title: SScMH_01_24mo_LA

description: SSc patient

value: skin biopsy

value: SSc patient

value: Rituximab


title: TR82

status: Public on Jan 01 2017

type: RNA

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.

data_processing: The analysis of raw data was performed with nSlover Analysis Software provided by NanoString Technologies. Data were collected as NanoString RCC files and provided as an Excel spreadsheet. The data were normalizeed to the geometric mean of the 90 most highly expressed miRNAs.

molecule: total RNA

organism: Homo sapiens

source_name: tonsils

label_protocol: RNA was not labeled; instead, RNA (33 ng/ul) was pre-processed following the NanoString manufacturer's protocol by the Ohio State Microarray Core Facility

extract_protocol: Ambion RecoverAll from Formalin Fixed Paraffin Embedded material

tag: tissue

value: tonsils

tag: disease state

value: oropharyngeal squamous cell carcinoma

tag: hpv status

value: HPV-


title: TR74

value: HPV+


title: TR71


title: ctrl_rep5

city: Guangzhou

first: Liang

last: Zhang

state: Guangdong

address: Xingnan Road 521

department: Translational Medicine Research Center

country: China

institute: Guangdong Women and Children Hospital

hyb_protocol: Labeled cDNAs were combined and hybridized to a custom microarray

scan_protocol: washing and scanning, image data were extracted using Agilent Feature Extraction software.

data_processing: Signals were normalized by using loess normalization.

source_name: pooled ctrl

label_protocol: The dual-color approach was adopted in our study, samples were labeled with Cy3 and common reference made up of several heathy controls were labeled with Cy5 by using klenow enzyme, respectively.

extract_protocol: Briefly, total RNA was extracted from nucleated cells using the Whole-Blood RNA Isolation Kit following the manufacturer’s instructions and formaldehyde agarose gel electrophoresis was used to check the quality of it. Purified RNA was reversely transcribed to cDNA and amplified using the Low-Input Quick AmpWT Labeling Kit (Agilent).

tag: reference

value: heathy controls

source_name: Whole-Blood

tag: disease

value: none, healthy control


title: PCOS_rep7

value: PCOS


title: SScMH_01_06mo_LA

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

country: USA

institute: Dartmouth Medical School

description: SSc patient

hyb_protocol: Fragmentation Buffer and Hybridization Buffer (Agilent Gene Expression Hybridization Kit) were added, and samples applied to Whole Human Genome microarrays

scan_protocol: Scanned on Axon scanner

data_processing: Images were quantified using GenePixPro

source_name: Sample: Human Tissue Biopsy

label_protocol: 200ng of total RNA was reversed transcribed using Agilent Quick-Amp Labeling Kit and labeled with Perkin Elmer Cy3

extract_protocol: Total RNA extracted using RNeasy Fibrous Tissue Mini following manufacturers protocol

treatment_protocol: Storage of human tissue in RNAlater

tag: subject

tag: treatment

source_name: Universal Human Reference

value: Universal Human Reference


title: PCOS_rep6


title: PCOS_rep5


title: ctrl_rep3


title: SScMH_01_24mo_LF

description: SSc patient


title: SScMH_01_12mo_LA

description: SSc patient


title: RegNorm_1026_LA

description: normal control

value: normal control


title: ctrl_rep8


title: ctrl_rep4


title: PCOS_rep8


title: RegNorm_1027_LA

description: normal control


title: SScMH_01_36mo_LA

description: SSc patient


title: ctrl_rep2


title: RegNorm_1024_LA

description: normal control


title: SScMH_01_12mo_LF

description: SSc patient


title: TR61


title: SScMH_01_06mo_LF

description: SSc patient


title: ctrl_rep1


title: RegNorm_1022_LA

description: normal control


title: PCOS_rep4


title: PCOS_rep3


title: MH_Norm_17_LF

description: normal control


title: TR66


title: TR36


title: TR78


title: TR9


title: TR65


title: TR75


title: TR38


title: TR22


title: TR15


title: MH_Norm_16_RA

description: normal control


title: PCOS_rep1


title: MH_Norm_17_LA

description: normal control


title: TR10


title: TR30


title: MH_Norm_14_LF

description: normal control


title: TR27


title: MH_Norm_16_RF

description: normal control


title: MH_Norm_15_LA

description: normal control


title: PCOS_rep2


title: MH_Norm_14_LA

description: normal control


title: MH_Norm_15_LF

description: normal control


title: MH_Norm_13_LF

description: normal control


title: MH_Norm_12_LA

description: normal control


title: MH_Norm_12_LF

description: normal control


title: MH_Norm_13_LA

description: normal control


title: TR46


title: CHP-902R

type: genomic

city: Gent

first: Pieter-Jan

last: Volders

address: De Pintelaan 185

country: Belgium

institute: Ghent University

hyb_protocol: Samples were hybridized on the custom array CGH arrays for 40 h at 65 °C.

scan_protocol: The samples were scanned at 5 µm resolution using a DNA microarray scanner G2505B (Agilent Technologies).

data_processing: The scan images were analyzed using the feature extraction software 9.5.3.1 (Agilent Technologies).

molecule: genomic DNA

source_name: Cell line

label_protocol: 400 ng of genomic DNA was labeled with Cy3-dCTP (GE Healthcare, Belgium) using a Bioprime array CGH genomic labeling system (Invitrogen, Belgium). In parallel, Kreatech gender-matched controls were labeled with Cy5-dCTP.

extract_protocol: The National Cancer Institute (NCI) provided DNA and RNA samples for all cell lines in the NCI 60 cancer cell line panel. For the neuroblastoma and T-ALL cell lines, RNA extraction was performed with the miRNeasy Mini Kit (QIAGEN) and DNA extraction with the QIAamp DNA Mini Kit (QIAGEN).

