title: Infected red blood cells 2

city: Saint Louis

first: Mei San

last: Tang

state: MO

address: 660 S Euclid, Campus Box 8118

department: Pathology & Immunology

institute: Washington University in St Louis

data_processing:
Raw reads aligned to the reference human genome Grch37 and the Ensembl reference transcriptome Grch37.82.gtf using Tophat (version 2.1.0) with the alignment parameter –library-type fr-firststrand, while keeping all other parameters at default settings.
Reads with mappability score (MAPQ) <30, as well as reads mapping to mitochondrial DNA and chromosome Y, were removed.
The number of filtered reads were subsequently counted for each gene using htseq-count, with the parameters --mode=union and --stranded=reverse.
Genome_build: Ensembl human reference genome Grch37
Supplementary_files_format_and_content: Raw counts of each gene generated using htseq-count

source_name: CD1c+ dendritic cells

growth_protocol: CD1c+ dendritic cells purified from peripheral blood mononuclear cells (PBMCs) from healthy donors cultured in RPMI with 10% human serum

extract_protocol:
Quiagen Rneasy Plus Micro Kit
TruSeq Poly A Stranded mRNA

treatment_protocol: CD1c+ dendritic cells incubated with Plasmodium falciparum shizonts, uninfected red blood cells or LPS for 6 h

value: CD1c+ dendritic cells


title: Lipopolysaccharides (LPS) 2

status: Public on Nov 11 2017

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell type


title: P4_D9_GMP

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

country: United Kingdom

institute: University of Cambridge

data_processing:
RNA-seq reads were aligned to hg19 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: hg19
Supplementary_files_format_and_content: HT-Seq counts (.txt)

source_name: cord blood

growth_protocol: Fresh cord blood from normal donors were obtained with informed consent. They were processed within 16-34h after collection. Mononuclear cells were isolated and CD34+ fraction was separated as described{Quek et al, Journal of Experimental Medicine 2016}.

extract_protocol:
Single cells were deposited in individual wells of 96 well plates, directly lysed according to the SmartSeq2 protocol and stored at -80C. No extraction protocol was performed
Single cell libraries for RNAseq were prepared using SmartSeq2 protocol (Picelli et al., Nature Protocols 2014) and the Illumina Nextera XT Index Kit (96 indexes, 384 samples, FC-131-1002) for cDNA tagmentation and indexing. ERCC RNA Spike-In Mix (Ambion, 4456740) are included.

treatment_protocol: Fresh Cord Blood cells were obtained and processed with ficoll to obtain mononuclear cells. CD34+ cells were purified using CD34 Microbead Kit and MACS  separation columns

value: Cord blood CD34+ haemopoietic stem and progenitor cells

tag: cell populations

value: GMP

tag: immunophenotype


title: Uninfected red blood cells 2


title: Control 2


title: P4_C9_GMP


title: P4_C12_GMP


title: Lipopolysaccharides (LPS) 1


title: P4_C11_GMP


title: Infected red blood cells 1


title: P4_C10_GMP


title: P4_H10_GMP


title: P4_B9_GMP


title: P4_G10_GMP


title: P4_B12_GMP


title: P4_B11_GMP


title: P4_F12_GMP


title: C4-2 EZH2

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Clinic sequence core using the pipeline Cassava 1.7.
Raw RIP-seq reads were aligned to human reference genome hg19 using Tophat (v1.4.0) with options: -p 4 --rg-id C4-2-EZH2 --max-multihits 20 --rg-sample C4-2-EZH2 --rg-platform illumina --rg-center MAYO --rg-library hg19 --solexa1.3-quals -r 150 --mate-std-dev 20
Raw count mapped to each RefSeq exon was calculated using RSeQC package. Hypergeometric test was applied to evaluate the significance of enrichment of RIP-seq reads at each exon. P values were then corrected using Benjamini-Hochberg procedure to control false discovery rate.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bigWig files describing the RIP-seq reads coverage.

molecule: total RNA

source_name: C4-2 EZH2

growth_protocol: LNCaP and C4-2 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
Whole cell lysates were incubated with EZH2 antibody and EZH2-RNA complexes were isolated with antibody.
Double-stranded cDNAs were generated from the reverse transcription of RNAs immunoprecipitated by EZH2 antibody and then fragmented by sonication. DNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

value: cultured prostate cancer cells

tag: rip-antibody

value: EZH2 (D2C9) XP Rabbit mAb (Cell Signaling Technology)


title: C4-2 input

source_name: C4-2 input


title: P4_B10_GMP


title: P4_A9_GMP


title: LNCaP input

source_name: LNCaP input

value: LNCaP


title: P4_A11_GMP


title: P4_D11_GMP


title: P3_H11_GMP


title: LNCaP EZH2

source_name: LNCaP EZH2


title: P4_A10_GMP


title: P3_G9_GMP


title: P3_G12_GMP


title: P3_G10_GMP


title: P3_G11_GMP


title: P3_H10_GMP


title: P3_F9_GMP


title: P3_F11_GMP


title: P3_F10_GMP


title: P3_F12_GMP


title: P3_E9_GMP


title: Control 1


title: P3_E11_GMP


title: P3_E10_GMP


title: P3_E12_GMP


title: P3_D11_GMP


title: P3_D12_GMP


title: P3_D9_GMP


title: P3_D10_GMP


title: P3_H9_GMP


title: P3_C12_GMP


title: P3_C11_GMP


title: P3_B9_GMP


title: WT (littermate controls for Thap1+/- (deltaexon2)) Cerebellum rep3

city: Tempe

first: Ben

last: Readhead

state: AZ

address: 797 E. Tyler Street

institute: ASU-Banner Neurodegenerative Disease Research Center

description:
Sample named as if striatal, but derived from cerebellum
Str2_12

data_processing:
Fastq files were aligned to mm10 using STAR read aligner
Mapped reads were summarized to count matrices using featureCounts function of subread
Counts adjusted by library size, normalized and logged (log2) using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text files including gene count matrix and log2 normalized gene expression data, across all samples

organism: Mus musculus

source_name: Cerebellum

extract_protocol:
Striatum or Cerebellum were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Sequencing libraries were prepared with the TruSeq RNA Sample Prep Kit v2 protocol (Illumina, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: Cerebellum

tag: age

value: Postnatal day 1 (P1)

tag: genotype

value: WT


title: WT (littermate controls for Thap1+/- (deltaexon2)) Striatum rep3

source_name: Striatum

value: Striatum


title: P3_B12_GMP


title: WT (littermate controls for Thap1+/- (deltaexon2)) Striatum rep2


title: P3_B11_GMP


title: Uninfected red blood cells 1


title: P3_B10_GMP


title: P3_A9_GMP


title: P3_A12_GMP


title: P3_A10_GMP


title: Thap1+/- (deltaexon2) Striatum rep2

value: Thap1+/- (deltaexon2)


title: Thap1+/- (deltaexon2) Striatum rep3


title: Thap1+/- (deltaexon2) Striatum rep1


title: P3_A11_GMP


title: WT (littermate controls for Thap1+/- (deltaexon2)) Striatum rep1


title: Thap1+/- (deltaexon2) Striatum rep4


title: P2_H11_GMP


title: P3_C9_GMP


title: P2_H10_GMP


title: P2_G9_GMP


title: WT (littermate controls for Thap1C54Y/+) Striatum rep4


title: WT (littermate controls for Thap1C54Y/+) Striatum rep1


title: P2_G12_GMP


title: WT (littermate controls for Thap1C54Y/+) Striatum rep2


title: P3_C10_GMP


title: P2_G11_GMP


title: Thap1C54Y/+ Striatum rep4


title: P2_G10_GMP


title: Thap1C54Y/+ Striatum rep3


title: Thap1C54Y/+ Striatum rep2


title: P2_F12_GMP


title: WT (littermate controls for Thap1+/- (deltaexon2)) Cerebellum rep4


title: Thap1C54Y/+ Striatum rep1


title: WT (littermate controls for Thap1+/- (deltaexon2)) Striatum rep4

description:
Sample named as if cerebellar, but derived from striatum
Cb2_12


title: WT (littermate controls for Thap1+/- (deltaexon2)) Cerebellum rep2


title: WT (littermate controls for Thap1+/- (deltaexon2)) Cerebellum rep1


title: P2_F10_GMP


title: P2_D11_GMP


title: Thap1+/- (deltaexon2) Cerebellum rep3


title: P2_D10_GMP


title: P2_D12_GMP


title: Thap1+/- (deltaexon2) Cerebellum rep4


title: P2_D9_GMP


title: WT (littermate controls for Thap1C54Y/+) Striatum rep3


title: P2_C9_GMP


title: P2_C10_GMP


title: P2_C12_GMP


title: P2_C11_GMP


title: Thap1+/- (deltaexon2) Cerebellum rep1


title: Thap1+/- (deltaexon2) Cerebellum rep2


title: WT (littermate controls for Thap1C54Y/+) Cerebellum rep4


title: WT (littermate controls for Thap1C54Y/+) Cerebellum rep3


title: P2_B9_GMP


title: WT (littermate controls for Thap1C54Y/+) Cerebellum rep2


title: WT (littermate controls for Thap1C54Y/+) Cerebellum rep1


title: P2_F11_GMP


title: P2_A9_GMP


title: P2_B11_GMP


title: Thap1C54Y/+ Cerebellum rep3


title: P2_F9_GMP


title: Thap1C54Y/+ Cerebellum rep4


title: Thap1C54Y/+ Cerebellum rep2


title: P2_A12_GMP


title: P2_A11_GMP


title: P2_A10_GMP


title: Thap1C54Y/+ Cerebellum rep1


title: EMX1_EMX1-ON_EXO1_KO_D10A_1

status: Public on Nov 10 2017

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

description: EMX1 EMX1-ON EXO1 KO D10A Indel DNA replicate1

library_source: genomic

data_processing:
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh37/hg19 human reference genome using BWA-MEM 0.7.9a-r786.
Genome_build: hg19 for human samples
Supplementary_files_format_and_content: Excel for Indels and Variations

molecule: genomic DNA

source_name: 293FT cells

growth_protocol: 293FT and HeLa cells from ATCC were maintained in DMEM (10566, Gibco/Thermo Fisher Scientific) + 10% FBS (16000-044, Gibco/Thermo Fisher Scientific) and have been tested for mycoplasma contamination free. Cryopreserved human peripheral blood mononuclear cells (PBMCs) were purchased from AllCells, LLC (PB003F). CD8+ T cells were pre-enriched from the PBMCs with Easysep Human CD8+ T cell enrichment kit (19053, Stemcell Technologies) according to the manufacturer’s protocol. The cells were then activated with Dynabeads Human T-Activator CD3/CD28 (LifeTech, 11131D) for 3 days in AIM V medium (Gibco, 0870112DK) supplemented with 10% FBS. The stimulated CD8+ T cells were then cultured in AIM V medium with 10% FBS and 100 IU/ml hIL2 (200-02-100, PeproTech).

extract_protocol:
For DNA, 72 hr after transfection, the genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre).
For DNA, DNA-seq libraries were prepared with Illumina TruSeq ChIP Sample Preparation Kit. Deep sequencing was performed on Illumina Hiseq 2500 and Hiseq X ten at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: To determine base substitution frequencies in the genomic DNA during HDR in cell lines, cells were co-transfected with 3 μg Cas9-expressing plasmid, 1.5 μg sgRNA-expressing plasmid and 100 pmol ssODNs, dsODNs or ds-plasmid donors by electroporation (program Q-001) with Cell Line Nucleofector® Kit V (VCA-1003) on Lonza Nuclepfectoe-2b. Electroporated cells were then plated into a 60-mm dish. To determine the indels in genomic DNA in cell lines, cells were seeded in a 24-well plate at a density of 1 × 105 per well and transfected with 1 μg Cas9-variant-expressing plasmid, 0.5 μg single sgRNA-expressing plasmid and 5.4 μl LipofectamineTM 2000 (Thermo Fisher Scientific) according to the manufacture’s instructions. After 24 hrs, blasticidin was added (ant-bl-1, InvivoGen) to the media at a final concentration of 10 μg/ml. To determine base substitutions during HDR, 4x106 T cells were electroporated with 30 pmol of siRNA (program EO-115) by using P3 Primary Cell 4D-Nucleofector® X Kit L (Lonza, V4XP-3024) on day 4. After 24 hrs, RNP mixture with or without 100 pmol of ssODN or dsODN donor and 2x105 transfected cells were combined in a Lonza 4D strip nucleocuvette and electroporated (program EO-115) by using P3 Primary Cell 4D-Nucleofector® X Kit. . After another 48 hours, cells were and lysed with QuickExtract DNA Extraction Solution for HDR taq-specific PCR amplification. To determine indel formation, 4x106 T cells were electroporated with 30 pmol of siRNA (program EO-115) by using P3 Primary Cell 4D-Nucleofector® X Kit L (Lonza, V4XP-3024) on day 4 or day 7. After 24 hrs, 8 μg of Cas9 protein (or its variants) and 2 μg of sgRNA were mixed and incubated for 10 min to allow RNP formation. RNP mixture and 2x105 cells were combined in a Lonza 4D strip nucleocuvette and electroporated (program EO-115) by using P3 Primary Cell 4D-Nucleofector® X Kit (V4XP-3032) on day 5 and day 8. After another 48 hours, Cells were collected and lysed with QuickExtract DNA Extraction Solution for PCR amplification.

