title: dbf4-A sld3-A +HU 45min BrdU-IP-ssSeq repeat 2

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
Reads were aligned to the yeast genome (sacCer3) using the Bowtie2 software. Only the consist pair reads were used for the further analysis.
The genome-wide reads coverage of Watson and Crick strand was calculated by BEDTools and  in-house Perl  programs.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were generated for Watson and Crick strand, scores represent the normalization reads density.

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: For G1 cell synchronization, alpha factor was added at cell density OD600=0.4-0.5 to finial concentration at 5ug/ml for wild type Bar1 and 50ng/ml for bar1 mutants.  After 3hr arrest at 30°C, the cell was released to fresh YPD medium with or without 200mM hydroxyurea.

extract_protocol:
The collected samples were incubated with 1% fresh-made formaldehyde at 25°C for 20mins, and quenched with 0.125M Glysine for 5mins.  The harvested cells were lysed with glass beads, and the chromatin pellet were washed and sonicated. The average DNA fragment size is about 200-400bp.  Sheared chromatin was immunoprecipitated with an protein-specific antibody. The chromatin was reverse-cross-linked and immunoprecipitated.  DNA was exacted with the Chelex-100 method
ssDNA library preparation method was modified from previous one (Meyer et al., 2012). To preserve the strand information, we use a specific RNA ligase, which also can ligated the ssDNAs in a sequence-independent way. The ssDNA library strand information was kept by sequential 3’ end and  5’ end ligation.

value: dbf4-A sld3-A

tag: media

value: YPD+HU

tag: cell cycle stage

value: S

value: Anti-BrdU (BD BioScience, 347580)


title: rad53-1 exon1∆ +HU 45min BrdU-IP-ssSeq

status: Public on Feb 11 2018

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

tag: genotype

tag: chip antibody


title: rad53-1 +HU 45min Pol ɛ ChIP-ssSeq repeat 1

value: Anti-FLAG (SIGMA,F1804)


title: dbf4-A sld3-A +HU 45min BrdU-IP-ssSeq repeat 1


title: rad53-1 +HU 45min MCM6 ChIP-ssSeq repeat 1


title: rad53-1 +HU 45min Rfa1 eSPAN


title: rad53-1 +HU 45min Rfa1 ChIP-ssSeq


title: WT +HU 45min Pol ɛ ChIP-ssSeq

value: wildtype


title: WT +HU 45min MCM6 ChIP-ssSeq


title: rad53-1 +HU 45min MCM6 ChIP-ssSeq repeat 2


title: rad53-1 +HU 45min Pol ɛ ChIP-ssSeq repeat 2


title: CAF+MCF10A EV rep2

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description:
CAF+MCF10A EV rep2
X18743_CAF.RNA.vec.EV.2.8.29.17_S4_L999_R1_001.fastq.bam.1

library_source: transcriptomic

data_processing:
Sequences were aligned to hg19 using Tophat2 with default settings
Gene expression level of Refseq coding genes were quantified using in-house R scripts
Count data were normalized using "edgeR"
Genome_build: hg19
Supplementary_files_format_and_content: edgeR normalized counts

molecule: total RNA

organism: Homo sapiens

source_name: breast cancer associated fibroblasts (CAF)

growth_protocol: CAF cells were grown in Iscove's modified dulbecco's media supplemented with 20% fetal bovine serum.

extract_protocol:
TRIZOL reagent (Invitrogen) was used to extract total RNA from cells following the manufacturer’s protocols.  RNA pellet was dissolved in RNase-free water, and subjected to library construction and deep sequencing.
poly(A) RNA-seq following Illumima's recommended protocol

treatment_protocol: For 2x10e5 recipient CAF cells, 2 μg of EV (based on protein measurement using BCA protein assay kit) resuspended in PBS was added.  RNA was extracted after 48 h.

tag: cell type

value: Primary CAF from a human breast tumor

tag: passage

tag: treatment

value: MCF10A EV


title: rad53-1 sml1∆ +HU 45min BrdU-IP-ssSeq repeat 2

value: rad53-1 sml1_delta


title: dbf4-A sld3-A +HU 45min input repeat 1


title: rad53-1 exon1∆ +HU 45min input


title: rad53-1 sml1∆ +HU 45min BrdU-IP-ssSeq repeat 1


title: rad53-1 sml1∆ +HU 45min input repeat 2


title: sml1∆ +HU 45min BrdU-IP-ssSeq repeat 1


title: rad53-1 sml1∆ +HU 45min input repeat 1


title: sml1∆ +HU 45min input repeat 2


title: dbf4-A sld3-A +HU 45min input repeat 2


title: H3k4me1_rn5

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the rn5 genome assembly using Bowtie2 with the default configuration
Peak calling was performed using MACS (Model-based Analysis of ChIP-Seq) (http://liulab.dfci.harvard.edu/MACS) with a p value cut off of 1x e9.
Genome_build: rn5
Supplementary_files_format_and_content: bed files were generated using Macs14

organism: Rattus norvegicus

source_name: Schwann cell

growth_protocol: primary rat schwann cell progenitors were induced to differentiate for 9 hours in the presence of cAMP

extract_protocol:
Lysates were clarified from sonicated nuclei and proteine-DNA complexes were isolated with antibody.
Schwann cells (~20 million cells) were cross-linked in 1% formaldehyde at room temperature for 10 min and then quenched with 125 mM glycine for 5 min. Cells were rinsed, resuspended in lysis buffer (50 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.25% Triton X-100 and 0.5% NP-40 and protease inhibitor cocktail) and incubated on ice for 10 min. Lysates were centrifuged and pellets were resuspended in nuclei washing buffer  (200 mM NaCl, 1 mM EDTA, 1 mM EGTA, 10 mM Tris pH 8.0, and protease inhibitor cocktail) with gentle rocking at 4°C. Nuclei were pelleted and resuspended in 1 ml of sonication buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 0.5 mM EGTA and protease inhibitor cocktail). Nuclear suspensions were sonicated with a Covaris S220 sonicator (total time 8 min). Antibody (chromatin: antibody = 4:1) was added to chromatin and incubated at 4°C overnight. Chromatin-protein complex was immunoprecipitated with protein A/G plus agarose beads and washed sequentially, twice with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.0], 150 mM NaCl), twice with high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.0], 500 mM NaCl) and twice with LiCl buffer (0.25 M LiCl, 1% IGEPAL CA630, 1% deoxycholic acid, 1 mM EDTA, 10 mM Tris [pH 8.0]) and once with 1xTE buffer. Immunoprecipitates were then eluted in elution buffer at 65°C for 1 h. Eluted chromatin was subjected to reverse-crosslink and chromatin fragment purification with QIAGEN PCR purification columns. ChIP-Seq libraries were prepared using NEBNext ChIP-Seq Library Prep Kit according to manufacturer’s instructions.

value: Schwann cell

tag: antibody

value: H3k4me1 (Abcam, ab8895)


title: CAF+MDA-MB-231 EV rep1

description:
CAF+MDA-MB-231 EV rep1
X18746_CAF.RNA.231.EV.1.8.29.17_S7_L999_R1_001.fastq.bam.1

value: MDA-MB-231 EV


title: sml1∆ +HU 45min BrdU-IP-ssSeq repeat 2


title: rad53-1 +HU 45min BrdU-IP-ssSeq repeat 1


title: sml1∆ +HU 45min input repeat 1


title: rad53-1 -HU 30min input

value: YPD


title: Cnpcre-cKO

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 whole genome using Tophat using default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file. Differential gene expression analysis was performed using Cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: Sciatic nerve

extract_protocol:
Sciatic nerves were removed, flash frozen on dry ice, and total RNA was harvested using Trizol reagent
Libraries were prepared according to Illumina's instructions accompanying Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001)

tag: strain background

value: mixed

tag: age

value: Postnatal day 6

tag: geneotype/variation

value: Hdac3f/f; Cnp-cre

tag: tissue

value: Sciatic nerve


title: rad53-1 -HU 30min BrdU-IP-ssSeq


title: rad53-1 +HU 45min input repeat 1


title: NPAI-R [67046]

status: Public on Feb 10 2018

city: Ann Arbor

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

description:
67046
Glioma implanted mouse model.
NRAS activated; TP53 knockdown; ATR knockdown; IDH1-R132H expression.
Processed data file: CuffDiff_rawCountsMatrix.txt

data_processing:
QC: We checked the quality of the raw reads data for each sample using FastQC (version 0.11.3) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content, etc.)
Alignment: We used the software package Tuxedo Suite for alignment, differential expression analysis, and post-analysis diagnostics. Briefly, we aligned reads to the reference transcriptome including both mRNAs and lncRNSs (UCSC mm10) using TopHat (version 2.0.3) and Bowtie (version 2.2.1). We used default parameter settings for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments.
QC: We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
Normalization and Quantitation: We used Cufflinks/CuffDiff (version 2.2.1) for expression quantitation, normalization, and differential expression analysis, using UCSC mm10.fa as the reference genome sequence. For this analysis, we used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package.
Differential Expression: We used locally developed scripts to format and annotate the differential expression data output from CuffDiff. Briefly, we identified genes and transcripts as being differentially expressed based on three criteria: test status = “OK”, FDR < 0.05 and fold change ≥ ± 1.5.
Annotation: We annotated genes and isoforms with NCBI Entrez GeneIDs and text descriptions. We further annotated differentially expressed genes with Gene Ontology (GO) terms using NCBI annotation.
Enrichment Testing: We used DAVID (version 6.7) for enrichment analysis of the set of differentially expressed genes to identify significantly enriched functional categories.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: CuffDiff_rawCountsMatrix.txt: Matrix of mapped read counts for each gene for each sample.

source_name: Implanted glioma brain tumor

growth_protocol: Brain tumors were generated in BL6 mice by implantation of 50,000 tumor neurospheres expression IDH1-R132H or control WT.

extract_protocol:
RNA was harvested using the RNeasy-Plus Kit (Qiagen; 74136) and assessed for quality using the TapeStation (Agilent). Samples with RNA Integrity Number of 8 or greater were rRNA depleted using Ribo Minus (Invitrogen;K1550-04).
rRNA-depleted samples were prepared using the TruSeq mRNA SamplePrep v2 kit (Illumina; RS-122-2001, RS-122-2002). The entire fraction of 0.1-3 ug of rRNA depleted total RNA was fragmented and copied into first-strand cDNA using reverse transcriptase and random primers. cDNA 3'-ends were adenylated and adapters were ligated. One of the adapters had a 6-nucleotide barcode that was unique for each sample, allowing us to multiplex in a HiSeq flow cell (Illumina). Products were purified and enriched by PCR to create the final cDNA library. Libraries were checked for quality and quantity by TapeStation (Agilent) and qPCR using a library quantification kit for Illumina platforms (Kapa Biosystems;KK4835). They were clustered on the cBot (Illumina) and sequenced 24 samples per lane on 6 lanes of a 50-cycle single end HiSeq 4000. HiSeq Control Software version 3.3.52 was used according to manufacturer's protocols. Demultiplexing and Fastq file generation was done using bcl2fastq version 2.17.1.14.

treatment_protocol: After 7 days of cell implantation, the animals were treated with 2 Gy of ionizing radiation (IR) per day during 2 weeks for a total of 20 Gy of IR.

tag: strain/background

value: Glioma brain tumor

tag: genotype/variation

value: NRAS-V12; shP53; shATRX; IDH1-R132H

value: IR 20Gy


title: NPA-C [69524]

description:
69524
Glioma implanted mouse model.
NRAS activated; TP53 knockdown; ATR knockdown.
Processed data file: CuffDiff_rawCountsMatrix.txt

value: NRAS-V12; shP53; shATRX

value: control


title: NPAI-C [67615]

description:
67615
Glioma implanted mouse model.
NRAS activated; TP53 knockdown; ATR knockdown; IDH1-R132H expression.
Processed data file: CuffDiff_rawCountsMatrix.txt


title: NPAI-R [69527]

description:
69527
Glioma implanted mouse model.
NRAS activated; TP53 knockdown; ATR knockdown; IDH1-R132H expression.
Processed data file: CuffDiff_rawCountsMatrix.txt


title: NPAI-R [67044]

description:
67044
Glioma implanted mouse model.
NRAS activated; TP53 knockdown; ATR knockdown; IDH1-R132H expression.
Processed data file: CuffDiff_rawCountsMatrix.txt


title: NPA-R [67040]

description:
67040
Glioma implanted mouse model.
NRAS activated; TP53 knockdown; ATR knockdown.
Processed data file: CuffDiff_rawCountsMatrix.txt


title: NPA-C [67035]

description:
67035
Glioma implanted mouse model.
NRAS activated; TP53 knockdown; ATR knockdown.
Processed data file: CuffDiff_rawCountsMatrix.txt


title: NPAI-C [67043]

description:
67043
Glioma implanted mouse model.
NRAS activated; TP53 knockdown; ATR knockdown; IDH1-R132H expression.
Processed data file: CuffDiff_rawCountsMatrix.txt


title: NPAI-C [67042]

description:
67042
Glioma implanted mouse model.
NRAS activated; TP53 knockdown; ATR knockdown; IDH1-R132H expression.
Processed data file: CuffDiff_rawCountsMatrix.txt


title: Dhhcre-cKO

value: Hdac3f/f; Dhh-cre


title: NPA-R [67614]

description:
67614
Glioma implanted mouse model.
NRAS activated; TP53 knockdown; ATR knockdown.
Processed data file: CuffDiff_rawCountsMatrix.txt


title: Dhhcre-Ctrl


title: GW26_PFC1_9

city: Beijing

first: Shu

last: Zhang

state: Beijing

address: Peking University, No.5 Yiheyuan Road Haidian District

country: China

institute: BIOPIC

description: polyA RNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
The first 8bp of read2 were used to split the mixed data into single cells according to the barcode sequences. The following 8bp were recorded and attached to the end of each read2 as unique molecular identifier (UMI). After that, reads1 were separated by the header of the corresponding read2 and then added UMI information. Hereafter, the split reads1 were trimmed off ploy(A) tail sequence and template switch oligo (TSO) sequence. Then we did quality control by removing out reads with adaptor contaminants (length < 37bp) and low-quality bases (N > 10%).
Subsequently, TopHat (version 2.0.12) was applied to align clean reads to the hg19 human transcriptome downloaded from UCSC.  Uniquely aligned reads were counted by the tool ‘htseq-count’ of HTSeq. According to the UMI information, transcripts with same UMI sequence of each gene were merged as one, thus the number of different UMIs for each gene was considered as the transcript counts of that gene without PCR bias for each sequenced cell.
The transcript counts of each cell were normalized to transcript per million (TPM), and the formula to calculate TPM is: the transcript counts of each gene divided by the sum of transcript counts of that cell, and multiplied by one million. TPM values were then normalized by log2(TPM/10 + 1) for the following analysis, since the sequencing depth of most single cell samples were less than 1,000,000 reads, we divided TPM values by 10.
Genome_build: hg19
Supplementary_files_format_and_content: xls files which include the TPM values of RefSeq genes.