tag: gender

tag: cancer subtype

value: Neuroblastoma

tag: origin

value: CMGG

source_name: gender-matched control


title: TR59


title: SK-N-SH

value: F


title: SK-N-BE-2c

value: M


title: MH_Norm_11_LA

description: normal control


title: NGP


title: MH_Norm_11_LF

description: normal control


title: CHP-134


title: SHEP


title: TR26


title: SK-N-AS


title: TR21


title: TR19


title: TR6


title: TR16


title: TR48


title: TR43


title: SH-SY5Y


title: PEER

value: T-cell acute lymphoblastic leukemia

value: DSMZ


title: NormUCLccws15

description: Normal Control

tag: sample type

value: 3mm skin punch biopsy

value: skin


title: MOLT-16


title: NormUCLccws18

description: Normal Control


title: TR51

value: tonsils


title: LOUCY


title: NormUCLccws19

description: Normal Control


title: NormUCLccws17

description: Normal Control


title: TR20

value: oropharyngeal squamous cell carcinoma


title: TR13


title: ALL-SIL


title: HPB-ALL


title: TALL-1


title: TR62


title: DND-41


title: IGROV1

value: Ovarian

value: NCI


title: Jurkat


title: TR33

value: HPV-


title: TR83

value: HPV+


title: lcSScUCLccws11

description: SSc sample

value: limited SSc patient


title: lcSScUCLccws13

description: SSc sample

value: Universal Human Reference


title: lcSScUCLccws12

description: SSc sample


title: CLB-GA


title: lcSScUCLccws08

description: SSc sample


title: lcSScUCLccws07

description: SSc sample


title: N206


title: lcSScUCLccws09

description: SSc sample


title: lcSScUCLccws10

description: SSc sample


title: wt DEX 5

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

hyb_protocol: Standard Affymetrix hybridization protocol (MOUSE GENE 2.1 atlas microarrays).

scan_protocol: Standard Affymetrix scanning protocol.

data_processing: The data were processed using oligo R package normalised using quantile normalisation.

label: biotin

organism: Mus musculus

source_name: Spinal cord of 6-10 week old C57BL/6J mice

label_protocol: RNA was labeled using the Affymetrix/Ambion WT Expression kit, combined with Affymetrix GeneChip WT terminal labeling kit.

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

tag: chronic treatment

value: WT

tag: acute treatment

value: DEX

tag: genotype/variation


title: Tg DEX 5

value: TG


title: Tg SAL 5

value: SAL


title: NB-1

value: Neuroblastoma

value: CMGG


title: TR79


title: TR77


title: CAKI-1

value: M

value: Renal


title: TR56


title: TR72


title: IMR-32


title: U251

value: CNS


title: lcSScUCLccws06

description: SSc sample

value: 3mm skin punch biopsy

value: skin


title: SNB-19


title: TR37

value: tonsils

value: oropharyngeal squamous cell carcinoma


title: lcSScUCLccws05

description: SSc sample


title: 2H 128μg/ml GR-SU_vs_control_4

city: Kagoshima City

first: Kentaro

last: Oyama

address: Sakuragaoka 8-35-1

country: Japan

institute: Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan

description: Gene expression after 2H

scan_protocol: The arrays were then scanned with an Agilent scanner (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Staphylococcus aureus subsp. aureus MW2

source_name: S.aureus 2H 128μg/ml GR-SU

label_protocol: Test and control cDNAs were labelled with Cy3 and Cy5 (GE Healthcare UK), respectively.

extract_protocol: Total RNA was extracted from the bacterial cells using a FastRNA Pro Blue Kit (MP Biomedicals, Cleveland, OH, USA) according to the manufacturer’s protocol.

tag: strain

source_name: S.aureus 2H 0μg/ml GR-SU


title: wt SAL 5


title: wt SAL 4


title: Tg SAL 4


title: TR25


title: Tg DEX 3


title: Tg DEX 4


title: wt DEX 4


title: 2H 128μg/ml GR-SU_vs_control_3

description: Gene expression after 2H


title: OVCAR-4

value: F

value: Ovarian

value: NCI


title: NCI-ADR-RES


title: PPY10

city: Bologna

first: Stefania

last: Purgato

address: via Selmi 3

department: Pharmacy and Biotechnology

country: Italy

institute: University of Bologna

description: ChIP-chip PPY10 cells for CENP-A

hyb_protocol: Manufacturer's NimbleScan Protocol.

scan_protocol: Manufacturer's NimbleScan Protocol.

data_processing:
Each feature on the array has a corresopnding log2-ratio that is provided in the GFF files. This is the ratio of the input singals for the experimental and test samples were were co-hybridized to the array. The log2-ratio is computed and scaled to center the ratio data round zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values of all features on the array from each log2-ratio values.
Normalized log-ratios ch1/ch2 (q-spline normalization).

organism: Pongo pygmaeus

source_name: CENP-A ChIP DNA from PPY10 cells

label_protocol: Standard NimbleGen protocol.

extract_protocol: 2x10E6 cells were harvested and washed in PBS. The cells were lysed in 5ml of Buffer I (85 mM KCl, 5.5% sucrose, 10 mM Tris pH 7.6, 0.5 mM Spermidine, 0.2 mM EDTA, 250 uM PMSF) and 5 ml of Buffer II (85 mM KCl, 5.5% sucrose, 10 mM Tris pH 7.6, 0.5 mM Spermidine, 0.2 mM EDTA, 250 uM PMSF, 0.1% NP-40). Nuclei were washed and resuspended in Buffer III (85 mM KCl, 5.5% sucrose, 10 mM Tris pH 7.6, 1.5 mM CaCl2, 3 mM MgCl2, 250 uM PMSF). Nuclei were digested with MNase (60 units/ml) and RNase A (3ug/ml) for 20 minutes at room temperature. Digestion was stopped adding EDTA (10mM final concentration). The supernatant containing the first soluble fraction of chromatin was recovered by centrifugation. After over-night incubation of chromatin in 5 mM NaCl buffer (10 mM Tris pH 7.5, 0.5 mM EDTA, 0.5 mM EGTA, 250 uM PMSF, 0.05% NP-40, 5 mM NaCl) on ice, the supernatant containing the second soluble fraction of chromatin was recovered. The chromatin was diluted in 50 mM NaCl buffer (10 mM Tris pH 7.5, 0.5 mM EDTA, 0.5 mM EGTA, 250 uM PMSF, 0.05% NP-40, 50 mM NaCl) and pre-cleared with protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 1 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of anti-CENP-A antibody at 4C. After incubation with protein A sepharose beads (50 µl) for 4 h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 15 min at 4C: 140 mM NaCl buffer (10 mM Tris pH 7.5, 0.5 mM EDTA, 0.5 mM EGTA, 250 uM PMSF, 0.05% NP-40, 140 mM NaCl) and 200 mM NaCl buffer (10 mM Tris pH 7.5, 0.5 mM EDTA, 0.5 mM EGTA, 250 uM PMSF, 0.05% NP-40, 200 mM NaCl). The protein-DNA complexes were eluted from the beads in 400 µl elution buffer (10 mM Tris pH 7.5, 0.5 mM EDTA, 0.5 mM EGTA, 250 uM PMSF, 0.05% NP-40, 50 mM NaCl, 1% SDS) at room temperature for 30 min. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input using Qiagen PCR Purification kit and was amplified using the Sigma-Aldrich Whole Genome Amplification kit.