tag: type

value: DNA

tag: 5'-end trimming of r1

tag: 3'-end trimming of r1


title: RNF2_RNF2-ON_SMUG1_KO_UDG_KO_D10A_1

description: RNF2 RNF2-ON SMUG1 KO UDG KO D10A Indel DNA replicate1


title: EMX1_EMX1_SMUG1_KO_UDG_KO_BE3_1

description: EMX1 EMX1 SMUG1 KO UDG KO BE3 Indel DNA replicate1


title: EMX1_EMX1-ON_EXO1_KO_Cas9_1

description: EMX1 EMX1-ON EXO1 KO Cas9 Indel DNA replicate1


title: P2_B12_GMP


title: EMX1_EMX1_APE1_KO_D10A_3

description: EMX1 EMX1 APE1 KO D10A Indel DNA replicate3


title: EMX1_EMX1_APE1_KO_dC9_3

description: EMX1 EMX1 APE1 KO dCas9 Indel DNA replicate3


title: EMX1_EMX1_APE1_KO_H8A_3

description: EMX1 EMX1 APE1 KO H840A Indel DNA replicate3


title: EMX1_EMX1-ON_MRE11_KD_D10A_3

description: EMX1 EMX1-ON MRE11 KD D10A Indel DNA replicatelicate3


title: EMX1_EMX1_APE1_KO_BE3_3

description: EMX1 EMX1 APE1 KO BE3 Indel DNA replicate3


title: EMX1_EMX1-ON_MRE11_KD_dC9_3

description: EMX1 EMX1-ON MRE11 KD dCas9 Indel DNA replicatelicate3


title: EMX1_EMX1-ON_MRE11_KD_H8A_3

description: EMX1 EMX1-ON MRE11 KD H840A Indel DNA replicatelicate3


title: EMX1_EMX1-ON_MRE11_KD_dC9_2

description: EMX1 EMX1-ON MRE11 KD dCas9 Indel DNA replicate2


title: EMX1_EMX1-ON_MRE11_KD_H8A_2

description: EMX1 EMX1-ON MRE11 KD H840A Indel DNA replicate2


title: EMX1_EMX1-ON_MRE11_KD_D10A_2

description: EMX1 EMX1-ON MRE11 KD D10A Indel DNA replicate2


title: EMX1_EMX1-ON_MRE11_KD_BE3_2

description: EMX1 EMX1-ON MRE11 KD BE3 Indel DNA replicate2


title: EMX1_EMX1-ON_MRE11_KD_dC9__1

description: EMX1 EMX1-ON MRE11 KD dCas9  Indel DNA replicate1


title: RNF2_RNF2-ON_APE1_KO_Cas9_2

description: RNF2 RNF2-ON APE1 KO Cas9 Indel DNA replicate2


title: EMX1_EMX1-ON_MRE11_KD_D10A__1

description: EMX1 EMX1-ON MRE11 KD D10A  Indel DNA replicate1


title: EMX1_EMX1-ON_MRE11_KD_H8A__1

description: EMX1 EMX1-ON MRE11 KD H840A  Indel DNA replicate1


title: RNF2_RNF2-ON_SMUG1_KO_UDG_KO_dC9_2

description: RNF2 RNF2-ON SMUG1 KO UDG KO dCas9 Indel DNA replicate2


title: EMX1_EMX1-ON_MRE11_KD_BE3__1

description: EMX1 EMX1-ON MRE11 KD BE3  Indel DNA replicate1


title: RNF2_RNF2-ON_SMUG1_KO_UDG_KO_H8A_2

description: RNF2 RNF2-ON SMUG1 KO UDG KO H840A Indel DNA replicate2


title: EMX1_EMX1-ON_EXO1_KO_H8A_1+RNF2_RNF2-ON_EXO1_KO_D10A_1

description: EMX1 EMX1-ON EXO1 KO H840A Indel DNA replicate1+RNF2 RNF2-ON EXO1 KO D10A Indel DNA replicate1


title: RNF2_RNF2-ON_APE1_KO_BE3_2

description: RNF2 RNF2-ON APE1 KO BE3 Indel DNA replicate2


title: EMX1_EMX1-ON_MRE11_KD_BE3_3

description: EMX1 EMX1-ON MRE11 KD BE3 Indel DNA replicate3


title: EMX1_EMX1-ON_EXO1_KO_BE3_1

description: EMX1 EMX1-ON EXO1 KO BE3 Indel DNA replicate1


title: RNF2_RNF2-ON_APE1_KO_BE3_1

description: RNF2 RNF2-ON APE1 KO BE3 Indel DNA replicate1


title: EMX1_EMX1_APE1_KO_Cas9_3

description: EMX1 EMX1 APE1 KO Cas9 Indel DNA replicate3


title: RNF2_RNF2-ON_APE1_KO_H8A_1

description: RNF2 RNF2-ON APE1 KO H840A Indel DNA replicate1


title: RNF2_RNF2-ON_EXO1_KO_dC9_1

description: RNF2 RNF2-ON EXO1 KO dCas9 Indel DNA replicate1


title: T_cell_FANCF_FANCF-ON_Day8_siA3_dC9_2

description: T cell FANCF FANCF-ON Day8 siA3 dCas9 Indel DNA replicate2

source_name: T cells

value: T cells


title: RNF2_RNF2-ON_SMUG1_KO_UDG_KO_H8A_1

description: RNF2 RNF2-ON SMUG1 KO UDG KO H840A Indel DNA replicate1


title: RNF2_RNF2-ON_EXO1_KO_BE3_2

description: RNF2 RNF2-ON EXO1 KO BE3 Indel DNA replicate2


title: RNF2_RNF2-ON_EXO1_KO_H8A_2

description: RNF2 RNF2-ON EXO1 KO H840A Indel DNA replicate2


title: RNF2_RNF2-ON_EXO1_KO_dC9_2 T_cell_FANCF_FANCF-ON_Day8_siA3_dC9_1

description: RNF2 RNF2-ON EXO1 KO dCas9 Indel DNA replicate2 and T cell FANCF FANCF-ON Day8 siA3 dCas9 Indel DNA replicate1


title: T_cell_FANCF_FANCF-ON_Day8_siCtrl_dC9_2

description: T cell FANCF FANCF-ON Day8 siCtrl dCas9 Indel DNA replicate2


title: RNF2_RNF2-ON_APE1_KO_D10A_1

description: RNF2 RNF2-ON APE1 KO D10A Indel DNA replicate1


title: T_cell_FANCF_FANCF-ON_Day8_siCtrl_dC9_1

description: T cell FANCF FANCF-ON Day8 siCtrl dCas9 Indel DNA replicate1


title: EMX1_EMX1-ON_EXO1_KO_dC9_3

description: EMX1 EMX1-ON EXO1 KO dCas9 Indel DNA replicate3


title: T_cell_FANCF_FANCF-ON_Day5_siA3_D10A_2

description: T cell FANCF FANCF-ON Day5 siA3 D10A Indel DNA replicate2


title: T_cell_FANCF_FANCF-ON_Day5_siA3_Cas9_1

description: T cell FANCF FANCF-ON Day5 siA3 Cas9 Indel DNA replicate1


title: T_cell_FANCF_FANCF-ON_Day5_siA3_D10A_1

description: T cell FANCF FANCF-ON Day5 siA3 D10A Indel DNA replicate1


title: RNF2_RNF2-ON_MRE11_KD_H8A_2 T_cell_FANCF_FANCF-ON_Day5_siCtrl_Cas9_2

description: RNF2 RNF2-ON MRE11 KD H840A Indel DNA replicate2 and T cell FANCF FANCF-ON Day5 siCtrl Cas9 Indel DNA replicate2


title: RNF2_RNF2-ON_siCtrl_Cas9_2 T_cell_FANCF_FANCF-ON_Day5_siCtrl_D10A_1

description: RNF2 RNF2-ON siCtrl Cas9 Indel DNA replicate2 and T cell FANCF FANCF-ON Day5 siCtrl D10A Indel DNA replicate1


title: RNF2_RNF2-ON_siCtrl_D10A_2 T_cell_FANCF_FANCF-ON_Day5_siCtrl_Cas9_1

description: RNF2 RNF2-ON siCtrl D10A Indel DNA replicate2 and T cell FANCF FANCF-ON Day5 siCtrl Cas9 Indel DNA replicate1


title: RNF2_RNF2-ON_SMUG1_KO_UDG_KO_D10A_2 T_cell_FANCF_FANCF-ON_Day5_siA3_Cas9_2

description: RNF2 RNF2-ON SMUG1 KO UDG KO D10A Indel DNA replicate2 and T cell FANCF FANCF-ON Day5 siA3 Cas9 Indel DNA replicate2


title: RNF2_RNF2-ON_SMUG1_KO_UDG_KO_dC9_1

description: RNF2 RNF2-ON SMUG1 KO UDG KO dCas9 Indel DNA replicate1


title: RNF2_RNF2-ON_siCtrl_BE3_2

description: RNF2 RNF2-ON siCtrl BE3 Indel DNA replicate2


title: RNF2_RNF2-ON_APE1_KO_H8A_2

description: RNF2 RNF2-ON APE1 KO H840A Indel DNA replicate2


title: RNF2_RNF2-ON_siCtrl_dC9_2 T_cell_FANCF_FANCF-ON_Day5_siCtrl_D10A_2

description: RNF2 RNF2-ON siCtrl dCas9 Indel DNA replicate2 and T cell FANCF FANCF-ON Day5 siCtrl D10A Indel DNA replicate2


title: RNF2_RNF2-ON_MRE11_KD_D10A_2 T_cell_FANCF_FANCF-ON_Day5_siA3_dC9_2

description: RNF2 RNF2-ON MRE11 KD D10A Indel DNA replicate2 and T cell FANCF FANCF-ON Day5 siA3 dCas9 Indel DNA replicate2


title: RNF2_RNF2-ON_MRE11_KD_Cas9_2

description: RNF2 RNF2-ON MRE11 KD Cas9 Indel DNA replicate2


title: RNF2_RNF2-ON_MRE11_KD_BE3_2

description: RNF2 RNF2-ON MRE11 KD BE3 Indel DNA replicate2


title: RNF2_RNF2-ON_MRE11_KD_H8A_1 T_cell_FANCF_FANCF-ON_Day8_siA3_D10A_2

description: RNF2 RNF2-ON MRE11 KD H840A Indel DNA replicate1 and T cell FANCF FANCF-ON Day8 siA3 D10A Indel DNA replicate2


title: RNF2_RNF2-ON_MRE11_KD_dC9_1 T_cell_FANCF_FANCF-ON_Day5_siA3_dC9_1

description: RNF2 RNF2-ON MRE11 KD dCas9 Indel DNA replicate1 and T cell FANCF FANCF-ON Day5 siA3 dCas9 Indel DNA replicate1


title: T_cell_FANCF_FANCF-ON_Day8_siCtrl_D10A_2

description: T cell FANCF FANCF-ON Day8 siCtrl D10A Indel DNA replicate2


title: T_cell_FANCF_FANCF-ON_Day8_siA3_Cas9_2

description: T cell FANCF FANCF-ON Day8 siA3 Cas9 Indel DNA replicate2


title: RNF2_RNF2-ON_siCtrl_dC9_1 T_cell_FANCF_FANCF-ON_Day8_siCtrl_Cas9_2

description: RNF2 RNF2-ON siCtrl dCas9 Indel DNA replicate1 and T cell FANCF FANCF-ON Day8 siCtrl Cas9 Indel DNA replicate2


title: RNF2_RNF2-ON_siCtrl_H8A_2

description: RNF2 RNF2-ON siCtrl H840A Indel DNA replicate2


title: RNF2_RNF2-ON_MRE11_KD_Cas9_1

description: RNF2 RNF2-ON MRE11 KD Cas9 Indel DNA replicate1


title: RNF2_RNF2-ON_MRE11_KD_BE3_1 T_cell_FANCF_FANCF-ON_Day8_siA3_D10A_1

description: RNF2 RNF2-ON MRE11 KD BE3 Indel DNA replicate1 and T cell FANCF FANCF-ON Day8 siA3 D10A Indel DNA replicate1


title: RNF2_RNF2-ON_siCtrl_H8A_1 T_cell_FANCF_FANCF-ON_Day8_siA3_Cas9_1

description: RNF2 RNF2-ON siCtrl H840A Indel DNA replicate1 and T cell FANCF FANCF-ON Day8 siA3 Cas9 Indel DNA replicate1


title: RNF2_RNF2-ON_siCtrl_D10A_1

description: RNF2 RNF2-ON siCtrl D10A Indel DNA replicate1


title: RNF2_RNF2-ON_EXO1_KO_H8A_1

description: RNF2 RNF2-ON EXO1 KO H840A Indel DNA replicate1


title: RNF2_RNF2-ON_siCtrl_BE3_1 T_cell_FANCF_FANCF-ON_Day8_siCtrl_Cas9_1

description: RNF2 RNF2-ON siCtrl BE3 Indel DNA replicate1 and T cell FANCF FANCF-ON Day8 siCtrl Cas9 Indel DNA replicate1


