title: Total 0-180 MAF Slbp10/12 Drosophila embryo (replicate 1)

description:
Slbp10_12_0_3h_1
processed data file: SLBP_Grp_mutants_normalized_counts.xlsx


title: Total 0-180 MAF grpfs1 Drosophila embryo (replicate 1)

status: Public on Jan 20 2017

type: SRA

city: Montreal

first: Fabio

middle: Alexis

last: Lefebvre

state: Quebec

address: 110 Ave des Pins

department: RNA biolog

country: Canada

institute: IRCM

description:
Chk1_ko_0_3h_1
processed data file: SLBP_Grp_mutants_normalized_counts.xlsx

library_source: transcriptomic

data_processing:
Read quality was assessed with FastQC v0.10.1.
No trimming was deemed necessary
Read alignment was performed with TopHat on dm3
Featurecount was used to extract read counts
The count files were used with DESeq for differential expression
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited files include normalized read counts for each sample

molecule: total RNA

organism: Drosophila melanogaster

growth_protocol: Oregon R was used as wt. The grpfs1 stock was kindly provided by the Theurkauf lab, and the Slbp10, Slbp12 and Slbp15 stock were obtained from the Duronio lab. Embryos were collected and dechorionated as previously described. 90-180 minutes AEL samples were collected over 90 minutes and kept at 25 C for 90 additional minutes, while 0-45 minutes AEL embryos.

extract_protocol:
For DAPI staining, embryos were fixed with formaldehyde as previously described and imaged by epifluorescence on a Leica DM5500B microscope equipped with a QImaging ExiAqua camera (QImaging). Cytoplasmic and nuclear extracts were derived from 90-180 minutes AEF wt embryos as previously described.
RNA-seq libraries were prepared for deep-sequencing using standard Illumina sequencing protocol with ribosomal depletion

tag: strain background

value: Oregon R

tag: embryonic stage

tag: genotype/variation

value: from transheterozygous mothers bearing the grpfs1 mutation

tag: sample type

value: Total mutant embryo extract


title: 20B_HighLight_HighO2

city: Richland

first: Ryan

middle: Scott

last: McClure

state: Washington

address: 902 Battelle Boulevard

country: USA

institute: Pacific Northwest National Laboratory

data_processing:
The75-base reads were aligned to the T. elongatus and M. ruber genomes using BWA
Resulting SAM files from BWA were then converted into counts for each gene in T. elongatus and M. ruber using HTSeq
Raw count files were then normalized using DESeq2
Genome_build: Thermosynechococcus elongatus BP1: NC_004113, M. ruber strain A RAST annotation
Supplementary_files_format_and_content: SS_BP1_Meio_Norm_Values.csv

organism:
Meiothermus ruber
Thermosynechococcus vestitus BP-1

growth_protocol: Growth took place in a bioreactor at pH 7.5, 52C, in modified BG-11 media (BP1 media, mM): 17.6 NaNO3, 0.3039 MgSO4∙7H2O, 0.175 KH2PO4, 0.2449 CaCl2∙2H2O, 0.0028 Na2EDTA, 0.0144 FeCl3. The mBG-11 was supplemented with 1 ml L-1 trace-mix (mM): 46.2544 H3BO3, 9.1458 MnCl2∙4H2O, 0.7720 ZnSO4∙7H2O, 1.6119 Na2MoO4∙2H2O, 0.3164 CuSO4∙5H2O, 0.1697 Co(NO3)2∙6H2O.

extract_protocol:
RNA was extracted using Promega following by DNAseI treatment
Template cDNA was prepared using the NuGen Ovation Universal RNAseq kit. Sequencing was carried using the Illumina NextSeq 500.

treatment_protocol: Three light levels were examined: low (197 µmol photons m-2 sec-1), mid (1190 µmol photons m-2 sec-1), and high (1995 µmol photons m-2 sec-1) all with oxygen at 7% of atmospheric levels .  Three oxygen levels were also examined: low (oxygen at 7% of atmosphere), mid (oxygen at 150% of atmosphere) and high (oxygen at 217% of atmosphere) all at a light level of 197 µmol photons m-2 sec-1.  T. elongatus was examined both axenically and with a hetertrophic partner of each of these six conditions.  The high light condition overlaps with the low oxygen condition for both axenic and co-culture experiments

tag: tissue

value: Planktonic cells

tag: oxygen

value: High

tag: light


title: 20A_HighLight_HighO2


title: 19B_HighLight_MidO2

value: Mid


title: Total 0-180 MAF ORER Drosophila embryo (replicate 2)

description:
ORER_0_3h_2
processed data file: SLBP_Grp_mutants_normalized_counts.xlsx

source_name: Total 0-180 MAF ORER Drosophila embryo

value: wild type

value: Total wt embryo extract


title: Nuclear 90-180 MAF ORER Drosophila embryo (replicate 1)

description:
J_nuclEmbWT_90_180MAF
processed data file: Spatiotemporal_RNA_distributions_embryogenesis_normalized_counts.xls

value: Nuclear blastoderm wt embryo extract


title: Total 0-180 MAF ORER Drosophila embryo (replicate 1)

description:
ORER_0_3h_1
processed data file: SLBP_Grp_mutants_normalized_counts.xlsx


title: 19A_HighLight_MidO2


title: Cytoplasmic 90-180 MAF ORER Drosophila embryo (replicate 2)

description:
I_cytoEmbWT_90_180MAF
processed data file: Spatiotemporal_RNA_distributions_embryogenesis_normalized_counts.xls

value: Cytoplasmic blastoderm wt embryo extract


title: Total 0-45 MAF ORER Drosophila embryo (replicate 2)

description:
M_TotEmbWT_0_45MAF
processed data file: Spatiotemporal_RNA_distributions_embryogenesis_normalized_counts.xls

source_name: Total 0-45 MAF ORER Drosophila embryo

value: 1 to 5; 0-45 min AEL

value: Total syncitial wt embryo extract


title: 18_2A_HighLight_LowO2

value: Low


title: Total 0-45 MAF ORER Drosophila embryo (replicate 1)

description:
L_TotEmbWT_0_45MAF
processed data file: Spatiotemporal_RNA_distributions_embryogenesis_normalized_counts.xls


title: 18_1B_HighLight_LowO2


title: 14A_LowLight_LowO2


title: Transcriptome from adult (C) goat

city: Chengdu

first: Jiangjiang

last: Zhu

state: Sichuan

address: #16, South Section, 1st Ring Road

department: Institute of Qinghai-Tibetan Plateau

country: China

institute: Southwest Uniersity for Nationalities

data_processing:
raw reads (raw data) were first determined by fastqc and filtered by removing the adapter sequences and potential contamination, i.e. reads with unknown base (N) greater than 10%, and low quality sequences (<Q20) , to obtain the clean data
All of the downstream analyses were based on high quality clean data.
TopHat2 method was used for sequence mapping and assembly with the whole genome (CHIR_1.0) as the reference sequence (ftp://ftp.ncbi.nlm.nih.gov/genomes/Capra_hircus/)
Assembled unigenes were annotated to the goat reference genome using BLAST. The unigene expression level was recorded according to the sum frequencies of compared reads. FPKM (expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced) was used for expression normalization. Gene Ontology (GO, http://www.geneontology.org) was performed using GOseq software
DEG was analyzed using DESeq method following the normalization of read count by Trimmed Mean of M values (TMM) . DEG were selected according to |log2(FoldChange)| > 1 and qvalue < 0.005 (normalized p value), which was then used for GO analysis
The software of Short Time-series Expression Miner (STEM) was used for expression pattern analysis
Gene co-expression analysis was performed to track the interactions among the DEG profiles
Supplementary_files_format_and_content: The excel file includes FPKM value of each sample

organism: Capra hircus

source_name: adult (C) goat

extract_protocol:
Total RNA was obtained from mammary tissue using the Trizol method, treated with RNase free DNase. The total RNA quality and purity were analyzed by agarose gel electrophoresis, Bioanalyzer 2100 and Nanodrop system (Agilent, CA, USA). The RIN value of RNA was better than 0.70. A Qubit® 2.0 Fluorometer equipment was used for RNA concentration determination.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: longissimus dorsi

tag: ages

value: 24 month

tag: growth stages

value: adult


title: 14B_LowLight_LowO2


title: Transcriptome from youth (Y) goat

source_name: youth (Y) goat

value: 9 month

value: youth


title: 13B_MidLight_LowO2


title: WS-FJ9-5

city: Nanjing

first: Qingwei

last: Zeng

address: 159 Longpan road

institute: Nanjing Forestry University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The filtered reads were obtained from raw data of three levels of exogenous soluble phosphate treated WS-FJ9 by filtering out adaptors, N-proportion (> 10%) and low quality (Q ≤ 20) reads. The de novo assembly for each treatment was performed to generate transcript assembly by using Trinity method with optimized k-mer length of 25. Contigs were firstly assembled from clean reads by SOAP denove, and then further extended and assembled to long sequence denominated “unigenes”.
Gene expression in transcript was calculated by reads per Kb per million reads (RPKM) method. The RPKM value of each gene was used in the consequent differential gene expression analysis. Differentially expressed genes were identified between two pairs of transcripts (WS-FJ9-0 versus WS-FJ9-5, WS-FJ9-5 versus WS-FJ9-20) by Cuffdiff and rigorously detected based on the description by Audic and Claverie (FDR ≤ 0.001 and |log2Ratio| ≥ 1) .
Genome_build: NA
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for WS-FJ9-0_RPKM.txt, WS-FJ9-5_RPKM.txt and WS-FJ9-20_RPKM.txt.

organism: Burkholderia multivorans

source_name: Phosphate-solubilizing bacterium

extract_protocol:
The bacterial cells were harvested and immediately frozen in liquid nitrogen for the next RNA extractionand. RNA was isolated with Trizol (Invitrogen, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using strand specific Illumina protocols

treatment_protocol: Bacteria were cultured under three levels of soluble phosphate (0, 5 and 20 mM).

tag: strain

value: Rhizospheric bacterium

tag: genotype

value: Wild type


title: 13A_MidLight_LowO2

value: Planktonic cells


title: WS-FJ9-20


title: WS-FJ9-0


title: Total 0-180 MAF grpfs1 Drosophila embryo (replicate 2)

description:
Chk1_ko_0_3h_2
processed data file: SLBP_Grp_mutants_normalized_counts.xlsx

value: Oregon R

value: from transheterozygous mothers bearing the grpfs1 mutation

value: Total mutant embryo extract


title: Nuclear 90-180 MAF ORER Drosophila embryo (replicate 2)

description:
K_nuclEmbWT_90_180MAF
processed data file: Spatiotemporal_RNA_distributions_embryogenesis_normalized_counts.xls

value: wild type


title: ATAC-seq Vh12/Vk4 Tg DKO B-1a [39308]

status: Public on Jan 19 2017

city: Vienna

first: Maria

last: Fischer

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology

library_source: genomic

data_processing:
For analysis of differential gene expression, the number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode set to ‘union’. The datasets were analyzed using the R package DESeq2 version 1.4.1. Sample normalizations and dispersion estimations were conducted using the default DESeq2 settings.
For ChIP-seq, the reads were aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9), using the Bowtie program version 12.5. Peaks were called with a P value of < 10-10 by using the MACS program version 1.3.6.1 with default parameters, a genome size of 2,654,911,517 bp (mm9) and a pro-B cell input sample. The identified peaks were then assigned to target genes as described previously.
For alignment of ATAC-seq reads, the Bowtie version 2.1.0 was used with the additional parameter -sensitive -X 5000.
Genome_build: MM9
Supplementary_files_format_and_content: text tab delim = TPM values in ASCII text format tab delimited; bigwig = bigWig Track format of read density coverage in reads per million (in some cases after extension to 150 base pairs)

molecule: genomic DNA

organism: Mus musculus

source_name: ATAC-seq Vh12/Vk4 Tg DKO B-1a

extract_protocol:
phenol-chloroform extraction
For strand specific RNA-sequencing, RNA was isolated with an RNeasy Plus Mini Kit (Qiagen), and mRNA was obtained by poly(A) selection with a Dynabeads mRNA purification kit (Invitrogen), followed by fragmentation by heating at 94 °C for 3 min (in fragmentation buffer). The fragmented mRNA was used as template for first-strand cDNA synthesis with random hexamers and a Superscript VILO cDNA Synthesis kit (Invitrogen). The second-strand cDNA was synthesized with 100 mM dATP, dCTP, dGTP and dUTP in the presence of RNase H, E. coli DNA polymerase I and DNA ligase (Invitrogen). Sequencing libraries were prepared with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-tailing module or NEBNext Ultra Ligation Module and NEBNext End Repair/dA-tailing module. For strandspecific RNA-sequencing, the uridines present in one cDNA strand were digested with uracil-Nglycosylase (New England Biolabs) as described10 followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems). Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS Library Quantification kit. For analysis of Bhlhe41 binding, Chromatin from 6x107 B-1a cells was prepared using a lysis buffer containing 0.25% SDS. The cells were subjected to ChIP as described11 with minor modifications. Anti-V5 agarose beads (Sigma- Aldrich) were used for precipitation. Sequencing libraries were prepared with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-tailing module or NEBNext Ultra Ligation Module and NEBNext End Repair/dA-tailing module followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems) and Illumina deep sequencing.  Open chromatin regions were mapped in sorted Vh12/Vk4 transgenic WT and DKO B-1a cells from the spleen of bone marrow chimeras by ATAC-seq, as described by Buenrostro et. al. with the following modification. The nuclei were prepared by incubation of cells with nuclear preparation buffer (0.30 M sucrose, 10 mM Tris, pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.1% NP40, 0.15 mM spermine, 0.5 mM spermidine and 2 mM 6AA) before the Tn5 treatment (3 × 104 cells with 4 ?l of the Nextera Tn5 transposase).