tag: cell type

value: lymphoblastoid cells

source_name: Input DNA from PPY10 cells


title: TR73

value: HPV+


title: 2H 128μg/ml GR-SU_vs_control_2

description: Gene expression after 2H


title: 2H 128μg/ml GR-SU_vs_control_1

description: Gene expression after 2H


title: TR18


title: TK-10


title: HCT-15

value: Colon


title: TR17


title: TR7


title: TR24


title: UO-31


title: TR29


title: A498


title: TR28


title: TR14


title: wt SAL 3

value: WT


title: NormUCLccws16

description: Normal Control

value: normal control

value: Universal Human Reference


title: Tg SAL 3

value: TG

value: SAL


title: wt DEX 2

value: DEX


title: SN12C

value: M

value: Renal


title: Tg DEX 2


title: wt DEX 3


title: Tg SAL 2


title: lcSScUCLccws14

description: SSc sample

value: 3mm skin punch biopsy

value: skin

value: limited SSc patient


title: Tg DEX 1


title: wt SAL 2


title: RXF-393


title: ACHN


title: TR11

value: tonsils

value: oropharyngeal squamous cell carcinoma


title: TR12


title: NCI-H460

value: Non-Small Cell Lung

value: NCI


title: TR67

value: HPV+


title: TR68


title: TR52

value: HPV-


title: TR49


title: R786-0


title: NCI-H522


title: EKVX


title: NPC H3K27ac-Rep2

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

description: ChIP-chip NPCs H3K27ac

hyb_protocol: The labeled ChIP DNA was hybridized for 16-18 h at 42C, and then washed  using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on a NimbleGen MS 200 Microarray scanner (Roche) using 100% laser power and 2μm resolution.

data_processing: Raw signal intensities were quantified from TIFF images using MS 200 Data Collection software. Microarray data were analysed in R using the bioconductor packages Beadarray and Limma according to the Epigenesys NimbleGen ChIP-on-chip protocol 43. Replicate probe values were collapsed to the arithmetic mean prior to generating log2 (ChIP/Input) ratios.

source_name: H3K27ac ChIP DNA from 46c differentiated NPC

label_protocol: Ten nanograms (optimal) of input or ChIP DNA were amplified using the WGA2 whole genome amplification kit (Sigma). Amplified material was labelled with Cy3 or Cy5 by random priming according to the NimbleGen ChIP-chip protocol (Roche). In total, 2 or 3 biological replicates with dye swaps were hybridized for 20 h and washed according to manufacturer´s protocol. A custom 3x720K mouse tiling array (NimbleGen, Roche) containing 179,493 unique probes from different genomic regions, with each probe represented by 4 replicates was used.

growth_protocol: N2B27 for 5 days

extract_protocol: Nuclei from 3x10^6 mESCs or sorted Sox1+ve NPCs were prepared and resuspended in NB-R (85 mM NaCl, 5.5% Sucrose, 10mM TrisHCl pH 7.5, 3 mM MgCl2, 1.5 mM CaCl2, 0.2 mM PMSF, 1 mM DTT), Micrococcal nuclease (MNase) digestion and native ChIP were performed as previously described (Eskeland et al. 2010, Pradeepa et al.2012)  Antibodies used for ChIP were; H3K4me1 (Abcam ab8895) and H3K27ac (Millipore 07-360).

treatment_protocol: Sox1-GFP positive NPCs were FACS sorted for Green channel after 5 days

value: 46c ESCs N2B27 differentiation in NPCs for 5 days and GFP sorted

tag: chip antibody

source_name: Input DNA from differentiated NPCs

tag: control type

value: input DNA


title: NCI-H322M


title: Tg SAL 1


title: wt DEX 1

value: WT


title: TR42

tag: tissue

tag: disease state


title: A549


title: wt SAL 1


title: RP10T VS RP14N

city: Beijng

first: bobby

last: zhang

address: DaTun road 15th

institute: IBP

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction(v10.7)

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Tumor

label_protocol: 10 µg of total RNA were primed with 2 µL Random Primer at 70℃ 5 min, then reversed transcribed at 40℃ 1.5 h,at last,labeled with Cy3-dCTP or Cy5-dCTP at 37℃ 1.5 h，70℃ 5 min.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: Nonkeratinizing Carcinoma

tag: age

tag: Sex

value: male

source_name: Adjacent non-tumor


title: NPC H3K27ac-Rep1

description: ChIP-chip NPCs H3K27ac


title: SF-268

value: F

value: CNS


title: TR39

tag: hpv status


title: RP10T VS RP12N


title: NCI-H226

value: M


title: TR55


title: RP10T VS RP11N


title: HOP-92


title: TR88


title: TR53


title: TR8


title: ESC H3K27ac-Rep2

description: ChIP-chip ESCs H3K27ac

source_name: H3K27ac ChIP DNA from 46c ESC

growth_protocol: GMEM+ Supplement

value: 46c ESCs

source_name: Input DNA from 46c ESCs


title: RP9T VS RP9N


title: NPC H3K4me1-Rep2

description: ChIP-chip NPCs H3K4me1

source_name: H3K4me1 ChIP DNA from 46c differentiated NPC


title: TR32

source_name: tonsils


title: ESC H3K27ac-Rep1

description: ChIP-chip ESCs H3K27ac


title: RP10T VS RP10N

value: female


title: NPC H3K4me1-Rep1

description: ChIP-chip NPCs H3K4me1


title: ESC H3K4me1-Rep2

description: ChIP-chip ESCs H3K4me1

source_name: H3K4me1 ChIP DNA from 46c ESC


title: SNB-75


title: TR23


title: S21DAP_replicate 2

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

hyb_protocol: After checking labeling efficiency, each 1,650ng of cyanine 3-labeled cRNA target was fragmented at 60°C for 30 min (Agilent Gene Expression Hybridization Kit) by adding 10X blocking agent and 25X fragmentation buffer. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent O.sativa GE 180K microarray. The arrays hybridized at 65oC for 17 h using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (C2505C) using one color scan setting for 4x180k array slides (Scan Area 175,546 with 54 x 10 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Fluorescence images of the hybridized arrays were generated using the Agilent DNA Microarray Scanner, and the intensities were extracted with Agilent Feature Extraction software ver.10.7.3.1.(Grid: 074336_D_F_20150401) The average flourescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3.1 (Agilent Technology, USA).