title: RNF2_RNF2-ON_siCtrl_Cas9_1 T_cell_FANCF_FANCF-ON_Day8_siCtrl_D10A_1

description: RNF2 RNF2-ON siCtrl Cas9 Indel DNA replicate1 and T cell FANCF FANCF-ON Day8 siCtrl D10A Indel DNA replicate1


title: EMX1_EMX1-ON_BE3_3

description: EMX1 EMX1-ON BE3 Indel DNA replicate3


title: RNF2_RNF2-ON_MRE11_KD_dC9_2

description: RNF2 RNF2-ON MRE11 KD dCas9 Indel DNA replicate2


title: EMX1_EMX1-ON_EXO1_KO_BE3_3

description: EMX1 EMX1-ON EXO1 KO BE3 Indel DNA replicate3


title: EMX1_EMX1_SMUG1_KO_UDG_KO_BE3_2

description: EMX1 EMX1 SMUG1 KO UDG KO BE3 Indel DNA replicate2


title: CDKN2A-6_H8A_2 VEGFA-2-OT1_H8A_2 VEGFA-3_H8A_2

description: CDKN2A-6 H840A Indel DNA replicate2 and VEGFA-2-OT1 H840A Indel DNA replicate2 and VEGFA-3 H840A Indel DNA replicate2


title: EMX1_EMX1-ON_EXO1_KO_H8A_3+RNF2_RNF2-ON_EXO1_KO_D10A_2

description: EMX1 EMX1-ON EXO1 KO H840A Indel DNA replicate3+RNF2 RNF2-ON EXO1 KO D10A Indel DNA replicate2


title: CDKN2A-6_D10A_2 RNA4_D10A-OT1_2 VEGFA-2_-OT1_D10A_2 VEGFA-3_D10A_2

description: CDKN2A-6 D10A Indel DNA replicate2 and RNA4 D10A-OT1 Indel DNA replicate2 and VEGFA-2 -OT1 D10A Indel DNA replicate2 and VEGFA-3 D10A Indel DNA replicate2


title: EMX1_EMX1-ON_EXO1_KO_Cas9_3+RNF2_RNF2-ON_EXO1_KO_Cas9_1

description: EMX1 EMX1-ON EXO1 KO Cas9 Indel DNA replicate3+RNF2 RNF2-ON EXO1 KO Cas9 Indel DNA replicate1


title: CDKN2A-6_Cas9_2 RNA4_Cas9-OT1_2 VEGFA-2_-OT1_Cas9_2 VEGFA-3_Cas9_2

description: CDKN2A-6 Cas9 Indel DNA replicate2 and RNA4 Cas9-OT1 Indel DNA replicate2 and VEGFA-2 -OT1 Cas9 Indel DNA replicate2 and VEGFA-3 Cas9 Indel DNA replicate2


title: RAG1-E_dC9_1 RNA4-OT1_A3Bm_dC9_1 VEGFA-2-OT1_A3Bm_dC9_1 VEGFA-3_A3Bm_dC9_1

description: RAG1-E dCas9 Indel DNA replicate1 and RNA4-OT1 A3Bm dCas9 Indel DNA replicate1 and VEGFA-2-OT1 A3Bm dCas9 Indel DNA replicate1 and VEGFA-3 A3Bm dCas9 Indel DNA replicate1


title: EMX1_EMX1-ON_EXO1_KO_D10A_3

description: EMX1 EMX1-ON EXO1 KO D10A Indel DNA replicate3


title: EMX1_EMX1-ON_EXO1_KO_dC9_2

description: EMX1 EMX1-ON EXO1 KO dCas9 Indel DNA replicate2


title: RAG1-E_H8A_1 VEGFA-2-OT1_A3Bm_H8A_1 VEGFA-3_A3Bm_H8A_1

description: RAG1-E H840A Indel DNA replicate1 and VEGFA-2-OT1 A3Bm H840A Indel DNA replicate1 and VEGFA-3 A3Bm H840A Indel DNA replicate1


title: EMX1_EMX1-ON_EXO1_KO_BE3_2+RNF2_RNF2-ON_EXO1_KO_D10A_1

description: EMX1 EMX1-ON EXO1 KO BE3 Indel DNA replicate2+RNF2 RNF2-ON EXO1 KO D10A Indel DNA replicate1


title: RAG1-E_D10A_1 RNA4-OT1_A3Bm_D10A_1 VEGFA-2-OT1_A3Bm_D10A_1 VEGFA-3_A3Bm_D10A_1

description: RAG1-E D10A Indel DNA replicate1 and RNA4-OT1 A3Bm D10A Indel DNA replicate1 and VEGFA-2-OT1 A3Bm D10A Indel DNA replicate1 and VEGFA-3 A3Bm D10A Indel DNA replicate1


title: EMX1_EMX1-ON_EXO1_KO_H8A_2

description: EMX1 EMX1-ON EXO1 KO H840A Indel DNA replicate2


title: RNF2_RNF2-ON_MRE11_KD_D10A_1

description: RNF2 RNF2-ON MRE11 KD D10A Indel DNA replicate1


title: RAG1-E_Cas9_1 RNA4-OT1_A3Bm_Cas9_1 VEGFA-2-OT1_A3Bm_Cas9_1 VEGFA-3_A3Bm_Cas9_1

description: RAG1-E Cas9 Indel DNA replicate1 and RNA4-OT1 A3Bm Cas9 Indel DNA replicate1 and VEGFA-2-OT1 A3Bm Cas9 Indel DNA replicate1 and VEGFA-3 A3Bm Cas9 Indel DNA replicate1


title: EMX1_EMX1_SMUG1_KO_UDG_KO_BE3_3

description: EMX1 EMX1 SMUG1 KO UDG KO BE3 Indel DNA replicate3


title: RNA4-OT1_A3B_dC9_1 VEGFA-2-OT1_A3B_dC9_1 VEGFA-3_A3B_dC9_1

description: RNA4-OT1 A3B dCas9 Indel DNA replicate1 and VEGFA-2-OT1 A3B dCas9 Indel DNA replicate1 and VEGFA-3 A3B dCas9 Indel DNA replicate1


title: EMX1_EMX1-ON_EXO1_KO_D10A_2+RNF2_RNF2-ON_APE1_KO_D10A_2

description: EMX1 EMX1-ON EXO1 KO D10A Indel DNA replicate2+RNF2 RNF2-ON APE1 KO D10A Indel DNA replicate2


title: VEGFA-2-OT1_A3B_H8A_1 VEGFA-3_A3B_H8A_1

description: VEGFA-2-OT1 A3B H840A Indel DNA replicate1 and VEGFA-3 A3B H840A Indel DNA replicate1


title: EMX1_EMX1-ON_EXO1_KO_Cas9_2

description: EMX1 EMX1-ON EXO1 KO Cas9 Indel DNA replicate2


title: EMX1_EMX1-ON_EXO1_KO_dC9_1

description: EMX1 EMX1-ON EXO1 KO dCas9 Indel DNA replicate1


title: FANCF,RNA4_up&dn_HDR_A3B_ds-plasmid_3

description: FANCF, RNA4 upstream and downstream HDR A3B ds-plasmid DNA replicate 3

data_processing:
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh37/hg19 human reference genome using BWA-MEM 0.7.9a-r786.
Genome_build: hg19 for human samples
Supplementary_files_format_and_content: Excel for Indels and Base Subtitutions

growth_protocol: 293FT from ATCC were maintained in DMEM (10566, Gibco/Thermo Fisher Scientific) + 10% FBS (16000-044, Gibco/Thermo Fisher Scientific) and have been tested for mycoplasma contamination free. Cryopreserved human peripheral blood mononuclear cells (PBMCs) were purchased from AllCells, LLC (PB003F). CD8+ T cells were pre-enriched from the PBMCs with Easysep Human CD8+ T cell enrichment kit (19053, Stemcell Technologies) according to the manufacturer’s protocol. The cells were then activated with Dynabeads Human T-Activator CD3/CD28 (LifeTech, 11131D) for 3 days in AIM V medium (Gibco, 0870112DK) supplemented with 10% FBS. The stimulated CD8+ T cells were then cultured in AIM V medium with 10% FBS and 100 IU/ml hIL2 (200-02-100, PeproTech).


title: RNA4-OT1_A3B_Cas9_1 VEGFA-2-OT1_A3B_Cas9_1 VEGFA-3_A3B_Cas9_1

description: RNA4-OT1 A3B Cas9 Indel DNA replicate1 and VEGFA-2-OT1 A3B Cas9 Indel DNA replicate1 and VEGFA-3 A3B Cas9 Indel DNA replicate1


title: CDKN2A-6_dC9_1 RNA4_dC9-OT1_1 VEGFA-2_-OT1_dC9_1 VEGFA-3_dC9_1

description: CDKN2A-6 dCas9 Indel DNA replicate1 and RNA4 dCas9-OT1 Indel DNA replicate1 and VEGFA-2 -OT1 dCas9 Indel DNA replicate1 and VEGFA-3 dCas9 Indel DNA replicate1


title: RNA4-OT1_A3B_D10A_1 VEGFA-2-OT1_A3B_D10A_1 VEGFA-3_A3B_D10A_1

description: RNA4-OT1 A3B D10A Indel DNA replicate1 and VEGFA-2-OT1 A3B D10A Indel DNA replicate1 and VEGFA-3 A3B D10A Indel DNA replicate1


title: FANCF,RNA4_up&dn_HDR_A3B_ds-plasmid_1

description: FANCF, RNA4 upstream and downstream HDR A3B ds-plasmid DNA replicate 1


title: FANCF,RNA4_up&dn_HDR_A3B_ds-plasmid_2

description: FANCF, RNA4 upstream and downstream HDR A3B ds-plasmid DNA replicate 2


title: CDKN2A-6_H8A_1 VEGFA-2-OT1_H8A_1 VEGFA-3_H8A_1

description: CDKN2A-6 H840A Indel DNA replicate1 and VEGFA-2-OT1 H840A Indel DNA replicate1 and VEGFA-3 H840A Indel DNA replicate1


title: FANCF_up_HDR_A3B_ssODN_3 FANCF_dn_HDR_A3B_ssODN_3

description: FANCF upstream HDR A3B ssODN DNA replicate 3 and FANCF downstream HDR A3B ssODN DNA replicate 3


title: FANCF_dn_HDR_A3B_ssODN_2

description: FANCF downstream HDR A3B ssODN DNA replicate 2


title: CDKN2A-6_D10A_1 RNA4_D10A-OT1_1 VEGFA-2_-OT1_D10A_1 VEGFA-3_D10A_1

description: CDKN2A-6 D10A Indel DNA replicate1 and RNA4 D10A-OT1 Indel DNA replicate1 and VEGFA-2 -OT1 D10A Indel DNA replicate1 and VEGFA-3 D10A Indel DNA replicate1


title: CDKN2A-6_Cas9_1 RNA4_Cas9-OT1_1 VEGFA-2_-OT1_Cas9_1_VEGFA-3_Cas9_1

description: CDKN2A-6 Cas9 Indel DNA replicate1 and RNA4 Cas9-OT1 Indel DNA replicate1 and VEGFA-2 -OT1 Cas9 Indel DNA replicate1 and  VEGFA-3 Cas9 Indel DNA replicate1


title: EMX1_A3Bm_dC9_2 FANCF_A3Bm_dC9_2 RNA4_A3Bm_dC9_2 ZSCAN2_A3Bm_dC9_2

description: EMX1 A3Bm dCas9 Indel DNA replicate2 and FANCF A3Bm dCas9 Indel DNA replicate2 and RNA4 A3Bm dCas9 Indel DNA replicate2 and ZSCAN2 A3Bm dCas9 Indel DNA replicate2


title: EMX1_A3Bm_Cas9_2 FANCF_A3Bm_Cas9_2 RNA4_A3Bm_Cas9_2 ZSCAN2_A3Bm_Cas9_2

description: EMX1 A3Bm Cas9 Indel DNA replicate2 and FANCF A3Bm Cas9 Indel DNA replicate2 and RNA4 A3Bm Cas9 Indel DNA replicate2 and ZSCAN2 A3Bm Cas9 Indel DNA replicate2


title: EMX1_A3Bm_D10A_2 FANCF_A3Bm_D10A_2 RNA4_A3Bm_D10A_2 ZSCAN2_A3Bm_D10A_2

description: EMX1 A3Bm D10A Indel DNA replicate2 and FANCF A3Bm D10A Indel DNA replicate2 and RNA4 A3Bm D10A Indel DNA replicate2 and ZSCAN2 A3Bm D10A Indel DNA replicate2