source_name: Cells From Prefrontal Cortex

extract_protocol:
Single cells were directly picked into 2.5ul cell lysis buffer the same as Smartseq2 except that we used barcoded reverse transcription primers instead of oligdT30VN primer. Further cell lysis, reverse transcription and amplification was referred to Smartseq2 with little modification.
Each cell was amplified for 18 cycles in total. The PCR product for each barcode 1 to barcode 96 was pooled together for purification and library construction. The libraries were sequenced on illumina platform for 1.8M 150bp pair-end reads per cell.

treatment_protocol: To maintain the cell activity, we dissected all prefrontal cortex from nine fetal brain in ice cold artificial cerebrospinal fluid containing 125.0 mM NaCl, 26.0 mM NaHCO3, 2.5 mM KCl, 2.0mM CaCl2, 1.0 mM MgCl2, 1.25 mM NaH2PO4 at a pH of 7.4 when oxygenated (95% O2 and 5% CO2).The PFC tissue was first digested in brain tissue digestion medium 1 (BTDM1, 2mg/ml collagenase IV (Gibco, Cat.17104-019) and 10 U/μl DNase I (NEB, Cat.M0303L) in hybradate E medium). After brief pipet to roughly digest the tissue into small pieces, brain tissue digestion medium 2 (BTDM2, 1mg/ml papain (Sigma, Cat.P4762) and 10 U/μl DNase I in hybradate E medium).

value: Prefrontal Cortex

tag: developmental stage

value: 26 weeks after gestation

tag: gender

value: female


title: GW26_PFC1_8

description: polyA RNA


title: GW26_PFC1_5

description: polyA RNA


title: GW26_PFC1_4

description: polyA RNA


title: GW26_PFC1_7

description: polyA RNA


title: GW26_PFC1_2

description: polyA RNA


title: GW26_PFC1_3

description: polyA RNA


title: NPAI-R [69526]

description:
69526
Glioma implanted mouse model.
NRAS activated; TP53 knockdown; ATR knockdown; IDH1-R132H expression.
Processed data file: CuffDiff_rawCountsMatrix.txt


title: NPA-C [69525]

description:
69525
Glioma implanted mouse model.
NRAS activated; TP53 knockdown; ATR knockdown.
Processed data file: CuffDiff_rawCountsMatrix.txt


title: rad53-1 +HU 45min BrdU-IP-ssSeq repeat 2

value: YPD+HU

value: S

value: Anti-BrdU (BD BioScience, 347580)


title: GW26_PFC1_1

description: polyA RNA


title: HX_005_re

city: Shanghai

first: Bo

last: Peng

address: 138 Yixueyuan Road

department: Institute for Translational Brain Research

institute: Fudan University

data_processing:
Quality control: 1) remove reads with adaptors; 2)remove reads in which unkown bases are more than 10%; 3)remove low qulity reads(the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5)
Hisat2 was used to align clean reads to the mouse genome
Htseq was used to estimate raw counts for each gene
FPKM was calculated using Stringtie
Edgr was use to detect differentially expressed genes
Genome_build: mm10

source_name: retina

extract_protocol:
Total RNA was extracted from retinal homogenate using the TriPure Isolation Reagent (Roche) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols. The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification.  We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

treatment_protocol: Mice were treated by either PLX5622, PLX, vehicle, or PLX5622 + control diet

value: PLX5622 + LPS

tag: strain

value: retina

value: adult


title: Cnpcre-Ctrl

value: mixed

value: Postnatal day 6


title: GW26_PFC1_10

description: polyA RNA


title: HX_106_re


title: HX_109_re


title: HX_006_re


title: GW23_PFC1_2

description: polyA RNA

value: 23 weeks after gestation

value: male


title: GW23_PFC1_1

description: polyA RNA


title: GW19_PFC1_3

description: polyA RNA

value: 19 weeks after gestation


title: HX_004_re

value: LPS + vehicle


title: HX_110_re


title: GW19_PFC1_1

description: polyA RNA


title: GW26_PFC1_6

description: polyA RNA


title: HX_003_re

value: microglial repopulation


title: GW16_PFC1_9

description: polyA RNA

value: 16 weeks after gestation


title: HX_002_re


title: HX_115_re


title: HX_112_re


title: GW16_PFC1_7

description: polyA RNA

value: Prefrontal Cortex


title: HX_030_RE


title: GW16_PFC1_6

description: polyA RNA


title: GW16_PFC1_8

description: polyA RNA


title: GW16_PFC1_5

description: polyA RNA


title: HX_037_RE


title: HX_206_re


title: HX_038_RE


title: rad53-1 +HU 45min input repeat 2

tag: media


title: HX_007_re


title: GW19_PFC1_2

description: polyA RNA


title: GW23_PFC1_3

description: polyA RNA


title: HX_034_RE


title: GW16_PFC1_4

description: polyA RNA


title: HX_036_RE


title: HX_032_RE


title: HX_Q01_RE


title: GW16_PFC1_2

description: polyA RNA


title: HX_201_re


title: HX_033_RE


title: GW16_PFC1_1

description: polyA RNA


title: HX_027_RE


title: HX_202_re


title: GW13_PFC1

description: polyA RNA

value: 13 weeks after gestation


title: GW16_PFC1_3

description: polyA RNA

value: female


title: HX_020_RE


title: GW12_PFC1

description: polyA RNA

value: 12 weeks after gestation


title: HX_215_re


title: GW10_PFC3

description: polyA RNA

value: 10 weeks after gestation


title: GW10_PFC2_2

description: polyA RNA


title: HX_029_RE


title: HX_204_re


title: HX_022_RE


title: HX_108_re


title: HX_024_RE


title: HX_214_re


title: HX_031_RE


title: GW10_PFC1_2

description: polyA RNA


title: HX_019_RE


title: GW10_PFC1_1

description: polyA RNA


title: GW10_PFC2_1

description: polyA RNA


title: HX_025_RE


title: HX_018_RE


title: GW09_PFC1

description: polyA RNA

value: 9 weeks after gestation


title: HX_028_RE


title: HX_021_RE


title: HX_203_re


title: HX_217_re


title: HX_026_RE


title: GW08_PFC1

description: polyA RNA

value: 8 weeks after gestation


title: HX_015_RE

value: retina


title: HX_010_RE

value: adult


title: HX_023_RE


title: HX_212_re


title: HX_389_RE


title: HX_008_RE


title: HX_016_RE


title: HX_211_re


title: HX_009_RE


title: HX_017_RE


title: PANC1 CTCF CGATGT

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

description: genomic DNA

data_processing:
CTCF ChIP-seq data of PANC1 cell line was mapped to HG19 reference genome by using BWA default parameters. Then genome-wide tag count density was computed in 100bp window size by using BALM program.
genome build: hg19
processed data files format and content: PANC1 CTCF processed data files are bedGraph format.

source_name: PANC1 Cancer Cell line

growth_protocol: PANC1 cells (ATCC #CRL-1469) were grown in DMEM supplemented with 10% FBS, 2mM L-glutamine and 1% Penicillin/Streptomycin until 75-90% confluent.

extract_protocol:
ChIP-seq library preparation is described in O’Geen et al (Methods Mol Biol. 2011;791:265-286) using protein A/G beads to collect the immunoprecipitates.
Approximately 5 x 10^7 MCF7 and PANC1 cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature, crosslinking was quenched with 0.125 M glycine for 5 minutes at room temperature and cell pellets were collected and stored at -80°C. Nuclei were digested with 2000U HindIII prior to dilute solid-surface ligation reactions. For the ChIP-Seq, the anti-CTCF antibody was from Cell Signaling Technology CTCF (D31H2) XP® Lot 1, 3418S.

tag: cell line

value: anti-CTCF


title: PANC1 CTCF CTTGTA

description: genomic DNA


title: PANC1 CTCF CAGATC

description: genomic DNA


title: HX_004_RE


title: PANC1 CTCF ATCACG

description: genomic DNA


title: MCF7 TCC

description: Tethered Chromosome Capture (TCC)

data_processing:
TCC reads were aligned to the hg19 genome assembly using bowtie version 0.12.5 with the default configurations except only reporting uniquely mapped reads
The algorithm HiCPeak developed in the paper (http://www.ncbi.nlm.nih.gov/pubmed/22675074), was applied to identified hundreds of thousands of Interacting Loci Pairs
genome build: hg19
processed data files format and content: The TCC processed data files are plain text files and each file contains hundreds of thousands of Interacting Loci Pairs (ILP) in lines. The format of an ILP is as follows and an example is given as follows: loci1_chromosome, loci2_chromosome, loci1_start, loci1_end, loci2_start,loci2_end, log_likelihood

source_name: MCF7 Cancer Cell line

extract_protocol:
TCC library preparation is described in the paper (http://www.nature.com/nbt/journal/v30/n1/full/nbt.2057.html)
Approximately 5 x 10^7 MCF7 and PANC1 cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature, crosslinking was quenched with 0.125 M glycine for 5 minutes at room temperature and cell pellets were collected and stored at -80°C. Nuclei were digested with 2000U HindIII prior to dilute solid-surface ligation reactions. For the ChIP-Seq, the anti-CTCF antibody was from Cell Signaling Technology CTCF (D31H2) XP® Lot 1, 3418S.


title: HX_213_re


title: PANC1 TCC

description: Tethered Chromosome Capture (TCC)


title: HX_012_RE


title: HX_014_RE


title: HX_006_RE


title: HX_003_RE


title: HX_011_RE


title: HX_002_RE


title: HX_013_RE

value: vehicle


title: HX_007_RE


title: HX_005_RE


title: HX_210_re


title: PP1723_2

status: Public on Feb 09 2018

city: Kansas City

first: Peter

last: Baumann

state: MO

institute: Stowers Institute for Medical Research

data_processing:
Reads were aligned to the S. pombe ASM294v2 genome from ensembl using the STAR aligner (v.2.5.2b) with the following parameters: -outFilterType BySJout --alignSJDBoverhangMin 5 --alignSJoverhangMin 10 --alignIntronMin 20 --alignIntronMax 2500 --twopassMode Basic.
A counts table for unambiguous uniquely mapped reads was generated using a custom R script. Coordinates for snu4 (II:467,488-467,615)and snu5 (II: 3,236,356-3,237,312) [GenBank: X16573.1] were manually curated based on alignment of the published sequences to the genome.
Differential gene expression analysis was performed with EdgeR (v.3.14.0) using the likelihood ratio test with the Benjamini-Hochberg false discovery rate correction. Genes with fewer than one counts per million in three or more libraries were filtered prior to differential expression analysis. Genes with absolute log2 fold change greater than 1 with an adjusted p-value less than 0.05 were considered differentially expressed.
Genome_build: S. pombe ASM294v2
Supplementary_files_format_and_content: Gene expression values from edgeR analysis in comma-separated text file.

organism: Schizosaccharomyces pombe

growth_protocol: YES rich media

extract_protocol:
Phenol Chloroform extraction
Ribo-depleted stranded RNA-seq libraries were constructed using the TruSeq SBS Kit v4 - HS kit (Illumina). The libraries were pooled and sequenced on a Illumina HiSeq 2500 for 100-bp single-end reads on two lanes.

value: pof8 deletion mutant


title: PP138_3

value: Wild Type


title: PP138_2


title: PP138_1


title: 181-8

city: seattle

first: Serge

last: Barcy

state: WA

address: 1900 Ninth Avenue

department: SCRI

institute: Seattle Children's

description: small RNA

data_processing:
Illumina bcl2fastq 1.8.3 was used for de-multiplexing and production of FASTQ sequence files. The FASTQ sequence files were merged for each sample and then filtered to remove reads that were flagged by Illumina software as low quality.
The FASTX(1) application was used to trim the 3’-end of sequence reads in order to remove the 3’ adaptor sequence (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) ; sequences without any 3’ adapter sequence as well as sequences of less than 17 nucleotides after trimming were removed. A Perl script was used to remove sequences with any amount of 5’ –adapter sequence (AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGACGATC).
FASTX was also used to collapse identical reads into single entries retaining the read count for each unique sequence. To filter out any sequencing errors, only sequence reads that occurred at least 5 times were retained for further analysis. Non-redundant sequences were then aligned to genomic (hg19) and mRNA sequence (hg19) using bowtie 2(2); sequences with perfect-match and 1bp mismatch alignments were retained for further analysis.
DESEq2 for read count normalization and differential expression analysis
Fasta files contain reads mapping to the human genome (Hg19) and mRNA database (miRBase 21)
A read count summary was obtained specifically for the YRNA (yrna_result _match .raw) or miRNA (mirna_result_match.raw) species using bowtie 2
The miRNA read count file (mirna_result_match.raw) was used as input data using the DESEq2 software in order to normalize the read counts obtained between the different samples (DESeq2 miRNA normalized read counts.txt)
Genome_build: reference genome hg19/miRBase 21.0
Supplementary_files_format_and_content: tab-delimited text files include normalized read count values for each sample determined by DESEq 2 using the hg19 (genomic and mRNA) reference genome
Supplementary_files_format_and_content: tab-delimited text files (.raw)include total read count values for each sample mapping to known miRNA and YRNA sequences
Supplementary_files_format_and_content: Exosome_mirbaseResultMatchRaw.txt: reads mapped against miRNA (mirbase21)
Supplementary_files_format_and_content: Exosome_yrnaResultMatchRaw.txt.gz: reads mapped against YRNA
Supplementary_files_format_and_content: Exosome_DESEq2normReadCounts.txt.gz: counts
Supplementary_files_format_and_content: Plasma_mirbaseResultMatchRaw.txt.gz: reads mapped against miRNA (mirbase21)
Supplementary_files_format_and_content: Plasma_DESEq2normReadCounts.txt.gz: DESEq2 normalized read counts mapping to miRNA

