title: 23d_Testis Germ cell_Control_Rep3

city: BRONX

first: PAMELA

last: STANLEY

state: NY

address: 1300 MORRIS PARK AVE

department: CELL BIOLOGY

institute: ALBERT EINSTEIN COLLEG OF MEDICINE

description: RMA expression value derived from Expression Console;Core Exon Analysis using Transcriptome Analysis Console

hyb_protocol: The fragmented and biotin labelled ss-cDNA were hybridised using GeneChip hybridisation, Wash and Stain Kit (ThermoFisher Scientific, Catalog number: 900720). The hybridised array was incubated for 16h at 45 degree celsius on GeneChip mouse Gene 2.0 ST Array. Gene Chips were  washed and stained in the Affymetrix Gene Chip Fluidics  Station 450.

scan_protocol: Gene Chips were scanned using Affymetrix GeneChip Scanner 3000 7G

data_processing: Raw Data were processed using Expression Console software.  Background corrections were applied to probe intensities; gene expression levels were summarized from the corrected intensities and then quantile normalized using the RMA algorithm.

source_name: Testis  germ cell,control3

label_protocol: The purified, sense-strand cDNA is fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues and breaks the DNA strand. The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin (ThermoFisher Scientific, Catalog number: 901525).

growth_protocol: Germ cells were isolated from testes of  23 day Control (6) and Mgat1 mutant (6) by a 2 step enzymatic process using Enzymatic Solution 1 (Collagenase, Dnase1) and Enzymatic Solution 2 (Dnase , Trypsin) accoding to method descibed in Chang et. al. Aliquots from each of the six control or mutant samples were pooled respectively, thoroughly mixed and  three replicates from control and mutant pools were used for the array.

extract_protocol: Germ cells were isolated as stated in growth protocol.  RNA was isolated from germ cells using Trizol reagent (Sigma) and cleaned up using RNeasy minielute clean up kit (Qiagen).  RNA integrity number assessed by 2100 Bioanalyser. Samples with RIN greater than 9 (100 ng RNA) were  submitted  to the  Genomics facility at Einstein for cDNA synthesis and microarray expression profiling (Affymetrix)

value: testis

value: germ cell

tag: genotype

value: 23 day

tag: background strain

value: FVB


title: 23d_Testis Germ cell_Mgat1mutant_Rep2

status: Public on Feb 13 2018

type: RNA

country: USA

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Testis  germ cell,mutant2

tag: tissue

tag: cell type

value: Mgat 1 mutant

tag: age


title: H827_rep2

city: New Taipei City

first: Sheng-Ming

last: Wu

address: No.291, Zhongzheng Rd., Zhonghe District

country: Taiwan

institute: Taipei Medical University Shuang-Ho Hospital

description: 18876_H827-1.txt:gProcessedSignal(normalized)

hyb_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.  Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Human GE  8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature (quantile normalization and log2 transformation).

organism: Homo sapiens

source_name: H827 cell without MDM

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent  Technologies, USA) during the in vitro transcription process.

extract_protocol: Total RNA was extracted with TRIzol (Invitrogen).

treatment_protocol: Human peripheral monoctyte cells (PBMCs) from lung cancer patients were collected. PBMCs were treated with GM-CSF and differentiated to MDM. MDM cells were cocultured with or without lung cancer cells for 24h. Total RNAs were extracted from H827 cancer cells.

tag: cell line

value: lung cancer cells

tag: cocultured with


title: Patient Derived Xenograft LTL-310R

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

hyb_protocol: 600ng labeled cRNA was hybridized on Agilent SurePrint G3 Human GE 8x60K Microarray (Design ID 028004)

scan_protocol: Slides were scanned with the Agilent DNA Microarray Scanner at a 3um scan resolution using the one colour and 20 bit tiff file settings

data_processing: Image files were processed with Agilent Feature Extraction 10.10 to produce spatially detrended and background subtracted gProcessedSignal intensities. Data were quantile normalized in GeneSpring 12.0.

source_name: Prostate Tumor

label_protocol: 100ng of total RNA was used as input for generation of Cyanine-3-labeled cRNA following Agilent’s One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.0.

extract_protocol: RNA were extracted by using the mirVana RNA Isolation Kit (Ambion, Burlington, Canada).  The quality and quantity of RNA were assessed with an Agilent 2100 Bioanalyzer (Caliper Technologies Corp., Canada)

value: prostate cancer tumor

tag: tumor foci

value: Patient Derived Xenograft


title: 22d_Testis Germ cell_Mgat1_mutant_1

hyb_protocol: The fragmented and biotin-labelled ss-cDNA was hybridised using GeneChip hybridization, wash and stain kit (ThermoFisher Scientific, Catalog number: 900720). The hybridized array was incubated for 16 h at 45 degree celsius on GeneChip mouse Gene 2.0 ST Array. Gene Chips were washed and stained in the Affymetrix Gene Chip Fluidics  Station 450.

source_name: Testis  germ cell,mutant1

label_protocol: The purified, sense-strand cDNA was fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues. The fragmented cDNA was labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA labeling reagent that is covalently linked to biotin (ThermoFisher Scientific, Catalog number: 901525).

growth_protocol: Germ cells were isolated from testes of individual  22 day Control (3) and Mgat1 conditional mutant mice (3)  by a two-step process using Enzymatic Solution 1 (Collagenase, Dnase1) and Enzymatic Solution 2 (Dnase , Trypsin) accoding to method descibed in Chang et. a (Chang et al., Biotechniques, 2011)

extract_protocol: Germ cells were isolated as stated in growth protocol.  RNA was isolated from germ cells using RNeasy mini kit (Qiagen) and cleaned up using RNeasy minielute clean up kit (Qiagen).  RNA integrity number(RIN)  was  assessed in a 2100 Bioanalyser. Samples with RIN greater than 9 (100 ng RNA) were  submitted  to the  Genomics facility at Einstein for cDNA synthesis and microarray expression profiling (Affymetrix)

value: Mgat1 mutant

value: 22 day


title: 23d_Testis Germ cell_Mgat1mutant_Rep1


title: 23d_Testis Germ cell_Control_Rep2

source_name: Testis  germ cell,control2

value: control


title: 22d_Testis Germ cell_Control_3


title: 23d_Testis Germ cell_Mgat1mutant_Rep3

source_name: Testis  germ cell,mutant3


title: Cic-/-_Clone_5_EGF+

city: Durham

first: Hai

last: Yan

state: NC

address: 199B-MSRB, Research Drive

department: Pathology

institute: Duke University

description:
5_EGF+
gene expression data from Cic-/- NSC culture in proliferation medium supplemented with EGF

hyb_protocol: Product generated from the label protocol was hybridized onto the Affymetrix GeneChip Mouse Gene 2.0 ST array in Affymetrix GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450 according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

scan_protocol: Arrays were scanned with Affymetrix GeneChip® Scanner 7G according to Affymetrix GeneChip protocols.

data_processing: The Robust Multichip Average (RMA) method was applied for data processing and normalization by R.

label: biotin

label_protocol: Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE). Hybridization targets were prepared with Ambion WT Expression Kit Life Technologies/Ambion (Grand Island, NY) and Affymetrix GeneChip WT Terminal Labeling Kit from total RNA.

growth_protocol: mNSCs were cultured following the NeuroCult protocol In vitro proliferation and differentiation of mouse neural stem and progenitor cells using NeuroCult.

extract_protocol: RNA was extracted by RNA miniprep kit (Zymo, Cat#11-328)

treatment_protocol: NSCs were cultured in standard NeuroCult proliferation medium supplemented with or without EGF for 24 hours.

tag: genotype/variation

value: conditional knockout  (Cicflox/flox)

value: postnatal day 4 (P4)

value: subventricular zone (SVZ)

value: neonatal mouse neural stem cell (NSC)

tag: treated with

value: EGF for 24 hr


title: LAIV_735_36h_1

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K mouse array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol.

source_name: Nasal Epithelial Cells

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Human nasal epithelial cells (hNECs) were obtained from non-diseased hosts during endoscopic sinus surgery for non-infection related conditions and grown in culture at the air-liquid interface (ALI) as previously described (Lane et al., 2004; Ramanathan and Lane, 2007; Ramanathan et al., 2007). Tissue processing, differentiation medium, and culture conditions have been previously described in detail (Fischer et al., 2015).  Seasonal influenza A virus A/Victoria/361/2011 (H3N2) and an antigenically-matched live attenuated influenza vaccine virus (LAIV; WT HA and NA, all other proteins from A/Ann Arbor/6/1960) were utilized in this study.  Viral seed stocks were obtained from Medimmune.

extract_protocol: All Trizol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Differentiated hNECs where infected at a multiplicity of infection (MOI) of 5 50% tissue culture infectious dose per cell.  All incubations were performed at 32oC in a humidified environment with 5% CO2.  Prior to infection, cells were apically washed with 200 μl DMEM (supplemented with 0.3% BSA, 2mM Glutamax, 100 U/ml Penicillin, and 100 µg/ml Streptomycin) and the basolateral media was refreshed with 500 μl of fresh LHC Basal Medium:DMEM-H.  The virus inoculum was added to the apical compartment in a volume of 100 μl and incubated for 2 hours, after which the inoculum was aspirated and the apical chamber was washed three times with 200 μl phosphate buffered saline containing calcium and magnesium (PBS+).  The plates were then returned to the incubator. Both apical washes and basolateral medium were collected and stored at -70oC. Virus production each time point was quantified by limited dilution infection of MDCKs using apical wash samples.  The TCID50 for each sample was calculated using the Reed-Muench algorithm (Reed, 1938).  RNA was isolated from Trizol homogenates from samples harvested at 24hpi and 36hpi.

