title: CAEBV, scRNA-seq

city: Bunkyo

first: Miki

last: Ando

state: Tokyo

address: Hongo 2-1-1

department: Hematology

country: Japan

institute: Juntendo University

data_processing:
Raw data were demultiplexed and quantified using Cell Ranger (v7.0.0, 10X Genomics). Downstream analyses used the Seurat R package (version 4.1.1).
Assembly: hg18
Supplementary files format and content: tsv
Supplementary files format and content: mtx

source_name: Peripehral blood

extract_protocol:
Approximately 0.12 x 10^6 cells, viability >80%, were used.Sample was suspended in 50 μl of ice - chilled phosphate-buffered saline + 0.04% bovine serum albumin (Thermo Fisher Scientific) and processed to yield scRNA-seq libraries using 10X Chromium Next Gem Single Cell 3’ Reagent Kits v 3.1 (Dual Index) (10x Genomics, Pleasanton, CA) following standard manufacturer protocols. A Bio-Rad T100 thermal cycler (Bio-Rad, Hercules, CA) was used for PCR. After library quality was assessed using Bioanalyzer 2100 (Agilent, Tokyo, Japan), samples were sequenced (Macrogen, Seoul, South Korea) on the HiseqX (Illumina, San Diego, CA) platform at a depth of 2,000,000 pair reads/sample.
Library was prepared using Chromium Single Cell 3ʹ v3.1 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ v3.1 protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ v3.1 protocol (10x Genomics).

value: Peripehral blood

value: CAEBV

tag: subject status

value: chronic active Epstein-Barr virus disease (CAEBV) patient


title: 203081450113_R08C01,Whole blood, Late-mid pregnancy, ID_26

status: Public on Jul 21 2025

type: genomic

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 117-2194 Health Sciences Mall

department: Faculty of Medicine

country: Canada

institute: University of British Columbia

description: ID_26, late-mid pregnancy timepoint

hyb_protocol: DNA was bisulfite converted using EZ-96 DNA Methylation kits (Zymo Research, Irvine, CA), hybridized to the MethylationEPIC BeadChip Infinium microarray v1.0 B5 (EPICv1) array using standard Illumina protocol

scan_protocol: Arrays were scanned with an Illumina HiScan

data_processing:
Noob, functional normalized, and batch corrected
[processed value definition]  DNA methylation beta value

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Whole blood

label_protocol: Standard Illumnia protocol

extract_protocol: Genomic DNA was extracted from whole blood using Qiagen DNeasy Kit according to standard instructions

tag: tissue

value: Whole blood

tag: pregnancytimepoint

value: Late-mid pregnancy

tag: maternalid

tag: Sex

value: F


title: 203081450078_R07C01,Whole blood, Late-mid pregnancy, ID_25

description: ID_25, late-mid pregnancy timepoint


title: 203081450078_R04C01,Whole blood, Late-mid pregnancy, ID_24

description: ID_24, late-mid pregnancy timepoint


title: 203081450078_R02C01,Whole blood, Late-mid pregnancy, ID_23

description: ID_23, late-mid pregnancy timepoint


title: 203081450078_R08C01,Whole blood, Late-mid pregnancy, ID_22

description: ID_22, late-mid pregnancy timepoint


title: 203081450024_R04C01,Whole blood, Late-mid pregnancy, ID_19

description: ID_19, late-mid pregnancy timepoint


title: 203081450024_R07C01,Whole blood, Late-mid pregnancy, ID_20

description: ID_20, late-mid pregnancy timepoint


title: 203081450037_R07C01,Whole blood, Late-mid pregnancy, ID_21

description: ID_21, late-mid pregnancy timepoint


title: 203081450024_R08C01,Whole blood, Late-mid pregnancy, ID_17

description: ID_17, late-mid pregnancy timepoint


title: 203081450024_R02C01,Whole blood, Late-mid pregnancy, ID_18

description: ID_18, late-mid pregnancy timepoint


title: 203081450037_R01C01,Whole blood, Late-mid pregnancy, ID_14

description: ID_14, late-mid pregnancy timepoint


title: 203081450022_R04C01,Whole blood, Late-mid pregnancy, ID_12

description: ID_12, late-mid pregnancy timepoint


title: 203081450022_R02C01,Whole blood, Late-mid pregnancy, ID_11

description: ID_11, late-mid pregnancy timepoint


title: D-NT2 Native DFF-ChIP Exp5 H3.3

status: Public on Jul 22 2025

type: SRA

city: Iowa City

first: Jeffery

middle: L

last: Meier

state: IA

address: SW34 GH, Department of Internal Medicine, University of Iowa. 200 Hawkins Drive

department: Departments of Internal Medicine and Epidemiology

country: USA

institute: University of Iowa and Iowa City Veterans Affairs Health Care System

description:
Library name: DFF-ChIP Exp5 D-NT2 H3.3
instrument model: Element Aviti24

library_source: genomic

data_processing:
Adapter trimming using trim_galore 0.6.
Alignment of trimmed reads to hg38 and FJ616285.1 using bowtie 1.2.2.
Deduplication of fragments based on their unique molecular index tags using awk and bash.
Conversion of deduped bed files into bedGraph and bigwig using bedtools genomecov and kentUtils bedGraphToBigWig programs.
Assembly: hg38, FJ616285.1
Supplementary files format and content: bigwig files containing pileup of DFF ChIP-Seq fragments across whole HCMV genomes.

growth_protocol: Culturing NT2 in DMEM with 10% FBS results in a sizeable proportion of cells expressing HCMV MIE protein within 24 hours of infection. Adding 10 µM retinoic acid (Sigma) further differentiates these cells. For the experiments in differentiated NT2 (D-NT2), the NT2 were cultured with retinoic acid for 10 days. On the day before the infection, the growth medium containing retinoic acid was removed, and the cells were cultured in DMEM with 10% FBS. HFF were isolated and cultured as described in the manuscript. Cells were maintained in Minimum Essential Medium and grown to confluence for at least one week before infection. All HFF used for these studies were at passage number ≤ 6.

extract_protocol:
Rapid nuclei isolation steps were performed on wet ice using ice-cold buffers as previously described (M. Li et al. 2020). Following DFF digestion, nuclei were lightly sonicated for 20s and the soluble material was immunoprecipitated with antibodies.
Library construction is detailed in the manuscript.

tag: cell line

tag: cell type

value: Neuronal cells

tag: chip antibody

value: H3.3 (Active Motif, 94491)

tag: batch

value: HCMV Towne BAC Infected 96 h


title: HFF Native DFF-ChIP Exp5 TBP

description:
Library name: DFF-ChIP Exp5 HFF TBP
instrument model: Element Aviti24

source_name: HFF

value: HFF

value: Human Foreskin Fibroblasts

value: TBP (Abcam, ab51841)


title: HFF Native DFF-ChIP Exp5 H3.3

description:
Library name: DFF-ChIP Exp5 HFF H3.3
instrument model: Element Aviti24


title: D-NT2 Native DFF-ChIP Exp5 TBP

description:
Library name: DFF-ChIP Exp5 D-NT2 TBP
instrument model: Element Aviti24


title: HFF Native DFF-ChIP Exp5 H3K4me3

description:
Library name: DFF-ChIP Exp5 HFF H3K4me3
instrument model: Element Aviti24

value: H3K4me3 (Abcam, ab8580)


title: 203077630102_R02C01,Whole blood, Late-mid pregnancy, ID_9

description: ID_9, late-mid pregnancy timepoint


title: D-NT2 Native DFF-ChIP Exp5 H3K4me3

description:
Library name: DFF-ChIP Exp5 D-NT2 H3K4me3
instrument model: Element Aviti24


title: 203077630102_R08C01,Whole blood, Late-mid pregnancy, ID_8

description: ID_8, late-mid pregnancy timepoint


title: 203077630122_R03C01,Whole blood, Late-mid pregnancy, ID_7

description: ID_7, late-mid pregnancy timepoint


title: 203077630122_R01C01,Whole blood, Late-mid pregnancy, ID_6

description: ID_6, late-mid pregnancy timepoint


title: 203072530208_R04C01,Whole blood, Late-mid pregnancy, ID_5

description: ID_5, late-mid pregnancy timepoint


title: 203072530208_R02C01,Whole blood, Late-mid pregnancy, ID_4

description: ID_4, late-mid pregnancy timepoint


title: 203081450113_R07C01,Whole blood, Late-mid pregnancy, ID_3

description: ID_3, late-mid pregnancy timepoint


title: 203077630086_R01C01,Whole blood, Late-mid pregnancy, ID_1

description: ID_1, late-mid pregnancy timepoint


title: 203077630086_R05C01,Whole blood, Late-mid pregnancy, ID_2

description: ID_2, late-mid pregnancy timepoint


title: 203081450037_R03C01,Whole blood, Late-mid pregnancy, ID_15

description: ID_15, late-mid pregnancy timepoint


title: 203081450023_R07C01,Whole blood, Late-mid pregnancy, ID_16

description: ID_16, late-mid pregnancy timepoint


title: 203081450023_R08C01,Whole blood, Late-mid pregnancy, ID_13

description: ID_13, late-mid pregnancy timepoint


title: 203081450113_R05C01,Whole blood, Early pregnancy, ID_25

description: ID_25, early pregnancy timepoint

value: Early pregnancy


title: 203081450023_R01C01,Whole blood, Late-mid pregnancy, ID_10

description: ID_10, late-mid pregnancy timepoint


title: 203081450113_R04C01,Whole blood, Early pregnancy, ID_24

description: ID_24, early pregnancy timepoint


title: 203081450078_R06C01,Whole blood, Early pregnancy, ID_22

description: ID_22, early pregnancy timepoint


title: 203081450113_R02C01,Whole blood, Early pregnancy, ID_23

description: ID_24, early pregnancy timepoint


title: 203081450078_R05C01,Whole blood, Early pregnancy, ID_21

description: ID_21, early pregnancy timepoint


title: 203081450024_R03C01,Whole blood, Early pregnancy, ID_15

description: ID_15, early pregnancy timepoint


title: 203081450024_R06C01,Whole blood, Early pregnancy, ID_17

description: ID_17, early pregnancy timepoint


title: 203081450037_R02C01,Whole blood, Early pregnancy, ID_18

description: ID_18, early pregnancy timepoint


title: 203081450037_R04C01,Whole blood, Early pregnancy, ID_19

description: ID_19, early pregnancy timepoint


title: 203081450037_R05C01,Whole blood, Early pregnancy, ID_20

description: ID_20, early pregnancy timepoint


title: 203081450023_R06C01,Whole blood, Early pregnancy, ID_13

description: ID_13, early pregnancy timepoint


title: 203081450024_R01C01,Whole blood, Early pregnancy, ID_14

description: ID_14, early pregnancy timepoint


title: 203081450113_R06C01,Whole blood, Early pregnancy, ID_26

description: ID_26, early pregnancy timepoint


title: 203081450023_R04C01,Whole blood, Early pregnancy, ID_12

description: ID_12, early pregnancy timepoint


title: 203081450022_R01C01,Whole blood, Early pregnancy, ID_10

description: ID_10, early pregnancy timepoint


title: 203077630102_R06C01,Whole blood, Early pregnancy, ID_8

description: ID_8, early pregnancy timepoint


title: 203077630122_R02C01,Whole blood, Early pregnancy, ID_9

description: ID_9, early pregnancy timepoint


title: 203081450023_R02C01,Whole blood, Early pregnancy, ID_11

description: ID_11, early pregnancy timepoint


title: 203077630086_R04C01,Whole blood, Early pregnancy, ID_5

description: ID_5, early pregnancy timepoint


title: 203077630102_R03C01,Whole blood, Early pregnancy, ID_7

description: ID_7, early pregnancy timepoint


title: 203077630086_R02C01,Whole blood, Early pregnancy, ID_4

description: ID_4, early pregnancy timepoint


title: 203077630102_R01C01,Whole blood, Early pregnancy, ID_6

description: ID_6, early pregnancy timepoint


title: 203072530208_R07C01,Whole blood, Early pregnancy, ID_3

description: ID_3, early pregnancy timepoint


title: 203072530208_R01C01,Whole blood, Early pregnancy, ID_1

description: ID_1, early pregnancy timepoint


title: 203072530208_R05C01,Whole blood, Early pregnancy, ID_2

description: ID_2, early pregnancy timepoint


title: MV411_Day17_Rep5_DR30

city: Newcastle

first: Heather

last: Lee

state: NSW

address: University Drive, Callaghan

country: Australia

institute: The University of Newcastle

data_processing:
bisulfite libraries were processed using Bismark (v0.22.3) and as previously described [Hunt, K. V. et al. sTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs. Scientific Reports (2022)] [Hunt, K. V. et al.  Protocol for targeted analysis of transposable element methylation levels and transcriptome in single cells using scTEM-seq. Protocol Exchange  (2022)].
After initial demultiplexing of primary Illumina indexes, Cutadapt (v2.10) [18] was used to demultiplex pools based on custom secondary indexes
Commands –g and -G were used to pass named forward and reverse index lists as a .fasta file to Cutadapt for demultiplexing
Bisulfite reads were trimmed using Trim Galore (v0.6.5). 10bp was trimmed from both the 5’ and 3’ ends to remove oligo sequences from reads.
Reads were mapped to Bowtie2 (v 2.4.1) indexed human genome (GRCh38) non-directionally and as paired end using Bismark (v0.22.3)
The methylation extraction module from Bismark was then used to produce coverage files (.cov) for methylation analysis.
Assembly: GRCh38
Supplementary files format and content: Bismark output file: genome-wide CpG methylation reports (CpG.cov.gz) are tab-delimited, use 1-based genomic coordinates and are in the following format: <chromosome> <position> <methylation rate>
Library strategy: TEM-seq

source_name: Peripheral blood

growth_protocol: Cell lines were maintained in tissue culture flasks (Greiner Bio-One) at 37°C, 5% CO2, and sub-cultured at 500,000 cells/mL every 2-3 days with fresh medium.  HL-60 cells were maintained in Iscove's Modified Dulbecco's media supplemented with 4mM GlutaMAX and 10% Fetal Bovine Serum (FBS). MOLM-13 and MV-4-11 cells were maintained in Roswell Park Memorial Institute 1640 media supplemented with 2mM GlutaMAX and 10% FBS.

extract_protocol:
Samples from of all (pooled) colonies per well, were collected by resuspending the MethoCult Optimum media (and colonies) in 3mL of standard culture media (IMDM or RPMI), centrifuging at 200xg for 5 mins, and resuspending the cell pellet in 20-50µL RLT PLUS buffer, before storage at −80°C.
TEM-seq of pooled colonies was performed as previously described using 5-10µL of cell lysate as input for bisulphite conversion, and 29 cycles for SINE Alu amplification. [Hunt, K. V. et al.  Protocol for targeted analysis of transposable element methylation levels and transcriptome in single cells using scTEM-seq. Protocol Exchange  (2022)]
[Hunt, K. V. et al. sTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs. Scientific Reports (2022)] [Hunt, K. V. et al.  Protocol for targeted analysis of transposable element methylation levels and transcriptome in single cells using scTEM-seq. Protocol Exchange  (2022)]

treatment_protocol:
Cell lines were treated with HMAs at various doses in suspension culture, every 24h for 72h total. All cell lines were treated with 100nM decitabine (DAC; Selleckchem #S1200), HL-60 cells were treated with 2000nM azacytidine (AZA; Selleckchem # S1782), and MOLM-13 and MV-4-11 cells were treated with 500nM AZA. Untreated cells (UNT) were given an equal volume of 0.1% DMSO in UltraPure™ DNase/RNase-Free Distilled Water (Thermo Fisher Scientific) and served as a control.
After treatment in suspension culture, cells were seeded in MethoCult Optimum (H4034; STEMCELL Technologies Inc.) at 500 cells/well in 6-well plates, with or without 30µM rosuvastatin (ROS) added to the MethoCult. Samples treated with ROS after DAC (DR30), with ROS only (R30), or without ROS (AZA, DAC or Unt) were then cultured at 37°C, 5% CO2 for a further 14 days. Cells were then collected at days 6, 10 or 17 of colony formation, as indicated.