source_name: plasma

extract_protocol:
A total of 1 mL of plasma was cleared of cellular debris by centrifugation at 3,000 g for 15 minutes at 4°C. The exosomal RNA was then isolated using the Qiagen exoRNeasy Serum/Plasma Midi Kit (Qiagen Germantown, MD). The RNA was then digested with RNase-free DNase I (Epicentre, Madison, WI) and re-purified on RNeasy MinElute columns (Qiagen Germantown, MD).
Template DNA molecules suitable for cluster generation were prepared using the NEBNext Small RNA-Seq Library Preparation Kit (New England BioLabs; Ipswhich, MA) according to the manufacturer’s instructions, except that following the RNA linker ligation, and after cDNA synthesis, the single stranded cDNA was fractionated using a 12% acrylamide-urea gel. cDNA fragments of 57-88 nt corresponding to inserts of 11-41 nt were excised and purified, in order to ensure that molecules with 17-35 nt inserts were recovered. Following the NEBNext protocol, the purified libraries were electrophoresed through a freshly cast 6% native acrylamide gel and library fragments of 128-158 nt corresponding to inserts of 11-41 nt were excised from the gel and recovered by overnight agitation at 37°C at 200 RPM in elution buffer, passage of the eluate through a 0.45 µm filter, and ethanol precipitation. The quality and size distribution of the amplified libraries were determined using Agilent 2100 Bioanalyzer High Sensitivity DNA microfluidic chips (Agilent Technologies; Santa Clara, CA) . Libraries were quantified using the KAPA Library Quantification Kit (Part Number: KK4824- Kapa Biosystems; Boston, MA).
The libraries were pooled at equimolar concentrations and diluted prior to loading onto a Illumina HiSeq Flow Cell v4 on the Illumina cBot cluster station (Illumina Inc., San Diego, CA). The libraries were extended and bridge amplified to create single sequence clusters using the HiSeq SR Cluster Kit v4 cBot. The flow cell carrying amplified clusters was loaded on the HiSeq 2500 sequencing system and sequenced with 50-nt single-end reads using the HiSeq SBS Kit v4. 10% ΦX174 phage DNA was spiked in all sequencing lanes for sequencer calibration. Real time image analysis and base calling were performed on the instrument using the HiSeq Sequencing Control Software v2.2.58. Illumina bcl2fastq v1.8.3 software was used for demultiplexing and production of FASTQ sequence files.
The samples were sequenced on two flowcells: C8B49ANXX and C89J5ANXX in order to generate a total of at least 14 million reads per sample

treatment_protocol: plasmas from KSHV+/HIV+ patients were collected after 2 years of ART treatment (lamivudine, tenofovir and efavirenz) , plasma from KSHV-/HIV+ patients were collected before ART therapy

value: F

value: Blood

tag: viral status

value: KSHV+/HIV+

tag: kshv oral shedding (copies/ml)

tag: kshv plasma viremia (copies/ml)

tag: hiv plasma viremia (copies/ml)

tag: absolute cd4 count

tag: art treatment

value: Pre ART


title: 174-5

description: small RNA

value: M


title: 131-6

description: small RNA

value: ND (below detection level)


title: 169-3

description: small RNA

value: KSHV+/HIV-

value: ND

value: NA (not available)

value: NA (not applicable)


title: 091-1

description: small RNA


title: 365-1

description: small RNA


title: 033-1

description: small RNA


title: 361-0

description: small RNA


title: 146-6

description: small RNA


title: 138-9

description: small RNA


title: 025-1

description: small exosomal RNA

source_name: Plasma exosomes

value: Blood (plasma)


title: HX_001_RE

tag: treatment

value: retina


title: HX_001_re

tag: age

value: adult


title: HX_209_re


title: 305-2

description: small exosomal RNA

value: KSHV-/HIV-


title: 023-7

description: small exosomal RNA

value: KSHV-/HIV+


title: 027-5

description: small exosomal RNA


title: 019-2

description: small exosomal RNA


title: 300-7

description: small exosomal RNA


title: RAS1nM_3

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description:
AG3_6
Expression profile of RAS-induced senescent IMR90 fibroblasts treated with 1nM Rapamycin (Rep3)

data_processing:
Sequence reads in Fastq format were generated from Illunina basecalls using Illumina's bcl2fastq (version 2.17).
Sequence reads were aligned to Ensembl GRCh37 genome build and gene models retrieved from Illumina's igenome using Tophat2 (v 2.0.11).
Number of reads on the genes were summarised  using featureCounts function avaialble in Rsubread R package(verion 1.22.3)
Genome_build: hg19
Supplementary_files_format_and_content: counts & reads counts on genes

growth_protocol: IMR90 fibroblasts were maintained in DMEM supplemented with 10% FBS.

extract_protocol:
Cells were scraped and homogenised in TRIzol® RNA isolation reagent, mixed with Chloroform in a 5:1 ratio, centrifuged at 15,000 rpm for 30 min and after successful phase separation, the top clear RNA-containing phase was purified using the RNAeasy® Mini Kit (Qiagen)
Libraries were prepared according to Illumina's kit instructions (mRNA stranded library prep kit)

treatment_protocol: Cells were transduced with retroviral OSKM or RAS expression and the next day treated with 1nM or 10nM Rapamycin. 2 days later the cells were also treated with 400 µg/ml G418 to select for cells carrying the OSKM and RAS transgene. RNA was collected 10 days after transduction.

tag: cell type

value: fibroblasts

tag: passage

tag: vector

value: RAS expressing vector

tag: treated with

value: 1nM Rapamycin

tag: days post-infection


title: RAS10nM_3

description:
AG3_7
Expression profile of RAS-induced senescent IMR90 fibroblasts treated with 10nM Rapamycin (Rep3)

value: 10nM Rapamycin


title: PP1723_3

tag: genotype/variation

value: pof8 deletion mutant


title: OSKM1nM_3

description:
AG3_3
Expression profile of OSKM-induced senescent IMR90 fibroblasts treated with 1nM Rapamycin (Rep3)

value: OSKM expressing vector


title: OSKM10nM_3

description:
AG3_4
Expression profile of OSKM-induced senescent IMR90 fibroblasts treated with 10nM Rapamycin (Rep3)


title: RAS_3

description:
AG3_5
Expression profile of RAS-induced senescent IMR90 fibroblasts (Rep3)


title: PP1723_1


title: OSKM_3

description:
AG3_2
Expression profile of OSKM-induced senescent IMR90 fibroblasts (Rep3)


title: RAS10nM_2

description:
AG2_7
Expression profile of RAS-induced senescent IMR90 fibroblasts treated with 10nM Rapamycin (Rep2)


title: OSKM_2

description:
AG2_2
Expression profile of OSKM-induced senescent IMR90 fibroblasts (Rep2)


title: RAS_2

description:
AG2_5
Expression profile of RAS-induced senescent IMR90 fibroblasts (Rep2)


title: OSKM1nM_2

description:
AG2_3
Expression profile of OSKM-induced senescent IMR90 fibroblasts treated with 1nM Rapamycin (Rep2)


title: RAS1nM_2

description:
AG2_6
Expression profile of RAS-induced senescent IMR90 fibroblasts treated with 1nM Rapamycin (Rep2)


title: RAS1nM_1

description:
AG1_6
Expression profile of RAS-induced senescent IMR90 fibroblasts treated with 1nM Rapamycin (Rep1)


title: 296-9

description: small exosomal RNA

tag: gender

value: F

tag: tissue


title: OSKM10nM_2

description:
AG2_4
Expression profile of OSKM-induced senescent IMR90 fibroblasts treated with 10nM Rapamycin (Rep2)

tag: cell line


title: Prolif_1

description:
AG1_1
Expression profile of proliferating IMR90 fibroblasts (Rep1)

value: empty vector (MSCV)


title: Sample_OmT3_2b

description: Expression profile of IMR90 + OSKM + a different shRNA targeting mTOR (Rep2)

data_processing:
Sequence reads in Fastq format were generated from Illunina basecalls using Illumina's bcl2fastq (version 2.17).
Sequence reads were aligned to Ensembl GRCh37 genome build and gene models retrieved from Illumina's igenome using Tophat2 (v 2.0.11).
Aligned reads were counted whithin exons using Rsubread (verion 1.22.3)
Genome_build: hg19
Supplementary_files_format_and_content: counts & reads counts on genes

extract_protocol:
RNA-Seq libraries were prepared following the Smartseq2 protocol (Picelli et al., 2014 Nat Protocols). Cells from a confluent 96-well were lysed in 50 µl lysis buffer. For reverse transcription, 2 µl lysis mix was used.
Nextera XT Library Preparation (Illumina)

treatment_protocol: Cells were transduced with retroviral OSKM expression and pGIPz-based vectors targeting p21CIP or mTOR and selected with 400 µg/ml G418. RNA was extracted after 14 or 20 days.

value: OSKM + pGIPz-based shRNA


title: OSKM1nM_1

description:
AG1_3
Expression profile of OSKM-induced senescent IMR90 fibroblasts treated with 1nM Rapamycin (Rep1)


title: Sample_OmT3_2c

description: Expression profile of IMR90 + OSKM + a different shRNA targeting mTOR (Rep3)


title: Sample_OmT3_1c


title: OSKM10nM_1

description:
AG1_4
Expression profile of OSKM-induced senescent IMR90 fibroblasts treated with 10nM Rapamycin (Rep1)


title: Sample_OmT3_2a

description: Expression profile of IMR90 + OSKM + a different shRNA targeting mTOR (Rep1)


title: OSKM_1

description:
AG1_2
Expression profile of OSKM-induced senescent IMR90 fibroblasts (Rep1)


title: Sample_OmT3_1b


title: Prolif_3

description:
AG3_1
Expression profile of proliferating IMR90 fibroblasts (Rep3)


title: Sample_O212_2b

description: Expression profile of IMR90 + OSKM + a different shRNA targeting p21CIP (Rep2)


title: Sample_OmT2_1b

description: Expression profile of IMR90 + OSKM + shRNA targeting mTOR (Rep2)


title: Sample_OmT2_2a

description: Expression profile of IMR90 + OSKM + shRNA targeting mTOR (Rep1)


title: Sample_O212_2c

description: Expression profile of IMR90 + OSKM + a different shRNA targeting p21CIP (Rep3)


title: Sample_OmT2_2c

description: Expression profile of IMR90 + OSKM + shRNA targeting mTOR (Rep3)


title: RAS_1

description:
AG1_5
Expression profile of RAS-induced senescent IMR90 fibroblasts (Rep1)


title: Prolif_2

description:
AG2_1
Expression profile of proliferating IMR90 fibroblasts (Rep2)


title: Sample_O212_2a

description: Expression profile of IMR90 + OSKM + a different shRNA targeting p21CIP (Rep1)


title: Sample_O212_1c


title: Sample_O212_1b


title: RAS10nM_1

description:
AG1_7
Expression profile of RAS-induced senescent IMR90 fibroblasts treated with 10nM Rapamycin (Rep1)


title: Sample_O211_2b

description: Expression profile of IMR90 + OSKM + shRNA targeting p21CIP (Rep2)


title: Sample_OmT3_1a


title: Sample_O211_1b


title: Sample_O211_2a

description: Expression profile of IMR90 + OSKM + shRNA targeting p21CIP (Rep1)


title: Sample_O211_1a


title: Sample_O211_1c

description: Expression profile of IMR90 + OSKM + shRNA targeting p21CIP (Rep3)


title: Sample_OmT2_2b


title: RPE1_hTERT_H2B_GFP_7.3_2_miRNA

city: Martinsried

first: Milena

last: Dürrbaum

address: Am Klopferspitz 18

department: Maintenance of Genome Stability

country: Germany

institute: Max Planck Institute of Biochemistry

description:
small RNA
normalized to RPE1_hTERT_H2B_GFP_11/ RPE1_hTERT_H2B_GFP_12/ RPE1_hTERT_H2B_GFP_13
processed data file:
RPE1_H2B_7.3.txt

data_processing:
If necessary, raw sequencing read ends were trimmed for low quality base calls using the FASTQ quality trimmer with the following parameters: “-Q33 -t 20 -l 17“ (28,33).
Sequencing adapters were removed with cutadapt.
Mapping to the human genome hg19 and miRNA identification was performed using mirdeep2 (v2.0.0.8) (33) with the following commands: “mapper.pl -e -h -i -j  -l 18 -m -p hg19 ‑q” and “miRDeep2.pl reads.fa hg19.fa genome.arf human_mature_rmspace.fa others_mature_rmspace.fa human_hairpin_rmspace.fa -d -t Human”.
The three biological replicates of aneuploid and the corresponding parental cell line were analyzed within the same analysis run. For subsequent normalization and differential expression analysis miRNA_expressed_all_samples.csv was used as an input for DESeq2.
To account for sequencing batch effects, paired replicate information in addition to condition information was input to the DESeq2 analysis for HCT116 5/4, RPE1 5/3 12/3 and RPE1* 21/3 and corresponding parental cell lines.
Genome_build: hg19
Supplementary_files_format_and_content: Tab- delimited text file containing the DeSeq2 normalized, log2 texpression fold changes of the aneuploid cell line to the control cell line (log2FoldChange). baseMean=mean of normalized counts for all samples;  lfcSE=standard error: condition treated vs untreated stat=Wald statistic: aneuploidy vs control;  pvalue=Wald test p-value: aneuploidy vs control; padj="Benjamini-Hochberg adjusted p-values

source_name: Retina pigmented epithelium cell line immortalized with hTERT

growth_protocol: Cells were maintained in 10 cm dishes in Dulbecco’s Modified Eagle Medium (DMEM) at 37°C and 5% CO2. Culture medium was supplemented with growth factors from 5% Fetal Calf Serum (FCS) and 1% Penicillin/ Streptavidin to avoid bacterial growth and contamination.

extract_protocol:
Total RNA, including small RNAs from 18 nucleotides upwards, was extracted using miRNeasy Mini Kit (QIAGEN).
TruSeq small RNA library preparation were performed by the Max Planck-Genome-Center Cologne, Germany.