value: Nasal Epithelial Cells

tag: infection

value: LAIV

tag: sampleID

tag: timepoint


title: 22d_Testis Germ cell_Mgat1_mutant_2

value: testis

value: germ cell


title: 22d_Testis Germ cell_Control_1

source_name: Testis  germ cell,control1

value: FVB


title: 23d_Testis Germ cell_Control_Rep1

value: 23 day


title: Cic-/-_Clone_6_EGF+

description:
6_EGF+
gene expression data from Cic-/- NSC culture in proliferation medium supplemented with EGF


title: Cic+/+_Clone_4_EGF-

description:
4_EGF-
gene expression data from Cic+/+ NSC culture in proliferation medium supplemented without EGF

value: wild trype control (Cic+/+)


title: Cic-/-_Clone_6_EGF-

description:
6_EGF-
gene expression data from Cic-/- NSC culture in proliferation medium supplemented without EGF


title: Cic-/-_Clone_7_EGF+

description:
7_EGF+
gene expression data from Cic-/- NSC culture in proliferation medium supplemented with EGF


title: Patient Derived Xenograft LTL-467

value: prostate cancer tumor


title: 22d_Testis Germ cell_Mgat1_mutant_3


title: MDA-hyb2

city: Hannover

first: Ralf

last: Hass

state: Germany

address: Carl-Neuberg-Str. 1

department: Gynecology

country: Germany

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE1_107_Sep09.xml’, except that the minimal number of replicates used to calculate population outliers was set to 5. Measurements of on-chip replicates were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by global linear scaling. For this, all gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be scaled (‘Array i’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)  A lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 10 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 10.

source_name: MDA-MB-231/MSC derived breast cancer hybrid

label_protocol: Synthesis of Cy3-labeled cRNA was performed with the ‘Quick Amp Labeling kit, one color’ (#5190-0442, Agilent Technologies) according to the manufacturer’s recommendations.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.


title: Cic-/-_Clone_5_EGF-

description:
5_EGF-
gene expression data from Cic-/- NSC culture in proliferation medium supplemented without EGF


title: MDA-MB-231-cherry

source_name: human breast carcinoma cell line

value: human breast carcinoma cell line MDA-MB-231


title: 22d_Testis Germ cell_Control_2


title: Cic-/-_Clone_7_EGF-

description:
7_EGF-
gene expression data from Cic-/- NSC culture in proliferation medium supplemented without EGF


title: Cic+/+_Clone_4_EGF+

description:
4_EGF+
gene expression data from Cic+/+ NSC culture in proliferation medium supplemented with EGF


title: Cic+/+_Clone_3_EGF+

description:
3_EGF+
gene expression data from Cic+/+ NSC culture in proliferation medium supplemented with EGF


title: Cic+/+_Clone_3_EGF-

description:
3_EGF-
gene expression data from Cic+/+ NSC culture in proliferation medium supplemented without EGF


title: Cic+/+_Clone_1_EGF-

description:
1_EGF-
gene expression data from Cic+/+ NSC culture in proliferation medium supplemented without EGF


title: MDA-hyb1

value: MDA-MB-231/MSC derived breast cancer hybrid


title: Cic+/+_Clone_2_EGF-

description:
2_EGF-
gene expression data from Cic+/+ NSC culture in proliferation medium supplemented without EGF


title: MSC051212-GFP P3

source_name: human mesenchymal stem/stroma cell

value: human mesenchymal stem/stroma cell (MSC)


title: Cic+/+_Clone_1_EGF+

description:
1_EGF+
gene expression data from Cic+/+ NSC culture in proliferation medium supplemented with EGF


title: placenta_deficient_mouse6_2

city: Adelaide

first: Rebecca

middle: L

last: Wilson

state: SA

address: Medical School North, Frome Rd

country: Australia

institute: University of Adelaide

description: Gene expression from a GD18.5 mouse placenta from a mother fed a deficient diet containing 10 mg/kg zinc

hyb_protocol: 3.5 µg of fragmented and labelled single-stranded cRNA was hybridised on Affymetrix MoGene 2.1 ST arrays and washed and stained following the Manual Target Preparation Guidelines for GeneChip Whole Transcript (WT) Expression Arrays.

scan_protocol: GeneChips were scanned according to standard Affymetrix protocols (Affymetrix Genechip Command Console program 3.2.0.1567, scanner PlateScanner M10)

data_processing: Data was RMA background corrected, and summarised using standard PLM approaches as implemented in the package affy  version 1.44,  and R version 3.2.1. Probe to gene mappings were as specified in v19.0.0 of the ENSG based CDF obtained from Brainarray. DABG was applied using a modified MAT model based on probe sequence information, and any undetectable genes and probes were removed before obtaining expression estimates under the PLM approach.

source_name: Placental tissue, GD18.5, deficient mother

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 250 ng total RNA following the Manual Target Preparation Guidelines for GeneChip Whole Transcript (WT) Expression Arrays.

growth_protocol: Seven-week-old C57Bl/6J female mice were fed either a zinc replete diet containing 40 mg/kg zinc  or a marginally zinc deficient diet containing 10 mg/kg zinc. They were maintained on a 12 h: 12 h light-dark cycle with both water and food provided ad libitum.

extract_protocol: Half a placenta (~50 mg tissue) was homogenised using a Powerlyzer® with seramic 1.4 mm beads. Total RNA was extracted using Trizol following manufacturers instructions

treatment_protocol: At gestational day 18.5 female mice were euthanised. Whole placentas were excised and snap frozen in liquid nitrogen. These samples were then stored at -80C until RNA was extracted.

tag: strain

value: Placenta

tag: gestational day


title: placenta_deficient_mouse5_2


title: placenta_deficient_mouse3_1


title: placenta_deficient_mouse4_1


title: placenta_deficient_mouse6_1


title: placenta_deficient_mouse1_1


title: placenta_control_mouse1_1replicate

description: Gene expression from a GD18.5 mouse placenta from a mother fed a control diet containing 40 mg/kg zinc

source_name: Placental tissue, GD18.5, control mother


title: placenta_deficient_mouse7_2


title: patient 7 AML QX

city: Xi'an City

first: Aili

last: He

address: NO.157 Xiwu Rd

department: Hematology

country: China

institute: The Second Affiliated Hospital of Xi'an Jiao Tong University

description: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA 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 DNA Microarray Scanner (part number G2511C).

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

scan_protocol: Assemble the slides into an slide holder. Place assembled slide holders into scanner carousel. Verify scan settings for one-color scans. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Open the Agilent Feature Extraction (FE) software. Add the images (.tif) to be extracted to the FE Project.  Set FE Project Properties. Check the Extraction Set Configuration. Save the FE Project (.fep) by selecting File > Save As and browse for desired location. Select Project > Start Extracting and export data to txt.

source_name: bone marrow

label_protocol: Add 1ug of total RNA to a 1.5-mL microcentrifuge tube. Add 1.2 μL of T7 Promoter Primer. Use nuclease-free water to bring the total reaction volume to 11.5 μL. Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes. Place the reactions on ice and incubate for 5 minutes.Briefly spin each sample tube in a microcentrifuge to drive down the contents from the tube walls and the lid. Return the tubes to ice. Add 8.5 μL of cDNA Master Mix to each sample tube and mix by pipetting up and down. Incubate samples at 40°C in a circulating water bath for 2 hours. Move samples to a 65°C circulating water bath and incubate for 15 minutes. Move samples to ice. Incubate for 5 minutes. Spin samples briefly in a microcentrifuge to drive down tube contents from the tube walls and lid. Immediately prior to use, gently mix the components listed in the following table in the order indicated for the Transcription Master Mix by pipetting at room temperature. Add 60 μL of Transcription Master Mix to each sample tube. Gently mix by pipetting. Incubate samples in a circulating water bath at 40°C for 2 hours.

extract_protocol: Bone marrow mononuclear cells (BMNCs) were isolated using lymphocyte separation liquid within eight hours after bone marrow samples were harvested and subjected for isolation of total cellular RNA, then stored at -80°C,Add 1ml Trizol per 5x10^6 cells.

value: bone marrow mononuclear cells

tag: disease state

value: acute myeloid leukemia

tag: gender

value: female

tag: age (years)

tag: cytogenetics risk category

value: Intermediate/Normal

tag: molecular abnormality

value: NO

tag: leukemia fab morphology code


title: placenta_deficient_mouse1_2

tag: tissue


title: patient 8 AML SCX

description: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA 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 DNA Microarray Scanner (part number G2512C).

tag: cell type

value: Not available


title: patient 9 AML XJW

description: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA 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 DNA Microarray Scanner (part number G2513C).