value: Peripheral blood

value: macrophage

tag: disease/cancer type

value: Biphenotypic B Myelomonocytic Leukemia

value: Male

tag: age

tag: replicate

tag: day

tag: treatment

tag: plate

tag: experiment name

value: statin combination


title: MV411_Day17_Rep5_R30


title: MV411_Day17_Rep4_DR30


title: MV411_Day17_Rep5_DAC


title: MV411_Day17_Rep4_Unt


title: MV411_Day17_Rep5_Unt


title: MV411_Day17_Rep4_DAC


title: MV411_Day17_Rep4_R30


title: MV411_Day17_Rep1_DAC

value: HL-MV-TEM


title: MV411_Day17_Rep1_DR30


title: MV411_Day17_Rep1_R30


title: MV411_Day17_Rep1_Unt


title: MV411_Day10_Rep3_AZA, t-c

value: time-course


title: MV411_Day17_Rep1_DAC, t-c


title: MV411_Day6_Rep2_AZA, t-c


title: MV411_Day17_Rep2_Unt, t-c


title: MV411_Day6_Rep3_DAC, t-c


title: MV411_Day10_Rep1_Unt, t-c


title: MV411_Day10_Rep3_DAC, t-c


title: MV411_Day17_Rep3_AZA, t-c


title: MV411_Day6_Rep3_Unt, t-c


title: MV411_Day6_Rep2_DAC, t-c


title: MV411_Day10_Rep2_AZA, t-c


title: MV411_Day6_Rep1_AZA, t-c


title: MV411_Day10_Rep3_Unt, t-c


title: MV411_Day10_Rep2_DAC, t-c


title: MV411_Day17_Rep1_Unt, t-c


title: MV411_Day17_Rep2_AZA, t-c


title: MV411_Day6_Rep3_AZA, t-c


title: MV411_Day17_Rep3_Unt, t-c


title: MV411_Day10_Rep2_Unt, t-c


title: MV411_Day17_Rep1_AZA, t-c


title: MOLM13_Day17_Rep4_Unt

value: acute myeloid leukemia

value: Acute myeloid leukemia (M5a)


title: MOLM13_Day17_Rep3_R30


title: MOLM13_Day17_Rep4_R30


title: MOLM13_Day17_Rep2_D30


title: MV411_Day6_Rep1_Unt, t-c


title: MOLM13_Day17_Rep3_DAC


title: MOLM13_Day17_Rep3_Unt


title: MV411_Day17_Rep3_DAC, t-c


title: MOLM13_Day17_Rep3_DR30


title: MOLM13_Day17_Rep4_DR30


title: MOLM13_Day17_Rep2_Unt


title: MOLM13_Day17_Rep2_DR30


title: MV411_Day6_Rep2_Unt, t-c


title: MOLM13_Day17_Rep4_DAC


title: MV411_Day6_Rep1_DAC, t-c


title: MOLM13_Day17_Rep1_DR30

value: MO-TEM


title: MOLM13_Day17_Rep2_DAC


title: MV411_Day17_Rep2_DAC, t-c


title: MOLM13_Day10_Rep3_AZA, t-c


title: MOLM13_Day6_Rep3_DAC, t-c


title: MOLM13_Day6_Rep2_AZA, t-c


title: MOLM13_Day17_Rep1_DAC, t-c


title: MOLM13_Day6_Rep3_Unt, t-c


title: MOLM13_Day10_Rep3_DAC, t-c


title: MOLM13_Day10_Rep1_Unt, t-c


title: MOLM13_Day17_Rep2_Unt, t-c


title: MOLM13_Day6_Rep2_DAC, t-c


title: MOLM13_Day10_Rep2_AZA, t-c


title: MV411_Day10_Rep1_AZA, t-c


title: MOLM13_Day17_Rep3_DAC, t-c


title: MOLM13_Day17_Rep1_DAC


title: MOLM13_Day10_Rep1_AZA, t-c


title: MOLM13_Day10_Rep2_DAC, t-c


title: MOLM13_Day6_Rep1_AZA, t-c


title: MOLM13_Day6_Rep2_Unt, t-c


title: MOLM13_Day6_Rep1_DAC, t-c


title: MOLM13_Day17_Rep3_Unt, t-c


title: MOLM13_Day10_Rep3_Unt, t-c


title: MOLM13_Day6_Rep3_AZA, t-c


title: MOLM13_Day17_Rep3_AZA, t-c


title: MOLM13_Day10_Rep2_Unt, t-c


title: MOLM13_Day17_Rep1_AZA, t-c


title: MOLM13_Day6_Rep1_Unt, t-c


title: MOLM13_Day10_Rep1_DAC, t-c


title: HL60_Day17_Rep4_R30

value: promyeloblast

value: Acute promyelocytic leukemia

value: Female


title: HL60_Day17_Rep4_Unt


title: HL60_Day17_Rep4_DAC


title: MOLM13_Day17_Rep2_AZA, t-c


title: HL60_Day17_Rep1_R30


title: HL60_Day17_Rep2_R30


title: HL60_Day17_Rep3_DAC


title: HL60_Day17_Rep2_DAC


title: HL60_Day17_Rep3_DR30


title: HL60_Day17_Rep1_DAC


title: HL60_Day17_Rep1_DR30


title: HL60_Day17_Rep2_DR30


title: MOLM13_Day17_Rep2_DAC, t-c


title: HL60_Day17_Rep3_Unt


title: HL60_Day17_Rep2_Unt


title: HL60_Day17_Rep1_Unt


title: HL60_Day17_Rep3_R30


title: HL60_Day17_Rep1_DAC, t-c


title: HL60_Day10_Rep3_AZA, t-c


title: HL60_Day17_Rep2_Unt, t-c


title: HL60_Day17_Rep1_Unt, t-c


title: HL60_Day10_Rep2_AZA, t-c


title: HL60_Day10_Rep3_Unt, t-c


title: HL60_Day10_Rep2_DAC, t-c


title: HL60_Day9_Rep3_AZA, t-c


title: HL60_Day10_Rep2_Unt, t-c


title: HL60_Day9_Rep2_AZA, t-c


title: HL60_Day17_Rep3_AZA, t-c


title: HL60_Day10_Rep1_Unt, t-c


title: HL60_Day9_Rep1_AZA, t-c


title: HL60_Day17_Rep2_AZA, t-c


title: HL60_Day17_Rep3_DAC, t-c


title: HL60_Day9_Rep3_Unt, t-c


title: HL60_Day9_Rep2_DAC, t-c


title: HL60_Day9_Rep1_DAC, t-c


title: HL60_Day17_Rep1_AZA, t-c


title: HL60_Day17_Rep2_DAC, t-c


title: HL60_Day10_Rep3_DAC, t-c


title: H10_MV_R2_P2, AZA

data_processing:
Bisulfite libraries were processed using Bismark (v0.22.3) and as previously described [Hunt, K. V. et al. sTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs. Scientific Reports (2022)] [Hunt, K. V. et al.  Protocol for targeted analysis of transposable element methylation levels and transcriptome in single cells using scTEM-seq. Protocol Exchange  (2022)].
After initial demultiplexing of primary Illumina indexes, Cutadapt (v2.10) [18] was used to demultiplex pools based on custom secondary indexes
Commands –g and -G were used to pass named forward and reverse index lists as a .fasta file to Cutadapt for demultiplexing
Bisulfite reads were trimmed using Trim Galore (v0.6.5). 10bp was trimmed from both the 5’ and 3’ ends to remove oligo sequences from reads.
Reads were mapped to Bowtie2 (v 2.4.1) indexed human genome (GRCh38) non-directionally and as paired end using Bismark (v0.22.3)
The methylation extraction module from Bismark was then used to produce coverage files (.cov) for methylation analysis. We excluded cells with coverage of less than 500 unique annotated TE (SINE-Alu) sites.
Assembly: GRCh38
Supplementary files format and content: Bismark output file: genome-wide CpG methylation reports (CpG.cov.gz) are tab-delimited, use 1-based genomic coordinates and are in the following format: <chromosome> <position> <methylation rate>
Library strategy: scTEM-Seq

growth_protocol: Cell lines (MOLM-13 and MV-4-11) were maintained in tissue culture flasks (Greiner Bio-One) at 37°C, 5% CO2, and sub-cultured at 500,000 cells/mL every 2-3 days with fresh medium. MOLM-13 and MV-4-11 cells were maintained in Roswell Park Memorial Institute 1640 media supplemented with 2mM GlutaMAX and 10% FBS.

extract_protocol:
At 72 hours, viable (propidium iodide negative) single cells were isolated by Fluoresence activated cell sorting (FACS) and sorted into 2.5µL of RLT PLUS buffer (Qiagen) containing 2.5U SUPERas-In (Thermo Fisher Scientific) in LoBind 96-well full skirted plates (Eppendorf) using indexed sorting on a FACS Aria II (BD Biosciences). Plates were sealed and briefly centrifuged before storage at -80°C for sequencing analyses.
scTEM-seq library preparation was performed as previously described. [Hunt, K. V. et al. sTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs. Scientific Reports (2022)]
[Hunt, K. V. et al. sTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs. Scientific Reports (2022)] [Hunt, K. V. et al.  Protocol for targeted analysis of transposable element methylation levels and transcriptome in single cells using scTEM-seq. Protocol Exchange  (2022)]

treatment_protocol: Cell lines were treated with HMAs at various doses in suspension culture, every 24h for 72h total. MOLM-13 and MV-4-11 were treated with 100nM decitabine (DAC; Selleckchem #S1200), or 500nM azacytidine (AZA; Selleckchem # S1782). Untreated cells (Unt) were given an equal volume of 0.1% DMSO in UltraPure™ DNase/RNase-Free Distilled Water (Thermo Fisher Scientific) and served as a control.

tag: disease

tag: protocol

value: TEM-Seq

value: azacytidine


title: HL60_Day9_Rep1_Unt, t-c

tag: tissue


title: HL60_Day17_Rep3_Unt, t-c


title: HL60_Day10_Rep1_DAC, t-c


title: H04_MV_R2_P2, AZA


title: HL60_Day9_Rep3_DAC, t-c


title: H01_MV_R2_P2, Unt

value: untreated


title: G10_MV_R2_P2, AZA


title: G05_MV_R2_P2, AZA


title: G03_MV_R2_P2, AZA


title: F11_MV_R2_P2, AZA


title: HL60_Day9_Rep2_Unt, t-c


title: G04_MV_R2_P2, AZA


title: F06_MV_R2_P2, AZA


title: HL60_Day10_Rep1_AZA, t-c


title: 203081450024_R05C01,Whole blood, Early pregnancy, ID_16

description: ID_16, early pregnancy timepoint

value: Whole blood

tag: pregnancytimepoint

value: Early pregnancy

value: F


title: E12_MV_R2_P2, Unt

value: Peripheral blood

value: macrophage

value: Biphenotypic B Myelomonocytic Leukemia


title: E09_MV_R2_P2, AZA

value: Male


title: E05_MV_R2_P2, AZA


title: F03_MV_R2_P2, AZA


title: F02_MV_R2_P2, AZA


title: C10_MV_R2_P2, DAC

value: decitabine


title: B01_MV_R2_P2, Unt


title: B06_MV_R2_P2, DAC


title: D10_MV_R2_P2, DAC


title: D12_MV_R2_P2, Unt


title: D05_MV_R2_P2, DAC


title: B12_MV_R2_P2, Unt


title: D09_MV_R2_P2, DAC


title: C05_MV_R2_P2, DAC


title: B04_MV_R2_P2, DAC


title: D03_MV_R2_P2, DAC


title: H11_MV_R2_P1, AZA


title: B08_MV_R2_P2, DAC


title: C04_MV_R2_P2, DAC


title: E04_MV_R2_P2, AZA


title: D04_MV_R2_P2, DAC


title: A03_MV_R2_P2, DAC


title: C12_MV_R2_P2, Unt


title: E01_MV_R2_P2, Unt


title: D02_MV_R2_P2, DAC


title: D01_MV_R2_P2, Unt


title: C02_MV_R2_P2, DAC


title: B05_MV_R2_P2, DAC


title: C09_MV_R2_P2, DAC


title: E10_MV_R2_P1, AZA


title: D04_MV_R2_P1, DAC


title: E04_MV_R2_P1, AZA


title: C02_MV_R2_P1, DAC


title: F01_MV_R2_P1, Unt


title: D01_MV_R2_P1, Unt


title: H05_MV_R2_P1, AZA


title: E01_MV_R2_P1, Unt


title: B05_MV_R2_P1, DAC


title: H08_MV_R2_P1, AZA


title: E03_MV_R2_P1, AZA


title: H02_MV_R2_P1, AZA


title: H07_MV_R2_P1, AZA


title: G05_MV_R2_P1, AZA


title: G03_MV_R2_P1, AZA


title: E06_MV_R2_P1, AZA


title: F02_MV_R2_P1, AZA


title: B10_MV_R2_P1, DAC


title: G10_MV_R2_P1, AZA


title: C01_MV_R2_P1, Unt


title: C03_MV_R2_P1, DAC


title: H04_MV_R2_P1, AZA


title: C05_MV_R2_P1, DAC


title: A03_MV_R2_P1, DAC


title: B03_MV_R2_P1, DAC


title: H06_MV_R1_P2, AZA


title: H02_MV_R1_P2, AZA


title: A08_MV_R2_P1, DAC


title: H09_MV_R1_P2, AZA


title: H03_MV_R1_P2, AZA


title: G07_MV_R1_P2, AZA


title: H10_MV_R1_P2, AZA


title: A02_MV_R2_P1, DAC


title: B04_MV_R2_P1, DAC


title: G08_MV_R1_P2, AZA


title: H05_MV_R1_P2, AZA


title: G09_MV_R1_P2, AZA


title: G10_MV_R1_P2, AZA


title: A09_MV_R2_P1, DAC


title: G12_MV_R1_P2, Unt


title: H08_MV_R1_P2, AZA


title: H11_MV_R1_P2, AZA


title: H01_MV_R1_P2, Unt


title: G11_MV_R1_P2, AZA


title: H07_MV_R1_P2, AZA


title: H04_MV_R1_P2, AZA


title: G06_MV_R1_P2, AZA


title: G04_MV_R1_P2, AZA


title: F08_MV_R1_P2, AZA


title: G05_MV_R1_P2, AZA


title: F09_MV_R1_P2, AZA


title: G01_MV_R1_P2, Unt


title: F05_MV_R1_P2, AZA


title: F10_MV_R1_P2, AZA


title: F11_MV_R1_P2, AZA


title: F02_MV_R1_P2, AZA


title: G03_MV_R1_P2, AZA


title: E10_MV_R1_P2, AZA


title: F12_MV_R1_P2, Unt


title: E09_MV_R1_P2, AZA


title: F03_MV_R1_P2, AZA


title: F01_MV_R1_P2, Unt


title: E12_MV_R1_P2, Unt


title: E08_MV_R1_P2, AZA


title: E07_MV_R1_P2, AZA


title: G02_MV_R1_P2, AZA


title: F07_MV_R1_P2, AZA


title: F04_MV_R1_P2, AZA


title: F06_MV_R1_P2, AZA


title: E06_MV_R1_P2, AZA


title: E05_MV_R1_P2, AZA


title: E01_MV_R1_P2, Unt


title: E02_MV_R1_P2, AZA


title: D12_MV_R1_P2, Unt


title: E04_MV_R1_P2, AZA


title: D10_MV_R1_P2, DAC


title: E03_MV_R1_P2, AZA


title: D09_MV_R1_P2, DAC


title: D06_MV_R1_P2, DAC


title: D04_MV_R1_P2, DAC


title: D07_MV_R1_P2, DAC


title: D02_MV_R1_P2, DAC


title: D05_MV_R1_P2, DAC


title: D01_MV_R1_P2, Unt


title: D03_MV_R1_P2, DAC


title: C12_MV_R1_P2, Unt


title: C10_MV_R1_P2, DAC


title: C08_MV_R1_P2, DAC


title: C09_MV_R1_P2, DAC


title: C06_MV_R1_P2, DAC


title: C07_MV_R1_P2, DAC


title: C04_MV_R2_P1, DAC


title: C05_MV_R1_P2, DAC


title: C04_MV_R1_P2, DAC


title: B11_MV_R1_P2, DAC


title: B12_MV_R1_P2, Unt


title: C03_MV_R1_P2, DAC


title: B08_MV_R1_P2, DAC


title: C02_MV_R1_P2, DAC


title: B07_MV_R1_P2, DAC


title: C01_MV_R1_P2, Unt


title: B01_MV_R1_P2, Unt


title: A12_MV_R1_P2, Unt


title: A09_MV_R1_P2, DAC


title: B02_MV_R1_P2, DAC


title: B06_MV_R1_P2, DAC


title: B10_MV_R1_P2, DAC


title: A06_MV_R1_P2, DAC


title: A11_MV_R1_P2, DAC


title: A05_MV_R1_P2, DAC


title: A03_MV_R1_P2, DAC


title: A02_MV_R1_P2, DAC


title: H09_MV_R1_P1, AZA


title: H01_MV_R1_P1, Unt


title: A04_MV_R1_P2, DAC


title: D08_MV_R1_P2, DAC


title: G09_MV_R1_P1, AZA


title: C04_MO_R2_P4, DAC

value: acute myeloid leukemia


title: G01_MO_R2_P4, Unt

value: Acute myeloid leukemia (M5a)


title: C05_MO_R2_P4, DAC


title: F03_MO_R2_P4, AZA


title: H02_MO_R2_P4, AZA


title: H04_MO_R2_P4, AZA


title: A03_MV_R1_P1, DAC


title: E02_MO_R2_P4, AZA


title: F10_MO_R2_P3, AZA


title: F02_MO_R2_P4, AZA


title: H09_MO_R2_P3, AZA


title: A09_MV_R1_P1, DAC


title: F02_MO_R2_P3, AZA


title: G01_MO_R2_P3, Unt


title: H03_MO_R2_P4, AZA


title: H10_MO_R2_P4, AZA


title: F01_MO_R2_P4, Unt


title: B09_MV_R1_P1, DAC


title: F01_MO_R2_P3, Unt


title: H01_MO_R2_P4, Unt


title: G04_MO_R2_P4, AZA


title: H02_MO_R2_P3, AZA


title: C01_MO_R2_P3, Unt


title: H11_MO_R1_P2, AZA


title: H07_MO_R1_P2, AZA


title: H03_MO_R1_P2, AZA


title: G12_MO_R1_P2, Unt


title: G05_MO_R1_P2, AZA


title: G11_MO_R1_P2, AZA


title: H02_MO_R1_P2, AZA


title: H08_MO_R1_P2, AZA


title: G10_MO_R1_P2, AZA


title: G07_MO_R1_P2, AZA


title: G08_MO_R1_P2, AZA


title: H09_MO_R1_P2, AZA


title: H04_MO_R1_P2, AZA


title: H05_MO_R1_P2, AZA


title: G09_MO_R1_P2, AZA


title: G04_MO_R1_P2, AZA


title: G06_MO_R1_P2, AZA


title: H01_MO_R1_P2, Unt


title: G03_MO_R1_P2, AZA


title: F12_MO_R1_P2, Unt


title: G02_MO_R1_P2, AZA


title: G01_MO_R1_P2, Unt


title: H10_MO_R1_P2, AZA


title: F10_MO_R1_P2, AZA


title: F08_MO_R1_P2, AZA


title: H06_MO_R1_P2, AZA


title: F02_MO_R1_P2, AZA


title: F06_MO_R1_P2, AZA


title: E10_MO_R1_P2, AZA


title: E05_MO_R1_P2, AZA


title: E01_MO_R1_P2, Unt


title: E06_MO_R1_P2, AZA


title: E12_MO_R1_P2, Unt


title: F04_MO_R1_P2, AZA


title: D04_MO_R1_P2, DAC


title: F01_MO_R1_P2, Unt


title: E04_MO_R1_P2, AZA


title: E02_MO_R1_P2, AZA


title: D10_MO_R1_P2, DAC


title: D03_MO_R1_P2, DAC


title: D12_MO_R1_P2, Unt


title: D05_MO_R1_P2, DAC


title: F05_MO_R1_P2, AZA


title: D06_MO_R1_P2, DAC


title: D02_MO_R1_P2, DAC


title: D01_MO_R1_P2, Unt


title: F03_MO_R1_P2, AZA


title: E03_MO_R1_P2, AZA


title: C12_MO_R1_P2, Unt


title: C10_MO_R1_P2, DAC


title: C06_MO_R1_P2, DAC


title: C05_MO_R1_P2, DAC


title: C09_MO_R1_P2, DAC


title: C03_MO_R1_P2, DAC


title: C02_MO_R1_P2, DAC


title: C01_MO_R1_P2, Unt


title: C04_MO_R1_P2, DAC


title: B09_MO_R1_P2, DAC


title: B10_MO_R1_P2, DAC


title: B07_MO_R1_P2, DAC


title: B11_MO_R1_P2, DAC


title: B03_MO_R1_P2, DAC


title: B05_MO_R1_P2, DAC


title: B06_MO_R1_P2, DAC


title: B12_MO_R1_P2, Unt


title: B08_MO_R1_P2, DAC


title: B02_MO_R1_P2, DAC


title: A12_MO_R1_P2, Unt


title: A11_MO_R1_P2, DAC


title: A09_MO_R1_P2, DAC


title: A10_MO_R1_P2, DAC


title: A07_MO_R1_P2, DAC


title: A05_MO_R1_P2, DAC


title: A03_MO_R1_P2, DAC


title: A04_MO_R1_P2, DAC


title: H8_MO_R1_P1, AZA


title: H9_MO_R1_P1, AZA


title: B04_MO_R1_P2, DAC


title: H10_MO_R1_P1, AZA


title: H5_MO_R1_P1, AZA


title: H6_MO_R1_P1, AZA


title: H3_MO_R1_P1, AZA


title: H4_MO_R1_P1, AZA


title: G11_MO_R1_P1, AZA


title: G9_MO_R1_P1, AZA


title: G8_MO_R1_P1, AZA


title: A08_MO_R1_P2, DAC


title: G7_MO_R1_P1, AZA


title: G6_MO_R1_P1, AZA


title: A06_MO_R1_P2, DAC


title: 6h, LL37, rep1

type: RNA

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

description: Gene expression data from human keratinocyte

hyb_protocol: The arrays were incubated in a GeneChip Hybridization Oven 645 for 16 hours at 45°C. The arrays were washed and stained on the GeneChip Fluidics Station 450 using GeneChip Hybridization, Wash, and Stain Kit (Applied Biosystems) by running FS450_0007 protocol.

scan_protocol: Array were scanned with GeneChip Scanner 3000 (Applied Biosystem)

data_processing: Data were analyzed in R using oligo and limma packages. clariomshumanhttranscriptcluster.db is used to annotate expressionset. lmFit used to fit linear model for each gene, followed by eBayes for differentially expressed gene analysis.

label: biotinylated

molecule: total RNA

source_name: Normal human skin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Normal human epidermal keratinocytes (NHEK) were isolated skin biopsies and cultured in Gibco Keratinocyte-SFM Medium with L-glutamine, supplemented with 0.4% bovine pituitary extract 0.1% human epidermal growth factor and 1% Penicillin-Streptomycin. Cell passage ranging from 4 to 6 were used.

extract_protocol: RNA was extracted using RNAeasy kit as per manufacturer's instruction.

treatment_protocol: Keratinocytes were treated with or without human cathelicidin peptide LL-37 for a period of 6-hours.

value: Normal human epidermal keratinocyte


title: A02_MO_R1_P2, DAC


title: H11_MO_R1_P1, AZA


title: G4_MO_R1_P1, AZA


title: G5_MO_R1_P1, AZA


title: H7_MO_R1_P1, AZA


title: G2_MO_R1_P1, AZA


title: F10_MO_R1_P1, AZA


title: H1_MO_R1_P1, Unt


title: F8_MO_R1_P1, AZA


title: F6_MO_R1_P1, AZA


title: F4_MO_R1_P1, AZA


title: G1_MO_R1_P1, Unt


title: G3_MO_R1_P1, AZA


title: G10_MO_R1_P1, AZA


title: F7_MO_R1_P1, AZA


title: F3_MO_R1_P1, AZA


title: F2_MO_R1_P1, AZA


title: F1_MO_R1_P1, Unt


title: E11_MO_R1_P1, AZA


title: E10_MO_R1_P1, AZA


title: E8_MO_R1_P1, AZA


title: E7_MO_R1_P1, AZA


title: E9_MO_R1_P1, AZA


title: E6_MO_R1_P1, AZA


title: E3_MO_R1_P1, AZA


title: E5_MO_R1_P1, AZA


title: E2_MO_R1_P1, AZA


title: F5_MO_R1_P1, AZA


title: E1_MO_R1_P1, Unt


title: D11_MO_R1_P1, DAC


title: F9_MO_R1_P1, AZA


title: E4_MO_R1_P1, AZA


title: 6h, LL37, rep3


title: D9_MO_R1_P1, DAC


title: F11_MO_R1_P1, AZA


title: D8_MO_R1_P1, DAC


title: 6h, LL37, rep2


title: D6_MO_R1_P1, DAC


title: D5_MO_R1_P1, DAC


title: D4_MO_R1_P1, DAC


title: D10_MO_R1_P1, DAC


title: D3_MO_R1_P1, DAC


title: D1_MO_R1_P1, Unt


title: 6h,unstim, rep2


title: D2_MO_R1_P1, DAC


title: 6h,unstim, rep3


title: C11_MO_R1_P1, DAC


title: C10_MO_R1_P1, DAC


title: C7_MO_R1_P1, DAC


title: C6_MO_R1_P1, DAC


title: C8_MO_R1_P1, DAC


title: C3_MO_R1_P1, DAC


title: C4_MO_R1_P1, DAC


title: 6h,unstim, rep1


title: C1_MO_R1_P1, Unt


title: B11_MO_R1_P1, DAC


title: B9_MO_R1_P1, DAC


title: C5_MO_R1_P1, DAC


title: B7_MO_R1_P1, DAC


title: B10_MO_R1_P1, DAC


title: B6_MO_R1_P1, DAC


title: B4_MO_R1_P1, DAC


title: B3_MO_R1_P1, DAC


title: C2_MO_R1_P1, DAC


title: B2_MO_R1_P1, DAC


title: B1_MO_R1_P1, Unt


title: A11_MO_R1_P1, DAC


title: B8_MO_R1_P1, DAC


title: A8_MO_R1_P1, DAC


title: A7_MO_R1_P1, DAC


title: A6_MO_R1_P1, DAC


title: A3_MO_R1_P1, DAC


title: A5_MO_R1_P1, DAC


title: A4_MO_R1_P1, DAC


title: A2_MO_R1_P1, DAC


title: H10_MV411_colonies_rep3, CpG

data_processing:
bisulfite libraries were processed using Bismark (v0.22.3) and as previously described [Hunt, K. V. et al. sTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs. Scientific Reports (2022)] [Hunt, K. V. et al.  Protocol for targeted analysis of transposable element methylation levels and transcriptome in single cells using scTEM-seq. Protocol Exchange  (2022)].
After initial demultiplexing of primary Illumina indexes, Cutadapt (v2.10) [18] was used to demultiplex pools based on custom secondary indexes
Commands –g and -G were used to pass named forward and reverse index lists as a .fasta file to Cutadapt for demultiplexing
Bisulfite reads were trimmed using Trim Galore (v0.6.5). 10bp was trimmed from both the 5’ and 3’ ends to remove oligo sequences from reads.
Reads were mapped to Bowtie2 (v 2.4.1) indexed human genome (GRCh38) non-directionally and as paired end using Bismark (v0.22.3)
The methylation extraction module from Bismark was then used to produce coverage files (.cov) for methylation analysis.
Assembly: GRCh38
Supplementary files format and content: Bismark output file: genome-wide CpG methylation reports (CpG.cov.gz) are tab-delimited, use 1-based genomic coordinates and are in the following format: <chromosome> <position> <methylation rate>
Following demultiplexing, squencing runs with multiple sequencing lanes per read were concatenated into single R1 and R2 fastq files, per sample using zcat and gzip.
Raw reads were trimmed in pair-end mode using Trim Galore (v0.6.5) and Cutadapt (v2.10), retaining unpaired reads.
Hisat2 (v2.1.0) was used to map and align trimmed and unpaired reads using default parameters (--phred33) to the human reference genome build (GRCh38), and samtools (v1.10) was used to sort by coordinate and generate bam files.
TEtranscripts (v2.2.1) was used to obtain raw gene and transposable element countreateds from unique and ambiguously aligned reads (bam files) using TEcountreated with the flags '--sortByPos --mode multi’. The GTF files used were generated as follows: 1) TEs (http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/rmsk.txt.gz; USCS repeating element Repeat Masker; hg38; 2021-09-03) and 2) genes (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_30/gencode.v30.annotation.gtf.gz; gencode Release 30; GRCh38.p12; 2019-04-08). To ensure the GTF files worked with TEtranscripts the gene GTF (from gencode) was updated by converting ‘M’ to ‘MT’ for mitochondrial genes in the chromosome column and removal of ‘Chr’ preceding each chromosome number. The TE GTF was generated from the repeat mask file  using the conversion tool from the TEtranscripts developers (http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/makeTEgtf.pl.gz) ‘perl makeTEgtf.pl -c 6 -s 7 -e 8 -o 10 -t 11 -n hg38_rmsk -f 13 -C 12 -S 2 rmsk.txt >> hg38_rmsk_TE.gtf’ and removing ‘chr’ from chromosome names ‘sed 's/chr//' hg38_rmsk_TE.gtf > hg38_rmsk_TE_NoChr.gtf’.    TEtranscripts the gene GTF (from gencode) was updated by converting ‘M’ to ‘MT’ for mitochondrial
Individual sample counts from TEtranscripts were collated into a single countreated table (tab-deliminated) and updated with relevant gene information from the gene GTF file.
Assembly: GRCh38
Supplementary files format and content: Count table (tab-deliminated) compiled from TEtranscripts results. First column contains gene (ensembl ID) and transposable element (TE) ID and column two contains hgnc symbol equiavelnt (gene IDs). Columns 3-7 contains TE information and columns 7-13  contains gene informations. Countreateds for individual samples are contained in column 14 onwards.
Library strategy: TEM-Seq

growth_protocol:
Cell lines were maintained in tissue culture flasks (Greiner Bio-One) at 37°C, 5% CO2, and sub-cultured at 500,000 cells/mL every 2-3 days with fresh medium.  HL-60 cells were maintained in Iscove's Modified Dulbecco's media supplemented with 4mM GlutaMAX and 10% Fetal Bovine Serum (FBS). MOLM-13 and MV-4-11 cells were maintained in Roswell Park Memorial Institute 1640 media supplemented with 2mM GlutaMAX and 10% FBS.
Treated cells were seeded in MethoCult Optimum (H4034; STEMCELL Technologies Inc.) at 500 cells/well in 6-well plates. Cells were then cultured at 37°C, 5% CO2 for 14 days to allow colony formation. Wells containing colonies were imaged using Cytation3 (Biotek). Individual colonies were manually plucked using a 20µL pipette tip into 100µL of media, centrifuged at 200xg for 5 mins, and then resuspended in 20µL of RLT PLUS buffer before storage at −80°C.

extract_protocol:
Individual colonies were manually plucked using a 20µL pipette tip into 100µL of media, centrifuged at 200xg for 5 mins, and then resuspended in 20µL of RLT PLUS buffer before storage at −80°C. Lysates from single colonies (HL-60: 7.5µL; MOLM-13 and MV-4-11: 2.5µL) were used to separate genomic DNA and mRNA by G&T separation and as previously described following 'scTEM-seq for low-input samples' [Hunt, K. V. et al. sTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs. Scientific Reports (2022)] [Hunt, K. V. et al.  Protocol for targeted analysis of transposable element methylation levels and transcriptome in single cells using scTEM-seq. Protocol Exchange  (2022)].
Single colony TEM-seq and parallel RNA-seq analysis was performed as described, with minor modifications. During single colony TEM-seq library preparation, the number of SINE Alu amplification cycles was reduced to 29. For RNA-seq analysis, 15 cycles of cDNA amplification were used. [Hunt, K. V. et al.  Protocol for targeted analysis of transposable element methylation levels and transcriptome in single cells using scTEM-seq. Protocol Exchange  (2022)]

treatment_protocol: Cell lines were treated with HMAs at various doses in suspension culture, every 24h for 72h total. All cell lines were treated with 100nM decitabine (DAC; Selleckchem #S1200), HL-60 cells were treated with 2000nM azacytidine (AZA; Selleckchem # S1782), and MOLM-13 and MV-4-11 cells were treated with 500nM AZA. Untreated cells (UNT) were given an equal volume of 0.1% DMSO in UltraPure™ DNase/RNase-Free Distilled Water (Thermo Fisher Scientific) and served as a control.

tag: paired sample_id

tag: processing protocol


title: H1_MV411_colonies_rep3, CpG

tag: cell line

tag: Sex


title: H11_MV411_colonies_rep3, CpG

tag: cell type


title: H3_MV411_colonies_rep3, CpG

tag: batch


title: H5_MV411_colonies_rep3, CpG

tag: disease/cancer type


title: H12_MV411_colonies_rep3, CpG

tag: age


title: H4_MV411_colonies_rep3, CpG


title: D7_MO_R1_P1, DAC


title: H7_MV411_colonies_rep3, CpG


title: A10_MO_R1_P1, DAC


title: H6_MV411_colonies_rep3, CpG


title: H8_MV411_colonies_rep3, CpG


title: G9_MV411_colonies_rep3, CpG


title: G7_MV411_colonies_rep3, CpG


title: G5_MV411_colonies_rep3, CpG


title: G12_MV411_colonies_rep3, CpG


title: G6_MV411_colonies_rep3, CpG


title: G10_MV411_colonies_rep3, CpG


title: G3_MV411_colonies_rep3, CpG


title: G2_MV411_colonies_rep3, CpG


title: G4_MV411_colonies_rep3, CpG


title: G1_MV411_colonies_rep3, CpG


title: F12_MV411_colonies_rep3, CpG


title: F11_MV411_colonies_rep3, CpG


title: F10_MV411_colonies_rep3, CpG


title: H2_MV411_colonies_rep3, CpG


title: G11_MV411_colonies_rep3, CpG


title: H9_MV411_colonies_rep3, CpG


title: F5_MV411_colonies_rep3, CpG


title: F9_MV411_colonies_rep3, CpG


title: F8_MV411_colonies_rep3, CpG


title: F7_MV411_colonies_rep3, CpG


title: G8_MV411_colonies_rep3, CpG


title: E7_MV411_colonies_rep3, CpG


title: F6_MV411_colonies_rep3, CpG


title: E11_MV411_colonies_rep3, CpG


title: E10_MV411_colonies_rep3, CpG


title: E6_MV411_colonies_rep3, CpG


title: F3_MV411_colonies_rep3, CpG


title: E8_MV411_colonies_rep3, CpG


title: E9_MV411_colonies_rep3, CpG


title: D10_MV411_colonies_rep3, CpG


title: D12_MV411_colonies_rep3, CpG


title: E12_MV411_colonies_rep3, CpG


title: F1_MV411_colonies_rep3, CpG


title: F4_MV411_colonies_rep3, CpG


title: E1_MV411_colonies_rep3, CpG


title: E2_MV411_colonies_rep3, CpG


title: D11_MV411_colonies_rep3, CpG


title: E4_MV411_colonies_rep3, CpG


title: D9_MV411_colonies_rep3, CpG


title: D8_MV411_colonies_rep3, CpG


title: F2_MV411_colonies_rep3, CpG


title: D7_MV411_colonies_rep3, CpG


title: D6_MV411_colonies_rep3, CpG


title: D5_MV411_colonies_rep3, CpG


title: D4_MV411_colonies_rep3, CpG


title: D3_MV411_colonies_rep3, CpG


title: D1_MV411_colonies_rep3, CpG


title: C11_MV411_colonies_rep3, CpG


title: C12_MV411_colonies_rep3, CpG


title: C9_MV411_colonies_rep3, CpG


title: C8_MV411_colonies_rep3, CpG


title: C6_MV411_colonies_rep3, CpG


title: C10_MV411_colonies_rep3, CpG


title: C5_MV411_colonies_rep3, CpG


title: D2_MV411_colonies_rep3, CpG


title: C4_MV411_colonies_rep3, CpG


title: C3_MV411_colonies_rep3, CpG


title: C1_MV411_colonies_rep3, CpG


title: C2_MV411_colonies_rep3, CpG


title: B11_MV411_colonies_rep3, CpG


title: B12_MV411_colonies_rep3, CpG


title: B10_MV411_colonies_rep3, CpG


title: C7_MV411_colonies_rep3, CpG


title: B6_MV411_colonies_rep3, CpG


title: B7_MV411_colonies_rep3, CpG


title: B3_MV411_colonies_rep3, CpG


title: B4_MV411_colonies_rep3, CpG


title: B5_MV411_colonies_rep3, CpG


title: B2_MV411_colonies_rep3, CpG


title: B1_MV411_colonies_rep3, CpG


title: A12_MV411_colonies_rep3, CpG


title: A11_MV411_colonies_rep3, CpG


title: A10_MV411_colonies_rep3, CpG


title: A9_MV411_colonies_rep3, CpG


title: B8_MV411_colonies_rep3, CpG


title: A3_MV411_colonies_rep3, CpG


title: A2_MV411_colonies_rep3, CpG


title: A5_MV411_colonies_rep3, CpG


title: H12_MV411_colonies_rep2, CpG


title: A4_MV411_colonies_rep3, CpG


title: B9_MV411_colonies_rep3, CpG


title: A7_MV411_colonies_rep3, CpG


title: A1_MV411_colonies_rep3, CpG


title: H11_MV411_colonies_rep2, CpG


title: H9_MV411_colonies_rep2, CpG


title: H7_MV411_colonies_rep2, CpG


title: A6_MV411_colonies_rep3, CpG


title: H6_MV411_colonies_rep2, CpG


title: H5_MV411_colonies_rep2, CpG


title: H10_MV411_colonies_rep2, CpG


title: H2_MV411_colonies_rep2, CpG


title: H4_MV411_colonies_rep2, CpG


title: H3_MV411_colonies_rep2, CpG


title: H1_MV411_colonies_rep2, CpG


title: G12_MV411_colonies_rep2, CpG


title: G11_MV411_colonies_rep2, CpG


title: A8_MV411_colonies_rep3, CpG


title: G10_MV411_colonies_rep2, CpG


title: G9_MV411_colonies_rep2, CpG


title: G8_MV411_colonies_rep2, CpG


title: H8_MV411_colonies_rep2, CpG


title: G7_MV411_colonies_rep2, CpG


title: G4_MV411_colonies_rep2, CpG


title: G6_MV411_colonies_rep2, CpG


title: G3_MV411_colonies_rep2, CpG


title: G5_MV411_colonies_rep2, CpG


title: F12_MV411_colonies_rep2, CpG


title: F11_MV411_colonies_rep2, CpG


title: F10_MV411_colonies_rep2, CpG


title: G1_MV411_colonies_rep2, CpG


title: G2_MV411_colonies_rep2, CpG


title: F9_MV411_colonies_rep2, CpG


title: F8_MV411_colonies_rep2, CpG


title: F7_MV411_colonies_rep2, CpG


title: F5_MV411_colonies_rep2, CpG


title: C9_MO_R1_P1, DAC


title: F3_MV411_colonies_rep2, CpG


title: F6_MV411_colonies_rep2, CpG


title: F1_MV411_colonies_rep2, CpG


title: E11_MV411_colonies_rep2, CpG


title: E12_MV411_colonies_rep2, CpG


title: E10_MV411_colonies_rep2, CpG


title: E9_MV411_colonies_rep2, CpG


title: F2_MV411_colonies_rep2, CpG


title: E7_MV411_colonies_rep2, CpG


title: E8_MV411_colonies_rep2, CpG


title: D12_MV411_colonies_rep2, CpG


title: E3_MV411_colonies_rep2, CpG


title: E1_MV411_colonies_rep2, CpG


title: E6_MV411_colonies_rep2, CpG


title: E5_MV411_colonies_rep2, CpG


title: E4_MV411_colonies_rep2, CpG


title: E2_MV411_colonies_rep2, CpG


title: D7_MV411_colonies_rep2, CpG


title: D4_MV411_colonies_rep2, CpG


title: D6_MV411_colonies_rep2, CpG


title: D11_MV411_colonies_rep2, CpG


title: D9_MV411_colonies_rep2, CpG


title: D8_MV411_colonies_rep2, CpG


title: F4_MV411_colonies_rep2, CpG


title: D2_MV411_colonies_rep2, CpG


title: D1_MV411_colonies_rep2, CpG


title: C11_MV411_colonies_rep2, CpG


title: C12_MV411_colonies_rep2, CpG


title: C9_MV411_colonies_rep2, CpG


title: C8_MV411_colonies_rep2, CpG


title: C7_MV411_colonies_rep2, CpG


title: C10_MV411_colonies_rep2, CpG


title: C6_MV411_colonies_rep2, CpG


title: C5_MV411_colonies_rep2, CpG


title: C1_MV411_colonies_rep2, CpG


title: B12_MV411_colonies_rep2, CpG


title: D10_MV411_colonies_rep2, CpG


title: C4_MV411_colonies_rep2, CpG


title: D5_MV411_colonies_rep2, CpG


title: C3_MV411_colonies_rep2, CpG


title: B9_MV411_colonies_rep2, CpG


title: B11_MV411_colonies_rep2, CpG


title: C2_MV411_colonies_rep2, CpG


title: B8_MV411_colonies_rep2, CpG


title: D3_MV411_colonies_rep2, CpG


title: B7_MV411_colonies_rep2, CpG


title: B4_MV411_colonies_rep2, CpG


title: B5_MV411_colonies_rep2, CpG


title: B10_MV411_colonies_rep2, CpG


title: B2_MV411_colonies_rep2, CpG


title: B1_MV411_colonies_rep2, CpG


title: B3_MV411_colonies_rep2, CpG


title: A11_MV411_colonies_rep2, CpG


title: A8_MV411_colonies_rep2, CpG


title: B6_MV411_colonies_rep2, CpG


title: A7_MV411_colonies_rep2, CpG


title: A12_MV411_colonies_rep2, CpG


title: A10_MV411_colonies_rep2, CpG


title: A6_MV411_colonies_rep2, CpG


title: A9_MV411_colonies_rep2, CpG


title: A5_MV411_colonies_rep2, CpG


title: A4_MV411_colonies_rep2, CpG


title: E3_MV411_colonies_rep3, CpG


title: A3_MV411_colonies_rep2, CpG


title: H12_MV411_colonies_rep1, CpG


title: A2_MV411_colonies_rep2, CpG


title: H11_MV411_colonies_rep1, CpG


title: H9_MV411_colonies_rep1, CpG


title: A1_MV411_colonies_rep2, CpG


title: H5_MV411_colonies_rep1, CpG


title: H6_MV411_colonies_rep1, CpG


title: H8_MV411_colonies_rep1, CpG


title: E5_MV411_colonies_rep3, CpG


title: H2_MV411_colonies_rep1, CpG


title: H1_MV411_colonies_rep1, CpG


title: H3_MV411_colonies_rep1, CpG


title: H4_MV411_colonies_rep1, CpG


title: G12_MV411_colonies_rep1, CpG


title: G10_MV411_colonies_rep1, CpG


title: G9_MV411_colonies_rep1, CpG


title: G8_MV411_colonies_rep1, CpG


title: G4_MV411_colonies_rep1, CpG


title: G5_MV411_colonies_rep1, CpG


title: G6_MV411_colonies_rep1, CpG


title: G7_MV411_colonies_rep1, CpG


title: G1_MV411_colonies_rep1, CpG


title: H10_MV411_colonies_rep1, CpG


title: F11_MV411_colonies_rep1, CpG


title: F10_MV411_colonies_rep1, CpG


title: H7_MV411_colonies_rep1, CpG


title: F8_MV411_colonies_rep1, CpG


title: F7_MV411_colonies_rep1, CpG


title: F9_MV411_colonies_rep1, CpG


title: F3_MV411_colonies_rep1, CpG


title: F2_MV411_colonies_rep1, CpG


title: F4_MV411_colonies_rep1, CpG


title: F5_MV411_colonies_rep1, CpG


title: F1_MV411_colonies_rep1, CpG


title: E11_MV411_colonies_rep1, CpG


title: E10_MV411_colonies_rep1, CpG


title: E8_MV411_colonies_rep1, CpG


title: G11_MV411_colonies_rep1, CpG


title: E7_MV411_colonies_rep1, CpG


title: E12_MV411_colonies_rep1, CpG


title: G2_MV411_colonies_rep1, CpG


title: E6_MV411_colonies_rep1, CpG


title: E2_MV411_colonies_rep1, CpG


title: E3_MV411_colonies_rep1, CpG


title: D12_MV411_colonies_rep1, CpG


title: F12_MV411_colonies_rep1, CpG


title: G3_MV411_colonies_rep1, CpG


title: F6_MV411_colonies_rep1, CpG


title: D11_MV411_colonies_rep1, CpG


title: E4_MV411_colonies_rep1, CpG


title: D10_MV411_colonies_rep1, CpG


title: D6_MV411_colonies_rep1, CpG


title: D5_MV411_colonies_rep1, CpG


title: E9_MV411_colonies_rep1, CpG


title: D2_MV411_colonies_rep1, CpG


title: D3_MV411_colonies_rep1, CpG


title: D1_MV411_colonies_rep1, CpG


title: C11_MV411_colonies_rep1, CpG


title: C10_MV411_colonies_rep1, CpG


title: C8_MV411_colonies_rep1, CpG


title: C9_MV411_colonies_rep1, CpG


title: C7_MV411_colonies_rep1, CpG


title: E5_MV411_colonies_rep1, CpG


title: E1_MV411_colonies_rep1, CpG


title: C5_MV411_colonies_rep1, CpG


title: C3_MV411_colonies_rep1, CpG


title: C2_MV411_colonies_rep1, CpG


title: C4_MV411_colonies_rep1, CpG


title: C1_MV411_colonies_rep1, CpG


title: B11_MV411_colonies_rep1, CpG


title: B12_MV411_colonies_rep1, CpG


title: B10_MV411_colonies_rep1, CpG


title: B8_MV411_colonies_rep1, CpG


title: D4_MV411_colonies_rep1, CpG


title: D9_MV411_colonies_rep1, CpG


title: D7_MV411_colonies_rep1, CpG


title: B7_MV411_colonies_rep1, CpG


title: C12_MV411_colonies_rep1, CpG


title: B9_MV411_colonies_rep1, CpG


title: B4_MV411_colonies_rep1, CpG


title: A12_MV411_colonies_rep1, CpG


title: B1_MV411_colonies_rep1, CpG


title: B3_MV411_colonies_rep1, CpG


title: A11_MV411_colonies_rep1, CpG


title: C6_MV411_colonies_rep1, CpG


title: A8_MV411_colonies_rep1, CpG


title: A10_MV411_colonies_rep1, CpG


title: A7_MV411_colonies_rep1, CpG


title: A5_MV411_colonies_rep1, CpG


title: A6_MV411_colonies_rep1, CpG


title: A3_MV411_colonies_rep1, CpG


title: B2_MV411_colonies_rep1, CpG


title: A4_MV411_colonies_rep1, CpG


title: B5_MV411_colonies_rep1, CpG


title: A2_MV411_colonies_rep1, CpG


title: A1_MV411_colonies_rep1, CpG


title: D8_MV411_colonies_rep1, CpG


title: A9_MV411_colonies_rep1, CpG


title: H6_Molm13_colony_rep3, CpG


title: H10_Molm13_colony_rep3, CpG


title: H11_Molm13_colony_rep3, CpG


title: H8_Molm13_colony_rep3, CpG


title: H9_Molm13_colony_rep3, CpG


title: H12_Molm13_colony_rep3, CpG


title: H4_Molm13_colony_rep3, CpG


title: H5_Molm13_colony_rep3, CpG


title: H3_Molm13_colony_rep3, CpG


title: H2_Molm13_colony_rep3, CpG


title: H1_Molm13_colony_rep3, CpG


title: G12_Molm13_colony_rep3, CpG


title: G9_Molm13_colony_rep3, CpG


title: G11_Molm13_colony_rep3, CpG


title: G8_Molm13_colony_rep3, CpG


title: G7_Molm13_colony_rep3, CpG


title: G4_Molm13_colony_rep3, CpG


title: G5_Molm13_colony_rep3, CpG


title: G6_Molm13_colony_rep3, CpG


title: G3_Molm13_colony_rep3, CpG


title: G2_Molm13_colony_rep3, CpG


title: B6_MV411_colonies_rep1, CpG


title: F12_Molm13_colony_rep3, CpG


title: G1_Molm13_colony_rep3, CpG


title: F9_Molm13_colony_rep3, CpG


title: F4_Molm13_colony_rep3, CpG


title: F6_Molm13_colony_rep3, CpG


title: F5_Molm13_colony_rep3, CpG


title: F2_Molm13_colony_rep3, CpG


title: F8_Molm13_colony_rep3, CpG


title: F7_Molm13_colony_rep3, CpG


title: F1_Molm13_colony_rep3, CpG


title: E12_Molm13_colony_rep3, CpG


title: E10_Molm13_colony_rep3, CpG


title: E9_Molm13_colony_rep3, CpG


title: E11_Molm13_colony_rep3, CpG


title: G10_Molm13_colony_rep3, CpG


title: E8_Molm13_colony_rep3, CpG


title: E6_Molm13_colony_rep3, CpG


title: E7_Molm13_colony_rep3, CpG


title: E4_Molm13_colony_rep3, CpG


title: E5_Molm13_colony_rep3, CpG


title: E3_Molm13_colony_rep3, CpG


title: F11_Molm13_colony_rep3, CpG


title: F10_Molm13_colony_rep3, CpG


title: H7_Molm13_colony_rep3, CpG


title: E2_Molm13_colony_rep3, CpG


title: D11_Molm13_colony_rep3, CpG


title: D10_Molm13_colony_rep3, CpG


title: D8_Molm13_colony_rep3, CpG


title: E1_Molm13_colony_rep3, CpG


title: D7_Molm13_colony_rep3, CpG


title: F3_Molm13_colony_rep3, CpG


title: D5_Molm13_colony_rep3, CpG


title: D4_Molm13_colony_rep3, CpG


title: D6_Molm13_colony_rep3, CpG


title: D3_Molm13_colony_rep3, CpG


title: D1_Molm13_colony_rep3, CpG


title: D2_Molm13_colony_rep3, CpG


title: C12_Molm13_colony_rep3, CpG


title: C10_Molm13_colony_rep3, CpG


title: C9_Molm13_colony_rep3, CpG


title: C8_Molm13_colony_rep3, CpG


title: C7_Molm13_colony_rep3, CpG


title: C6_Molm13_colony_rep3, CpG


title: C4_Molm13_colony_rep3, CpG


title: C3_Molm13_colony_rep3, CpG


title: C5_Molm13_colony_rep3, CpG


title: C1_Molm13_colony_rep3, CpG


title: D12_Molm13_colony_rep3, CpG


title: B12_Molm13_colony_rep3, CpG


title: B9_Molm13_colony_rep3, CpG


title: C2_Molm13_colony_rep3, CpG


title: B8_Molm13_colony_rep3, CpG


title: B6_Molm13_colony_rep3, CpG


title: D9_Molm13_colony_rep3, CpG


title: B11_Molm13_colony_rep3, CpG


title: B3_Molm13_colony_rep3, CpG


title: B10_Molm13_colony_rep3, CpG


title: B2_Molm13_colony_rep3, CpG


title: B4_Molm13_colony_rep3, CpG


title: B1_Molm13_colony_rep3, CpG


title: A11_Molm13_colony_rep3, CpG


title: B5_Molm13_colony_rep3, CpG


title: A8_Molm13_colony_rep3, CpG


title: A12_Molm13_colony_rep3, CpG


title: B7_Molm13_colony_rep3, CpG


title: C11_Molm13_colony_rep3, CpG


title: A7_Molm13_colony_rep3, CpG


title: A5_Molm13_colony_rep3, CpG


title: A3_Molm13_colony_rep3, CpG


title: A4_Molm13_colony_rep3, CpG


title: A10_Molm13_colony_rep3, CpG


title: A9_Molm13_colony_rep3, CpG


title: A2_Molm13_colony_rep3, CpG


title: A1_Molm13_colony_rep3, CpG


title: H10_Molm13_colony_rep2, CpG


title: H11_Molm13_colony_rep2, CpG


title: H9_Molm13_colony_rep2, CpG


title: H6_Molm13_colony_rep2, CpG


title: H8_Molm13_colony_rep2, CpG


title: H4_Molm13_colony_rep2, CpG


title: H12_Molm13_colony_rep2, CpG


title: H3_Molm13_colony_rep2, CpG


title: H1_Molm13_colony_rep2, CpG


title: G12_Molm13_colony_rep2, CpG


title: H2_Molm13_colony_rep2, CpG


title: G10_Molm13_colony_rep2, CpG


title: G9_Molm13_colony_rep2, CpG


title: G11_Molm13_colony_rep2, CpG


title: A6_Molm13_colony_rep3, CpG


title: G6_Molm13_colony_rep2, CpG


title: G5_Molm13_colony_rep2, CpG


title: G7_Molm13_colony_rep2, CpG


title: G8_Molm13_colony_rep2, CpG


title: G4_Molm13_colony_rep2, CpG


title: G3_Molm13_colony_rep2, CpG


title: F12_Molm13_colony_rep2, CpG


title: G1_Molm13_colony_rep2, CpG


title: F10_Molm13_colony_rep2, CpG


title: G2_Molm13_colony_rep2, CpG


title: F9_Molm13_colony_rep2, CpG


title: H7_Molm13_colony_rep2, CpG


title: F11_Molm13_colony_rep2, CpG


title: H5_Molm13_colony_rep2, CpG


title: F7_Molm13_colony_rep2, CpG


title: F5_Molm13_colony_rep2, CpG


title: F6_Molm13_colony_rep2, CpG


title: F3_Molm13_colony_rep2, CpG


title: F2_Molm13_colony_rep2, CpG


title: F8_Molm13_colony_rep2, CpG


title: E11_Molm13_colony_rep2, CpG


title: E12_Molm13_colony_rep2, CpG


title: E10_Molm13_colony_rep2, CpG


title: E9_Molm13_colony_rep2, CpG


title: F1_Molm13_colony_rep2, CpG


title: E8_Molm13_colony_rep2, CpG


title: E7_Molm13_colony_rep2, CpG


title: E6_Molm13_colony_rep2, CpG


title: E4_Molm13_colony_rep2, CpG


title: E3_Molm13_colony_rep2, CpG


title: E2_Molm13_colony_rep2, CpG


title: E1_Molm13_colony_rep2, CpG


title: E5_Molm13_colony_rep2, CpG


title: D9_Molm13_colony_rep2, CpG


title: D12_Molm13_colony_rep2, CpG


title: D10_Molm13_colony_rep2, CpG


title: F4_Molm13_colony_rep2, CpG


title: D11_Molm13_colony_rep2, CpG


title: D8_Molm13_colony_rep2, CpG


title: D6_Molm13_colony_rep2, CpG


title: D5_Molm13_colony_rep2, CpG


title: D4_Molm13_colony_rep2, CpG


title: D3_Molm13_colony_rep2, CpG


title: D7_Molm13_colony_rep2, CpG


title: C10_Molm13_colony_rep2, CpG


title: C12_Molm13_colony_rep2, CpG


title: D2_Molm13_colony_rep2, CpG


title: D1_Molm13_colony_rep2, CpG


title: C7_Molm13_colony_rep2, CpG


title: C9_Molm13_colony_rep2, CpG


title: C6_Molm13_colony_rep2, CpG


title: C11_Molm13_colony_rep2, CpG


title: C5_Molm13_colony_rep2, CpG


title: C4_Molm13_colony_rep2, CpG


title: C2_Molm13_colony_rep2, CpG


title: B11_Molm13_colony_rep2, CpG


title: B10_Molm13_colony_rep2, CpG


title: C3_Molm13_colony_rep2, CpG


title: C1_Molm13_colony_rep2, CpG


title: B8_Molm13_colony_rep2, CpG


title: B12_Molm13_colony_rep2, CpG


title: B9_Molm13_colony_rep2, CpG


title: B5_Molm13_colony_rep2, CpG


title: B4_Molm13_colony_rep2, CpG


title: C8_Molm13_colony_rep2, CpG


title: B6_Molm13_colony_rep2, CpG


title: B3_Molm13_colony_rep2, CpG


title: B1_Molm13_colony_rep2, CpG


title: A12_Molm13_colony_rep2, CpG


title: A11_Molm13_colony_rep2, CpG


title: A7_Molm13_colony_rep2, CpG


title: A9_Molm13_colony_rep2, CpG


title: A5_Molm13_colony_rep2, CpG


title: A8_Molm13_colony_rep2, CpG


title: A10_Molm13_colony_rep2, CpG


title: A6_Molm13_colony_rep2, CpG


title: H12_Molm13_colony_rep1, CpG


title: A4_Molm13_colony_rep2, CpG


title: A3_Molm13_colony_rep2, CpG


title: A2_Molm13_colony_rep2, CpG


title: H10_Molm13_colony_rep1, CpG


title: B7_Molm13_colony_rep2, CpG


title: A1_Molm13_colony_rep2, CpG


title: H5_Molm13_colony_rep1, CpG


title: H8_Molm13_colony_rep1, CpG


title: H4_Molm13_colony_rep1, CpG


title: H7_Molm13_colony_rep1, CpG


title: H9_Molm13_colony_rep1, CpG


title: H6_Molm13_colony_rep1, CpG


title: H2_Molm13_colony_rep1, CpG


title: H3_Molm13_colony_rep1, CpG


title: H1_Molm13_colony_rep1, CpG


title: G11_Molm13_colony_rep1, CpG


title: G12_Molm13_colony_rep1, CpG


title: G10_Molm13_colony_rep1, CpG


title: B2_Molm13_colony_rep2, CpG


title: G9_Molm13_colony_rep1, CpG


title: G8_Molm13_colony_rep1, CpG


title: G6_Molm13_colony_rep1, CpG


title: G7_Molm13_colony_rep1, CpG


title: G4_Molm13_colony_rep1, CpG


title: G5_Molm13_colony_rep1, CpG


title: G2_Molm13_colony_rep1, CpG


title: H11_Molm13_colony_rep1, CpG


title: G3_Molm13_colony_rep1, CpG


title: G1_Molm13_colony_rep1, CpG


title: F12_Molm13_colony_rep1, CpG


title: F6_Molm13_colony_rep1, CpG


title: F10_Molm13_colony_rep1, CpG


title: F7_Molm13_colony_rep1, CpG


title: F8_Molm13_colony_rep1, CpG


title: F11_Molm13_colony_rep1, CpG


title: F9_Molm13_colony_rep1, CpG


title: F5_Molm13_colony_rep1, CpG


title: F3_Molm13_colony_rep1, CpG


title: E12_Molm13_colony_rep1, CpG


title: E11_Molm13_colony_rep1, CpG


title: E10_Molm13_colony_rep1, CpG


title: F2_Molm13_colony_rep1, CpG


title: E9_Molm13_colony_rep1, CpG


title: E8_Molm13_colony_rep1, CpG


title: E7_Molm13_colony_rep1, CpG


title: F4_Molm13_colony_rep1, CpG


title: E6_Molm13_colony_rep1, CpG


title: E5_Molm13_colony_rep1, CpG


title: E4_Molm13_colony_rep1, CpG


title: E2_Molm13_colony_rep1, CpG


title: E3_Molm13_colony_rep1, CpG


title: D12_Molm13_colony_rep1, CpG


title: D10_Molm13_colony_rep1, CpG


title: E1_Molm13_colony_rep1, CpG


title: D9_Molm13_colony_rep1, CpG


title: D8_Molm13_colony_rep1, CpG


title: D7_Molm13_colony_rep1, CpG


title: D6_Molm13_colony_rep1, CpG


title: D1_Molm13_colony_rep1, CpG


title: D3_Molm13_colony_rep1, CpG


title: F1_Molm13_colony_rep1, CpG


title: C11_Molm13_colony_rep1, CpG


title: C8_Molm13_colony_rep1, CpG


title: C10_Molm13_colony_rep1, CpG


title: C5_Molm13_colony_rep1, CpG


title: C7_Molm13_colony_rep1, CpG


title: C4_Molm13_colony_rep1, CpG


title: C9_Molm13_colony_rep1, CpG


title: C3_Molm13_colony_rep1, CpG


title: D11_Molm13_colony_rep1, CpG


title: C2_Molm13_colony_rep1, CpG


title: B9_Molm13_colony_rep1, CpG


title: B12_Molm13_colony_rep1, CpG


title: B11_Molm13_colony_rep1, CpG


title: D2_Molm13_colony_rep1, CpG


title: B6_Molm13_colony_rep1, CpG


title: B7_Molm13_colony_rep1, CpG


title: B8_Molm13_colony_rep1, CpG


title: D5_Molm13_colony_rep1, CpG


title: D4_Molm13_colony_rep1, CpG


title: B5_Molm13_colony_rep1, CpG


title: B3_Molm13_colony_rep1, CpG


title: C12_Molm13_colony_rep1, CpG


title: B4_Molm13_colony_rep1, CpG


title: A12_Molm13_colony_rep1, CpG


title: B2_Molm13_colony_rep1, CpG


title: B1_Molm13_colony_rep1, CpG


title: A9_Molm13_colony_rep1, CpG


title: A11_Molm13_colony_rep1, CpG


title: A10_Molm13_colony_rep1, CpG


title: A7_Molm13_colony_rep1, CpG


title: C6_Molm13_colony_rep1, CpG


title: C1_Molm13_colony_rep1, CpG


title: A5_Molm13_colony_rep1, CpG


title: A2_Molm13_colony_rep1, CpG


title: A3_Molm13_colony_rep1, CpG


title: B10_Molm13_colony_rep1, CpG


title: H11_HL60_colonies_rep3, CpG

value: promyeloblast


title: H12_HL60_colonies_rep3, CpG

value: Acute promyelocytic leukemia


title: H9_HL60_colonies_rep3, CpG

value: Female


title: H7_HL60_colonies_rep3, CpG

value: TEM-Seq


title: H3_HL60_colonies_rep3, CpG

value: azacytidine


title: H6_HL60_colonies_rep3, CpG


title: A6_Molm13_colony_rep1, CpG


title: G11_HL60_colonies_rep3, CpG

value: untreated


title: G5_HL60_colonies_rep3, CpG


title: G8_HL60_colonies_rep3, CpG


title: G12_HL60_colonies_rep3, CpG


title: A1_Molm13_colony_rep1, CpG


title: G6_HL60_colonies_rep3, CpG


title: G2_HL60_colonies_rep3, CpG


title: H5_HL60_colonies_rep3, CpG


title: G9_HL60_colonies_rep3, CpG


title: G1_HL60_colonies_rep3, CpG


title: A8_Molm13_colony_rep1, CpG


title: H1_HL60_colonies_rep3, CpG


title: G7_HL60_colonies_rep3, CpG


title: A4_Molm13_colony_rep1, CpG


title: G3_HL60_colonies_rep3, CpG


title: H8_HL60_colonies_rep3, CpG


title: H10_HL60_colonies_rep3, CpG


title: F12_HL60_colonies_rep3, CpG


title: F11_HL60_colonies_rep3, CpG


title: F10_HL60_colonies_rep3, CpG


title: F7_HL60_colonies_rep3, CpG


title: F9_HL60_colonies_rep3, CpG


title: F8_HL60_colonies_rep3, CpG


title: E8_HL60_colonies_rep3, CpG


title: E10_HL60_colonies_rep3, CpG


title: F6_HL60_colonies_rep3, CpG


title: E5_HL60_colonies_rep3, CpG


title: F5_HL60_colonies_rep3, CpG


title: E11_HL60_colonies_rep3, CpG


title: E9_HL60_colonies_rep3, CpG


title: F4_HL60_colonies_rep3, CpG


title: E6_HL60_colonies_rep3, CpG


title: E4_HL60_colonies_rep3, CpG


title: F2_HL60_colonies_rep3, CpG


title: E12_HL60_colonies_rep3, CpG


title: F3_HL60_colonies_rep3, CpG


title: E3_HL60_colonies_rep3, CpG


title: E7_HL60_colonies_rep3, CpG


title: E2_HL60_colonies_rep3, CpG


title: E1_HL60_colonies_rep3, CpG


title: D12_HL60_colonies_rep3, CpG


title: F1_HL60_colonies_rep3, CpG


title: D11_HL60_colonies_rep3, CpG


title: D8_HL60_colonies_rep3, CpG


title: D7_HL60_colonies_rep3, CpG


title: D6_HL60_colonies_rep3, CpG


title: D5_HL60_colonies_rep3, CpG


title: D3_HL60_colonies_rep3, CpG


title: D4_HL60_colonies_rep3, CpG


title: D2_HL60_colonies_rep3, CpG


title: H4_HL60_colonies_rep3, CpG


title: D9_HL60_colonies_rep3, CpG


title: H2_HL60_colonies_rep3, CpG


title: C11_HL60_colonies_rep3, CpG


title: C8_HL60_colonies_rep3, CpG


title: C6_HL60_colonies_rep3, CpG


title: D1_HL60_colonies_rep3, CpG


title: C9_HL60_colonies_rep3, CpG


title: C4_HL60_colonies_rep3, CpG


title: C5_HL60_colonies_rep3, CpG


title: C10_HL60_colonies_rep3, CpG


title: C3_HL60_colonies_rep3, CpG


title: C1_HL60_colonies_rep3, CpG


title: B12_HL60_colonies_rep3, CpG


title: C7_HL60_colonies_rep3, CpG


title: B11_HL60_colonies_rep3, CpG


title: D10_HL60_colonies_rep3, CpG


title: B10_HL60_colonies_rep3, CpG


title: B9_HL60_colonies_rep3, CpG


title: B7_HL60_colonies_rep3, CpG


title: B3_HL60_colonies_rep3, CpG


title: B5_HL60_colonies_rep3, CpG


title: B2_HL60_colonies_rep3, CpG


title: C12_HL60_colonies_rep3, CpG


title: B6_HL60_colonies_rep3, CpG


title: B4_HL60_colonies_rep3, CpG


title: B8_HL60_colonies_rep3, CpG


title: B1_HL60_colonies_rep3, CpG


title: A8_HL60_colonies_rep3, CpG


title: A12_HL60_colonies_rep3, CpG


title: C2_HL60_colonies_rep3, CpG


title: A7_HL60_colonies_rep3, CpG


title: A11_HL60_colonies_rep3, CpG


title: A1_HL60_colonies_rep3, CpG


title: A6_HL60_colonies_rep3, CpG


title: A9_HL60_colonies_rep3, CpG


title: A5_HL60_colonies_rep3, CpG


title: H9_HL60_colonies_rep2, CpG


title: H12_HL60_colonies_rep2, CpG


title: A10_HL60_colonies_rep3, CpG


title: H11_HL60_colonies_rep2, CpG


title: A2_HL60_colonies_rep3, CpG


title: H10_HL60_colonies_rep2, CpG


title: H8_HL60_colonies_rep2, CpG


title: H7_HL60_colonies_rep2, CpG


title: H6_HL60_colonies_rep2, CpG


title: H3_HL60_colonies_rep2, CpG


title: H2_HL60_colonies_rep2, CpG


title: H5_HL60_colonies_rep2, CpG


title: H4_HL60_colonies_rep2, CpG


title: A4_HL60_colonies_rep3, CpG


title: H1_HL60_colonies_rep2, CpG


title: G8_HL60_colonies_rep2, CpG


title: G10_HL60_colonies_rep2, CpG


title: A3_HL60_colonies_rep3, CpG


title: G11_HL60_colonies_rep2, CpG


title: G6_HL60_colonies_rep2, CpG


title: G9_HL60_colonies_rep2, CpG


title: G7_HL60_colonies_rep2, CpG


title: G5_HL60_colonies_rep2, CpG


title: G10_HL60_colonies_rep3, CpG


title: G4_HL60_colonies_rep2, CpG


title: G3_HL60_colonies_rep2, CpG


title: F11_HL60_colonies_rep2, CpG


title: F12_HL60_colonies_rep2, CpG


title: F5_HL60_colonies_rep2, CpG


title: F9_HL60_colonies_rep2, CpG


title: G1_HL60_colonies_rep2, CpG


title: F3_HL60_colonies_rep2, CpG


title: G2_HL60_colonies_rep2, CpG


title: F10_HL60_colonies_rep2, CpG


title: F6_HL60_colonies_rep2, CpG


title: G12_HL60_colonies_rep2, CpG


title: F1_HL60_colonies_rep2, CpG


title: F2_HL60_colonies_rep2, CpG


title: F7_HL60_colonies_rep2, CpG


title: F8_HL60_colonies_rep2, CpG


title: E12_HL60_colonies_rep2, CpG


title: E9_HL60_colonies_rep2, CpG


title: E11_HL60_colonies_rep2, CpG


title: E8_HL60_colonies_rep2, CpG


title: E7_HL60_colonies_rep2, CpG


title: E5_HL60_colonies_rep2, CpG


title: E6_HL60_colonies_rep2, CpG


title: E3_HL60_colonies_rep2, CpG


title: D10_HL60_colonies_rep2, CpG


title: D12_HL60_colonies_rep2, CpG


title: E1_HL60_colonies_rep2, CpG


title: D11_HL60_colonies_rep2, CpG


title: D9_HL60_colonies_rep2, CpG


title: F4_HL60_colonies_rep2, CpG


title: D8_HL60_colonies_rep2, CpG


title: D3_HL60_colonies_rep2, CpG


title: D5_HL60_colonies_rep2, CpG


title: C12_HL60_colonies_rep2, CpG


title: D2_HL60_colonies_rep2, CpG


title: D1_HL60_colonies_rep2, CpG


title: C9_HL60_colonies_rep2, CpG


title: D6_HL60_colonies_rep2, CpG


title: D7_HL60_colonies_rep2, CpG


title: C11_HL60_colonies_rep2, CpG


title: C10_HL60_colonies_rep2, CpG


title: E4_HL60_colonies_rep2, CpG


title: E2_HL60_colonies_rep2, CpG


title: C6_HL60_colonies_rep2, CpG


title: D4_HL60_colonies_rep2, CpG


title: G4_HL60_colonies_rep3, CpG


title: C8_HL60_colonies_rep2, CpG


title: C7_HL60_colonies_rep2, CpG


title: E10_HL60_colonies_rep2, CpG


title: C5_HL60_colonies_rep2, CpG


title: C2_HL60_colonies_rep2, CpG


title: C3_HL60_colonies_rep2, CpG


title: B12_HL60_colonies_rep2, CpG


title: C4_HL60_colonies_rep2, CpG


title: B9_HL60_colonies_rep2, CpG


title: B11_HL60_colonies_rep2, CpG


title: C1_HL60_colonies_rep2, CpG


title: B7_HL60_colonies_rep2, CpG


title: B8_HL60_colonies_rep2, CpG


title: B6_HL60_colonies_rep2, CpG


title: B4_HL60_colonies_rep2, CpG


title: B5_HL60_colonies_rep2, CpG


title: B2_HL60_colonies_rep2, CpG


title: B3_HL60_colonies_rep2, CpG


title: B1_HL60_colonies_rep2, CpG


title: A12_HL60_colonies_rep2, CpG


title: A10_HL60_colonies_rep2, CpG


title: A9_HL60_colonies_rep2, CpG


title: A11_HL60_colonies_rep2, CpG


title: A8_HL60_colonies_rep2, CpG


title: A6_HL60_colonies_rep2, CpG


title: A7_HL60_colonies_rep2, CpG


title: A5_HL60_colonies_rep2, CpG


title: A2_HL60_colonies_rep2, CpG


title: A4_HL60_colonies_rep2, CpG


title: A3_HL60_colonies_rep2, CpG


title: A1_HL60_colonies_rep2, CpG


title: H12_HL60_colonies_rep1, CpG


title: B10_HL60_colonies_rep2, CpG


title: H9_HL60_colonies_rep1, CpG


title: H11_HL60_colonies_rep1, CpG


title: H8_HL60_colonies_rep1, CpG


title: H6_HL60_colonies_rep1, CpG


title: H5_HL60_colonies_rep1, CpG


title: H10_HL60_colonies_rep1, CpG


title: H4_HL60_colonies_rep1, CpG


title: H3_HL60_colonies_rep1, CpG


title: H2_HL60_colonies_rep1, CpG


title: H7_HL60_colonies_rep1, CpG


title: G10_HL60_colonies_rep1, CpG


title: G9_HL60_colonies_rep1, CpG


title: G8_HL60_colonies_rep1, CpG


title: H1_HL60_colonies_rep1, CpG


title: G7_HL60_colonies_rep1, CpG


title: G3_HL60_colonies_rep1, CpG


title: G11_HL60_colonies_rep1, CpG


title: G6_HL60_colonies_rep1, CpG


title: G1_HL60_colonies_rep1, CpG


title: G5_HL60_colonies_rep1, CpG


title: G2_HL60_colonies_rep1, CpG


title: F12_HL60_colonies_rep1, CpG


title: F11_HL60_colonies_rep1, CpG


title: F8_HL60_colonies_rep1, CpG


title: F9_HL60_colonies_rep1, CpG


title: F5_HL60_colonies_rep1, CpG


title: E10_HL60_colonies_rep1, CpG


title: E11_HL60_colonies_rep1, CpG


title: F4_HL60_colonies_rep1, CpG


title: F2_HL60_colonies_rep1, CpG


title: F1_HL60_colonies_rep1, CpG


title: F3_HL60_colonies_rep1, CpG


title: E8_HL60_colonies_rep1, CpG


title: E6_HL60_colonies_rep1, CpG