title: FANCF_dsODN_A3B_1

description: FANCF dsODN A3B DNA replicate 1

source_name: FANCF dsODN A3B DNA replicate 1


title: FANCF_ssODN_A3Bm_3

description: FANCF ssODN A3Bm DNA replicate 3

source_name: FANCF ssODN A3Bm DNA replicate 3


title: FANCF_ssODN_A3Bm_2

description: FANCF ssODN A3Bm DNA replicate 2

source_name: FANCF ssODN A3Bm DNA replicate 2


title: EMX1_A3Bm_H8A_2 FANCF_A3Bm_H8A_2 RNA4_A3Bm_H8A_2 ZSCAN2_A3Bm_H8A_2

description: EMX1 A3Bm H840A Indel DNA replicate2 and FANCF A3Bm H840A Indel DNA replicate2 and RNA4 A3Bm H840A Indel DNA replicate2 and ZSCAN2 A3Bm H840A Indel DNA replicate2


title: FANCF_ssODN_A3Bm_1

description: FANCF ssODN A3Bm DNA replicate 1

source_name: FANCF ssODN A3Bm DNA replicate 1


title: RNA4_ssODN_A3B_1

description: RNA4 ssODN A3B DNA replicate 1

source_name: RNA4 ssODN A3B DNA replicate 1


title: RNA4_ssODN_A3B_2

description: RNA4 ssODN A3B DNA replicate 2

source_name: RNA4 ssODN A3B DNA replicate 2


title: EMX1_A3B_H8A_2 FANCF_A3B_H8A_2 RNA4_A3B_H8A_2 ZSCAN2_A3B_H8A_2

description: EMX1 A3B H840A Indel DNA replicate2 and FANCF A3B H840A Indel DNA replicate2 and RNA4 A3B H840A Indel DNA replicate2 and ZSCAN2 A3B H840A Indel DNA replicate2


title: FANCF,RNA4_ssODN_A3B_3

description: FANCF, RNA4 ssODN A3B DNA replicate 3

source_name: FANCF, RNA4 ssODN A3B DNA replicate 3


title: EMX1_A3B_D10A_2 FANCF_A3B_D10A_2 RNA4_A3B_D10A_2 ZSCAN2_A3B_D10A_2

description: EMX1 A3B D10A Indel DNA replicate2 and FANCF A3B D10A Indel DNA replicate2 and RNA4 A3B D10A Indel DNA replicate2 and ZSCAN2 A3B D10A Indel DNA replicate2


title: EMX1_A3B_Cas9_2 FANCF_A3B_Cas9_2 RNA4_A3B_Cas9_2 ZSCAN2_A3B_Cas9_2

description: EMX1 A3B Cas9 Indel DNA replicate2 and FANCF A3B Cas9 Indel DNA replicate2 and RNA4 A3B Cas9 Indel DNA replicate2 and ZSCAN2 A3B Cas9 Indel DNA replicate2


title: EMX1_dC9_2 FANCF_dC9_2 RNA4_dC9_2 ZSCAN2_dC9_2

description: EMX1 dCas9 Indel DNA replicate2 and FANCF dCas9 Indel DNA replicate2 and RNA4 dCas9 Indel DNA replicate2 and ZSCAN2 dCas9 Indel DNA replicate2


title: FANCF_ssODN_A3B_2

description: FANCF ssODN A3B DNA replicate 2

source_name: FANCF ssODN A3B DNA replicate 2


title: FANCFssODN_3

description: FANCFssODN DNA replicate 3

source_name: FANCFssODN DNA replicate 3


title: EMX1_H8A_2 FANCF_H8A_2 RNA4_H8A_2 ZSCAN2_H8A_2

description: EMX1 H840A Indel DNA replicate2 and FANCF H840A Indel DNA replicate2 and RNA4 H840A Indel DNA replicate2 and ZSCAN2 H840A Indel DNA replicate2


title: RNA4_ssODN_1 FANCF_ssODN_A3B_1

description: RNA4 ssODN DNA replicate 1 and FANCF ssODN A3B DNA replicate 1


title: FANCF_dsODN_A3B_3

description: FANCF dsODN A3B DNA replicate 3

source_name: FANCF dsODN A3B DNA replicate 3


title: EMX1_Cas9_2 FANCF_Cas9_2 RNA4_Cas9_2 ZSCAN2_Cas9_2

description: EMX1 Cas9 Indel DNA replicate2 and FANCF Cas9 Indel DNA replicate2 and RNA4 Cas9 Indel DNA replicate2 and ZSCAN2 Cas9 Indel DNA replicate2


title: FANCF_ssODN_2

description: FANCF ssODN DNA replicate 2

source_name: FANCF ssODN DNA replicate 2


title: EMX1_A3Bm_dC9_1 FANCF_A3Bm_dC9_1 RNA4_A3Bm_dC9_1 ZSCAN2_A3Bm_dC9_1 VEGFA_A3Bm_dC9_1

description: EMX1 A3Bm dCas9 Indel DNA replicate1 and FANCF A3Bm dCas9 Indel DNA replicate1 and RNA4 A3Bm dCas9 Indel DNA replicate1 and ZSCAN2 A3Bm dCas9 Indel DNA replicate1 and VEGFA A3Bm dCas9 Indel DNA replicate1


title: FANCF_ssODN_1

description: FANCF ssODN DNA replicate 1

source_name: FANCF ssODN DNA replicate 1


title: EMX1_A3Bm_D10A_1 FANCF_A3Bm_D10A_1 RNA4_A3Bm_D10A_1 ZSCAN2_A3Bm_D10A_1 and_VEGFA_A3Bm_D10A_1

description: EMX1 A3Bm D10A Indel DNA replicate1 and FANCF A3Bm D10A Indel DNA replicate1 and RNA4 A3Bm D10A Indel DNA replicate1 and ZSCAN2 A3Bm D10A Indel DNA replicate1 and and VEGFA A3Bm D10A Indel DNA replicate1


title: FANCF,RNA4_ssODN_NT_3

description: FANCF, RNA4 ssODN Non-transfected DNA replicate 3


title: EMX1_D10A_2 FANCF_D10A_2 RNA4_D10A_2 ZSCAN2_D10A_2

description: EMX1 D10A Indel DNA replicate2 and FANCF D10A Indel DNA replicate2 and RNA4 D10A Indel DNA replicate2 and ZSCAN2 D10A Indel DNA replicate2


title: EMX1_A3Bm_Cas9_1 FANCF_A3Bm_Cas9_1 RNA4_A3Bm_Cas9_1 ZSCAN2_A3Bm_Cas9_1 VEGFA_A3Bm_Cas9_1

description: EMX1 A3Bm Cas9 Indel DNA replicate1 and FANCF A3Bm Cas9 Indel DNA replicate1 and RNA4 A3Bm Cas9 Indel DNA replicate1 and ZSCAN2 A3Bm Cas9 Indel DNA replicate1 and VEGFA A3Bm Cas9 Indel DNA replicate1


title: EMX1_A3B_dC9_1 FANCF_A3B_dC9_1 RNA4_A3B_dC9_1 ZSCAN2_A3B_dC9_1 VEGFA_A3B_dC9_1

description: EMX1 A3B dCas9 Indel DNA replicate1 and FANCF A3B dCas9 Indel DNA replicate1 and RNA4 A3B dCas9 Indel DNA replicate1 and ZSCAN2 A3B dCas9 Indel DNA replicate1 and VEGFA A3B dCas9 Indel DNA replicate1


title: FANCF,RNA4_ssODN_NT_1

description: FANCF, RNA4 ssODN Non-transfected DNA replicate 1


title: EMX1_A3B_dC9_2 FANCF_A3B_dC9_2 RNA4_A3B_dC9_2 ZSCAN2_A3B_dC9_2

description: EMX1 A3B dCas9 Indel DNA replicate2 and FANCF A3B dCas9 Indel DNA replicate2 and RNA4 A3B dCas9 Indel DNA replicate2 and ZSCAN2 A3B dCas9 Indel DNA replicate2


title: EMX1_A3B_H8A_1 FANCF_A3B_H8A_1 RNA4_A3B_H8A_1 ZSCAN2_A3B_H8A_1 VEGFA_A3B_H8A_1

description: EMX1 A3B H840A Indel DNA replicate1 and FANCF A3B H840A Indel DNA replicate1 and RNA4 A3B H840A Indel DNA replicate1 and ZSCAN2 A3B H840A Indel DNA replicate1 and VEGFA A3B H840A Indel DNA replicate1


title: EMX1_A3B_D10A_1 FANCF_A3B_D10A_1 RNA4_A3B_D10A_1 ZSCAN2_A3B_D10A_1 VEGFA_A3B_D10A_1

description: EMX1 A3B D10A Indel DNA replicate1 and FANCF A3B D10A Indel DNA replicate1 and RNA4 A3B D10A Indel DNA replicate1 and ZSCAN2 A3B D10A Indel DNA replicate1 and VEGFA A3B D10A Indel DNA replicate1


title: IRF8 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4)

city: Debrecen

first: Gergely

last: Nagy

address: Egyetem ter 1.

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

data_processing:
Samples were aligned by bwa v0.7.10 using default parameters.
Bam files were generated and indexed with samtools v0.1.19 using default parameters.
Tag directories were generated with homer v4.2 makeTagDirectory using -checkGC parameter.
Region calling for histone ChIP-seq samples was done with homer v4.2 findPeaks using -center -size 1000 -minDist 2500 parameters.
Peak calling for ATAC-seq and factor ChIP-seq samples was done with macs2 2.0.10 using -B --SPMR parameters.
mm10 ENCODE blacklist were subtracted from the peak lists.
Annotation was created with homer v4.2 annotatePeaks.pl using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: annotation file

source_name: bone marrow

growth_protocol: Isolation and differentiation were completed as described earlier (Daniel et al., 2014). Isolated bone marrow-derived cells were differentiated for 6 days in the presence of L929 supernatant.

extract_protocol:
Mouse bone marrow-derived macrophages were cross-linked using DSG and formaldehyde-based double cross-linking method and processed for ChIP.
Libraries were prepared either with Ovation Ultralow Library Systems (Nugen) or TruSeq ChIP library systems (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Cells were polarized on the 6th day of the differentiation with IL-4 (20ng/ml) for the indicated period of time.

tag: treatment

value: 8-12 weeks

value: bone marrow-derived macrophages

tag: chip antibody


title: JUNB ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4)

value: JUNB (sc-46x)


title: C/EBPa ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4)

value: CEBPa (sc-61X)


title: JUNB ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF


title: EMX1_A3B_Cas9_1 FANCF_A3B_Cas9_1 RNA4_A3B_Cas9_1 ZSCAN2_A3B_Cas9_1 VEGFA_A3B_Cas9_1

description: EMX1 A3B Cas9 Indel DNA replicate1 and FANCF A3B Cas9 Indel DNA replicate1 and RNA4 A3B Cas9 Indel DNA replicate1 and ZSCAN2 A3B Cas9 Indel DNA replicate1 and VEGFA A3B Cas9 Indel DNA replicate1


title: IRF8 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF


title: EMX1_H8A_1 FANCF_H8A_1 RNA4_H8A_1 ZSCAN2_H8A_1

description: EMX1 H840A Indel DNA replicate1 and FANCF H840A Indel DNA replicate1 and RNA4 H840A Indel DNA replicate1 and ZSCAN2 H840A Indel DNA replicate1


title: RNA4_ssODN_2 FANCF_dsODN_A3B_2

description: RNA4 ssODN DNA replicate 2 and FANCF dsODN A3B DNA replicate 2


title: EMX1_Cas9_1 FANCF_Cas9_1 RNA4_Cas9_1 ZSCAN2_Cas9_1

description: EMX1 Cas9 Indel DNA replicate1 and FANCF Cas9 Indel DNA replicate1 and RNA4 Cas9 Indel DNA replicate1 and ZSCAN2 Cas9 Indel DNA replicate1


title: EMX1_A3Bm_H8A_1 FANCF_A3Bm_H8A_1 RNA4_A3Bm_H8A_1 ZSCAN2_A3Bm_H8A_1 VEGFA_A3Bm_H8A_1

description: EMX1 A3Bm H840A Indel DNA replicate1 and FANCF A3Bm H840A Indel DNA replicate1 and RNA4 A3Bm H840A Indel DNA replicate1 and ZSCAN2 A3Bm H840A Indel DNA replicate1 and VEGFA A3Bm H840A Indel DNA replicate1


title: VEGFA-3_NT_3

description: VEGFA-3 NT Indel DNA replicate3


title: RNA-Seq analysis of Stat6KO mouse BMDM cells differentiated in the presence of MCSF (6h_ctrl, rep2)

data_processing:
alignment with TopHat v2.0.7 using default parameters
calculating RPKM values by cufflinks v2.0.2 using default parameters
Genome_build: mm10
Supplementary_files_format_and_content: table (tsv) of expressed genes

extract_protocol:
Total RNA was isolated from cells using Tri Reagent (MRC) according to the manufacturer’s protocol.
Indexed cDNA libraries were prepared from 1 µg of total RNA following the TruSeq™ RNA Sample Preparation Kit (Illumina, Inc.) protocol. Briefly, the mRNA Poly-A was selected on oligo (dT) magnetic beads and fragmented by divalent cations at 94°C for 5 min. Reverse transcription was performed using SuperScript II reverse transcriptase (Life Technologies, Inc.) and random primers. After second strand cDNA synthesis, fragments were end repaired, A-tailed and ligated with indexed adapters. cDNA libraries were purified and size selected after PCR with AMPure XP beads (Beckman Coulter, Inc, Fullerton, C.A USA).