organism: Oryza sativa

source_name: seed after 21 days after pollination

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

growth_protocol: All four tissues in this study were prepared from Oryza sativa L. cv. Ilmi. Leaves and roots were harvested separately 14 days after sowing in soil. The flower before pollination was collected in the range of 0.5-1.5cm of the panicle (P1cm). The flower after 20-30 day of pollination was collected the internal ripening stage of grains.

extract_protocol: Total RNA was isolated from tissues by Hybrid-RTM (GeneAll) extraction following the manufacturer’s manual. The dried RNA pellet was dissolved with RNase-free water. The concentration was determined by spectrophotometry (NanoDrop, ND1000, Lab Tech), and the integrity of the RNA was determined by electrophoresis (Agilent Bioanalyzer 2100). The RNA was then stored at -80℃ until required. For experimental reproducibility.

tag: cultivar

value: Ilmi

value: seed after 21 days after pollination


title: P1cm_replicate 2

source_name: panicle at 1 cm

treatment_protocol: All four tissues in this study were prepared from Oryza sativa L. cv. Ilmi. Leaves and roots were harvested separately 14 days after sowing in soil. The flower before pollination was collected in the range of 0.5-1.5cm of the panicle (P1cm). The flower after 20-30 day of pollination was collected the internal ripening stage of grains.

value: panicle at 1 cm


title: SF-295

source_name: Cell line

tag: gender

source_name: gender-matched control


title: SF-539

tag: cancer subtype


title: ESC H3K4me1-Rep1

description: ChIP-chip ESCs H3K4me1


title: S21DAP_replicate 1


title: RP8T VS RP8N


title: OVCAR-5

value: Ovarian

tag: origin


title: TR54

value: tonsils

value: oropharyngeal squamous cell carcinoma


title: TR50

value: HPV-


title: P1cm_replicate 1


title: SK-OV-3

value: NCI


title: RP10T VS RP13N


title: TR57


title: TR60


title: Root_replicate 2

source_name: root

value: root


title: NCI-H23

value: Non-Small Cell Lung


title: OVCAR-3


title: OVCAR-8


title: MCF7

value: Breast


title: Root_replicate 1


title: HL-60

value: Leukemia


title: CCRF-CEM

value: F


title: Leaf_replicate 1

source_name: leaf

value: leaf


title: K-562


title: rLEC HNF4α transduction + AZA treatment, biological rep3 mRNA

city: Jette

first: jennifer

last: bolleyn

address: Laarbeeklaan 103

institute: Vrije universiteit Brussel

description: Gene expression data from HNF4a transduced rLEC exposed to a non-cytotoxic concentration of 20 µM 5' azacytidine for 7 days

hyb_protocol: 3.5 μg fragmented and labeled ssDNA was hybridized to a Rat transcriptome array 1.0 and then placed in a Genechip Hybridization Oven-645 (Affymetrix) rotating at 60 rpm at 45 ºC for 16 h. After incubation, arrays were washed on a Genechip Fluidics Station-450 (Affymetrix) and stained with the Affymetrix HWS kit as indicated by the manufacturer’s protocols.

scan_protocol: The chips were scanned with an Affymetrix Gene-Chip Scanner-3000-7G

data_processing: Robust Multiarray Analysis and detection above background for data summarization, normalisation and quality control were done with Affymetrix expression console software

organism: Rattus norvegicus

source_name: rLEC transduced with a lentiviral vector containing HNF4a and exposed to 20 µM of azacytidine  for 7 days

label_protocol: Total RNA (100 ng) was used for amplification and converted into biotinylated sense-strand DNA using the Genechip® WT PLUS Reagent kit following the manufacturer’s instructions (Affymetrix).

growth_protocol: rLEC were isolated from 8-day old male Sprague-Dawley rats, subcultivated and cryoperserved as previously described. Cryoperserved rLEC, previously collected at passage 12 were subcultivated at 75% confluency and rLEC growth medium was changed every two days.

extract_protocol: Total RNA enriched with small RNA (≤ 200nt) was isolated using the mirVana™miRNA isolation kit (Ambion, Inc., USA) according to the manufacturer’s instructions.

treatment_protocol: rLECs were transduced at 50% confluency with a viral titer of 2.09 x 109 TU/ml. After transduction, the cells were subcultivated at 75% confluency. rLECs containing the lentiviral vectors encoding HNF4α were puromycin selected (twice). 10 µg/ml puromycin was added to the growth medium and the cells were incubated at 37°C for 24 hours. After the puromycin selection, cells were washed and growth medium was changed. This was done every 2 days until 75% confluency was reached. AZA treatment consisted of the exposure to the non-cytotoxic concentration of 20 µM 5' azacytidine for 7 days.

value: male

value: liver


title: Leaf_replicate 2


title: rLEC HNF4α transduction + AZA treatment, biological rep1 mRNA


title: HOP-62


title: rLEC HNF4α transduction + AZA treatment, biological rep2 mRNA


title: rLEC AZA treatment, biological rep3 mRNA

description: Gene expression data from rLEC exposed to a non-cytotoxic concentration of 20 µM 5' azacytidine for 7 days

source_name: rLEC exposed to 20 µM of azacytidine for 7 days


title: SK-MEL-5

value: Melanoma


title: rLEC AZA treatment, biological rep1 mRNA


title: SR

value: M


title: rLEC HNF4α transduction, biological rep3 mRNA

description: Gene expression data from HNF4a transduced rLEC

source_name: rLEC transduced with a lentiviral vector containing HNF4a


title: MDA-MB-435


title: MOLT-4


title: RPMI-8226


title: UACC-62


title: rLEC AZA treatment, biological rep2 mRNA


title: rLEC HNF4α transduction, biological rep1 mRNA


title: rLEC HNF4α transduction, biological rep2 mRNA


title: PC-3

value: Prostate


title: rLEC control condition, biological rep1 mRNA

description: Gene expression data from untreated rLEC

source_name: untreated rLEC


title: SK-MEL-28


title: rLEC control condition, biological rep3 mRNA


title: DU-145


title: M14


title: A_acido_WAX_Xyl_Post_rep3

city: Richland

first: Brady

last: Lee

state: Washington

address: 902 Battelle Boulevard

institute: Pacific Northwest National Laboratory

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
Log2-transformed RMA data files were imported into ArrayStar 4 software (DNASTAR, Inc., Madison, WI) and the mean expression levels of three replicate arrays for each condition were considered.

