title: ROOT ZONE II (1.5mm) REP 3 [RNA-seq]

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

description:
Z2 Rep 3
D3-2_S6
processed data file:
RNAseq_Genediff_pilot
RNAseq_Isoformsdiff_pilot

data_processing:
The paired end reads were mapped to the A. thaliana var. Columbia reference genome (TAIR10) using TopHat. Multi-step process of transcriptome assembly and differential expression analysis was done using the Cufflinks tool. Reads that map to each transcript were counted and normalized based on fragment length and total reads. Normalized counts were expressed in terms of FPKM values (fragments per kilobase of transcript per million mapped fragments). FPKM is directly proportional to abundance of the transcript. The expression data was generated at a False Discovery Rate = 0.01 (FDR=0.01). At this FDR, a total of 33,234 genes were tested.
Expression quantification and differential gene expression analysis were performed using cufflinks and cuffdiff respectively (version 2.2.1) with default parameters. The cuffdiff output files were parsed with custom scripts to generate the final annotated tables of differentially expressed genes.
Genome_build: TAIR10
Supplementary_files_format_and_content: differential gene expression

source_name: solid media plates; 24 hr light grown

growth_protocol: Arabidopsis thaliana var. Columbia (COL-0) seedlings were grown on sterile solid media plates containing 0.5 % phytagel. The plates were vertically placed in growth chambers with continuous light (80-100 µmol m -2) at a constant temperature of 19° C.  Two Arabidopsis thaliana Col-0 cell culture lines were used: Wild Type (WT) and ARG1 KO SALK_024542C line (ARG1 T-DNA insertion knockout), all cell cultures derived from hypocotyls. Tissue culture cells were plated on 60mm round, nutrient agar Petri plates cultured in a horizontal position until turnover and installation into the BRIC hardware.  All of the sub-culturing on the plates was conducted in the laboratory of the PIs and the University of Florida.  Plates were planted in a laminar flow hood and stored in sterile Biotransfer Boxes (BT). Plates with cells were kept in the dark and at ambient temperature.  Preparation of specialized plates and biology  Petri plates.   Because of their configuration within the BRIC flight hardware, sterility was maintained on all surfaces (interior and exterior) of the Petri plates. The media in the plates for BRIC had to be 5mm deep or less to accommodate the biology and the PDFU cover hardware. For a 60mm dish, this calculates out to 6.7 mLs. After pouring, the plates are allowed to solidify, and then transferred to a sterile Biotransporter (to maintain sterility of external surface) until planting.  Preparation of cell culture plates.  The liquid media from a sterile cell suspension was decanted, and the cells were washed once with fresh liquid media, and then decanted again. A sterile scoop was used to place about 1 gram of cells in the surface on the plate and disperse evenly across the surface. The cover was replaced, but not taped, and transferred to a sterile BT.  The BT was wrapped in black cloth and stored at room temperature. The same day plates were transported by car to the Kennedy Space Center, NASA for the same night (3:00 AM) Turn Over. The ground control plates were turned over 48 hours later.   BRIC Spaceflight Hardware  The hardware for this experiment was the NASA BRIC-LED (Biological Research In a Canister – Light Emitting Diode). The LED component of the hardware was disabled and all biology was held in the dark for the duration of the experiment. The BRIC-LED canisters hold six 60 mm diameter Petri plates in small sub-compartments called PDFUs (Petri Dish Fixation Units). The PDFUs allow an externally activated fixation step without manipulating the samples. We were allocated 10 PDFUs: 5 in BRIC A and 5 in BRIC B. The 2 replicate plates of WT cultured cells and the 3 replicate plates of ARG1 KO were distributed among the BRIC A canister. The 2 replicate plates of WT cultured cells were distributed among the BRIC B canister. One of the PDFU slots in each BRIC was used to hold a HOBO™ data logger to record temperature. The HOBO temperature data collection begins immediately after the biology is sealed in the BRICs, 24 hours before launch.   An additional set of Petri plates within BRIC hardware, identical to that launched for Spaceflight, was prepared for the Ground Control. The Ground Control was housed in the OES (Orbital Environmental Simulator) chamber in the Spaceflight Life Sciences Laboratory (SLSL) at Kennedy Space Center (KSC). The Ground Control was initiated with a precise 24 hour delay to enable the OES environment to be programmed with the environmental profile taken from telemetry of the Space Shuttle. Nominally, the Ground Control BRIC hardware and samples experienced the same external environment profile as the hardware and samples on the Space Shuttle. Environmental parameters that are controlled on the OES and made identical to flight are cabin temperature, humidity and CO2 concentration.

extract_protocol:
Total RNA was extracted from these frozen samples using Picopure RNA isolation kit (Arcturus®, Life technologies). RNA concentration was determined on a Qubit (Thermo Fisher/Life Technologies, Inc) and sample quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).
Library preparation:  Five ng of total RNA was used for cDNA library construction using CloneTech SMART-Seq V3 ultra low input RNA kit for sequencing (Clontech Laboratories, Inc,) according to manufacturer's protocol. Briefly, 1st strand cDNA was primed by the SMART-SMARTer II A oligonucleotide and then base-pairs with these additional nucleotides, creating an extended template. The reverse transcriptase then switches templates and continues transcribing to the end of the oligonucleotide, resulting full-length cDNA that contains an anchor sequence that serves as a universal priming site for second strand synthesis. cDNA was amplified with primer II A for 10 PCR cycles. Then Illumina sequencing libraries were generated with 120 pg of cDNA using Illumina Nextera DNA Sample Preparation Kit (Cat#: FC-131-1024) per manufacturer’s instructions. Briefly, 120 pg of cDNA was fragmented by tagmentation reaction and then adapter sequences added onto template cDNA by PCR amplification. Libraries were quantitated by Bioanalyzer and qPCR (Kapa Biosystems, catalog number: KK4824). Finally, the libraries were pooled by equal molar concentration and sequenced by Illumina 2X150 NextSeq 500 (Illumina Inc., CA, U.S.).
Illumina sequencing:  Sequencing experiments were performed at the Interdisciplinary Center for Biotechnology Research (ICBR) gene expression and sequencing core, University of Florida. In preparation for sequencing, barcoded libraries were sized on the bioanalyzer, quantitated by QUBIT and qPCR (Kapa Biosystems, catalog number: KK4824). Individual samples were pooled equimolarly at 4 nM. This “working pool” was used as input in the NextSeq500 instrument sample preparation protocol (Illumina, Part # 15048776, Rev A). Typically, a 1.3 pM library concentration resulted in optimum clustering density in our instrument (i.e., ~200,000 clusters per mm2). Samples were sequenced on a single flowcell, using a 2x150 cycles (paired-end) configuration. A typical sequencing run in the NextSeq500 produced 750-800 million paired-end reads with a Q30>=85%. For RNA seq, around 40 million reads/sample provided sufficient depth for transcriptome analysis.

treatment_protocol: Plants were grown for 8 days

tag: cultivar

tag: genotype/variation

value: WT

tag: age

value: 8 days old plants, light grown

tag: tissue

value: Roots

tag: tissue subtype

value: 1.5mm sections including root elongation and root hair zone

tag: biosource type

value: RNAlater fixed_sample


title: P09_S02_CSF

status: Public on Oct 27 2018

type: SRA

city: Phoenix

first: Kendall

last: Van Keuren-Jensen

state: AZ

address: 445 N. Fifth Street

country: USA

institute: The Translational Genomics Research Institute

library_source: transcriptomic

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt), with an adapter sequence of TGGAATTCTCGGGTGCCAAGG. Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data archive contains RPM read counts for miRNAs / piRNAs / tRNAs / GENCODE annotations / circular RNAs.

molecule: total RNA

organism: Homo sapiens

source_name: Cerebrospinal fluid

extract_protocol:
RNA was isolated using MiRVana Paris (Ambion).
TruSeq Small RNA library prep kit (Illumina) was used. Samples were multiplexed. Strand specificity is non-stranded. Type of starting material is total RNA.

tag: condition

value: Intraventricular Brain Hemorrhage

tag: anatomical location

value: Entire brain

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: MiRVana Paris (Ambion)


title: HeLa Mitotic Chromatin 5C R1T1

city: München

first: Marlies

middle: E

last: Oomen

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

description: MO5CM-Hela-M-C-combined__5158-TalLmoHindIIIDA.score.sorted.subset.singletonFiltered.anchorFiltered.symmetrical.selfMerged.scaled-200000000.balanced__15000__6.balanced.matrix

library_source: genomic

data_processing:
Library strategy: 5C-Seq
Mapping onto custom build genome based on 5C primer.  For more details see supplemental methods of Oomen et al, BioRxiv 2018 (https://www.biorxiv.org/content/early/2018/07/11/365866) and https://github.com/dekkerlab/cworld-dekker
Binning and balancing to obtain contact matrix files. For more details see supplemental methods of Oomen et al, BioRxiv 2018 (https://www.biorxiv.org/content/early/2018/07/11/365866) and https://github.com/dekkerlab/cworld-dekker
Genome_build: Custom built based on 5C primers, originally used in Hnisz et al, Science 2016
Supplementary_files_format_and_content: Insulation score calling and heatmap generation calling using cWorld pipeline (cworlds-dekker : https://github.com/dekkerlab/cworld-dekker). For more details see supplemental methods of Oomen et al, BioRxiv 2018 (https://www.biorxiv.org/content/early/2018/07/11/365866)

molecule: genomic DNA

source_name: HeLa-S3 cells

growth_protocol: HeLa-S3 cells were cultured glutamax DMEM supplemented with 10% heat-inactivated FBS and penicillin-streptomycin

extract_protocol:
For each 5C library, 25 million cells or the equivalent in mitotic chromatin clusters from HeLa S3  were used as input. Cells  were crosslinked for 10 minutes at room temperature in a final concentration of 1%  formaldehyde. Glycine was added to quench crosslinking and pellets were frozen at -80C until 5C library generation
5C was performed  according to published protocols (Dostie et al., 2006; Hnisz et al., 2016).

treatment_protocol: Cells were harvested as non-synchrous without treatment or arrested in mitosis using 24hr Thymidine treatment and 12hr Nocodazole (mitotic cells). Mitotic chromatin was purified from mitotic cells using percoll gradients.