value: cells differentiated in the presence of MCSF (6h_ctrl)


title: RNA-Seq analysis of Stat6KO mouse BMDM cells differentiated in the presence of MCSF (6h_ctrl, rep1)


title: RNA-Seq analysis of Stat6KO mouse BMDM cells differentiated in the presence of MCSF (6hIL4, rep2)

value: cells differentiated in the presence of MCSF (6hIL4)


title: T_cell_FANCF_FANCF-ON_Day5_siCtrl_dC9DNA_1

description: T cell FANCF FANCF-ON Day5 siCtrl dCas9DNA Indel DNA replicate1


title: RNA-Seq analysis of Stat6KO mouse BMDM cells differentiated in the presence of MCSF (6hIL4, rep1)


title: VEGFA-3_dC9_3

description: VEGFA-3 dCas9 Indel DNA replicate3


title: FANCF,RNA4_ssODN_NT_2

description: FANCF, RNA4 ssODN Non-transfected DNA replicate 2


title: RNA-Seq analysis of Stat6KO mouse BMDM cells differentiated in the presence of MCSF (3h_ctrl, rep2)

value: cells differentiated in the presence of MCSF (3h_ctrl)


title: FANCF_dn_HDR_A3Bm_ssODN_3

description: FANCF downstream HDR A3Bm ssODN DNA replicate 3


title: RNA-Seq analysis of Stat6KO mouse BMDM cells differentiated in the presence of MCSF (3h_ctrl, rep1)


title: VEGFA-3_H8A_3

description: VEGFA-3 H840A Indel DNA replicate3


title: T_cell_FANCF_FANCF-ON_Day5_siCtrl_dC9_2

description: T cell FANCF FANCF-ON Day5 siCtrl dCas9 Indel DNA replicate2


title: RNA-Seq analysis of Stat6KO mouse BMDM cells differentiated in the presence of MCSF (3hIL4, rep1)

value: cells differentiated in the presence of MCSF (3hIL4)


title: RNF2_RNF2-ON_SMUG1_KO_UDG_KO_BE3_2

description: RNF2 RNF2-ON SMUG1 KO UDG KO BE3 Indel DNA replicate2


title: RNF2_RNF2-ON_SMUG1_KO_UDG_KO_Cas9_2

description: RNF2 RNF2-ON SMUG1 KO UDG KO Cas9 Indel DNA replicate2


title: RNA-Seq analysis of Stat6KO mouse BMDM cells differentiated in the presence of MCSF (24h_ctrl, rep1)

value: cells differentiated in the presence of MCSF (24h_ctrl)


title: RNA-Seq analysis of Stat6KO mouse BMDM cells differentiated in the presence of MCSF (24h_ctrl, rep2)


title: EMX1_dC9_1 FANCF_dC9_1 RNA4_dC9_1 ZSCAN2_dC9_1

description: EMX1 dCas9 Indel DNA replicate1 and FANCF dCas9 Indel DNA replicate1 and RNA4 dCas9 Indel DNA replicate1 and ZSCAN2 dCas9 Indel DNA replicate1


title: C/EBPa ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF


title: RNF2_RNF2-ON_APE1_KO_dC9_2

description: RNF2 RNF2-ON APE1 KO dCas9 Indel DNA replicate2


title: RNA-Seq analysis of Stat6KO mouse BMDM cells differentiated in the presence of MCSF (24hIL4, rep2)

value: cells differentiated in the presence of MCSF (24hIL4)


title: EMX1_D10A_1 FANCF_D10A_1 RNA4_D10A_1 ZSCAN2_D10A_1 VEGFA-3_D10A_1

description: EMX1 D10A Indel DNA replicate1 and FANCF D10A Indel DNA replicate1 and RNA4 D10A Indel DNA replicate1 and ZSCAN2 D10A Indel DNA replicate1 and VEGFA-3 D10A Indel DNA replicate1


title: RNF2_RNF2-ON_EXO1_KO_Cas9_2

description: RNF2 RNF2-ON EXO1 KO Cas9 Indel DNA replicate2


title: RNA-Seq analysis of Stat6KO mouse BMDM cells differentiated in the presence of MCSF (24hIL4, rep1)


title: RNF2_RNF2-ON_SMUG1_KO_UDG_KO_BE3_1

description: RNF2 RNF2-ON SMUG1 KO UDG KO BE3 Indel DNA replicate1


title: RNA-Seq analysis of Stat6KO mouse BMDM cells differentiated in the presence of MCSF (1h_ctrl, rep2)

value: cells differentiated in the presence of MCSF (1h_ctrl)


title: RNA-Seq analysis of Stat6KO mouse BMDM cells differentiated in the presence of MCSF (1hIL4, rep2)

value: cells differentiated in the presence of MCSF (1hIL4)


title: RNF2_RNF2-ON_SMUG1_KO_UDG_KO_Cas9_1

description: RNF2 RNF2-ON SMUG1 KO UDG KO Cas9 Indel DNA replicate1


title: RNF2_RNF2-ON_APE1_KO_dC9_1

description: RNF2 RNF2-ON APE1 KO dCas9 Indel DNA replicate1


title: RNA-Seq analysis of Stat6KO mouse BMDM cells differentiated in the presence of MCSF (1h_ctrl, rep1)


title: RNF2_RNF2-ON_APE1_KO_Cas9_1

description: RNF2 RNF2-ON APE1 KO Cas9 Indel DNA replicate1


title: RNA-Seq analysis of Stat6KO mouse BMDM cells differentiated in the presence of MCSF (1hIL4, rep1)


title: VEGFA-3_D10A_3

description: VEGFA-3 D10A Indel DNA replicate3


title: RNA-Seq analysis of Stat6KO mouse BMDM cells differentiated in the presence of MCSF (rep2)


title: VEGFA_A3Bm_H840A_3 EMX1_EMX1_SMUG1_KO_UDG_KO_dCas9_3

description: VEGFA A3Bm H840A Indel DNA replicate3 and EMX1 EMX1 SMUG1 KO UDG KO dCas9 Indel DNA replicate3


title: VEGFA_A3Bm_D10A_3 EMX1_EMX1_SMUG1_KO_UDG_KO_H8A_3

description: VEGFA A3Bm D10A Indel DNA replicate3 and EMX1 EMX1 SMUG1 KO UDG KO H840A Indel DNA replicate3


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (6h_ctrl, rep4)

value: wild type


title: HeLa_FANCF_FANCF-ON_NT_3 HeLa_RAG1_RAG1-ON_NT_3 HeLa_VEGFA_VEGFA-ON_NT_3

description: HeLa FANCF FANCF-ON NT Indel DNA replicate3 and HeLa RAG1 RAG1-ON NT Indel DNA replicate3 and HeLa VEGFA VEGFA-ON NT Indel DNA replicate3

source_name: HeLa cells

value: HeLa


title: RNA-Seq analysis of Stat6KO mouse BMDM cells differentiated in the presence of MCSF (rep1)


title: RNA-Seq analysis of Stat6KO mouse BMDM cells differentiated in the presence of MCSF (3hIL4, rep2)


title: VEGFA-3_Cas9_3

description: VEGFA-3 Cas9 Indel DNA replicate3


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (6h_ctrl, rep2)


title: EMX1,FANCF,RNA4,RNA4-OT1,VEGFA-2-OT1,VEGFA-3,ZSCAN2_A3Bm_dC9_3

description: EMX1 A3Bm dCas9 Indel DNA replicate3 and FANCF A3Bm dCas9 Indel DNA replicate3 and RNA4 A3Bm dCas9 Indel DNA replicate3 and RNA4-OT1 A3Bm dCas9 Indel DNA replicate3 and VEGFA-2-OT1 A3Bm dCas9 Indel DNA replicate3 and VEGFA-3 A3Bm dCas9 Indel DNA replicate3 and ZSCAN2 A3Bm dCas9 Indel DNA replicate3


title: EMX1,FANCF,RNA4,RNA4-OT1,VEGFA-2-OT1,VEGFA-3,ZSCAN2_A3Bm_H8A_3

description: EMX1 A3Bm H840A Indel DNA replicate3 and FANCF A3Bm H840A Indel DNA replicate3 and RNA4 A3Bm H840A Indel DNA replicate3 and RNA4-OT1 A3Bm H840A Indel DNA replicate3 and VEGFA-2-OT1 A3Bm H840A Indel DNA replicate3 and VEGFA-3 A3Bm H840A Indel DNA replicate3 and ZSCAN2 A3Bm H840A Indel DNA replicate3


title: EMX1,FANCF,RNA4,RNA4-OT1,VEGFA-2-OT1,VEGFA-3,ZSCAN2_A3Bm_D10A_3

description: EMX1 A3Bm D10A Indel DNA replicate3 and FANCF A3Bm D10A Indel DNA replicate3 and RNA4 A3Bm D10A Indel DNA replicate3 and RNA4-OT1 A3Bm D10A Indel DNA replicate3 and VEGFA-2-OT1 A3Bm D10A Indel DNA replicate3 and VEGFA-3 A3Bm D10A Indel DNA replicate3 and ZSCAN2 A3Bm D10A Indel DNA replicate3


title: VEGFA_A3B_Cas9_3

description: VEGFA A3B Cas9 Indel DNA replicate3


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (6h_ctrl, rep1)


title: HeLa_FANCF_FANCF-ON_NT_2 HeLa_RAG1_RAG1-ON_NT_2 HeLa_VEGFA_VEGFA-ON_NT_2

description: HeLa FANCF FANCF-ON NT Indel DNA replicate2 and HeLa RAG1 RAG1-ON NT Indel DNA replicate2 and HeLa VEGFA VEGFA-ON NT Indel DNA replicate2


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (6hIL4, rep2)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (6hIL4, rep4)


title: EMX1,FANCF,RNA4,RNA4-OT1,VEGFA-2-OT1,VEGFA-3,ZSCAN2_A3Bm_Cas9_3

description: EMX1 A3Bm Cas9 Indel DNA replicate3 and FANCF A3Bm Cas9 Indel DNA replicate3 and RNA4 A3Bm Cas9 Indel DNA replicate3 and RNA4-OT1 A3Bm Cas9 Indel DNA replicate3 and VEGFA-2-OT1 A3Bm Cas9 Indel DNA replicate3 and VEGFA-3 A3Bm Cas9 Indel DNA replicate3 and ZSCAN2 A3Bm Cas9 Indel DNA replicate3


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (6hIL4, rep3)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (3h_ctrl, rep4)


title: VEGFA_A3Bm_H840A_2 EMX1_EMX1_SMUG1_KO_UDG_KO_dCas9_2

description: VEGFA A3Bm H840A Indel DNA replicate2 and EMX1 EMX1 SMUG1 KO UDG KO dCas9 Indel DNA replicate2


title: VEGFA_A3Bm_D10A_2 EMX1_EMX1_SMUG1_KO_UDG_KO_H8A_2

description: VEGFA A3Bm D10A Indel DNA replicate2 and EMX1 EMX1 SMUG1 KO UDG KO H840A Indel DNA replicate2


title: EMX1,FANCF,RNA4,RNA4-OT1,VEGFA-2-OT1,VEGFA-3,ZSCAN2_A3B_dC9_3

description: EMX1 A3B dCas9 Indel DNA replicate3 and FANCF A3B dCas9 Indel DNA replicate3 and RNA4 A3B dCas9 Indel DNA replicate3 and RNA4-OT1 A3B dCas9 Indel DNA replicate3 and VEGFA-2-OT1 A3B dCas9 Indel DNA replicate3 and VEGFA-3 A3B dCas9 Indel DNA replicate3 and ZSCAN2 A3B dCas9 Indel DNA replicate3


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (3h_ctrl, rep2)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (3h_ctrl, rep1)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (6h_ctrl, rep3)


title: EMX1,FANCF,RNA4,RNA4-OT1,VEGFA-2-OT1,VEGFA-3,ZSCAN2_A3B_D10A_3

description: EMX1 A3B D10A Indel DNA replicate3 and FANCF A3B D10A Indel DNA replicate3 and RNA4 A3B D10A Indel DNA replicate3 and RNA4-OT1 A3B D10A Indel DNA replicate3 and VEGFA-2-OT1 A3B D10A Indel DNA replicate3 and VEGFA-3 A3B D10A Indel DNA replicate3 and ZSCAN2 A3B D10A Indel DNA replicate3


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (3hIL4, rep4)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (3hIL4, rep1)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (3hIL4, rep2)


title: VEGFA_A3B_Cas9_2

description: VEGFA A3B Cas9 Indel DNA replicate2


title: EMX1,FANCF,RNA4,RNA4-OT1,VEGFA-2-OT1,VEGFA-3,ZSCAN2_A3B_Cas9_3

description: EMX1 A3B Cas9 Indel DNA replicate3 and FANCF A3B Cas9 Indel DNA replicate3 and RNA4 A3B Cas9 Indel DNA replicate3 and RNA4-OT1 A3B Cas9 Indel DNA replicate3 and VEGFA-2-OT1 A3B Cas9 Indel DNA replicate3 and VEGFA-3 A3B Cas9 Indel DNA replicate3 and ZSCAN2 A3B Cas9 Indel DNA replicate3