organism: Alicyclobacillus acidocaldarius

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Alicyclobacillus acidocaldarius ATCC27009/DSM446 was grown to mid-log phase (O.D.600nm 0.5) aerobically at 60°C in modified 402 medium with using wheat arabinoxylan as the carbon source.  At this point, the medium was spiked with a second sugar to induce catabolite repression

extract_protocol: Total RNA was extracted using the RNeasy Midi kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect Bacteria Reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality was determined by analysis with an Agilent 2100 bioanalyzer.  RNA concentration was measured using a NanoDrop ND-1000 micro-spectrophotometer

treatment_protocol: Experiments were performed with glucose and xylose to induce changes in transcription.  Samples were taken for RNA extraction just prior to addition of sugar and immediately after addition of the sugar.

value: Wild-type

tag: grown with

value: wheat arabinoxylan (WAX)

tag: spiked with

value: xylose

tag: time point

value: immediately after addition of the second sugar


title: UACC-257


title: SK-MEL-2


title: A_acido_WAX_Xyl_Pre_rep2

tag: genotype/variation

value: just prior to addition of the 2nd sugar


title: A_acido_WAX_Xyl_Pre_rep3

tag: strain


title: MALME-3M

value: NCI


title: rLEC control condition, biological rep2 mRNA


title: PPY15

description: ChIP-chip PPY15 cells for CENP-A

source_name: CENP-A ChIP DNA from PPY15 cells

tag: cell type

value: lymphoblastoid cells

source_name: Input DNA from PPY15 cells


title: PPY17

description: ChIP-chip PPY17 cells for CENP-A

source_name: CENP-A ChIP DNA from PPY17 cells

source_name: Input DNA from PPY17 cells


title: A_acido_WAX_Xyl_Post_rep1


title: MDA-MB-468


title: A_acido_WAX_Xyl_Post_rep2


title: LOXIMVI


title: A_acido_WAX_Xyl_Pre_rep1


title: PAB13

description: ChIP-chip PAB13 cells for CENP-A

organism: Pongo abelii

source_name: CENP-A ChIP DNA from PAB13 cells

source_name: Input DNA from PAB13 cells


title: HT29

value: Colon


title: Pg35405 Data from Strain ATCC 35405

city: Chiyoda-ku

first: Kazuyuki

last: Ishihara

state: Tokyo

address: Misakicho 2-1-14

department: Microbiolgy

institute: Tokyo Dental College

description: Wild type

hyb_protocol: 1. Fragmentation of Cy3 labeled cRNA was carried out at 60°C for 30 min.  2. Stop fragmentation.  3. Hybridization was performed at 65°C for 17 h with agitation in Hybrioven.

scan_protocol: Scanned by Agilent Technologies Microarray Scanner.

data_processing: Normalization (RMA) was used GeneSpring GX software.

organism: Treponema denticola

source_name: Microorganism frequently isolated from lesion of chronic periodontitis

label_protocol: Cy3 label with Input Quick-Amp WT Labeling Kit (Agilent Technologies, Santa Clara, CA)

growth_protocol: T. denticola strains were grown in TYGVS medium at 37°C under anaerobic condition.  After the strains reached exponentially growing phase (OD660 ~0.2), chloramphenicol was added at 1 µg/ml and incubated for 4 h.

extract_protocol: TRIzol reagent (Invitorogen, Carlsbad, CA)

tag: strain background

value: wild type


title: TDE-0719 Data from Strain KT-3

description: TDE_0719:: ermF ermAM, Emr

value: Deficient mutant of TDE-0719


title: A_acido_WAX_Glu_Pre_rep2

value: glucose


title: KM12


title: A_acido_WAX_Glu_Pre_rep1


title: MDA-MB-231

value: F

value: Breast


title: A_acido_WAX_Glu_Post_rep3


title: BT-549


title: HS578T


title: A_acido_WAX_Glu_Pre_rep3


title: A_acido_WAX_Glu_Post_rep2


title: A_acido_WAX_Glu_Post_rep1


title: Serum_free-rep4.2

status: Public on Dec 24 2016

city: Vienna

first: Gerald

last: Klanert

address: Muthgasse 18

department: Department of Biotechnology

country: Austria

institute: University of Natural Resources and Biotechnology

description:
control.c1_4.2
Biological replicate 4 of 4. Technical replicate 2 of 2. RNA sample taken at early day 2.

hyb_protocol: 825 ng of each sample were pooled with the CRP, and fragmented at 60 °C for 30 minutes in a reaction volume of 30 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent. On completion of the fragmentation, 30 µl of 2x GEx Agilent hybridization buffer HI-RPM were added and hybridized to Agilent SurePrint Custom GE 4x44K microarrays (G2514F - 047308) for 17 hours at 65 °C. After hybridization, microarrays were washed for 1 minute with 37 °C GE Wash buffer 2 (Agilent), containing 0.005% Triton X-102.

scan_protocol: Agilent Technologies Scanner G2505C US83703555. Images were quantified using Agilent Feature Extraction Software (version 11.5.1.1) using default parameters (protocol GE2_1105_Oct12 and Grid 047308_D_F_20130212).

data_processing: LOESS and AQUANTILE with minimum background correction.

organism: Cricetulus griseus

source_name: reference pool

label_protocol: 200 ng of each sample were labeled using the Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Kit (V. 6.5, May 2010, Agilent) according to the manufacturer's protocol.

growth_protocol: Serum-containing cells were cultivated in 1:1 DMEM/Ham's F12 media (Biochrom, Germany) supplemented with 5% fetal calf serum (PAA, Austria) and 4 mM L-Glutamine at 37 °C, 7% CO2 and humidified air. Serum-free and suspension adapted CHO-K1 cells were grown in CD CHO (Gibco, Carlsbad, CA) supplemented with 8 mM L-Glutamine and 0.2% anti-clumping agent (Gibco, Carlsbad, CA).

extract_protocol: Total RNA extracted using TRI reagent® (Sigma-Aldrich, St. Louis, MO) following manufacturer's instructions.