value: male


title: placenta_deficient_mouse5_1


title: patient 6 AML CYY

description: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA 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 DNA Microarray Scanner (part number G2510C).

value: FLT3 postive


title: patient 10 AML ZBR

description: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA 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 DNA Microarray Scanner (part number G2514C).


title: patient 3 IDA CHQ

description: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA 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 DNA Microarray Scanner (part number G2507C).

value: iron-deficiency anemia


title: placenta_deficient_mouse4_2


title: placenta_deficient_mouse7_1


title: patient 5 IDA JLL

description: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA 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 DNA Microarray Scanner (part number G2509C).


title: placenta_control_mouse10_2


title: placenta_deficient_mouse2_1


title: placenta_control_mouse9_1


title: placenta_control_mouse8_2


title: placenta_control_mouse10_1


title: patient 2 IDA XLX

description: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA 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 DNA Microarray Scanner (part number G2506C).


title: placenta_control_mouse8_1


title: placenta_control_mouse7_2


title: placenta_control_mouse1_2


title: Patient Derived Xenograft LTL-484

value: Patient Derived Xenograft


title: placenta_control_mouse6_2


title: placenta_control_mouse3_2


title: patient 1 IDA SHN

description: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA 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 DNA Microarray Scanner (part number G2505C).


title: placenta_control_mouse4_1


title: placenta_control_mouse3_1


title: placenta_control_mouse6_1


title: C1_RamDA_mESC_10pg_CF12

status: Public on Feb 12 2018

type: SRA

city: Tsukuba

first: Hiroaki

last: Tateno

state: Ibaraki

address: Tsukuba Central 2, 1-1-1 Umezono

country: Japan

institute: National Institute of Advanced Industrial Science and Technology (AIST)

library_source: transcriptomic

data_processing:
FASTQ files were generated using bcl2fastq (v2.16.0.10).
For RamDA-seq and C1-RamDA-seq data with living cells, fastq-mcf (version 1.04.807) was used for adapter trimming with the parameters '-l 36 --lowcomplex-pct 74 --homopolymer- pct 74 -k 4' for RamDA-seq and '-L 75 -l 46 -k 4 -q 30' for C1-RamDA-seq. The reads were mapped to the mouse genome (mm10) using HISAT2 with the parameters '--dta-cufflinks -p 4 -k 5 -X 800 --sp 1000,1000'. Uniquely mapped reads were selected using the bamtools ‘filter’ command with the parameters '-isMapped true -tag NH:1' and samtools ‘view’ command with the parameter ‘-q 40’. BigWig files were generated using deepTools (version 2.2.4). The transcript-level expression levels were quantified using sailfish (version 0.9.2). The transcript-level expression levels were also calculated using Bowtie2 (version 2.2.6) with the parameters '-k 100 -X 800' and eXpress (version 1.5.1) with the parameter '--no-bias-correct'.
For each scRNA-seq method data with 10 pg of diluted RNA, fastq-mcf (version 1.04.807) was used to trim adapter sequences and generate read lengths of 42 nt with the parameters ‘-L 42 -l 42 -k 4 -q 30 -S’. For comparison, we also prepared R1 reads of rdRNA-seq and paRNA-seq data. The reads were mapped to the mouse genome (mm10) using HISAT2 (version 2.0.1) with parameters ‘--dta-cufflinks -p 4 -k 5 --sp 1000,1000’. Uniquely mapped reads were selected using the bamtools (version 2.0.1;) 53 ‘filter’ command with the parameters `-isMapped true -tag NH:1` and the samtools (version 2.0.1)54 ‘view’ command with the parameter ‘-q 40’. BigWig files were generated using deepTools (version 2.2.4). Sailfish (version 0.9.2) was used to quantify transcript-level expressions.
For bulk poly(A) and total RNA-seq data, fastq-mcf was used to trim adapter sequences with the parameters ‘-l 50 --lowcomplex-pct 36 --homopolymer-pct 36 -k 4 -S’. The reads were mapped to the mouse genome (mm10) using HISAT2 with the parameters '--dta-cufflinks --rna-strandness RF -k 5 --no-mixed --no-discordant --sp 1000,1000'. Properly (i.e., convergent read pairs) and uniquely mapped reads were selected using the bamtools ‘filter’ command and samtools ‘view’ command with the parameter ‘-q 40’. For genome-guided transcriptome assembly, Cufflinks (version 2.2.1) was used with the parameters ‘--multi-read-correct --frag-bias-correct -M $mask --library-type fr-unstranded’. A GTF file of tRNA and rRNA annotations in GENCODE (vM9) were provided to mask the genome. Cuffcompare was used to annotate transcripts with transfrag class codes with respect to the GENCODE (vM9) annotation. According to the Cuffcompare class codes, we selected (1) unnannotated transcripts with class codes of "i", "o", "u", "x", or "s" and (2) unannotated splicing variant transcripts (‘j’ class (potentially novel isoform)) with at least one unannotated splice junction. We then removed (1) unannotated transcripts with exons located within 100 bp of the tRNA or rRNA annotations in GECODE or RepeatMasker, or pseudogene annotations in GENCODE (‘2wayconspseudos’), and (2) unannotated transcripts with lengths that were not monger than 200 bp. These filtered unannotated gene models were further merged with gene models in GENCODE vM9.
Genome_build: mm10
Supplementary_files_format_and_content: txt, gtf, bigWig

source_name: ES_diluted total RNA

growth_protocol: 5G6GR mouse ES cells were used for bulk and single-cell RNA-seq. The cells were cultured in a feeder-free gelatin-coated dish in 10% fetal calf serum containing Glasgow minimal essential medium (GMEM; Sigma-Aldrich), 1000 U/mL leukemia inhibitory factor (ESGRO; Invitrogen), 100 µmol/l 2-mercaptoethanol (Nacalai Tesque), 1× non-essential amino acids (Life Technologies), 1 mmol/L sodium pyruvate (Life Technologies), 2 mmol/L L-glutamine (Nacalai Tesque), 0.5× penicillin/streptomycin (Life Technologies), 0.5 ug/ml puromycin (Sigma) and 10 µg/mL blasticidin (Life Technologies).

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit (Qiagen). For ribosomal RNA depleted total RNA-seq, depletion of rRNA from 1 µg of ES total RNA was performed by using GeneRead rRNA Depletion Kits (Qiagen). For single-cell RamDA-seq, single cells were directly sorted into the cell lysis buffer containing RNasein plus (Promega), Cell Lysis Buffer (Roche), NP40 (Thermo), and RNase free water (TaKaRa). For averaged G1-phase cell lysate sample, 180 cells were sorted into 180 µl of the cell lysis buffer and individually divided into 1 μl in a 96-well PCR plate after well-mixing to lyse the cells. The cell lysate solution was stored at -80ºC until use.
For bulk RNA-seq, the libraries were constructed by using a commercial kit (NEBNext Ultra Directional RNA Library Prep Kit for Illumina; NEB) in accordance with the manufacturer’s protocol, with slight modifications during the reverse-transcription and PCR steps. SMART-Seq v4 libraries were prepared according to manufacture's instructions accompanying the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech). For library construction of RamDA-seq and C1-RamDA-seq, refer to the protocol in "Single-cell full-length total RNA sequencing uncovers dynamics of non-polyadenylated RNAs, recursive splicing and enhancer RNAs". For rRNA-depleted RNA-seq using 1 and 10 ng of diluted total RNA, sequencing libraries were prepared with KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems) according to the manufacturer’s protocol. C1-SMART-Seq v4 libraries were prepared using Fluidigm C1 with the script "Full-length mRNA Sequencing" was downloaded from Script Hub (https://jp.fluidigm.com/c1openapp/scripthub)in accordance with the manufacturer’s protocol. For analyses of plate-to-plate variability (batch effect) of RamDA-seq, we prepared RamDA-seq library DNA by using the advanced method of RamDA-seq (refer to the protocol in "Single-cell full-length total RNA sequencing uncovers dynamics of non-polyadenylated RNAs, recursive splicing and enhancer RNAs").

treatment_protocol: For the assessment of PrE differentiation, 5G6GR ES cells were cultured in differentiation medium containing 100 mmol/l dexamethasone rather than blasticidin. The cells are cultured for 72 hours.

value: Embryonic stem (ES) cell

tag: sample type

value: purified total RNA

tag: starting amount

value: 10 pg

tag: cell cycle phase

value: All phase

tag: method subtype


title: C1_RamDA_mESC_10pg_CF10


title: placenta_control_mouse2_1


title: placenta_control_mouse7_1


title: C1_RamDA_mESC_10pg_CF11


title: C1_RamDA_mESC_10pg_CG03


title: C1_RamDA_mESC_10pg_CF09


title: C1_RamDA_mESC_10pg_CG01


title: C1_RamDA_mESC_10pg_CG02


title: placenta_control_mouse5_1


title: C1_RamDA_mESC_10pg_CF08


title: C1_RamDA_mESC_10pg_CF07


title: placenta_control_mouse1_1


title: patient 4 IDA WXY

description: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA 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 DNA Microarray Scanner (part number G2508C).