tag: protocol

tag: enzyme

value: HindIII

tag: cell type

value: Human adenocarcinoma cells

tag: cell line


title: ROOT ZONE I (0.5mm) REP 1 [RNA-seq]

description:
Z1 Rep 1
C1-2_S1
processed data file:
RNAseq_Genediff_pilot
RNAseq_Isoformsdiff_pilot

organism: Arabidopsis thaliana

value: 0.5mm from the tip including the root cap


title: ROOT ZONE I (0.5mm) REP 3 [RNA-seq]

description:
Z1 Rep 3
C3-2_S3
processed data file:
RNAseq_Genediff_pilot
RNAseq_Isoformsdiff_pilot


title: P30_S01_CSF


title: ROOT ZONE II (1.5mm) REP 1 [RNA-seq]

description:
Z2 Rep 1
D1-2_S4
processed data file:
RNAseq_Genediff_pilot
RNAseq_Isoformsdiff_pilot


title: P27_S02_CSF


title: ROOT ZONE II (1.5mm) REP 2 [RNA-seq]

description:
Z2 Rep 2
D2-2_S5
processed data file:
RNAseq_Genediff_pilot
RNAseq_Isoformsdiff_pilot


title: P05_S06_CSF


title: ROOT ZONE I (0.5mm) REP 2 [RNA-seq]

description:
Z1 Rep 2
C2-2_S2
processed data file:
RNAseq_Genediff_pilot
RNAseq_Isoformsdiff_pilot


title: P28_S02_CSF


title: P25_S01_CSF


title: P28_S01_CSF


title: P29_S01_CSF


title: P29_S06_CSF


title: P10_S06_CSF


title: P27_S04_CSF


title: P10_S07_CSF


title: Dm_Input_S4

city: Swansea

first: Tomas

middle: Nicholas

last: Generalovic

state: West Glamorgan

address: Swansea University, Singleton Campus

department: Bioscience

country: United Kingdom

institute: Swansea University

data_processing:
Sequence data quality checked using FastQC (v0.11.7).
Adapter sequences removed using Cutadapt (v1.16) with parameters; --trim-n -f fastq -q 15,15 -u -2 -U -2.
Sequenced reads mapped to respective reference genomes (D. melanogaster; GCA_000001215.4 and Nicrophorus vespilloides; GCA_001412225.1) using BWA mem (v0.7.17) parameters; bwa mem -M and sorted for high-quality maps using AWK (v4.1.3) parameters; F '\t' '($0 ~/^@/ || $5 > 59)’. High quality reads were converted to Bam files using Samtools (v1.9) flagstat command.
Duplicates reads were removed using Picard (v2.17.11) parameters; (REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT).
Drosophila melanogaster MACS2 genome build; dm. Nicrophorus vespilloides MACS2 genome build; 1.70e8.
bed files generated using MACS2; (v2.1.0) using parameters; callpeaks -B --keep-dup 100 representing summits of all peaks.
Genome_build: D. melanogaster; GCA_000001215.4 and Nicrophorus vespilloides; GCA_001412225.1
Supplementary_files_format_and_content: bed files generated using MACS2

organism: Drosophila melanogaster

source_name: 3rd instar staged larvae

growth_protocol: Drosophila melanogaster stocks were reared in yeast-based food vials (Manchester Fly Facility). Nicrophorus vespilloides mature adults were fed decapitated Tenebrio sp. (Live foods direct, UK) twice weekly ad libitum. Both insect species maintained on a 16: 8-hour light: dark cycle at 22 ± 1 °С with humidity of 55-65%.

extract_protocol:
Fragmented chromatin was processed through Chromatraps® ChIP protocol using 30 µg of chromatin.
ChIP-Seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (#E7645S).

treatment_protocol: Drosophila melanogaster 3rd instar larvae were collected (30 individuals per biological replicate) and flash frozen in liquid nitrogen. Nicrophorus vespilloides neural tissue (one brain per replicate) was extracted in under 10 minutes via dissection in ice-cold Phosphate Buffered Saline (PBS) outlined in Cunningham et al., (2014) and flash-frozen in liquid nitrogen. Collected samples were suspended in PBS and homogenised using a hand-held Pellet Pestle® Motor (Kontes, UK) for a total of 2.5 minutes made up of 30 seconds homogenization and five seconds rest. DNA was cross-linked to chromatin using 1% formaldehyde for 10 minutes on wet ice at 4 ˚C. Fixation of DNA was quenched using 0.65 M Glycine and the homogenate was collected by spinning at 6000 x g for five minutes (4 ˚C). Drosophila melanogaster samples were treated with 800 µL hypertonic buffer for 10 minutes followed by 500 µL lysis buffer for another 10 minutes. Nicrophorus vespilloides samples were treated with 500 µL hypertonic buffer, incubated for 10 minutes followed by another 10 minutes in 300 µL lysis buffer. Drosophila melanogaster samples were sonicated for a total of 10 minutes and Nicrophorus vespilloides samples sonicated for a total of 8 minutes using a Bioruptor sonicator (Diagenode) on high power in 30 second intervals.

tag: strain

value: Oregon-R

tag: antibody

value: H3K4me3 (Chromatrap®, #700010)

tag: developmental stage

value: 3rd instar staged larvae

value: 3rd instar larvae


title: Dm_H3K4me3_ChIP_S4


title: P34_S01_CSF


title: CD90- 17_(MTA-1_0)

type: RNA

city: Amsterdam

first: Olga

middle: N

last: Karpus

address: Meibergdreef 69-71

department: Tytgat Institute for Liver and Intestinal research

country: Netherlands

institute: Academic Medical Center

description: C57BL/6J mice were used for colon isolation and flow-sorting experiments

hyb_protocol: The GeneChip Hybridization, Wash and Stain Kit (#900720) is used for the for the hybridizations, washing, and staining of the chips. Affymetrix Clariom® D array HT (Affymetrix) according to the standard protocols of the Dutch Genomics Service and Support Provider  (MAD, Science Park, University of Amsterdam, Netherlands)

scan_protocol: The GeneChip Hybridization, Wash and Stain Kit (#900720) is used for scanning of the chips.

data_processing:
The Affymetrix Command Console (v1.1) and Expression Console software (v1.1) are used to measure the performance of the washing, staining and scanning of the chips, and provide the data stored in DTT format and Cell Intensity File (*.cel) for each GeneChip processed.
Robust Multichip Average (RMA) normalization.

organism: Mus musculus

source_name: sorted colon fibroblasts Epcam-CD45-CD31-GP38+

label_protocol: 2 ng RNA was amplified and labeled using 3’ IVT pico kit Affymetrix RNA amplification kit (Nugene) according to manufacturer’s protocol

extract_protocol: RNA from the colons was extracted with Agencourt RNAdvance Cell v2 kit (Beckman Coulter, Beverly, Massachusetts, USA) according to manufacturers’ protocol including DNA digestion step. RNA integrity and concentration were quantified with BioAnalyzer (Agilent Technologies).

value: colon

tag: sorted population


title: CD90+ 20_(MTA-1_0)


title: CD90- 19_(MTA-1_0)


title: CD90+ 16_(MTA-1_0)


title: CD90- 15_(MTA-1_0)


title: Dm_H3K4me3_ChIP_S3


title: CD90+ 18_(MTA-1_0)


title: 2572_KCV_1_26_CC

city: Nashville

first: Kasey

last: Vickers

state: TN

address: 312B Preston Research Building

institute: Vanderbilt University

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt), with a 3' adapter sequence of TGGAATTCTCGGGTGCCAAGGAACTC. Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data archive contains RPM read counts for miRNAs / piRNAs / tRNAs / GENCODE annotations.

source_name: Plasma

extract_protocol:
Total RNA was isolated using miRNAeasy columns with Qiazol. Size selection method was Pippen prep.
TruSeq Small RNA library prep kit (Illumina) was the library construction kit used. Multiplexing was not used. Strand specificity was non-stranded. Type of starting material was total RNA.

value: Healthy Control

value: High density lipoprotein

value: miRNeasy (Qiagen)


title: 2572_KCV_1_28_CHL001

value: Systemic Lupus Erythematosus


title: 2572_KCV_1_25_VK


title: 2572_KCV_1_30_CHL003


title: CD90+ 14_(MTA-1_0)


title: Dm_Input_S2


title: Dm_Input_S1


title: ROOT ZONE II (1.5mm) REP 2

hyb_protocol: Amplified and labeled cDNA (5 µg/sample) was fragmented and hybridized with rotation onto Affymetrix GeneChip Arabidopsis ATH1 Genome Arrays for 16h at 45°C. Arrays were washed on a Fluidics Station 450 (Affymetrix) with the Hybridization Wash and Stain Kit (Affymetrix) and the Washing Procedure FS450_0004.

scan_protocol: scan was performed using Affymetrix GeneChip Scanner 3000 7G

data_processing: The MAS5 data was generated by using the Affymetrix Expression Console software using default analysis settings and global scaling as normalization method.

label: biotin

label_protocol: cDNA was synthesized using Ovation Pico WTA System (NuGEN Technologies Inc.) and cDNA was labeled using Encore Biotin Module (NuGEN Technologies Inc.)

extract_protocol: Total RNA was extracted from these frozen samples using Picopure RNA isolation kit (Arcturus®, Life technologies). RNA concentration was determined on a Qubit (Thermo Fisher/Life Technologies, Inc) and sample quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).

treatment_protocol: Plants were grown for 8 days.