tag: cell line

value: different cell lines

tag: tissue derivation

value: Chinese Hamster Ovary

tag: sample type

value: reference pool

tag: passage

tag: condition

value: serum free


title: Serum_free-rep3.1

description:
control.c2_3.1
Biological replicate 3 of 4. Technical replicate 1 of 2. RNA sample taken at early day 2.


title: Serum_free-rep4.1

description:
control.c1_4.1
Biological replicate 4 of 4. Technical replicate 1 of 2. RNA sample taken at early day 2.


title: T47D


title: SW-620

value: M


title: Serum_free-rep2.2

description:
control.c2_2.2
Biological replicate 2 of 4. Technical replicate 2 of 2. RNA sample taken at late day 2.


title: HCC-2998


title: HCT-116


title: H2O_4

status: Public on Dec 23 2016

city: Leuven

first: Vera

middle: van

last: Noort

address: Kasteelpark Arenberg 20, bus 2460

department: Microbial and Molecular systems

institute: KU Leuven

description: Botrytis cinerea treated A. thaliana leaves (2 replicates) vs control (water) treated A. thaliana leaves (2 replicates), (4 samples in total)

hyb_protocol: A mixture of fragmented biotinylated DNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix GeneChip® Arabidopsis Tiling 1.0R Arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix)

data_processing:
[signal.txt] Background correction, log2 transformation and interslide normalization were performed with the Affymetrix Tiling Analysis Software - Version 1.1, Build 2. Since the tiling arrays were based on the A. thaliana genome sequence of the 2007’s version of the TAIR database, the corresponding TAIR7 genome annotation was used for the analysis of the tiling array data. All steps of our strategy are illustrated in Figure S1. In a first step the average log2 intensities of biological replicates were calculated and a threshold value of 8.8 was chosen to identify transcriptionally active probes. This threshold was determined by comparing the log2 intensity distribution of genomic regions with known expression status (expressed and not expressed). Probes with log2 intensities below the threshold that were surrounded by transcriptionally active probes were considered active and vice versa to remove the effect of probes with poor hybridization properties. Secondly, groups of 4-13 successive transcriptionally active probes were combined into short transcriptionally active regions (TARs). Selection of even smaller regions would lead to a high number of false positives and to the identification of very small genes that are difficult to amplify in later stage, while all active regions of 14-15 successive probes were already annotated (TAIR7), supporting our choice of size limits. In a third step, TARs were withheld if the number of transcriptionally active probes was smaller in the control than in the BC treatment and if the average log2 intensity of all probes in the smallest of the two regions was at least 1.4 higher in the BC treatment than in the control. Both rules were based on the tiling array results for genomic regions that were known to be induced upon BC treatment. The former rule was added because of the frequent occurrence of probes having zero intensity in one of the four hybridizations. In small regions these zero values can have substantial influence on the average log2 intensity leading to false positive calls. The threshold for upregulation by BC was refined by comparing qRT-PCR and tiling array results for 30 selected TARs. All upregulations of 1.4 or more (corresponding to 2.6 fold or more) in the tiling arrays could be confirmed by qRT-PCR supporting our choice of threshold (data not shown). Finally, each selected region was compared to the A. thaliana TAIR7 genome annotation and only regions that were located in intergenic regions, introns or pseudogenes were withheld.
[Supp_data_positions_TARs_BotrytisCin.txt] first column: attributes; second column: log transformed, normalized and background corrected intensity; third, fourth, fifth column : position on chromosome (Chr (TAIR7), start (TAIR7),stop (TAIR7)); sixth, seventh, eighth column : position on chromosome (Chr (TAIR10), start (TAIR10), stop(TAIR10))

label: Biotin

organism: Arabidopsis thaliana

source_name: A. thaliana leaves (4 weeks old)

label_protocol: Samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Double-Stranded DNA Terminal Labeling Kit.

growth_protocol: Seeds of Arabidopsis thaliana wild-type ecotype Columbia-0 (Col-0) were obtained from the European A. thaliana stock Centre (NASC; http://nasc.nott.ac.uk/home.html).They were sown on ‘Zaai- en Stekgrond’ (DCM, Sint-Katelijne-Waver, Belgium) and grown in a growth chamber with 21°C temperature, 75% humidity and a 12h day-light cycle with a light intensity of approximately 120 μmol m-2s-1.

extract_protocol: After 48h treatment, RNA from A. thaliana leaves was isolated by the guanidinium isothiocyanate method (TRIzol reagent; Invitrogen, Carlsbad, USA) followed by purification using the RNeasy Mini Kit (Qiagen, Valencia, USA). First, approximately 100 mg plant material was crushed in liquid nitrogen, 1 ml of TRIzol reagent was added and samples were mixed and incubated for 5 min at room temperature. Following centrifugation (20,000 x g, 10 min, 4°C) the supernatant was transferred to a fresh tube and 200 µl of chloroform was added. The thoroughly mixed samples were incubated for 2 min at room temperature and the upper aqueous phase was transferred to a fresh tube after centrifugation (20,000 x g, 15 min, 4°C). An equal volume of 70% ethanol was added after which the samples were thoroughly shaken and applied onto a Qiagen column. The procedure was continued according to the manufacturer’s instructions. To selectively use mRNA for the tiling array analysis, RNA is converted into cDNA via an oligodT primer and reverse transcriptase. This cDNA was then used as a template for generation of cRNA.

treatment_protocol: Rosette leaves from soil-grown four-week old A. thaliana plants were sprayed evenly with a spore suspension of 5 x 105 spores/ml in PDB. After inoculation, plants were kept at 100% relative humidity.. Control plants were mock treated by spraying with H2O. The treated plants were kept at 100% relative humidity for 48h.

tag: treatment

value: H2O (control)

tag: tissue

value: leaves


title: Bot_4

source_name: A. thaliana leaves (4 weeks old, sprayed with  5 x 105 Botrytis cinerea B05.10 spores/ml in PDB).