title: Cic+/+_Clone_2_EGF+

description:
2_EGF+
gene expression data from Cic+/+ NSC culture in proliferation medium supplemented with EGF

tag: genotype/variation

value: wild trype control (Cic+/+)

tag: age

value: postnatal day 4 (P4)

value: subventricular zone (SVZ)

value: neonatal mouse neural stem cell (NSC)

tag: treated with

value: EGF for 24 hr


title: placenta_control_mouse9_2

tag: strain

value: Placenta


title: placenta_control_mouse5_2

tag: gestational day


title: C1_RamDA_mESC_10pg_CF05


title: C1_RamDA_mESC_10pg_CF06


title: C1_RamDA_mESC_10pg_CF02


title: C1_RamDA_mESC_10pg_CF03


title: C1_RamDA_mESC_10pg_CF01


title: C1_RamDA_mESC_10pg_CE07


title: C1_RamDA_mESC_10pg_CE09


title: C1_RamDA_mESC_10pg_CE11


title: C1_RamDA_mESC_10pg_CE05


title: C1_RamDA_mESC_10pg_CE12


title: C1_RamDA_mESC_10pg_CE08


title: C1_RamDA_mESC_10pg_CE10


title: C1_RamDA_mESC_10pg_CE04


title: placenta_control_mouse2_2


title: C1_RamDA_mESC_10pg_CE06


title: C1_RamDA_mESC_10pg_CE02


title: C1_RamDA_mESC_10pg_CE01


title: C1_RamDA_mESC_10pg_CD12


title: C1_RamDA_mESC_10pg_CD09


title: C1_RamDA_mESC_10pg_CE03


title: C1_RamDA_mESC_10pg_CD08


title: C1_RamDA_mESC_10pg_CD06


title: C1_RamDA_mESC_10pg_CF04


title: C1_RamDA_mESC_10pg_CD05


title: C1_RamDA_mESC_10pg_CD10


title: C1_RamDA_mESC_10pg_CD11


title: C1_RamDA_mESC_10pg_CD07


title: C1_RamDA_mESC_10pg_CD03


title: C1_RamDA_mESC_10pg_CD02


title: C1_RamDA_mESC_10pg_CD01


title: C1_RamDA_mESC_10pg_CC12


title: C1_RamDA_mESC_10pg_CC09


title: C1_RamDA_mESC_10pg_CC11


title: C1_RamDA_mESC_10pg_CC10


title: C1_RamDA_mESC_10pg_CC08


title: C1_RamDA_mESC_10pg_CC05


title: C1_RamDA_mESC_10pg_CD04


title: C1_RamDA_mESC_10pg_CC02


title: C1_RamDA_mESC_10pg_CC04


title: C1_RamDA_mESC_10pg_CC01


title: C1_RamDA_mESC_10pg_CC06


title: C1_RamDA_mESC_10pg_CC07


title: C1_RamDA_mESC_10pg_CC03


title: C1_RamDA_mESC_10pg_CB11


title: C1_RamDA_mESC_10pg_CB05


title: C1_RamDA_mESC_10pg_CB07


title: C1_RamDA_mESC_10pg_CB08


title: C1_RamDA_mESC_10pg_CB01


title: C1_RamDA_mESC_10pg_CB04


title: C1_RamDA_mESC_10pg_CB02


title: C1_RamDA_mESC_10pg_CB06


title: C1_RamDA_mESC_10pg_CA11


title: C1_RamDA_mESC_10pg_CB09


title: C1_RamDA_mESC_10pg_CA12


title: C1_RamDA_mESC_10pg_CA09


title: C1_RamDA_mESC_10pg_CA10


title: C1_RamDA_mESC_10pg_CA08


title: C1_RamDA_mESC_10pg_CA04


title: C1_RamDA_mESC_10pg_CA05


title: C1_RamDA_mESC_10pg_CA03


title: C1_RamDA_mESC_10pg_CB12


title: C1_RamDA_mESC_10pg_CB10


title: C1_RamDA_mESC_10pg_CA02


title: SRC-3 ChIP-Seq

city: Houston

first: Bokai

last: Zhu

state: Texas

address: One Baylor Plaza, M813

department: MCB

institute: Baylor College of Medicine

library_source: genomic

data_processing:
The sequences identified were mapped to the mouse genome (NCBI37/UCSC mm9) using BOWTIE function in Galaxy. Only the sequences uniquely mapped with no more than 2 mismatches were kept and used as valid reads. PCR duplicates were also removed.
Peak calling was carried out by MACS (version 1.4.2 20120305) in Galaxy/Cistrome (options --mfold 10, 30 --pvalue 1e-5)
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated by RPKM normalization.

molecule: genomic DNA

source_name: liver

extract_protocol:
Lysates were clarified from sonicated nuclei and Protein-DNA complexes were isolated with antibody.
Illumina sequencing libraries were prepared from the ChIP by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina NextSeq 500 (75 nt reads, single-end).

value: liver

value: 10 weeks old

tag: chip antibody

value: SRC-3 (5E11) Rabbit mAb #2126 CST


title: C1_RamDA_mESC_10pg_CA01


title: C1_RamDA_mESC_10pg_CA07


title: RamDA_Batch_effect_mES_PrE_B2_BH10_ES

source_name: ES_single cell

value: MoFlo sorted cell

value: single cell

value: RamDA-seq


title: RamDA_Batch_effect_mES_PrE_B2_BH05_PrE

source_name: PrE_single cell

value: Primitive endoderm (PE) cell


title: RamDA_Batch_effect_mES_PrE_B2_BH08_ES

value: Embryonic stem (ES) cell


title: RamDA_Batch_effect_mES_PrE_B2_BG11_ES


title: RamDA_Batch_effect_mES_PrE_B2_BH12_ES


title: RamDA_Batch_effect_mES_PrE_B2_BH02_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BG10_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BH06_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BG08_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BH04_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BG12_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BG09_ES


title: RamDA_Batch_effect_mES_PrE_B2_BH01_ES


title: RamDA_Batch_effect_mES_PrE_B2_BG05_ES


title: RamDA_Batch_effect_mES_PrE_B2_BG04_ES


title: RamDA_Batch_effect_mES_PrE_B2_BG02_PrE


title: C1_RamDA_mESC_10pg_CB03

value: purified total RNA


title: RamDA_Batch_effect_mES_PrE_B2_BG01_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BG03_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BF11_ES


title: RamDA_Batch_effect_mES_PrE_B2_BH09_ES


title: RamDA_Batch_effect_mES_PrE_B2_BF12_ES


title: RamDA_Batch_effect_mES_PrE_B2_BH03_ES


title: RamDA_Batch_effect_mES_PrE_B2_BH11_ES


title: RamDA_Batch_effect_mES_PrE_B2_BF09_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BF08_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BF10_ES


title: RamDA_Batch_effect_mES_PrE_B2_BG07_ES


title: RamDA_Batch_effect_mES_PrE_B2_BG06_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BF03_ES


title: RamDA_Batch_effect_mES_PrE_B2_BE11_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BE10_ES


title: RamDA_Batch_effect_mES_PrE_B2_BF04_ES


title: RamDA_Batch_effect_mES_PrE_B2_BF02_ES


title: RamDA_Batch_effect_mES_PrE_B2_BF06_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BF01_ES


title: RamDA_Batch_effect_mES_PrE_B2_BE07_ES


title: RamDA_Batch_effect_mES_PrE_B2_BE04_ES


title: RamDA_Batch_effect_mES_PrE_B2_BH07_ES


title: RamDA_Batch_effect_mES_PrE_B2_BE06_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BE05_ES


title: RamDA_Batch_effect_mES_PrE_B2_BE03_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BE02_ES


title: RamDA_Batch_effect_mES_PrE_B2_BE01_ES


title: RamDA_Batch_effect_mES_PrE_B2_BD12_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BD11_ES


title: RamDA_Batch_effect_mES_PrE_B2_BD10_ES


title: RamDA_Batch_effect_mES_PrE_B2_BD09_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BF05_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BD05_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BD02_ES


title: RamDA_Batch_effect_mES_PrE_B2_BD08_ES


title: RamDA_Batch_effect_mES_PrE_B2_BF07_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BD01_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BC12_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BD04_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BD03_ES


title: RamDA_Batch_effect_mES_PrE_B2_BC10_ES


title: RamDA_Batch_effect_mES_PrE_B2_BD07_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BE12_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BC09_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BE09_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BC11_ES


title: RamDA_Batch_effect_mES_PrE_B2_BE08_ES


title: RamDA_Batch_effect_mES_PrE_B2_BC07_ES


title: RamDA_Batch_effect_mES_PrE_B2_BC08_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BC06_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BC04_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BC03_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BC02_ES


title: RamDA_Batch_effect_mES_PrE_B2_BC05_ES


title: RamDA_Batch_effect_mES_PrE_B2_BB11_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BC01_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BB10_ES


title: RamDA_Batch_effect_mES_PrE_B2_BD06_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BB12_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BB09_ES


title: RamDA_Batch_effect_mES_PrE_B2_BB08_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BB07_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BB06_ES


title: RamDA_Batch_effect_mES_PrE_B2_BB04_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BA12_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BB05_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BB03_ES