value: mixed

value: Vh12/Vk4 Tg Bhlhe41-/- Bhlhe40-/-

tag: cell type

value: splenic B-1a cells from bone marrow chimeras (Vh12/Vk4 Tg DKO donor (CD45.2+) and B6.SJL (CD45.1+) recipient)

tag: cell preparation

value: Ex-vivo, FACS sorted

tag: cell sorting strategy


title: ATAC-seq Vh12/Vk4 Tg B-1a [39307]

source_name: ATAC-seq Vh12/Vk4 Tg B-1a

value: Vh12/Vk4 Tg

value: splenic B-1a cells from bone marrow chimeras (Vh12/Vk4 Tg donor (CD45.2+) and B6.SJL (CD45.1+) recipient)


title: Bhlhe41 ChIP-seq Vh12/Vk4 Tg B-1a; spike in [38807_SI]

value: Vh12/Vk4 Tg Bhlhe41Tag/Tag

value: splenic B-1a cells

value: Ex-vivo, MACS sorted

value: MACS depletion of cells, expressing CD23, CD4, CD8, TCRβ, TCRγδ, NK1.1, CD11c, CD11b, Gr-1, Ter119

tag: chip antibody

value: anti-V5 antibody (clone V5-10)


title: RNA-seq Vh12/Vk4 Tg DKO B-1a [27545]

description: Cells sorted from an individual mouse for expression analysis; SuperScript® VILO™ cDNA Synthesis, strand-specific

molecule: polyA RNA

source_name: RNA-seq Vh12/Vk4 Tg DKO B-1a

extract_protocol:
Rneasy Plus Mini Kit, Dynabeads mRNA purification kit
For strand specific RNA-sequencing, RNA was isolated with an RNeasy Plus Mini Kit (Qiagen), and mRNA was obtained by poly(A) selection with a Dynabeads mRNA purification kit (Invitrogen), followed by fragmentation by heating at 94 °C for 3 min (in fragmentation buffer). The fragmented mRNA was used as template for first-strand cDNA synthesis with random hexamers and a Superscript VILO cDNA Synthesis kit (Invitrogen). The second-strand cDNA was synthesized with 100 mM dATP, dCTP, dGTP and dUTP in the presence of RNase H, E. coli DNA polymerase I and DNA ligase (Invitrogen). Sequencing libraries were prepared with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-tailing module or NEBNext Ultra Ligation Module and NEBNext End Repair/dA-tailing module. For strandspecific RNA-sequencing, the uridines present in one cDNA strand were digested with uracil-Nglycosylase (New England Biolabs) as described10 followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems). Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS Library Quantification kit. For analysis of Bhlhe41 binding, Chromatin from 6x107 B-1a cells was prepared using a lysis buffer containing 0.25% SDS. The cells were subjected to ChIP as described11 with minor modifications. Anti-V5 agarose beads (Sigma- Aldrich) were used for precipitation. Sequencing libraries were prepared with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-tailing module or NEBNext Ultra Ligation Module and NEBNext End Repair/dA-tailing module followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems) and Illumina deep sequencing.  Open chromatin regions were mapped in sorted Vh12/Vk4 transgenic WT and DKO B-1a cells from the spleen of bone marrow chimeras by ATAC-seq, as described by Buenrostro et. al. with the following modification. The nuclei were prepared by incubation of cells with nuclear preparation buffer (0.30 M sucrose, 10 mM Tris, pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.1% NP40, 0.15 mM spermine, 0.5 mM spermidine and 2 mM 6AA) before the Tn5 treatment (3 × 104 cells with 4 ?l of the Nextera Tn5 transposase).

value: peritoneal cavity B-1a cells


title: RNA-seq DKO B-1a [27344]

description: Cells sorted from pooled mice for expression analysis; SuperScript® VILO™ cDNA Synthesis, strand-specific

source_name: RNA-seq DKO B-1a

value: Bhlhe41-/- Bhlhe40-/-


title: RNA-seq Vh12/Vk4 Tg B-1a [27539]

source_name: RNA-seq Vh12/Vk4 Tg B-1a


title: RNA-seq Vh12/Vk4 Tg DKO B-1a [27542]


title: RNA-seq Vh12/Vk4 Tg B-1a [27536]


title: 18_2B_HighLight_LowO2

value: Planktonic cells

value: Low

value: High


title: Cytoplasmic 90-180 MAF ORER Drosophila embryo (replicate 1)

description:
G_cytoEmbWT_90_180MAF
processed data file: Spatiotemporal_RNA_distributions_embryogenesis_normalized_counts.xls

value: Oregon R

value: wild type

value: Cytoplasmic blastoderm wt embryo extract


title: Transcriptome from kid (G) goat

source_name: kid (G) goat

value: longissimus dorsi

value: 2 month

value: kid


title: RNA-seq DKO B-1a [27342]

value: Ex-vivo, FACS sorted


title: RNA-seq WT B-1a [27340]

source_name: RNA-seq WT B-1a

value: Wild-type


title: 2776-TL-0004

city: Gainesville

first: Tanmay

last: Lele

state: FL

address: Bldg 723, Room 329

department: Chemical Engineering

institute: University of Florida

data_processing: Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using the Genomic Services Laboratory unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Raw reads were mapped to the reference mouse genome mm9 using TopHat v2.0 (Langmead et al. 2009). The alignment metrics of the mapped reads were estimated using SAMtools (Li et al. 2009). Aligned reads were imported to the commercial data analysis platform AvadisNGS (Strand Scientifics, CA, USA). After quality inspection, the aligned reads were filtered on the basis of read quality metrics; reads with a base quality score of less than 30, alignment score of less than 95, and mapping quality of less than 40 were removed. Remaining reads were then filtered on the basis of their read statistics; missing mates, translocated, unaligned, and flipped reads were removed. The reads list was then filtered to remove duplicates. Samples were grouped and transcript abundance was quantified for this final read list using Trimmed Means of M-values as the normalization method (Robinson and Oshlack 2010). Output data utilized for all subsequent comparisons were summarized as normalized signal values generated by AvadisNGS. Differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions, and the p-value of the differentially expressed gene list was estimated by z-score calculations using Benjamini Hochberg corrections of 0.05 for false-discovery rate (Benjamini and Hochberg 1995). A   gene   ontology (GO)  analysis  was  performed  on  the  list  of  differentially expressed  mRNAs  between  samples.  Database for Annotation, Visualization   and Integrated Discovery (DAVID) v6.7 (Huang et al., 2009a; Huang et al., 2009b) was used for this analysis.   A functional annotation enrichment analysis was performed; functional annotation clustering based on biological processes, cellular components, and molecular functions demonstrating enrichment in the dataset was examined. Ingenuity Pathway Analysis (IPA,  Ingenuity® Systems, Redwood City, CA, USA) software was used to analyze the unique canonical pathways, biological functions, and networks  affected by LINC complex disruption on each substrate.  Additionally, a two-way analysis of variance was applied to significant substrate rigidity and LINC complex disruption main effects as well as their interaction. Additional GO-based analyses were performed using DAVID for genes that were significantly affected in the interaction analysis.

source_name: SS-GFP-KDEL-1 kPa

growth_protocol: The SS-GFP-KDEL (control) and SS-HA-SUN1L-KDEL (LINC complex disrupted) cells were cultured in Dulbecco’s modified Eagle’s medium with 4.5 g/l glucose (Mediatech, Manassas, VA, USA) supplemented with 10% Donor Bovine Serum (DBS) (Gibco, Grand Island, NY, USA) and 1% penicillin-streptomycin (Mediatech), and were maintained at 37°C in a humidified environment with 5% CO2. Cells were trypsinized, seeded on hydrogel, and induced by adding 1 µg/ml doxycycline hyclate (Sigma, St. Louis, MO, USA) for 48 hr prior to lysis or fixation. For myosin inhibition, Y27 (EMD Millipore, Billerica, MA, USA) and blebbistatin (EMD Millipore) were added to the cell medium at final concentrations of 25 μM and 10 μM, respectively, for 48 hr prior to lysing or fixing.

extract_protocol:
After 48 hr of seeding on substrates, cells were lysed using QIAzol Lysis Reagent (Qiagen Sciences, Germantown, MD USA) following the manufacturer’s protocol. The cell lysate was immediately stored at -80°C and transported on dry ice to the Genomic Services Laboratory (HudsonAlpha, Huntsville, AL, USA) for RNA isolation and sequencing. Total RNA containing both mRNA as well as microRNA fractions was extracted from the cell lysate using the miRNeasy Kit with on-column DNase treatment (Qiagen Inc., Valencia, CA, USA) according to the manufacturer's protocol. The final elution was performed in 30 µl of RNase-free sterile distilled water. The concentration and integrity of the extracted total RNA were estimated using the Qubit® 2.0 Fluorometer (Invitrogen)and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA, USA), respectively. RNA samples with RNA integrity numbers (RIN) of at least 7.0 were used for further processing.
Five hundred nanograms of total RNA for samples with RIN values of greater than 7.0 was required for downstream RNA-seq applications. One microliter of a 1:100 dilution of ERCC spike-in consisting of either Mix 1 or Mix 2 (Invitrogen) was added to each sample. Polyadenylated RNAs were isolated using NEBNext Magnetic Oligo d(T)25 Beads. The NEBNext mRNA Library Prep Reagent Set for Illumina (New England BioLabs Inc., Ipswich, MA, USA) was used to prepare individually bar-coded next-generation sequencing expression libraries. Library quality was assessed using the Qubit 2.0 Fluorometer, and the library concentration was estimated by utilizing a DNA 1000 Chip on an Agilent 2100 Bioanalyzer. Accurate quantification for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA). Each library was diluted to a final concentration of 12.5 nM and pooled in an equimolar ratio prior to clustering. Paired-end sequencing (25 million reads per sample, 50-bp) was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc., San Diego, CA, USA)

tag: cell line

value: NIH 3T3

tag: substrate stiffness (kpa)

tag: linc complex

value: Control (SS-GFP-KDEL)

tag: myosin inhibition

value: No


title: RNA-seq WT B-1a [27338]

tag: strain background

tag: genotype/variation


title: 18_1A_HighLight_LowO2

tag: tissue


title: I1_plate9_H_12

city: Barcelona

first: Lars

last: Velten

address: C. Dr. Aiguader 88, P05

department: Bioinformatics and Genomics

country: Spain

institute: CRG

data_processing:
Demultiplexing. Perl 5.10.1
Trim off remaining poly-A tails, if applicable. Perl 5.10.1
Align reads to the human genome using GSNAP with default settings, expected paired-end length=400bp and allowable deviation from expected paired-end length=100bp. GSNAP version 2012-01-11
Count reads overlapping uniquely with mRNA genes. Python2.7/HTSeq
Remove cells with less than 750 genes at a minimum of 10 reads per gene. R-3.1.2
Remove genes with less than 10 reads in at least 5 cells. R-3.1.2
Fit error models to the readcount data for normalization. R-3.1.2 / scde
Remove cells with large overdispersion of the correlated component (theta_Corr < 0.45). R-3.1.2
Normalize data using posterior odds ratio, see manuscript. R-3.1.2
Genome_build: Homo Sapiens 37.68, with ERCC spike in sequences appended
Supplementary_files_format_and_content: Comma separated text file. First column: ENSEMBL Gene id. Second column: Raw read count.

organism: Homo sapiens

source_name: Lin-CD34+CD38+ bone marrow

extract_protocol:
Fresh bone marrow mononuclear cells were stained with fluorescence labeled antibodies against CD34, CD38, CD45RA, CD90, CD49f, CD135, CD10, CD7 and a lineage cocktail consisting of CD4, CD8, CD11b, CD14, CD19, CD20, CD56 and CD235a. Single Lin-CD34+CD38- and LinCD34+CD38+ HSPCs were sorted into lysis buffer.
Whole transcriptome amplification was performed using the smart-seq2 protocol (Picelli et al., 2013), but using 5uL of a modified RT buffer containing 1x SMART First Strand Buffer (Clontech), 1mM DTT (Clontech), 1uM template switching oligo (Exiqon), 10U/uL SMARTScribe (Clontech) and 1U/uL RNASin (Promega). ERCC spike-ins were included at a final dilution of 1:1,000,000. Libraries were constructed using a home-made Tn5 transposase (Picelli et al., 2014 and Hennig et al., manuscript in preparation).

tag: fsc-a

tag: fsc-h

tag: ssc-a

tag: ssc-h

tag: lin

tag: facs time


title: I1_plate9_H_11


title: I1_plate9_H_7


title: I1_plate9_H_5


title: I1_plate9_H_10


title: I1_plate9_H_9


title: I1_plate9_H_2


title: Bhlhe41 ChIP-seq Vh12/Vk4 Tg B-1a [38807]

source_name: Bhlhe41 ChIP-seq Vh12/Vk4 Tg B-1a

value: mixed

value: Vh12/Vk4 Tg Bhlhe41Tag/Tag

tag: cell type

value: splenic B-1a cells

value: Ex-vivo, MACS sorted

value: MACS depletion of cells, expressing CD23, CD4, CD8, TCRβ, TCRγδ, NK1.1, CD11c, CD11b, Gr-1, Ter119

value: anti-V5 antibody (clone V5-10)


title: I1_plate9_H_3


title: I1_plate9_H_4


title: I1_plate9_H_1


title: I1_plate9_H_6


title: I1_plate9_G_11


title: I1_plate9_G_12


title: I1_plate9_G_10


title: I1_plate9_G_9


title: I1_plate9_G_8


title: I1_plate9_G_7


title: I1_plate9_G_6


title: I1_plate9_G_5


title: ChIP-seq input pro-B cell [10195]