value: Botrytis cinerea


title: Bot_3


title: H2O_1


title: 1772122326_H10

status: Public on Oct 06 2016

type: SRA

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: ESMoleculeCounts.cef

library_source: transcriptomic

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA synthesis. In some reads, one of the three Gs has been replaced by an A by the Illumina HiSeq software, representing failed base calling at that position. We rejected cells that had less than 2000 mRNA molecules, more than 26,000 mRNA molecules (putative doublets) as well as cells that formed a separate cluster with no specific gene expression (putative damaged or dead cells). Genes that were detected at less than 4 molecules in the whole datasets were eliminated.
Genome_build: UCSC mm10 and UCSC hg19
Supplementary_files_format_and_content: Tab-delimited table of total number of detected mRNA molecules from each gene in each cell identified by the "Title" field in Samples list. Mitochondrial genes and genes with less than 4 molecules have been omitted. The first two lines of each file are table metadata (see https://github.com/linnarsson-lab/ceftools)

molecule: polyA RNA

source_name: stem cells

growth_protocol: Wild-type CD1 mice were mated overnight and noon of the day was considered E0.5. Mothers were killed and embryos were dissected out of the uterine horn between the time points E11.5 and E18.5. Adult CD1 animals were dissected at P19 to P27. Human tissue was collected at Addenbrooke’s Hospital (Cambridge, UK) and dissected in HIBERNATE medium (Gibco). Samples were shipped overnight on ice (in HIBERNATE solution) to Sweden. For the embryonic stem cells (hES DA),  iCell DopaNeurons from Cellular Dynamics International (DNC-301030001, lot #6003358) were differentiated following the manufacturer’s recommendations and harvested at day 5 and 21.

extract_protocol:
Human embryo ventral midbrain dissection was performed on ice in neuronal N2 culturing media. 10-17  tissue pieces were collected for each experiment. The tissue pieces were dissociated using the Papain dissociation system (Worthington) following manufacturers recommendations, adjusting incubation time based on tissue piece size to 25-45 mins. Using glass pipettes of increasingly smaller tip diameter, the cell suspension was then filtered with 20um filter (Partec) and cells kept in N2 media, and cells loaded into C1 chips for cell capture.
Fluidigm C1 Autoprep System  Cells medium (10-17 micrometer) microfluidic was used to capture the cells. 14 microlitre of cell suspension (approx. 800 cells/microlitre in N2 culturing medium with DNaseI) was mixed with 7 microlitre C1 Suspension Reagent after filtering. Single-cells were then captured for 30 min at 4°C using the “Cell Load (1772x/1773x)” script. The protocol for Lysis, RT and PCR was performed as previously described  (Islam et al., Nat Methods. 2014 Feb;11(2):163-6). Amplified cDNA was harvested with 13 microlitre Harvest Reagent and cDNA library quality was measured on an Agilent BioAnalyzer. Cell barcoding and fragmentation was performed in a single step using Tn5 DNA transposase as described previously. 1 microlitre Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were resuspended in 20 microlitre Binding and Blocking buffer (10mM Tris, 250mM NaCl, 5mM EDTA, 0.5% SDS) and added to each well. After 15 min incubation at room temperature, all wells were pooled, the beads washed once with 100 microlitre Washing buffer (10mM Tris-150mM NaCl, 0.02% Tween), once in 100 microlitre Qiagen Qiaquick PB and then twice using 100 microlitre Washing buffer. Restriction was performed to cleave 3’ fragments: the beads were incubated in 100 microlitre restriction mix (1x NEB CutSmart, 0.4 U/microlitre PvuI-HF enzyme) for 1h at 37°C. Finally, the beads were washed three times with Washing buffer, then resuspended in 30 μl ddH2O and incubated for 10 min at 70°C to elute the DNA. AMPure beads XP (Beckman Coulter) were used at 1.8x volume and eluted in 30 microlitre to remove short fragments.

value: stem cells

tag: Sex

tag: age

tag: inferred cell type


title: 1772122326_H05

description: ESMoleculeCounts.cef


title: 1772122326_H07

description: ESMoleculeCounts.cef


title: 1772122326_H08

description: ESMoleculeCounts.cef


title: 1772122326_H04

description: ESMoleculeCounts.cef


title: 1772122326_H11

description: ESMoleculeCounts.cef


title: 1772122326_H03

description: ESMoleculeCounts.cef


title: Serum_free-rep1.2

description:
control.c1_1.2
Biological replicate 1 of 4. Technical replicate 2 of 2. RNA sample taken at late day 2.


title: Serum-rep2.1

description:
serum.p17_2.1
Biological replicate 2 of 4. Technical replicate 1 of 2. RNA sample taken at late day 3.

value: serum


title: Serum-rep3.2

description:
serum.p17_3.2
Biological replicate 3 of 4. Technical replicate 2 of 2. RNA sample taken at early day 3.


title: Serum_free-rep3.2

description:
control.c2_3.2
Biological replicate 3 of 4. Technical replicate 2 of 2. RNA sample taken at early day 2.


title: Serum-rep1.2

description:
serum.p18_1.2
Biological replicate 1 of 4. Technical replicate 2 of 2. RNA sample taken at late day 3.


title: Serum-rep4.1

description:
serum.p18_4.1
Biological replicate 4 of 4. Technical replicate 1 of 2. RNA sample taken at early day 3.


title: Serum_free-rep2.1

description:
control.c2_2.1
Biological replicate 2 of 4. Technical replicate 1 of 2. RNA sample taken at late day 2.


title: Serum_free-rep1.1

description:
control.c1_1.1
Biological replicate 1 of 4. Technical replicate 1 of 2. RNA sample taken at late day 2.


title: Serum-rep2.2

description:
serum.p17_2.2
Biological replicate 2 of 4. Technical replicate 2 of 2. RNA sample taken at late day 3.


title: 1772122326_G11

description: ESMoleculeCounts.cef


title: COLO205

source_name: Cell line

tag: gender

tag: cancer subtype

tag: origin

value: NCI

source_name: gender-matched control


title: 1772122326_G10

description: ESMoleculeCounts.cef


title: 1772122326_G08

description: ESMoleculeCounts.cef


title: 1772122326_G06

description: ESMoleculeCounts.cef


title: 1772122326_G03

description: ESMoleculeCounts.cef


title: 1772122326_F06

description: ESMoleculeCounts.cef


title: 1772122326_F10

description: ESMoleculeCounts.cef


title: Serum-rep1.1

description:
serum.p18_1.1
Biological replicate 1 of 4. Technical replicate 1 of 2. RNA sample taken at late day 3.