title: RamDA_Batch_effect_mES_PrE_B2_BA11_ES


title: RamDA_Batch_effect_mES_PrE_B2_BB01_ES


title: RamDA_Batch_effect_mES_PrE_B2_BA10_ES


title: RamDA_Batch_effect_mES_PrE_B2_BA07_ES


title: RamDA_Batch_effect_mES_PrE_B2_BA06_ES


title: RamDA_Batch_effect_mES_PrE_B2_BA08_ES


title: RamDA_Batch_effect_mES_PrE_B2_BA04_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BA03_ES


title: RamDA_Batch_effect_mES_PrE_E2_CH09_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CH12_ES


title: RamDA_Batch_effect_mES_PrE_E2_CH08_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CH11_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CH07_ES


title: RamDA_Batch_effect_mES_PrE_E2_CH10_ES


title: RamDA_Batch_effect_mES_PrE_E2_CH06_ES


title: RamDA_Batch_effect_mES_PrE_E2_CH05_ES


title: RamDA_Batch_effect_mES_PrE_E2_CH03_ES


title: RamDA_Batch_effect_mES_PrE_E2_CH02_ES


title: RamDA_Batch_effect_mES_PrE_B2_BA09_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BA05_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CG07_ES


title: RamDA_Batch_effect_mES_PrE_E2_CG12_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CH01_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CG08_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CG06_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CG10_ES


title: RamDA_Batch_effect_mES_PrE_B2_BA02_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CG02_PrE


title: RamDA_Batch_effect_mES_PrE_B2_BA01_ES


title: RamDA_Batch_effect_mES_PrE_E2_CG03_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CG11_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CF10_ES


title: RamDA_Batch_effect_mES_PrE_E2_CH04_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CG04_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CF07_ES


title: RamDA_Batch_effect_mES_PrE_E2_CF11_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CG01_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CF12_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CF05_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CF06_ES


title: RamDA_Batch_effect_mES_PrE_B2_BB02_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CF04_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CG09_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CF03_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CF02_ES


title: RamDA_Batch_effect_mES_PrE_E2_CG05_ES


title: RamDA_Batch_effect_mES_PrE_E2_CE10_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CF01_ES


title: RamDA_Batch_effect_mES_PrE_E2_CE12_ES


title: RamDA_Batch_effect_mES_PrE_E2_CE11_ES


title: RamDA_Batch_effect_mES_PrE_E2_CF09_ES


title: RamDA_Batch_effect_mES_PrE_E2_CE09_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CE07_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CF08_ES


title: RamDA_Batch_effect_mES_PrE_E2_CE02_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CE06_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CE04_ES


title: RamDA_Batch_effect_mES_PrE_E2_CE08_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CD08_ES


title: RamDA_Batch_effect_mES_PrE_E2_CE03_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CE05_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CD06_ES


title: RamDA_Batch_effect_mES_PrE_E2_CE01_ES


title: RamDA_Batch_effect_mES_PrE_E2_CD04_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CD09_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CD11_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CD07_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CD10_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CC12_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CD05_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CD12_ES


title: RamDA_Batch_effect_mES_PrE_E2_CD03_ES


title: RamDA_Batch_effect_mES_PrE_E2_CC10_ES


title: RamDA_Batch_effect_mES_PrE_E2_CD02_ES


title: RamDA_Batch_effect_mES_PrE_E2_CC08_ES


title: RamDA_Batch_effect_mES_PrE_E2_CC07_ES


title: RamDA_Batch_effect_mES_PrE_E2_CC06_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CD01_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CB10_ES


title: RamDA_Batch_effect_mES_PrE_E2_CB11_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CC01_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CC04_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CC02_ES


title: RamDA_Batch_effect_mES_PrE_E2_CB12_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CB06_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CB08_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CC11_ES


title: RamDA_Batch_effect_mES_PrE_E2_CC09_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CB01_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CB03_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CB04_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CB02_ES


title: RamDA_Batch_effect_mES_PrE_E2_CB05_ES


title: RamDA_Batch_effect_mES_PrE_E2_CA10_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CA11_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CC03_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CA09_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CA07_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CA08_ES


title: RamDA_Batch_effect_mES_PrE_E2_CA02_ES


title: RamDA_Batch_effect_mES_PrE_E2_CA05_ES


title: RamDA_Batch_effect_mES_PrE_E2_CA03_ES


title: RamDA_Batch_effect_mES_PrE_E2_CB09_ES


title: RamDA_Batch_effect_mES_PrE_E2_CA04_PrE


title: RamDA_Batch_effect_mES_PrE_E2_CA06_ES


title: RamDA_Batch_effect_mES_PrE_E2_CC05_ES


title: RamDA_Batch_effect_mES_PrE_E2_CA01_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DH08_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DH11_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DH10_ES


title: RamDA_Batch_effect_mES_PrE_E2_CA12_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DG11_ES


title: RamDA_Batch_effect_mES_PrE_B1_DH12_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DH09_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DG10_ES


title: RamDA_Batch_effect_mES_PrE_B1_DG08_ES


title: RamDA_Batch_effect_mES_PrE_B1_DG07_ES


title: RamDA_Batch_effect_mES_PrE_B1_DG05_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DG06_ES


title: RamDA_Batch_effect_mES_PrE_B1_DG04_ES


title: RamDA_Batch_effect_mES_PrE_B1_DF11_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DF10_ES


title: RamDA_Batch_effect_mES_PrE_B1_DF08_ES


title: RamDA_Batch_effect_mES_PrE_B1_DF09_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DF06_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DG02_ES


title: RamDA_Batch_effect_mES_PrE_B1_DF07_ES


title: RamDA_Batch_effect_mES_PrE_B1_DF12_ES


title: RamDA_Batch_effect_mES_PrE_B1_DG03_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DG01_ES


title: RamDA_Batch_effect_mES_PrE_B1_DF02_ES


title: RamDA_Batch_effect_mES_PrE_B1_DE11_ES


title: RamDA_Batch_effect_mES_PrE_B1_DF01_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DE12_ES


title: RamDA_Batch_effect_mES_PrE_B1_DF05_ES


title: RamDA_Batch_effect_mES_PrE_B1_DF04_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DF03_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DE10_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DE06_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DE07_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DE09_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DE08_ES


title: RamDA_Batch_effect_mES_PrE_B1_DG12_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DH01_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DH06_ES


title: RamDA_Batch_effect_mES_PrE_B1_DH07_ES


title: RamDA_Batch_effect_mES_PrE_B1_DH02_ES


title: RamDA_Batch_effect_mES_PrE_B1_DH04_ES


title: RamDA_Batch_effect_mES_PrE_B1_DE04_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DH03_ES


title: RamDA_Batch_effect_mES_PrE_B1_DH05_ES


title: RamDA_Batch_effect_mES_PrE_B1_DE05_ES


title: RamDA_Batch_effect_mES_PrE_B1_DE03_ES


title: RamDA_Batch_effect_mES_PrE_B1_DE01_ES


title: RamDA_Batch_effect_mES_PrE_B1_DD10_ES


title: RamDA_Batch_effect_mES_PrE_B1_DD11_ES


title: RamDA_Batch_effect_mES_PrE_B1_DD12_ES


title: RamDA_Batch_effect_mES_PrE_E2_CB07_ES


title: RamDA_Batch_effect_mES_PrE_B1_DE02_ES


title: RamDA_Batch_effect_mES_PrE_B1_DD04_ES


title: RamDA_Batch_effect_mES_PrE_B1_DD05_ES


title: RamDA_Batch_effect_mES_PrE_B1_DD06_ES


title: RamDA_Batch_effect_mES_PrE_B1_DD07_ES


title: RamDA_Batch_effect_mES_PrE_B1_DD08_ES


title: RamDA_Batch_effect_mES_PrE_B1_DD03_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DC12_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DD09_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DC11_ES


title: RamDA_Batch_effect_mES_PrE_B1_DC10_ES


title: RamDA_Batch_effect_mES_PrE_B1_DC09_ES


title: RamDA_Batch_effect_mES_PrE_B1_DC08_ES


title: RamDA_Batch_effect_mES_PrE_B1_DC03_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DC04_ES


title: RamDA_Batch_effect_mES_PrE_B1_DC05_ES


title: RamDA_Batch_effect_mES_PrE_B1_DC07_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DC01_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DB12_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DC02_ES


title: RamDA_Batch_effect_mES_PrE_B1_DB11_ES


title: RamDA_Batch_effect_mES_PrE_B1_DB10_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DB09_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DB08_ES


title: RamDA_Batch_effect_mES_PrE_B1_DB07_ES


title: RamDA_Batch_effect_mES_PrE_B1_DB06_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DD02_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DB04_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DB05_ES


title: RamDA_Batch_effect_mES_PrE_B1_DC06_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DB01_ES


title: RamDA_Batch_effect_mES_PrE_B1_DA10_ES


title: RamDA_Batch_effect_mES_PrE_B1_DA11_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DA12_ES


title: RamDA_Batch_effect_mES_PrE_B1_DA08_ES


title: RamDA_Batch_effect_mES_PrE_B1_DA09_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DB02_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DB03_ES


title: RamDA_Batch_effect_mES_PrE_B1_DA07_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DA05_ES