tag: cultivar

tag: genotype

value: WT

value: Root

tag: tissue part

value: 1.5mm sections including root elongation and root hair zone

value: 8 days old

value: RNAlater fixed_sample


title: T21-100-3 dataset II

city: Tartu

first: Hindrek

last: Teder

address: Tiigi 61b

country: Estonia

institute: The Competence Centre on Health Technologies

description:
acoustically sheared
TAC-seq_trisomy2_UMI1.tsv
TAC-seq_trisomy2_UMI2.tsv
TAC-seq_trisomy2_UMI3.tsv

data_processing:
BCLs were converted and demultiplexed to FASTQs by sample using Illumina's bcl2fastq2 (version 2.20) with --barcode-mismatches 0 and --no-lane-splitting
Reads were converted to FASTA format, trimmed to 62 bp, shorter than 62 bp reads were removed using FASTX-Toolkit (version 0.0.14)
UMI subsequences were joined using AWK
Reads were demultiplexed by target sequence using FASTX-Toolkit with 5 mismatches
Target sequence (54 bp) were trimmed, reads with N nucleotide were removed using FASTX-Toolkit
Identical UMI sequences (8 bp) were merged using FASTX-Toolkit
Read and molecule counts were calculated per sample and target using different UMI thresholds (1-3)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file containing sample name, targeted locus, read and molecule counts at fixed UMI threshold

extract_protocol:
Genomic DNAs from GM01359 and GM04616 cell lines (NIGMS Human Genetic Cell Repository at the Coriell Institute of Medical Research (USA)) were extracted using DNeasy Blood and Tissue kit (Qiagen). To mimic cfDNA, the genomic DNAs were fragmented to 150-200 bp using Covaris M220 Focused-ultrasonicator (Thermo Fisher) with following settings: 50 μl volume, 10% duty cycle, 75 W peak incident power, 200 cycles per burst and 360 s. Concentrations were quantified by Qubit dsDNA HS (Thermo Fisher).
10 ng of acoustically sheared (Covaris) cell-free like DNAs were combined to create excess rates of chromosome 21 above diploidy level, that mimic 10 to 20% fetal fraction. 100% fraction is the GM04616 cell line DNA with trisomy 21. Samples were pipetted into strip tubes, adding 1 μl of 10 µM TAC-seq probe mixture and 1 µl 10× hybridization buffer, containing 100 mM Tris-HCl (pH 7.5) (Sigma-Aldrich), 500 mM KCl (Sigma-Aldrich), 0.2% Tween-20 (Sigma-Aldrich) and 0.1 mM EDTA (Sigma-Aldrich). The final hybridization volume was 12 µl. The content was mixed on vortex and centrifuged briefly. Strip tubes were placed on thermocycler, denatured 2 min at 98°C, following hybridization at 60°C overnight. After hybridization, thermostable ligase reaction master mix was added on thermocycler, keeping constant (60°C) hybridization temperature. Following, 3 µl Taq DNA ligase mixture, containing 1.5 µl 10× Taq DNA ligation buffer (NEB) and 1.5 µl Taq DNA ligase (5 U/µl; NEB) was added to each individual reaction tube and mixed by pipetting. Ligation reaction was stopped after 20 min incubation by placing reaction tubes on ice. 25 μl of previously combined Dynabeads MyOne Carboxylic Acid beads (3 µl) (Thermo Fisher) and 22 µl of capture buffer was added to ice-cooled ligated sample. The content was mixed by vortex. The capture was carried out for 20 min at RT, and after that the samples were placed on DynaMag-96 Side Magnet (Thermo Fisher) holding 8-well strip tubes on VersiPlate Frame (Thermo Fisher). The clean supernatant was removed.Then, strip tubes were removed from the magnet and 18 µl of PCR master mix was added directly to beads. The master mix contained 1× proofreading HOT FIREPol Blend Master Mix (SolisBiodyne, Tartu, Estonia) and 250 nM TAC-seq Left primer. In addition to universal TAC-seq Left, 12 different TAC-seq barcode oligonucleotides were used to introduce a six-nucleotide barcode to each studied sample. For that, 2 µl of 5 µM TAC-seq Barcoded primers were added individually to each PCR reaction. Strip tubes were closed with clean domed caps, mixed on vortex until all beads were suspended. The reaction was incubated at 95°C for 12 min, followed by two cycles of 95°C for 20 s, 57°C for 60 s and 72°C for 20 s. In addition, 18 cycles of 95°C for 20 s, 65°C for 20 s and 72°C for 10 s with a final extension at 72°C for 1 min using the default ramp speed of the T100 cycler (Bio-Rad) were performed. PCR products were pooled together into 1.5 ml tube. The pooled tube was placed on magnet to remove carboxylated beads before the following column purification. Clear supernatant was purified with DNA Clean & Concentrator-5 column (Zymo Research) and eluted with 30 µl EB. The library was size-selected using AMPure XP beads (Beckman Coulter) in a single-step selection to reduce 81 bp linear PCR double-stranded by-product. Beads were added 1:1 ratio of the purified PCR product, incubated for 5 min at room temperature and captured by a magnet for 3 min. After incubation on magnet, the supernatant was discarded and the remaining beads were centrifuged at 500 ×g for 10 s. After centrifugation, the beads were placed again on the magnet and all remaining supernatant was removed. The beads were eluted directly without ethanol washing in 20 µl of EB and incubated for 1 min at RT. Finally, the eluted library was transferred to a clean tube after 1 min incubation on the magnet. The library (single 180 bp product) was visualized on a TapeStation High Sensitivity D1000 ScreenTape (Agilent Technologies).
Library was analyzed by Illumina MiSeq instrument using custom LNA barcode primer, 10 pM loading concentration, 62 bp for read-1 and 6 bp for barcode read-2

tag: t21 cell line

tag: t21 cell line proportion

tag: t18 cell line

tag: t18 cell line proportion


title: ROOT ZONE II (1.5mm) REP 3

tag: tissue

tag: age

tag: biosource type


title: ROOT ZONE II (1.5mm) REP 1


title: ROOT ZONE I (0.5mm) REP 2


title: Dm_Input_S3


title: ROOT ZONE I (0.5mm) REP 1


title: ROOT ZONE I (0.5mm) REP 3


title: CD90- 13_(MTA-1_0)


title: P35_S01_CSF

tag: condition

value: Intraventricular Brain Hemorrhage

tag: anatomical location

value: Entire brain

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: MiRVana Paris (Ambion)


title: Dm_H3K4me3_ChIP_S1

tag: strain

value: Oregon-R

tag: antibody

value: H3K4me3 (Chromatrap®, #700010)


title: T21-100-2 dataset II


title: T21-20-1 dataset II


title: Dm_H3K4me3_ChIP_S2

tag: developmental stage

value: 3rd instar staged larvae

value: 3rd instar larvae


title: 2572_KCV_1_29_CHL002


title: T21-100-1 dataset II


title: T21-0-3 dataset II


title: T21-10-1 dataset II


title: T21-20-2 dataset II


title: 2572_KCV_1_27_AE

value: Healthy Control


title: DLD-1 pLVX-NC

city: Guangzhou

first: han

last: kai

state: Guangdong

address: Dongfeng Road East

country: China

institute: Sun Yat-sen university cancer center

description:
microRNA
microRNA microarray in DLD-1 cells transfected with negative control plasmid

hyb_protocol: The labeled cRNA over the procession of  inspissation and desiccation and then redissolved with water. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent Microarray Scanner (part number G2505C).

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing:
Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, miRNAs that at least 3 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.
Differentially expressed miRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed miRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts.

source_name: DLD-1 cells, negative control

label_protocol: Sample labeling and array hybridization were performed according to the Agilent miRNA Microarray Systemwith miRNA Complete Labeling and Hyb Kit protocol (Agilent Technology). Briefly, total miRNA from each sample was labeled with Cyanine 3-pCp under the action of T4 RNA ligase.

growth_protocol: Human colorectal carcinoma cell line DLD-1 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum.  The culture conditions were 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis

treatment_protocol: DLD-1 cells transfected with circLONP2 overexpressing plasmid or negative control plasmid were treated with Trizol reagent for further microRNA extraction.

tag: cell type

value: colorectal carcinoma cell line

tag: cell line

tag: genotype/variation


title: m4 Sca1+Gli1ZsGreen-

hyb_protocol: The GeneChip Hybridization, Wash and Stain Kit (#900720) is used for the for the hybridizations, washing, and staining of the chips. Affymetrix GeneChip® HT MG-430 PM 16-Array Plate and Gene Titan MC system (Affymetrix) according to the standard protocols of the Dutch Genomics Service and Support Provider  (MAD, Science Park, University of Amsterdam, Netherlands)

data_processing: The Affymetrix Command Console (v1.1) and Expression Console software (v1.1) are used to measure the performance of the washing, staining and scanning of the chips, and provide the data stored in DTT format and Cell Intensity File (*.cel) for each GeneChip processed.

label: Biotin

treatment_protocol: Gli1CreERT2-ZsGreen mice were intraperitoneally injected with 1 mg tamoxifen for 5 consecutive days. At day 6 animals were sacificed and colons were isolated.

tag: strain background

tag: mouse id#

tag: time point

value: 5 days after tamoxifen injection

value: colon

value: colon fibroblasts Epcam-CD45-CD31-GP38+

tag: sorted population


title: m3 Sca1+Gli1ZsGreen-

tag: tissue


title: m4 Sca1+Gli1ZsGreendim


title: m4 Sca1-Gli1ZsGreen-


title: m3 Sca1-Gli1ZsGreen-


title: m2 Sca1-Gli1ZsGreen-


title: m4 Sca1+Gli1ZsGreenhigh


title: m1 Sca1+Gli1ZsGreen-


title: m2 Sca1+Gli1ZsGreen-


title: m3 Sca1+Gli1ZsGreendim


title: Desiccated_2

city: Austin

first: Xun

last: Wang

state: Texas

address: 2506 Speedway, NMS 3.236

department: Department of Molecular Biosciences

institute: University of Texas at Austin

description:
des_vs_plate.csv
des_vs_stationary.csv
des_vs_log.csv

data_processing:
The sequencing data was mapped to the A. baumannii 17978 genome and analyzed by CLC Genomics Workbench software 11.0 to generate RPKM values. The coding sequences were used for genome annotation instead of all the genes.
Baggerley's test was performed on desiccated samples compared with each of the three growth conditions.
The Baggerley's test generated a p-value associated with the weighted proportion fold change for each gene in each comparison.
We used an FDR corrected p<0.01 as the cutoff for a significant change.
Genome_build: CP000521
Supplementary_files_format_and_content: The comma separated values (.csv) files contain feature ID, weighted propotions fold change and the FDR corrected p-value for each CDS obtained from Baggerley's test comparing desiccated samples to samples from each growth condition.

organism: Acinetobacter baumannii

source_name: Bacteria suspension

growth_protocol: A. baumannii 17978 was streaked out onto LB agar plates and incubated at 37C overight to generate the LB agar samples (sample 1 and 2). The strain was inoculated into liquid LB medium overnight to generate the stationary samples (sample 3 and 4). The stationary phase bacteria were diluted to OD600 ~0.01 and re-grow to OD600 ~0.3 to generate the log phase samples (sample 5 and 6).

extract_protocol:
Ambion RNA extraction kit (Thermo Fisher) was used.
RNA libraries were prepared for sequencing using standard Illumina protocols (NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®)

treatment_protocol: For desiccation (sample 7 and 8), A. baumannii grown on an LB agar plate was scraped into LB medium and diluted to OD600 of 0.5. Inocula of 0.5mL were added into 6 wells of a 6-well plates in duplicate. The two plates were desiccated for 24h. Then TRI reagent was added to each well for rehydration and cell lysis and suspensions of 6 wells were pooled to one sample.