title: 1772122326_F09

description: ESMoleculeCounts.cef


title: 1772122326_F11

description: ESMoleculeCounts.cef


title: 1772122326_F05

description: ESMoleculeCounts.cef


title: 1772122326_F12

description: ESMoleculeCounts.cef


title: 1772122326_F04

description: ESMoleculeCounts.cef


title: 1772122326_F03

description: ESMoleculeCounts.cef


title: Serum-rep4.2

description:
serum.p18_4.2
Biological replicate 4 of 4. Technical replicate 2 of 2. RNA sample taken at early day 3.


title: 1772122326_F01

description: ESMoleculeCounts.cef


title: 1772122326_E12

description: ESMoleculeCounts.cef


title: 1772122326_E08

description: ESMoleculeCounts.cef


title: 1772122326_G05

description: ESMoleculeCounts.cef


title: 1772122326_G02

description: ESMoleculeCounts.cef


title: 1772122326_H02

description: ESMoleculeCounts.cef


title: 1772122326_E06

description: ESMoleculeCounts.cef


title: 1772122326_D11

description: ESMoleculeCounts.cef


title: 1772122326_E02

description: ESMoleculeCounts.cef


title: 1772122326_E07

description: ESMoleculeCounts.cef


title: 1772122326_D09

description: ESMoleculeCounts.cef


title: 1772122326_G04

description: ESMoleculeCounts.cef


title: 1772122326_E03

description: ESMoleculeCounts.cef


title: 1772122326_E10

description: ESMoleculeCounts.cef


title: 1772122326_D10

description: ESMoleculeCounts.cef


title: 1772122326_E11

description: ESMoleculeCounts.cef


title: 1772122326_G12

description: ESMoleculeCounts.cef


title: 1772122326_D01

description: ESMoleculeCounts.cef


title: 1772122326_D05

description: ESMoleculeCounts.cef


title: 1772122326_C09

description: ESMoleculeCounts.cef


title: 1772122326_D06

description: ESMoleculeCounts.cef


title: 1772122326_C11

description: ESMoleculeCounts.cef


title: 1772122326_C06

description: ESMoleculeCounts.cef


title: 1772122326_C07

description: ESMoleculeCounts.cef


title: 1772122326_C05

description: ESMoleculeCounts.cef


title: 1772122326_D07

description: ESMoleculeCounts.cef


title: 1772122326_C04

description: ESMoleculeCounts.cef


title: 1772122326_C01

description: ESMoleculeCounts.cef


title: 1772122326_B12

description: ESMoleculeCounts.cef


title: 1772122326_B11

description: ESMoleculeCounts.cef


title: 1772122326_B10

description: ESMoleculeCounts.cef


title: 1772122326_B07

description: ESMoleculeCounts.cef


title: Serum-rep3.1

description:
serum.p17_3.1
Biological replicate 3 of 4. Technical replicate 1 of 2. RNA sample taken at early day 3.


title: 1772122326_B05

description: ESMoleculeCounts.cef


title: 1772122326_A10

description: ESMoleculeCounts.cef


title: 1772122326_A07

description: ESMoleculeCounts.cef


title: 1772122326_A05

description: ESMoleculeCounts.cef


title: 1772122326_A09

description: ESMoleculeCounts.cef


title: 1772122326_A12

description: ESMoleculeCounts.cef


title: 1772122326_A03

description: ESMoleculeCounts.cef


title: 1772122326_A04

description: ESMoleculeCounts.cef


title: 1772122326_A08

description: ESMoleculeCounts.cef


title: 1772122326_A02

description: ESMoleculeCounts.cef


title: 1772122326_A01

description: ESMoleculeCounts.cef


title: 1772122325_H09

description: ESMoleculeCounts.cef


title: 1772122326_C10

description: ESMoleculeCounts.cef


title: 1772122325_H01

description: ESMoleculeCounts.cef


title: 1772122325_H08

description: ESMoleculeCounts.cef


title: 1772122325_G08

description: ESMoleculeCounts.cef


title: 1772122325_G03

description: ESMoleculeCounts.cef


title: 1772122325_F08

description: ESMoleculeCounts.cef


title: 1772122325_G04

description: ESMoleculeCounts.cef


title: 1772122325_F07

description: ESMoleculeCounts.cef


title: 1772122325_F05

description: ESMoleculeCounts.cef

value: eRglf


title: 1772122325_F02

description: ESMoleculeCounts.cef


title: 1772122325_F01

description: ESMoleculeCounts.cef


title: 1772122326_B03

description: ESMoleculeCounts.cef


title: 1772122325_E06

description: ESMoleculeCounts.cef


title: 1772122325_F09

description: ESMoleculeCounts.cef


title: 1772122325_E09

description: ESMoleculeCounts.cef


title: 1772122325_E08

description: ESMoleculeCounts.cef


title: 1772122325_E04

description: ESMoleculeCounts.cef


title: 1772122325_D09

description: ESMoleculeCounts.cef


title: 1772122325_E05

description: ESMoleculeCounts.cef


title: 1772122325_D08

description: ESMoleculeCounts.cef


title: 1772122325_D04

description: ESMoleculeCounts.cef


title: 1772122325_D01

description: ESMoleculeCounts.cef


title: 1772122325_D07

description: ESMoleculeCounts.cef


title: 1772122325_D06

description: ESMoleculeCounts.cef


title: 1772122325_C08

description: ESMoleculeCounts.cef


title: 1772122325_C12

description: ESMoleculeCounts.cef


title: 1772122325_E03

description: ESMoleculeCounts.cef


title: 1772122325_C11

description: ESMoleculeCounts.cef


title: 1772122326_D08

description: ESMoleculeCounts.cef


title: 1772122325_C04

description: ESMoleculeCounts.cef


title: 1772122325_C03

description: ESMoleculeCounts.cef


title: 1772122325_C07

description: ESMoleculeCounts.cef


title: 1772122325_C05

description: ESMoleculeCounts.cef


title: 1772122325_B09

description: ESMoleculeCounts.cef


title: 1772122325_B11

description: ESMoleculeCounts.cef


title: 1772122325_B07

description: ESMoleculeCounts.cef


title: 1772122325_B08

description: ESMoleculeCounts.cef


title: 1772122325_B03

description: ESMoleculeCounts.cef


title: 1772122325_B02

description: ESMoleculeCounts.cef


title: 1772122326_A11

description: ESMoleculeCounts.cef


title: 1772122325_A12

description: ESMoleculeCounts.cef


title: 1772122325_D10

description: ESMoleculeCounts.cef


title: 1772122325_B01

description: ESMoleculeCounts.cef


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