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24h_ctrl, rep4)


title: EMX1_dC9_3 FANCF_dC9_3 RNA4_dC9_3 RNA4-OT1_dC9_3 VEGFA-2-OT1_dC9_3 ZSCAN2_dC9_3

description: EMX1 dCas9 Indel DNA replicate3 and FANCF dCas9 Indel DNA replicate3 and RNA4 dCas9 Indel DNA replicate3 and RNA4-OT1 dCas9 Indel DNA replicate3 and VEGFA-2-OT1 dCas9 Indel DNA replicate3 and ZSCAN2 dCas9 Indel DNA replicate3


title: EMX1_H8A_3 FANCF_H8A_3 RNA4_H8A_3 RNA4-OT1_H8A_3 VEGFA-2-OT1_H8A_3 ZSCAN2_H8A_3

description: EMX1 H840A Indel DNA replicate3 and FANCF H840A Indel DNA replicate3 and RNA4 H840A Indel DNA replicate3 and RNA4-OT1 H840A Indel DNA replicate3 and VEGFA-2-OT1 H840A Indel DNA replicate3 and ZSCAN2 H840A Indel DNA replicate3


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24h_ctrl, rep3)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24h_ctrl, rep2)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (6hIL4, rep1)


title: EMX1_D10A_3 FANCF_D10A_3 RNA4_D10A_3 RNA4-OT1_D10A_3 VEGFA-2-OT1_D10A_3 ZSCAN2_D10A_3

description: EMX1 D10A Indel DNA replicate3 and FANCF D10A Indel DNA replicate3 and RNA4 D10A Indel DNA replicate3 and RNA4-OT1 D10A Indel DNA replicate3 and VEGFA-2-OT1 D10A Indel DNA replicate3 and ZSCAN2 D10A Indel DNA replicate3


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24h_ctrl, rep1)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4, rep3)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4, rep4)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (3h_ctrl, rep3)


title: EMX1_Cas9_3 FANCF_Cas9_3 RNA4_Cas9_3 RNA4-OT1_Cas9_3 VEGFA-2-OT1_Cas9_3 ZSCAN2_Cas9_3

description: EMX1 Cas9 Indel DNA replicate3 and FANCF Cas9 Indel DNA replicate3 and RNA4 Cas9 Indel DNA replicate3 and RNA4-OT1 Cas9 Indel DNA replicate3 and VEGFA-2-OT1 Cas9 Indel DNA replicate3 and ZSCAN2 Cas9 Indel DNA replicate3


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4, rep2)


title: CDKN2A-6_dC9_2 RNA4_dC9-OT1_2 VEGFA-2_-OT1_dC9_2 VEGFA-3_dC9_2

description: CDKN2A-6 dCas9 Indel DNA replicate2 and RNA4 dCas9-OT1 Indel DNA replicate2 and VEGFA-2 -OT1 dCas9 Indel DNA replicate2 and VEGFA-3 dCas9 Indel DNA replicate2


title: EMX1_EMX1_SMUG1_KO_UDG_KO_Cas9_1

description: EMX1 EMX1 SMUG1 KO UDG KO Cas9 Indel DNA replicate1


title: EMX1_EMX1_SMUG1_KO_UDG_KO_D10A_1

description: EMX1 EMX1 SMUG1 KO UDG KO D10A Indel DNA replicate1


title: EMX1,FANCF,RNA4,RNA4-OT1,VEGFA-2-OT1,VEGFA-3,ZSCAN2_A3B_H8A_3

description: EMX1 A3B H840A Indel DNA replicate3 and FANCF A3B H840A Indel DNA replicate3 and RNA4 A3B H840A Indel DNA replicate3 and RNA4-OT1 A3B H840A Indel DNA replicate3 and VEGFA-2-OT1 A3B H840A Indel DNA replicate3 and VEGFA-3 A3B H840A Indel DNA replicate3 and ZSCAN2 A3B H840A Indel DNA replicate3


title: EMX1_EMX1-ON_MRE11_KD_Cas9_3

description: EMX1 EMX1-ON MRE11 KD Cas9 Indel DNA replicate3


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1h_ctrl, rep4)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1h_ctrl, rep3)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (3hIL4, rep3)


title: VEGFA_A3B_D10A_2

description: VEGFA A3B D10A Indel DNA replicate2


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1h_ctrl, rep2)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1h_ctrl, rep1)


title: RNA4-OT1_A3Bm_H8A_2

description: RNA4-OT1 A3Bm H840A Indel DNA replicate2


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4, rep3)


title: RNA4-OT1_H8A_2

description: RNA4-OT1 H840A Indel DNA replicate2


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4, rep2)


title: HeLa_FANCF_FANCF-ON_dC9_3 HeLa_RAG1_RAG1-ON_dC9_3 HeLa_VEGFA_VEGFA-ON_dC9_3

description: HeLa FANCF FANCF-ON dCas9 Indel DNA replicate3 and HeLa RAG1 RAG1-ON dCas9 Indel DNA replicate3 and HeLa VEGFA VEGFA-ON dCas9 Indel DNA replicate3


title: HeLa_FANCF_FANCF-ON_H8A_3 HeLa_RAG1_RAG1-ON_H8A_3 HeLa_VEGFA_VEGFA-ON_H8A_3

description: HeLa FANCF FANCF-ON H840A Indel DNA replicate3 and HeLa RAG1 RAG1-ON H840A Indel DNA replicate3 and HeLa VEGFA VEGFA-ON H840A Indel DNA replicate3


title: RNA4-OT1_A3B_H8A_2

description: RNA4-OT1 A3B H840A Indel DNA replicate2


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4, rep1)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (0h_rep4)

value: cells differentiated in the presence of MCSF (0h)


title: HeLa_FANCF_FANCF-ON_D10A_3 HeLa_RAG1_RAG1-ON_D10A_3 HeLa_VEGFA_VEGFA-ON_D10A_3

description: HeLa FANCF FANCF-ON D10A Indel DNA replicate3 and HeLa RAG1 RAG1-ON D10A Indel DNA replicate3 and HeLa VEGFA VEGFA-ON D10A Indel DNA replicate3

value: DNA


title: HeLa_FANCF_FANCF-ON_Cas9_3 HeLa_RAG1_RAG1-ON_Cas9_3 HeLa_VEGFA_VEGFA-ON_Cas9_3

description: HeLa FANCF FANCF-ON Cas9 Indel DNA replicate3 and HeLa RAG1 RAG1-ON Cas9 Indel DNA replicate3 and HeLa VEGFA VEGFA-ON Cas9 Indel DNA replicate3


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (0h_rep3)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (0h_rep2)


title: GRO-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4)

description:
mm_BMDM_1hIL4_GRO
nascent RNA

data_processing:
Library strategy: GRO-Seq
alignment with bwa v0.7.10 using default parameters
bam generation with samtools v0.1.19 using default parameters
tag directory generation with homer v4.2 makeTagDirectory using -checkGC parameter
transcript calling with homer v4.2 findPeaks using-style groseq -tssSize 200 -minBodySize 300 -maxBodySize 3000 -tssFold 5 -bodyFold 2 -endFold 10 -fragLength 35
annotation was created with homer v4.2 annotatePeaks.pl using default parameters
Genome_build: mm10
Supplementary_files_format_and_content: annotation file

extract_protocol:
Nuclei isolation was performed using buffer containing 10mM Tris-HCl, pH 7.4; 2mM MgCl2; 3mM CaCl2; 0.5% NP40; 10% Glycerol; 1mM DTT supplemented with protease inhibitors (prior to use) and RNase inhibitor (SUPERase-In, prior to use). Nuclear Run-On (NRO) reactions were performed in the presence of Br-UTP in duplicates containing ~10x106 nuclei and pooled for nascent RNA enrichment, using BrdU antibody coated agarose beads. Beads were washed and NRO RNA was eluted and quantified by Qubit fluorometer.
Approximately 100ng NRO RNA was used for end-repair with T4 PNK (3’-end de-phosphorylation) and Cap-Clip Acid Pyrophosphatase (de-capping). Libraries were prepared with NEBNext Small RNA Library Prep set for Illumina and sequenced on HiSeq 2500.

treatment_protocol: Mouse bone marrow-derived macrophages were treated with IL-4 (20 ng/ml; 1, hour).


title: RNA4-OT1_A3Bm_H8A_1_

description: RNA4-OT1 A3Bm H840A Indel DNA replicate1


title: EMX1_EMX1-ON_MRE11_KD_Cas9_2

description: EMX1 EMX1-ON MRE11 KD Cas9 Indel DNA replicate2


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (0h_rep1)


title: RNA4-OT1_H8A_1

description: RNA4-OT1 H840A Indel DNA replicate1


title: GRO-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl)

description:
mm_BMDM_CTR_GRO
nascent RNA


title: RNA4-OT1_A3B_H8A_1

description: RNA4-OT1 A3B H840A Indel DNA replicate1


title: ATAC-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4, rep1)

extract_protocol:
Mouse bone marrow-derived macrophages were lysed with the following lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL). After lysis, nuclei were subjected to tagmentation.
Nextera DNA Library Prep Kit was used for library generation according to manufacturer's protocol.


title: ATAC-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl, rep2)

value: cells differentiated in the presence of MCSF (ctrl)


title: HeLa_FANCF_FANCF-ON_Cas9_2 HeLa_RAG1_RAG1-ON_Cas9_2 HeLa_VEGFA_VEGFA-ON_Cas9_2

description: HeLa FANCF FANCF-ON Cas9 Indel DNA replicate2 and HeLa RAG1 RAG1-ON Cas9 Indel DNA replicate2 and HeLa VEGFA VEGFA-ON Cas9 Indel DNA replicate2


title: HeLa_FANCF_FANCF-ON_D10A_2 HeLa_RAG1_RAG1-ON_D10A_2 HeLa_VEGFA_VEGFA-ON_D10A_2

description: HeLa FANCF FANCF-ON D10A Indel DNA replicate2 and HeLa RAG1 RAG1-ON D10A Indel DNA replicate2 and HeLa VEGFA VEGFA-ON D10A Indel DNA replicate2


title: HeLa_FANCF_FANCF-ON_H8A_2 HeLa_RAG1_RAG1-ON_H8A_2 HeLa_VEGFA_VEGFA-ON_H8A_2

description: HeLa FANCF FANCF-ON H840A Indel DNA replicate2 and HeLa RAG1 RAG1-ON H840A Indel DNA replicate2 and HeLa VEGFA VEGFA-ON H840A Indel DNA replicate2


title: ATAC-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl, rep1)

value: 8-12 weeks


title: EMX1_EMX1_APE1_KO_BE3_2

description: EMX1 EMX1 APE1 KO BE3 Indel DNA replicate2


title: HeLa_FANCF_FANCF-ON_dC9_2 HeLa_RAG1_RAG1-ON_dC9_2 HeLa_VEGFA_VEGFA-ON_dC9_2

description: HeLa FANCF FANCF-ON dCas9 Indel DNA replicate2 and HeLa RAG1 RAG1-ON dCas9 Indel DNA replicate2 and HeLa VEGFA VEGFA-ON dCas9 Indel DNA replicate2


title: ATAC-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4, rep2)

value: bone marrow-derived macrophages


title: STAT6 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4_rep1)

treatment_protocol: Mouse bone marrow-derived macrophages were treated with (1) IL-4 (20 ng/ml; 1, 6 or 24 hours) as indicated or (2) were pretreated with IL-4 (20 ng/ml) for 24 hours then LPS (100ng/ml) were added for 1 hours.


title: STAT6 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (6hIL4_rep2)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4, rep4)


title: EMX1_EMX1_APE1_KO_BE3_1

description: EMX1 EMX1 APE1 KO BE3 Indel DNA replicate1


title: STAT6 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4_rep2)


title: EMX1_EMX1_APE1_KO_dC9_2

description: EMX1 EMX1 APE1 KO dCas9 Indel DNA replicate2


title: STAT6 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (6hIL4_rep1)


title: EMX1_EMX1_APE1_KO_D10A_2

description: EMX1 EMX1 APE1 KO D10A Indel DNA replicate2


title: STAT6 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4_rep2)


title: EMX1_EMX1_APE1_KO_H8A_2

description: EMX1 EMX1 APE1 KO H840A Indel DNA replicate2


title: STAT6 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4_rep1)


title: EMX1_EMX1_APE1_KO_Cas9_2

description: EMX1 EMX1 APE1 KO Cas9 Indel DNA replicate2


title: STAT6 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep2)


title: VEGFA_dC9_2

description: VEGFA dCas9 Indel DNA replicate2


title: VEGFA_H8A_2

description: VEGFA H840A Indel DNA replicate2


title: STAT6 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep1)


title: p65 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4_1hLPS_rep2)

value: cells differentiated in the presence of MCSF (24hIL4_1hLPS)


title: p65 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_1hLPS_rep2)

value: cells differentiated in the presence of MCSF (ctrl_1hLPS)


title: VEGFA_Cas9_2 EMX1_EMX1-ON_MRE11_KD_1

description: VEGFA Cas9 Indel DNA replicate2 and EMX1 EMX1-ON MRE11 KD Indel DNA replicate1


title: EMX1_EMX1-ON_BE3_2

description: EMX1 EMX1-ON BE3 Indel DNA replicate2


title: VEGFA_D10A_2

description: VEGFA D10A Indel DNA replicate2


title: p65 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4_1hLPS_rep1)


title: p65 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4_ctrl_rep2)

value: cells differentiated in the presence of MCSF (24hIL4_ctrl)


title: EMX1_EMX1_APE1_KO_H8A_1

description: EMX1 EMX1 APE1 KO H840A Indel DNA replicate1


title: EMX1_EMX1_APE1_KO_dC9_1

description: EMX1 EMX1 APE1 KO dCas9 Indel DNA replicate1


title: EMX1_EMX1-ON_BE3_1

description: EMX1 EMX1-ON BE3 Indel DNA replicate1


title: p65 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_ctrl_rep2)

value: cells differentiated in the presence of MCSF (ctrl_ctrl)


title: p65 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4_ctrl_rep1)


title: sgCDKN2A-6_NT_3

description: sgCDKN2A-6 NT Indel DNA replicate3


title: p65 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_ctrl_rep1)


title: sgCDKN2A-6_dC9_3

description: sgCDKN2A-6 dCas9 Indel DNA replicate3


title: p300 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4_rep2)


title: sgCDKN2A-6_D10A_3

description: sgCDKN2A-6 D10A Indel DNA replicate3


title: sgCDKN2A-6_Cas9_3

description: sgCDKN2A-6 Cas9 Indel DNA replicate3


title: RAG1-E_Cas9_3

description: RAG1-E Cas9 Indel DNA replicate3


title: p300 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep2)


title: p300 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep1)


title: HeLa_FANCF_FANCF-ON_NT_1 HeLa_RAG1_RAG1-ON_NT_1 HeLa_VEGFA_VEGFA-ON_NT_1

description: HeLa FANCF FANCF-ON NT Indel DNA replicate1 and HeLa RAG1 RAG1-ON NT Indel DNA replicate1 and HeLa VEGFA VEGFA-ON NT Indel DNA replicate1


title: ZSCAN2_CDKN2A-ON_A3B_H8A_2 ZSCAN2_RAG1-ON_A3B_H8A_2 ZSCAN2_VEGFA-ON_A3B_H8A_2

description: ZSCAN2 CDKN2A-ON A3B H840A Indel DNA replicate2 and ZSCAN2 RAG1-ON A3B H840A Indel DNA replicate2 and ZSCAN2 VEGFA-ON A3B H840A Indel DNA replicate2


title: RNA Pol II-pS2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4_1hLPS_rep2)

value: RNA Pol II-pS2 (ab5095)


title: HeLa_FANCF_FANCF-ON_dC9_1 HeLa_RAG1_RAG1-ON_dC9_1 HeLa_VEGFA_VEGFA-ON_dC9_1

description: HeLa FANCF FANCF-ON dCas9 Indel DNA replicate1 and HeLa RAG1 RAG1-ON dCas9 Indel DNA replicate1 and HeLa VEGFA VEGFA-ON dCas9 Indel DNA replicate1


title: p65 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_1hLPS_rep1)


title: ZSCAN2_CDKN2A-ON_A3B_D10A_2 ZSCAN2_RAG1-ON_A3B_D10A_2 ZSCAN2_VEGFA-ON_A3B_D10A_2

description: ZSCAN2 CDKN2A-ON A3B D10A Indel DNA replicate2 and ZSCAN2 RAG1-ON A3B D10A Indel DNA replicate2 and ZSCAN2 VEGFA-ON A3B D10A Indel DNA replicate2


title: RNA Pol II-pS2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_1hLPS_rep2)


title: RNA Pol II-pS2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4_1hLPS_rep1)


title: RNA Pol II-pS2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_1hLPS_rep1)


title: RNA4_CDKN2A-ON_H8A_Cas9_2 RNA4_RAG1-ON_A3B_H8A_2 RNA4_VEGFA-ON_A3B_H8A_2

description: RNA4 CDKN2A-ON H840A Cas9 Indel DNA replicate2 and RNA4 RAG1-ON A3B H840A Indel DNA replicate2 and RNA4 VEGFA-ON A3B H840A Indel DNA replicate2


title: RNA Pol II-pS2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4_ctrl_rep2)


title: RNA4_CDKN2A-ON_A3B_dC9_2 RNA4_RAG1-ON_A3B_dC9_2 RNA4_VEGFA-ON_A3B_dC9_2

description: RNA4 CDKN2A-ON A3B dCas9 Indel DNA replicate2 and RNA4 RAG1-ON A3B dCas9 Indel DNA replicate2 and RNA4 VEGFA-ON A3B dCas9 Indel DNA replicate2


title: HeLa_FANCF_FANCF-ON_H8A_1 HeLa_RAG1_RAG1-ON_H8A_1 HeLa_VEGFA_VEGFA-ON_H8A_1

description: HeLa FANCF FANCF-ON H840A Indel DNA replicate1 and HeLa RAG1 RAG1-ON H840A Indel DNA replicate1 and HeLa VEGFA VEGFA-ON H840A Indel DNA replicate1


title: RNA Pol II-pS2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4_ctrl_rep1)


title: RNA Pol II-pS2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_ctrl_rep2)


title: RNA4_CDKN2A-ON_D10A_Cas9_2 RNA4_RAG1-ON_A3B_D10A_2 RNA4_VEGFA-ON_A3B_D10A_2

description: RNA4 CDKN2A-ON D10A Cas9 Indel DNA replicate2 and RNA4 RAG1-ON A3B D10A Indel DNA replicate2 and RNA4 VEGFA-ON A3B D10A Indel DNA replicate2


title: RNA Pol II-pS2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_ctrl_rep1)


title: sgCDKN2A-6_H8A_3

description: sgCDKN2A-6 H840A Indel DNA replicate3


title: HeLa_FANCF_FANCF-ON_Cas9_1 HeLa_RAG1_RAG1-ON_Cas9_1 HeLa_VEGFA_VEGFA-ON_Cas9_1

description: HeLa FANCF FANCF-ON Cas9 Indel DNA replicate1 and HeLa RAG1 RAG1-ON Cas9 Indel DNA replicate1 and HeLa VEGFA VEGFA-ON Cas9 Indel DNA replicate1


title: p300 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4_rep1)


title: FANCF_CDKN2A-ON_A3B_dC9_2 FANCF_RAG1-ON_A3B_dC9_2 FANCF_VEGFA-ON_A3B_dC9_2

description: FANCF CDKN2A-ON A3B dCas9 Indel DNA replicate2 and FANCF RAG1-ON A3B dCas9 Indel DNA replicate2 and FANCF VEGFA-ON A3B dCas9 Indel DNA replicate2


title: FANCF_CDKN2A-ON_A3B_D10A_2 FANCF_RAG1-ON_A3B_D10A_2 FANCF_VEGFA-ON_A3B_D10A_2

description: FANCF CDKN2A-ON A3B D10A Indel DNA replicate2 and FANCF RAG1-ON A3B D10A Indel DNA replicate2 and FANCF VEGFA-ON A3B D10A Indel DNA replicate2


title: RNA Pol II-pS5 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4_1hLPS_rep2)

value: RNA Pol II-pS5 (ab5131)


title: HeLa_FANCF_FANCF-ON_D10A_1 HeLa_RAG1_RAG1-ON_D10A_1 HeLa_VEGFA_VEGFA-ON_D10A_1

description: HeLa FANCF FANCF-ON D10A Indel DNA replicate1 and HeLa RAG1 RAG1-ON D10A Indel DNA replicate1 and HeLa VEGFA VEGFA-ON D10A Indel DNA replicate1


title: ZSCAN2_CDKN2A-ON_A3B_dC9_1 ZSCAN2_RAG1-ON_A3B_dC9_1 ZSCAN2_VEGFA-ON_A3B_dC9_1

description: ZSCAN2 CDKN2A-ON A3B dCas9 Indel DNA replicate1 and ZSCAN2 RAG1-ON A3B dCas9 Indel DNA replicate1 and ZSCAN2 VEGFA-ON A3B dCas9 Indel DNA replicate1


title: RNA Pol II-pS5 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4_1hLPS_rep1)


title: ZSCAN2_CDKN2A-ON_A3B_H8A_1 ZSCAN2_RAG1-ON_A3B_H8A_1 ZSCAN2_VEGFA-ON_A3B_H8A_1

description: ZSCAN2 CDKN2A-ON A3B H840A Indel DNA replicate1 and ZSCAN2 RAG1-ON A3B H840A Indel DNA replicate1 and ZSCAN2 VEGFA-ON A3B H840A Indel DNA replicate1


title: RNA Pol II-pS5 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_1hLPS_rep1)


title: RNA Pol II-pS5 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4_ctrl_rep1)


title: RNA Pol II-pS5 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4_ctrl_rep2)


title: RNA Pol II-pS5 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_ctrl_rep2)


title: RNA Pol II-pS5 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_ctrl_rep1)


title: VEGFA_dC9_Indel_3

description: VEGFA dCas9 Indel DNA replicate 3


title: RNA4_CDKN2A-ON_A3B_dC9_1 RNA4_RAG1-ON_A3B_dC9_1 RNA4_VEGFA-ON_A3B_dC9_1

description: RNA4 CDKN2A-ON A3B dCas9 Indel DNA replicate1 and RNA4 RAG1-ON A3B dCas9 Indel DNA replicate1 and RNA4 VEGFA-ON A3B dCas9 Indel DNA replicate1


title: RNA4_CDKN2A-ON_D10A_Cas9_1 RNA4_RAG1-ON_A3B_D10A_1 RNA4_VEGFA-ON_A3B_D10A_1

description: RNA4 CDKN2A-ON D10A Cas9 Indel DNA replicate1 and RNA4 RAG1-ON A3B D10A Indel DNA replicate1 and RNA4 VEGFA-ON A3B D10A Indel DNA replicate1


title: VEGFA_H8A_Indel_3

description: VEGFA H840A Indel DNA replicate 3


title: FANCF_CDKN2A-ON_A3B_dC9_1 FANCF_RAG1-ON_A3B_dC9_1 FANCF_VEGFA-ON_A3B_dC9_1

description: FANCF CDKN2A-ON A3B dCas9 Indel DNA replicate1 and FANCF RAG1-ON A3B dCas9 Indel DNA replicate1 and FANCF VEGFA-ON A3B dCas9 Indel DNA replicate1


title: RNA Pol II-pS2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep2)


title: RNA Pol II-pS2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4_rep1)


title: RNA Pol II-pS2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep1)


title: VEGFA_D10A_Indel_3

description: VEGFA D10A Indel DNA replicate 3


title: FANCF_CDKN2A-ON_A3B_D10A_1 FANCF_RAG1-ON_A3B_D10A_1 FANCF_VEGFA-ON_A3B_D10A_1

description: FANCF CDKN2A-ON A3B D10A Indel DNA replicate1 and FANCF RAG1-ON A3B D10A Indel DNA replicate1 and FANCF VEGFA-ON A3B D10A Indel DNA replicate1


title: RNA Pol II-pS5 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_1hLPS_rep2)


title: RNA Pol II-pS5 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4_rep2)


title: RNA Pol II-pS5 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4_rep1)


title: PU1 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4_rep2)


title: CDKN2A-6_NT_1 EMX1_NT_1 FANCF_NT_1 RNA4_NT_1 ZSCAN2_NT_1 RAG1-E_NT_1 VEGFA-3_NT_1

description: CDKN2A-6 NT Indel DNA replicate1 and EMX1 NT Indel DNA replicate1 and FANCF NT Indel DNA replicate1 and RNA4 NT Indel DNA replicate1 and ZSCAN2 NT Indel DNA replicate1 and RAG1-E NT Indel DNA replicate1 and VEGFA-3 NT Indel DNA replicate1


title: VEGFA_Cas9_Indel_3

description: VEGFA Cas9 Indel DNA replicate 3


title: RNA Pol II-pS5 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep2)


title: CDKN2A-6_NT_2 EMX1_NT_2 FANCF_NT_2 RNA4_NT_2 ZSCAN2_NT_2 RAG1-E_NT_2 VEGFA-3_NT_2

description: CDKN2A-6 NT Indel DNA replicate2 and EMX1 NT Indel DNA replicate2 and FANCF NT Indel DNA replicate2 and RNA4 NT Indel DNA replicate2 and ZSCAN2 NT Indel DNA replicate2 and RAG1-E NT Indel DNA replicate2 and VEGFA-3 NT Indel DNA replicate2


title: RNA Pol II-pS5 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep1)


title: ZSCAN2_CDKN2A-ON_A3B_D10A_1 ZSCAN2_RAG1-ON_A3B_D10A_1 ZSCAN2_VEGFA-ON_A3B_D10A_1

description: ZSCAN2 CDKN2A-ON A3B D10A Indel DNA replicate1 and ZSCAN2 RAG1-ON A3B D10A Indel DNA replicate1 and ZSCAN2 VEGFA-ON A3B D10A Indel DNA replicate1


title: RAG1-E_dC9_2 RNA4-OT1_A3Bm_dC9_2 VEGFA-2-OT1_A3Bm_dC9_2 VEGFA-3_A3Bm_dC9_2