source_name: ChIP-seq input pro-B cell

value: pro-B cells

tag: cell preparation

value: pro-B culture


title: I1_plate9_G_4


title: I1_plate9_G_3


title: I1_plate9_F_12


title: I1_plate9_H_8


title: I1_plate9_G_1


title: I1_plate9_G_2


title: I1_plate9_F_9


title: I1_plate9_F_8


title: I1_plate9_F_11


title: I1_plate9_E_9


title: I1_plate9_E_8


title: I1_plate9_F_10


title: I1_plate9_F_6


title: I1_plate9_F_5


title: I1_plate9_F_4


title: I1_plate9_E_4


title: I1_plate9_F_2


title: I1_plate9_E_10


title: I1_plate9_F_1


title: I1_plate9_E_11


title: I1_plate9_D_9


title: I1_plate9_E_7


title: I1_plate9_D_7


title: I1_plate9_D_8


title: I1_plate9_F_7


title: I1_plate9_E_6


title: I1_plate9_F_3


title: 2776-TL-0036

source_name: SS-GFP-KDEL-308 kPa-Y27

value: Yes, with Y27632


title: I1_plate9_E_2


title: I1_plate9_E_12


title: I1_plate9_E_3


title: I1_plate9_D_5


title: I1_plate9_E_5


title: I1_plate9_E_1


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title: I1_plate9_D_1


title: I1_plate9_D_11


title: I1_plate9_D_3


title: I1_plate9_D_10


title: I1_plate9_C_12


title: I1_plate9_D_6


title: I1_plate9_D_4


title: I1_plate9_D_2


title: I1_plate9_C_11


title: I1_plate9_C_10


title: I1_plate9_C_4


title: I1_plate9_C_8


title: I1_plate9_C_5


title: I1_plate9_C_6


title: I1_plate9_C_3


title: I1_plate9_C_2


title: I1_plate9_B_9


title: I1_plate9_B_8


title: I1_plate9_B_12


title: I1_plate9_B_11


title: I1_plate9_B_5


title: I1_plate9_B_4


title: I1_plate9_C_1


title: I1_plate9_B_7


title: I1_plate9_B_6


title: I1_plate9_B_10


title: I1_plate9_C_9


title: I1_plate9_B_3


title: I1_plate9_A_10


title: I1_plate9_A_8


title: I1_plate9_B_2


title: I1_plate9_A_7


title: I1_plate9_A_11


title: I1_plate9_B_1


title: I1_plate9_A_9


title: I1_plate9_A_12


title: I1_plate9_C_7


title: I1_plate9_A_4


title: I1_plate9_A_5


title: I1_plate9_A_6


title: I1_plate9_A_1


title: I1_plate8_H_11


title: I1_plate9_A_2


title: I1_plate8_H_10


title: I1_plate8_H_6


title: I1_plate9_A_3


title: I1_plate8_H_9


title: I1_plate8_H_8


title: I1_plate8_H_4


title: I1_plate8_H_7


title: I1_plate8_H_2


title: I1_plate8_H_1


title: I1_plate8_G_12


title: I1_plate8_H_3


title: I1_plate8_G_10


title: I1_plate8_H_12


title: I1_plate8_G_11


title: I1_plate8_G_6


title: I1_plate8_G_3


title: I1_plate8_G_4


title: I1_plate8_G_2


title: I1_plate8_G_1


title: I1_plate8_G_8


title: I1_plate8_F_12


title: I1_plate8_F_11


title: I1_plate8_F_10


title: I1_plate8_H_5


title: I1_plate8_F_7


title: I1_plate8_F_4


title: I1_plate8_F_5


title: I1_plate8_F_1


title: I1_plate8_F_6


title: I1_plate8_F_3


title: I1_plate8_E_12


title: I1_plate8_F_2


title: I1_plate8_G_9


title: I1_plate8_E_9


title: I1_plate8_E_11


title: I1_plate8_E_10


title: I1_plate8_E_8


title: I1_plate8_E_7


title: I1_plate8_G_5


title: I1_plate8_E_6


title: I1_plate8_G_7


title: I1_plate8_E_5


title: I1_plate8_E_1


title: I1_plate8_F_9


title: I1_plate8_D_11


title: I1_plate8_E_3


title: I1_plate8_E_4


title: I1_plate8_E_2


title: I1_plate8_D_12


title: I1_plate8_D_10


title: I1_plate8_D_9


title: I1_plate8_F_8


title: I1_plate8_D_8


title: I1_plate8_D_5


title: I1_plate8_D_7


title: I1_plate8_D_6


title: I1_plate8_D_1


title: I1_plate8_D_2


title: I1_plate8_D_4


title: I1_plate8_C_11


title: I1_plate8_D_3


title: I1_plate8_C_8


title: I1_plate8_C_12


title: I1_plate8_C_10


title: I1_plate8_C_9


title: I1_plate8_C_6


title: I1_plate8_C_2


title: I1_plate8_C_7


title: I1_plate8_C_3


title: I1_plate8_C_1


title: I1_plate8_C_5


title: I1_plate8_B_11


title: I1_plate8_B_10


title: I1_plate8_B_8


title: I1_plate8_B_7


title: I1_plate8_B_6


title: I1_plate8_B_12


title: I1_plate8_B_5


title: I1_plate8_B_3


title: I1_plate8_B_2


title: I1_plate8_B_1


title: I1_plate8_A_11


title: I1_plate8_A_10


title: I1_plate8_A_7


title: I1_plate8_A_9


title: I1_plate8_A_12


title: I1_plate8_A_5


title: I1_plate8_A_4


title: I1_plate8_A_3


title: I1_plate7_H_11


title: I1_plate8_A_1


title: I1_plate7_H_12


title: I1_plate8_A_2


title: I1_plate8_B_9


title: I1_plate7_H_10


title: I1_plate7_H_9


title: I1_plate7_H_6


title: I1_plate7_H_5


title: I1_plate8_B_4


title: I1_plate7_H_8


title: I1_plate7_H_7


title: I1_plate7_H_4


title: I1_plate8_C_4


title: I1_plate7_H_3


title: I1_plate7_H_2


title: I1_plate7_H_1


title: I1_plate8_A_8


title: I1_plate8_A_6


title: I1_plate7_G_10


title: I1_plate7_G_12


title: I1_plate7_G_8


title: I1_plate7_G_9


title: I1_plate7_G_7


title: I1_plate7_G_3


title: I1_plate7_G_4


title: I1_plate7_G_5


title: I1_plate7_F_12


title: I1_plate7_G_2


title: I1_plate7_F_11


title: I1_plate7_F_9


title: I1_plate7_F_8


title: I1_plate7_F_10


title: I1_plate7_F_7


title: I1_plate7_F_6


title: I1_plate7_F_5


title: I1_plate7_F_3


title: I1_plate7_E_12


title: I1_plate7_F_2


title: I1_plate7_F_1


title: I1_plate7_E_11


title: I1_plate7_E_10


title: I1_plate7_G_11


title: I1_plate7_G_6


title: I1_plate7_F_4


title: I1_plate7_E_5


title: I1_plate7_E_6


title: I1_plate7_E_7


title: I1_plate7_E_8


title: I1_plate7_E_4


title: I1_plate7_G_1


title: I1_plate7_E_2


title: I1_plate7_E_1


title: I1_plate7_D_11


title: I1_plate7_D_12


title: I1_plate7_D_9


title: I1_plate7_E_3


title: I1_plate7_D_8


title: I1_plate7_D_6


title: I1_plate7_D_5


title: I1_plate7_D_4


title: I1_plate7_D_7


title: I1_plate7_D_1


title: I1_plate7_E_9


title: I1_plate7_C_12


title: I1_plate7_C_10


title: I1_plate7_C_11


title: I1_plate7_C_9


title: I1_plate7_C_8


title: I1_plate7_C_7


title: I1_plate7_C_6


title: I1_plate7_D_10


title: I1_plate7_C_5


title: I1_plate7_B_12


title: I1_plate7_B_11


title: I1_plate7_C_2


title: I1_plate7_C_4


title: I1_plate7_C_1


title: I1_plate7_C_3


title: I1_plate7_B_10


title: I1_plate7_B_9


title: I1_plate7_B_6


title: I1_plate7_B_4


title: I1_plate7_D_2


title: I1_plate7_B_7


title: I1_plate7_B_5


title: I1_plate7_A_12


title: I1_plate7_B_1


title: I1_plate7_D_3


title: I1_plate7_B_8


title: I1_plate7_A_10


title: I1_plate7_A_11


title: I1_plate7_B_3


title: I1_plate7_B_2


title: I1_plate7_A_7


title: I1_plate7_A_5


title: I1_plate7_A_6


title: I1_plate7_A_8


title: I1_plate7_A_4


title: I1_plate7_A_3


title: I1_plate7_A_9


title: I1_plate7_A_2


title: I1_plate6_H_11


title: I1_plate6_H_8


title: I1_plate6_H_10


title: I1_plate6_H_9


title: I1_plate6_H_12


title: I1_plate7_A_1


title: I1_plate6_H_7


title: I1_plate6_H_5


title: I1_plate6_H_4


title: I1_plate6_H_3


title: I1_plate6_H_2


title: I1_plate6_H_1


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title: I1_plate6_H_6


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title: I1_plate6_F_4


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title: I1_plate6_F_9


title: I1_plate6_F_10


title: I1_plate6_G_6


title: I1_plate6_F_7


title: I1_plate6_G_8


title: I1_plate6_F_8


title: I1_plate6_G_10


title: I1_plate6_F_11


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title: I1_plate6_F_2


title: I1_plate6_E_8


title: I1_plate6_E_11


title: I1_plate6_F_3


title: I1_plate6_E_6


title: I1_plate6_E_12


title: I1_plate6_G_3


title: I1_plate6_E_9


title: I1_plate6_G_5


title: I1_plate6_E_7


title: I1_plate6_G_4


title: I1_plate6_F_12


title: I1_plate6_F_1


title: I1_plate6_G_2


title: I1_plate6_E_5


title: I1_plate6_E_2


title: I1_plate6_E_1


title: I1_plate6_D_11


title: I1_plate6_D_12


title: I1_plate6_D_7


title: I1_plate6_D_10


title: I1_plate6_D_8


title: I1_plate6_E_3


title: I1_plate6_D_3


title: I1_plate6_D_5


title: I1_plate6_D_2


title: I1_plate6_D_4


title: I1_plate6_C_12


title: I1_plate6_E_4


title: I1_plate6_D_6


title: I1_plate6_C_8


title: I1_plate6_C_10


title: I1_plate6_C_7


title: I1_plate6_F_5


title: I1_plate6_C_6


title: I1_plate6_C_5


title: I1_plate6_C_4


title: I1_plate6_C_1


title: I1_plate6_C_3


title: I1_plate6_C_2


title: I1_plate6_B_12


title: I1_plate6_D_9


title: I1_plate6_D_1


title: I1_plate6_C_9


title: I1_plate6_C_11


title: I1_plate6_B_10


title: I1_plate6_B_11


title: I1_plate6_B_9


title: I1_plate6_B_3


title: I1_plate6_B_8


title: I1_plate6_B_5


title: I1_plate6_B_6


title: I1_plate6_B_2


title: I1_plate6_B_4


title: I1_plate6_B_1


title: I1_plate6_A_10


title: I1_plate6_A_12


title: I1_plate6_A_8


title: I1_plate6_A_7


title: I1_plate6_A_11


title: I1_plate6_A_5


title: I1_plate6_B_7


title: I1_plate6_A_9


title: I1_plate6_A_6


title: I1_plate6_A_3


title: I1_plate6_A_1


title: I1_plate6_A_4


title: I1_plate6_A_2


title: I1_plate5_H_12


title: I1_plate5_H_11


title: I1_plate5_H_10


title: I1_plate5_H_9


title: I1_plate5_H_8


title: I1_plate5_H_6


title: I1_plate5_H_7


title: I1_plate5_H_3


title: I1_plate5_H_1


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title: I1_plate5_G_2


title: I1_plate5_G_7


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title: I1_plate5_F_7


title: I1_plate5_F_6


title: I1_plate5_H_5


title: I1_plate5_F_5


title: I1_plate5_F_4


title: I1_plate5_F_3


title: I1_plate5_F_2


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title: I1_plate4_D_6


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title: I1_plate4_D_2


title: I1_plate4_B_2


title: I1_plate4_B_6


title: I1_plate4_B_7


title: I1_plate4_C_11


title: I1_plate4_B_4


title: I1_plate4_B_1


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title: I1_plate4_B_3


title: I1_plate4_A_8


title: I1_plate4_A_11


title: I1_plate4_A_6


title: I1_plate4_C_6


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title: I1_plate4_A_5


title: I1_plate4_A_4


title: I1_plate4_A_3


title: I1_plate3_H_12


title: I1_plate3_H_11


title: I1_plate4_B_5


title: I1_plate3_H_10


title: I1_plate3_H_9


title: I1_plate3_H_8


title: I1_plate4_A_7


title: I1_plate3_H_7


title: I1_plate3_H_6


title: I1_plate4_A_9


title: I1_plate3_H_5


title: I1_plate3_G_12


title: I1_plate3_H_1


title: I1_plate3_H_2


title: I1_plate4_B_10


title: I1_plate3_H_4


title: I1_plate3_G_8


title: I1_plate4_A_2


title: I1_plate3_G_10


title: I1_plate3_G_7


title: I1_plate3_G_3


title: I1_plate3_H_3


title: I1_plate3_G_9


title: I1_plate3_G_2


title: I1_plate3_G_5


title: I1_plate3_G_1


title: I1_plate3_F_11


title: I1_plate3_F_10


title: I1_plate3_F_12


title: I1_plate3_F_9


title: I1_plate3_F_7


title: I1_plate3_F_8


title: I1_plate3_G_11


title: I1_plate3_F_6


title: I1_plate3_F_3


title: I1_plate3_F_2


title: I1_plate3_F_5


title: I1_plate4_A_1


title: I1_plate3_G_6


title: I1_plate3_F_1


title: I1_plate3_E_11


title: I1_plate3_E_10


title: I1_plate3_E_12


title: I1_plate3_E_8


title: I1_plate3_E_9


title: I1_plate3_E_2


title: I1_plate3_D_12


title: I1_plate3_D_11


title: I1_plate3_E_7


title: I1_plate3_E_6


title: I1_plate3_E_4


title: I1_plate3_E_1


title: I1_plate3_E_3


title: I1_plate3_D_8


title: I1_plate3_D_10


title: I1_plate3_D_9


title: I1_plate3_D_7


title: I1_plate3_D_6


title: I1_plate3_D_4


title: I1_plate3_F_4


title: I1_plate3_D_5


title: I1_plate3_D_2


title: I1_plate3_D_1


title: I1_plate3_D_3


title: I1_plate3_C_12


title: I1_plate3_C_10


title: I1_plate3_C_9


title: I1_plate3_E_5


title: I1_plate3_C_3


title: I1_plate3_C_5


title: I1_plate3_G_4


title: I1_plate3_C_7


title: I1_plate3_C_8


title: I1_plate3_C_2


title: I1_plate3_B_11


title: I1_plate3_B_8


title: I1_plate3_B_12


title: I1_plate3_B_5


title: I1_plate3_B_2


title: I1_plate3_A_12


title: I1_plate3_A_11


title: I1_plate3_A_10


title: I1_plate3_A_8


title: I1_plate3_C_4


title: I1_plate3_B_7


title: I1_plate3_B_1


title: I1_plate3_A_9


title: I1_plate3_A_7


title: I1_plate3_C_1


title: I1_plate3_C_11


title: I1_plate3_B_4


title: I1_plate3_B_6


title: I1_plate3_A_6


title: I1_plate19_G_10

source_name: Lin-CD34+CD38- bone marrow


title: I1_plate3_A_4


title: I1_plate19_G_9


title: I1_plate3_B_9


title: I1_plate19_G_3


title: I1_plate3_A_2


title: I1_plate3_B_10


title: I1_plate19_G_11


title: I1_plate19_G_1


title: I1_plate3_A_1


title: I1_plate19_G_5


title: I1_plate3_A_5


title: I1_plate3_B_3


title: I1_plate3_A_3


title: I1_plate19_G_12


title: I1_plate19_F_9


title: I1_plate19_F_6


title: I1_plate19_F_11


title: I1_plate19_G_7


title: I1_plate19_F_3


title: I1_plate19_F_5


title: I1_plate19_F_7


title: I1_plate19_F_10


title: I1_plate19_F_4


title: I1_plate19_E_11


title: I1_plate19_F_12


title: I1_plate19_E_10


title: I1_plate19_F_1


title: I1_plate19_D_12


title: I1_plate19_E_12


title: I1_plate19_E_5


title: I1_plate19_E_7


title: I1_plate19_G_4


title: I1_plate19_G_6


title: I1_plate19_E_6


title: I1_plate19_E_4


title: I1_plate19_E_1


title: I1_plate19_E_3


title: I1_plate19_D_11


title: I1_plate19_D_1


title: I1_plate19_C_10


title: I1_plate19_C_11


title: I1_plate19_C_6


title: I1_plate19_C_5


title: I1_plate19_C_4


title: I1_plate19_D_5


title: I1_plate19_D_7


title: I1_plate19_D_10


title: I1_plate19_D_9


title: I1_plate19_D_4


title: I1_plate19_C_9


title: I1_plate19_B_10


title: I1_plate19_B_9


title: I1_plate19_B_7


title: I1_plate19_E_9


title: I1_plate19_B_4


title: I1_plate19_C_7


title: I1_plate19_C_3


title: I1_plate19_C_1


title: I1_plate19_D_3


title: I1_plate19_B_12


title: I1_plate19_A_12


title: I1_plate19_A_10


title: I1_plate19_A_6


title: I1_plate19_D_6


title: I1_plate19_B_6


title: I1_plate18_H_8


title: I1_plate19_B_5


title: I1_plate19_B_3


title: I1_plate19_A_5


title: I1_plate19_B_1


title: I1_plate19_A_11


title: I1_plate18_H_1


title: I1_plate19_A_9


title: I1_plate19_C_12


title: I1_plate19_A_7


title: I1_plate19_A_4


title: I1_plate3_C_6


title: I1_plate19_A_3


title: I1_plate19_A_1


title: I1_plate18_G_7


title: I1_plate18_H_12


title: I1_plate18_G_3


title: I1_plate18_G_1


title: I1_plate18_F_12


title: I1_plate18_H_6


title: I1_plate19_B_11


title: I1_plate18_F_8


title: I1_plate18_H_3


title: I1_plate18_H_7


title: I1_plate18_G_12


title: I1_plate18_H_5


title: I1_plate18_H_2


title: I1_plate18_G_8


title: I1_plate18_G_11


title: I1_plate18_G_6


title: I1_plate18_F_1


title: I1_plate18_E_7


title: I1_plate18_E_8


title: I1_plate18_H_11


title: I1_plate18_E_6


title: I1_plate18_G_2


title: I1_plate18_F_11


title: I1_plate18_F_5


title: I1_plate18_F_6


title: I1_plate18_G_5


title: I1_plate18_E_12


title: I1_plate18_F_2


title: I1_plate18_F_7


title: I1_plate18_E_11


title: I1_plate18_D_12


title: I1_plate18_D_11


title: I1_plate18_D_7


title: I1_plate18_E_1


title: I1_plate18_E_3


title: I1_plate18_D_3


title: I1_plate18_D_5


title: I1_plate18_E_5


title: I1_plate18_D_2


title: I1_plate18_D_8


title: I1_plate18_E_2


title: I1_plate18_F_3


title: I1_plate18_D_6


title: I1_plate18_D_1


title: I1_plate18_C_8


title: I1_plate18_C_2


title: I1_plate18_C_6


title: I1_plate18_C_11


title: I1_plate18_B_12


title: I1_plate18_C_7


title: I1_plate18_B_11


title: I1_plate18_B_3


title: I1_plate18_B_2


title: I1_plate18_C_1


title: I1_plate18_A_12


title: I1_plate18_B_7


title: I1_plate18_A_11


title: I1_plate18_C_5


title: I1_plate18_A_6


title: I1_plate18_C_12


title: I1_plate18_A_5


title: I1_plate18_A_3


title: I1_plate18_B_5


title: I1_plate17_H_11


title: I1_plate18_B_1


title: I1_plate17_H_9


title: I1_plate18_C_3


title: I1_plate18_A_7


title: I1_plate18_A_8


title: I1_plate17_H_8


title: I1_plate18_A_2


title: I1_plate18_A_1


title: I1_plate17_H_3


title: I1_plate17_G_12


title: I1_plate17_H_2


title: I1_plate18_B_8


title: I1_plate17_G_8


title: I1_plate17_G_9


title: I1_plate18_B_6


title: I1_plate17_H_6


title: I1_plate17_H_7


title: I1_plate17_H_1


title: I1_plate17_H_4


title: I1_plate17_H_5


title: I1_plate17_G_4


title: I1_plate17_G_3


title: I1_plate17_G_5


title: I1_plate17_G_10


title: I1_plate17_F_8


title: I1_plate17_G_6


title: I1_plate17_F_11


title: I1_plate17_G_2


title: I1_plate17_G_1


title: I1_plate17_H_12


title: I1_plate17_F_6


title: I1_plate17_H_10


title: I1_plate17_G_7


title: I1_plate17_F_3


title: I1_plate17_F_10


title: I1_plate17_F_2


title: I1_plate17_F_1


title: I1_plate17_E_12


title: I1_plate17_F_7


title: I1_plate17_E_10


title: I1_plate17_E_9


title: I1_plate17_F_9


title: I1_plate17_E_7


title: I1_plate17_E_6


title: I1_plate17_G_11


title: I1_plate17_F_5


title: I1_plate17_F_4


title: I1_plate17_E_5


title: I1_plate17_E_3


title: I1_plate17_E_11


title: I1_plate17_D_12


title: I1_plate17_D_8


title: I1_plate17_D_7


title: I1_plate17_E_8


title: I1_plate17_D_11


title: I1_plate17_D_10


title: I1_plate17_E_4


title: I1_plate17_E_2


title: I1_plate17_F_12


title: I1_plate17_D_6


title: I1_plate17_D_2


title: I1_plate17_D_4


title: I1_plate17_C_11


title: I1_plate17_C_7


title: I1_plate17_C_9


title: I1_plate17_C_6


title: I1_plate17_C_10


title: I1_plate17_C_12


title: I1_plate17_D_1


title: I1_plate17_E_1


title: I1_plate17_C_8


title: I1_plate17_C_1


title: I1_plate17_D_9


title: I1_plate17_D_3


title: I1_plate17_D_5


title: I1_plate17_C_5


title: I1_plate17_C_2


title: I1_plate17_B_11


title: I1_plate17_B_12


title: I1_plate17_B_10


title: I1_plate17_B_9


title: I1_plate17_A_12


title: I1_plate17_B_1


title: I1_plate17_B_5


title: I1_plate17_B_3


title: I1_plate17_B_4


title: I1_plate17_A_11


title: I1_plate17_B_2


title: I1_plate17_B_6


title: I1_plate17_C_3


title: I1_plate17_C_4


title: I1_plate17_A_4


title: I1_plate17_A_9


title: I1_plate17_A_10


title: I1_plate17_A_3


title: I1_plate17_B_8


title: I1_plate17_A_8


title: I1_plate17_A_5


title: I1_plate17_A_1


title: I1_plate17_A_6


title: I1_plate16_H_12


title: I1_plate16_H_9


title: I1_plate17_B_7


title: I1_plate17_A_7


title: I1_plate16_H_11


title: I1_plate16_H_10


title: I1_plate16_H_8


title: I1_plate16_H_5


title: I1_plate16_H_7


title: I1_plate16_H_3


title: I1_plate16_H_6


title: I1_plate16_H_4


title: I1_plate16_G_8


title: I1_plate16_H_1


title: I1_plate16_G_12


title: I1_plate16_G_6


title: I1_plate16_G_9


title: I1_plate17_A_2


title: I1_plate16_G_2


title: I1_plate16_G_5


title: I1_plate16_G_7


title: I1_plate16_F_11


title: I1_plate16_G_4


title: I1_plate16_F_10


title: I1_plate16_F_8


title: I1_plate16_G_3


title: I1_plate16_F_4


title: I1_plate16_F_3


title: I1_plate16_H_2


title: I1_plate16_G_11


title: I1_plate16_G_1


title: I1_plate16_F_5


title: I1_plate16_F_6


title: I1_plate16_F_7


title: I1_plate16_E_12


title: I1_plate16_F_1


title: I1_plate16_F_12


title: I1_plate16_F_9


title: I1_plate16_E_11


title: I1_plate16_E_8


title: I1_plate16_E_5


title: I1_plate16_E_7


title: I1_plate16_E_9


title: I1_plate16_G_10


title: I1_plate16_E_4


title: I1_plate16_E_3


title: I1_plate16_E_6


title: I1_plate16_E_1


title: I1_plate16_D_12


title: I1_plate16_D_8


title: I1_plate16_D_11


title: I1_plate16_F_2


title: I1_plate16_D_7


title: I1_plate16_C_12


title: I1_plate16_C_10


title: I1_plate16_D_6


title: I1_plate16_D_2


title: I1_plate16_D_5


title: I1_plate16_D_4


title: I1_plate16_C_11


title: I1_plate16_C_9


title: I1_plate16_E_2


title: I1_plate16_D_10


title: I1_plate16_C_7


title: I1_plate16_C_6


title: I1_plate16_C_5


title: I1_plate16_C_8


title: I1_plate16_C_2


title: I1_plate16_C_3


title: I1_plate16_D_9


title: I1_plate16_C_4


title: I1_plate16_B_12


title: I1_plate16_C_1


title: I1_plate16_B_10


title: I1_plate16_D_1


title: I1_plate16_B_11


title: I1_plate16_B_9


title: I1_plate16_B_6


title: I1_plate16_B_8


title: I1_plate16_D_3


title: I1_plate16_A_11


title: I1_plate16_B_1


title: I1_plate16_B_2


title: I1_plate16_B_3


title: I1_plate16_B_5


title: I1_plate16_B_4


title: I1_plate16_A_12


title: I1_plate16_A_9


title: I1_plate16_A_10


title: I1_plate16_A_8


title: I1_plate16_A_6


title: I1_plate16_A_7


title: I1_plate16_A_3


title: I1_plate16_A_2


title: I1_plate16_A_1


title: I1_plate15_H_12


title: I1_plate16_B_7


title: I1_plate15_H_10


title: I1_plate15_H_9


title: I1_plate15_H_8


title: I1_plate15_H_5


title: I1_plate15_H_7


title: I1_plate15_H_2


title: I1_plate15_H_6


title: I1_plate15_H_3


title: I1_plate15_H_4


title: I1_plate15_H_1


title: I1_plate15_G_12


title: I1_plate15_G_9


title: I1_plate15_G_7


title: I1_plate15_G_10


title: I1_plate15_G_5


title: I1_plate15_G_6


title: I1_plate15_G_8


title: I1_plate15_G_11


title: I1_plate16_A_5


title: I1_plate16_A_4


title: I1_plate15_G_4


title: I1_plate15_G_2


title: I1_plate15_G_3


title: I1_plate15_H_11


title: I1_plate15_G_1


title: I1_plate15_F_12


title: I1_plate15_F_11


title: I1_plate15_F_10


title: I1_plate15_F_7


title: I1_plate15_F_6


title: I1_plate15_F_8


title: I1_plate15_F_9


title: I1_plate15_F_5


title: I1_plate15_F_4


title: I1_plate15_F_2


title: I1_plate15_F_3


title: I1_plate15_E_12


title: I1_plate15_E_8


title: I1_plate15_E_9


title: I1_plate15_E_10


title: I1_plate15_E_7


title: I1_plate15_E_6


title: I1_plate15_E_5


title: I1_plate15_E_1


title: I1_plate15_E_2


title: I1_plate15_D_12


title: I1_plate15_E_3


title: I1_plate15_E_4


title: I1_plate15_E_11


title: I1_plate15_D_11


title: I1_plate15_D_9


title: I1_plate15_D_10


title: I1_plate15_D_7


title: I1_plate15_D_6


title: I1_plate15_D_4


title: I1_plate15_D_5


title: I1_plate15_D_3


title: I1_plate15_D_2


title: I1_plate15_D_1


title: I1_plate15_F_1


title: I1_plate15_C_12


title: I1_plate15_C_11


title: I1_plate15_C_10


title: I1_plate15_C_7


title: I1_plate15_C_6


title: I1_plate15_C_8


title: I1_plate15_C_9


title: I1_plate15_B_12


title: I1_plate15_C_4


title: I1_plate15_B_8


title: I1_plate15_B_11


title: I1_plate15_B_7


title: I1_plate15_B_9


title: I1_plate15_B_5


title: I1_plate15_B_10


title: I1_plate15_C_5


title: I1_plate15_C_3


title: I1_plate15_D_8


title: I1_plate15_B_6


title: I1_plate15_C_1


title: I1_plate15_B_4


title: I1_plate15_B_2


title: I1_plate15_B_3


title: I1_plate15_B_1


title: I1_plate15_A_11


title: I1_plate15_A_8


title: I1_plate15_A_12


title: I1_plate15_A_10


title: I1_plate15_A_9


title: I1_plate15_A_7


title: I1_plate15_A_6


title: I1_plate15_A_5


title: I1_plate15_C_2


title: I1_plate15_A_3


title: I1_plate15_A_4


title: I1_plate15_A_2


title: I1_plate11_H_10


title: I1_plate11_H_9


title: I1_plate11_H_7


title: I1_plate11_H_11


title: I1_plate15_A_1


title: I1_plate11_H_2


title: I1_plate11_H_8


title: I1_plate11_H_12


title: I1_plate11_H_5


title: I1_plate11_H_3


title: I1_plate11_G_10


title: I1_plate11_G_11


title: I1_plate11_H_1


title: I1_plate11_G_12


title: I1_plate11_G_9


title: I1_plate11_G_8


title: I1_plate11_G_6


title: I1_plate11_G_5


title: I1_plate11_G_3


title: I1_plate11_G_7


title: I1_plate11_G_4


title: I1_plate11_G_2


title: I1_plate11_F_12


title: I1_plate11_G_1


title: I1_plate11_F_11


title: I1_plate11_F_10


title: I1_plate11_F_9


title: I1_plate11_H_6


title: I1_plate11_H_4


title: I1_plate11_F_5


title: I1_plate11_F_4


title: I1_plate11_F_3


title: I1_plate11_F_7


title: I1_plate11_E_12


title: I1_plate11_F_2


title: I1_plate11_E_8


title: I1_plate11_E_9


title: I1_plate11_E_7


title: I1_plate11_F_8


title: I1_plate11_E_6


title: I1_plate11_E_4


title: I1_plate11_E_11


title: I1_plate11_E_2


title: I1_plate11_E_10


title: I1_plate11_E_5


title: I1_plate11_E_3


title: I1_plate11_E_1


title: I1_plate11_D_12


title: I1_plate11_D_11


title: I1_plate11_D_10


title: I1_plate11_D_9


title: I1_plate11_D_8


title: I1_plate11_D_6


title: I1_plate11_D_5


title: I1_plate11_F_6


title: I1_plate11_D_4


title: I1_plate11_F_1


title: I1_plate11_D_3


title: I1_plate11_D_2


title: I1_plate11_C_11


title: I1_plate11_C_10


title: I1_plate11_D_1


title: I1_plate11_C_12


title: I1_plate11_C_9


title: I1_plate11_C_6


title: I1_plate11_C_8


title: I1_plate11_C_3


title: I1_plate11_C_2


title: I1_plate11_C_1


title: I1_plate11_B_12


title: I1_plate11_C_5


title: I1_plate11_B_9


title: I1_plate11_C_4


title: I1_plate11_B_5


title: I1_plate11_B_6


title: I1_plate11_B_4


title: I1_plate11_B_7


title: I1_plate11_B_3


title: I1_plate11_D_7


title: I1_plate11_B_1


title: I1_plate11_A_11


title: I1_plate11_C_7


title: I1_plate11_A_10


title: I1_plate11_A_12


title: I1_plate11_B_10


title: I1_plate11_A_8


title: I1_plate11_A_6


title: I1_plate11_A_3


title: I1_plate11_A_2


title: I1_plate11_B_8


title: I1_plate11_A_7


title: I1_plate11_A_5


title: I1_plate11_A_4


title: I1_plate11_A_1


title: I1_plate11_B_11


title: I1_plate16_E_10


title: I1_plate10_H_9


title: I1_plate10_H_10


title: I1_plate10_H_5


title: I1_plate10_H_6


title: I1_plate10_H_4


title: I1_plate10_H_1


title: I1_plate10_H_7


title: I1_plate10_H_2


title: I1_plate10_G_12


title: I1_plate10_G_10


title: I1_plate11_A_9


title: I1_plate10_G_9


title: I1_plate10_H_12


title: I1_plate10_G_11


title: I1_plate10_G_8


title: I1_plate10_H_11


title: I1_plate10_F_12


title: I1_plate10_G_5


title: I1_plate10_H_8


title: I1_plate10_F_11


title: I1_plate10_G_2


title: I1_plate10_G_7


title: I1_plate10_G_1


title: I1_plate10_F_10


title: I1_plate11_B_2


title: I1_plate10_F_7


title: I1_plate10_F_8


title: I1_plate10_F_6


title: I1_plate10_F_4


title: I1_plate10_F_9


title: I1_plate10_F_5


title: I1_plate10_F_1


title: I1_plate10_E_12


title: I1_plate10_E_11


title: I1_plate10_E_10


title: I1_plate10_G_6


title: I1_plate10_E_7


title: I1_plate10_E_6


title: I1_plate10_E_5


title: I1_plate10_E_9


title: I1_plate10_G_4


title: I1_plate10_E_2


title: I1_plate10_E_8


title: I1_plate10_D_11


title: I1_plate10_D_10


title: I1_plate10_E_1


title: I1_plate10_D_9


title: I1_plate10_D_8


title: I1_plate10_D_5


title: I1_plate10_D_4


title: I1_plate10_D_12


title: I1_plate10_D_6


title: I1_plate10_D_1


title: I1_plate10_C_12


title: I1_plate10_D_2


title: I1_plate10_C_11


title: I1_plate10_F_2


title: I1_plate10_C_9


title: I1_plate10_C_8


title: I1_plate10_C_7


title: I1_plate10_C_10


title: I1_plate10_C_5


title: I1_plate10_E_4


title: I1_plate10_C_2


title: I1_plate10_B_11


title: I1_plate10_B_10


title: I1_plate10_C_4


title: I1_plate10_B_12


title: I1_plate10_C_1


title: I1_plate10_B_9


title: I1_plate10_B_6


title: I1_plate10_B_5


title: I1_plate10_B_4


title: I1_plate10_B_2


title: I1_plate10_A_9


title: I1_plate10_A_11


title: I1_plate10_A_10


title: I1_plate10_B_8


title: I1_plate10_A_7


title: I1_plate10_C_6


title: I1_plate10_A_8


title: I1_plate10_A_2


title: I1_plate10_A_1


title: I1_plate10_B_1


title: I1_plate10_A_12


title: I1_plate10_D_7


title: islet_single_cell_artemether_10

first: Christoph

last: Bock

address: Lazarettgasse 14

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
Trimming of adapter sequences was performed with trimmomatic (v 0.32) minimum read length after trimming: 25
Alignment of the trimmed reads to the human transcriptome (hg19 GRCh37 ftp://ftp.ensembl.org/pub/release-74/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh37.74.cdna.all.fa.gz) was performed with bowtie1 (v 1.1)
Calculation of normalized transcript-wise expression estimates (RPKM values) was performed based on the transcriptome alignments using the R (v 3.1.2) package BitSeq (v 1.10.0). Function: getExpression() with uniform=FALSE
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include transcript-wise RPKM values or read counts for each sample

source_name: pancreatic islet

extract_protocol:
To disassociate islets into single cells, islets were incubated in Accutase (Life technology) in 37 °C for 20 min, neutralized by CMRL medium. Purification of single cells was performed by flow cytometry cell sorting on a Moflo AstriosEQ (Beckman Coulter, Miami)
cDNA synthesis and enrichment was performed following the Smart-seq2 protocol as described (Picelli et al., 2014).

treatment_protocol: Islets were cultured in CMRL medium (Life technology) supplemented with 10% FBS, 2 mM glutamine, 100 U/mL penicillin, and 100 µg/mL streptomycin. Artemether treatment was administered for the indicated period of time.

tag: assigned cell type

value: alpha

tag: treatment length

tag: cell count


title: islet_single_cell_artemether_12

value: delta


title: islet_single_cell_artemether_9


title: islet_single_cell_artemether_7

value: beta


title: islet_single_cell_artemether_4


title: islet_single_cell_artemether_3


title: islet_single_cell_artemether_6


title: islet_single_cell_artemether_8


title: islet_single_cell_artemether_1


title: I1_plate10_A_6


title: I1_plate10_A_4


title: islet_single_cell_artemether_11


title: islet_single_cell_artemether_5

value: acinar


title: islet_single_cell_artemether_13

value: pp


title: I1_plate10_B_7


title: I1_plate10_A_5


title: I2_plate15_H_4

extract_protocol:
Fresh bone marrow mononuclear cells were stained with fluorescence labeled antibodies against CD34, CD38, CD45RA, CD90, CD49f, CD135, CD10, CD7 and a lineage cocktail consisting of CD4, CD8, CD11b, CD14, CD19, CD20, CD56 and CD235a. Single Lin-CD34+CD38- and LinCD34+CD38+ HSPCs were sorted into lysis buffer.
Whole transcriptome amplifcation was performed using the QUARTZ-Seq protocol (Sasagawa et al., 2013). ERCC spike ins were included into the lysis buffer at a final dilution of 1:2,000,000. Libraries were constructed using Nextera Tn5 (Illumina) following the protocol provided, but using 1/4 of all volumes.

tag: fsc-w

tag: ssc-w


title: I2_plate15_H_11


title: I2_plate15_H_12


title: I2_plate15_G_12


title: I2_plate15_H_5


title: I2_plate15_H_1


title: I2_plate15_H_6


title: I2_plate15_H_7


title: I2_plate15_H_8


title: I2_plate15_H_9


title: islet_single_cell_artemether_2


title: I2_plate15_H_3


title: I2_plate15_H_10


title: I2_plate15_G_11


title: I2_plate15_G_8


title: I2_plate15_G_9


title: I2_plate15_G_2


title: I2_plate15_G_6


title: I2_plate15_G_4


title: I2_plate15_G_5


title: I2_plate15_G_10


title: I2_plate15_G_7


title: I2_plate15_F_10


title: I2_plate15_G_1


title: I2_plate15_H_2


title: I2_plate15_F_9


title: I2_plate15_F_8


title: I2_plate15_F_12


title: I2_plate15_F_7


title: I2_plate15_F_3


title: I2_plate15_F_5


title: I2_plate15_E_8


title: I2_plate15_E_9


title: I2_plate15_E_10


title: I2_plate15_E_12


title: I2_plate15_F_2


title: I2_plate15_E_6


title: I2_plate15_E_11


title: I2_plate15_F_1


title: I2_plate15_F_4


title: I2_plate15_E_1


title: I2_plate15_E_5


title: I2_plate15_F_11


title: I2_plate15_E_4


title: I2_plate15_D_12


title: I2_plate15_G_3


title: I2_plate15_D_10


title: I2_plate15_E_3


title: I2_plate15_D_7


title: I2_plate15_E_2


title: I2_plate15_D_8


title: I2_plate15_D_9


title: I2_plate15_D_11


title: I2_plate15_D_6


title: I2_plate15_D_4


title: I2_plate15_D_5


title: I2_plate15_F_6


title: I2_plate15_D_3


title: I2_plate15_C_12


title: I2_plate15_D_1


title: I2_plate15_C_11


title: I2_plate15_E_7


title: I2_plate15_C_4


title: I2_plate15_C_2


title: I2_plate15_C_10


title: I2_plate15_C_9


title: I2_plate15_C_7


title: I2_plate15_B_12


title: I2_plate15_C_6


title: I2_plate15_C_5


title: I2_plate15_C_8


title: I2_plate15_B_10


title: I2_plate15_C_3


title: I2_plate15_B_8


title: I2_plate15_B_6


title: I2_plate15_B_7


title: I2_plate15_B_4


title: I2_plate15_B_11


title: I2_plate15_B_9


title: I2_plate15_C_1


title: I2_plate15_B_5


title: I2_plate15_B_2


title: I2_plate15_B_3


title: I2_plate15_B_1


title: I2_plate15_A_12


title: I2_plate15_A_11


title: I2_plate15_D_2


title: I2_plate15_A_9


title: I2_plate15_A_7


title: I2_plate15_A_6


title: I2_plate15_A_2


title: I2_plate15_A_1


title: I2_plate15_A_5


title: I2_plate14_H_8


title: I2_plate14_H_6


title: I2_plate14_H_4


title: I2_plate14_H_7


title: I2_plate14_H_12


title: I2_plate15_A_3


title: I2_plate14_H_3


title: I2_plate15_A_4


title: I2_plate14_H_11


title: I2_plate14_H_5


title: I2_plate14_G_9


title: I2_plate14_G_10


title: I2_plate14_H_10


title: I2_plate14_H_9


title: I2_plate14_G_8


title: I2_plate14_G_11


title: I2_plate14_H_1


title: I2_plate14_G_6


title: I2_plate14_H_2


title: I2_plate15_A_10


title: I2_plate14_G_7


title: I2_plate14_G_5


title: I2_plate15_A_8


title: I2_plate14_G_12


title: I2_plate14_G_4


title: I2_plate14_G_3


title: I2_plate14_G_2


title: I2_plate14_G_1


title: I2_plate14_F_12


title: I2_plate14_F_9


title: I2_plate14_F_8


title: I2_plate14_F_10


title: I2_plate14_F_11


title: I2_plate14_F_7


title: I2_plate14_F_1


title: I2_plate14_F_3


title: I2_plate14_E_11


title: I2_plate14_F_5


title: I2_plate14_F_4


title: I2_plate14_F_2


title: I2_plate14_E_6


title: I2_plate14_E_7


title: I2_plate14_E_4


title: I2_plate14_E_10


title: I2_plate14_E_8


title: I2_plate14_E_3


title: I2_plate14_E_9


title: I2_plate14_E_5


title: I2_plate14_E_1


title: I2_plate14_D_12


title: I2_plate14_D_10


title: I2_plate14_E_2


title: I2_plate14_D_11


title: I2_plate14_D_9


title: I2_plate14_D_8


title: I2_plate14_D_6


title: I2_plate14_F_6


title: I2_plate14_E_12


title: I2_plate14_D_7


title: I2_plate14_D_4


title: I2_plate14_D_5


title: I2_plate14_C_9


title: I2_plate14_C_12


title: I2_plate14_C_11


title: I2_plate14_C_10


title: I2_plate14_D_3


title: I2_plate14_D_2


title: I2_plate14_D_1


title: I2_plate14_C_4


title: I2_plate14_C_2


title: I2_plate14_C_8


title: I2_plate14_B_12


title: I2_plate14_C_3


title: I2_plate14_C_1


title: I2_plate14_B_11


title: I2_plate14_C_7


title: I2_plate14_B_9


title: I2_plate14_B_10


title: I2_plate14_B_6


title: I2_plate14_B_7


title: I2_plate14_B_5


title: I2_plate14_B_2


title: I2_plate14_B_1


title: I2_plate14_B_3


title: I2_plate14_A_12


title: I2_plate14_B_4


title: I2_plate14_A_11


title: I2_plate14_A_10


title: I2_plate14_A_9


title: I2_plate14_A_6


title: I2_plate14_A_5


title: I2_plate14_A_3


title: I2_plate14_A_1


title: I2_plate14_A_2


title: I2_plate14_A_8


title: I2_plate14_C_6


title: I2_plate12_H_12

source_name: Lin-CD34+CD38+CD45RA-CD90+ bone marrow


title: I2_plate12_H_11


title: I2_plate14_B_8


title: I2_plate12_H_8


title: I2_plate12_H_10


title: I2_plate14_A_4


title: I2_plate12_H_7


title: I2_plate12_H_6


title: I2_plate12_H_5


title: I2_plate12_H_4


title: I2_plate12_H_3


title: I2_plate12_H_9


title: I2_plate12_H_2


title: I2_plate12_G_12


title: I2_plate12_H_1


title: I2_plate12_G_9


title: I2_plate14_C_5


title: I2_plate12_G_8


title: I2_plate12_G_7


title: I2_plate12_G_5


title: I2_plate12_G_4


title: I2_plate12_G_2


title: I2_plate12_G_3


title: I2_plate12_F_11


title: I2_plate12_F_8


title: I2_plate12_F_10


title: I2_plate12_F_7


title: I2_plate12_F_1


title: I2_plate12_F_3


title: I2_plate12_E_12


title: I2_plate12_F_2


title: I2_plate12_E_11


title: I2_plate12_G_11


title: I2_plate12_F_6


title: I2_plate12_G_10


title: I2_plate12_F_5


title: I2_plate12_E_9


title: I2_plate12_E_8


title: I2_plate12_E_7


title: I2_plate12_G_6


title: I2_plate12_G_1


title: I2_plate12_F_12


title: I2_plate12_E_5


title: I2_plate12_E_4


title: I2_plate12_E_1


title: I2_plate12_E_3


title: I2_plate12_F_4


title: I2_plate12_E_2


title: I2_plate12_D_10


title: I2_plate12_F_9


title: I2_plate12_D_11


title: I2_plate12_E_10


title: I2_plate12_D_2


title: I2_plate12_D_7


title: I2_plate12_D_5


title: I2_plate12_D_4


title: I2_plate12_D_6


title: I2_plate12_C_12


title: I2_plate12_D_3


title: I2_plate12_D_1


title: I2_plate12_D_9


title: I2_plate12_C_9


title: I2_plate12_C_10


title: I2_plate12_D_8


title: I2_plate12_C_8


title: I2_plate12_C_7


title: I2_plate12_C_6


title: I2_plate12_D_12


title: I2_plate12_C_4


title: I2_plate12_C_3


title: I2_plate12_C_5


title: I2_plate12_C_1


title: I2_plate12_B_12


title: I2_plate12_B_9


title: I2_plate12_B_10


title: I2_plate12_B_11


title: I2_plate12_C_11


title: I2_plate12_B_8


title: I2_plate12_B_7


title: I2_plate12_B_6


title: I2_plate12_B_5


title: I2_plate12_E_6


title: I2_plate12_B_2


title: I2_plate12_B_1


title: I2_plate12_B_3


title: I2_plate12_A_11


title: I2_plate12_A_12


title: I2_plate12_A_10


title: I2_plate12_A_8


title: I2_plate12_A_7


title: I2_plate12_A_9


title: I2_plate12_C_2


title: I2_plate12_A_5


title: I2_plate12_A_3


title: I2_plate12_A_6


title: I2_plate11_H_10


title: I2_plate12_B_4


title: I2_plate14_A_7


title: I2_plate11_H_6


title: I2_plate11_H_8


title: I2_plate11_H_9


title: I2_plate11_H_12


title: I2_plate11_H_5


title: I2_plate11_H_7


title: I2_plate12_A_4


title: I2_plate11_G_11


title: I2_plate11_G_12


title: I2_plate11_H_3


title: I2_plate11_G_10


title: I2_plate11_G_5


title: I2_plate11_H_4


title: I2_plate11_G_4


title: I2_plate11_G_8


title: I2_plate11_G_1


title: I2_plate11_H_1


title: I2_plate11_H_2


title: I2_plate11_G_6


title: I2_plate12_A_2


title: I2_plate12_A_1


title: I2_plate11_G_3


title: I2_plate11_F_12


title: I2_plate11_H_11


title: I2_plate11_F_11


title: I2_plate11_F_10


title: I2_plate11_F_9


title: I2_plate11_G_9


title: I2_plate11_F_7


title: I2_plate11_F_8


title: I2_plate11_F_4


title: I2_plate11_G_7


title: I2_plate11_F_5


title: I2_plate11_F_3


title: I2_plate11_F_1


title: I2_plate11_F_2


title: I2_plate11_E_10


title: I2_plate11_E_12


title: I2_plate11_E_9


title: I2_plate11_E_11


title: I2_plate11_E_8


title: I2_plate11_E_6


title: I2_plate11_E_7


title: I2_plate11_E_5


title: I2_plate11_F_6


title: I2_plate11_E_4


title: I2_plate11_E_3


title: I2_plate11_E_2


title: I2_plate11_E_1


title: I2_plate11_D_12


title: I2_plate11_D_11


title: I2_plate11_D_10


title: I2_plate11_D_9


title: I2_plate11_D_8


title: I2_plate11_D_7


title: I2_plate11_D_5


title: I2_plate11_D_4


title: I2_plate11_D_1


title: I2_plate11_C_10


title: I2_plate11_C_12


title: I2_plate11_D_2


title: I2_plate11_D_3


title: I2_plate11_C_7


title: I2_plate11_C_9


title: I2_plate11_C_4


title: I2_plate11_C_8


title: I2_plate11_C_3


title: I2_plate11_C_5


title: I2_plate11_C_2


title: I2_plate11_C_1


title: I2_plate11_B_12


title: I2_plate11_B_11


title: I2_plate11_B_9


title: I2_plate11_B_8


title: I2_plate11_B_7


title: I2_plate11_D_6


title: I2_plate11_B_4


title: I2_plate11_B_6


title: I2_plate11_B_2


title: I2_plate11_B_3


title: I2_plate11_C_11


title: I2_plate11_A_9


title: I2_plate11_A_11


title: I2_plate11_A_8


title: I2_plate11_A_7


title: I2_plate11_A_5


title: I2_plate11_A_10


title: I2_plate11_A_6


title: I2_plate11_B_1


title: I2_plate11_A_12


title: I2_plate11_C_6


title: I2_plate11_A_4


title: I2_plate11_A_1


title: I2_plate10_H_11


title: I2_plate11_B_10


title: I2_plate10_H_10


title: I2_plate11_A_2


title: I2_plate11_B_5


title: I2_plate10_H_12


title: I2_plate10_H_7


title: I2_plate10_H_8


title: I2_plate10_H_6


title: I2_plate10_H_5


title: I2_plate10_H_3


title: I2_plate10_H_4


title: I2_plate10_H_2


title: I2_plate10_H_1


title: I2_plate10_G_12


title: I2_plate10_G_11


title: I2_plate10_G_10


title: I2_plate10_G_8


title: I2_plate10_G_6


title: I2_plate10_G_9


title: I2_plate10_G_3


title: I2_plate10_G_4


title: I2_plate10_G_7


title: I2_plate10_F_10


title: I2_plate10_F_11


title: I2_plate10_F_7


title: I2_plate10_G_1


title: I2_plate10_F_12


title: I2_plate10_F_9


title: I2_plate10_H_9


title: I2_plate10_F_4


title: I2_plate10_F_5


title: I2_plate10_F_6


title: I2_plate10_F_3


title: I2_plate10_F_1


title: I2_plate10_F_2


title: I2_plate10_E_11


title: I2_plate10_E_10


title: I2_plate10_E_12


title: I2_plate10_E_9


title: I2_plate10_G_5


title: I2_plate10_E_7


title: I2_plate10_E_8


title: I2_plate11_A_3


title: I2_plate10_E_6


title: I2_plate10_E_5


title: I2_plate10_E_4


title: I2_plate10_E_3


title: I2_plate10_E_1


title: I2_plate10_F_8


title: I2_plate10_E_2


title: I2_plate10_D_11


title: I2_plate10_D_12


title: I2_plate10_D_9


title: I2_plate10_D_8


title: I2_plate10_D_7


title: I2_plate10_D_10


title: I2_plate10_D_6


title: I2_plate10_G_2


title: I2_plate10_D_4


title: I2_plate10_C_10


title: I2_plate10_C_12


title: I2_plate10_D_1


title: I2_plate10_C_11


title: I2_plate10_D_2


title: I2_plate10_C_9


title: I2_plate10_C_8


title: I2_plate10_C_7


title: I2_plate10_C_3


title: I2_plate10_C_6


title: I2_plate10_C_2


title: I2_plate10_C_5


title: I2_plate10_B_11


title: I2_plate10_C_4


title: I2_plate10_C_1


title: I2_plate10_B_12


title: I2_plate10_B_10


title: I2_plate10_D_5


title: I2_plate10_B_9


title: I2_plate10_B_4


title: I2_plate10_B_7


title: I2_plate10_B_5


title: I2_plate10_B_6


title: I2_plate10_D_3


title: I2_plate10_B_3


title: I2_plate11_G_2


title: I2_plate10_B_2


title: I2_plate10_B_1


title: I2_plate10_A_11


title: I2_plate10_A_6


title: I2_plate10_A_10


title: I2_plate10_A_9


title: I2_plate10_A_4


title: I2_plate10_A_7


title: I2_plate10_A_8


title: I2_plate10_A_12


title: I2_plate10_A_5


title: I2_plate10_A_1


title: I2_plate10_A_3


title: I2_plate9_H_4


title: I2_plate10_A_2


title: I2_plate9_H_10


title: I2_plate9_H_3


title: I2_plate9_H_5


title: I2_plate9_H_1


title: I2_plate9_H_2


title: I2_plate9_G_10


title: I2_plate9_G_12


title: I2_plate9_H_6


title: I2_plate9_H_7


title: I2_plate9_G_11


title: I2_plate9_G_9


title: I2_plate9_G_8


title: I2_plate9_H_11


title: I2_plate9_H_12


title: I2_plate9_H_9


title: I2_plate9_H_8


title: I2_plate9_G_3


title: I2_plate9_G_4


title: I2_plate9_G_6


title: I2_plate9_G_5


title: I2_plate9_G_1


title: I2_plate9_F_12


title: I2_plate9_G_2


title: I2_plate9_F_9


title: I2_plate9_F_7


title: I2_plate9_F_6


title: I2_plate9_F_8


title: I2_plate9_E_12


title: I2_plate9_F_5


title: I2_plate9_F_1


title: I2_plate9_F_4


title: I2_plate9_E_9


title: I2_plate9_E_10


title: I2_plate9_E_11


title: I2_plate9_E_7


title: I2_plate10_B_8


title: I2_plate9_E_6


title: I2_plate9_E_5


title: I2_plate9_E_3


title: I2_plate9_E_2


title: I2_plate9_E_1


title: I2_plate9_E_4


title: I2_plate9_F_10


title: I2_plate9_D_11


title: I2_plate9_D_10


title: I2_plate9_F_2


title: I2_plate9_D_7


title: I2_plate9_D_8


title: I2_plate9_D_9


title: I2_plate9_E_8


title: I2_plate9_D_6


title: I2_plate9_D_2


title: I2_plate9_D_5


title: I2_plate9_C_11


title: I2_plate9_C_12


title: I2_plate9_D_1


title: I2_plate9_C_9


title: I2_plate9_C_8


title: I2_plate9_D_3


title: I2_plate9_C_7


title: I2_plate9_C_10


title: I2_plate9_G_7


title: I2_plate9_F_3


title: I2_plate9_C_4


title: I2_plate9_C_2


title: I2_plate9_C_3


title: I2_plate9_C_1


title: I2_plate9_B_12


title: I2_plate9_B_9


title: I2_plate9_D_4


title: I2_plate9_B_10


title: I2_plate9_B_7


title: I2_plate9_B_5


title: I2_plate9_B_6


title: I2_plate9_C_6


title: I2_plate9_B_4


title: I2_plate9_B_1


title: I2_plate9_D_12


title: I2_plate9_B_3


title: I2_plate9_A_12


title: I2_plate9_C_5


title: I2_plate9_A_11


title: I2_plate9_A_6


title: I2_plate9_A_9


title: I2_plate9_A_8


title: I2_plate9_A_10


title: I2_plate9_A_3


title: I2_plate9_A_1


title: I2_plate8_H_12


title: I2_plate8_H_11


title: I2_plate9_B_8


title: I2_plate8_H_9


title: I2_plate9_B_2


title: I2_plate8_H_7


title: I2_plate8_H_10


title: I2_plate8_H_5


title: I2_plate8_H_6


title: I2_plate8_H_4


title: I2_plate8_H_2


title: I2_plate8_G_12


title: I2_plate9_A_4


title: I2_plate8_H_1


title: I2_plate9_A_5


title: I2_plate8_G_11


title: I2_plate8_H_3


title: I2_plate8_G_10


title: I2_plate9_A_2


title: I2_plate8_G_7


title: I2_plate8_G_8


title: I2_plate8_G_9


title: I2_plate8_G_4


title: I2_plate8_G_6


title: I2_plate8_G_1


title: I2_plate8_G_5


title: I2_plate8_F_11


title: I2_plate8_H_8


title: I2_plate8_G_3


title: I2_plate8_F_12


title: I2_plate8_G_2


title: I2_plate8_F_10


title: I2_plate8_F_6


title: I2_plate8_F_8


title: I2_plate8_F_4


title: I2_plate8_F_1


title: I2_plate8_F_5


title: I2_plate8_F_3


title: I2_plate8_F_2


title: I2_plate8_E_7


title: I2_plate8_E_8


title: I2_plate8_E_9


title: I2_plate8_E_12


title: I2_plate8_E_5


title: I2_plate8_F_9


title: I2_plate8_E_6


title: I2_plate9_B_11


title: I2_plate8_D_12


title: I2_plate8_D_11


title: I2_plate8_E_2


title: I2_plate8_F_7


title: I2_plate9_F_11


title: I2_plate8_D_8


title: I2_plate8_D_9


title: I2_plate8_E_4


title: I2_plate8_E_3


title: I2_plate8_D_10


title: I2_plate8_E_11


title: I2_plate8_D_5


title: I2_plate8_D_6


title: I2_plate9_A_7


title: I2_plate8_D_7


title: I2_plate8_D_1


title: I2_plate8_D_4


title: I2_plate8_E_10


title: I2_plate8_D_2


title: I2_plate8_E_1


title: I2_plate8_C_11


title: I2_plate8_C_10


title: I2_plate8_C_9


title: I2_plate8_C_8


title: I2_plate8_C_7


title: I2_plate8_C_6


title: I2_plate8_C_3


title: I2_plate8_C_1


title: I2_plate8_C_5


title: I2_plate8_B_12


title: I2_plate8_B_8


title: I2_plate8_B_10


title: I2_plate8_B_11


title: I2_plate8_C_4


title: I2_plate8_C_2


title: I2_plate8_B_9


title: I2_plate8_B_7


title: I2_plate8_B_5


title: I2_plate8_B_4


title: I2_plate8_B_6


title: I2_plate8_B_3


title: I2_plate8_A_9


title: I2_plate8_B_1


title: I2_plate8_A_10


title: I2_plate8_A_8


title: I2_plate8_A_7


title: I2_plate8_A_6


title: I2_plate8_A_5


title: I2_plate8_A_4


title: I2_plate8_A_2


title: I2_plate8_A_1


title: I2_plate7_H_12


title: I2_plate7_H_9


title: I2_plate7_H_8


title: I2_plate7_H_7


title: I2_plate8_B_2


title: I2_plate7_H_3


title: I2_plate7_H_5


title: I2_plate8_A_11


title: I2_plate7_H_11


title: I2_plate7_H_10


title: I2_plate7_H_6


title: I2_plate7_H_1


title: I2_plate8_A_12


title: I2_plate7_H_2


title: I2_plate7_G_11


title: I2_plate7_G_12


title: I2_plate7_H_4


title: I2_plate7_G_10


title: I2_plate7_G_8


title: I2_plate7_G_9


title: I2_plate7_G_7


title: I2_plate7_G_5


title: I2_plate8_A_3


title: I2_plate7_G_4


title: I2_plate7_G_3


title: I2_plate8_D_3


title: I2_plate7_G_1


title: I2_plate7_F_12


title: I2_plate7_F_10


title: I2_plate7_G_2


title: I2_plate7_F_8


title: I2_plate7_F_7


title: I2_plate7_F_11


title: I2_plate7_F_9


title: I2_plate7_F_2


title: I2_plate7_F_3


title: I2_plate7_F_6


title: I2_plate7_F_5


title: I2_plate7_F_4


title: I2_plate7_E_12


title: I2_plate7_E_6


title: I2_plate7_E_7


title: I2_plate7_E_8


title: I2_plate7_E_11


title: I2_plate7_G_6


title: I2_plate7_E_2


title: I2_plate7_E_4


title: I2_plate7_E_3


title: I2_plate7_F_1


title: I2_plate7_E_5


title: I2_plate7_E_1


title: I2_plate7_D_12


title: I2_plate7_D_11


title: I2_plate7_D_9


title: I2_plate7_D_10


title: I2_plate7_D_8


title: I2_plate7_D_6


title: I2_plate7_E_10


title: I2_plate7_D_7


title: I2_plate7_D_4


title: I2_plate7_D_3


title: I2_plate7_D_5


title: I2_plate7_D_1


title: I2_plate7_C_12


title: I2_plate7_C_11


title: I2_plate7_C_9


title: I2_plate7_E_9


title: I2_plate7_C_6


title: I2_plate7_C_7


title: I2_plate7_C_5


title: I2_plate7_C_4


title: I2_plate7_B_9


title: I2_plate7_B_10


title: I2_plate7_C_8


title: I2_plate7_C_1


title: I2_plate7_C_3


title: I2_plate7_C_2


title: I2_plate7_B_7


title: I2_plate7_B_8


title: I2_plate7_B_2


title: I2_plate7_B_1


title: I2_plate7_D_2


title: I2_plate7_B_6


title: I2_plate7_A_6


title: I2_plate7_A_12


title: I2_plate8_C_12


title: I2_plate7_A_9


title: I2_plate7_B_4


title: I2_plate7_B_12


title: I2_plate7_A_7


title: I2_plate7_C_10


title: I2_plate7_B_5


title: I2_plate7_B_11


title: I2_plate7_B_3


title: I2_plate7_A_10


title: I2_plate7_A_8


title: I2_plate7_A_4


title: I2_plate7_A_5


title: I2_plate7_A_2


title: I2_plate7_A_3


title: I2_plate6_H_11


title: I2_plate7_A_1


title: I2_plate6_H_12


title: I2_plate7_A_11


title: I2_plate6_H_9


title: I2_plate6_H_10


title: I2_plate6_H_7


title: I2_plate6_H_5


title: I2_plate6_H_6


title: I2_plate6_H_3


title: I2_plate6_H_2


title: I2_plate6_H_1


title: I2_plate6_G_11


title: I2_plate6_G_9


title: I2_plate6_G_8


title: I2_plate6_G_6


title: I2_plate6_G_10


title: I2_plate6_G_7


title: I2_plate6_G_4


title: I2_plate6_G_1


title: I2_plate6_G_3


title: I2_plate6_G_2


title: I2_plate6_F_12


title: I2_plate6_F_11


title: I2_plate6_H_4


title: I2_plate6_F_8


title: I2_plate6_F_9


title: I2_plate6_F_7


title: I2_plate6_F_4


title: I2_plate6_F_10


title: I2_plate6_H_8


title: I2_plate6_G_12


title: I2_plate6_F_6


title: I2_plate6_E_12


title: I2_plate6_F_3


title: I2_plate6_F_5


title: I2_plate6_E_11


title: I2_plate6_F_1


title: I2_plate6_E_10


title: I2_plate6_E_9


title: I2_plate6_E_8


title: I2_plate6_E_7


title: I2_plate6_G_5


title: I2_plate6_E_6


title: I2_plate6_E_1


title: I2_plate6_E_5


title: I2_plate6_E_4


title: I2_plate6_E_3


title: I2_plate6_D_12


title: I2_plate6_E_2


title: I2_plate6_D_11


title: I2_plate6_D_10


title: I2_plate6_F_2


title: I2_plate6_D_6


title: I2_plate6_D_7


title: I2_plate6_D_1


title: I2_plate6_D_5


title: I2_plate6_D_3


title: I2_plate6_D_4


title: I2_plate6_D_8


title: I2_plate6_D_9


title: I2_plate6_C_10


title: I2_plate6_C_7


title: I2_plate6_D_2


title: I2_plate6_C_12


title: I2_plate6_C_8


title: I2_plate6_C_9


title: I2_plate6_C_11


title: I2_plate6_C_4


title: I2_plate6_C_2


title: I2_plate6_C_3


title: I2_plate6_C_5


title: I2_plate6_B_8


title: I2_plate6_B_9


title: I2_plate6_B_12


title: I2_plate6_B_7


title: I2_plate6_B_11


title: I2_plate6_B_10


title: I2_plate6_B_4


title: I2_plate6_B_6


title: I2_plate6_B_3


title: I2_plate6_B_1


title: I2_plate6_A_12


title: I2_plate6_C_6


title: I2_plate6_B_2


title: I2_plate6_A_11


title: I2_plate6_A_9


title: I2_plate6_A_8


title: I2_plate6_C_1


title: I2_plate6_A_3


title: I2_plate5_H_11


title: I2_plate6_A_10


title: I2_plate6_A_2


title: I2_plate6_A_7


title: I2_plate6_A_6


title: I2_plate5_H_12


title: I2_plate6_A_5


title: I2_plate5_H_10


title: I2_plate6_A_1


title: I2_plate5_H_8


title: I2_plate5_H_7


title: I2_plate6_B_5


title: I2_plate5_H_5


title: I2_plate5_H_6


title: I2_plate5_H_9


title: I2_plate5_H_4


title: I2_plate5_H_1


title: I2_plate5_H_3


title: I2_plate5_H_2


title: I2_plate5_G_12


title: I2_plate5_G_11


title: I2_plate5_G_9


title: I2_plate5_G_8


title: I2_plate5_G_7


title: I2_plate6_A_4


title: I2_plate5_G_6


title: I2_plate5_G_3


title: I2_plate5_F_10


title: I2_plate5_G_2


title: I2_plate5_F_8


title: I2_plate5_G_1


title: I2_plate5_F_6


title: I2_plate5_F_12


title: I2_plate5_G_4


title: I2_plate5_F_9


title: I2_plate5_F_1


title: I2_plate5_F_5


title: I2_plate5_F_2


title: I2_plate5_F_7


title: I2_plate5_E_12


title: I2_plate5_F_4


title: I2_plate5_F_3


title: I2_plate5_E_11


title: I2_plate5_G_10


title: I2_plate5_E_10


title: I2_plate5_E_7


title: I2_plate5_E_6


title: I2_plate5_E_3


title: I2_plate5_E_5


title: I2_plate5_E_8


title: I2_plate5_E_2


title: I2_plate5_E_4


title: I2_plate5_E_1


title: I2_plate5_F_11


title: I2_plate5_G_5


title: I2_plate5_D_7


title: I2_plate5_D_10


title: I2_plate5_D_4


title: I2_plate5_D_5


title: I2_plate5_D_6


title: I2_plate5_D_9


title: I2_plate5_D_3


title: I2_plate5_D_8


title: I2_plate5_C_11


title: I2_plate5_D_12


title: I2_plate5_C_10


title: I2_plate5_E_9


title: I2_plate5_D_1


title: I2_plate5_C_12


title: I2_plate5_C_8


title: I2_plate5_C_9


title: I2_plate5_C_7


title: I2_plate5_D_2


title: I2_plate5_C_2


title: I2_plate5_B_12


title: I2_plate5_C_1


title: I2_plate5_B_10


title: I2_plate5_C_3


title: I2_plate5_C_4


title: I2_plate5_B_9


title: I2_plate5_D_11


title: I2_plate5_B_8


title: I2_plate5_B_7


title: I2_plate5_B_6


title: I2_plate5_B_5


title: I2_plate5_B_4


title: I2_plate5_C_6


title: I2_plate5_B_3


title: I2_plate5_B_2


title: I2_plate5_A_11


title: I2_plate5_C_5


title: I2_plate5_A_12


title: I2_plate5_B_1


title: I2_plate5_A_10


title: I2_plate5_A_9


title: I2_plate5_A_8


title: I2_plate5_B_11


title: I2_plate5_A_7


title: I2_plate5_A_5


title: I2_plate5_A_6


title: I2_plate5_A_2


title: I2_plate4_H_9


title: I2_plate5_A_4


title: I2_plate4_H_8


title: I2_plate4_H_12


title: I2_plate5_A_1


title: I2_plate4_H_11


title: I2_plate5_A_3


title: I2_plate4_H_10


title: I2_plate4_H_6


title: I2_plate4_H_7


title: I2_plate4_H_5


title: I2_plate4_H_4


title: I2_plate4_H_2


title: I2_plate4_H_3


title: I2_plate4_H_1


title: Normal_35

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

description: Tncg

data_processing:
Library strategy: DREAM
Sequencing reads were mapped to SmaI sites in the human genome (hg19) and signatures corresponding to methylated (starting with CCGGG) and unmethylated (starting with GGG) CpG were enumerated for each SmaI/XmaI site.
At each SmaI/XmaI site, let sm be the number of tags corresponding to methylated CpG (i.e., tags starting with CCGGG) and u be the number of tags corresponding to unmethylated CpG (i.e., tags starting with GGG), the methylation value was calculated as 100%*(c*sm/(c*sm+u)), where c is the correction factor based on observed vs expected methylation of spiked-in standards.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated plain text files

source_name: Normal T lymphocytes

extract_protocol:
DNA isolation: Red blood cells (RBCs) were lysed in the RBC lysis solution containing 155 mM ammonium chloride, 10 mM potassium bicarbonate and 1 mM EDTA. White blood cells (WBCs) were isolated as a pellet by centrifugation. The WBC pellet was then lysed in the solution containing 2% sodium dodecyl sulphate and 25 mM EDTA. Proteins were precipitated by adding 1/3 volume of 10 M ammonium acetate and removed as a pellet by centrifugation. DNA was precipitated from the supernatant with isopropanol, washed with 70% ethanol and dissolved in TE (10 mM TRIS pH 8.0, 1 mM EDTA).
Five micrograms of genomic DNA spiked with 5 methylation standards with defined methylation levels of 0, 25, 50, 75, and 100% were digested with 100 units of SmaI endonuclease (NEB) for 3 hours at 25°C. Subsequently, 100 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA was purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA) and eluted in TRIS-HCl 10 mM pH 8.5 (EB). Eluted DNA was supplemented with NEB buffer #2, dCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3'>5' exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3' DNA ends created by XmaI digestion and added 3' dA tails to all fragments.
Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA).

