d13_Scar_RNAseq_1

description:
Hs_H1_BG058_d13_Scar_RNAseq_1_merged
processed data file: lncrna_ko_rpkm.txt

source_name: LHFPL3-AS2 KO hESCs were differentiated to the PP2 stage


title: Non-cancer 3 [SH56827_Cell3]

description:
miRNA
XB0884


title: 65    Aged    B


title: 63    Aged    B


title: 64    Aged    B


title: Hs_H1_BG065_d13_LINC00479_38_RNAseq_1

description:
Hs_H1_BG065_d13_LINC00479_38_RNAseq_1_merged
processed data file: lncrna_ko_rpkm.txt

source_name: LINC00479 KO hESCs were differentiated to the PP2 stage


title: Non-cancer 3 [SH55M13_Cell4]

description:
miRNA
XB0881

source_name: Serum


title: 62    Aged    B


title: Hs_H1_BG52_TUNAR_16_d13_RNAseq_1

description:
BG52_TUNAR-16_d13_S8_L001
processed data file: lncrna_ko_rpkm.txt

source_name: TUNAR KO hESCs were differentiated to the PP2 stage

value: TUNAR-/-


title: 61    Aged    B

value: Caucasian


title: Hs_H1_BG51_TUNAR_21_d13_RNAseq_1

description:
BG51_TUNAR-21_d13_S7_L001
processed data file: lncrna_ko_rpkm.txt


title: 70    Aged    B

value: peripheral blood


title: 60    Aged    B


title: Hs_H1_BG058_d13_GATA6-AS1_7_RNAseq_1

description:
Hs_H1_BG058_d13_GATA6-AS1_7_RNAseq_1_merged
processed data file: lncrna_ko_rpkm.txt

source_name: GATA6-AS1 KO hESCs were differentiated to the PP2 stage

value: H1 ES cells


title: 58    Aged    B


title: 59    Aged    B


title: 56    Aged    B


title: Non-cancer 3 [SH55M08_Cell3]

description:
miRNA
XB0872


title: Non-cancer 3 [SH55M13_Cell1]

description:
miRNA
XB0878


title: 54    Aged    B


title: Hs_H1_BG063_d13_PDX1_RNAseq_1

description:
Hs_H1_BG063_d13_PDX1_RNAseq_1_merged
processed data file: lncrna_ko_rpkm.txt

source_name: PDX1 KO hESCs were differentiated to the PP2 stage

value: ES-derived late pancreatic progenitor cells


title: Non-cancer 3 [SH55M08_Cell2]

description:
miRNA
XB0871


title: Non-cancer 3 [SH55M06_Cell4]

description:
miRNA
XB0869


title: 52    Aged    B


title: 53    Aged    B


title: 51    Aged    B


title: Non-cancer 3 [SH55M06_Cell2]

description:
miRNA
XB0867


title: 50    Aged    B


title: Non-cancer 3 [SH55M06_Cell1]

description:
miRNA
XB0866


title: 49    Aged    B


title: Hs_H1_BG063_d13_LINC00479_15_RNAseq_1

description:
Hs_H1_BG063_d13_LINC00479_15_RNAseq_1_merged
processed data file: lncrna_ko_rpkm.txt


title: Non-cancer 3 [SH56224_Cell4]

description:
miRNA
XB0861


title: Hs_H1_BG113_d13_ctrl_RNAseq_1

description:
Hs_H1_BG113_d13_ctrl_RNAseq_1_S7_L001
processed data file: lncrna_ko_rpkm.txt

value: WT


title: 55    Aged    B


title: 48    Aged    B


title: 47    Aged    B


title: Hs_H1_BG111_d13_ctrl_RNAseq_1

description:
Hs_H1_BG111_d13_ctrl_RNAseq_1_S4_L001
processed data file: lncrna_ko_rpkm.txt

value: polyA, stranded


title: Non-cancer 3 [SH56828_Cell4]

description:
miRNA
XB0854


title: 45    Aged    B


title: 43    Aged    B


title: 46    Aged    B


title: 42    Aged    B


title: Hs_H1_BG130_d13_CRISPRctrl_RNAseq_2

description:
Hs_H1_BG130_d13_CRISPRctrl_RNAseq_2_S15_L004
processed data file: lncrna_ko_rpkm.txt


title: 44    Aged    B


title: 41    Aged    B


title: Hs_H1_BG023_d13_PDX1_RNAseq_1

description:
BG23_PDX1_d13_S5_L001
processed data file: lncrna_ko_rpkm.txt


title: 39    Aged    B


title: 38    Aged    B


title: Hs_H1_BG063_d13_ctrl_RNAseq_1

description:
Hs_H1_BG063_d13_ctrl_RNAseq_1_merged
processed data file: lncrna_ko_rpkm.txt


title: 35    Aged    B


title: 34    Aged    B


title: Hs_H1_BG020_d13_ctrl_RNAseq_1

description:
Hs_H1_BG020_d13_ctrl_RNAseq_1_S8_L004
processed data file: lncrna_ko_rpkm.txt


title: 33    Aged    B


title: Hs_H1_BG062_d3_Alien_7_RNAseq_1

description:
Hs_H1_BG062_d3_Alien_7_RNAseq_1_merged
processed data file: lncrna_ko_rpkm.txt

source_name: LINC00261 KO hESCs were differentiated to the definitive endoderm stage

value: ES-derived definitive endoderm cells


title: 30    Aged    B

value: Female


title: 29    Aged    B

value: Hematopoietic Stem Cells (HSCs)


title: 32    Aged    B


title: Non-cancer 3 [SH56824_Cell4]

description:
miRNA
XB0853

value: serum


title: Hs_H1_BG049_d3_Alien-GATA6-AS1_RNAseq_1

description:
BG49_Alien-GATA6-AS1_d3_S6_L001
processed data file: lncrna_ko_rpkm.txt


title: Hs_H1_BG129_d13_CRISPRctrl_RNAseq_1

description:
Hs_H1_BG129_d13_CRISPRctrl_RNAseq_1_S19_L004
processed data file: lncrna_ko_rpkm.txt


title: Non-cancer 3 [SH56824_Cell3]

description:
miRNA
XB0852


title: 25    Aged    B


title: 26    Aged    B


title: Hs_H1_BG043_d3_445F12.1_34_RNAseq_1

description:
Hs_H1_BG043_d3_445F12_1_34_RNAseq_1_merged
processed data file: lncrna_ko_rpkm.txt

source_name: RP11-445F12.1 KO hESCs were differentiated to the definitive endoderm stage


title: 27    Aged    B