title: RamDA_Batch_effect_mES_PrE_B1_DA06_ES


title: RamDA_Batch_effect_mES_PrE_B1_DA01_ES


title: RamDA_Batch_effect_mES_PrE_B1_DA04_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DA03_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DD01_ES


title: RamDA_Batch_effect_mES_PrE_E1_AH03_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AH12_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AH11_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DA02_ES


title: RamDA_Batch_effect_mES_PrE_E1_AH08_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AH02_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AH10_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AH09_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AH07_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AH06_ES


title: RamDA_Batch_effect_mES_PrE_E1_AG10_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AH05_ES


title: RamDA_Batch_effect_mES_PrE_E1_AG05_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AG07_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AG04_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AH04_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AG12_ES


title: RamDA_Batch_effect_mES_PrE_E1_AH01_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AG08_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AG09_ES


title: RamDA_Batch_effect_mES_PrE_E1_AF09_ES


title: RamDA_Batch_effect_mES_PrE_E1_AF07_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AG06_ES


title: RamDA_Batch_effect_mES_PrE_E1_AG03_ES


title: RamDA_Batch_effect_mES_PrE_E1_AF04_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AF02_ES


title: RamDA_Batch_effect_mES_PrE_E1_AF12_ES


title: RamDA_Batch_effect_mES_PrE_E1_AF10_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AE11_ES


title: RamDA_Batch_effect_mES_PrE_E1_AF01_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AG02_ES


title: RamDA_Batch_effect_mES_PrE_E1_AF11_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AE12_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AF08_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AG01_ES


title: RamDA_Batch_effect_mES_PrE_E1_AE07_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AG11_ES


title: RamDA_Batch_effect_mES_PrE_E1_AE08_ES


title: RamDA_Batch_effect_mES_PrE_E1_AE10_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AE06_ES


title: RamDA_Batch_effect_mES_PrE_E1_AE05_ES


title: RamDA_Batch_effect_mES_PrE_E1_AE01_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AE09_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AD12_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AE04_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AD11_PrE


title: RamDA_Batch_effect_mES_PrE_B1_DG09_ES


title: RamDA_Batch_effect_mES_PrE_E1_AD09_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AE02_ES


title: RamDA_Batch_effect_mES_PrE_E1_AF06_ES


title: RamDA_Batch_effect_mES_PrE_E1_AF05_ES


title: RamDA_Batch_effect_mES_PrE_E1_AF03_ES


title: RamDA_Batch_effect_mES_PrE_E1_AD10_ES


title: RamDA_Batch_effect_mES_PrE_E1_AD06_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AD07_ES


title: RamDA_Batch_effect_mES_PrE_E1_AD02_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AD04_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AC09_ES


title: RamDA_Batch_effect_mES_PrE_E1_AC08_ES


title: RamDA_Batch_effect_mES_PrE_E1_AC12_ES


title: RamDA_Batch_effect_mES_PrE_E1_AC10_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AC02_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AC07_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AC11_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AB11_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AB10_ES


title: RamDA_Batch_effect_mES_PrE_E1_AC04_ES


title: RamDA_Batch_effect_mES_PrE_E1_AD05_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AB06_ES


title: RamDA_Batch_effect_mES_PrE_E1_AD08_ES


title: RamDA_Batch_effect_mES_PrE_E1_AB12_ES


title: RamDA_Batch_effect_mES_PrE_E1_AB08_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AB07_ES


title: RamDA_Batch_effect_mES_PrE_E1_AB09_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AA12_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AD03_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AC01_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AB03_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AA10_ES


title: RamDA_Batch_effect_mES_PrE_E1_AA08_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AD01_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AB05_ES


title: RamDA_Batch_effect_mES_PrE_E1_AB04_ES


title: RamDA_Batch_effect_mES_PrE_E1_AA06_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AB01_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AA05_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AB02_ES


title: RamDA_Batch_effect_mES_PrE_E1_AC06_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AC03_PrE