tag: growth condition

value: desiccated bacteria


title: T21-10-3 dataset II

tag: t21 cell line

tag: t21 cell line proportion

tag: t18 cell line

tag: t18 cell line proportion


title: m2 Sca1+Gli1ZsGreendim


title: igf3-dsRNA-1

city: Wuxi

first: Lanmei

address: East Shanshui Road 9

institute: Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the C. carpio v3 reference genome using Hisat2 aligner with default parameters.
The mapped reads from each sample were assembled using StringTie v1.3.3b, then assembled transcripts were annotated using gﬀcompare program (v 0.10.1) from the stringTie packageand. The unknown transcripts were used to lncRNA identification using CPAT, NR and Pfam.
The RPKM value was used to estimate the expression levels of lncRNAs and mRNAs in every sample.
Differential expression analyses in the control and igf3-dsRNA groups were performed using the R package (edgeR 3.22.3), an absolute value of |log2 (fold change)| > 1 and an adjusted P-value of < 0.05 were set as the filter criteria for significant differential expression.
Genome_build: C. carpio v3
Supplementary_files_format_and_content: tab-delimited text files include rawcount number for each Sample

organism: Cyprinus carpio

source_name: gonad

growth_protocol: Juvenile fishes were 8 weeks post hatching (10.92 ± 0.14 g), and maintained in the water aquaculture experimental facilities during the acclimation and experimental periods. Maintained under 12-h light/dark cycles at 28 ± 1 °C, and fed twice daily with special aquatic compound feed (Tech-bank Co., Ltd., Ningbo, China).

extract_protocol:
Total RNA was isolated using the standard TRIzol (Invitrogen) protocol
Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit (Life Technology). The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio-analyzer. Strand-specific libraries were constructed by following the manufacturer’s instructions (Illumina).
Illumina HiSeq X Ten for 2 × 150 bp pair-end sequencing

treatment_protocol: Juvenile C. carpio were randomly divided into two groups with 15 fishes per group. The experimental group was injected intraperitoneally of igf3 dsRNA at a dose of 5 μg/g body weight, the control group was injected intraperitoneally of H2O at an equal dose based on gram body weight. Gonad samples were obtained at 24 h after injection, and 9 fish samples were obtained per group.

value: gonad

tag: age

value: 8 weeks post hatching

value: FFRC

tag: genotype


title: CAF-Exos: CAF-derived exosomes

city: Shanghai

first: xing

last: qin

state: Shanghai

address: Zhizaoju load 639

institute: Shanghai Jiaotong University

description: miRNA expression data from CAF-derived exosomes

hyb_protocol: Biotin-labeled sample were hybridized for 16 h at 48°C on an Affymetrix miRNA 3.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: Affymetrix GeneChip Command Console software (version 4.0, Affymetrix) was used to get raw data and then RMA normalization method was taken. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Primary cultured CAFs

label_protocol: Exosomal RNA were tailed with Poly A. FlashTag Biotin HSR labeled RNA were prepared according to the standard Affymetrix protocol from 1 μg total RNA (FlashTag™ Biotin HSR RNA Labeling Kit For miRNA Arrays, 2012, Affymetrix).

growth_protocol: NFs and CAFs were cultured in Dulbecco's Modified Eagle Medium (DMEM, Gibco-BRL) supplemented with 10% fetal bovine serum (Gibco-BRL), 100 units/mL penicillin, and 100 μg/mL streptomycin at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol: Exosomal RNA was extracted using mirVanaTM miRNA Isolation Kit (Ambion, USA) according to the manufacturer's instructions.

treatment_protocol: NFs or CAFs cultured to confluency were incubated with serum-free DMEM for 48 h. The CM was collected and filtered through a 0.22 μm PVDF filter. Exosomes were purified from NF- or CAF-CM using ultracentrifugation and placed on ice in the Lysis/Binding Buffer.

value: head and neck cancer-associated fibroblast exosomes

tag: cell passages

value: The fifth generation


title: Desiccated_1

tag: strain


title: control-3

value: WT


title: T21-20-3 dataset II


title: T21-10-2 dataset II


title: m3 Sca1+Gli1ZsGreenhigh

tag: cell type


title: igf3-dsRNA-2


title: igf3-dsRNA-3


title: control-2


title: Log phase_1

source_name: Bacteria culture

value: bacteria grown to log phase


title: Nv_Input_S4

organism: Nicrophorus vespilloides

source_name: Whole adult brain

tag: antibody

tag: developmental stage

value: Sexually mature adult

value: adult whole brain


title: T21-0-2 dataset II


title: DLD-1 pLVX-circLONP2

description:
microRNA
microRNA microarray in DLD-1 cells transfected with circLONP2 overexpressing plasmid

source_name: DLD-1 cells, circLONP2 overexpression

tag: cell line

tag: genotype/variation


title: NF-Exos: NF-derived exosomes

description: miRNA expression data from NF-derived exosomes

source_name: Primary cultured NFs

value: normal fibroblast exosomes


title: Unaffected family member [0030]

type: genomic

city: La Jolla

first: Neil

last: Chi

state: CA

address: 9500 Gilman Drive

department: Medicine

institute: University of California, San Diego

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).  After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

scan_protocol: After allele-specific staining BeadChip arrays were coated with staining reagents (LX1, LX2, XC3 and XC4)/ethanol , dried for 1 hour and scanned on a HiScan Instrument (Illumina).

data_processing:
Genomic DNA from saliva sampeles were genotyped using Illumina HumanCoreExome-12 v1-1 BeadChip arrays
Genotype: AA,AB,BB,or NC (no call)

label: Cy5, Cy3

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

extract_protocol: Saliva samples were collected and genomic DNA (gDNA) was purified using the QIAamp DNA Blood Mini Kit (Qiagen; 51104).

tag: group

value: Control


title: T21-0-1 dataset II


title: Proband [0024]

value: Cardiomyopathy


title: LB agar_2

value: bacteria grown on LB agar plates


title: Log phase_2


title: m1 Sca1+Gli1ZsGreendim

tag: strain background

tag: mouse id#

tag: time point

value: 5 days after tamoxifen injection

tag: sorted population


title: LB agar_1

tag: growth condition


title: Unaffected family member [0012]


title: Unaffected family member [0029]


title: Stationary phase_2

value: bacteria grown to stationary phase


title: Unaffected family member [0010]


title: Nv_H3K4me3_ChIP_S4

value: H3K4me3 (Chromatrap®, #700010)

tag: tissue


title: control-1


title: Nv_Input_S3


title: Trinity_A. argotaenia2

city: hangzhou

first: chengchao

last: zhang

address: Xuelin Street No.16

institute: Hangzhou Normal University

data_processing:
The paired-end sequencing was performed on an Illumina Hiseq 4000 platform
The reads containing adaptor, low quality bases and undetermined bases were  removed
The processed data (*txt) was generated using software Trinity 2.4.0
The TPM values were contained in the processed data (*txt).
Genome_build: Trinity.gene.fasta
Supplementary_files_format_and_content: fasta

organism: Amentotaxus argotaenia

source_name: Trinity_A. argotaenia_fresh twigs

growth_protocol: The growth conditions were set at 25 ± 1°C with a light/dark cycle of 12/12 h and a 60%–70% relative humidity

extract_protocol:
Total RNAs were extracted using Trizol reagent (Qiagen, Hilden, Germany) according to the manufacturer’s procedure. The quantity and purity of RNAs were analyzed using a Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: three years

tag: phenotype

value: non-taxol producing (NTP) tree

value: fresh twigs (wood+needles)


title: Unaffected family member [0008]


title: Cardiomyopathy family member [0013]


title: m1 Sca1-Gli1ZsGreen-

value: colon

value: colon fibroblasts Epcam-CD45-CD31-GP38+


title: m2 Sca1+Gli1ZsGreenhigh


title: Trinity_A. argotaenia3

tag: age


title: Nv_H3K4me3_ChIP_S3


title: m1 Sca1+Gli1ZsGreenhigh


title: Trinity_T. grandis3

organism: Torreya grandis

source_name: Trinity_T. grandis_fresh twigs


title: Stationary phase_1


title: Nv_Input_S2


title: Unaffected family member [0020]


title: Nv_H3K4me3_ChIP_S2


title: Unaffected family member [0004]


title: Trinity_A. argotaenia1


title: Nv_Input_S1


title: Nv_H3K4me3_ChIP_S1


title: Trinity_T. grandis1


title: Cardiomyopathy family member [0002]


title: Trinity_P. chienii1

organism: Pseudotaxus chienii

source_name: Trinity_P. chienii_fresh twigs

value: taxol-producing (TP)


title: Cardiomyopathy family member [0001]


title: Trinity_P. chienii3


title: monocyte_treated_exosomes_rep4 [miRNA]

status: Public on Oct 26 2018

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Standard Agilent scanning protocol with Agilent SureScan microarray scanner (G2505C).

data_processing: Scanned images were processed with Agilent Feature Extraction v10.7 with default parameters to obtain raw data. Raw data were imported in R and processed using the limma package, performing background correction with normexp method and quantile normalization. After normalization, expression levels for replicate probes were collapsed using the avereps function and finally microRNA-level signals were obtained selecting the probe with the highest mean expression across samples, among the probes targeting the same microRNA.

source_name: monocyte co-cultured with melanoma exosomes

label_protocol: Total RNA from each sample was labeled according to the manufacturers recommendations.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with Ambion miRVANA kit according to the protocol provided by the manufacturer.

treatment_protocol: 300,000 CD14+ cells were co-cultured for 24 hours with 50 µg of exosomes isolated from the INT12 melanoma cell line generated in our laboratory

tag: subject status

value: healthy donor

value: CD14+ monocytes

tag: cocultivated with

value: 50 µg exosomes isolated from the INT12 melanoma cell line


title: monocyte_treated_exosomes_rep5 [miRNA]


title: monocyte_treated_exosomes_rep3 [miRNA]


title: Trinity_P. chienii2


title: monocyte_untreated_rep3 [miRNA]

source_name: untreated monocyte

value: none (untreated control)


title: monocyte_untreated_rep4 [miRNA]


title: monocyte_treated_exosomes_rep2 [miRNA]


title: monocyte_treated_exosomes_rep1 [miRNA]


title: Trinity_T. grandis2


title: monocyte_untreated_rep2 [miRNA]


title: monocyte_untreated_rep1 [miRNA]


title: monocyte_untreated_rep5 [miRNA]


title: Heart-Infarct area-IGF1-168 h-rep3

city: Düsseldorf

first: Axel

last: Gödecke

address: Moorenstrasse 5

department: Cardiovascular Physiology

institute: Heinrich-Heine-Universität - UKD

hyb_protocol: 600ng fragmented and Cy3-labeled cRNA was hybridized to the Microarray (G4852B) according to the manufacturer's protocol (One-Color Microarray-Based Gene Expression Analysis / Low Input Quick Amp Labeling; Agilent Technologies) at 65°C for 17 hours in the hybridization rotator.