tag: cell line origin

value: Human retina, pigmented epithelium

tag: aneuploidy

value: trisomy of chromosome 7

tag: stable expression

value: H2B tagged with GFP


title: RPE1_hTERT_H2B_GFP_7.3_3_miRNA


title: RPE1_hTERT_H2B_GFP_7.3_1_miRNA


title: RPE1_hTERT_H2B_GFP_12_miRNA

description:
small RNA
processed data file:
RPE1_H2B_7.3.txt

value: modal no. 46, near diploid


title: Sample_OmT2_1c


title: RPE1_hTERT_H2B_GFP_11_miRNA


title: RPE1_hTERT_H2B_GFP_21.3_2_miRNA

description:
small RNA
normalized to RPE1_hTERT_H2B_GFP_1/ RPE1_hTERT_H2B_GFP_2/ RPE1_hTERT_H2B_GFP_3
processed data file:
RPE1_H2B_21.3.txt

value: trisomy of chromosome 21


title: RPE1_hTERT_H2B_GFP_21.3_3_miRNA


title: RPE1_hTERT_H2B_GFP_21.3_1_miRNA


title: Sample_OmT2_1a


title: RPE1_hTERT_H2B_GFP_2_miRNA

description:
small RNA
processed data file:
RPE1_H2B_21.3.txt


title: RPE1_hTERT_H2B_GFP_3_miRNA


title: Sample_O212_1a


title: RPE1_hTERT_5.3_12.3_2_miRNA

description:
small RNA
normalized to RPE1_hTERT_1/ RPE1_hTERT_2/ RPE1_hTERT_3
processed data file:
RPE1_5.3_12.3.txt

value: trisomy of chromosome 5, trisomy of chromosome 12


title: Sample_O211_2c


title: RPE1_hTERT_H2B_GFP_1_miRNA


title: RPE1_hTERT_5.3_12.3_3_miRNA


title: RPE1_hTERT_3_miRNA

description:
small RNA
processed data file:
RPE1_5.3_12.3.txt


title: RPE1_hTERT_5.3_12.3_1_miRNA


title: RPE1_hTERT_2_miRNA


title: HCT116_H2B_GFP_3.3.c11_3_miRNA

description:
small RNA
normalized to HCT116_H2B_GFP_1/HCT116_H2B_GFP_2/ HCT116_H2B_GFP_3
processed data file:
HCT116_H2B_3.3c11.txt

source_name: Human colorectal cell line

value: Human colon carcinoma

value: trisomy of chromosome 3


title: RPE1_hTERT_1_miRNA


title: HCT116_H2B_GFP_3.3.c11_2_miRNA


title: RPE1_hTERT_H2B_GFP_13_miRNA


title: HCT116_18.3.c2_1_miRNA

description:
small RNA
normalized to HCT116_H2B_GFP_1/HCT116_H2B_GFP_2/ HCT116_H2B_GFP_3
processed data file:
HCT116_18.3c2.txt

value: trisomy of chromosome 18


title: HCT116_18.3.c2_2_miRNA


title: HCT116_18.3.c2_3_miRNA


title: HCT116_H2B_GFP_8.3.c7_3_miRNA

description:
small RNA
normalized to HCT116_H2B_GFP_1/HCT116_H2B_GFP_2/ HCT116_H2B_GFP_3
processed data file:
HCT116_H2B_8.3c7.txt

value: trisomy of chromosome 8


title: HCT116_H2B_GFP_3.3.c11_1_miRNA


title: HCT116_5.4_2_miRNA

description:
small RNA
normalized to HCT116_1/ HCT116_2/ HCT116_3
processed data file:
HCT116_5.4.txt

value: tetrasomy of chromosome 5


title: HCT116_5.4_3_miRNA


title: HCT116_H2B_GFP_1_miRNA

description:
small RNA
processed data file:
HCT116_H2B_8.3c7.txt

value: modal no. 45, near diploid


title: HCT116_H2B_GFP_2_miRNA


title: HCT116_H2B_GFP_8.3.c7_2_miRNA


title: HCT116_5.4_1_miRNA


title: HCT116_H2B_GFP_3_miRNA


title: HCT116_H2B_GFP_8.3.c7_1_miRNA


title: HCT116_1_miRNA

description:
small RNA
processed data file:
HCT116_5.4.txt


title: HCT116_3_miRNA


title: HCT116_2_miRNA


title: RPE1_hTERT_H2B_GFP_2

description:
processed data file:
RPE1_H2B_21.3.txt

data_processing:
Sequencing adapters were removed from the raw sequences with cutadapt.
Sequencing reads were mapped to the human genome using TopHat (v2.0.10) with the following parameters: “tophat2 -g1 -G”.
RefSeq information in the GTF file was downloaded from the UCSC genome browser. featureCounts (v1.4.3) was used to generate the count matrix with the same GTF file as for the alignment with the following parameters: “-t exon -g gene_id”.
Normalization and differential expression analysis was performed using the R/Bioconductor package DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Tab- delimited text file containing the DeSeq2 normalized, log2 texpression fold changes of the aneuploid cell line to thecontrol cell line (log2FoldChange). baseMean=mean of normalized counts for all samples;  lfcSE=standard error: condition treated vs untreated stat=Wald statistic: aneuploidy vs control;  pvalue=Wald test p-value: aneuploidy vs control; padj="Benjamini-Hochberg adjusted p-values

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN).
TruSeq RNA library preparation and Illumina HiSeq2500 sequencing with 25 million 100bp single reads per library were performed by the Max Planck-Genome-Center Cologne, Germany.


title: RPE1_hTERT_H2B_GFP_21.3_3

description:
normalized to RPE1_hTERT_H2B_GFP_1/ RPE1_hTERT_H2B_GFP_2/ RPE1_hTERT_H2B_GFP_3
processed data file:
RPE1_H2B_21.3.txt


title: RPE1_hTERT_H2B_GFP_1

description:
processed data file:
RPE1_H2B_21.3.txt


title: RPE1_hTERT_H2B_GFP_3

description:
processed data file:
RPE1_H2B_21.3.txt


title: RPE1_hTERT_H2B_GFP_21.3_1


title: RPE1_hTERT_5.3_12.3_3

description:
normalized to RPE1_hTERT_1/ RPE1_hTERT_2/ RPE1_hTERT_3
processed data file:
RPE1_5.3_12.3.txt


title: RPE1_hTERT_5.3_12.3_1


title: RPE1_hTERT_5.3_12.3_2


title: RPE1_hTERT_3

description:
processed data file:
RPE1_5.3_12.3.txt


title: RPE1_hTERT_2

description:
processed data file:
RPE1_5.3_12.3.txt


title: HCT116_H2B_GFP_8.3.c7_2

description:
normalized to HCT116_H2B_GFP_1/HCT116_H2B_GFP_2/ HCT116_H2B_GFP_3
processed data file:
HCT116_H2B_8.3c7.txt


title: RPE1_hTERT_1

description:
processed data file:
RPE1_5.3_12.3.txt


title: HCT116_H2B_GFP_2

description:
processed data file:
HCT116_H2B_8.3c7.txt


title: HCT116_5.4_1

description:
normalized to HCT116_1/ HCT116_2/ HCT116_3
processed data file:
HCT116_5.4.txt


title: HCT116_H2B_GFP_1


title: HCT116_5.4_2


title: HCT116_H2B_GFP_3


title: HCT116_5.4_3


title: HCT116_1

description:
processed data file:
HCT116_5.4.txt


title: HCT116_2

description:
processed data file:
HCT116_5.4.txt


title: Sample_OSKM_7

description: Barcode: GGACTCCT-AAGGAGTA

data_processing:
Sequence reads in Fastq format were generated from Illunina basecalls using Illumina's bcl2fastq (version 2.17).
Sequence reads were aligned to Ensembl GRCh37 genome build and gene models retrieved from Illumina's igenome using Tophat2 (v 2.0.11).
Aligned reads were counted whithin exons using Rsubread (verion 1.22.3)
Genome_build: h19
Supplementary_files_format_and_content: counts on genes

source_name: IMR90 fibroblast

extract_protocol:
RNA-Seq libraries were prepared following the Smartseq2 protocol (Picelli et al., 2014 Nat Protocols).
Nextera XT Library Preparation (Illumina)

treatment_protocol: Cells were transduced with retroviral OSKM expressing or control vectors followed by a lentiviral shRNA library and selected with G418 and puromycin, respectively. Cells were passaged at regular intervals to allow for bypass of the senescence growth arrest. After 56 days, OSKM-infected library cells were sorted into three 96-well plates by flow cytometry for single-cell RNA-Seq.

value: IMR90 fibroblast

tag: transduction

value: OSKM + shRNA control vector


title: Sample_OSKM_9

description: Barcode: TAGGCATG-GCGTAAGA


title: RPE1_hTERT_H2B_GFP_21.3_2


title: HCT116_3

description:
processed data file:
HCT116_5.4.txt


title: Sample_OSKM_64

description: Barcode: GTAGAGGA-CTAAGCCT


title: Sample_OSKM_63

description: Barcode: GTAGAGGA-AAGGAGTA


title: Sample_OSKM_8

description: Barcode: GGACTCCT-CTAAGCCT


title: Sample_OSKM_6

description: Barcode: GGACTCCT-ACTGCATA


title: Sample_OSKM_62

description: Barcode: GTAGAGGA-ACTGCATA


title: Sample_OSKM_61

description: Barcode: GTAGAGGA-GTAAGGAG


title: Sample_OSKM_60

description: Barcode: GTAGAGGA-AGAGTAGA


title: Sample_OSKM_59

description: Barcode: GTAGAGGA-TATCCTCT


title: Sample_OSKM_55

description: Barcode: AAGAGGCA-AAGGAGTA


title: Sample_OSKM_57

description: Barcode: GTAGAGGA-GCGTAAGA


title: Sample_OSKM_56

description: Barcode: AAGAGGCA-CTAAGCCT


title: Sample_OSKM_54

description: Barcode: AAGAGGCA-ACTGCATA


title: Sample_OSKM_53

description: Barcode: AAGAGGCA-GTAAGGAG


title: HCT116_H2B_GFP_8.3.c7_3


title: Sample_OSKM_52

description: Barcode: AAGAGGCA-AGAGTAGA


title: Sample_OSKM_5

description: Barcode: GGACTCCT-GTAAGGAG


title: Sample_OSKM_49

description: Barcode: AAGAGGCA-GCGTAAGA


title: Sample_OSKM_4

description: Barcode: GGACTCCT-AGAGTAGA


title: HCT116_H2B_GFP_8.3.c7_1


title: Sample_OSKM_51

description: Barcode: AAGAGGCA-TATCCTCT


title: Sample_OSKM_46

description: Barcode: CGAGGCTG-ACTGCATA


title: Sample_OSKM_47

description: Barcode: CGAGGCTG-AAGGAGTA


title: Sample_OSKM_45

description: Barcode: CGAGGCTG-GTAAGGAG


title: Sample_OSKM_48

description: Barcode: CGAGGCTG-CTAAGCCT


title: Sample_OSKM_41

description: Barcode: CGAGGCTG-GCGTAAGA


title: Sample_OSKM_42

description: Barcode: CGAGGCTG-CTCTCTAT


title: Sample_OSKM_40

description: Barcode: GCTACGCT-CTAAGCCT


title: Sample_OSKM_44

description: Barcode: CGAGGCTG-AGAGTAGA


title: Sample_OSKM_43

description: Barcode: CGAGGCTG-TATCCTCT


title: Sample_OSKM_39

description: Barcode: GCTACGCT-AAGGAGTA


title: Sample_OSKM_38

description: Barcode: GCTACGCT-ACTGCATA


title: Sample_OSKM_37

description: Barcode: GCTACGCT-GTAAGGAG


title: Sample_OSKM_58

description: Barcode: GTAGAGGA-CTCTCTAT


title: Sample_OSKM_36

description: Barcode: GCTACGCT-AGAGTAGA


title: Sample_OSKM_35

description: Barcode: GCTACGCT-TATCCTCT


title: Sample_OSKM_34

description: Barcode: GCTACGCT-CTCTCTAT


title: Sample_OSKM_31

description: Barcode: CAGAGAGG-AAGGAGTA


title: Sample_OSKM_33

description: Barcode: GCTACGCT-GCGTAAGA


title: Sample_OSKM_30

description: Barcode: CAGAGAGG-ACTGCATA


title: Sample_OSKM_32

description: Barcode: CAGAGAGG-CTAAGCCT


title: Sample_OSKM_2

description: Barcode: GGACTCCT-CTCTCTAT


title: Sample_OSKM_29

description: Barcode: CAGAGAGG-GTAAGGAG


title: Sample_OSKM_27

description: Barcode: CAGAGAGG-TATCCTCT


title: Sample_OSKM_28

description: Barcode: CAGAGAGG-AGAGTAGA


title: Sample_OSKM_23

description: Barcode: CTCTCTAC-AAGGAGTA


title: Sample_OSKM_3

description: Barcode: GGACTCCT-TATCCTCT


title: Sample_OSKM_25

description: Barcode: CAGAGAGG-GCGTAAGA


title: Sample_OSKM_26

description: Barcode: CAGAGAGG-CTCTCTAT


title: Sample_OSKM_21

description: Barcode: CTCTCTAC-GTAAGGAG


title: Sample_OSKM_1

description: Barcode: GGACTCCT-GCGTAAGA


title: Sample_OSKM_22

description: Barcode: CTCTCTAC-ACTGCATA


title: Sample_OSKM_19

description: Barcode: CTCTCTAC-TATCCTCT


title: Sample_OSKM_24

description: Barcode: CTCTCTAC-CTAAGCCT


title: Sample_OSKM_20

description: Barcode: CTCTCTAC-AGAGTAGA


title: Sample_OSKM_15

description: Barcode: TAGGCATG-AAGGAGTA


title: Sample_OSKM_18

description: Barcode: CTCTCTAC-CTCTCTAT


title: Sample_OSKM_17

description: Barcode: CTCTCTAC-GCGTAAGA


title: Sample_OSKM_14

description: Barcode: TAGGCATG-ACTGCATA


title: Sample_OSKM_11

description: Barcode: TAGGCATG-TATCCTCT


title: Sample_OSKM_13

description: Barcode: TAGGCATG-GTAAGGAG


title: Sample_OSKM_16

description: Barcode: TAGGCATG-CTAAGCCT


title: Sample_OSKM_10

description: Barcode: TAGGCATG-CTCTCTAT


title: Sample_EV_5

description: Barcode: TAAGGCGA-GTAAGGAG

value: Empty control vectors


title: Sample_EV_9

description: Barcode: CGTACTAG-GCGTAAGA


title: Sample_EV_8

description: Barcode: TAAGGCGA-CTAAGCCT


title: Sample_EV_7

description: Barcode: TAAGGCGA-AAGGAGTA


title: Sample_EV_3

description: Barcode: TAAGGCGA-TATCCTCT


title: Sample_EV_4

description: Barcode: TAAGGCGA-AGAGTAGA


title: Sample_OSKM_12

description: Barcode: TAGGCATG-AGAGTAGA


title: Sample_EV_32

description: Barcode: TCCTGAGC-CTAAGCCT


title: Sample_EV_31

description: Barcode: TCCTGAGC-AAGGAGTA


title: Sample_EV_28

description: Barcode: TCCTGAGC-AGAGTAGA


title: Sample_EV_29

description: Barcode: TCCTGAGC-GTAAGGAG


title: Sample_EV_27

description: Barcode: TCCTGAGC-TATCCTCT


title: Sample_EV_25

description: Barcode: TCCTGAGC-GCGTAAGA


title: Sample_EV_24

description: Barcode: AGGCAGAA-CTAAGCCT


title: Sample_EV_26

description: Barcode: TCCTGAGC-CTCTCTAT


title: Sample_EV_2

description: Barcode: TAAGGCGA-CTCTCTAT


title: Sample_EV_1

description: Barcode: TAAGGCGA-GCGTAAGA


title: Sample_EV_22

description: Barcode: AGGCAGAA-ACTGCATA


title: Sample_EV_20

description: Barcode: AGGCAGAA-AGAGTAGA


title: Sample_EV_21

description: Barcode: AGGCAGAA-GTAAGGAG


title: Sample_EV_18

description: Barcode: AGGCAGAA-CTCTCTAT


title: Sample_EV_16

description: Barcode: CGTACTAG-CTAAGCCT


title: Sample_EV_17

description: Barcode: AGGCAGAA-GCGTAAGA


title: Sample_EV_13

description: Barcode: CGTACTAG-GTAAGGAG


title: Sample_EV_19

description: Barcode: AGGCAGAA-TATCCTCT


title: Sample_EV_15

description: Barcode: CGTACTAG-AAGGAGTA


title: Sample_EV_12

description: Barcode: CGTACTAG-AGAGTAGA


title: Sample_EV_11

description: Barcode: CGTACTAG-TATCCTCT


title: Sample_EV_14

description: Barcode: CGTACTAG-ACTGCATA


title: Sample_B2_9

description: Barcode: GCTACGCT-TCGACTAG

value: OSKM + shRNA library


title: Sample_EV_10

description: Barcode: CGTACTAG-CTCTCTAT


title: Sample_EV_30

description: Barcode: TCCTGAGC-ACTGCATA


title: Sample_B2_93

description: Barcode: CCTAAGAC-CTCTCTAT


title: Sample_B2_94

description: Barcode: CGATCAGT-CTCTCTAT


title: Sample_B2_91

description: Barcode: TAGCGCTC-CTCTCTAT


title: Sample_B2_90

description: Barcode: ATGCGCAG-CTCTCTAT


title: Sample_EV_23

description: Barcode: AGGCAGAA-AAGGAGTA


title: Sample_B2_89

description: Barcode: TACGCTGC-CTCTCTAT


title: Sample_B2_88

description: Barcode: CGGAGCCT-CTCTCTAT


title: Sample_EV_6

description: Barcode: TAAGGCGA-ACTGCATA


title: Sample_B2_87

description: Barcode: GCGTAGTA-CTCTCTAT


title: Sample_B2_95

description: Barcode: TGCAGCTA-CTCTCTAT


title: Sample_B2_86

description: Barcode: GGAGCTAC-CTCTCTAT


title: Sample_B2_82

description: Barcode: CGAGGCTG-TTATGCGA


title: Sample_B2_84

description: Barcode: GTAGAGGA-TTATGCGA


title: Sample_B2_78

description: Barcode: TAGGCATG-TTATGCGA


title: Sample_B2_81

description: Barcode: GCTACGCT-TTATGCGA


title: Sample_B2_7

description: Barcode: CTCTCTAC-TCGACTAG


title: Sample_B2_75

description: Barcode: AGGCAGAA-TTATGCGA


title: Sample_B2_74

description: Barcode: CGTACTAG-TTATGCGA


title: Sample_B2_76

description: Barcode: TCCTGAGC-TTATGCGA


title: Sample_B2_73

description: Barcode: TAAGGCGA-TTATGCGA


title: Sample_B2_72

description: Barcode: GTAGAGGA-GAGCCTTA


title: Sample_B2_70

description: Barcode: CGAGGCTG-GAGCCTTA


title: Sample_B2_69

description: Barcode: GCTACGCT-GAGCCTTA


title: Sample_B2_71

description: Barcode: AAGAGGCA-GAGCCTTA


title: Sample_B2_77

description: Barcode: GGACTCCT-TTATGCGA


title: Sample_B2_96

description: Barcode: TCGACGTC-CTCTCTAT


title: Sample_B2_92

description: Barcode: ACTGAGCG-CTCTCTAT


title: Sample_B2_6

description: Barcode: TAGGCATG-TCGACTAG


title: Sample_B2_68

description: Barcode: CAGAGAGG-GAGCCTTA


title: Sample_B2_83

description: Barcode: AAGAGGCA-TTATGCGA


title: Sample_B2_67

description: Barcode: CTCTCTAC-GAGCCTTA


title: Sample_B2_66

description: Barcode: TAGGCATG-GAGCCTTA


title: Sample_B2_79

description: Barcode: CTCTCTAC-TTATGCGA


title: Sample_B2_65

description: Barcode: GGACTCCT-GAGCCTTA


title: Sample_B2_60

description: Barcode: GTAGAGGA-AAGGCTAT


title: Sample_B2_62

description: Barcode: CGTACTAG-GAGCCTTA


title: Sample_B2_5

description: Barcode: GGACTCCT-TCGACTAG


title: Sample_B2_58

description: Barcode: CGAGGCTG-AAGGCTAT


title: Sample_B2_59

description: Barcode: AAGAGGCA-AAGGCTAT


title: Sample_B2_64

description: Barcode: TCCTGAGC-GAGCCTTA


title: Sample_B2_57

description: Barcode: GCTACGCT-AAGGCTAT


title: Sample_B2_55

description: Barcode: CTCTCTAC-AAGGCTAT


title: Sample_B2_52

description: Barcode: TCCTGAGC-AAGGCTAT


title: Sample_B2_50

description: Barcode: CGTACTAG-AAGGCTAT


title: Sample_B2_4

description: Barcode: TCCTGAGC-TCGACTAG


title: Sample_B2_49

description: Barcode: TAAGGCGA-AAGGCTAT


title: Sample_B2_56

description: Barcode: CAGAGAGG-AAGGCTAT


title: Sample_B2_47

description: Barcode: AAGAGGCA-CTATTAAG


title: Sample_B2_53

description: Barcode: GGACTCCT-AAGGCTAT


title: Sample_B2_46

description: Barcode: CGAGGCTG-CTATTAAG


title: Sample_B2_63

description: Barcode: AGGCAGAA-GAGCCTTA


title: Sample_B2_51

description: Barcode: AGGCAGAA-AAGGCTAT


title: Sample_B2_39

description: Barcode: AGGCAGAA-CTATTAAG


title: Sample_B2_40

description: Barcode: TCCTGAGC-CTATTAAG


title: Sample_B2_41

description: Barcode: GGACTCCT-CTATTAAG


title: Sample_B2_38

description: Barcode: CGTACTAG-CTATTAAG


title: Sample_B2_45

description: Barcode: GCTACGCT-CTATTAAG


title: Sample_B2_44

description: Barcode: CAGAGAGG-CTATTAAG


title: Sample_B2_35

description: Barcode: AAGAGGCA-CCTAGAGT


title: Sample_B2_61

description: Barcode: TAAGGCGA-GAGCCTTA


title: Sample_B2_33

description: Barcode: GCTACGCT-CCTAGAGT


title: Sample_B2_48

description: Barcode: GTAGAGGA-CTATTAAG


title: Sample_B2_3

description: Barcode: AGGCAGAA-TCGACTAG


title: Sample_B2_42

description: Barcode: TAGGCATG-CTATTAAG


title: Sample_B2_43

description: Barcode: CTCTCTAC-CTATTAAG


title: Sample_B2_30

description: Barcode: TAGGCATG-CCTAGAGT


title: Sample_B2_2

description: Barcode: CGTACTAG-TCGACTAG


title: Sample_B2_36

description: Barcode: GTAGAGGA-CCTAGAGT


title: Sample_B2_32

description: Barcode: CAGAGAGG-CCTAGAGT


title: Sample_B2_54

description: Barcode: TAGGCATG-AAGGCTAT


title: Sample_OSKM_50

description: Barcode: AAGAGGCA-CTCTCTAT


title: Sample_B2_34

description: Barcode: CGAGGCTG-CCTAGAGT


title: Sample_B2_28

description: Barcode: TCCTGAGC-CCTAGAGT


title: Sample_B2_29

description: Barcode: GGACTCCT-CCTAGAGT


title: Sample_B2_26

description: Barcode: CGTACTAG-CCTAGAGT


title: Sample_B2_31

description: Barcode: CTCTCTAC-CCTAGAGT


title: Sample_B2_27

description: Barcode: AGGCAGAA-CCTAGAGT


title: Sample_B2_20

description: Barcode: CAGAGAGG-TTCTAGCT


title: Sample_B2_22

description: Barcode: CGAGGCTG-TTCTAGCT


title: Sample_B2_23

description: Barcode: AAGAGGCA-TTCTAGCT


title: Sample_B2_1

description: Barcode: TAAGGCGA-TCGACTAG


title: Sample_B2_18

description: Barcode: TAGGCATG-TTCTAGCT


title: Sample_B2_17

description: Barcode: GGACTCCT-TTCTAGCT


title: Sample_B2_21

description: Barcode: GCTACGCT-TTCTAGCT


title: Sample_B2_15

description: Barcode: AGGCAGAA-TTCTAGCT


title: Sample_B2_16

description: Barcode: TCCTGAGC-TTCTAGCT


title: Sample_B2_14

description: Barcode: CGTACTAG-TTCTAGCT


title: Sample_B2_25

description: Barcode: TAAGGCGA-CCTAGAGT


title: Sample_B1_9

description: Barcode: CCTAAGAC-TCGACTAG


title: Sample_B2_12

description: Barcode: GTAGAGGA-TCGACTAG


title: Sample_B2_13

description: Barcode: TAAGGCGA-TTCTAGCT


title: Sample_B2_11

description: Barcode: AAGAGGCA-TCGACTAG


title: Sample_B1_95

description: Barcode: TGCAGCTA-TTATGCGA


title: Sample_B1_96

description: Barcode: TCGACGTC-TTATGCGA


title: Sample_B1_92

description: Barcode: ACTGAGCG-TTATGCGA


title: Sample_B1_93

description: Barcode: CCTAAGAC-TTATGCGA


title: Sample_B2_24

description: Barcode: GTAGAGGA-TTCTAGCT


title: Sample_B1_91

description: Barcode: TAGCGCTC-TTATGCGA


title: Sample_B1_94

description: Barcode: CGATCAGT-TTATGCGA


title: Sample_B2_37

description: Barcode: TAAGGCGA-CTATTAAG


title: Sample_B2_19

description: Barcode: CTCTCTAC-TTCTAGCT


title: Sample_B1_8

description: Barcode: ACTGAGCG-TCGACTAG


title: Sample_B1_88

description: Barcode: CGGAGCCT-TTATGCGA


title: Sample_B1_86

description: Barcode: GGAGCTAC-TTATGCGA


title: Sample_B1_89

description: Barcode: TACGCTGC-TTATGCGA


title: Sample_B1_85

description: Barcode: ACTCGCTA-TTATGCGA


title: Sample_B2_10

description: Barcode: CGAGGCTG-TCGACTAG


title: Sample_B1_84

description: Barcode: TCGACGTC-GAGCCTTA


title: Sample_B1_80

description: Barcode: ACTGAGCG-GAGCCTTA


title: Sample_B2_8

description: Barcode: CAGAGAGG-TCGACTAG


title: Sample_B1_81

description: Barcode: CCTAAGAC-GAGCCTTA


title: Sample_B1_76

description: Barcode: CGGAGCCT-GAGCCTTA


title: Sample_B1_77

description: Barcode: TACGCTGC-GAGCCTTA


title: Sample_B1_75

description: Barcode: GCGTAGTA-GAGCCTTA


title: Sample_B1_73

description: Barcode: ACTCGCTA-GAGCCTTA


title: Sample_B1_78

description: Barcode: ATGCGCAG-GAGCCTTA


title: Sample_B1_7

description: Barcode: TAGCGCTC-TCGACTAG


title: Sample_B1_74

description: Barcode: GGAGCTAC-GAGCCTTA


title: Sample_B1_72

description: Barcode: TCGACGTC-AAGGCTAT


title: Sample_B1_71

description: Barcode: TGCAGCTA-AAGGCTAT


title: Sample_B1_70

description: Barcode: CGATCAGT-AAGGCTAT


title: Sample_B1_82

description: Barcode: CGATCAGT-GAGCCTTA


title: Sample_B1_69

description: Barcode: CCTAAGAC-AAGGCTAT


title: Sample_B1_90

description: Barcode: ATGCGCAG-TTATGCGA


title: Sample_B1_87

description: Barcode: GCGTAGTA-TTATGCGA


title: Sample_B1_67

description: Barcode: TAGCGCTC-AAGGCTAT


title: Sample_B1_83

description: Barcode: TGCAGCTA-GAGCCTTA


title: Sample_B1_6

description: Barcode: ATGCGCAG-TCGACTAG


title: Sample_B1_68

description: Barcode: ACTGAGCG-AAGGCTAT


title: Sample_B1_66

description: Barcode: ATGCGCAG-AAGGCTAT


title: Sample_B1_64

description: Barcode: CGGAGCCT-AAGGCTAT


title: Sample_B1_79

description: Barcode: TAGCGCTC-GAGCCTTA


title: Sample_B1_63

description: Barcode: GCGTAGTA-AAGGCTAT


title: Sample_B1_61

description: Barcode: ACTCGCTA-AAGGCTAT


title: Sample_B1_60

description: Barcode: TCGACGTC-CTATTAAG


title: Sample_B1_5

description: Barcode: TACGCTGC-TCGACTAG


title: Sample_B1_59

description: Barcode: TGCAGCTA-CTATTAAG


title: Sample_B1_56

description: Barcode: ACTGAGCG-CTATTAAG


title: Sample_B1_55

description: Barcode: TAGCGCTC-CTATTAAG


title: Sample_B1_65

description: Barcode: TACGCTGC-AAGGCTAT


title: Sample_B1_53

description: Barcode: TACGCTGC-CTATTAAG


title: Sample_B1_51

description: Barcode: GCGTAGTA-CTATTAAG


title: Sample_B1_52

description: Barcode: CGGAGCCT-CTATTAAG


title: Sample_B1_4

description: Barcode: CGGAGCCT-TCGACTAG


title: Sample_B1_50

description: Barcode: GGAGCTAC-CTATTAAG


title: Sample_B1_49

description: Barcode: ACTCGCTA-CTATTAAG


title: Sample_B1_47

description: Barcode: TGCAGCTA-GCGTAAGA


title: Sample_B1_3

description: Barcode: GCGTAGTA-TCGACTAG


title: Sample_B1_40

description: Barcode: CGGAGCCT-GCGTAAGA


title: Sample_B1_41

description: Barcode: TACGCTGC-GCGTAAGA


title: Sample_B1_45

description: Barcode: CCTAAGAC-GCGTAAGA


title: Sample_B1_39

description: Barcode: GCGTAGTA-GCGTAAGA


title: Sample_B1_48

description: Barcode: TCGACGTC-GCGTAAGA


title: Sample_B1_42

description: Barcode: ATGCGCAG-GCGTAAGA


title: Sample_B1_44

description: Barcode: ACTGAGCG-GCGTAAGA


title: Sample_B1_46

description: Barcode: CGATCAGT-GCGTAAGA


title: Sample_B1_38

description: Barcode: GGAGCTAC-GCGTAAGA


title: Sample_B1_37

description: Barcode: ACTCGCTA-GCGTAAGA


title: Sample_B1_58

description: Barcode: CGATCAGT-CTATTAAG


title: Sample_B1_57

description: Barcode: CCTAAGAC-CTATTAAG


title: Sample_B1_36

description: Barcode: TCGACGTC-CCTAGAGT


title: Sample_B1_54

description: Barcode: ATGCGCAG-CTATTAAG


title: Sample_B1_35

description: Barcode: TGCAGCTA-CCTAGAGT


title: Sample_B1_34

description: Barcode: CGATCAGT-CCTAGAGT


title: Sample_B1_30

description: Barcode: ATGCGCAG-CCTAGAGT


title: Sample_B1_33

description: Barcode: CCTAAGAC-CCTAGAGT


title: Sample_B1_32

description: Barcode: ACTGAGCG-CCTAGAGT


title: Sample_B1_2

description: Barcode: GGAGCTAC-TCGACTAG


title: Sample_B1_31

description: Barcode: TAGCGCTC-CCTAGAGT


title: Sample_B1_43

description: Barcode: TAGCGCTC-GCGTAAGA


title: Sample_B1_27

description: Barcode: GCGTAGTA-CCTAGAGT


title: Sample_B1_25

description: Barcode: ACTCGCTA-CCTAGAGT


title: Sample_B1_28

description: Barcode: CGGAGCCT-CCTAGAGT


title: Sample_B1_1

description: Barcode: ACTCGCTA-TCGACTAG


title: Sample_B1_13

description: Barcode: ACTCGCTA-TTCTAGCT


title: Sample_B1_21

description: Barcode: CCTAAGAC-TTCTAGCT


title: Sample_B1_26

description: Barcode: GGAGCTAC-CCTAGAGT


title: Sample_B2_85

description: Barcode: ACTCGCTA-CTCTCTAT


title: Sample_B1_23

description: Barcode: TGCAGCTA-TTCTAGCT


title: Sample_MA94

description: Barcode: CGAGGCTG-GCGTAAGA


title: Sample_B1_22

description: Barcode: CGATCAGT-TTCTAGCT


title: Sample_MA95

description: Barcode: AAGAGGCA-GCGTAAGA


title: Sample_B2_80

description: Barcode: CAGAGAGG-TTATGCGA


title: Sample_MA91

description: Barcode: CTCTCTAC-GCGTAAGA


title: Sample_MA93

description: Barcode: GCTACGCT-GCGTAAGA


title: Sample_B1_19

description: Barcode: TAGCGCTC-TTCTAGCT


title: Sample_B1_24

description: Barcode: TCGACGTC-TTCTAGCT


title: Sample_B1_62

description: Barcode: GGAGCTAC-AAGGCTAT


title: Sample_MA90

description: Barcode: TAGGCATG-GCGTAAGA


title: Sample_MA96

description: Barcode: GTAGAGGA-GCGTAAGA


title: Sample_MA8

description: Barcode: CAGAGAGG-CTCTCTAT


title: Sample_MA92

description: Barcode: CAGAGAGG-GCGTAAGA


title: Sample_MA88

description: Barcode: TCCTGAGC-GCGTAAGA


title: Sample_MA85

description: Barcode: TAAGGCGA-GCGTAAGA


title: Sample_MA87

description: Barcode: AGGCAGAA-GCGTAAGA


title: Sample_MA89

description: Barcode: GGACTCCT-GCGTAAGA


title: Sample_MA86

description: Barcode: CGTACTAG-GCGTAAGA


title: Sample_B1_29

description: Barcode: TACGCTGC-CCTAGAGT


title: Sample_B1_20

description: Barcode: ACTGAGCG-TTCTAGCT


title: Sample_MA9

description: Barcode: GCTACGCT-CTCTCTAT


title: Sample_MA83

description: Barcode: AAGAGGCA-CTAAGCCT


title: Sample_MA7

description: Barcode: CTCTCTAC-CTCTCTAT


title: Sample_MA80

description: Barcode: CAGAGAGG-CTAAGCCT


title: Sample_MA78

description: Barcode: TAGGCATG-CTAAGCCT


title: Sample_MA81

description: Barcode: GCTACGCT-CTAAGCCT


title: Sample_MA79

description: Barcode: CTCTCTAC-CTAAGCCT


title: Sample_MA77

description: Barcode: GGACTCCT-CTAAGCCT


title: Sample_MA75

description: Barcode: AGGCAGAA-CTAAGCCT


title: Sample_MA76

description: Barcode: TCCTGAGC-CTAAGCCT


title: Sample_MA72

description: Barcode: GTAGAGGA-AAGGAGTA


title: Sample_MA70

description: Barcode: CGAGGCTG-AAGGAGTA


title: Sample_MA73

description: Barcode: TAAGGCGA-CTAAGCCT


title: Sample_MA74

description: Barcode: CGTACTAG-CTAAGCCT


title: Sample_MA6

description: Barcode: TAGGCATG-CTCTCTAT


title: Sample_MA69

description: Barcode: GCTACGCT-AAGGAGTA


title: Sample_MA68

description: Barcode: CAGAGAGG-AAGGAGTA


title: Sample_MA64

description: Barcode: TCCTGAGC-AAGGAGTA


title: Sample_MA65

description: Barcode: GGACTCCT-AAGGAGTA


title: Sample_MA67

description: Barcode: CTCTCTAC-AAGGAGTA


title: Sample_MA66

description: Barcode: TAGGCATG-AAGGAGTA


title: Sample_MA63

description: Barcode: AGGCAGAA-AAGGAGTA


title: Sample_MA62

description: Barcode: CGTACTAG-AAGGAGTA


title: Sample_MA60

description: Barcode: GTAGAGGA-ACTGCATA


title: Sample_MA84

description: Barcode: GTAGAGGA-CTAAGCCT


title: Sample_MA59

description: Barcode: AAGAGGCA-ACTGCATA


title: Sample_MA82

description: Barcode: CGAGGCTG-CTAAGCCT


title: Sample_MA5

description: Barcode: GGACTCCT-CTCTCTAT


title: Sample_MA58

description: Barcode: CGAGGCTG-ACTGCATA


title: Sample_MA55

description: Barcode: CTCTCTAC-ACTGCATA


title: Sample_MA54

description: Barcode: TAGGCATG-ACTGCATA


title: Sample_MA57

description: Barcode: GCTACGCT-ACTGCATA


title: Sample_MA56

description: Barcode: CAGAGAGG-ACTGCATA


title: Sample_MA52

description: Barcode: TCCTGAGC-ACTGCATA


title: Sample_MA53

description: Barcode: GGACTCCT-ACTGCATA


title: Sample_MA71

description: Barcode: AAGAGGCA-AAGGAGTA


title: Sample_MA49

description: Barcode: TAAGGCGA-ACTGCATA


title: Sample_MA50

description: Barcode: CGTACTAG-ACTGCATA


title: Sample_MA4

description: Barcode: TCCTGAGC-CTCTCTAT


title: Sample_MA51

description: Barcode: AGGCAGAA-ACTGCATA


title: Sample_MA48

description: Barcode: GTAGAGGA-GTAAGGAG


title: Sample_MA61

description: Barcode: TAAGGCGA-AAGGAGTA


title: Sample_MA46

description: Barcode: CGAGGCTG-GTAAGGAG


title: Sample_MA45

description: Barcode: GCTACGCT-GTAAGGAG


title: Sample_MA43

description: Barcode: CTCTCTAC-GTAAGGAG


title: Sample_MA44

description: Barcode: CAGAGAGG-GTAAGGAG


title: Sample_MA47

description: Barcode: AAGAGGCA-GTAAGGAG


title: Sample_MA3

description: Barcode: AGGCAGAA-CTCTCTAT


title: Sample_MA42

description: Barcode: TAGGCATG-GTAAGGAG


title: Sample_MA40

description: Barcode: TCCTGAGC-GTAAGGAG


title: Sample_MA37

description: Barcode: TAAGGCGA-GTAAGGAG


title: Sample_MA41

description: Barcode: GGACTCCT-GTAAGGAG


title: Sample_MA38

description: Barcode: CGTACTAG-GTAAGGAG


title: Sample_MA36

description: Barcode: GTAGAGGA-AGAGTAGA


title: Sample_MA39

description: Barcode: AGGCAGAA-GTAAGGAG


title: Sample_MA34

description: Barcode: CGAGGCTG-AGAGTAGA


title: Sample_MA32

description: Barcode: CAGAGAGG-AGAGTAGA


title: Sample_MA35

description: Barcode: AAGAGGCA-AGAGTAGA


title: Sample_MA33

description: Barcode: GCTACGCT-AGAGTAGA


title: Sample_MA31

description: Barcode: CTCTCTAC-AGAGTAGA


title: Sample_MA30

description: Barcode: TAGGCATG-AGAGTAGA


title: Sample_MA29

description: Barcode: GGACTCCT-AGAGTAGA


title: Sample_MA28

description: Barcode: TCCTGAGC-AGAGTAGA


title: Sample_MA2

description: Barcode: CGTACTAG-CTCTCTAT


title: Sample_MA27

description: Barcode: AGGCAGAA-AGAGTAGA


title: Sample_MA26

description: Barcode: CGTACTAG-AGAGTAGA


title: Sample_MA25

description: Barcode: TAAGGCGA-AGAGTAGA


title: Sample_MA24

description: Barcode: GTAGAGGA-TATCCTCT


title: Sample_MA23

description: Barcode: AAGAGGCA-TATCCTCT


title: Sample_MA20

description: Barcode: CAGAGAGG-TATCCTCT


title: Sample_MA1

description: Barcode: TAAGGCGA-CTCTCTAT


title: Sample_MA16

description: Barcode: TCCTGAGC-TATCCTCT


title: Sample_MA21

description: Barcode: GCTACGCT-TATCCTCT


title: Sample_MA22

description: Barcode: CGAGGCTG-TATCCTCT


title: Sample_MA19

description: Barcode: CTCTCTAC-TATCCTCT


title: Sample_MA17

description: Barcode: GGACTCCT-TATCCTCT


title: Sample_MA14

description: Barcode: CGTACTAG-TATCCTCT


title: Sample_MA13

description: Barcode: TAAGGCGA-TATCCTCT


title: Sample_MA10

description: Barcode: CGAGGCTG-CTCTCTAT


title: Sample_MA12

description: Barcode: GTAGAGGA-CTCTCTAT


title: Sample_MA11

description: Barcode: AAGAGGCA-CTCTCTAT


title: Vector_36_S306_L001

description: single cells with these vectors were used as input

extract_protocol:
RNA-Seq libraries were prepared following the iCELL8 Single-Cell protocol (WaferGen Biosystems).
Nextera XT Library Preparation (Illumina) adapted for iCELL8 Single-Cell libraries (WaferGen Biosystems)

treatment_protocol: Cells were transduced with retroviral OSKM expression or control vectors followed by lentiviral shRNA vectors and selected with G418 and puromycin, respectively. At 16 days post-infection, cells were dispensed on the iCELL8 microchip.

tag: flow cell lane


title: Vector_40_S310_L002


title: Vector_39_S309_L001


title: Vector_37_S307_L002


title: Vector_37_S307_L001


title: Vector_38_S308_L002


title: Vector_40_S310_L001


title: Vector_36_S306_L002


title: Vector_35_S305_L002


title: Vector_39_S309_L002


title: Vector_38_S308_L001


title: Vector_34_S304_L002


title: Sample_MA18

description: Barcode: TAGGCATG-TATCCTCT


title: Vector_35_S305_L001


title: Vector_34_S304_L001


title: Vector_32_S302_L002


title: Vector_31_S301_L001


title: Vector_33_S303_L001


title: Vector_31_S301_L002


title: Vector_32_S302_L001


title: Sample_MA15

description: Barcode: AGGCAGAA-TATCCTCT


title: Vector_29_S299_L002


title: Vector_29_S299_L001


title: Vector_28_S298_L001


title: Vector_30_S300_L001


title: Vector_28_S298_L002


title: Vector_27_S297_L002


title: Vector_27_S297_L001


title: Vector_33_S303_L002


title: Vector_30_S300_L002


title: Vector_26_S296_L002


title: Vector_23_S293_L002


title: Vector_25_S295_L001


title: Vector_21_S291_L001


title: Vector_24_S294_L001


title: Vector_25_S295_L002


title: Vector_20_S290_L001


title: Vector_20_S290_L002


title: Vector_21_S291_L002


title: Vector_26_S296_L001


title: Vector_22_S292_L001


title: Vector_23_S293_L001


title: Vector_22_S292_L002


title: Vector_18_S288_L001


title: Vector_16_S286_L002


title: Vector_17_S287_L002


title: Vector_24_S294_L002


title: Vector_17_S287_L001


title: Vector_16_S286_L001


title: Vector_19_S289_L002


title: Vector_19_S289_L001


title: Vector_15_S285_L002


title: Vector_18_S288_L002


title: Vector_13_S283_L002


title: Vector_15_S285_L001


title: Vector_13_S283_L001


title: Vector_12_S282_L001


title: Vector_12_S282_L002


title: Vector_09_S279_L001


title: Vector_11_S281_L001


title: Vector_09_S279_L002


title: Vector_10_S280_L001


title: Vector_10_S280_L002


title: Vector_11_S281_L002


title: Vector_05_S275_L001


title: Vector_06_S276_L002


title: Vector_14_S284_L002


title: Vector_07_S277_L002


title: Vector_05_S275_L002


title: Vector_03_S273_L002


title: Vector_04_S274_L001


title: Vector_03_S273_L001


title: Vector_08_S278_L002


title: Vector_07_S277_L001


title: Vector_01_S271_L001


title: Vector_01_S271_L002


title: Vector_02_S272_L002


title: Pos_20_S20_L002

description: isolated RNA from a bulk population of these cells was used as input for preparation of the libraries