title: RamDA_Batch_effect_mES_PrE_E1_AA11_ES


title: RamDA_Batch_effect_mES_PrE_E1_AA04_PrE


title: RamDA_mESC_1ng_03

value: 1 ng


title: RamDA_mESC_1ng_02

value: All phase


title: RamDA_Batch_effect_mES_PrE_E1_AA09_ES


title: RamDA_Batch_effect_mES_PrE_E1_AA01_ES


title: RamDA_Batch_effect_mES_PrE_E1_AA07_PrE


title: KAPA_riboE_mESC_1ng_01

value: KAPA RNA HyperPrep Kit with RiboErase


title: RamDA_Batch_effect_mES_PrE_E1_AA02_ES


title: RamDA_mESC_1ng_01


title: RamDA_mESC_10pg_DH09

value: 10 pg


title: RamDA_mESC_10pg_DH11


title: RamDA_mESC_10pg_DH12


title: KAPA_riboE_mESC_10ng_02

value: 10 ng


title: KAPA_riboE_mESC_10ng_03


title: RamDA_Batch_effect_mES_PrE_E1_AA03_PrE


title: RamDA_mESC_10pg_DH10


title: KAPA_riboE_mESC_1ng_02


title: KAPA_riboE_mESC_10ng_01


title: RamDA_mESC_10pg_DH07


title: RamDA_mESC_10pg_DH05


title: RamDA_mESC_10pg_DH06


title: RamDA_mESC_10pg_DH08


title: RamDA_mESC_10pg_DH04


title: KAPA_riboE_mESC_1ng_03


title: RamDA_mESC_10pg_DG11


title: RamDA_mESC_10pg_DH02


title: RamDA_Batch_effect_mES_PrE_E1_AE03_PrE


title: RamDA_mESC_10pg_DH01


title: RamDA_mESC_10pg_DG09


title: RamDA_mESC_10pg_DG10


title: RamDA_mESC_10pg_DG07


title: RamDA_mESC_10pg_DG08


title: RamDA_mESC_10pg_DG03


title: RamDA_mESC_10pg_DG05


title: RamDA_mESC_10pg_DH03


title: RamDA_mESC_10pg_DG04


title: RamDA_mESC_10pg_DG02


title: RamDA_mESC_10pg_DG01


title: RamDA_mESC_10pg_DF11


title: RamDA_mESC_10pg_DF10


title: RamDA_mESC_10pg_DF07


title: RamDA_mESC_10pg_DF08


title: RamDA_mESC_10pg_DF12


title: RamDA_mESC_10pg_DG12


title: RamDA_mESC_10pg_DF04


title: RamDA_mESC_10pg_DF05


title: RamDA_mESC_10pg_DF03


title: RamDA_mESC_10pg_DF02


title: RamDA_mESC_10pg_DG06


title: RamDA_mESC_10pg_DE11


title: RamDA_mESC_10pg_DE09


title: RamDA_mESC_10pg_DF01


title: RamDA_mESC_10pg_DE07


title: RamDA_mESC_10pg_DE06


title: RamDA_mESC_10pg_DE08


title: RamDA_mESC_10pg_DE10


title: RamDA_mESC_10pg_DE12


title: RamDA_mESC_10pg_DE04


title: RamDA_mESC_10pg_DF06


title: RamDA_mESC_10pg_DF09


title: RamDA_mESC_10pg_DE05


title: RamDA_mESC_10pg_DD12


title: RamDA_mESC_10pg_DE01


title: RamDA_mESC_10pg_DE02


title: RamDA_mESC_10pg_DD10


title: RamDA_mESC_10pg_DD11


title: RamDA_mESC_10pg_DD09


title: RamDA_mESC_10pg_DE03


title: RamDA_mESC_10pg_DD04


title: RamDA_mESC_10pg_DD07


title: RamDA_mESC_10pg_DD03


title: RamDA_mESC_10pg_DC11


title: RamDA_mESC_10pg_DC12


title: RamDA_mESC_10pg_DC09


title: RamDA_mESC_10pg_DC08


title: RamDA_mESC_10pg_DC06


title: RamDA_mESC_10pg_DC07


title: RamDA_mESC_10pg_DC03


title: RamDA_mESC_10pg_DC10


title: RamDA_mESC_10pg_DC04


title: RamDA_mESC_10pg_DC05


title: RamDA_mESC_10pg_DB11


title: RamDA_mESC_10pg_DC02


title: RamDA_mESC_10pg_DC01


title: RamDA_mESC_10pg_DD08


title: RamDA_mESC_10pg_DB10


title: RamDA_mESC_10pg_DD06


title: RamDA_mESC_10pg_DB12


title: RamDA_mESC_10pg_DD05


title: RamDA_mESC_10pg_DB09


title: RamDA_mESC_10pg_DD02


title: RamDA_mESC_10pg_DB07


title: RamDA_mESC_10pg_DB06


title: RamDA_mESC_10pg_DB05


title: RamDA_mESC_10pg_DD01


title: RamDA_mESC_10pg_DB04


title: RamDA_mESC_10pg_DB02


title: RamDA_mESC_10pg_DB03


title: RamDA_mESC_10pg_DA12


title: RamDA_mESC_10pg_DB01


title: RamDA_mESC_10pg_DA11


title: RamDA_mESC_10pg_DA10


title: RamDA_mESC_10pg_DA08


title: RamDA_mESC_10pg_DA06


title: RamDA_mESC_10pg_DA07


title: RamDA_mESC_10pg_DA09


title: RamDA_mESC_10pg_DA04


title: C1_SMART_V4_mESC_10pg_AH12

value: C1-SMART-Seq v4


title: C1_SMART_V4_mESC_10pg_AH11


title: RamDA_mESC_10pg_DB08


title: C1_SMART_V4_mESC_10pg_AH08


title: C1_SMART_V4_mESC_10pg_AH09


title: C1_SMART_V4_mESC_10pg_AH06


title: C1_SMART_V4_mESC_10pg_AH07


title: C1_SMART_V4_mESC_10pg_AH05


title: C1_SMART_V4_mESC_10pg_AH03


title: C1_SMART_V4_mESC_10pg_AH04


title: C1_SMART_V4_mESC_10pg_AH02


title: C1_SMART_V4_mESC_10pg_AH01


title: RamDA_mESC_10pg_DA05


title: C1_SMART_V4_mESC_10pg_AG09


title: C1_SMART_V4_mESC_10pg_AG12


title: C1_SMART_V4_mESC_10pg_AG06


title: C1_SMART_V4_mESC_10pg_AG10


title: C1_SMART_V4_mESC_10pg_AG07


title: C1_SMART_V4_mESC_10pg_AG08


title: C1_SMART_V4_mESC_10pg_AG03


title: RamDA_mESC_10pg_DA01


title: C1_SMART_V4_mESC_10pg_AG02


title: C1_SMART_V4_mESC_10pg_AH10


title: C1_SMART_V4_mESC_10pg_AG11


title: C1_SMART_V4_mESC_10pg_AG05


title: C1_SMART_V4_mESC_10pg_AF12


title: C1_SMART_V4_mESC_10pg_AG01


title: C1_SMART_V4_mESC_10pg_AF08


title: C1_SMART_V4_mESC_10pg_AF06


title: C1_SMART_V4_mESC_10pg_AF07


title: C1_SMART_V4_mESC_10pg_AF11


title: C1_SMART_V4_mESC_10pg_AF10


title: C1_SMART_V4_mESC_10pg_AF03


title: C1_SMART_V4_mESC_10pg_AF02


title: C1_SMART_V4_mESC_10pg_AF05


title: C1_SMART_V4_mESC_10pg_AF09


title: C1_SMART_V4_mESC_10pg_AF04


title: C1_SMART_V4_mESC_10pg_AE11


title: C1_SMART_V4_mESC_10pg_AE12


title: C1_SMART_V4_mESC_10pg_AE09


title: C1_SMART_V4_mESC_10pg_AE02


title: C1_SMART_V4_mESC_10pg_AE07


title: C1_SMART_V4_mESC_10pg_AE01


title: C1_SMART_V4_mESC_10pg_AE06


title: RamDA_mESC_10pg_DA03


title: C1_SMART_V4_mESC_10pg_AD11


title: C1_SMART_V4_mESC_10pg_AD12


title: C1_SMART_V4_mESC_10pg_AD09


title: C1_SMART_V4_mESC_10pg_AE05


title: C1_SMART_V4_mESC_10pg_AD08


title: C1_SMART_V4_mESC_10pg_AD10


title: C1_SMART_V4_mESC_10pg_AD07


title: C1_SMART_V4_mESC_10pg_AE08


title: C1_SMART_V4_mESC_10pg_AF01


title: C1_SMART_V4_mESC_10pg_AD01


title: C1_SMART_V4_mESC_10pg_AD02


title: C1_SMART_V4_mESC_10pg_AC10


title: C1_SMART_V4_mESC_10pg_AD03


title: C1_SMART_V4_mESC_10pg_AC11


title: C1_SMART_V4_mESC_10pg_AD04


title: C1_SMART_V4_mESC_10pg_AC09


title: C1_SMART_V4_mESC_10pg_AC03


title: C1_SMART_V4_mESC_10pg_AC05


title: C1_SMART_V4_mESC_10pg_AC08


title: C1_SMART_V4_mESC_10pg_AC01


title: C1_SMART_V4_mESC_10pg_AE10


title: C1_SMART_V4_mESC_10pg_AB12


title: C1_SMART_V4_mESC_10pg_AC06


title: C1_SMART_V4_mESC_10pg_AB08


title: C1_SMART_V4_mESC_10pg_AC02


title: C1_SMART_V4_mESC_10pg_AD06


title: C1_SMART_V4_mESC_10pg_AB07


title: C1_SMART_V4_mESC_10pg_AB10


title: C1_SMART_V4_mESC_10pg_AB02


title: C1_SMART_V4_mESC_10pg_AB03


title: C1_SMART_V4_mESC_10pg_AB05


title: C1_SMART_V4_mESC_10pg_AB04


title: C1_SMART_V4_mESC_10pg_AA12


title: C1_SMART_V4_mESC_10pg_AB06


title: C1_SMART_V4_mESC_10pg_AB09


title: C1_SMART_V4_mESC_10pg_AB01


title: C1_SMART_V4_mESC_10pg_AC04


title: C1_SMART_V4_mESC_10pg_AA11


title: C1_SMART_V4_mESC_10pg_AA10


title: RamDA_Batch_effect_mES_PrE_E1_AC05_ES


title: C1_SMART_V4_mESC_10pg_AA07


title: C1_SMART_V4_mESC_10pg_AA09


title: C1_SMART_V4_mESC_10pg_AC12


title: C1_SMART_V4_mESC_10pg_AA06


title: C1_SMART_V4_mESC_10pg_AA05


title: C1_SMART_V4_mESC_10pg_AA03


title: C1_SMART_V4_mESC_10pg_AA08


title: H10 RA PR30P5 vs M1P5

city: Montpellier

first: Rachel

last: AUDO

address: 1919 route de Mende

country: France

hyb_protocol: Cy3 and Cy5 labelled aRNA samples were mixed in equal proportions (700 pmol) and fragmented with the RNA Fragmentation Reagents (Ambion) to enhance aRNA hybridization, dried up to 60ul of final volume, and hybridized on INDAC oligonucleotide microarrays. Labeled probes (60 µl) were mixed with 60 µl of 4X hybridization buffer and 120 µl of deionised formamide, denatured at 95°C for 5min and hybridized at 37°C for 12 hours with the Automated Slide Processor (ASP) of Amersham. Slides were successively washed at 37°C in 1X SCC/0.2% SDS for 20 min, in 0.1X SCC/0.2% SDS for 2x10 min, in 0.1X SCC for 10 min, rinsed in isopropanol and air dried.

scan_protocol: Images were obtained with a GenePix 4200AL (Axon Instruments) at 10 um resolution and 5% of laser power.

data_processing: The data was normalized using LOESS (Locally Weighted Scatterplot Smoothing) method from the LIMMA package (from Bioconductor)

source_name: RA PR30P5

label_protocol: Amino allyl aRNA was labelled according the Dye Coupling and Labeled aRNA Cleanup protocol of the Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion) 700 pmol of incorporated dye was used for hybridization.

growth_protocol: Synovial fibroblasts were extracted from synovium obtained from  patients meeting the American College of Rheumatology criteria for RA (revised 1987), who had undergone surgery for synovectomy or total joint replacement surgery. Synovial fibroblasts were cultured in RPMI-1640 supplemented with 10% fetal calf serum (FCS)

extract_protocol: The total RNA from 4x105 cells were extracted by TRIZol (Invitrogen, Cergy Pontoise, France) and purified by precipitation in the LiCl. The purity of the mRNA, thus obtained, was checked by Agilent Bioanalyser

treatment_protocol: For experimentation, the FCS in the media was progressively decreased from 10% to 1%, with final starvation for 12 hours in RPMI-media containing 1% FCS

tag: cell decsription (gender-age of patient)

value: synovial fibroblast

tag: gender-age of patient

value: female-46 years

tag: sensitivity to trail induced apoptosis

value: resistant

value: female-87 years

source_name: RA M1P5

tag: cell description

value: sensitive


title: H12 RA PR8P5 vs PR19P8

source_name: RA PR8P5

value: female-52 years

value: female-50 years

source_name: RA PR19P8


title: C1_SMART_V4_mESC_10pg_AA01


title: C1_SMART_V4_mESC_10pg_AA02


title: C1_RamDA_mESC_10pg_CH12


title: C1_RamDA_mESC_10pg_CH11


title: H11 RA M1P5 vs PR8P5


title: H8 RA PR28P6 vs PR32P4

source_name: RA PR28P6

value: female-48 years

value: female-62 years

source_name: RA PR32P4


title: C1_SMART_V4_mESC_10pg_AA04

value: Embryonic stem (ES) cell


title: C1_SMART_V4_mESC_10pg_AC07

value: purified total RNA


title: CD31-45- cells [cd3145 cell 92]

city: London

first: Magnus

middle: David

last: Lynch

address: 28th Floor, Tower Wing, Guy's Campus

department: Centre for Stem Cells and Regenerative Medicine

country: United Kingdom

institute: King's College London

description:
cd3145 cell 92
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv

data_processing:
Reads were mapped to hg19 reference genome with Tophat.
For single cell RNA sequencing, gene-specific expression was quantified using featureCounts.
For spatial RNA sequencing, maximal exonic read density was quantified for each gene.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.csv: Comma-separated text files include gene expression quantification.