scan_protocol: The Microarrays were scannt with the Agilent Microarray Scanner G2505C (protocol: AgilentG3_GX_1color; dye: green; scan region: Agilent HD; scan area: 61x21.6 mm; scan resolution 3µm; tiff file: 20 bit; green PMT gain: 100%). Signal intensities on 20 bit tiff images were calculated by Feature Extraction software (FE, Vers. 12.0.3.2; Agilent Technologies; Grid Template: 074809_D_F_20171030; Protocol: GE1_1200_Jun14; MetricSet: GE1_QCMT_Jun14).

data_processing: Probe signal intensities were quantile normalized across all samples to reduce inter-array variability. Input data pre-processing was concluded by baseline transformation to the median of all samples. Data analyses were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies).

source_name: heart -anterior wall- 45 min. ischemia: IGF1 1 µg/g/d (in PBS, 0.1 % BSA)

label_protocol: Synthesis of cDNA and subsequent fluorescent labelling of cRNA was performed according to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis / Low Input Quick Amp Labeling; Agilent Technologies).

growth_protocol: Mice were housed in conventional cages with a 12-h light/dark cycle and had ad libitum access to food and water.

extract_protocol: Infarcted areas were excised after the indicated times. Total RNA was isolated from heart tissue of the area at risk using the Fibrous Tissue RNeasy Kit (Qiagen, Hilden, Germany; #74704) according to manufacturer’s instruction and used for array analyses.  Labelled cRNA was hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarrays and scanned as described in the manufactors' protocol.

treatment_protocol: Mice were anaesthetized by 2% isoflurane, orotracheally intubated, and ventilated with oxygen enriched gas (40% oxygen) using a rodent ventilator (Minivent Microventilator, Hugo Sachs, Germany). Mice were placed in a supine position on a warming plate (Uno, Zevenaar, The Netherlands) to keep body temperature at 37.5°C, and received buprenorphine (0.1 mg/kg body weight, s.c.) for analgesia. Electrocardiography (ECG) was recorded continuously. After lateral thoracotomy, the pericardium was dissected and a 7-0 surgical prolene suture was cautiously passed underneath the left anterior descending coronary artery (LAD) at a position 1 mm from the tip of the left auricle. The suture ends were passed through a silicon tubing to form a snare occluder. Myocardial ischemia was produced by tightening the snare and confirmed by blanching of the myocardium and change in ECG (decrease in S wave amplitude). After 45 min, the snare occluder was opened to initiate reperfusion. Afterwards, the suture was removed and the chest was closed. Animals of the IGF1 groups received 40 ng/g mature recombinant IGF1 (Milteny Biotec GmbH, Bergisch Gladbach, Germany) subcutaneously as bolus at the begin of reperfusion. In addition, IGF1 was administered continuously for the first three days of reperfusion (1 µg/g/d) using micro-osmotic pumps (Alzet, 1003D) that were implanted subcutaneously. At the end of experimental procedures, mice were extubated after they regained spontaneous breathing. Animals received buprenorphine (0.05 ‑ 0.1mg/kg body weight, s.c.) every 8 hours up to five days for postoperative analgesia.

tag: strain

tag: Sex

value: male

value: heart -anterior wall


title: Heart-Infarct area-vehicle-168 h-rep4

source_name: heart -anterior wall- 45 min. ischemia: vehicle (PBS, 0.1 % BSA)


title: Heart-Infarct area-vehicle-48 h-rep1


title: Heart-Infarct area-IGF1-168 h-rep2


title: Heart-Infarct area-IGF1-48 h-rep4


title: Heart-Infarct area-vehicle-168 h-rep3


title: Heart-Infarct area-vehicle-168 h-rep2


title: Heart-Infarct area-IGF1-48 h-rep3


title: Heart-Infarct area-vehicle-48 h-rep4


title: Heart-Infarct area-IGF1-24 h-rep4


title: Heart-Infarct area-IGF1-24 h-rep1


title: Heart-Infarct area-IGF1-24 h-rep3


title: Heart-Infarct area-IGF1-24 h-rep2


title: Heart-Infarct area-vehicle-48 h-rep3


title: Heart-Infarct area-IGF1-168 h-rep4


title: Heart-Infarct area-vehicle-48 h-rep2


title: Heart-Infarct area-IGF1-48 h-rep1


title: Heart-Infarct area-vehicle-24 h-rep1


title: Array 4_Cum_68h

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

description: Biological replicate 1 of 3

hyb_protocol: The hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects using the expression array protocol.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing: Signal intensity data files were normalized and analyzed using the FlexArray 1.6.1 software (Genome Quebec, URL: http://genomequebec.mcgill.ca/FlexArray). The first step in the data processing was to remove the background of intensity files using a simple background subtraction. Data were then normalized for dye bias using a within-array loess and a between-array « quantile » normalization to minimize array effects. To calculate fold changes of probe intensity, normalized data were assessed using the e Bayes moderated t-test (LIMMA) included in the FlexArray software. A False Discovery Rate algorithm (Benjamini-Hochberg) was also applied.

organism: Bos taurus

source_name: Cumulus cells

label_protocol:
amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Thermo Fisher).
The labelling aRNA was done using  the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

extract_protocol: Total RNA extraction using the PicoPure RNA Isolation Kit from Thermo Fisher.

treatment_protocol:
six dairy cows were stimulated with FSH given twice daily for three days followed by an FSH withdrawal period of 68h « 68h condition ». For the « 68h +Cetro » condition, the GnRH agonist Cetrorelix (Cetrotide, Merckx-Serono), which inhibits LH secretion, was given from day 2 of FSH stimulation until COC recovery 68h following the last FSH injection (12mg per day for 5 days).
collect protocol: The recovered COC were washed twice in TLH solution and were then collected in Petri dishes containing PBS and polyvinyl alcohol (PVA). The COC were washed three times with PBS-PVA in different dishes, transferred into 1.5 ml conical tubes, and vortexed in 150µl PBS for 2min. Cells were placed into a new dish to collect oocytes and cumulus cells (CC) separately into new 1.5-ml conical tubes. The CC were washed by centrifugation three times in 150µl PBS. Cells were then snap frozen in liquid nitrogen and conserved at  80°C

tag: breed (cattle)

value: holstein

tag: cell type

value: Cumulus cells

tag: time

value: 68 hours

tag: treatment

source_name: Cumulus cells_Cetrorelix

value: Cetrorelix 12mg/day


title: Array 6_Cum_68h

description: Biological replicate 3 of 3


title: Heart-Infarct area-IGF1-48 h-rep2


title: Heart-Infarct area-vehicle-24 h-rep3


title: Heart-Infarct area-vehicle-168 h-rep1


title: Array 1_Cum_68h-Cetro

description: Biological replicate 1 of 3


title: Heart-Infarct area-IGF1-168 h-rep1


title: Heart-Infarct area-vehicle-24 h-rep4


title: Array 3_Cum_68h-Cetro

description: Biological replicate 3 of 3


title: Cell17 (RNA-seq)

city: New Haven

first: Jun

last: Lu

state: CT

address: 10 Amistad St.

department: Yale Stem Cell Center

institute: Yale University

description:
HalfCell#17
NW_half_cell_K562_RNAseq_processed_data.gct

data_processing:
Data were mapped to hg19 using TopHat using gtf files based on UCSC gene definition downloaded from the GenePattern server.
Aligned reads were quantified using the CuffDiff program, by using UCSC gtf definition for hg19, to obtain RPKM values.
Genome_build: hg19
Supplementary_files_format_and_content: gct file format (tab delimited text file); contains RPKM values

growth_protocol: The human K562 cell line was originated from American Type Culture Collection (ATCC), and was maintained in RPMI 1640 media supplemented with 10% FBS at the cell density between 2 × 105 and 2 × 106 per ml and incubated at 37°C with 5% CO2.

extract_protocol:
Cells were washed once with cold PBS (Life Technologies) and diluted to < 1000 cells/ml. Prior to picking single cells, 10 µl of lysis buffer (0.25% Triton-X100, 4 units (U) recombinant RNase Inhibitor, Takara) was deposited in each PCR tube. To ensure single cell resolution, we performed most experiments by hand-picking of single cells under microscope. The diluted cell mixture was placed on the cover of a petridish, and single cells without close neighbours were manually picked by using a 10 µl pipette, with each cell contained within less than 1 µl of volume. Single cells were then added into the lysis buffer. The single-cell lysates were stored at −80 °C. The lysate was split, and half of the lysate was used for RNAseq analaysis. For the cells 1 to 20, the data were paired with the small RNA sequencing data. For cell 21, both halves of the same cell were subjected to RNAseq, yielding data for 21_1 and 21_2.
Library was prepared using SMART-Seq v4 kit

treatment_protocol: No treatment

tag: sample type

value: single K562 cell


title: Array 5_Cum_68h

description: Biological replicate 2 of 3


title: Array 2_Cum_68h-Cetro

description: Biological replicate 2 of 3


title: Cell21-2 (RNA-seq)

description:
HalfCell#21-2
NW_half_cell_K562_RNAseq_processed_data.gct


title: Cell15 (RNA-seq)

description:
HalfCell#15
NW_half_cell_K562_RNAseq_processed_data.gct


title: Cell20 (RNA-seq)

description:
HalfCell#20
NW_half_cell_K562_RNAseq_processed_data.gct


title: Cell18 (RNA-seq)

description:
HalfCell#18
NW_half_cell_K562_RNAseq_processed_data.gct


title: Cell16 (RNA-seq)

description:
HalfCell#16
NW_half_cell_K562_RNAseq_processed_data.gct


title: Cell13 (RNA-seq)

description:
HalfCell#13
NW_half_cell_K562_RNAseq_processed_data.gct


title: Cell14 (RNA-seq)

description:
HalfCell#14
NW_half_cell_K562_RNAseq_processed_data.gct


title: Cell10 (RNA-seq)

description:
HalfCell#10
NW_half_cell_K562_RNAseq_processed_data.gct


title: Cell9 (RNA-seq)

description:
HalfCell#9
NW_half_cell_K562_RNAseq_processed_data.gct


title: Cell19 (RNA-seq)

description:
HalfCell#19
NW_half_cell_K562_RNAseq_processed_data.gct


title: Cell4 (RNA-seq)

description:
HalfCell#4
NW_half_cell_K562_RNAseq_processed_data.gct


title: Heart-Infarct area-vehicle-24 h-rep2


title: Cell12 (RNA-seq)

description:
HalfCell#12
NW_half_cell_K562_RNAseq_processed_data.gct


title: Cell11 (RNA-seq)

description:
HalfCell#11
NW_half_cell_K562_RNAseq_processed_data.gct


title: Cell8 (RNA-seq)

description:
HalfCell#8
NW_half_cell_K562_RNAseq_processed_data.gct


title: Cell7 (RNA-seq)

description:
HalfCell#7
NW_half_cell_K562_RNAseq_processed_data.gct


title: Cell6 (RNA-seq)

description:
HalfCell#6
NW_half_cell_K562_RNAseq_processed_data.gct


title: Cell5 (RNA-seq)

description:
HalfCell#5
NW_half_cell_K562_RNAseq_processed_data.gct


title: Cell15 (small RNA-seq)

data_processing:
Remove ligation adaptor sequence
Remove reads less than 16 in length
Map to miRNA database (miRBase v21) using miRDeep2 package program
Normalize reads to reflect the fraction among all miRNA reads
log2 transform
Genome_build: mm10
Supplementary_files_format_and_content: gct file format (tab delimited text file); contains normalized miRNA fraction among total miRNA content

extract_protocol:
Cells were washed once with cold PBS (Life Technologies) and diluted to < 1000 cells/ml. Prior to picking single cells, 10 µl of lysis buffer (0.25% Triton-X100, 4 units (U) recombinant RNase Inhibitor, Takara) was deposited in each PCR tube. To ensure single cell resolution, we performed most experiments by hand-picking of single cells under microscope. The diluted cell mixture was placed on the cover of a petridish, and single cells without close neighbours were manually picked by using a 10 µl pipette, with each cell contained within less than 1 µl of volume. Single cells were then added into the lysis buffer. The single-cell lysates were stored at −80 °C. After thawing, the lysates were incubated at 72 °C for 20 min to release small RNAs for reaction.
Small RNA library preparation: Single-cell or half-cell lysate (5 µl) was subjected to 3’ adaptor ligation by adding 5.24 µl of 3’ adapter ligation reaction mixture (1 pmole 3’ adapter, 1.66 µl 50% PEG 8000, NEB, 250 U T4 RNA Ligase 2 truncated KQ, NEB M0373S, 0.83 µl 10× T4 RNA ligase buffer, NEB, 20 U recombinant RNase Inhibitor, Takara) and the reaction was incubated at 30 °C for 6 hours followed by 4 °C for 10 hours. Next, 5 µl adaptor-digestion mixture was added (10 pmole RT primer, 5 U Lambda exonuclease, NEB, 5 U 5’ deadenylase, NEB) and the reaction was incubated at 30 °C for 15 min followed by 37 °C for 15 min. Next, 5 µl 5’ adapter ligation reaction mixture was added (10 pmole 5’ adapter oligo, 10 U T4 RNA ligase 1, Thermo Fisher, 1 µl T4 RNA ligase buffer, Thermo Fisher, 2 µl 50% PEG 8000, NEB) and incubated at 37 °C for 1 hour. Reverse transcription reaction was performed with three steps and was performed with M-MLV reverse transcriptase (RT) (Invitrogen 28025-013). First, 5 µl of RT reaction mix was added (10 pmole RT primer) and the reaction was incubated at 65 °C for 5 minutes. Second, the mix of 2.1 µl 5x First Strand buffer (Invitrogen), 0.3 µl H2O and 0.8 µl of 0.1M DTT (Invitrogen) was added and incubated at 42 °C for 30 minutes. Third, 3.3 µl of RT reaction was added (0.6ul M-MLV reverse transcriptase, 1 µl 5x First Strand buffer (Invitrogen), 0.3 µl H2O, 0.8 µl of 0.1M DTT, Invitrogen and 0.6 µl 10mM dNTP mix, Invitrogen) and the reaction was incubated at 42 °C for 2 h. The first PCR amplification was carried out by adding 35 µl of the reagents (3.5 µl 10xThermoPol Reaction Buffer (NEB), 0.7 µl 10mM dNTP mix (Invitrogen), 35 pmole RT primer oligo, 35 pmole PCR primer oligo, 0.5 µl Taq DNA Polymerase (NEB), 23.3 µl H2O) and incubating at 98 °C for 30 seconds followed by 13 cycles of 98 °C for 10 seconds, 60 °C  for 30 seconds and 72 °C  for 30 seconds and a final incubation at 72 °C for 5 minutes. At last, 1 µl of the amplified product was transferred to a fresh tube and to a 25 µl of second PCR reaction consisting of 10 µM indexed primer, 10 µM RP1 primer, 2.5 µl 10x ThermoPol Reaction buffer, 0.5 µl Taq DNA Polymerase (NEB), 0.5 µl 10mM dNTP mix (Invitrogen), followed by a 30 second incubation at 98 °C, 13 cycles of 98 °C for 10 seconds, 67 °C for 30 seconds and 72 °C for 30 seconds and a final incubation at 72 °C for 5 minutes. PCR product of ~140 bp were gel-purified after 2nd PCR on a 8% acrylamide gel. Gels were prepared by adding 9.3 ml Protein Gel Mix (American Bioanalytical AB13021), 3.6ml 10x TBE, 23.1 ml water, 600 µl 10% ammonium persulfate (Sigma Aldrich), and 30 µl TEMED (American Bioanalytical). Samples were prepared by adding 1/5 volume of 6X Gel loading dye purple (New England BioLabs). Electrophoresis was performed at 140V for 80 minutes. After electrophoresis, the gel was stained in 15 ml water containing 1.5 µl GelStar Nucleic Acid Gel Stain (LONZA) for 15 minutes. All barcoded small RNA libraries were sequenced on an Illumina HiSeq 2000 instrument.


title: Cell12 (small RNA-seq)


title: Cell14 (small RNA-seq)


title: Cell3 (RNA-seq)

description:
HalfCell#3
NW_half_cell_K562_RNAseq_processed_data.gct


title: Cell2 (RNA-seq)

description:
HalfCell#2
NW_half_cell_K562_RNAseq_processed_data.gct


title: Cell1 (RNA-seq)

description:
HalfCell#1
NW_half_cell_K562_RNAseq_processed_data.gct


title: Cell8 (small RNA-seq)


title: Cell4 (small RNA-seq)


title: Cell5 (small RNA-seq)


title: Cell2 (small RNA-seq)


title: Cell3 (small RNA-seq)


title: Cell20 (small RNA-seq)


title: Cell19 (small RNA-seq)


title: Cell18 (small RNA-seq)


title: Cell17 (small RNA-seq)


title: Cell7 (small RNA-seq)


title: Cell13 (small RNA-seq)


title: Cell6 (small RNA-seq)


title: Cell9 (small RNA-seq)


title: Cell10 (small RNA-seq)


title: Cell1 (small RNA-seq)


title: Cell11 (small RNA-seq)


title: Cell16 (small RNA-seq)


title: TDC : Gene expression data of TDC sorted from spleens of naive C57BL/6 mice

first: Mirela

last: Kuka

address: Via Olgettina, 58

institute: Vita-Salute San Raffaele University

hyb_protocol: Microarray gene expression was performed by the Laboratory of Molecular Technology (NCI), with Affymetrix 430 2.0 GeneChip technology after RNA was amplified with a NuGEN WT-Ovation kit (Nugen).

data_processing: Microarray data analysis was performed with Partek Genomics Suite 6.6 (St Louis, MO, USA).

source_name: Spleen

extract_protocol: Total RNA was isolated with the RNeasy Micro kit (Qiagen) from 1,000 to 4,000 cells that were double or triple sorted from B6 splenocytes.

treatment_protocol: Total cell suspensions from spleens of naive C57BL/6 mice were made by gently mashing the debris through 40-μM nylon mesh. Viable cells were counted by Trypan Blue exclusion. The three indicated  populations were identified upon cell surface staining with antibodies to CD11c, MHC-II, and TCRb. Cells underwent two or three rounds of sequential sorting to reach a purity of ≥99%

value: TDC

value: spleen


title: DC: Gene expression data of dendritic cells sorted from spleens of naive C57BL/6 mice

scan_protocol: Microarray gene expression was performed by the Laboratory of Molecular Technology (NCI), with Affymetrix 430 2.0 GeneChip technology after RNA was amplified with a NuGEN WT-Ovation kit (Nugen).

value: DC


title: 32D-EpoR_with_Epo_simulation_Rep_2

city: Kowloon Tong

first: Jiahai

last: Shi

state: Kowloon

address: Department of Biomedical Sciences, 1F, Block 1, To, 1F, Block 1, To Yu, 1F, Block 1, To Yuen Building

country: Hong Kong

institute: City University of Hong Kong

hyb_protocol: Agilent expression arrays were hybridized according to the Agilent standard hybridization protocol. The hybridization cocktail consisted of 800 ng cy-dye labeled cRNA for each sample, Agilent hybridization blocking components, and fragmentation buffer. The hybridization cocktails were fragmented at 60°C for 30 minutes, and then Agilent 2X hybridization buffer was added to the cocktail prior to application to the array. The arrays were then hybridized for 16 hours at 65°C in an Agilent rotor oven set to maximum speed. The arrays were treated with Agilent Wash Buffer 1 at room temperature for 2 minutes, and then AgilentWash Buffer 2 for 2 minutes at 37°C. The arrays were then dipped briefly in acetonitrile before a final 30 second wash in Agilent Wash 3 Stabilization and Drying Solution, in the hood using a stir plate and stir bar at room temperature.

scan_protocol: Arrays were scanned using an Agilent scanner G2505C and the data was extracted using Agilent’s Feature Extraction software v10.1.1.1 set to the default one-color gene expression protocol.

data_processing: Data were analyzed using the limma package from Bioconductor. A quantile method was applied to achieve consistency between arrays.

label_protocol: Cy-dye labeled cRNA samples were prepared using Agilent’s Low Input Quick Amp Sample Labeling Kit. Input was 200ng total RNA. Briefly, first and second strand cDNA are generated using MMLV-RT enzyme and an oligo-dT based primer. In vitro transcription is performed using T7 RNA polymerase and either cyanine 3-CTP or cyanine 5-CTP, creating a direct incorporation of dye into the cRNA.

growth_protocol: 32D-EpoR cells were maintained  in RPMI medium with 10% FBS and 10% WEHI medium. For experiments, cells were washed and cultured in RPMI medium with only 10% FBS without any WEHI medium.

extract_protocol: Total RNA was prepared using the RNA purification kit from Qiagen following the manufacturer's protocol.

treatment_protocol: After cultured in the absence of Epo and WEHI medium, cells were treated with 10 u/ml Epo in the Epo treatment group, while the control group received no Epo treatment.

tag: cell line


title: GD15_Placenta_FOXA2_cKO_1

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

data_processing:
raw sequence files were first chekced for quality by FASTQC.
quality trimmed with fqtrim (v 0.9.4) phred 30, min length 20
mapped with hisat2 (v 2.0.3)
counted mapped reads with featureCounts and Ensembl version 89 annotation
edgeR-robust DE analysis with genes filtered at rowSum cpm>1
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text file with raw read counts for each gene

source_name: Placenta

growth_protocol: All samples were from mice at  day 15 of pregnancy

extract_protocol:
Qiagen rneasy kit
Illumina Tru-seq Stranded Ribo-zero kit

treatment_protocol: For establishment of preganancy in Foxa2 cKO mice,  intraperitoneal injections of 10 μg recombinant mouse LIF (BioLegend) at 1000 h and 1800 h were given to mice on GD4 to rescue implantation. On GD15, placenta and fetal brain were dissected.

value: Placenta

tag: genotype/variation

value: FOXA2 knockout (uterus)


title: GD15_Brain_M2

source_name: Maternal brain

value: Maternal brain

value: FOXA2 Wildtype


title: GD15_Placenta_2


title: GD15_Brain_M3


title: GD15_Placenta_FOXA2_cKO_2


title: 32D-EpoR_with_Epo_simulation_Rep_1


title: GD15_Brain_F1

source_name: Fetal brain

value: Fetal brain


title: GD15_Brain_M1


title: GD15_Placenta_1


title: GD15_Placenta_3


title: GD15_Placenta_FOXA2_cKO_3


title: T: Gene expression data of T cells sorted from spleens of naive C57BL/6 mice

label_protocol: Microarray gene expression was performed by the Laboratory of Molecular Technology (NCI), with Affymetrix 430 2.0 GeneChip technology after RNA was amplified with a NuGEN WT-Ovation kit (Nugen).

value: T


title: KO_rep 3

city: Chicago

first: Navdeep

middle: S

last: Chandel

address: 240 E Huron

institute: Northwestern University

data_processing:
Base calls performed using BCL2fastq.
RNAseq reads were aligned to the mm10 genome assembly using tophat.
Reads were counted on the exons of mm10 genes using Htseq.
differential gene expression was performed using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text, edgeR output containing normalized expression values. Bigwig of RNAseq tracks in positive and minus strands.

source_name: KO_lung endothelial cells

extract_protocol:
Cells were lysed with RLT buffer + 0.1% b-mercaptoethanol from the RNeasy Plus Micro Kit (Qiagen) and stored at -80˚C until RNA was extracted. RNA isolation were performed using the RNAeasy Plus Micro Kit (Qiagen) following the manufacturer’s instructions with an additional on-column DNase treatment using RNase-free DNase Set (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with tamoxifen to induce loss of QPC on days P0-P4. ECs were harvested on P15.

tag: strain background

value: post natal day 15

value: a subunit of mitochondrial complex III (QPC) knockout

value: lung endothelial cells


title: 32D-EpoR_without_Epo_simulation_Rep_2


title: GD15_Brain_F3


title: GD15_Brain_M4


title: 32D-EpoR_without_Epo_simulation_Rep_1


title: KO_rep 1


title: GD15_Brain_F4


title: GD15_Placenta_FOXA2_cKO_4


title: WT_rep 4

source_name: WT_lung endothelial cells

value: wild type


title: KO_rep 4


title: KO_rep 2


title: GD15_Placenta_4


title: GD15_Brain_F2


title: WT_rep 2


title: WT_rep 1


title: Cultured FL5.12 murine cells [FL52_G08_S176]

city: Cambridge

first: Sanjay

last: Prakadan

state: MA

address: 77 Massachusetts Ave, E25-356

institute: Massachusetts Institute of Technology

description:
FL52_G08_S176
fl5_rsem.txt

data_processing:
Illumina bcl2fastq2.17.1.14 was used to generate fastqs from bcl files
TopHat was used to align data
RSEM was used to generate estimates of transcripts per million reads for each single cell
Genome_build: human: hg19, mouse: mm10
Supplementary_files_format_and_content: cd8_rsem.txt: Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
Supplementary_files_format_and_content: gbmt_rsem.txt: Human Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
Supplementary_files_format_and_content: gbmut_rsem.txt: Human Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
Supplementary_files_format_and_content: l1201_rsem.txt: Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
Supplementary_files_format_and_content: fl5_rsem.txt: Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y

source_name: Transcriptome of single murine FL5.12 cell following measurement with sSMR device

extract_protocol:
Smart-seq 2
Illumina Nextera XT

value: Cultured FL5.12 murine cells


title: Cultured FL5.12 murine cells [FL52_H01_S181]

description:
FL52_H01_S181
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_H02_S182]

description:
FL52_H02_S182
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_H07_S187]

description:
FL52_H07_S187
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_H09_S189]

description:
FL52_H09_S189
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_G10_S178]

description:
FL52_G10_S178
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_H11_S191]

description:
FL52_H11_S191
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_H06_S186]

description:
FL52_H06_S186
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_H05_S185]

description:
FL52_H05_S185
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_H03_S183]

description:
FL52_H03_S183
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_G12_S180]

description:
FL52_G12_S180
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_H08_S188]

description:
FL52_H08_S188
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_H04_S184]

description:
FL52_H04_S184
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_H10_S190]

description:
FL52_H10_S190
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_G11_S179]

description:
FL52_G11_S179
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_H12_S192]

description:
FL52_H12_S192
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_G05_S173]

description:
FL52_G05_S173
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_G04_S172]

description:
FL52_G04_S172
fl5_rsem.txt


title: WT_rep 3


title: Cultured FL5.12 murine cells [FL52_G07_S175]

description:
FL52_G07_S175
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_F12_S168]

description:
FL52_F12_S168
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_F10_S166]

description:
FL52_F10_S166
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_G09_S177]

description:
FL52_G09_S177
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_G02_S170]

description:
FL52_G02_S170
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_F11_S167]

description:
FL52_F11_S167
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_G03_S171]

description:
FL52_G03_S171
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_E12_S156]

description:
FL52_E12_S156
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_F06_S162]

description:
FL52_F06_S162
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_F01_S157]

description:
FL52_F01_S157
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_F03_S159]

description:
FL52_F03_S159
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_E09_S153]

description:
FL52_E09_S153
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_E11_S155]

description:
FL52_E11_S155
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_F08_S164]

description:
FL52_F08_S164
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_F07_S163]

description:
FL52_F07_S163
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_E10_S154]

description:
FL52_E10_S154
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_E04_S148]

description:
FL52_E04_S148
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_F02_S158]

description:
FL52_F02_S158
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_E08_S152]

description:
FL52_E08_S152
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_G01_S169]

description:
FL52_G01_S169
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_E05_S149]

description:
FL52_E05_S149
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_F04_S160]

description:
FL52_F04_S160
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_E01_S145]

description:
FL52_E01_S145
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_E07_S151]

description:
FL52_E07_S151
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_E06_S150]

description:
FL52_E06_S150
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_F09_S165]

description:
FL52_F09_S165
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_D10_S142]

description:
FL52_D10_S142
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_D09_S141]

description:
FL52_D09_S141
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_D07_S139]

description:
FL52_D07_S139
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_D08_S140]

description:
FL52_D08_S140
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_D11_S143]

description:
FL52_D11_S143
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_D12_S144]

description:
FL52_D12_S144
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_E02_S146]

description:
FL52_E02_S146
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_E03_S147]

description:
FL52_E03_S147
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_F05_S161]

description:
FL52_F05_S161
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_D06_S138]

description:
FL52_D06_S138
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_D04_S136]

description:
FL52_D04_S136
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_D03_S135]

description:
FL52_D03_S135
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_C09_S129]

description:
FL52_C09_S129
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_C11_S131]

description:
FL52_C11_S131
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_D02_S134]

description:
FL52_D02_S134
fl5_rsem.txt


title: Cell21-1 (RNA-seq)

description:
HalfCell#21-1
NW_half_cell_K562_RNAseq_processed_data.gct


title: Cultured FL5.12 murine cells [FL52_C07_S127]

description:
FL52_C07_S127
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_D05_S137]

description:
FL52_D05_S137
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_C10_S130]

description:
FL52_C10_S130
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_C04_S124]

description:
FL52_C04_S124
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_C06_S126]

description:
FL52_C06_S126
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_G06_S174]

description:
FL52_G06_S174
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_C12_S132]

description:
FL52_C12_S132
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_C05_S125]

description:
FL52_C05_S125
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_C03_S123]

description:
FL52_C03_S123
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_C02_S122]

description:
FL52_C02_S122
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_B12_S120]

description:
FL52_B12_S120
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_B11_S119]

description:
FL52_B11_S119
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_B06_S114]

description:
FL52_B06_S114
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_B10_S118]

description:
FL52_B10_S118
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_B05_S113]

description:
FL52_B05_S113
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_B08_S116]

description:
FL52_B08_S116
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_B04_S112]

description:
FL52_B04_S112
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_B09_S117]

description:
FL52_B09_S117
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_C08_S128]

description:
FL52_C08_S128
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_B03_S111]

description:
FL52_B03_S111
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_B02_S110]

description:
FL52_B02_S110
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_D01_S133]

description:
FL52_D01_S133
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_B01_S109]

description:
FL52_B01_S109
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_A12_S108]

description:
FL52_A12_S108
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_A10_S106]

description:
FL52_A10_S106
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_C01_S121]

description:
FL52_C01_S121
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_A09_S105]

description:
FL52_A09_S105
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_A03_S99]

description:
FL52_A03_S99
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_A05_S101]

description:
FL52_A05_S101
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_A11_S107]

description:
FL52_A11_S107
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_A06_S102]

description:
FL52_A06_S102
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_A07_S103]

description:
FL52_A07_S103
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_A02_S98]

description:
FL52_A02_S98
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_A04_S100]

description:
FL52_A04_S100
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_A01_S97]

description:
FL52_A01_S97
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_H12_S192]

description:
FL51b_H12_S192
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_H10_S190]

description:
FL51b_H10_S190
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_B07_S115]

description:
FL52_B07_S115
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_H07_S187]

description:
FL51b_H07_S187
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_H06_S186]

description:
FL51b_H06_S186
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_H09_S189]

description:
FL51b_H09_S189
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_H05_S185]

description:
FL51b_H05_S185
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_H08_S188]

description:
FL51b_H08_S188
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_H04_S184]

description:
FL51b_H04_S184
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_H02_S182]

description:
FL51b_H02_S182
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_H03_S183]

description:
FL51b_H03_S183
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_H01_S181]

description:
FL51b_H01_S181
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL52_A08_S104]

description:
FL52_A08_S104
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_G12_S180]

description:
FL51b_G12_S180
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_H11_S191]

description:
FL51b_H11_S191
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_G09_S177]

description:
FL51b_G09_S177
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_G10_S178]

description:
FL51b_G10_S178
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_G06_S174]

description:
FL51b_G06_S174
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_G08_S176]

description:
FL51b_G08_S176
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_G03_S171]

description:
FL51b_G03_S171
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_G04_S172]

description:
FL51b_G04_S172
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_G02_S170]

description:
FL51b_G02_S170
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_F11_S167]

description:
FL51b_F11_S167
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_G01_S169]

description:
FL51b_G01_S169
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_F09_S165]

description:
FL51b_F09_S165
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_G05_S173]

description:
FL51b_G05_S173
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_F06_S162]

description:
FL51b_F06_S162
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_F05_S161]

description:
FL51b_F05_S161
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_G11_S179]

description:
FL51b_G11_S179
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_E11_S155]

description:
FL51b_E11_S155
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_F02_S158]

description:
FL51b_F02_S158
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_F01_S157]

description:
FL51b_F01_S157
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_G07_S175]

description:
FL51b_G07_S175
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_F07_S163]

description:
FL51b_F07_S163
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_F03_S159]

description:
FL51b_F03_S159
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_F12_S168]

description:
FL51b_F12_S168
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_F10_S166]

description:
FL51b_F10_S166
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_E12_S156]

description:
FL51b_E12_S156
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_E06_S150]

description:
FL51b_E06_S150
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_E08_S152]

description:
FL51b_E08_S152
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_E10_S154]

description:
FL51b_E10_S154
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_E09_S153]

description:
FL51b_E09_S153
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_E07_S151]

description:
FL51b_E07_S151
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_F08_S164]

description:
FL51b_F08_S164
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_D11_S143]

description:
FL51b_D11_S143
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_E04_S148]

description:
FL51b_E04_S148
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_E05_S149]

description:
FL51b_E05_S149
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_E02_S146]

description:
FL51b_E02_S146
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_D10_S142]

description:
FL51b_D10_S142
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_E03_S147]

description:
FL51b_E03_S147
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_D07_S139]

description:
FL51b_D07_S139
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_E01_S145]

description:
FL51b_E01_S145
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_D08_S140]

description:
FL51b_D08_S140
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_F04_S160]

description:
FL51b_F04_S160
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_D12_S144]

description:
FL51b_D12_S144
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_D03_S135]

description:
FL51b_D03_S135
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_D05_S137]

description:
FL51b_D05_S137
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_D06_S138]

description:
FL51b_D06_S138
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_D02_S134]

description:
FL51b_D02_S134
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_D04_S136]

description:
FL51b_D04_S136
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_D01_S133]

description:
FL51b_D01_S133
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_C12_S132]

description:
FL51b_C12_S132
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_C09_S129]

description:
FL51b_C09_S129
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_C11_S131]

description:
FL51b_C11_S131
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_C10_S130]

description:
FL51b_C10_S130
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_D09_S141]

description:
FL51b_D09_S141
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_C06_S126]

description:
FL51b_C06_S126
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_C07_S127]

description:
FL51b_C07_S127
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_C08_S128]

description:
FL51b_C08_S128
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_C05_S125]

description:
FL51b_C05_S125
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_C04_S124]

description:
FL51b_C04_S124
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_C02_S122]

description:
FL51b_C02_S122
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_C03_S123]

description:
FL51b_C03_S123
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_C01_S121]

description:
FL51b_C01_S121
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_B12_S120]

description:
FL51b_B12_S120
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_B11_S119]

description:
FL51b_B11_S119
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_B10_S118]

description:
FL51b_B10_S118
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_B07_S115]

description:
FL51b_B07_S115
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_B06_S114]

description:
FL51b_B06_S114
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_B08_S116]

description:
FL51b_B08_S116
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_B03_S111]

description:
FL51b_B03_S111
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_B02_S110]

description:
FL51b_B02_S110
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_B01_S109]

description:
FL51b_B01_S109
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_A11_S107]

description:
FL51b_A11_S107
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_A12_S108]

description:
FL51b_A12_S108
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_A10_S106]

description:
FL51b_A10_S106
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_A09_S105]

description:
FL51b_A09_S105
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_A07_S103]

description:
FL51b_A07_S103
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_A06_S102]

description:
FL51b_A06_S102
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_H12_S96]

description:
FL51a_H12_S96
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_A02_S98]

description:
FL51b_A02_S98
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_B09_S117]

description:
FL51b_B09_S117
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_B05_S113]

description:
FL51b_B05_S113
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_A01_S97]

description:
FL51b_A01_S97
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_A03_S99]

description:
FL51b_A03_S99
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_A08_S104]

description:
FL51b_A08_S104
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_A05_S101]

description:
FL51b_A05_S101
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_A04_S100]

description:
FL51b_A04_S100
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_H11_S95]

description:
FL51a_H11_S95
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51b_B04_S112]

description:
FL51b_B04_S112
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_H08_S92]

description:
FL51a_H08_S92
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_H10_S94]

description:
FL51a_H10_S94
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_H07_S91]

description:
FL51a_H07_S91
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_H09_S93]

description:
FL51a_H09_S93
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_H05_S89]

description:
FL51a_H05_S89
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_H03_S87]

description:
FL51a_H03_S87
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_H01_S85]

description:
FL51a_H01_S85
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_H02_S86]

description:
FL51a_H02_S86
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_H06_S90]

description:
FL51a_H06_S90
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_G12_S84]

description:
FL51a_G12_S84
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_G11_S83]

description:
FL51a_G11_S83
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_G10_S82]

description:
FL51a_G10_S82
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_G09_S81]

description:
FL51a_G09_S81
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_G07_S79]

description:
FL51a_G07_S79
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_G08_S80]

description:
FL51a_G08_S80
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_G06_S78]

description:
FL51a_G06_S78
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_G05_S77]

description:
FL51a_G05_S77
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_H04_S88]

description:
FL51a_H04_S88
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_G03_S75]

description:
FL51a_G03_S75
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_G01_S73]

description:
FL51a_G01_S73
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_F10_S70]

description:
FL51a_F10_S70
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_F12_S72]

description:
FL51a_F12_S72
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_G02_S74]

description:
FL51a_G02_S74
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_F11_S71]

description:
FL51a_F11_S71
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_F07_S67]

description:
FL51a_F07_S67
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_G04_S76]

description:
FL51a_G04_S76
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_F06_S66]

description:
FL51a_F06_S66
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_F09_S69]

description:
FL51a_F09_S69
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_F05_S65]

description:
FL51a_F05_S65
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_F01_S61]

description:
FL51a_F01_S61
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_F02_S62]

description:
FL51a_F02_S62
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_F04_S64]

description:
FL51a_F04_S64
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_F03_S63]

description:
FL51a_F03_S63
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_E12_S60]

description:
FL51a_E12_S60
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_E11_S59]

description:
FL51a_E11_S59
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_E08_S56]

description:
FL51a_E08_S56
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_E07_S55]

description:
FL51a_E07_S55
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_E10_S58]

description:
FL51a_E10_S58
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_E04_S52]

description:
FL51a_E04_S52
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_E05_S53]

description:
FL51a_E05_S53
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_E03_S51]

description:
FL51a_E03_S51
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_E06_S54]

description:
FL51a_E06_S54
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_F08_S68]

description:
FL51a_F08_S68
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_E02_S50]

description:
FL51a_E02_S50
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_D12_S48]

description:
FL51a_D12_S48
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_E01_S49]

description:
FL51a_E01_S49
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_D07_S43]

description:
FL51a_D07_S43
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_D06_S42]

description:
FL51a_D06_S42
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_D10_S46]

description:
FL51a_D10_S46
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_D09_S45]

description:
FL51a_D09_S45
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_D11_S47]

description:
FL51a_D11_S47
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_C12_S36]

description:
FL51a_C12_S36
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_D05_S41]

description:
FL51a_D05_S41
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_D04_S40]

description:
FL51a_D04_S40
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_D01_S37]

description:
FL51a_D01_S37
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_D02_S38]

description:
FL51a_D02_S38
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_D08_S44]

description:
FL51a_D08_S44
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_C11_S35]

description:
FL51a_C11_S35
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_D03_S39]

description:
FL51a_D03_S39
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_C08_S32]

description:
FL51a_C08_S32
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_C10_S34]

description:
FL51a_C10_S34
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_E09_S57]

description:
FL51a_E09_S57
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_C06_S30]

description:
FL51a_C06_S30
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_C05_S29]

description:
FL51a_C05_S29
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_C07_S31]

description:
FL51a_C07_S31
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_C09_S33]

description:
FL51a_C09_S33
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_C04_S28]

description:
FL51a_C04_S28
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_B12_S24]

description:
FL51a_B12_S24
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_C02_S26]

description:
FL51a_C02_S26
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_B11_S23]

description:
FL51a_B11_S23
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_C03_S27]

description:
FL51a_C03_S27
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_B10_S22]

description:
FL51a_B10_S22
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_B09_S21]

description:
FL51a_B09_S21
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_B08_S20]

description:
FL51a_B08_S20
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_B07_S19]

description:
FL51a_B07_S19
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_B06_S18]

description:
FL51a_B06_S18
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_B05_S17]

description:
FL51a_B05_S17
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_B04_S16]

description:
FL51a_B04_S16
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_B03_S15]

description:
FL51a_B03_S15
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_A11_S11]

description:
FL51a_A11_S11
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_B02_S14]

description:
FL51a_B02_S14
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_A12_S12]

description:
FL51a_A12_S12
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_B01_S13]

description:
FL51a_B01_S13
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_A09_S9]

description:
FL51a_A09_S9
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_A06_S6]

description:
FL51a_A06_S6
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_A07_S7]

description:
FL51a_A07_S7
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_A10_S10]

description:
FL51a_A10_S10
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_A04_S4]

description:
FL51a_A04_S4
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_A08_S8]

description:
FL51a_A08_S8
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_A05_S5]

description:
FL51a_A05_S5
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_A03_S3]

description:
FL51a_A03_S3
fl5_rsem.txt


title: Cultured FL5.12 murine cells [FL51a_A02_S2]

description:
FL51a_A02_S2
fl5_rsem.txt


title: Cultured L1210 cells [L1210serial_H12_S288]

description:
L1210serial_H12_S288
l1210_rsem.txt

source_name: Transcriptome of single L1210 leukemia cell following measurement with sSMR device

value: Cultured L1210 cells