title: F7_HL60_colonies_rep1, CpG


title: E9_HL60_colonies_rep1, CpG


title: F10_HL60_colonies_rep1, CpG


title: E7_HL60_colonies_rep1, CpG


title: F6_HL60_colonies_rep1, CpG


title: G4_HL60_colonies_rep1, CpG


title: E3_HL60_colonies_rep1, CpG


title: E1_HL60_colonies_rep1, CpG


title: E2_HL60_colonies_rep1, CpG


title: D9_HL60_colonies_rep1, CpG


title: G12_HL60_colonies_rep1, CpG


title: E5_HL60_colonies_rep1, CpG


title: D11_HL60_colonies_rep1, CpG


title: E4_HL60_colonies_rep1, CpG


title: D10_HL60_colonies_rep1, CpG


title: E12_HL60_colonies_rep1, CpG


title: D6_HL60_colonies_rep1, CpG


title: D8_HL60_colonies_rep1, CpG


title: D7_HL60_colonies_rep1, CpG


title: D5_HL60_colonies_rep1, CpG


title: D3_HL60_colonies_rep1, CpG


title: D4_HL60_colonies_rep1, CpG


title: D2_HL60_colonies_rep1, CpG


title: C11_HL60_colonies_rep1, CpG


title: D1_HL60_colonies_rep1, CpG


title: C10_HL60_colonies_rep1, CpG


title: C6_HL60_colonies_rep1, CpG


title: C9_HL60_colonies_rep1, CpG


title: C12_HL60_colonies_rep1, CpG


title: C7_HL60_colonies_rep1, CpG


title: C5_HL60_colonies_rep1, CpG


title: C3_HL60_colonies_rep1, CpG


title: C2_HL60_colonies_rep1, CpG


title: B12_HL60_colonies_rep1, CpG


title: C4_HL60_colonies_rep1, CpG


title: B10_HL60_colonies_rep1, CpG


title: B9_HL60_colonies_rep1, CpG


title: B11_HL60_colonies_rep1, CpG


title: B7_HL60_colonies_rep1, CpG


title: B6_HL60_colonies_rep1, CpG


title: B5_HL60_colonies_rep1, CpG


title: B8_HL60_colonies_rep1, CpG


title: B4_HL60_colonies_rep1, CpG


title: B2_HL60_colonies_rep1, CpG


title: B3_HL60_colonies_rep1, CpG


title: C8_HL60_colonies_rep1, CpG


title: A12_HL60_colonies_rep1, CpG


title: A11_HL60_colonies_rep1, CpG


title: A9_HL60_colonies_rep1, CpG


title: A10_HL60_colonies_rep1, CpG


title: A8_HL60_colonies_rep1, CpG


title: A5_HL60_colonies_rep1, CpG


title: C1_HL60_colonies_rep1, CpG


title: A4_HL60_colonies_rep1, CpG


title: A2_HL60_colonies_rep1, CpG


title: A7_HL60_colonies_rep1, CpG


title: A3_HL60_colonies_rep1, CpG


title: B1_HL60_colonies_rep1, CpG


title: A6_HL60_colonies_rep1, CpG


title: A1_HL60_colonies_rep1, CpG


title: D10_MV411_colonies_rep2, RNA

library_source: transcriptomic

data_processing:
bisulfite libraries were processed using Bismark (v0.22.3) and as previously described [Hunt, K. V. et al. sTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs. Scientific Reports (2022)] [Hunt, K. V. et al.  Protocol for targeted analysis of transposable element methylation levels and transcriptome in single cells using scTEM-seq. Protocol Exchange  (2022)].
After initial demultiplexing of primary Illumina indexes, Cutadapt (v2.10) [18] was used to demultiplex pools based on custom secondary indexes
Commands –g and -G were used to pass named forward and reverse index lists as a .fasta file to Cutadapt for demultiplexing
Bisulfite reads were trimmed using Trim Galore (v0.6.5). 10bp was trimmed from both the 5’ and 3’ ends to remove oligo sequences from reads.
Reads were mapped to Bowtie2 (v 2.4.1) indexed human genome (GRCh38) non-directionally and as paired end using Bismark (v0.22.3)
The methylation extraction module from Bismark was then used to produce coverage files (.cov) for methylation analysis.
Assembly: GRCh38
Supplementary files format and content: Bismark output file: genome-wide CpG methylation reports (CpG.cov.gz) are tab-delimited, use 1-based genomic coordinates and are in the following format: <chromosome> <position> <methylation rate>
Following demultiplexing, squencing runs with multiple sequencing lanes per read were concatenated into single R1 and R2 fastq files, per sample using zcat and gzip.
Raw reads were trimmed in pair-end mode using Trim Galore (v0.6.5) and Cutadapt (v2.10), retaining unpaired reads.
Hisat2 (v2.1.0) was used to map and align trimmed and unpaired reads using default parameters (--phred33) to the human reference genome build (GRCh38), and samtools (v1.10) was used to sort by coordinate and generate bam files.
TEtranscripts (v2.2.1) was used to obtain raw gene and transposable element countreateds from unique and ambiguously aligned reads (bam files) using TEcountreated with the flags '--sortByPos --mode multi’. The GTF files used were generated as follows: 1) TEs (http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/rmsk.txt.gz; USCS repeating element Repeat Masker; hg38; 2021-09-03) and 2) genes (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_30/gencode.v30.annotation.gtf.gz; gencode Release 30; GRCh38.p12; 2019-04-08). To ensure the GTF files worked with TEtranscripts the gene GTF (from gencode) was updated by converting ‘M’ to ‘MT’ for mitochondrial genes in the chromosome column and removal of ‘Chr’ preceding each chromosome number. The TE GTF was generated from the repeat mask file  using the conversion tool from the TEtranscripts developers (http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/makeTEgtf.pl.gz) ‘perl makeTEgtf.pl -c 6 -s 7 -e 8 -o 10 -t 11 -n hg38_rmsk -f 13 -C 12 -S 2 rmsk.txt >> hg38_rmsk_TE.gtf’ and removing ‘chr’ from chromosome names ‘sed 's/chr//' hg38_rmsk_TE.gtf > hg38_rmsk_TE_NoChr.gtf’.    TEtranscripts the gene GTF (from gencode) was updated by converting ‘M’ to ‘MT’ for mitochondrial
Individual sample counts from TEtranscripts were collated into a single countreated table (tab-deliminated) and updated with relevant gene information from the gene GTF file.
Assembly: GRCh38
Supplementary files format and content: Count table (tab-deliminated) compiled from TEtranscripts results. First column contains gene (ensembl ID) and transposable element (TE) ID and column two contains hgnc symbol equiavelnt (gene IDs). Columns 3-7 contains TE information and columns 7-13  contains gene informations. Countreateds for individual samples are contained in column 14 onwards.

molecule: polyA RNA

value: RNA-Seq


title: D8_MV411_colonies_rep2, RNA


title: D7_MV411_colonies_rep2, RNA


title: D6_MV411_colonies_rep2, RNA


title: D9_MV411_colonies_rep2, RNA


title: D4_MV411_colonies_rep2, RNA


title: 24 hr Irradiated USFKD, Replicate 3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from 24 hr Irradiated USFKD

hyb_protocol: Five and one half micrograms (5.5 μg) of amplified biotin-cDNAs were fragmented and hybridized to each array for 16 hours at 45°C in a rotating hybridization oven. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0001.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Expression Console Software (AGCC; Version 1.2) using the SST-RMA algorithm to generate .CHP files.

label: biotin

organism: Mus musculus

source_name: M12 B lymphocytes

label_protocol: Three hundred nanograms (300 ng) of total RNA were amplified and labeled as directed using the Affymetrix WT Plus Reagent Kit (WT Plus Kit).

growth_protocol: Murine M12 germinal center B lymphocytes were cultured at 37oC/5% CO2 in RPMI 1640 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.01% penicillin/streptomycin, and 50 mM β-mercaptoethanol

extract_protocol: Total RNA was extracted using Qiagen Rneasy Plus according to the manufacturer's instructions

treatment_protocol: For USF depletion, cells were stably transduced with lentiviral particles that encoded shRNAs targeting either USF1 or USF2. Puromycin-resistent clones were selected after 7-10 days in culture and USF depletion confirmed by Western blot. For irradiation, cells were exposed to ionizing radiation (5 Gy) at room temperature using a Gammacell 220 cobalt-60 irradiator (MDS Nordion), and allowed to grow for 1 or 7 days under normal culture conditions before RNA harvest.

value: B Lymphocytes


title: D3_MV411_colonies_rep2, RNA


title: 7 Day Irradiated Control, Replicate 2

description: Gene expression from 7 Day Irradiated Control


title: D2_MV411_colonies_rep2, RNA


title: 7 Day Irradiated USFKD, Replicate 2

description: Gene expression from 7 Day Irradiated USFKD


title: 24 hr Irradiated Control, Replicate 1

description: Gene expression from 24 hr Irradiated Control


title: Untreated USFKD, Replicate 3

description: Gene expression from Untreated USFKD


title: 7 Day  Irradiated USFKD, Replicate 3


title: D5_MV411_colonies_rep2, RNA


title: 7 Day Irradiated USFKD, Replicate 1


title: 7 Day Irradiated Control, Replicate 1


title: C9_MV411_colonies_rep2, RNA


title: C11_MV411_colonies_rep2, RNA


title: Untreated Control, Replicate 3

description: Gene expression from Untreated Control


title: 24 hr Irradiated USFKD, Replicate 2


title: D1_MV411_colonies_rep2, RNA


title: C12_MV411_colonies_rep2, RNA


title: 24 hr Irradiated USFKD, Replicate 1


title: Untreated Control, Replicate 1

description: Gene expression from Untreated Control


title: D12_HL60_colonies_rep1, CpG


title: C8_MV411_colonies_rep2, RNA


title: 7 Day Irradiated Control, Replicate 3


title: 24 hr Irradiated Control, Replicate 2


title: C10_MV411_colonies_rep2, RNA


title: Untreated USFKD, Replicate 1

description: Gene expression from Untreated USFKD


title: C6_MV411_colonies_rep2, RNA


title: C4_MV411_colonies_rep2, RNA


title: C1_MV411_colonies_rep2, RNA


title: B11_MV411_colonies_rep2, RNA


title: B10_MV411_colonies_rep2, RNA


title: B9_MV411_colonies_rep2, RNA


title: C2_MV411_colonies_rep2, RNA


title: B6_MV411_colonies_rep2, RNA


title: B5_MV411_colonies_rep2, RNA


title: B7_MV411_colonies_rep2, RNA


title: Untreated Control, Replicate 2

description: Gene expression from Untreated Control


title: C7_MV411_colonies_rep2, RNA


title: B8_MV411_colonies_rep2, RNA


title: 24 hr Irradiated Control, Replicate 3


title: Untreated USFKD, Replicate 2

description: Gene expression from Untreated USFKD


title: C5_MV411_colonies_rep2, RNA


title: B1_MV411_colonies_rep2, RNA


title: A11_MV411_colonies_rep2, RNA


title: B2_MV411_colonies_rep2, RNA


title: A12_MV411_colonies_rep2, RNA


title: A9_MV411_colonies_rep2, RNA


title: A10_MV411_colonies_rep2, RNA


title: A7_MV411_colonies_rep2, RNA


title: A6_MV411_colonies_rep2, RNA


title: B4_MV411_colonies_rep2, RNA


title: B12_MV411_colonies_rep2, RNA


title: A5_MV411_colonies_rep2, RNA


title: H9_MV411_colonies_rep1, RNA


title: A4_MV411_colonies_rep2, RNA


title: A3_MV411_colonies_rep2, RNA


title: A1_MV411_colonies_rep2, RNA


title: H8_MV411_colonies_rep1, RNA


title: H12_MV411_colonies_rep1, RNA


title: H5_MV411_colonies_rep1, RNA


title: A2_MV411_colonies_rep2, RNA


title: H4_MV411_colonies_rep1, RNA


title: H11_MV411_colonies_rep1, RNA


title: H10_MV411_colonies_rep1, RNA


title: H6_MV411_colonies_rep1, RNA


title: H7_MV411_colonies_rep1, RNA


title: Amniotic fluid

city: Shenzhen

first: Tong

last: Zhang

address: Longgang District Maternity & Child Healthcare Hospital of Shenzhen City

country: China

description: Hybridized to Cytoscan750K

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CHAS 4.3.0) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CHAS 4.3.0. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

source_name: Amniotic fluid

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA is extracted from prenatal specimens or aborted tissue using the Qiagen DNA Blood mini kit. The quality and quantity of DNA were evaluated by spectrophotometer and agarose gel electrophoresis.

value: female


title: villus

institute: Longgang District Maternity & Child Healthcare Hospital of Shenzhen City

description: Hybridized to Cytoscan750K

source_name: villus


title: H3_MV411_colonies_rep1, RNA

value: Peripheral blood


title: H2_MV411_colonies_rep1, RNA

value: macrophage


title: H1_MV411_colonies_rep1, RNA

value: Biphenotypic B Myelomonocytic Leukemia


title: G12_MV411_colonies_rep1, RNA

value: Male


title: G8_MV411_colonies_rep1, RNA

value: decitabine


title: G9_MV411_colonies_rep1, RNA


title: G10_MV411_colonies_rep1, RNA


title: G7_MV411_colonies_rep1, RNA


title: G5_MV411_colonies_rep1, RNA


title: F9_MV411_colonies_rep1, RNA


title: G1_MV411_colonies_rep1, RNA


title: F10_MV411_colonies_rep1, RNA


title: F8_MV411_colonies_rep1, RNA


title: G3_MV411_colonies_rep1, RNA


title: G4_MV411_colonies_rep1, RNA


title: F3_MV411_colonies_rep1, RNA


title: G6_MV411_colonies_rep1, RNA


title: F12_MV411_colonies_rep1, RNA


title: G2_MV411_colonies_rep1, RNA


title: B3_MV411_colonies_rep2, RNA


title: F11_MV411_colonies_rep1, RNA


title: F7_MV411_colonies_rep1, RNA


title: F2_MV411_colonies_rep1, RNA


title: F4_MV411_colonies_rep1, RNA


title: F1_MV411_colonies_rep1, RNA


title: G11_MV411_colonies_rep1, RNA


title: E12_MV411_colonies_rep1, RNA


title: E11_MV411_colonies_rep1, RNA


title: E9_MV411_colonies_rep1, RNA


title: E8_MV411_colonies_rep1, RNA


title: E6_MV411_colonies_rep1, RNA


title: E7_MV411_colonies_rep1, RNA


title: E5_MV411_colonies_rep1, RNA


title: E4_MV411_colonies_rep1, RNA


title: E10_MV411_colonies_rep1, RNA


title: F6_MV411_colonies_rep1, RNA


title: E3_MV411_colonies_rep1, RNA


title: E2_MV411_colonies_rep1, RNA


title: F5_MV411_colonies_rep1, RNA


title: E1_MV411_colonies_rep1, RNA


title: D10_MV411_colonies_rep1, RNA


title: D7_MV411_colonies_rep1, RNA


title: D11_MV411_colonies_rep1, RNA


title: D5_MV411_colonies_rep1, RNA


title: D6_MV411_colonies_rep1, RNA


title: D4_MV411_colonies_rep1, RNA


title: D3_MV411_colonies_rep1, RNA


title: D12_MV411_colonies_rep1, RNA


title: D2_MV411_colonies_rep1, RNA


title: D9_MV411_colonies_rep1, RNA


title: D8_MV411_colonies_rep1, RNA


title: D1_MV411_colonies_rep1, RNA


title: C11_MV411_colonies_rep1, RNA


title: C12_MV411_colonies_rep1, RNA


title: C10_MV411_colonies_rep1, RNA


title: C7_MV411_colonies_rep1, RNA


title: C8_MV411_colonies_rep1, RNA


title: C5_MV411_colonies_rep1, RNA


title: C6_MV411_colonies_rep1, RNA


title: C9_MV411_colonies_rep1, RNA


title: C4_MV411_colonies_rep1, RNA


title: C3_MV411_colonies_rep1, RNA


title: C2_MV411_colonies_rep1, RNA


title: C1_MV411_colonies_rep1, RNA


title: B12_MV411_colonies_rep1, RNA


title: B11_MV411_colonies_rep1, RNA


title: B10_MV411_colonies_rep1, RNA


title: B8_MV411_colonies_rep1, RNA


title: B7_MV411_colonies_rep1, RNA


title: B3_MV411_colonies_rep1, RNA


title: A11_MV411_colonies_rep1, RNA


title: A12_MV411_colonies_rep1, RNA


title: B1_MV411_colonies_rep1, RNA


title: A10_MV411_colonies_rep1, RNA


title: B4_MV411_colonies_rep1, RNA


title: A9_MV411_colonies_rep1, RNA


title: A7_MV411_colonies_rep1, RNA


title: A8_MV411_colonies_rep1, RNA


title: A6_MV411_colonies_rep1, RNA


title: A5_MV411_colonies_rep1, RNA


title: A3_MV411_colonies_rep1, RNA


title: A1_MV411_colonies_rep1, RNA


title: H12_Molm13_colony_rep3, RNA

value: acute myeloid leukemia


title: B9_MV411_colonies_rep1, RNA


title: H11_Molm13_colony_rep3, RNA

value: Acute myeloid leukemia (M5a)


title: H10_Molm13_colony_rep3, RNA


title: B6_MV411_colonies_rep1, RNA


title: B5_MV411_colonies_rep1, RNA


title: H9_Molm13_colony_rep3, RNA


title: H8_Molm13_colony_rep3, RNA


title: H5_Molm13_colony_rep3, RNA


title: H7_Molm13_colony_rep3, RNA


title: B2_MV411_colonies_rep1, RNA


title: H6_Molm13_colony_rep3, RNA


title: C3_MV411_colonies_rep2, RNA


title: H3_Molm13_colony_rep3, RNA


title: H2_Molm13_colony_rep3, RNA


title: H1_Molm13_colony_rep3, RNA


title: G10_Molm13_colony_rep3, RNA


title: G11_Molm13_colony_rep3, RNA


title: G9_Molm13_colony_rep3, RNA


title: A4_MV411_colonies_rep1, RNA


title: A2_MV411_colonies_rep1, RNA


title: G7_Molm13_colony_rep3, RNA


title: G6_Molm13_colony_rep3, RNA


title: G8_Molm13_colony_rep3, RNA


title: G4_Molm13_colony_rep3, RNA


title: G3_Molm13_colony_rep3, RNA


title: G2_Molm13_colony_rep3, RNA


title: G5_Molm13_colony_rep3, RNA


title: F11_Molm13_colony_rep3, RNA


title: F12_Molm13_colony_rep3, RNA


title: H4_Molm13_colony_rep3, RNA


title: F10_Molm13_colony_rep3, RNA


title: F9_Molm13_colony_rep3, RNA


title: F8_Molm13_colony_rep3, RNA


title: F7_Molm13_colony_rep3, RNA


title: F6_Molm13_colony_rep3, RNA


title: G1_Molm13_colony_rep3, RNA


title: F5_Molm13_colony_rep3, RNA


title: F4_Molm13_colony_rep3, RNA


title: G12_Molm13_colony_rep3, RNA


title: F1_Molm13_colony_rep3, RNA


title: E12_Molm13_colony_rep3, RNA


title: E11_Molm13_colony_rep3, RNA


title: E9_Molm13_colony_rep3, RNA


title: F3_Molm13_colony_rep3, RNA


title: E10_Molm13_colony_rep3, RNA


title: E8_Molm13_colony_rep3, RNA


title: E6_Molm13_colony_rep3, RNA


title: E5_Molm13_colony_rep3, RNA


title: E2_Molm13_colony_rep3, RNA


title: E1_Molm13_colony_rep3, RNA


title: E3_Molm13_colony_rep3, RNA


title: E4_Molm13_colony_rep3, RNA


title: E7_Molm13_colony_rep3, RNA


title: D12_Molm13_colony_rep3, RNA


title: D11_Molm13_colony_rep3, RNA


title: A8_MV411_colonies_rep2, RNA


title: D10_Molm13_colony_rep3, RNA


title: D9_Molm13_colony_rep3, RNA


title: D5_Molm13_colony_rep3, RNA


title: D4_Molm13_colony_rep3, RNA


title: D3_Molm13_colony_rep3, RNA


title: D6_Molm13_colony_rep3, RNA


title: D7_Molm13_colony_rep3, RNA


title: D2_Molm13_colony_rep3, RNA


title: D8_Molm13_colony_rep3, RNA


title: F2_Molm13_colony_rep3, RNA


title: C10_Molm13_colony_rep3, RNA


title: C12_Molm13_colony_rep3, RNA


title: D1_Molm13_colony_rep3, RNA


title: C11_Molm13_colony_rep3, RNA


title: C6_Molm13_colony_rep3, RNA


title: C8_Molm13_colony_rep3, RNA


title: C9_Molm13_colony_rep3, RNA


title: C5_Molm13_colony_rep3, RNA


title: C7_Molm13_colony_rep3, RNA


title: C3_Molm13_colony_rep3, RNA


title: C2_Molm13_colony_rep3, RNA


title: C4_Molm13_colony_rep3, RNA


title: C1_Molm13_colony_rep3, RNA


title: B10_Molm13_colony_rep3, RNA


title: B11_Molm13_colony_rep3, RNA


title: B12_Molm13_colony_rep3, RNA


title: B9_Molm13_colony_rep3, RNA


title: B8_Molm13_colony_rep3, RNA


title: B7_Molm13_colony_rep3, RNA


title: B6_Molm13_colony_rep3, RNA


title: B3_Molm13_colony_rep3, RNA


title: A11_Molm13_colony_rep3, RNA


title: A9_Molm13_colony_rep3, RNA


title: B2_Molm13_colony_rep3, RNA


title: A12_Molm13_colony_rep3, RNA


title: B4_Molm13_colony_rep3, RNA


title: B1_Molm13_colony_rep3, RNA


title: B5_Molm13_colony_rep3, RNA


title: A8_Molm13_colony_rep3, RNA


title: A10_Molm13_colony_rep3, RNA


title: A5_Molm13_colony_rep3, RNA


title: A3_Molm13_colony_rep3, RNA


title: A2_Molm13_colony_rep3, RNA


title: A7_Molm13_colony_rep3, RNA


title: A6_Molm13_colony_rep3, RNA


title: H11_Molm13_colony_rep2, RNA


title: A1_Molm13_colony_rep3, RNA


title: H10_Molm13_colony_rep2, RNA


title: A4_Molm13_colony_rep3, RNA


title: H9_Molm13_colony_rep2, RNA


title: H6_Molm13_colony_rep2, RNA


title: H4_Molm13_colony_rep2, RNA


title: H1_Molm13_colony_rep2, RNA


title: H5_Molm13_colony_rep2, RNA


title: H3_Molm13_colony_rep2, RNA


title: G12_Molm13_colony_rep2, RNA


title: G10_Molm13_colony_rep2, RNA


title: G11_Molm13_colony_rep2, RNA


title: G9_Molm13_colony_rep2, RNA


title: G8_Molm13_colony_rep2, RNA


title: G6_Molm13_colony_rep2, RNA


title: G2_Molm13_colony_rep2, RNA


title: G3_Molm13_colony_rep2, RNA


title: G1_Molm13_colony_rep2, RNA


title: F12_Molm13_colony_rep2, RNA


title: G7_Molm13_colony_rep2, RNA


title: F10_Molm13_colony_rep2, RNA


title: H12_Molm13_colony_rep2, RNA


title: F11_Molm13_colony_rep2, RNA


title: F6_Molm13_colony_rep2, RNA


title: F7_Molm13_colony_rep2, RNA


title: F8_Molm13_colony_rep2, RNA


title: H2_Molm13_colony_rep2, RNA


title: H8_Molm13_colony_rep2, RNA


title: F9_Molm13_colony_rep2, RNA


title: F4_Molm13_colony_rep2, RNA


title: H7_Molm13_colony_rep2, RNA


title: F2_Molm13_colony_rep2, RNA


title: F5_Molm13_colony_rep2, RNA


title: F3_Molm13_colony_rep2, RNA


title: F1_Molm13_colony_rep2, RNA


title: E11_Molm13_colony_rep2, RNA


title: E10_Molm13_colony_rep2, RNA


title: G5_Molm13_colony_rep2, RNA


title: G4_Molm13_colony_rep2, RNA


title: E9_Molm13_colony_rep2, RNA


title: E8_Molm13_colony_rep2, RNA


title: E7_Molm13_colony_rep2, RNA


title: E5_Molm13_colony_rep2, RNA


title: D12_Molm13_colony_rep2, RNA


title: E4_Molm13_colony_rep2, RNA


title: E3_Molm13_colony_rep2, RNA


title: D11_Molm13_colony_rep2, RNA


title: E1_Molm13_colony_rep2, RNA


title: D7_Molm13_colony_rep2, RNA


title: D10_Molm13_colony_rep2, RNA


title: D6_Molm13_colony_rep2, RNA


title: D5_Molm13_colony_rep2, RNA


title: D8_Molm13_colony_rep2, RNA


title: D3_Molm13_colony_rep2, RNA


title: D2_Molm13_colony_rep2, RNA


title: D4_Molm13_colony_rep2, RNA


title: C10_Molm13_colony_rep2, RNA


title: E12_Molm13_colony_rep2, RNA


title: D1_Molm13_colony_rep2, RNA


title: C11_Molm13_colony_rep2, RNA


title: C8_Molm13_colony_rep2, RNA


title: E6_Molm13_colony_rep2, RNA


title: C7_Molm13_colony_rep2, RNA


title: C5_Molm13_colony_rep2, RNA


title: C4_Molm13_colony_rep2, RNA


title: C6_Molm13_colony_rep2, RNA


title: C3_Molm13_colony_rep2, RNA


title: C1_Molm13_colony_rep2, RNA


title: C2_Molm13_colony_rep2, RNA


title: E2_Molm13_colony_rep2, RNA


title: B12_Molm13_colony_rep2, RNA


title: D9_Molm13_colony_rep2, RNA


title: B10_Molm13_colony_rep2, RNA


title: B11_Molm13_colony_rep2, RNA


title: B8_Molm13_colony_rep2, RNA


title: C12_Molm13_colony_rep2, RNA


title: B6_Molm13_colony_rep2, RNA


title: B3_Molm13_colony_rep2, RNA


title: B5_Molm13_colony_rep2, RNA


title: B2_Molm13_colony_rep2, RNA


title: B1_Molm13_colony_rep2, RNA


title: B4_Molm13_colony_rep2, RNA


title: A12_Molm13_colony_rep2, RNA


title: A9_Molm13_colony_rep2, RNA


title: A8_Molm13_colony_rep2, RNA


title: C9_Molm13_colony_rep2, RNA


title: A7_Molm13_colony_rep2, RNA


title: A6_Molm13_colony_rep2, RNA


title: A10_Molm13_colony_rep2, RNA


title: A4_Molm13_colony_rep2, RNA


title: A5_Molm13_colony_rep2, RNA


title: A3_Molm13_colony_rep2, RNA


title: A2_Molm13_colony_rep2, RNA


title: H11_Molm13_colony_rep1, RNA


title: H10_Molm13_colony_rep1, RNA


title: B9_Molm13_colony_rep2, RNA


title: A1_Molm13_colony_rep2, RNA


title: H8_Molm13_colony_rep1, RNA


title: H9_Molm13_colony_rep1, RNA


title: H7_Molm13_colony_rep1, RNA


title: B7_Molm13_colony_rep2, RNA


title: H5_Molm13_colony_rep1, RNA


title: H6_Molm13_colony_rep1, RNA


title: H4_Molm13_colony_rep1, RNA


title: H2_Molm13_colony_rep1, RNA


title: H3_Molm13_colony_rep1, RNA


title: G10_Molm13_colony_rep1, RNA


title: A11_Molm13_colony_rep2, RNA


title: G12_Molm13_colony_rep1, RNA


title: G11_Molm13_colony_rep1, RNA


title: G9_Molm13_colony_rep1, RNA


title: G8_Molm13_colony_rep1, RNA


title: G5_Molm13_colony_rep1, RNA


title: G7_Molm13_colony_rep1, RNA


title: G6_Molm13_colony_rep1, RNA


title: G2_Molm13_colony_rep1, RNA


title: G1_Molm13_colony_rep1, RNA


title: G4_Molm13_colony_rep1, RNA


title: G3_Molm13_colony_rep1, RNA


title: F9_Molm13_colony_rep1, RNA


title: F11_Molm13_colony_rep1, RNA


title: H12_Molm13_colony_rep1, RNA


title: F12_Molm13_colony_rep1, RNA


title: F8_Molm13_colony_rep1, RNA


title: F5_Molm13_colony_rep1, RNA


title: F10_Molm13_colony_rep1, RNA


title: F6_Molm13_colony_rep1, RNA


title: F4_Molm13_colony_rep1, RNA


title: F3_Molm13_colony_rep1, RNA


title: H1_Molm13_colony_rep1, RNA


title: E12_Molm13_colony_rep1, RNA


title: E9_Molm13_colony_rep1, RNA


title: F7_Molm13_colony_rep1, RNA


title: E11_Molm13_colony_rep1, RNA


title: E7_Molm13_colony_rep1, RNA


title: E10_Molm13_colony_rep1, RNA


title: F2_Molm13_colony_rep1, RNA


title: E5_Molm13_colony_rep1, RNA


title: F1_Molm13_colony_rep1, RNA


title: E8_Molm13_colony_rep1, RNA


title: E3_Molm13_colony_rep1, RNA


title: E4_Molm13_colony_rep1, RNA


title: E2_Molm13_colony_rep1, RNA


title: E1_Molm13_colony_rep1, RNA


title: D12_Molm13_colony_rep1, RNA


title: D10_Molm13_colony_rep1, RNA


title: D11_Molm13_colony_rep1, RNA


title: D8_Molm13_colony_rep1, RNA


title: D9_Molm13_colony_rep1, RNA


title: D7_Molm13_colony_rep1, RNA


title: D6_Molm13_colony_rep1, RNA


title: D5_Molm13_colony_rep1, RNA


title: D1_Molm13_colony_rep1, RNA


title: D4_Molm13_colony_rep1, RNA


title: D2_Molm13_colony_rep1, RNA


title: C12_Molm13_colony_rep1, RNA


title: C11_Molm13_colony_rep1, RNA


title: C10_Molm13_colony_rep1, RNA


title: D3_Molm13_colony_rep1, RNA


title: E6_Molm13_colony_rep1, RNA


title: C8_Molm13_colony_rep1, RNA


title: C9_Molm13_colony_rep1, RNA


title: C6_Molm13_colony_rep1, RNA


title: C5_Molm13_colony_rep1, RNA


title: C4_Molm13_colony_rep1, RNA


title: C2_Molm13_colony_rep1, RNA


title: C1_Molm13_colony_rep1, RNA


title: B12_Molm13_colony_rep1, RNA


title: B11_Molm13_colony_rep1, RNA


title: B10_Molm13_colony_rep1, RNA


title: B7_Molm13_colony_rep1, RNA


title: B8_Molm13_colony_rep1, RNA


title: B9_Molm13_colony_rep1, RNA


title: B6_Molm13_colony_rep1, RNA


title: B4_Molm13_colony_rep1, RNA


title: B5_Molm13_colony_rep1, RNA


title: B3_Molm13_colony_rep1, RNA


title: B2_Molm13_colony_rep1, RNA


title: A12_Molm13_colony_rep1, RNA


title: A11_Molm13_colony_rep1, RNA


title: A7_Molm13_colony_rep1, RNA


title: A8_Molm13_colony_rep1, RNA


title: A5_Molm13_colony_rep1, RNA


title: A10_Molm13_colony_rep1, RNA


title: A6_Molm13_colony_rep1, RNA


title: A4_Molm13_colony_rep1, RNA


title: A9_Molm13_colony_rep1, RNA


title: B1_Molm13_colony_rep1, RNA


title: C7_Molm13_colony_rep1, RNA


title: C3_Molm13_colony_rep1, RNA


title: A2_Molm13_colony_rep1, RNA