source_name: Human Dermal Cells

extract_protocol:
Separated papillary and reticular dermis samples were transferred to lysis buffer containing 2-mercaptoethanol (PureLink RNA micro scale kit, Invitrogen) and homogenized for 2 minutes using a mechanical homogenizer (Polytron, Kinematica). Subsequent RNA extraction was performed using the PureLink micro kit according to the manufacturer’s instructions.
Library preparation was performed with SmartSeq2 followed by the Nextera XT protocol (Illumina). Sequencing was performed on the Illumina HiSeq 2000 or HiSeq 2500 with TruSeq SBS v3 chemistry.

treatment_protocol: Spatial RNA sequencing was performed using fresh human skin samples (from three separate individuals). Skin samples were incubated with Dispase II (Stemcell Technologies) for 1h at 37° C permitting separation of the epidermis. The dermis was separated into papillary (upper 100 μm) reticular (200-500 μm) dermis by microdissection under a dissecting microscope. For single cell RNA sequencing, single cells were isolated by flow cytometry and sorted into individual wells of a 96 well plate containing 2μl lysis buffer (0.2% (vol/vol) Triton X-100 and 2 U/ul recombinant RNase inhibitor (Clontech).

value: Primary dermal fibroblasts

tag: cell subpopulation


title: C1_RamDA_mESC_10pg_CH09

value: All phase


title: C1_RamDA_mESC_10pg_CH10


title: H6 RA PR25P4 vs PR24

source_name: RA PR25P4

value: female-39 years

value: male-55 years

source_name: RA PR24


title: CD31-45- cells [cd3145 cell 90]

description:
cd3145 cell 90
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: C1_RamDA_mESC_10pg_CH07

value: 10 pg


title: CD31-45- cells [cd3145 cell 89]

description:
cd3145 cell 89
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: H7 RA PR24 vs PR28P6


title: H5 RA PR16P4 vs PR25P4

source_name: RA PR16P4

value: female-68 years


title: H9 RA PR32P4 vs PR30P5

value: synovial fibroblast


title: H2 RA PR18P8 vs PR21P8

source_name: RA PR18P8

value: female-30 years

value: female-36 years

source_name: RA PR21P8


title: H4 RA PR22P6 vs PR16P4

source_name: RA PR22P6

value: resistant


title: CD31-45- cells [cd3145 cell 88]

description:
cd3145 cell 88
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: H1 RA PR19P8 vs PR18P8

value: sensitive


title: H3 RA PR21P8 vs PR22P6

value: female-52 years


title: CD31-45- cells [cd3145 cell 85]

description:
cd3145 cell 85
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 86]

description:
cd3145 cell 86
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: C1_RamDA_mESC_10pg_CH03

source_name: ES_diluted total RNA


title: CD31-45- cells [cd3145 cell 87]

description:
cd3145 cell 87
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 83]

description:
cd3145 cell 83
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 84]

description:
cd3145 cell 84
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: C1_RamDA_mESC_10pg_CH05


title: CD31-45- cells [cd3145 cell 91]

description:
cd3145 cell 91
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: C1_RamDA_mESC_10pg_CH06


title: CD31-45- cells [cd3145 cell 82]

description:
cd3145 cell 82
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: C1_RamDA_mESC_10pg_CH08


title: C1_RamDA_mESC_10pg_CH01


title: C1_RamDA_mESC_10pg_CG12


title: CD31-45- cells [cd3145 cell 81]

description:
cd3145 cell 81
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: RamDA_mESC_10pg_DA02

value: RamDA-seq


title: CD31-45- cells [cd3145 cell 80]

description:
cd3145 cell 80
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: C1_RamDA_mESC_10pg_CH04


title: C1_RamDA_mESC_10pg_CG09


title: CD31-45- cells [cd3145 cell 76]

description:
cd3145 cell 76
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 77]

description:
cd3145 cell 77
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: C1_SMART_V4_mESC_10pg_AD05

value: C1-SMART-Seq v4


title: C1_RamDA_mESC_10pg_CG10


title: C1_RamDA_mESC_10pg_CG07


title: CD31-45- cells [cd3145 cell 79]

description:
cd3145 cell 79
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: C1_RamDA_mESC_10pg_CG08


title: CD31-45- cells [cd3145 cell 75]

description:
cd3145 cell 75
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: C1_RamDA_mESC_10pg_CH02


title: C1_RamDA_mESC_10pg_CG04


title: C1_SMART_V4_mESC_10pg_AG04


title: CD31-45- cells [cd3145 cell 72]

description:
cd3145 cell 72
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: C1_RamDA_mESC_10pg_CG06


title: CD31-45- cells [cd3145 cell 73]

description:
cd3145 cell 73
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 71]

description:
cd3145 cell 71
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: C1_RamDA_mESC_10pg_CG05


title: CD31-45- cells [cd3145 cell 69]

description:
cd3145 cell 69
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 70]

description:
cd3145 cell 70
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 66]

description:
cd3145 cell 66
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: C1_RamDA_mESC_10pg_CG11


title: CD31-45- cells [cd3145 cell 74]

description:
cd3145 cell 74
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 68]

description:
cd3145 cell 68
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 78]

description:
cd3145 cell 78
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 65]

description:
cd3145 cell 65
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 63]

description:
cd3145 cell 63
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 62]

description:
cd3145 cell 62
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 61]

description:
cd3145 cell 61
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 60]

description:
cd3145 cell 60
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 58]

description:
cd3145 cell 58
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 59]

description:
cd3145 cell 59
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 56]

description:
cd3145 cell 56
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 55]

description:
cd3145 cell 55
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 54]

description:
cd3145 cell 54
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 53]

description:
cd3145 cell 53
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 52]

description:
cd3145 cell 52
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 67]

description:
cd3145 cell 67
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 50]

description:
cd3145 cell 50
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 48]

description:
cd3145 cell 48
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 64]

description:
cd3145 cell 64
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 46]

description:
cd3145 cell 46
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 44]

description:
cd3145 cell 44
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 45]

description:
cd3145 cell 45
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 49]

description:
cd3145 cell 49
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 51]

description:
cd3145 cell 51
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 41]

description:
cd3145 cell 41
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 47]

description:
cd3145 cell 47
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 43]

description:
cd3145 cell 43
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 38]

description:
cd3145 cell 38
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 40]

description:
cd3145 cell 40
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 36]

description:
cd3145 cell 36
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 37]

description:
cd3145 cell 37
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 39]

description:
cd3145 cell 39
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 42]

description:
cd3145 cell 42
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 35]

description:
cd3145 cell 35
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 57]

description:
cd3145 cell 57
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 32]

description:
cd3145 cell 32
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 30]

description:
cd3145 cell 30
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 33]

description:
cd3145 cell 33
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 29]

description:
cd3145 cell 29
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 28]

description:
cd3145 cell 28
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 31]

description:
cd3145 cell 31
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 26]

description:
cd3145 cell 26
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 23]

description:
cd3145 cell 23
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 25]

description:
cd3145 cell 25
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 21]

description:
cd3145 cell 21
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 22]

description:
cd3145 cell 22
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 19]

description:
cd3145 cell 19
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 15]

description:
cd3145 cell 15
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 20]

description:
cd3145 cell 20
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 24]

description:
cd3145 cell 24
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 13]

description:
cd3145 cell 13
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 34]

description:
cd3145 cell 34
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 14]

description:
cd3145 cell 14
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 11]

description:
cd3145 cell 11
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 17]

description:
cd3145 cell 17
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 16]

description:
cd3145 cell 16
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 7]

description:
cd3145 cell 7
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 12]

description:
cd3145 cell 12
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 6]

description:
cd3145 cell 6
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 8]

description:
cd3145 cell 8
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 27]

description:
cd3145 cell 27
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 10]

description:
cd3145 cell 10
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 9]

description:
cd3145 cell 9
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 4]

description:
cd3145 cell 4
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 1]

description:
cd3145 cell 1
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 5]

description:
cd3145 cell 5
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-CD45-CD90+ cells [cd90 cell92]

description:
cd90 cell92
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-45- cells [cd3145 cell 3]

description:
cd3145 cell 3
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-45- cells [cd3145 cell 18]

description:
cd3145 cell 18
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-CD45-CD90+ cells [cd90 cell91]

description:
cd90 cell91
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell87]

description:
cd90 cell87
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: C1_SMART_V4_mESC_10pg_AB11


title: CD31-45- cells [cd3145 cell 2]

description:
cd3145 cell 2
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-.
PolyA
processed data file: CD3145.csv


title: CD31-CD45-CD90+ cells [cd90 cell86]

description:
cd90 cell86
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell89]

description:
cd90 cell89
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell88]

description:
cd90 cell88
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell84]

description:
cd90 cell84
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell83]

description:
cd90 cell83
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell81]

description:
cd90 cell81
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell80]

description:
cd90 cell80
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell77]

description:
cd90 cell77
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell78]

description:
cd90 cell78
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell82]

description:
cd90 cell82
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell79]

description:
cd90 cell79
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell76]

description:
cd90 cell76
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell75]

description:
cd90 cell75
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell73]

description:
cd90 cell73
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv