title: Westar, rep1

description: Library name: Sample1


title: patient22

status: Public on Jun 25 2025

type: SRA

city: San Francisco

first: Isabelle

last: Liu

state: California

department: Department of Biochemistry and Biophysics

country: USA

institute: UCSF

description: Library name: Sample22

library_source: transcriptomic

data_processing:
Bam files were input into Pacbio's Iso-Seq analysis pipeline. First, patient samples were demultiplexed by PCR and SMRTbell barcodes using the lima package.
The isoseq-refine tool was used for further read refinement, including polyA tail trimming and concatemer removal, resulting in Full-Length Non-Chimeric (FLNC) reads that capture complete transcript structures with minimal errors. Then the ‘cluster’ command was called to cluster reads that represent the same transcript.
Following the generation of FLNC reads, the data was aligned to the reference genome using minimap2.
Transcript isoform quantification was performed using the bambu package in the quantification mode.
Assembly: hg38, gencode v47
Supplementary files format and content: a csv file of transcript TPM values generated by bambu for all samples

molecule: total RNA

organism: Homo sapiens

source_name: meningioma

extract_protocol:
Meningiomas were removed, flash frozen in liquid nitrogen, mechanically lysed using a TissueLyser II, and RNA was extracted from the lysed tissue using the Qiagen AllPrep DNA/RNA/miRNA Universal Kit (CAT# 80224).
Long-read RNA-seq libraries were constructed using the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, PacBio Iso-Seq Express Oligo Kit and SMRTbell express template prep kit 3.0 according to the manufacturer’s protocol.

tag: tissue

value: meningioma


title: R4817, rep3

city: Hangzhou

first: Mengjie

last: Gong

address: Yuhangtang Road-866

country: China

institute: Zhejiang University

data_processing:
All clean reads were mapped to B. napus ZS11 v0 genome by HISAT2 v2.2.1 to obtain FeatureCounts
Assembly: Brassica napus ZS11
Supplementary files format and content: The csv file includes counts for each sample.

organism: Brassica napus

source_name: shoot apices

growth_protocol: in the field

extract_protocol:
Total RNAs were extracted using steadyPure RNA Extraction Kit without Lysis Buffer (Accurate Biology, AG21024, China).
The nine polyA-selected RNA-sequencing libraryies of R5044, R5159 and R5161 harbouring BnaC3.LFY haplotype 1, and another nine of R4168, R4210 and R4817 harbouring BnaC3.LFY haplotype 2 were constructed and sequenced by Novogene Co., Ltd. (Beijing, China) using the Illunima platform.

value: shoot apices

tag: haplotype


title: EL.CS2.m.004.Epithelium

city: Chicago

first: CRI

last: Bioinformatics

state: IL

address: 5801 S. Ellis Ave.

institute: University of Chicago

description: Library name: DSP-1001660009340-A-C08

data_processing:
Sequencing files were processed into DCC format using the GeoMx NGS Pipeline software v1.0. GeoMx counts were log2 transformed in preparation for statistic data analysis.
Assembly: GRCh38.p13
Supplementary files format and content: DCC files include raw read counts along with RTS_IDs for each ROI
Supplementary files format and content: PKC file includes probe metadata describing the targets and is needed to interpret RTS_IDs in the DCC files

source_name: Epithelium

extract_protocol:
FFPE tissue sections (5 μm) sliced consecutively to Deep Viusal Proteomics samples were processed following the Nanostring GeoMx user manual (MAN-10132-04). In brief, tissue slides were deparaffinized and rehydrated, followed by protein target retrieval using antigen retrieval buffer (Tris-EDTA) for 20 min in a pressure cooker. RNA target retrieval was accomplished by a digest with proteinase K for 15 min at 37°C. Tissue was post-fixed in 10% NBF, followed by an overnight hybridization at 37°C with the RNA probes (Human Whole Transcriptome Atlas, 18,000 protein-coding genes coupled to UV-cleavable oligonucleotide barcodes). Excess probes were removed the next day by washing the samples twice in stringent washes at 37°C, followed by an incubation period in blocking buffer W (Nanostring LOT#:2-23020032). Thereafter, tissue was stained using conjugated primary antibodies targeting pan-cytokeratin (mouse monoclonal antibody, Novus NBP2-33200AF488, 1:100) and vimentin (mouse monoclonal IgG1κ, Santa Cruz sc-373717, 1:100) as well as the SYTO13 nuclear stain (ThermoFisher Scientific, S7575) for one hour at room temperature. For transcriptomics data acquisition, slides were placed on the GeoMx Digital Spatial Profiler (DSP) and scanned in 20x magnification. Based on immunofluorescence images, regions of interest (ROI) were collected under supervision of an experienced pathologist (AB) and matched to the regions selected in DVP. Upon ROI selection, oligonucleotide barcodes were collected into a 96-well plate by UV-ablation while precisely separating compartments in each region.
Sequencing libraries were prepared using the Illumina TruSeq technology for the ligation of sequencing adaptors and amplification. Amplified libraries were purified using two rounds of Ampure XP magnetic bead cleanup (ratio 1.2:1 (beads: library)) (HighPrep PCR from MAGBIO (Cat#: AC-60500). Purified libraries were sequenced in an Illumina NovaSeq flowcell PE50 at a depth of 100x /μm2.

value: Ovarian Cancer, Tumor

tag: cell type

value: Epithelium

tag: cohort

value: SBT


title: R4817, rep2


title: EL.CS2.m.006.Stroma

description: Library name: DSP-1001660009340-A-D01

source_name: Stroma

value: Stroma


title: EL.CS2.m.003.Stroma

description: Library name: DSP-1001660009340-A-C07


title: R4817, rep1


title: 4T1 cells, in vitro heterogeneity, lineage tracing cassette library, rep 2

city: Cambridge

first: Kathryn

last: Yost

state: Massachusetts

address: 455 Main St

department: Biology

institute: Whitehead Institute

description: Library name: PEtracer_4T1_invitro_rep2_LTC

library_source: transcriptomic single cell

data_processing:
All scRNA-seq data was processed using the Cellranger software package (version 7.1.0). To capture lineage information a custom reference genome was constructed by appending the 2171 lineage tracing cassette sequences to the human hg38 genome build. Both gene expression and lineage tracing cassette libraries were then aligned to this reference using default parameters. Since the reference contains all 2171 30bp barcode sequences the integration barcode (intBC) of each lineage tracing cassette read can be determined based on which element in the reference it aligns to. A custom Python script was used to extract lineage information from the bam alignment file generated by Cellranger. This script iterated through all reads aligned to a tracing cassette sequence. For each read the lineage mark (LM) sequence at each edit site was determined based on the alignment. For each UMI the number of supporting reads was calculated and the LM for each site set to the LM with the most read support (ties broken randomly). UMIs were then aggregated by intBC, cellBC, and the set of LMs detected across the three edit sites to generate a final LM table. scRNA-seq data for puromycin and blasticidin barcode libraries was aligned using Cellranger to a custom reference. This reference included puromycin and blasticidin resistance cassette sequences with ‘N’s indicating the positions of the 10nt random barcodes. A custom Python script was used to extract the barcode sequence from each read aligned to these elements, generate a consensus barcode for each UMI, and aggregate UMIs by barcode for each cell. To separate barcode calls corresponding to real integrations from sequencing errors and ambient RNA, for each 10x capture a Gaussian mixture model was fitted to the distribution of UMIs per barcode per cell. Barcode calls corresponding to the lower peak were excluded as likely errors. pegRNA libraries were processed using the “CRISPR Guide Capture” feature of Cellranger. pegRNA protospacer mismatch calls supported by <3 UMIs were filtered out and careful quality control performed to exclude cells with multiple pegRNA integrations as these cells could confound our estimation of protospacer mismatch kinetics. Cells with multiple pegRNA calls were removed as well as cells with lineage cassette reads where more than one edit site had an LM installed.
Assembly: mm10
Supplementary files format and content: Processed data barcodes/features/matrix and filtered_counts.h5 files contain the filtered_feature_bc_matrix transcript count matrix outputs from Cellranger. BlastBC_counts.csv, PuroBC_counts.csv, allele_counts.csv, and mapping_counts.csv files contain unfiltered static barcode, lineage tracing cassette allele, and intBC mapping count data.

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Single cell suspensions were washed with PBS + 0.04% BSA and captured using the 10X Genomics Next GEM Single Cell 3ʹ Kit v3.1
Gene expression libraries were prepared using the 10X Genomics Next GEM Single Cell 3ʹ Kit v3.1 according to the manufacturer's instructions. Targeted lineage tracing cassette, puromycin/blasticidin barcode, and pegRNA libraries were prepared from amplified cDNA using two or three rounds of PCR with target-specific amplification primers and sample indexing primers.

tag: cell line

tag: treatment


title: patient21

description: Library name: Sample21


title: 4T1 cells, in vitro heterogeneity, lineage tracing cassette library, rep 1

description: Library name: PEtracer_4T1_invitro_rep1_LTC


title: patient20

description: Library name: Sample20


title: EL.CS2.m.003.Epithelium

description: Library name: DSP-1001660009340-A-C06


title: patient19

description: Library name: Sample19


title: R4210, rep3


title: MPRA_GMSM-K_DNA_biological replicate 3

city: Seattle

first: Robert

middle: A.

last: Cornell

state: WA

address: 1959 NE Pacific Street

department: Oral Health Sciences

institute: University of Washington

description: Library name: MPRA_DNA3

library_source: other

data_processing:
All raw reads were processed regardless of quality score. Reads with the expected in-line multiplexing barcode for each sample followed by the spacer sequence were identified. Demultiplexed reads were then used to determine the number of unique occurrences of 9 bp sequences in the barcoded region of the reporter construct. Barcodes that exactly matched designed sequences were written to a file along with the barcode's count. All other reads and barcodes were discarded.
Assembly: hg19
Supplementary files format and content: The processed data file "MPRA_RawBarcodeCounts_allSamples.txt" contains the raw, unnormalized barcode counts for all samples: four RNA, one pre-transfection plamsid DNA and three post-transfection plasmid DNA.

molecule: other

source_name: GMSM-K

extract_protocol:
Forty eight hours post transfection RNA and DNA were extracted from four replicates using Quick-DNA/RNA Miniprep kit (Zymo Research) as per manufacturer’s instructions.
Isolated RNA was treated with Turbo DNaseI (ThermoFisher) as per manufacturer’s instructions. First strand of cDNA was synthesized with SuperScript III First-Strand Synthesis System (Thermo Fisher Scientific). The barcodes including the flanking sequence were amplified from cDNA, the post-transfection plasmid DNA and plasmid DNA samples (prior to transfection) with Phusion High-Fidelity PCR Master Mix (NEB) that yielded barcode sequences that were flanked with NheI and MfeI restriction enzyme sites. The products were digested with NheI and MfeI and then ligated to custom sequencing adapters with PE2 indexing barcodes and phased P1 barcodes. This product was further amplified and sequenced on the Illumina platform.

value: GMSM-K

value: fetal oral epithelial


title: Westar, rep2

description: Library name: Sample2

data_processing:
All clean reads were mapped to B. napus Westar v0 genome by HISAT2 v2.2.1 to obtain FeatureCounts
Assembly: Brassica napus Westar
Supplementary files format and content: The csv file includes counts for each sample.

growth_protocol: in the chamber

extract_protocol:
Total RNAs were extracted using steadyPure RNA Extraction Kit without Lysis Buffer (Accurate Biology, AG21024, China).
Th polyA-selected RNA-sequencing libraryies of Westar wild-type and BnaC3.lfy△I2 were constructed and sequenced by Novogene Co., Ltd. (Beijing, China) using the Illunima platform.


title: adjacent_1599104

type: RNA

city: sheng yang

first: li

middle: rui

last: ming

address: san hao jie

institute: china medical school

description: adjacent

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays (4x44K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The lncRNAs that at least half of samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed lncRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information.

source_name: whole adjacent tissue

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: RCC and matched non-tumor hepar tissues

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Tissues from RCC surgury and promptly frozen in liquid nitrogen.

value: whole adjacent tissue

tag: gender

value: male

tag: age


title: EL.CS2.m.002.Epithelium

description: Library name: DSP-1001660009340-A-C04


title: R4210, rep2


title: EL.CS2.m.002.Stroma

description: Library name: DSP-1001660009340-A-C05


title: Rcc tissue_2080951

description: Renal cell carcinoma

source_name: whole Rcc tissue

value: whole Rcc tissue

value: female


title: adjacent_2075354

description: adjacent


title: MPRA_GMSM-K_DNA_biological replicate 2

description: Library name: MPRA_DNA2


title: patient18

description: Library name: Sample18


title: patient17

description: Library name: Sample17


title: adjacent_2080951

description: adjacent


title: EL.CS2.m.001.Stroma

description: Library name: DSP-1001660009340-A-C03


title: Rcc tissue_1599104

description: Renal cell carcinoma


title: MPRA_GMSM-K_Plasmid_library

description: Library name: MPRA_Plasmid


title: EL.CS2.m.001.Epithelium

description: Library name: DSP-1001660009340-A-C02


title: Rcc tissue_2075354

description: Renal cell carcinoma


title: R4168, rep3


title: patient16

description: Library name: Sample16


title: R4168, rep2


title: R4210, rep1


title: patient15

description: Library name: Sample15


title: MPRA_GMSM-K_RNA_biological replicate 4

description: Library name: MPRA_RNA4


title: EL.CS1.m.012.Stroma

description: Library name: DSP-1001660009340-A-C01


title: R4168, rep1


title: patient14

description: Library name: Sample14


title: MPRA_GMSM-K_DNA_biological replicate 1

description: Library name: MPRA_DNA1


title: MPRA_GMSM-K_RNA_biological replicate 3

description: Library name: MPRA_RNA3


title: EL.CS1.m.011.Stroma

description: Library name: DSP-1001660009340-A-B11


title: patient13

description: Library name: Sample13


title: R5161, rep3


title: MPRA_GMSM-K_RNA_biological replicate 2

description: Library name: MPRA_RNA2


title: EL.CS1.m.011.Epithelium

description: Library name: DSP-1001660009340-A-B10


title: patient12

description: Library name: Sample12


title: R5161, rep2


title: MPRA_GMSM-K_RNA_biological replicate 1

description: Library name: MPRA_RNA1


title: patient11

description: Library name: Sample11


title: Sample_YsM-6_IGO_12855_F_6

city: New York

first: Yinwen

last: Liang

email: liangy@mskcc.org, liangyinwen@gmail.com

state: New York

address: 1275 york avenue

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

data_processing:
ATAC-seq reads were filtered for quality and 3' trimmed for adapter sequences. Reads were aligned to mouse assembly mm10 using bowtie2 (v2.3.4.1) with default parameters. To create density files, read overlap density was calculated with an extension of 0 bp and the signal was then normalized to the size factor calculation in DESeq2 and created using the BEDTools suite.
Assembly: mm10
Supplementary files format and content: BigWig files containing normalized read density

molecule: genomic DNA

source_name: mouse embryonic yolk sac

extract_protocol:
The yolk sac and gut tube were dissected from E8.75 (12 somite) Afp-GFP/+ embryos, disassocated into single cells, and applied to fluorescence-activated cell sorting to obtain high viability YsVE (GFP+) and YsMes (GFP-) cells from yolk sac samples and GutVE (GFP+) from gut tube samples. From each sample 10,000-30,000 cells were processed for ATAC-seq
Omni-ATAC protocol

value: mouse embryonic yolk sac

tag: genotype

value: Afp-GFP/+

value: YsMes


title: Sample_YsM-4_IGO_12855_F_3


title: R5159, rep3


title: patient10

description: Library name: Sample10


title: EL.CS1.m.009.Stroma

description: Library name: DSP-1001660009340-A-B07


title: patient9

description: Library name: Sample9


title: Sample_0125YsM2_IGO_12855_D_10


title: EL.CS1.m.008.Stroma

description: Library name: DSP-1001660009340-A-B05


title: R5161, rep1


title: patient8

description: Library name: Sample8


title: EL.CS1.m.012.Epithelium

description: Library name: DSP-1001660009340-A-B12


title: Sample_0126YsM3_IGO_12855_D_12


title: EL.CS1.m.010.Epithelium

description: Library name: DSP-1001660009340-A-B08


title: R5044, rep3


title: EL.CS1.m.008.Epithelium

description: Library name: DSP-1001660009340-A-B04


title: Sample_YsE-5_IGO_12855_F_5

value: YsVE


title: R5044, rep2


title: R5159, rep2


title: patient6

description: Library name: Sample6


title: patient7

description: Library name: Sample7


title: EL.CS1.m.009.Epithelium

description: Library name: DSP-1001660009340-A-B06


title: R5044, rep1


title: EL.CS1.m.007.Epithelium

description: Library name: DSP-1001660009340-A-B02


title: patient5

description: Library name: Sample5


title: Sample_0126YsE3_IGO_12855_D_11


title: EL.CS1.m.006.Stroma

description: Library name: DSP-1001660009340-A-B01


title: Sample_0125YsE1_IGO_12855_D_9


title: R5159, rep1


title: patient4

description: Library name: Sample4


title: EL.CS1.m.006.Epithelium

description: Library name: DSP-1001660009340-A-A12


title: patient3

description: Library name: Sample3


title: Sample_emVE-3_IGO_12855_F_4

source_name: mouse embryonic gut

value: mouse embryonic gut

value: GutVE


title: EL.CS1.m.005.Stroma

description: Library name: DSP-1001660009340-A-A11


title: Sample_emVE-2_IGO_12855_F_1


title: patient1

description: Library name: Sample1

value: meningioma


title: EL.CS1.m.005.Epithelium

description: Library name: DSP-1001660009340-A-A10

value: Ovarian Cancer, Tumor


title: Sample_0125emVE_IGO_12855_D_8


title: EL.CS1.m.004.Stroma

description: Library name: DSP-1001660009340-A-A09


title: Sample_YsE-4_IGO_12855_F_2


title: EL.CS1.m.003.Stroma

description: Library name: DSP-1001660009340-A-A07


title: L9_0968-rep 3

city: Changsha

first: Ning ning

last: Yan

state: Hunan

address: Changsha University of Science & Technology

institute: 长沙理工大学

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing low quality reads from raw data, and the Q20, Q30 and GC content of the clean data were calculated.
Then the clean reads were compared to the reference genome of Lacticaseibacillus paracasei L9 (NZ_CP012148).
Bowtie 2-2.2.3
Assembly: GCF_001244395.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Lacticaseibacillus paracasei

source_name: bacteria

growth_protocol: The mutants were cultured with MRS Broth (HuanKai Microbial, Guangdong, China) at 37oC with the addition of 10 μg/mL erythromycin (EM).

extract_protocol:
Total RNA was extracted using the Trizol method.The quantity of RNA was determined using a NanoDropTM ND-2000 spectrophotometer obtained from Thermo Fisher (USA). The integrity and total amount quality of RNA were assessed using an Agilent Technologies 2100 Bioanalyzer (Santa Clara, CA).
The RNA-seq transcriptome library was prepared using the TruSeqTM RNA library kit with 2 μg of extracted RNA. mRNA was purified from total RNA using probes to remove rRNA.First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then the RNaseH was used to degrade the RNA. The second strand of cDNA was synthesized by replacing dTTP with dUTP in the DNA polymerase I system. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. Then USER Enzyme was used to degrade the second strand of cDNA containing Uracil. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion HighFidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: 0.05% glycine deoxycholate (GDCA, Sigma-Aldrich, Germany ) was added to the medium to collect the cells when they were cultured to the logarithmic growth phase

value: bacteria


title: L9_0968-rep 2


title: L9_0968-rep 1


title: D0 CD34+ HSPCs_Sample 4_HIV exposed

city: Pretoria

first: Candice

middle: Laverne

last: Hendricks

state: Gauteng

address: 15 Bophelo Road, Prinshof Campus, University of Pretoria, Gezinaa

department: Medical Immunology

country: South Africa

institute: University of Pretoria

description:
Gene expression data from umbilical cord blood derived CD34+ HSPCs in an HIV exposed infant
Sample 4_HIV exposed

hyb_protocol: The GeneChip™ Hybridization, Wash and Stain Kit was used to hybridise chips in an Affymetrix GeneChip® Hybridisation Oven-645 (Serial #:C0115380), rotating at 60 rpm at 45°C for 17 hours, followed by washing and staining.

scan_protocol: Chips were scanned using the Affymetrix GeneChip® Scanner (Serial#: 54716570) to generate intensity CEL files

data_processing: The CEL files which have intensity values for all probes present on the scanned chips were imported into the Affymetrix Transcriptome Analysis Console (TAC) v4.0.3 software. Normalization and summarization of the CEL file data was done using SST-RMA algorithm to generate gene level CHP file. The Pos vs Neg AUC Threshold was set at 0.7. All samples passed this threshold; hence, the CHP files were used for differential gene expression analysis on the TAC v4.0.3 software to calculate fold change

label: Propritary DNA labeling reagents

source_name: CD34+ UCB HSPCs

label_protocol: The cDNA was labelled by terminal deoxynucleotidyl transferase (TdT) using the proprietary DNA Labeling Reagent (supplied with the GeneChip™ 3’ IVT Pico Kit) that is covalently linked to biotin

growth_protocol: Experiments were performed on freshly isolated cells thus no growth protocol was employed

extract_protocol: The RNA of enriched CD34+ HSPCs was extracted using the Qiagen RNeasy Micro Plus kit according to manufacturer's instructions.

treatment_protocol: UCB CD34+ HSPCs were isolated from the mononuclear layer of umbilical cord blood using magnetic isolation with a CD34+ Microbead kit.

value: Umbilical cord blood CD34+ Haematopoietic stem/progenitor cells

tag: subject status

value: HIV exposed infant


title: EL.CS1.m.004.Epithelium

description: Library name: DSP-1001660009340-A-A08

value: Epithelium

value: SBT


title: L9_melA-rep 3


title: D0 CD34+ HSPCs_Sample 1_HIV exposed

description:
Gene expression data from umbilical cord blood derived CD34+ HSPCs in an HIV exposed infant
Sample 1_HIV exposed


title: EL.CS1.m.001.Epithelium

description: Library name: DSP-1001660009340-A-A02


title: L9_melA-rep 2


title: circulating plasma miRNA

city: Boston

first: Worawan

middle: B

last: Limpitikul

state: MA

address: 55 Fruit Street

institute: Massachusetts General Hospital

description: This sample represents expression data for 21 miRNA for 4541 subjects.

hyb_protocol: see manufacter protocol: https://docs.abcam.com/pdf/kits/FirePlex-miRNA-Assay.pdf

scan_protocol: Millipore Guava HT

data_processing:
To account for potential batch effect across different plates, replicates of synthetic reference RNA (“RefRNA”) were run on each plate. The geometric mean of all RefRNA replicates was used to calculate per-plate scaling factors to normalize each plate. To account for sample volume input and other technical factors, a second normalization step was performed across all samples: the geometric mean of all subject samples was used to normalize each individual sample
Processed data value: mean fluorescent intensity (MFI)

source_name: plasma

label_protocol: not provided

extract_protocol: Whole blood was centrifuged at 3,000 g for 15 min and the top layer (plasma) was collected.

value: plasma

tag: diagnosis

value: acute coronary syndrome


title: D0 CD34+ HSPCs_Sample 4_HIV unexposed

description:
Gene expression data from umbilical cord blood derived CD34+ HSPCs in an HIV unexposed infant
Sample 4_HIV unexposed

value: HIV unexposed infant


title: L9_melA-rep 1


title: patient2

description: Library name: Sample2


title: D0 CD34+ HSPCs_Sample 5_HIV unexposed

description:
Gene expression data from umbilical cord blood derived CD34+ HSPCs in an HIV unexposed infant
Sample 5_HIV unexposed


title: Transitional AT2_2

status: Public on Jun 24 2025

city: Philadelphia

first: Michael

last: Beers

state: PA

address: 3450 Hamilton Walk

institute: University of Pennsylvania

description: Library name: I73T_CD51+_2

data_processing:
RNA-SEQ Fastq files from paired end reads were trimmed, processed and evaluated for quality control using fastp. Resulting files were aligned against the mouse genome (mm10) using bowtie2 and quantified via featureCounts. Duplicate reads and chimeric fragments were flagged and excluded from the analysis.
scRNA-seq Fastq files were aligned to the mm10 reference genome using STARSolo
Downstream processing was performed using Seurat v3
Assembly: mm10
Supplementary files format and content: tab seperated files

source_name: Lung

extract_protocol: scRNASeq Libraries were prepared using Illumina stranded total RNA accordine to manufacture instructions.  Total RNA for RNA-Seq was processed from cell pellets using the RNAeasy kit from Qiagen following manufacture instructions.

treatment_protocol: For scRNA-seq single cell suspensions were prepared by physical and enzymatic dissociation (Collagenase, DNase, Dispase) followed by MACS sorting by LS columns with CD45+ and CD31 cell removal using CD45 and CD31 micobeads. For flow cytometery RNA-seq single cell suspension were stainined with an antibody mix to identify AT2 cells and transitional AT2 cells. AT2 cells were identified as CD45-CD31-Epcam+CD104-MHCII hiCD51- and transitional At2 cells  CD45-CD31-Epcam+CD104-MHCII hiCD51+. Dead cells were excluded by Dapi staining. iAT2s were collected from matrigel dropplets via enzymatic digestion followed by immediate freezing of the cell pellets

value: Lung

value: Tamoxifen


title: Transitional AT2_3

description: Library name: I73T_CD51+_3


title: Transitional AT2_1

description: Library name: I73T_CD51+_1


title: B6_AT2_3

description: Library name: B6_CD51-_3

value: SftpcWT/WT


title: D0 CD34+ HSPCs_Sample 3_HIV exposed

description:
Gene expression data from umbilical cord blood derived CD34+ HSPCs in an HIV exposed infant
Sample 3_HIV exposed


title: I73T_AT2_1

description: Library name: I73T_CD51-_1


title: B6_AT2_1

description: Library name: B6_CD51-_1


title: B6_AT2_2

description: Library name: B6_CD51-_2


title: I73T_AT2_d14_4

description: Library name: AT2-24


title: D0 CD34+ HSPCs_Sample 2_HIV unexposed

description:
Gene expression data from umbilical cord blood derived CD34+ HSPCs in an HIV unexposed infant
Sample 2_HIV unexposed


title: EL.CS1.m.003.Epithelium

description: Library name: DSP-1001660009340-A-A06


title: I73T_AT2_d14_2

description: Library name: AT2-22


title: EL.CS1.m.002.Epithelium

description: Library name: DSP-1001660009340-A-A04


title: WT_12

description: Library name: AT2-20


title: D0 CD34+ HSPCs_Sample 3_HIV unexposed

description:
Gene expression data from umbilical cord blood derived CD34+ HSPCs in an HIV unexposed infant
Sample 3_HIV unexposed


title: WT_11

description: Library name: AT2-19


title: WT_10

description: Library name: AT2-18


title: WT_9

description: Library name: AT2-17


title: WT_8

description: Library name: AT2-14


title: I73T_AT2_3

description: Library name: I73T_CD51-_3


title: WT_7

description: Library name: AT2-13


title: I73T_AT2_2

description: Library name: I73T_CD51-_2


title: WT_6

description: Library name: AT2-10


title: I73T_AT2_d3_4

description: Library name: AT2-8


title: I73T_AT2_d3_1

description: Library name: AT2-5


title: I73T_AT2_d3_2

description: Library name: AT2-6


title: I73T_AT2_d14_3

description: Library name: AT2-23


title: D0 CD34+ HSPCs_Sample 1_HIV unexposed

description:
Gene expression data from umbilical cord blood derived CD34+ HSPCs in an HIV unexposed infant
Sample 1_HIV unexposed


title: D0 CD34+ HSPCs_Sample 2_HIV exposed

description:
Gene expression data from umbilical cord blood derived CD34+ HSPCs in an HIV exposed infant
Sample 2_HIV exposed


title: I73T_AT2_d14_1

description: Library name: AT2-21


title: WT_3

description: Library name: AT2-3


title: WT_2

description: Library name: AT2-2


title: WT_1

description: Library name: AT2-1


title: HoxA7 TPO-GFP+CD41-  K1v2-undifferentiation-sorted

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
BWA align
HTSEQ count
log2 FPKM transform
Assembly: mm9
Supplementary files format and content: Heme_mm9_log2FPKM_7_18_18.txt log2FPKM

source_name: ex vivo sorted reticulocytes from H2KGFP BM-adoptively transferred day11  mice

growth_protocol: ex vivo cell sorted

extract_protocol:
RNAeasy
total stranded

treatment_protocol: genetic transformation and time differential

value: bone marrow

value: reticulocytes


title: HoxA7 TPO-GFP+CD41-  K5-undifferentiation-sorted


title: HoxA7 TPO-GFP+CD41-  K3-undifferentiation-sorted


title: HoxA7 TPO-GFP+CD41-  K2-undifferentiation-sorted


title: HoxA7 TPO-GFP+CD41-  K1-undifferentiation-sorted


title: HoxA7 TPO-GFP+CD41+ K5-differentiation-sorted

source_name: ex vivo sorted reticulocytes from HoxA7-TPO (K3)-adoptively transferred day6  mice


title: HoxA7 TPO-GFP+CD41+ K3-differentiation-sorted


title: WT_5

description: Library name: AT2-9


title: HoxA7 TPO-GFP+CD41+ K1-differentiation-sorted


title: I73T_AT2_d3_3

description: Library name: AT2-7


title: HepG2_hsa-miR-1912_rep1

city: Seoul

first: Myeongjune

last: Go

address: Yonsei-ro,Seodaemun-gu

department: College of Medicine

country: South Korea

institute: Yonsei University

description: Gene expression after miR-1912 treatment

hyb_protocol: The Cy3-labeled aRNAs were resuspended in 50㎕ of hybridization solution (Agilent technologies, CA).After labeled aRNAs were placed on Agilent SurePrint G3 Human GE 8x60K array (Agilent technologies, CA) and covered by a Gasket 8-plex slide (Agilent technologies, CA). The slides were hybridized for 17hr at 65 ℃ oven. The hybridized slides were washed in 2 X SSC, 0.1 % SDS for 2 min, 1 X SSC for 3 min, and then 0.2 X SSC for 2 min at room temperature. The slides were centrifuged at 3000 rpm for 20 sec to dry.

scan_protocol: The micro arrays were scanned with the Agilent C scanner and the images were processed with the Agilent Feature Extraction v10.7.3.1 software

data_processing: The data were processed based on quantile normalization method using the GeneSpring GX 11.5.1 (Agilent technologies, CA). Each measured values were normalized to the 75% of all measurement from the array.

source_name: HepG2, hsa-miR-1912 treated

label_protocol: Each total RNA sample (200ng) was labeled and amplified using Low Input Quick Amp labeling kit (Agilent technologies, CA) following manufacturer's instrurction.

growth_protocol: HepG2 Cells [ATCC, HB-8065] were cultured with DMEM supplemented by 10% FBS containing 1% P/S. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2 and passaged every 4-5 days.

extract_protocol: Total RNAs were extracted with miRNeasy micro kit (Qiagen, Hiden, Germany) according to the manufacturer's instruction.

treatment_protocol: 2 × 10 5 of HepG2 cells were transfected with final concentration 40 nM of microRNA mimics by Lipofectamine 2000 according to manufacturer's instrument. The cells were incubated in DMEM supplemented with 10% FBS and 1% P/S on normal culture condition for 24 hours. Then the culture media was changed to DMEM supplemented with 10% DLPS and 1% P/S on normal culture condition for 24 hours.


title: FAB@MN-4

city: Chongqing

first: Tao

last: Chen

address: No.426, Songshi North Road, Yubei District

institute: Stomatological Hospital of Chongqing Medical University

description:
Library name: sample8
H4

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 and  |log2FoldChange| > 1 found by DESeq2 were assigned as differentially expressed.
Assembly: GRCh38-2020-A
Supplementary files format and content: gene_fpkm.xls

source_name: hypertrophic scar

extract_protocol:
HSFs were seeded at a density of 1 × 10^5 cells/well in a 24-well plate and cultured for 24 hours in DMEM containing 10% FBS. Subsequently, the cells were treated with FAB NPs for 4 hours, followed by 10 mins of illumination, and then incubated for another 24 hours. Total RNA was extracted using TRIzol reagent (Invitrogen, USA), and the integrity of the RNA was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). RNA samples were prepared using total RNA as a template. Initially, mRNA was extracted from total RNA using magnetic beads coated with poly-T oligonucleotides. This mRNA was then fragmented under high temperatures in the presence of divalent cations, using a 5X First Strand Synthesis Reaction Buffer. The synthesis of the first cDNA strand was achieved using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). This was followed by the synthesis of the second cDNA strand using DNA Polymerase I and RNase H. Exonuclease and polymerase activities were employed to transform remaining overhangs into blunt ends. Subsequent to the adenylation of the 3' ends of the DNA fragments, adapters containing hairpin loop structures were attached, setting the stage for hybridization. cDNA fragments ranging in size from 370-420 bp were isolated using the AMPure XP system (Beckman Coulter, Beverly, USA). Amplification of these fragments was then carried out using Phusion High-Fidelity DNA Polymerase, along with universal PCR primers and an Index (X) Primer. The PCR products were purified within the AMPure XP system, and the library's quality was evaluated using an Agilent Bioanalyzer 2100 system. Indexed samples were clustered on the cBot Cluster Generation System using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer's guidelines. Post-clustering, the library was sequenced on the Illumina Novaseq platform, producing 150 bp paired-end reads and thereby acquiring the sequence data of the fragments.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: hypertrophic scar

value: primary cell

value: fibroblast


title: FAB@MN-3

description:
Library name: sample7
H3


title: FAB@MN-2

description:
Library name: sample6
H2


title: WT_4

description: Library name: AT2-4


title: Control-2

description:
Library name: sample2
C2


title: Control-4

description:
Library name: sample4
C4


title: HepG2_hsa-miR-N.C_rep1

description: Gene expression after miR-N.C treatment

source_name: HepG2, hsa-miR-N.C treated

value: control


title: HepG2_hsa-miR-224_rep1

description: Gene expression after miR-224 treatment

source_name: HepG2, hsa-miR-224 treated


title: FAB@MN-1

description:
Library name: sample5
H1


title: Control-3

description:
Library name: sample3
C3


title: Control-1

description:
Library name: sample1
C1


title: Fulvestrant Resistant MCF-7 cells, Cold Atmospheric Plasma 600s 2

city: Goyang

first: Sooseong

last: Choi

institute: Dongguk university

description: Library name: Sample 10

data_processing:
FastQC v0.11.7 - quality check for data before raw sequence analysis
Trimmomatic 0.38 - trimming process
HISAT2 version 2.1.0 - mapping high throughput sequencing data in reference genome
StringTie version 2.1.3b - assembly of potential transcript using sequencing information in reference
Assembly: hg38
Supplementary files format and content: txt files include FPKM and TPM values for each samples

growth_protocol: A breast cancer cell line MCF-7 and T47D were purchased from the American Type Culture Collection (ATCC) (Manassas, VA, USA) and cultured in RPMI-1640 medium (Gibco, Los Angeles, CA, USA) supplemented with 10% FBS (Gibco) and 2% Penicillin and Streptomycin (Gibco) maintained at 37 °C in 5% CO2

extract_protocol:
RNA was extracted using Direct-zol RNA Miniprep Kit (Zymo Research, Irvine, CA, USA).
Libraries for RNA-seq were constructed using TruSeq Stranded Total RNA Library Prep Gold Kit (Sample 1 ~ 4) and TruSeq Stranded Total RNA with Ribo-Zero H/M/R_Gold (Sample 5 ~ 10)

treatment_protocol:
To construct fulvestrant resistant breast cancer cell lines, MCF-7 and T47D cells were continually exposed to increased doses of fulvestrant for 32 weeks, up to 4.0 and 3.0 nM.
The CAP device, a type of mesh - DBD (Dielectric Barrier Discharge), was manufactured at the Plasma Bioscience Research Center (Kwangwoon University, Korea). CAP was treated onto the cell in culture media for 600 sec at 0.12 kV, using argon gas flow of 1.5 L/min, with operation frequency 12.89 kHz.

value: epithelial cells

value: FulR_MCF-7 cells were treated with cold atmospheric plasma for 600s.


title: Fulvestrant Resistant MCF-7 cells, Cold Atmospheric Plasma 0s 2

description: Library name: Sample 8

value: FulR_MCF-7 cells were treated with cold atmospheric plasma for 0s.


title: Fulvestrant Resistant T47D cells, Cold Atmospheric Plasma 600s 1

description: Library name: Sample 3

value: FulR_T47D cells were treated with cold atmospheric plasma for 600s.


title: Fulvestrant Resistant T47D cells, Cold Atmospheric Plasma 600s 2

description: Library name: Sample 4


title: T47D cells, Cold Atmospheric Plasma 0s 2

description: Library name: Sample 6

value: T47D cells were treated with cold atmospheric plasma for 0s.


title: Fulvestrant Resistant T47D cells, Cold Atmospheric Plasma 0s 2

description: Library name: Sample 2

value: FulR_T47D cells were treated with cold atmospheric plasma for 0s.


title: Fulvestrant Resistant T47D cells, Cold Atmospheric Plasma 0s 1

description: Library name: Sample 1


title: Fulvestrant Resistant MCF-7 cells, Cold Atmospheric Plasma 0s 1

description: Library name: Sample 7


title: HoxA7 TPO-GFP+CD41+ K1v2-differentiation-sorted


title: HoxA7 TPO-GFP+CD41+ K2-differentiation-sorted


title: pADamID-RPE_H2AXwt2_tracr_10h_r2_damonly_sample

city: Amsterdam

first: Xabier

last: Vergara

state: North Holland

address: Plesmalaan 121

department: Molecular Genetics

country: Netherlands

institute: Netherlands Cancer Institute

description:
Library name: 7703_14_R2_Dam_WT2_tracr_CTGGAGAATA-TCCATACAAC_S14_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"

data_processing:
We processed the DNA sequencing data using the previously published computational pipeline (https://github.com/vansteensellab/pADamID_ABCB1_Novaseq)
Assembly: hg38
Supplementary files format and content: There are two processed data formats: (1) -gatc.counts.txt.gz, read counts per gatc sequence in the genome used for domainograms and (2) -20kb.bw, bigwig file at 20kb resolution
Library strategy: DamID-Seq

growth_protocol: Culturing methods per cell line are described in the manuscript

extract_protocol:
genomic DNA was extracted using the Bioline kit (details in methods section)
We followed pA-DamID library preparation protocol used for NOVAseq (details in methods section)

treatment_protocol: Trearment per sample are described in the manuscript

value: hTERT-immortalized retinal pigment epithelial

value: wildtype

tag: antibody

tag: transfection

tag: timepoint

tag: batch


title: E2185_ABCB1_DMSO_DAM-gatc.counts.txt.gz

description:
Library name: 7260_4_E2185_ABCB1_DMSO_DAM_CTTCGGAATC-CGTCGGTAAG_S4_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"

value: DMSO


title: E2185_ABCB1_DNApki_DAM-gatc.counts.txt.gz

description:
Library name: 7260_13_E2185_ABCB1_DNApki_DAM_TTGTGAAGGC-TCGTCAGTAC_S13_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: E2185_ABCB1_ATMi_DAM-gatc.counts.txt.gz

description:
Library name: 7260_7_E2185_ABCB1_ATMi_DAM_ACTTCAACAG-GCGTGAGCAT_S7_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_H2AXwt2_tracr_10h_r1_damonly_sample

description:
Library name: 7703_13_R1_Dam_WT2_tracr_GTGAGAGTAT-ATCTGTGAGG_S13_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: E2185_ABCB1_DMSO_LMNB2-gatc.counts.txt.gz

description:
Library name: 7260_5_E2185_ABCB1_DMSO_LMNB2_AACCACACTA-CCTCTGCTGA_S5_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_H2AXwt1_tracr_10h_r2_damonly_sample

description:
Library name: 7703_2_R2_Dam_WT1_tracr_CGGATTGATC-AGTCACAACA_S2_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_48h_r1_gH2AX_sample

description:
Library name: 7633_43_R1_48A_gH2AX_TTGTGAAGGC-TCGTCAGTAC_S43_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_48h_r2_gH2AX_sample

description:
Library name: 7633_46_R2_48A_gH2AX_CCTCTGTCAT-CGTATCGATT_S46_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_48h_r1_gH2AX_sample

description:
Library name: 7633_35_R1_48T_gH2AX_bis_AACCACACTA-CCTCTGCTGA_S35_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r2_H3K27me3_sample

description:
Library name: 7122_35_E2137_ID11_10h_RPE1_ABCB1_H3K27me3_R4_CTGGAGAATA-TCCATACAAC_S1_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: T47D cells, Cold Atmospheric Plasma 0s 1

description: Library name: Sample 5


title: Fulvestrant Resistant MCF-7 cells, Cold Atmospheric Plasma 600s 1

description: Library name: Sample 9


title: pADamID-RPE_tracr_10h_r1_H3K27me3_sample

description:
Library name: 7070_15_E2061_tracr_H3K27me3_G7_GCGAGATGGA-ACACTCTACT_S16_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: E2185_ABCB1_ATRi_DAM-gatc.counts.txt.gz

description:
Library name: 7260_10_E2185_ABCB1_ATRi_DAM_AGGATACGGT-AACCACGTCA_S10_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S4_R1_ATRi_gH2AX_sample

description:
Library name: 7908_9_S4_Rep1_gH2AX_ATRi_GACAATTAGC-CCGGTCATGA_S9_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r2_H3K27me3_sample

description:
Library name: 7122_29_E2137_ID05_10h_RPE1_tracr_H3K27me3_R4_TCGACGTTGG-GATAAGTGTG_S40_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: E2185_ABCB1_ATRi_LMNB2-gatc.counts.txt.gz

description:
Library name: 7260_11_E2185_ABCB1_ATRi_LMNB2_GCTACAGGTC-TTATGCAGGA_S11_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S3_R1_DNAPKi_gH2AX_sample

description:
Library name: 7908_8_S4_Rep1_LMNB2_ATRi_CAACCATACA-ACCGGTTATA_S8_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S1_R1_DMSO_gH2AX_sample

description:
Library name: 7908_6_S3_Rep1_LMNB2_DNAPKi_CGGATTGATC-AGTCACAACA_S6_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S2_R1_ATMi_gH2AX_sample

description:
Library name: 7908_7_S1_Rep1_LMNB2_DMSO_GTAGGCCGTT-GCCACTGTCT_S7_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S3_R3_DNAPKi_Dam_sample

description:
Library name: 7908_43_S3_Rep3_Dam_DNAPKi_GTCGACTCCT-TGCCGTTAGC_S43_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S4_R1_ATRi_LMNB2_sample

description:
Library name: 7908_4_S3_Rep1_gH2AX_DNAPKi_ACAAGAACCT-CGATACTGAA_S4_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S2_R3_ATMi_Dam_sample

description:
Library name: 7908_42_S2_Rep3_Dam_ATMi_CTGAGCTTGT-CTTCTTGCGT_S42_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S4_R3_ATRi_Dam_sample

description:
Library name: 7908_44_S4_Rep3_Dam_ATRi_TTGTGAAGGC-TCGTCAGTAC_S44_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S1_R3_DMSO_Dam_sample

description:
Library name: 7908_41_S1_Rep3_Dam_DMSO_CCTCTGTCAT-CGTATCGATT_S41_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: E2185_ABCB1_ATMi_LMNB2-gatc.counts.txt.gz

description:
Library name: 7260_8_E2185_ABCB1_ATMi_LMNB2_TGGACAATAG-GAGTCCTGTG_S8_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_48h_r2_gH2AX_sample

description:
Library name: 7633_38_R2_48T_gH2AX_TGGACAATAG-GAGTCCTGTG_S38_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S2_R1_ATMi_LMNB2_sample

description:
Library name: 7908_2_S1_Rep1_gH2AX_DMSO_ACTTAGATCG-CGGAATTCTT_S2_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S3_R3_DNAPKi_gH2AX_sample

description:
Library name: 7908_38_S3_Rep3_gH2AX_DNAPKi_CATTGAGCTA-ACTTCACATC_S38_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r1_H3K27me3_sample

description:
Library name: 7070_22_E2061_ABCB1_gH2AX_G10_AGAGGCACGA-ACGTGGAATT_S22_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S4_R2_ATRi_Dam_sample

description:
Library name: 7908_29_S4_Rep2_Dam_ATRi_TAAGCCACGC-TTACGAACGA_S29_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S1_R3_DMSO_gH2AX_sample

description:
Library name: 7908_36_S1_Rep3_gH2AX_DMSO_AACCACACTA-CCTCTGCTGA_S36_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S4_R3_ATRi_gH2AX_sample

description:
Library name: 7908_39_S4_Rep3_gH2AX_ATRi_CTCATCATCT-TAAGCCTCTA_S39_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S2_R3_ATMi_gH2AX_sample

description:
Library name: 7908_37_S2_Rep3_gH2AX_ATMi_CTTCGGAATC-CGTCGGTAAG_S37_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S3_R1_DNAPKi_LMNB2_sample

description:
Library name: 7908_3_S5_Rep1_LMNB2_tracer_AGAGTATGTG-AGATGGCTTC_S3_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S1_R2_DMSO_Dam_sample

description:
Library name: 7908_26_S1_Rep2_Dam_DMSO_TTGCAATGCG-CGAGACTTCA_S26_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S4_R2_ATRi_gH2AX_sample

description:
Library name: 7908_24_S4_Rep2_gH2AX_ATRi_CATTATCGCT-CGAGTTGCTT_S24_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S2_R2_ATMi_gH2AX_sample

description:
Library name: 7908_22_S2_Rep2_gH2AX_ATMi_GTGAGAGTAT-ATCTGTGAGG_S22_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S3_R2_DNAPKi_Dam_sample

description:
Library name: 7908_28_S3_Rep2_Dam_DNAPKi_TCAATCAGAG-GACTCTGGTT_S28_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S3_R2_DNAPKi_gH2AX_sample

description:
Library name: 7908_23_S3_Rep2_gH2AX_DNAPKi_TTCTACCGGC-TACTCGTAAG_S23_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S1_R1_DMSO_LMNB2_sample

description:
Library name: 7908_1_S2_Rep1_LMNB2_ATMi_GATCAACAAG-AAGCACTGTC_S1_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S4_R2_ATRi_LMNB2_sample

description:
Library name: 7908_19_S4_Rep2_LMNB2_ATRi_TGTTCGCTCT-ACTTGCGTGT_S19_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S1_R2_DMSO_gH2AX_sample

description:
Library name: 7908_21_S1_Rep2_gH2AX_DMSO_CTGGAGAATA-TCCATACAAC_S21_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S3_R2_DNAPKi_LMNB2_sample

description:
Library name: 7908_18_S3_Rep2_LMNB2_DNAPKi_AGGTATTCGG-AGATGTGCGC_S18_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S2_R2_ATMi_LMNB2_sample

description:
Library name: 7908_17_S2_Rep2_LMNB2_ATMi_ACGGCCTACA-TCTCACTCTA_S17_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"

value: lymphoblast cells isolated from the bone marrow


title: S4_R1_ATRi_Dam_sample

description:
Library name: 7908_14_S4_Rep1_Dam_ATRi_CGTCTAGTAA-TTAATCCAGC_S14_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S1_R2_DMSO_LMNB2_sample

description:
Library name: 7908_16_S1_Rep2_LMNB2_DMSO_CACGTAAGAG-TCAATCCGCG_S16_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S3_R1_DNAPKi_Dam_sample

description:
Library name: 7908_13_S3_Rep1_Dam_DNAPKi_TCTTAGGTGG-GATCACTGGT_S13_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S2_R1_ATMi_Dam_sample

description:
Library name: 7908_12_S2_Rep1_Dam_ATMi_TCGACGTTGG-GATAAGTGTG_S12_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S1_R1_DMSO_Dam_sample

description:
Library name: 7908_11_S1_Rep1_Dam_DMSO_AAGAGTACGA-GCAAGGACGT_S11_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r6_gH2AX_sample

description:
Library name: 7789_6_R1_RPE1_ABCB1_gH2AX_AAGGTACCGT-CTGATCTTGT_S6_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r10_LMNB2_sample

description:
Library name: 7789_5_R1_RPE1_ABCB1_LMNB2_AATCCAGGAT-CATGCAGAGT_S5_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r6_Dam_sample

description:
Library name: 7789_4_R1_RPE1_ABCB1_dam_TAAGGCGATC-GTTAGCACAA_S4_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: S2_R2_ATMi_Dam_sample

description:
Library name: 7908_27_S2_Rep2_Dam_ATMi_AACATAAGGC-GTTAGCTTAG_S27_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-K562_cr6_10h_r2_gH2AX_sample

description:
Library name: 7789_42_R2_K562_ABCB1_gH2AX_AGAACCGGAC-TCCTACCATA_S42_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-K562_cr6_10h_r2_LMNB2_sample

description:
Library name: 7789_41_R2_K562_ABCB1_LMNB2_GCAACCTGAG-GTTCATTGCG_S41_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-K562_tracr_10h_r2_Dam_sample

description:
Library name: 7789_37_R2_K562_tracr_dam_ACGTGCATCG-CAGTCAGTTG_S37_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-K562_tracr_10h_r2_gH2AX_sample

description:
Library name: 7789_39_R2_K562_tracr_gH2AX_GACAATGCGG-TTGTTGAGTG_S39_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r6_gH2AX_sample

description:
Library name: 7789_3_R1_RPE1_tracr_gH2AX_TGATTCCACA-CTCTAGCCGT_S3_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-K562_tracr_10h_r2_LMNB2_sample

description:
Library name: 7789_38_R2_K562_tracr_LMNB2_GCGATGCAGA-TCTTCGTGTA_S38_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-K562_cr6_10h_r2_Dam_sample

description:
Library name: 7789_40_R2_K562_ABCB1_Dam_AAGTGGCATT-AGAACAATCG_S40_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-K562_cr6_10h_r1_Dam_sample

description:
Library name: 7789_34_R1_K562_ABCB1_Dam_CCACTTGGAT-AATCTCGGTT_S34_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-K562_cr6_10h_r1_gH2AX_sample

description:
Library name: 7789_36_R1_K562_ABCB1_gH2AX_GCATAGCCAA-TGGTTCCTGG_S36_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-K562_tracr_10h_r1_LMNB2_sample

description:
Library name: 7789_32_R1_K562_tracr_LMNB2_CTCATTCTGC-TTGAAGCGGT_S32_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-K562_cr6_10h_r1_LMNB2_sample

description:
Library name: 7789_35_R1_K562_ABCB1_LMNB2_TCAGACTGGT-TCGATTACGC_S35_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-K562_tracr_10h_r1_gH2AX_sample

description:
Library name: 7789_33_R1_K562_tracr_gH2AX_AACAGTGACT-ATCGCAGTGT_S33_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53BRCA1dKO_cr6_10h_r3_LMNB2_sample

description:
Library name: 7789_29_R2_p53BRCA1_ABCB1_LMNB2_AGTCGACGTA-CCATGGAACA_S29_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-K562_tracr_10h_r1_Dam_sample

description:
Library name: 7789_31_R1_K562_tracr_Dam_CACACTGTTG-TGCATTGGTT_S31_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r10_LMNB2_sample

description:
Library name: 7789_2_R1_RPE1_tracr_LMNB2_CAACAGGTAG-GACGATAGTG_S2_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53KO_cr6_10h_r3_LMNB2_sample

description:
Library name: 7789_23_R2_p53_ABCB1_LMNB2_TATGATGCAG-AGGCCAGTTG_S23_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r6_Dam_sample

description:
Library name: 7789_1_R1_RPE1_tracr_Dam_CGTGGCAGAA-TCTTCCGATG_S1_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53KO_tracr_10h_r3_LMNB2_sample

description:
Library name: 7789_20_r2_p53KO_tracr_LMNB2_AGAACCTACA-AGTGTACGGT_S20_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53BRCA1dKO_tracr_10h_r3_LMNB2_sample

description:
Library name: 7789_26_R2_p53BRCA1_ABCB1_gH2AX_TTGGCTCCAA-GTCTGATCCG_S26_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53BRCA1dKO_cr6_10h_r3_Dam_sample

description:
Library name: 7789_28_R2_p53BRCA1_ABCB1_Dam_TATCCAGTTC-TGAGCTACGT_S28_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: E2185_ABCB1_DNApki_LMNB2-gatc.counts.txt.gz

description:
Library name: 7260_14_E2185_ABCB1_DNApki_LMNB2_GTCGACTCCT-TGCCGTTAGC_S14_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53KO_tracr_10h_r3_Dam_sample

description:
Library name: 7789_19_R2_p53KO_tracr_Dam_GTGCTATCGA-TTAAGCACCG_S19_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53KO_cr6_10h_r3_Dam_sample

description:
Library name: 7789_22_r2_p53ko_ABCB1_Dam_CTCAGAATTC-ACAGAGACCG_S22_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53BRCA1dKO_tracr_10h_r3_Dam_sample

description:
Library name: 7789_25_r2_p53BRCAdKO_tracr_Dam_AGAGGCACGA-ACGTGGAATT_S25_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r11_LMNB2_sample

description:
Library name: 7789_14_r2_RPE1_ABCB1_LMNB2_GTCTTCTCGA-TGGTGCCAAC_S14_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r7_gH2AX_sample

description:
Library name: 7789_12_R2_RPE1_tracr_gH2AX_TCCAGCGAAG-GTTCTATGTC_S12_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r11_LMNB2_sample

description:
Library name: 7789_11_R2_RPE1_tracr_LMNB2_TCGGAGACCT-AAGGTTACTC_S11_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r7_Dam_sample

description:
Library name: 7789_13_R2_RPE1_ABCB1_Dam_GTACTAAGAG-CGCTCTAGAT_S13_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO1_ABCB1_10h_r1_LMNB2_sample

description:
Library name: 7703_9_R1_LMNB2_KO2_ABCB1_TCTTAGGTGG-GATCACTGGT_S9_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEWT1_ABCB1_10h_r2_Dam_sample

description:
Library name: 7703_8_R2_Dam_WT1_ABCB1_CGTCTAGTAA-TTAATCCAGC_S8_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO2_ABCB1_10h_r2_gH2AX_sample

description:
Library name: 7703_64_R2_gH2AX_KO3_ABCB1_AATCCAGGAT-CATGCAGAGT_S64_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEWT2_ABCB1_10h_r2_LMNB2_sample

description:
Library name: 7703_62_R2_LMNB2_WT2_ABCB1_TGATTCCACA-CTCTAGCCGT_S62_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO2_tracr_10h_r2_gH2AX_sample

description:
Library name: 7703_60_R2_gH2AX_KO3_tracr_GTCTTCTCGA-TGGTGCCAAC_S60_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r11_Dam_sample

description:
Library name: 7789_10_R2_RPE1_tracr_Dam_TTAAGTGCGT-ACCTGTCGCT_S10_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEWT2_tracr_10h_r1_LMNB2_sample

description:
Library name: 7703_57_R1_LMNB2_WT2_tracr_TCGGAGACCT-AAGGTTACTC_S57_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEWT2_tracr_10h_r2_LMNB2_sample

description:
Library name: 7703_58_R2_LMNB2_WT2_tracr_TCCAGCGAAG-GTTCTATGTC_S58_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO1_ABCB1_10h_r2_gH2AX_sample

description:
Library name: 7703_55_R2_gH2AX_KO2_ABCB1_TATGATGCAG-AGGCCAGTTG_S55_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO2_tracr_10h_r1_gH2AX_sample

description:
Library name: 7703_59_R1_gH2AX_KO3_tracr_GTACTAAGAG-CGCTCTAGAT_S59_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEWT2_ABCB1_10h_r1_LMNB2_sample

description:
Library name: 7703_61_R1_LMNB2_WT2_ABCB1_CAACAGGTAG-GACGATAGTG_S61_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO2_ABCB1_10h_r1_gH2AX_sample

description:
Library name: 7703_63_R1_gH2AX_KO3_ABCB1_TAAGGCGATC-GTTAGCACAA_S63_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEWT1_ABCB1_10h_r2_LMNB2_sample

description:
Library name: 7703_53_R2_LMNB2_WT1_ABCB1_ATGGTGTATC-GCAATTGTGG_S53_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO1_ABCB1_10h_r1_gH2AX_sample

description:
Library name: 7703_54_R1_gH2AX_KO2_ABCB1_CTCAGAATTC-ACAGAGACCG_S54_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO1_tracr_10h_r2_gH2AX-20kb.bw

description:
Library name: 7703_50_R2_gH2AX_KO2_tracr_TCAGACTGGT-TCGATTACGC_S50_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO1_tracr_10h_r2_LMNB2_sample

description:
Library name: 7703_4_R2_LMNB2_KO2_tracr_ACAAGAACCT-CGATACTGAA_S4_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO1_tracr_10h_r1_gH2AX_sample

description:
Library name: 7703_49_R1_gH2AX_KO2_tracr_CCACTTGGAT-AATCTCGGTT_S49_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEWT1_tracr_10h_r2_LMNB2_sample

description:
Library name: 7703_48_R2_LMNB2_WT1_tracr_AACAGTGACT-ATCGCAGTGT_S48_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEWT2_ABCB1_10h_r2_gH2AX_sample

description:
Library name: 7703_45_R2_gH2AX_WT2_ABCB1_GACAATGCGG-TTGTTGAGTG_S45_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEWT2_ABCB1_10h_r1_gH2AX_sample

description:
Library name: 7703_44_R1_gH2AX_WT2_ABCB1_TTCGTTCACA-CTGATTAGTG_S44_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO2_ABCB1_10h_r1_Dam_sample

description:
Library name: 7703_42_R1_Dam_KO3_ABCB1_TATCCAGTTC-TGAGCTACGT_S42_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r7_gH2AX_sample

description:
Library name: 7789_15_r2_RPE1_ABCB1_gH2AX_ATACACAGAG-AGTCAGAAGG_S15_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEWT2_tracr_10h_r1_gH2AX_sample

description:
Library name: 7703_39_R1_gH2AX_WT2_tracr_CTTGCGAAGA-AATGACGCGG_S39_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO1_tracr_10h_r1_LMNB2_sample

description:
Library name: 7703_3_R1_LMNB2_KO2_tracr_ACTGGCAAGA-TGTTGTCCAT_S3_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO2_tracr_10h_r1_Dam_sample

description:
Library name: 7703_37_R1_Dam_KO3_tracr_TCCTACGTGC-TAGGTGCTAT_S37_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEWT2_tracr_10h_r2_gH2AX_sample

description:
Library name: 7703_40_R2_gH2AX_WT2_tracr_TGGCACGAAC-CCTGACTCTT_S40_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEWT1_ABCB1_10h_r2_gH2AX_sample

description:
Library name: 7703_34_R2_gH2AX_WT1_ABCB1_CTGAGCTTGT-CTTCTTGCGT_S34_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO1_ABCB1_10h_r2_Dam_sample

description:
Library name: 7703_32_R2_Dam_KO2_ABCB1_TTGTGAAGGC-TCGTCAGTAC_S32_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO2_tracr_10h_r2_Dam_sample

description:
Library name: 7703_38_R2_Dam_KO3_tracr_CCACGATAAC-CATGCCTGAC_S38_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO1_ABCB1_10h_r1_Dam_sample

description:
Library name: 7703_31_R1_Dam_KO2_ABCB1_GCCAAGTAAC-TGCGTGATGA_S31_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO1_tracr_10h_r1_Dam_sample

description:
Library name: 7703_25_R1_Dam_KO2_tracr_CTTCGGAATC-CGTCGGTAAG_S25_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO2_ABCB1_10h_r2_LMNB2_sample

description:
Library name: 7703_22_R2_LMNB2_KO3_ABCB1_AACATAAGGC-GTTAGCTTAG_S22_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEWT1_tracr_10h_r2_gH2AX_sample

description:
Library name: 7703_28_R2_gH2AX_WT1_tracr_ACTTCAACAG-GCGTGAGCAT_S28_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEWT2_ABCB1_10h_r1_Dam_sample

description:
Library name: 7703_19_R1_Dam_WT2_ABCB1_AGGCTGGAGA-CAACTGTCAT_S19_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO2_tracr_10h_r2_LMNB2_sample

description:
Library name: 7703_16_R2_LMNB2_KO3_tracr_TGTTCGCTCT-ACTTGCGTGT_S16_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEWT2_ABCB1_10h_r2_Dam_sample

description:
Library name: 7703_20_R2_Dam_WT2_ABCB1_TAAGCCACGC-TTACGAACGA_S20_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO2_ABCB1_10h_r1_LMNB2_sample

description:
Library name: 7703_21_R1_LMNB2_KO3_ABCB1_TCAATCAGAG-GACTCTGGTT_S21_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r8_Dam_sample

description:
Library name: 7633_9_R1_10A_dam_ACCTTCGGAC-GACCGTAGAT_S9_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r9_LMNB2_sample

description:
Library name: 7633_5_R2_10T_LMNB2_ACAAGAACCT-CGATACTGAA_S5_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO1_ABCB1_10h_r2_LMNB2_sample

description:
Library name: 7703_10_R2_LMNB2_KO2_ABCB1_TCGACGTTGG-GATAAGTGTG_S10_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r5_gH2AX_sample

description:
Library name: 7633_6_R2_10T_gH2AX_AGAGTATGTG-AGATGGCTTC_S6_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO1_tracr_10h_r2_Dam_sample

description:
Library name: 7703_26_R2_Dam_KO2_tracr_AACCACACTA-CCTCTGCTGA_S26_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO2_ABCB1_10h_r2_Dam_sample

description:
Library name: 7703_43_R2_Dam_KO3_ABCB1_AGTCGACGTA-CCATGGAACA_S43_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r5_Dam_sample

description:
Library name: 7633_4_R2_10T_dam_ACTGGCAAGA-TGTTGTCCAT_S4_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_48h_r1_Dam_sample

description:
Library name: 7633_41_R1_48A_dam_GCTACAGGTC-TTATGCAGGA_S41_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_48h_r2_Dam_sample

description:
Library name: 7633_44_R2_48A_dam_GTCGACTCCT-TGCCGTTAGC_S44_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_48h_r2_LMNB2_sample

description:
Library name: 7633_37_R2_48T_LMNB2_ACTTCAACAG-GCGTGAGCAT_S37_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_48h_r1_LMNB2_sample

description:
Library name: 7633_42_R1_48A_LMNB2_GCCAAGTAAC-TGCGTGATGA_S42_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r4_gH2AX_sample

description:
Library name: 7633_3_R1_10T_gH2AX_CGGATTGATC-AGTCACAACA_S3_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_48h_r1_Dam_sample

description:
Library name: 7633_33_R1_48T_dam_CATTGAGCTA-ACTTCACATC_S33_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_48h_r2_LMNB2_sample

description:
Library name: 7633_45_R2_48A_LMNB2_CTGAGCTTGT-CTTCTTGCGT_S45_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_48h_r2_Dam_sample

description:
Library name: 7633_36_R2_48T_dam_GTACAGCGGA-CAATCTGTGT_S36_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_48h_r1_LMNB2_sample

description:
Library name: 7633_34_R1_48T_LMNB2_CTTCGGAATC-CGTCGGTAAG_S34_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_24h_r2_gH2AX_sample

description:
Library name: 7633_30_R2_24A_gH2AX_TTGCAATGCG-CGAGACTTCA_S30_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_24h_r4_LMNB2_sample

description:
Library name: 7633_29_R2_24A_LMNB2_AACATAAGGC-GTTAGCTTAG_S29_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_24h_r4_Dam_sample

description:
Library name: 7633_28_R2_24A_dam_TCAATCAGAG-GACTCTGGTT_S28_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPEKO2_tracr_10h_r1_LMNB2_sample

description:
Library name: 7703_15_R1_LMNB2_KO3_tracr_TGACAAGAGG-AATCTGTTGG_S15_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_24h_r3_LMNB2_sample

description:
Library name: 7633_26_R1_24A_LMNB2_AGGCTGGAGA-CAACTGTCAT_S26_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_24h_r3_Dam_sample

description:
Library name: 7633_25_R1_24T_dam_true_AATCGAACTC-ACGAACCTTA_S25_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_24h_r2_gH2AX_sample

description:
Library name: 7633_22_R2_24T_gH2AX_AGGTATTCGG-AGATGTGCGC_S22_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_24h_r4_LMNB2_sample

description:
Library name: 7633_21_R2_24T_LMNB2_TGTTCGCTCT-ACTTGCGTGT_S21_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r8_Dam_sample

description:
Library name: 7633_1_R1_10T_dam_CAACCATACA-ACCGGTTATA_S1_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_24h_r4_Dam_sample

description:
Library name: 7633_20_R2_24T_dam_TGACAAGAGG-AATCTGTTGG_S20_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_24h_r3_LMNB2_sample

description:
Library name: 7633_18_R1_24T_LMNB2_GTGAGAGTAT-ATCTGTGAGG_S18_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_24h_r3_Dam_sample

description:
Library name: 7633_17_R1_24A_dam_TTCTACCGGC-TACTCGTAAG_S17_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r5_Dam_sample

description:
Library name: 7633_12_R2_10A_dam_TCTTAGGTGG-GATCACTGGT_S12_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r9_LMNB2_sample

description:
Library name: 7633_13_R2_10A_LMNB2_TCGACGTTGG-GATAAGTGTG_S13_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r8_LMNB2_sample

description:
Library name: 7633_10_R1_10A_LMNB2_TATCATGTCG-TAATCTGCAC_S10_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r5_gH2AX_sample

description:
Library name: 7633_14_R2_10A_gH2AX_AAGAGTACGA-GCAAGGACGT_S14_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53BRCA1dKO_cr6_10h_r1_LMNB2_sample

description:
Library name: 7580_8_R1_DEF_ABCB1_LMNB2_CGTCTAGTAA-TTAATCCAGC_S8_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53BRCA1dKO_cr6_10h_r1_Dam_sample

description:
Library name: 7580_2_R1_DEF_ABCB1_Dam_CGGATTGATC-AGTCACAACA_S2_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53KO_tracr_10h_r2_LMNB2_sample

description:
Library name: 7580_27_R2_PRO_tracr_LMNB2_GTACAGCGGA-CAATCTGTGT_S27_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53KO_cr6_10h_r2_LMNB2_sample

description:
Library name: 7580_28_R2_PRO_ABCB1_LMNB2_ACTTCAACAG-GCGTGAGCAT_S28_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r8_LMNB2_sample

description:
Library name: 7633_2_R1_10T_LMNB2_GTAGGCCGTT-GCCACTGTCT_S2_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53BRCA1dKO_cr6_10h_r2_LMNB2_sample

description:
Library name: 7580_26_R2_DEF_ABCB1_LMNB2_AACCACACTA-CCTCTGCTGA_S26_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53KO_cr6_10h_r2_Dam_sample

description:
Library name: 7580_22_R2_PRO_ABCB1_Dam_AACATAAGGC-GTTAGCTTAG_S22_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53KO_tracr_10h_r1_Dam_sample

description:
Library name: 7580_3_R1_PRO_tracr_Dam_ACTGGCAAGA-TGTTGTCCAT_S3_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r4_gH2AX_sample

description:
Library name: 7633_11_R1_10A_gH2AX_CGTCTAGTAA-TTAATCCAGC_S11_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53KO_tracr_10h_r1_LMNB2_sample

description:
Library name: 7580_9_R1_PRO_tracr_LMNB2_TCTTAGGTGG-GATCACTGGT_S9_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53BRCA1dKO_tracr_10h_r1_LMNB2_sample

description:
Library name: 7580_7_R1_DEF_tracr_LMNB2_TATCATGTCG-TAATCTGCAC_S7_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53BRCA1dKO_cr6_10h_r2_Dam_sample

description:
Library name: 7580_20_R2_DEF_ABCB1_Dam_TAAGCCACGC-TTACGAACGA_S20_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53KO_tracr_10h_r2_Dam_sample

description:
Library name: 7580_21_R2_PRO_tracr_Dam_TCAATCAGAG-GACTCTGGTT_S21_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_24h_r1_gH2AX-20kb.bw

description:
Library name: 7633_27_R1_24A_gH2AX_TAAGCCACGC-TTACGAACGA_S27_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53BRCA1dKO_tracr_10h_r2_Dam_sample

description:
Library name: 7580_19_R2_DEF_tracr_Dam_AGGCTGGAGA-CAACTGTCAT_S19_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53BRCA1dKO_tracr_10h_r1_Dam_sample

description:
Library name: 7580_1_R1_DEF_tracr_Dam_GTAGGCCGTT-GCCACTGTCT_S1_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53KO_cr6_10h_r1_Dam_sample

description:
Library name: 7580_4_R1_PRO_ABCB1_Dam_ACAAGAACCT-CGATACTGAA_S4_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_24h_r1_gH2AX_sample

description:
Library name: 7633_19_R1_24T_gH2AX_CTGGAGAATA-TCCATACAAC_S19_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE1_tracr_DMSO_10h_r3_LMNB2_sample

description:
Library name: 7260_2_E2185_Tracr_DMSO_LMNB2_CATTATCGCT-CGAGTTGCTT_S2_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53KO_cr6_10h_r1_LMNB2_sample

description:
Library name: 7580_10_R1_PRO_ABCB1_LMNB2_TCGACGTTGG-GATAAGTGTG_S10_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r3_gH2AX_sample

description:
Library name: 7122_36_E2137_ID12_10h_RPE1_ABCB1_gH2AX_R4_TGACAAGAGG-AATCTGTTGG_S3_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r3_H3K9me3_sample

description:
Library name: 7122_34_E2137_ID10_10h_RPE1_ABCB1_H3K9me3_R4_GTGAGAGTAT-ATCTGTGAGG_S37_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r7_LMNB2_sample

description:
Library name: 7122_32_E2137_ID08_10h_RPE1_ABCB1_LMNB2_R4_CACGTAAGAG-TCAATCCGCG_S39_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r3_H3K9me2_sample

description:
Library name: 7122_33_E2137_ID09_10h_RPE1_ABCB1_H3K9me2_R4_TTCTACCGGC-TACTCGTAAG_S38_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r3_Dam_sample

description:
Library name: 7122_31_E2137_ID07_10h_RPE1_ABCB1_Dam_R4_ACGGCCTACA-TCTCACTCTA_S42_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r3_H3K9me3_sample

description:
Library name: 7122_28_E2137_ID04_10h_RPE1_tracr_H3K9me3_R4_TCTTAGGTGG-GATCACTGGT_S29_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r3_H3K9me2_sample

description:
Library name: 7122_27_E2137_ID03_10h_RPE1_tracr_H3K9me2_R4_CGTCTAGTAA-TTAATCCAGC_S35_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r3_gH2AX_sample

description:
Library name: 7122_30_E2137_ID06_10h_RPE1_tracr_gH2AX_R4_AAGAGTACGA-GCAAGGACGT_S41_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r3_Dam_sample

description:
Library name: 7122_25_E2137_ID01_10h_RPE1_tracr_Dam_R4_ACCTTCGGAC-GACCGTAGAT_S33_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r2_H3K9me3_sample

description:
Library name: 7122_22_E2071_ID10_10h_RPE1_ABCB1_H3K9me3_R2_AGAACCTACA-AGTGTACGGT_S30_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r7_LMNB2_sample

description:
Library name: 7122_26_E2137_ID02_10h_RPE1_tracr_LMNB2_R4_TATCATGTCG-TAATCTGCAC_S34_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPEp53BRCA1dKO_tracr_10h_r2_LMNB2_sample

description:
Library name: 7580_25_R2_DEF_tracr_LMNB2_CTTCGGAATC-CGTCGGTAAG_S25_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r2_gH2AX_sample

description:
Library name: 7122_24_E2071_ID12_10h_RPE1_ABCB1_gH2AX_R2_CTCAGAATTC-ACAGAGACCG_S32_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r7_Dam_sample

description:
Library name: 7070_20_E2061_ABCB1_H3K27me3_E8_GACAATGCGG-TTGTTGAGTG_S20_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r2_H3K9me3_sample

description:
Library name: 7122_16_E2071_ID04_10h_RPE1_tracr_H3K9me3_R2_CCACTTGGAT-AATCTCGGTT_S23_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"