value: Normal T lymphocytes

tag: diagnosis

value: Healthy

tag: vital status

tag: overall survival

tag: gender

value: unknown

tag: age

tag: cytogenetic risk

tag: peripheral blasts

tag: bone marrow blasts

tag: wbc

tag: platelets

tag: dnmt3a mutation

tag: idh mutation

tag: npm1 mutation


title: Normal_34

description: Tjmc

tag: tissue


title: Normal_33

description: Tajs


title: I2_plate4_G_12

tag: fsc-a

tag: fsc-h

tag: ssc-a

tag: ssc-h

tag: lin

tag: facs time


title: Normal_31

description: Gklg

source_name: Normal granulocytes

value: Normal granulocytes

tag: diagnosis

tag: vital status

tag: overall survival

tag: gender


title: Normal_30

description: Gcag

tag: age

tag: cytogenetic risk

tag: peripheral blasts

tag: bone marrow blasts


title: Normal_32

description: Gp

tag: wbc

tag: platelets

tag: dnmt3a mutation

tag: idh mutation


title: I2_plate4_G_11

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-w


title: I2_plate4_G_8

tag: ssc-a

tag: ssc-h

tag: lin

tag: facs time


title: Normal_29

source_name: Cord blood CD34 positive cells

tag: tissue

value: Cord blood CD34 positive cells

tag: diagnosis

tag: vital status

tag: overall survival

tag: gender

tag: npm1 mutation


title: Normal_27

source_name: Cord blood mononuclear cells

value: Cord blood mononuclear cells

tag: age

tag: cytogenetic risk

tag: peripheral blasts

tag: bone marrow blasts

tag: wbc

tag: platelets


title: I2_plate4_G_5

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-w


title: I2_plate4_G_6

tag: ssc-a

tag: ssc-h

tag: lin

tag: facs time


title: Normal_26

tag: tissue

tag: diagnosis

tag: vital status

tag: overall survival

tag: dnmt3a mutation

tag: idh mutation


title: Normal_25

tag: gender

tag: age

tag: cytogenetic risk

tag: peripheral blasts

tag: bone marrow blasts

tag: npm1 mutation


title: Normal_24

tag: wbc

tag: platelets


title: I2_plate4_G_1

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h


title: I2_plate4_G_7

tag: lin

tag: facs time


title: I2_plate4_G_3


title: Normal_23

tag: tissue

tag: diagnosis

tag: vital status

tag: overall survival

tag: dnmt3a mutation

tag: idh mutation


title: I2_plate4_G_2


title: I2_plate4_G_10


title: I2_plate4_G_4


title: I2_plate4_F_11


title: Normal_20

tag: gender

tag: age

tag: cytogenetic risk

tag: peripheral blasts

tag: bone marrow blasts

tag: npm1 mutation


title: Normal_19

tag: wbc

tag: platelets


title: Normal_22


title: I2_plate4_F_9

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h


title: Normal_18

tag: tissue

tag: diagnosis

tag: vital status

tag: overall survival


title: I2_plate4_F_10

tag: lin

tag: facs time


title: Normal_16

source_name: Normal peripheral blood leukocytes

value: Normal peripheral blood leukocytes

tag: gender

tag: age

tag: cytogenetic risk

tag: peripheral blasts

tag: dnmt3a mutation

tag: idh mutation


title: Normal_17

tag: bone marrow blasts

tag: wbc

tag: platelets

tag: npm1 mutation


title: Normal_28


title: I2_plate4_F_8

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h


title: I2_plate4_F_6

tag: lin

tag: facs time


title: Normal_15

tag: tissue

tag: diagnosis

tag: vital status

tag: overall survival

tag: gender

tag: age


title: I2_plate4_F_3


title: I2_plate4_F_2


title: I2_plate4_F_4


title: Normal_13

tag: cytogenetic risk

tag: peripheral blasts

tag: bone marrow blasts

tag: wbc

tag: dnmt3a mutation

tag: idh mutation


title: Normal_12

tag: platelets

tag: npm1 mutation


title: Normal_14


title: I2_plate4_F_12

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h


title: I2_plate4_G_9

tag: lin

tag: facs time


title: Normal_21

tag: tissue

tag: diagnosis

tag: vital status

tag: overall survival

tag: gender

tag: age


title: Normal_11

tag: cytogenetic risk

tag: peripheral blasts

tag: bone marrow blasts

tag: wbc

tag: dnmt3a mutation

tag: idh mutation


title: I2_plate4_E_12

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a


title: Normal_10

tag: platelets

tag: npm1 mutation


title: Normal_09

tag: tissue

tag: diagnosis


title: I2_plate4_E_11

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: I2_plate4_F_1


title: I2_plate4_F_7


title: I2_plate4_E_9


title: Normal_08

tag: vital status

tag: overall survival

tag: gender

tag: age

tag: cytogenetic risk

tag: peripheral blasts


title: Normal_07

tag: bone marrow blasts

tag: wbc

tag: dnmt3a mutation

tag: idh mutation


title: I2_plate4_E_10

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a


title: Normal_05

tag: tissue

tag: diagnosis

tag: platelets

tag: npm1 mutation


title: I2_plate4_E_5

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: I2_plate4_E_6


title: Normal_03

tag: vital status

tag: overall survival

tag: gender

tag: age

tag: cytogenetic risk

tag: peripheral blasts


title: I2_plate4_E_8

tag: fsc-a

tag: fsc-w


title: I2_plate4_E_7

tag: fsc-h

tag: ssc-a


title: Normal_02

tag: tissue

tag: diagnosis

tag: bone marrow blasts

tag: wbc

tag: dnmt3a mutation

tag: idh mutation


title: I2_plate4_F_5

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: I2_plate4_E_2


title: AML_96

description: Z

source_name: AML patient bone marrow

value: AML patient bone marrow

value: Acute myeloid leukemia (AML)

tag: vital status

value: Dead

tag: overall survival

value: 1.27 years

tag: gender

value: M

tag: age

value: 48 years

value: adverse risk

value: 86 percent

value: 93 percent

value: 77700 per uL

tag: platelets

value: 89000 per uL

value: wild-type

tag: npm1 mutation


title: Normal_01

description: Btq

value: Healthy

value: unknown

tag: cytogenetic risk

tag: peripheral blasts


title: I2_plate4_D_12

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a


title: I2_plate4_E_1


title: AML_93

description: W

tag: tissue

tag: diagnosis

value: 0.63 years

value: 63 years

value: favorable risk

value: 35 percent

tag: bone marrow blasts

value: 61 percent

tag: wbc

value: 62200 per uL

value: 34000 per uL

tag: dnmt3a mutation

tag: idh mutation

value: mutation-positive


title: AML_95

description: Y

value: AML patient bone marrow

value: Acute myeloid leukemia (AML)

tag: vital status

value: Dead

tag: overall survival

value: 0.89 years

value: F

value: 36 years

value: 83 percent

value: 69000 per uL


title: AML_92

description: V

value: Alive

value: 11.01 years

tag: gender

value: M

tag: age

value: 39 years

value: intermediate risk

value: 9 percent

value: 31 percent

value: 41600 per uL

value: wild-type


title: I2_plate4_E_4

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: I2_plate4_D_11

tag: fsc-a

tag: fsc-w


title: Normal_06

value: Normal peripheral blood leukocytes

value: Healthy

value: unknown

tag: cytogenetic risk

tag: peripheral blasts

tag: platelets

tag: npm1 mutation


title: I2_plate4_D_10

tag: fsc-h

tag: ssc-a


title: AML_91

description: T

tag: tissue

value: AML patient bone marrow

tag: diagnosis

value: Acute myeloid leukemia (AML)

value: Dead

value: 0.6 years

value: 77 years

value: 27 percent

tag: bone marrow blasts

value: 85 percent

tag: wbc

value: 16900 per uL

value: 42000 per uL

tag: dnmt3a mutation

tag: idh mutation

value: mutation-positive


title: AML_90

description: S

tag: vital status

tag: overall survival

value: 1.52 years

tag: gender

value: M

tag: age

value: 68 years

value: intermediate risk

value: 51 percent

value: 55 percent

value: 55200 per uL

value: 11000 per uL


title: I2_plate4_D_9

tag: fsc-a

tag: fsc-w

tag: ssc-w

tag: ssc-h

tag: lin

tag: facs time


title: I2_plate4_D_7

tag: fsc-h

tag: ssc-a


title: AML_89

description: R

tag: tissue

value: AML patient bone marrow

tag: diagnosis

value: Acute myeloid leukemia (AML)

value: 0.75 years

value: F

value: 61 years

tag: cytogenetic risk

tag: peripheral blasts

value: 74 percent

value: 73 percent

tag: platelets

tag: npm1 mutation


title: AML_94

description: X

tag: vital status

value: Dead

tag: overall survival

value: 14 years

value: 75 years

value: adverse risk

value: 94 percent

tag: bone marrow blasts

tag: wbc

value: 29600 per uL

value: 18000 per uL

tag: dnmt3a mutation

value: wild-type

tag: idh mutation


title: I2_plate4_D_4

tag: fsc-a

tag: fsc-w

tag: ssc-w

tag: ssc-h


title: AML_87

description: N

value: 1.9 years

tag: gender

tag: age

value: 21 years

value: favorable risk

value: 54 percent

value: 52 percent

value: 63400 per uL


title: AML_88

description: O

tag: tissue

value: AML patient bone marrow

tag: diagnosis

value: Acute myeloid leukemia (AML)

value: 6.31 years

value: M

value: 20 years

value: intermediate risk

value: 83 percent

value: 81 percent

value: 58000 per uL


title: I2_plate4_D_6

tag: fsc-h

tag: ssc-a

tag: lin

tag: facs time


title: I2_plate4_D_5


title: I2_plate4_D_8


title: I2_plate4_D_2


title: I2_plate4_E_3


title: I2_plate4_D_1


title: AML_85

description: L

tag: vital status

value: Dead

tag: overall survival

value: 0.79 years

value: F

value: 17 years

tag: cytogenetic risk

value: adverse risk

tag: peripheral blasts

value: 95 percent

value: 82 percent

tag: platelets

value: 38000 per uL

tag: npm1 mutation


title: AML_83

description: J

value: AML patient bone marrow

value: 1.43 years

value: 31 years

value: 89 percent

tag: bone marrow blasts

value: 88 percent

tag: wbc

value: 69000 per uL

tag: dnmt3a mutation

value: wild-type

tag: idh mutation

value: mutation-positive


title: I2_plate4_C_11

tag: fsc-a

tag: fsc-w

tag: ssc-w

tag: ssc-h


title: I2_plate4_C_10

tag: fsc-h

tag: ssc-a


title: I2_plate4_C_12

tag: lin

tag: facs time


title: AML_80

description: G

tag: tissue

tag: diagnosis

value: Acute myeloid leukemia (AML)

tag: vital status

tag: overall survival

value: 0.13 years

tag: gender

value: M

tag: age

value: 63 years

value: 28 percent

value: 35 percent

value: 9200 per uL

value: 19000 per uL


title: AML_82

description: I

value: Dead

value: 0.61 years

value: 27 years

tag: cytogenetic risk

value: adverse risk

tag: peripheral blasts

value: 76 percent

tag: bone marrow blasts

value: 69 percent

tag: wbc

value: 95400 per uL

tag: platelets

value: 55000 per uL

tag: npm1 mutation


title: AML_79

description: F

value: AML patient bone marrow

value: Alive

value: 15.42 years

value: F

value: 59 years

value: intermediate risk

value: 95 percent

value: 86 percent

tag: dnmt3a mutation

value: wild-type

tag: idh mutation


title: I2_plate4_C_9

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h


title: AML_78

tag: tissue

tag: diagnosis

value: Acute myeloid leukemia (AML)

tag: vital status

value: Dead

tag: overall survival

value: 0.13 years

value: M

value: 62 years

value: 92 percent

value: 42500 per uL

value: 40000 per uL

value: mutation-positive


title: AML_86

description: M

value: AML patient bone marrow

value: 1.47 years

tag: gender

tag: age

value: 52 years

tag: cytogenetic risk

tag: peripheral blasts

value: 88 percent


title: I2_plate4_C_8

tag: lin

tag: facs time


title: AML_75

value: 2.71 years

value: F

value: 48 years

value: intermediate risk

value: 0 percent

tag: bone marrow blasts

value: 21 percent

tag: wbc

value: 4100 per uL

tag: platelets

tag: dnmt3a mutation

tag: idh mutation

tag: npm1 mutation


title: I2_plate4_C_7

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: ssc-w

tag: ssc-h


title: AML_77

tag: tissue

tag: diagnosis

value: Acute myeloid leukemia (AML)

tag: vital status

value: Dead

tag: overall survival

value: 0.31 years

tag: gender

tag: age

value: 31 years

value: 8 percent

value: 94 percent

value: 2500 per uL

value: 28000 per uL

value: wild-type


title: I2_plate4_C_6

tag: lin

tag: facs time


title: I2_plate4_C_5


title: I2_plate4_C_4


title: AML_84

description: K

value: AML patient bone marrow

value: Alive

value: 15 years

value: M

value: 37 years

tag: cytogenetic risk

value: favorable risk

tag: peripheral blasts

value: 30 percent

tag: bone marrow blasts

value: 36 percent

tag: wbc

value: 52500 per uL

tag: platelets

value: 18000 per uL

tag: dnmt3a mutation


title: I2_plate4_D_3

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a


title: I2_plate4_C_3

tag: ssc-w

tag: ssc-h


title: AML_73

tag: tissue

tag: diagnosis

value: Acute myeloid leukemia (AML)

tag: vital status

tag: overall survival

value: 2.64 years

value: F

value: 65 years

value: intermediate risk

value: 0 percent

value: 52 percent

value: 8500 per uL

tag: idh mutation

tag: npm1 mutation

value: mutation-positive


title: AML_74

value: AML patient bone marrow

value: Dead

value: 0.76 years

tag: gender

tag: age

value: 45 years

tag: cytogenetic risk

value: adverse risk

tag: peripheral blasts

value: 5 percent

value: 64 percent

value: 5300 per uL

value: 52000 per uL

value: wild-type


title: AML_72

value: Acute myeloid leukemia (AML)

value: 1.6 years

value: F

value: 49 years

value: 84 percent

tag: bone marrow blasts

value: 85 percent

tag: wbc

value: 13500 per uL

tag: platelets

tag: dnmt3a mutation


title: I2_plate4_C_1

tag: fsc-a

tag: fsc-w

tag: fsc-h

tag: ssc-a

tag: lin

tag: facs time