title: Vector_04_S274_L002


title: Vector_08_S278_L001


title: Vector_14_S284_L001


title: Pos_20_S20_L001


title: Pos_19_S19_L001


title: Vector_06_S276_L001


title: Pos_18_S18_L002


title: Pos_15_S15_L002


title: Pos_18_S18_L001


title: Pos_16_S16_L002


title: Pos_17_S17_L001


title: Pos_17_S17_L002


title: Vector_02_S272_L001


title: Pos_16_S16_L001


title: Pos_14_S14_L001


title: Pos_12_S12_L002


title: Pos_15_S15_L001


title: Pos_09_S9_L001


title: Pos_08_S8_L001


title: Pos_07_S7_L001


title: Pos_12_S12_L001


title: Pos_13_S13_L001


title: Pos_13_S13_L002


title: Pos_10_S10_L001


title: Pos_19_S19_L002


title: Pos_14_S14_L002


title: Pos_11_S11_L001


title: Pos_11_S11_L002


title: Pos_09_S9_L002


title: Pos_10_S10_L002


title: Pos_08_S8_L002


title: Pos_07_S7_L002


title: Pos_05_S5_L002


title: Pos_06_S6_L002


title: Pos_02_S2_L002


title: Pos_04_S4_L001


title: Pos_03_S3_L002


title: Pos_06_S6_L001


title: Pos_01_S1_L002


title: OSKM_UBE_39_S59_L002

value: OSKM + shUBE2E1 #1-2 vectors


title: OSKM_UBE_38_S58_L001


title: OSKM_UBE_40_S60_L001


title: OSKM_UBE_39_S59_L001


title: OSKM_UBE_33_S53_L002


title: Pos_05_S5_L001


title: Pos_04_S4_L002


title: Pos_01_S1_L001


title: Pos_02_S2_L001


title: OSKM_UBE_38_S58_L002


title: OSKM_UBE_37_S57_L001


title: Pos_03_S3_L001


title: OSKM_UBE_40_S60_L002


title: OSKM_UBE_35_S55_L002


title: OSKM_UBE_34_S54_L002


title: OSKM_UBE_35_S55_L001


title: OSKM_UBE_30_S50_L002


title: OSKM_UBE_32_S52_L002


title: OSKM_UBE_29_S49_L001


title: OSKM_UBE_36_S56_L002


title: OSKM_UBE_36_S56_L001


title: OSKM_UBE_34_S54_L001


title: OSKM_UBE_31_S51_L002


title: OSKM_UBE_32_S52_L001


title: OSKM_UBE_31_S51_L001


title: OSKM_UBE_25_S45_L002


title: OSKM_UBE_25_S45_L001


title: OSKM_UBE_29_S49_L002


title: OSKM_UBE_28_S48_L002


title: OSKM_UBE_37_S57_L002


title: OSKM_UBE_24_S44_L002


title: OSKM_UBE_33_S53_L001


title: OSKM_UBE_22_S42_L002


title: OSKM_UBE_27_S47_L002


title: OSKM_UBE_23_S43_L001


title: OSKM_UBE_26_S46_L002


title: OSKM_UBE_24_S44_L001


title: OSKM_UBE_30_S50_L001


title: OSKM_UBE_21_S41_L002


title: OSKM_UBE_21_S41_L001


title: OSKM_UBE_19_S39_L002


title: OSKM_UBE_20_S40_L001


title: OSKM_UBE_28_S48_L001


title: OSKM_UBE_27_S47_L001


title: OSKM_UBE_19_S39_L001


title: OSKM_UBE_26_S46_L001


title: OSKM_UBE_18_S38_L002


title: OSKM_UBE_20_S40_L002


title: OSKM_UBE_17_S37_L002


title: OSKM_UBE_18_S38_L001


title: OSKM_UBE_16_S36_L001


title: OSKM_UBE_17_S37_L001


title: OSKM_UBE_16_S36_L002


title: OSKM_UBE_15_S35_L002


title: OSKM_UBE_23_S43_L002


title: OSKM_UBE_15_S35_L001


title: OSKM_UBE_13_S33_L002


title: OSKM_UBE_14_S34_L001


title: OSKM_UBE_14_S34_L002


title: OSKM_UBE_13_S33_L001


title: OSKM_UBE_12_S32_L002


title: OSKM_UBE_22_S42_L001


title: OSKM_UBE_12_S32_L001


title: OSKM_UBE_11_S31_L001


title: OSKM_UBE_10_S30_L001


title: OSKM_UBE_10_S30_L002


title: OSKM_UBE_11_S31_L002


title: OSKM_UBE_09_S29_L002


title: OSKM_UBE_05_S25_L002


title: OSKM_UBE_05_S25_L001


title: OSKM_UBE_06_S26_L002


title: OSKM_UBE_04_S24_L001


title: OSKM_UBE_03_S23_L001


title: OSKM_UBE_02_S22_L001


title: OSKM_UBE_03_S23_L002


title: OSKM_UBE_01_S21_L002


title: OSKM_UBE_07_S27_L001


title: OSKM_UBE_09_S29_L001


title: OSKM_shp53_39_S99_L002

value: OSKM + shp53 vector


title: OSKM_shp53_40_S100_L001


title: OSKM_shp53_40_S100_L002


title: OSKM_UBE_01_S21_L001


title: OSKM_shp53_39_S99_L001


title: OSKM_UBE_06_S26_L001


title: OSKM_shp53_38_S98_L001


title: OSKM_shp53_38_S98_L002


title: OSKM_shp53_37_S97_L002


title: OSKM_UBE_08_S28_L001


title: OSKM_UBE_08_S28_L002


title: OSKM_shp53_35_S95_L001


title: OSKM_shp53_37_S97_L001


title: OSKM_shp53_36_S96_L002


title: OSKM_shp53_36_S96_L001


title: OSKM_shp53_34_S94_L002


title: OSKM_UBE_04_S24_L002


title: OSKM_shp53_35_S95_L002


title: OSKM_UBE_07_S27_L002


title: OSKM_UBE_02_S22_L002


title: OSKM_shp53_34_S94_L001


title: OSKM_shp53_33_S93_L001


title: OSKM_shp53_33_S93_L002


title: OSKM_shp53_31_S91_L002


title: OSKM_shp53_32_S92_L001


title: OSKM_shp53_31_S91_L001


title: OSKM_shp53_32_S92_L002


title: OSKM_shp53_29_S89_L002


title: OSKM_shp53_30_S90_L002


title: OSKM_shp53_30_S90_L001


title: OSKM_shp53_27_S87_L001


title: OSKM_shp53_29_S89_L001


title: OSKM_shp53_28_S88_L001


title: OSKM_shp53_27_S87_L002


title: OSKM_shp53_28_S88_L002


title: OSKM_shp53_26_S86_L002


title: OSKM_shp53_26_S86_L001


title: OSKM_shp53_25_S85_L002


title: OSKM_shp53_25_S85_L001


title: OSKM_shp53_24_S84_L002


title: OSKM_shp53_21_S81_L002


title: OSKM_shp53_24_S84_L001


title: OSKM_shp53_23_S83_L002


title: OSKM_shp53_20_S80_L002


title: OSKM_shp53_20_S80_L001


title: OSKM_shp53_19_S79_L002


title: OSKM_shp53_18_S78_L002


title: OSKM_shp53_17_S77_L001


title: OSKM_shp53_16_S76_L001


title: OSKM_shp53_19_S79_L001


title: OSKM_shp53_17_S77_L002


title: OSKM_shp53_15_S75_L002


title: OSKM_shp53_13_S73_L001


title: OSKM_shp53_15_S75_L001


title: OSKM_shp53_13_S73_L002


title: OSKM_shp53_18_S78_L001


title: OSKM_shp53_23_S83_L001


title: OSKM_shp53_14_S74_L002


title: OSKM_shp53_21_S81_L001


title: OSKM_shp53_22_S82_L002


title: OSKM_shp53_16_S76_L002


title: OSKM_shp53_11_S71_L002


title: OSKM_shp53_10_S70_L001


title: OSKM_shp53_14_S74_L001


title: OSKM_shp53_12_S72_L002


title: OSKM_shp53_09_S69_L001


title: OSKM_shp53_08_S68_L001


title: OSKM_shp53_12_S72_L001


title: OSKM_shp53_07_S67_L001


title: OSKM_shp53_22_S82_L001


title: OSKM_shp53_09_S69_L002


title: OSKM_shp53_06_S66_L002


title: OSKM_shp53_06_S66_L001


title: OSKM_shp53_05_S65_L001


title: OSKM_shp53_05_S65_L002


title: OSKM_shp53_11_S71_L001


title: OSKM_shp53_08_S68_L002


title: OSKM_shp53_10_S70_L002


title: OSKM_shp53_04_S64_L001


title: OSKM_shp53_04_S64_L002


title: OSKM_shp53_03_S63_L001


title: OSKM_shp53_03_S63_L002


title: OSKM_shp53_02_S62_L001


title: OSKM_shp53_02_S62_L002


title: OSKM_shp53_01_S61_L002


title: OSKM_shp53_01_S61_L001


title: OSKM_shp53_07_S67_L002


title: OSKM_shp21_38_S138_L002

value: OSKM + shp21 #1-2-3 vectors


title: OSKM_shp21_39_S139_L002


title: OSKM_shp21_40_S140_L001


title: OSKM_shp21_38_S138_L001


title: OSKM_shp21_37_S137_L002


title: OSKM_shp21_36_S136_L002


title: OSKM_shp21_36_S136_L001


title: OSKM_shp21_35_S135_L001


title: OSKM_shp21_35_S135_L002


title: OSKM_shp21_37_S137_L001


title: OSKM_shp21_40_S140_L002


title: OSKM_shp21_34_S134_L002


title: OSKM_shp21_34_S134_L001


title: OSKM_shp21_33_S133_L002


title: OSKM_shp21_31_S131_L002


title: OSKM_shp21_32_S132_L001


title: OSKM_shp21_33_S133_L001


title: OSKM_shp21_31_S131_L001


title: OSKM_shp21_32_S132_L002


title: OSKM_shp21_30_S130_L002


title: OSKM_shp21_39_S139_L001


title: OSKM_shp21_30_S130_L001


title: OSKM_shp21_29_S129_L002


title: OSKM_shp21_29_S129_L001


title: OSKM_shp21_28_S128_L002


title: OSKM_shp21_28_S128_L001


title: OSKM_shp21_27_S127_L002


title: OSKM_shp21_27_S127_L001


title: OSKM_shp21_26_S126_L002


title: OSKM_shp21_26_S126_L001


title: OSKM_shp21_25_S125_L001


title: OSKM_shp21_25_S125_L002


title: OSKM_shp21_23_S123_L001


title: OSKM_shp21_19_S119_L002


title: OSKM_shp21_18_S118_L001


title: OSKM_shp21_21_S121_L001


title: OSKM_shp21_18_S118_L002


title: OSKM_shp21_23_S123_L002


title: OSKM_shp21_16_S116_L002


title: OSKM_shp21_19_S119_L001


title: OSKM_shp21_22_S122_L001


title: OSKM_shp21_17_S117_L001


title: OSKM_shp21_17_S117_L002


title: OSKM_shp21_21_S121_L002


title: OSKM_shp21_20_S120_L002


title: OSKM_shp21_20_S120_L001


title: OSKM_shp21_24_S124_L001


title: OSKM_shp21_16_S116_L001


title: OSKM_shp21_24_S124_L002


title: OSKM_shp21_15_S115_L002


title: OSKM_shp21_14_S114_L002


title: OSKM_shp21_12_S112_L002


title: OSKM_shp21_13_S113_L002


title: OSKM_shp21_13_S113_L001


title: OSKM_shp21_12_S112_L001


title: OSKM_shp21_11_S111_L001


title: OSKM_shp21_11_S111_L002


title: OSKM_shp21_22_S122_L002


title: OSKM_shp21_10_S110_L002


title: OSKM_shp21_10_S110_L001


title: OSKM_shp21_09_S109_L002


title: OSKM_shp21_08_S108_L002


title: OSKM_shp21_05_S105_L002


title: OSKM_shp21_15_S115_L001


title: OSKM_shp21_14_S114_L001


title: OSKM_shp21_09_S109_L001


title: OSKM_shp21_07_S107_L002


title: OSKM_shp21_04_S104_L002


title: OSKM_shp21_04_S104_L001


title: OSKM_shp21_03_S103_L002


title: OSKM_shp21_06_S106_L002


title: OSKM_shp21_08_S108_L001


title: OSKM_shp21_05_S105_L001


title: OSKM_shp21_06_S106_L001


title: OSKM_shp21_03_S103_L001


title: OSKM_shp21_01_S101_L001


title: OSKM_shp21_02_S102_L002


title: OSKM_shp21_01_S101_L002


title: OSKM_shp21_02_S102_L001


title: OSKM_MYOT_39_S179_L001

value: OSKM + shMYOT #1-2 vectors


title: OSKM_MYOT_40_S180_L001


title: OSKM_MYOT_38_S178_L002


title: OSKM_MYOT_39_S179_L002


title: OSKM_MYOT_40_S180_L002


title: OSKM_MYOT_37_S177_L001


title: OSKM_MYOT_38_S178_L001


title: OSKM_MYOT_36_S176_L001


title: OSKM_MYOT_36_S176_L002


title: OSKM_MYOT_37_S177_L002


title: OSKM_shp21_07_S107_L001


title: OSKM_MYOT_33_S173_L001


title: OSKM_MYOT_34_S174_L001


title: OSKM_MYOT_35_S175_L002


title: OSKM_MYOT_32_S172_L001


title: OSKM_MYOT_34_S174_L002


title: OSKM_MYOT_29_S169_L001


title: OSKM_MYOT_31_S171_L001


title: OSKM_MYOT_30_S170_L002


title: OSKM_MYOT_29_S169_L002


title: OSKM_MYOT_33_S173_L002


title: OSKM_MYOT_28_S168_L002


title: OSKM_MYOT_27_S167_L001


title: OSKM_MYOT_27_S167_L002


title: OSKM_MYOT_30_S170_L001


title: OSKM_MYOT_28_S168_L001


title: OSKM_MYOT_31_S171_L002


title: OSKM_MYOT_24_S164_L001


title: OSKM_MYOT_24_S164_L002


title: OSKM_MYOT_23_S163_L002


title: OSKM_MYOT_26_S166_L002


title: OSKM_MYOT_22_S162_L002


title: OSKM_MYOT_22_S162_L001


title: OSKM_MYOT_21_S161_L002


title: OSKM_MYOT_23_S163_L001


title: OSKM_MYOT_32_S172_L002


title: OSKM_MYOT_35_S175_L001


title: OSKM_MYOT_21_S161_L001


title: OSKM_MYOT_20_S160_L002


title: OSKM_MYOT_26_S166_L001


title: OSKM_MYOT_25_S165_L001


title: OSKM_MYOT_19_S159_L001


title: OSKM_MYOT_25_S165_L002


title: OSKM_MYOT_17_S157_L002


title: OSKM_MYOT_19_S159_L002


title: OSKM_MYOT_20_S160_L001


title: OSKM_MYOT_16_S156_L001


title: OSKM_MYOT_18_S158_L001


title: OSKM_MYOT_13_S153_L002


title: OSKM_MYOT_14_S154_L002


title: OSKM_MYOT_15_S155_L002


title: OSKM_MYOT_17_S157_L001


title: OSKM_MYOT_15_S155_L001


title: OSKM_MYOT_18_S158_L002


title: OSKM_MYOT_12_S152_L002


title: OSKM_MYOT_16_S156_L002


title: OSKM_MYOT_13_S153_L001


title: OSKM_MYOT_14_S154_L001


title: OSKM_MYOT_11_S151_L001


title: OSKM_MYOT_11_S151_L002


title: OSKM_MYOT_10_S150_L001


title: OSKM_MYOT_09_S149_L002


title: OSKM_MYOT_09_S149_L001


title: OSKM_MYOT_08_S148_L002


title: OSKM_MYOT_08_S148_L001


title: OSKM_MYOT_07_S147_L002


title: OSKM_MYOT_05_S145_L002


title: OSKM_MYOT_06_S146_L001


title: OSKM_MYOT_06_S146_L002


title: OSKM_MYOT_04_S144_L002


title: OSKM_MYOT_05_S145_L001


title: OSKM_MYOT_03_S143_L001


title: OSKM_MYOT_04_S144_L001


title: OSKM_MYOT_12_S152_L001


title: OSKM_MYOT_02_S142_L002


title: OSKM_MYOT_01_S141_L001


title: OSKM_MYOT_01_S141_L002


title: OSKM_MYOT_03_S143_L002


title: OSKM_MYOT_07_S147_L001


title: OSKM_MTOR_39_S219_L002

value: OSKM + shMTOR #1-2-3 vectors


title: OSKM_MYOT_02_S142_L001


title: OSKM_MTOR_38_S218_L002


title: OSKM_MYOT_10_S150_L002


title: OSKM_MTOR_38_S218_L001


title: OSKM_MTOR_37_S217_L002


title: OSKM_MTOR_39_S219_L001


title: OSKM_MTOR_35_S215_L002


title: OSKM_MTOR_37_S217_L001


title: OSKM_MTOR_36_S216_L002


title: OSKM_MTOR_34_S214_L002


title: OSKM_MTOR_35_S215_L001


title: OSKM_MTOR_40_S220_L002


title: OSKM_MTOR_31_S211_L001


title: OSKM_MTOR_32_S212_L002


title: OSKM_MTOR_32_S212_L001


title: OSKM_MTOR_31_S211_L002


title: OSKM_MTOR_34_S214_L001


title: OSKM_MTOR_33_S213_L002


title: OSKM_MTOR_29_S209_L002


title: OSKM_MTOR_28_S208_L002


title: OSKM_MTOR_28_S208_L001


title: OSKM_MTOR_29_S209_L001


title: OSKM_MTOR_30_S210_L002


title: OSKM_MTOR_26_S206_L002


title: OSKM_MTOR_25_S205_L002


title: OSKM_MTOR_27_S207_L002


title: OSKM_MTOR_25_S205_L001


title: OSKM_MTOR_27_S207_L001


title: OSKM_MTOR_24_S204_L001


title: OSKM_MTOR_26_S206_L001


title: OSKM_MTOR_23_S203_L001


title: OSKM_MTOR_22_S202_L002


title: OSKM_MTOR_22_S202_L001


title: OSKM_MTOR_40_S220_L001


title: OSKM_MTOR_33_S213_L001


title: OSKM_MTOR_20_S200_L002


title: OSKM_MTOR_30_S210_L001


title: OSKM_MTOR_21_S201_L001


title: OSKM_MTOR_20_S200_L001


title: OSKM_MTOR_19_S199_L002


title: OSKM_MTOR_19_S199_L001


title: OSKM_MTOR_36_S216_L001


title: OSKM_MTOR_17_S197_L002


title: OSKM_MTOR_24_S204_L002


title: OSKM_MTOR_15_S195_L001


title: OSKM_MTOR_17_S197_L001


title: OSKM_MTOR_18_S198_L001


title: OSKM_MTOR_23_S203_L002


title: OSKM_MTOR_14_S194_L001


title: OSKM_MTOR_13_S193_L001


title: OSKM_MTOR_12_S192_L002


title: OSKM_MTOR_21_S201_L002


title: OSKM_MTOR_13_S193_L002


title: OSKM_MTOR_14_S194_L002


title: OSKM_MTOR_11_S191_L002


title: OSKM_MTOR_11_S191_L001


title: OSKM_MTOR_16_S196_L002


title: OSKM_MTOR_10_S190_L002


title: OSKM_MTOR_10_S190_L001


title: OSKM_MTOR_09_S189_L002


title: OSKM_MTOR_18_S198_L002


title: OSKM_MTOR_08_S188_L002


title: OSKM_MTOR_08_S188_L001


title: OSKM_MTOR_16_S196_L001


title: OSKM_MTOR_07_S187_L001


title: OSKM_MTOR_15_S195_L002


title: OSKM_MTOR_06_S186_L002


title: OSKM_MTOR_06_S186_L001


title: OSKM_MTOR_05_S185_L002


title: OSKM_MTOR_04_S184_L002


title: OSKM_MTOR_05_S185_L001


title: OSKM_MTOR_01_S181_L002


title: OSKM_MTOR_12_S192_L001


title: OSKM_MTOR_03_S183_L002


title: OSKM_MTOR_04_S184_L001


title: OSKM_MTOR_03_S183_L001


title: OSKM_MTOR_02_S182_L002


title: OSKM_38_S258_L002


title: OSKM_39_S259_L001


title: OSKM_40_S260_L002


title: OSKM_40_S260_L001


title: OSKM_37_S257_L002


title: OSKM_38_S258_L001


title: OSKM_36_S256_L002


title: OSKM_MTOR_07_S187_L002


title: OSKM_37_S257_L001


title: OSKM_36_S256_L001


title: OSKM_34_S254_L002


title: OSKM_35_S255_L001


title: OSKM_34_S254_L001


title: OSKM_32_S252_L001


title: OSKM_32_S252_L002


title: OSKM_33_S253_L001


title: OSKM_MTOR_01_S181_L001


title: OSKM_MTOR_02_S182_L001


title: OSKM_31_S251_L002


title: OSKM_31_S251_L001


title: OSKM_35_S255_L002


title: OSKM_30_S250_L001


title: OSKM_29_S249_L002


title: OSKM_30_S250_L002


title: OSKM_39_S259_L002


title: OSKM_29_S249_L001


title: OSKM_28_S248_L001


title: OSKM_28_S248_L002


title: OSKM_26_S246_L002


title: OSKM_27_S247_L001


title: OSKM_26_S246_L001


title: OSKM_25_S245_L001


title: OSKM_25_S245_L002


title: OSKM_24_S244_L002


title: OSKM_24_S244_L001


title: OSKM_33_S253_L002


title: OSKM_23_S243_L002


title: OSKM_23_S243_L001


title: OSKM_22_S242_L001


title: OSKM_22_S242_L002


title: OSKM_21_S241_L002


title: OSKM_19_S239_L001


title: OSKM_21_S241_L001


title: OSKM_20_S240_L001


title: OSKM_19_S239_L002


title: OSKM_18_S238_L001


title: OSKM_20_S240_L002


title: OSKM_17_S237_L002


title: OSKM_18_S238_L002


title: OSKM_27_S247_L002


title: OSKM_15_S235_L001


title: OSKM_15_S235_L002


title: OSKM_17_S237_L001


title: OSKM_16_S236_L001


title: OSKM_MTOR_09_S189_L001


title: OSKM_16_S236_L002


title: OSKM_13_S233_L001


title: OSKM_13_S233_L002


title: OSKM_14_S234_L001


title: OSKM_10_S230_L002


title: OSKM_14_S234_L002


title: OSKM_12_S232_L002


title: OSKM_09_S229_L002


title: OSKM_10_S230_L001


title: OSKM_09_S229_L001


title: OSKM_08_S228_L001


title: OSKM_07_S227_L002


title: OSKM_07_S227_L001


title: OSKM_08_S228_L002


title: OSKM_05_S225_L002


title: OSKM_06_S226_L001


title: OSKM_05_S225_L001


title: OSKM_03_S223_L002


title: OSKM_04_S224_L002


title: OSKM_04_S224_L001


title: OSKM_03_S223_L001


title: OSKM_02_S222_L002


title: OSKM_02_S222_L001


title: Neg_10_S270_L002

description: H2O was used as input

source_name: no cell

value: no cell

value: no vector


title: OSKM_12_S232_L001


title: OSKM_01_S221_L001


title: OSKM_01_S221_L002


title: OSKM_11_S231_L002


title: Neg_10_S270_L001

description: H2O was used as input


title: Neg_09_S269_L001

description: H2O was used as input


title: OSKM_11_S231_L001


title: Neg_07_S267_L001

description: H2O was used as input


title: Neg_08_S268_L002

description: H2O was used as input


title: Neg_07_S267_L002

description: H2O was used as input


title: Neg_06_S266_L002

description: H2O was used as input


title: Neg_05_S265_L002

description: H2O was used as input


title: OSKM_06_S226_L002


title: Neg_06_S266_L001

description: H2O was used as input


title: Neg_05_S265_L001

description: H2O was used as input


title: Neg_04_S264_L001

description: H2O was used as input


title: Neg_03_S263_L002

description: H2O was used as input


title: Neg_04_S264_L002

description: H2O was used as input


title: Neg_03_S263_L001

description: H2O was used as input


title: Neg_02_S262_L002

description: H2O was used as input


title: Neg_09_S269_L002

description: H2O was used as input


title: Neg_02_S262_L001

description: H2O was used as input


title: icell8 458

data_processing:
Sequence reads in Fastq format were generated from Illunina basecalls using Illumina's bcl2fastq (version 2.17).
Sequence reads were aligned to Ensembl GRCh37 genome build and gene models retrieved from Illumina's igenome using Tophat2 (v 2.0.11).
Aligned reads were counted whithin exons using Rsubread (verion 1.22.3)
Genome_build: h19
Supplementary_files_format_and_content: counts of genes


title: icell8 452


title: icell8 454


title: icell8 459


title: icell8 455


title: Neg_01_S261_L001

description: H2O was used as input


title: Neg_01_S261_L002

description: H2O was used as input


title: icell8 453


title: Neg_08_S268_L001

description: H2O was used as input


title: icell8 460

value: control vector


title: icell8 448


title: icell8 446


title: icell8 449


title: icell8 456


title: icell8 457


title: icell8 451


title: icell8 442


title: icell8 443

description:
Neg_29
H2O was used as input


title: icell8 444


title: icell8 450


title: icell8 447


title: icell8 441

description:
Pos_27
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 440

description:
Pos_29
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 438

description:
Pos_28
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 439


title: icell8 435


title: icell8 437


title: icell8 432

description:
Pos_30
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 436


title: icell8 431


title: icell8 428

description:
Neg_28
H2O was used as input


title: icell8 429


title: icell8 426


title: icell8 425


title: icell8 430


title: icell8 434

description:
Neg_30
H2O was used as input


title: icell8 445


title: icell8 424


title: icell8 422


title: icell8 421


title: icell8 418


title: icell8 416


title: icell8 417


title: icell8 427


title: icell8 420


title: icell8 414


title: icell8 415


title: icell8 412


title: icell8 419


title: icell8 413


title: icell8 433


title: icell8 409


title: icell8 410


title: icell8 411


title: icell8 407


title: icell8 408


title: icell8 423


title: icell8 406


title: icell8 400


title: icell8 405


title: icell8 404

description:
Neg_22
H2O was used as input


title: icell8 402


title: icell8 403


title: icell8 399


title: icell8 397


title: icell8 395


title: icell8 394


title: icell8 393


title: icell8 392

description:
Neg_23
H2O was used as input


title: icell8 389


title: icell8 391


title: icell8 390


title: icell8 396


title: icell8 386


title: icell8 387

description:
Neg_24
H2O was used as input


title: icell8 388

description:
Pos_24
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 398