description: RAG1-E dCas9 Indel DNA replicate2 and RNA4-OT1 A3Bm dCas9 Indel DNA replicate2 and VEGFA-2-OT1 A3Bm dCas9 Indel DNA replicate2 and VEGFA-3 A3Bm dCas9 Indel DNA replicate2


title: RAG1-E_H8A_2 VEGFA-2-OT1_A3Bm_H8A_2 VEGFA-3_A3Bm_H8A_2

description: RAG1-E H840A Indel DNA replicate2 and VEGFA-2-OT1 A3Bm H840A Indel DNA replicate2 and VEGFA-3 A3Bm H840A Indel DNA replicate2


title: PU1 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4_rep1)


title: PU1 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep2)


title: RNA4_CDKN2A-ON_H8A_Cas9_1 RNA4_RAG1-ON_A3B_H8A_1 RNA4_VEGFA-ON_A3B_H8A_1

description: RNA4 CDKN2A-ON H840A Cas9 Indel DNA replicate1 and RNA4 RAG1-ON A3B H840A Indel DNA replicate1 and RNA4 VEGFA-ON A3B H840A Indel DNA replicate1


title: RAG1-E_D10A_2 RNA4-OT1_A3Bm_D10A_2 VEGFA-2-OT1_A3Bm_D10A_2 VEGFA-3_A3Bm_D10A_2

description: RAG1-E D10A Indel DNA replicate2 and RNA4-OT1 A3Bm D10A Indel DNA replicate2 and VEGFA-2-OT1 A3Bm D10A Indel DNA replicate2 and VEGFA-3 A3Bm D10A Indel DNA replicate2


title: HDAC3 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4_rep2)


title: RAG1-E_Cas9_2 RNA4-OT1_A3Bm_Cas9_2 VEGFA-2-OT1_A3Bm_Cas9_2 VEGFA-3_A3Bm_Cas9_2

description: RAG1-E Cas9 Indel DNA replicate2 and RNA4-OT1 A3Bm Cas9 Indel DNA replicate2 and VEGFA-2-OT1 A3Bm Cas9 Indel DNA replicate2 and VEGFA-3 A3Bm Cas9 Indel DNA replicate2


title: RNA Pol II-pS2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4_rep2)


title: RNA4-OT1_A3B_dC9_2 VEGFA-2-OT1_A3B_dC9_2 VEGFA-3_A3B_dC9_2

description: RNA4-OT1 A3B dCas9 Indel DNA replicate2 and VEGFA-2-OT1 A3B dCas9 Indel DNA replicate2 and VEGFA-3 A3B dCas9 Indel DNA replicate2


title: VEGFA-2-OT1_A3B_H8A_2 VEGFA-3_A3B_H8A_2

description: VEGFA-2-OT1 A3B H840A Indel DNA replicate2 and VEGFA-3 A3B H840A Indel DNA replicate2


title: HDAC3 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4_rep1)


title: HDAC3 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep1)


title: RNA4-OT1_A3B_D10A_2 VEGFA-2-OT1_A3B_D10A_2 VEGFA-3_A3B_D10A_2

description: RNA4-OT1 A3B D10A Indel DNA replicate2 and VEGFA-2-OT1 A3B D10A Indel DNA replicate2 and VEGFA-3 A3B D10A Indel DNA replicate2


title: RNA4-OT1_A3B_Cas9_2 VEGFA-2-OT1_A3B_Cas9_2 VEGFA-3_A3B_Cas9_2

description: RNA4-OT1 A3B Cas9 Indel DNA replicate2 and VEGFA-2-OT1 A3B Cas9 Indel DNA replicate2 and VEGFA-3 A3B Cas9 Indel DNA replicate2


title: T_cell_RNA4_up_HDR_dsODN_siA3_2 EMX1_EMX1-ON_dC9_3

description: T cell RNA4 upstream HDR dsODN siA3 DNA replicate 2 and EMX1 EMX1-ON dCas9 Indel DNA replicate3


title: HDAC2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4_rep1)


title: T_cell_RNA4_up_HDR_dsODN_siA3_1 RAG1-E_dC9_3 EMX1_EMX1-ON_dC9_2

description: T cell RNA4 upstream HDR dsODN siA3 DNA replicate 1 and RAG1-E dCas9 Indel DNA replicate3 and EMX1 EMX1-ON dCas9 Indel DNA replicate2


title: HDAC3 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep2)


title: T_cell_RNA4_up_HDR_ssODN_siA3_1 T_cell_RNA4_dn_HDR_ssODN_siA3_1 RAG1-E_H8A_3 EMX1_EMX1-ON_H8A_2

description: T cell RNA4 upstream HDR ssODN siA3 DNA replicate 1 and T cell RNA4 downstream HDR ssODN siA3 DNA replicate 1 and RAG1-E H840A Indel DNA replicate3 and EMX1 EMX1-ON H840A Indel DNA replicate2


title: HDAC2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep1)


title: T_cell_RNA4_up_HDR_ssODN_siA3_2 T_cell_RNA4_dn_HDR_ssODN_siA3_2 EMX1_EMX1-ON_H8A_3

description: T cell RNA4 upstream HDR ssODN siA3 DNA replicate 2 and T cell RNA4 downstream HDR ssODN siA3 DNA replicate 2 and EMX1 EMX1-ON H840A Indel DNA replicate3


title: T_cell_RNA4_dn_HDR_dsODN_siCtrl_2 VEGFA_A3B_D10A_3

description: T cell RNA4 downstream HDR dsODN siCtrl DNA replicate 2 and VEGFA A3B D10A Indel DNA replicate3


title: HDAC1 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4_rep2)


title: HDAC1 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4_rep1)


title: PU1 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep1)


title: HDAC2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep2)


title: HDAC1 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep1)


title: T_cell_RNA4_up_HDR_dsODN_siCtrl_1 T_cell_RNA4_dn_HDR_dsODN_siCtrl_1 RAG1-E_D10A_3 EMX1_EMX1-ON_D10A_2

description: T cell RNA4 upstream HDR dsODN siCtrl DNA replicate 1 and T cell RNA4 downstream HDR dsODN siCtrl DNA replicate 1 and RAG1-E D10A Indel DNA replicate3 and EMX1 EMX1-ON D10A Indel DNA replicate2


title: T_cell_RNA4_up_HDR_dsODN_siCtrl_2 T_cell_RNA4_dn_HDR_dsODN_siA3_1 EMX1_EMX1-ON_D10A 3

description: T cell RNA4 upstream HDR dsODN siCtrl DNA replicate 2 and T cell RNA4 downstream HDR dsODN siA3 DNA replicate 1 and EMX1 EMX1-ON D10A DNA replicate3


title: T_cell_RNA4_up_HDR_ssODN_siCtrl_2 T_cell_RNA4_dn_HDR_ssODN_siCtrl_2 EMX1_EMX1-ON_Cas9_3

description: T cell RNA4 upstream HDR ssODN siCtrl DNA replicate 2 and T cell RNA4 downstream HDR ssODN siCtrl DNA replicate 2 and EMX1 EMX1-ON Cas9 Indel DNA replicate3


title: T_cell_RNA4_up_HDR_ssODN_siCtrl_1 T_cell_RNA4_dn_HDR_ssODN_siCtrl_1 RAG1-E_Cas9_3 EMX1_EMX1-ON_Cas9_2

description: T cell RNA4 upstream HDR ssODN siCtrl DNA replicate 1 and T cell RNA4 downstream HDR ssODN siCtrl DNA replicate 1 and RAG1-E Cas9 Indel DNA replicate3 and EMX1 EMX1-ON Cas9 Indel DNA replicate2


title: H3K27Ac ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4_rep2)


title: H3K27Ac ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep1)


title: HDAC2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4_rep2)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4_3hLPS_rep3)

data_processing:
alignment with TopHat v2.0.7 using default parameters
calculating RPKM values by cufflinks v2.0.2 using default parameters
Genome_build: mm10
Supplementary_files_format_and_content: table (tsv) of fpkm values

treatment_protocol: Mouse bone marrow-derived macrophages were pretreated with IL-4 (20 ng/ml) for 24 hours then LPS (100ng/ml) were added for 3 hours.

value: cells differentiated in the presence of MCSF (24hIL4_3hLPS)


title: H3K27Ac ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep2)


title: T_cell_RNA4_HDR_NT_1

description: T cell RNA4 HDR Non-transfected DNA replicate 1


title: RNA4_up_HDR_A3B_dsODN_3 RNA4_CDKN2A-ON_A3B_Cas9_2 RNA4_RAG1-ON_A3B_Cas9_2 RNA4_VEGFA-ON_A3B_Cas9_2

description: RNA4 upstream HDR A3B dsODN DNA replicate 3 and RNA4 CDKN2A-ON A3B Cas9 Indel DNA replicate2 and RNA4 RAG1-ON A3B Cas9 Indel DNA replicate2 and RNA4 VEGFA-ON A3B Cas9 Indel DNA replicate2


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_3hLPS_rep3)

value: cells differentiated in the presence of MCSF (ctrl_3hLPS)


title: RNA4_up_HDR_A3B_dsODN_2 RNA4_CDKN2A-ON_A3B_Cas9_1 RNA4_RAG1-ON_A3B_Cas9_1 RNA4_VEGFA-ON_A3B_Cas9_1

description: RNA4 upstream HDR A3B dsODN DNA replicate 2 and RNA4 CDKN2A-ON A3B Cas9 Indel DNA replicate1 and RNA4 RAG1-ON A3B Cas9 Indel DNA replicate1 and RNA4 VEGFA-ON A3B Cas9 Indel DNA replicate1


title: FANCF_up_HDR_A3B_dsODN_3

description: FANCF upstream HDR A3B dsODN DNA replicate 3


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4_ctrl_rep3)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_ctrl_rep3)


title: FANCF_dn_HDR_A3B_dsODN_3 EMX1_EMX1_SMUG1_KO_UDG_KO_H8A_1

description: FANCF downstream HDR A3B dsODN DNA replicate 3 and EMX1 EMX1 SMUG1 KO UDG KO H840A Indel DNA replicate1


title: FANCF_up_HDR_A3B_dsODN_2 RNA4_dn_HDR_A3B_dsODN_2 VEGFA_A3Bm_Cas9_3

description: FANCF upstream HDR A3B dsODN DNA replicate 2 and RNA4 downstream HDR A3B dsODN DNA replicate 2 and VEGFA A3Bm Cas9 Indel DNA replicate3


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_3hLPS_rep2)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4_ctrl_rep2)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4_3hLPS_rep2)


title: RNA4_up_HDR_A3Bm_ssODN_3 ZSCAN2_CDKN2A-ON_A3B_Cas9_2 ZSCAN2_RAG1-ON_A3B_Cas9_2 ZSCAN2_VEGFA-ON_A3B_Cas9_2

description: RNA4 upstream HDR A3Bm ssODN DNA replicate 3 and ZSCAN2 CDKN2A-ON A3B Cas9 Indel DNA replicate2 and ZSCAN2 RAG1-ON A3B Cas9 Indel DNA replicate2 and ZSCAN2 VEGFA-ON A3B Cas9 Indel DNA replicate2


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4_3hLPS_rep1)


title: FANCF_up_HDR_A3Bm_ssODN_3

description: FANCF upstream HDR A3Bm ssODN DNA replicate 3


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_3hLPS_rep1)


title: FANCF_up_HDR_A3Bm_ssODN_2 FANCF_dn_HDR_A3Bm_ssODN_2 RNA4_dn_HDR_A3Bm_ssODN_2 VEGFA_A3Bm_dC9_3

description: FANCF upstream HDR A3Bm ssODN DNA replicate 2 and FANCF downstream HDR A3Bm ssODN DNA replicate 2 and RNA4 downstream HDR A3Bm ssODN DNA replicate 2 and VEGFA A3Bm dCas9 Indel DNA replicate3


title: FANCF,RNA4_up&dn_HDR_A3B_dsODN_1 VEGFA_A3Bm_Cas9_2

description: FANCF, RNA4 upstream and downstream HDR A3B dsODN DNA replicate 1 and VEGFA A3Bm Cas9 Indel DNA replicate2


title: FANCF_up_HDR_A3Bm_ssODN_1 RNA4_up_HDR_A3Bm_ssODN_1 RNA4_dn_HDR_A3Bm_ssODN_1 VEGFA_A3Bm_dC9_2

description: FANCF upstream HDR A3Bm ssODN DNA replicate 1 and RNA4 upstream HDR A3Bm ssODN DNA replicate 1 and RNA4 downstream HDR A3Bm ssODN DNA replicate 1 and VEGFA A3Bm dCas9 Indel DNA replicate2


title: H3K27Ac ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4_rep1)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4_ctrl_rep1)


title: RNA4_dn_HDR_A3B_ssODN_3 FANCF_dn_HDR_A3B_dsODN_2 ZSCAN2_CDKN2A-ON,ZSCAN2_RAG1-ON,ZSCAN2_VEGFA-ON_A3B_dC9_2

description: RNA4 downstream HDR A3B ssODN DNA replicate 3 and FANCF downstream HDR A3B dsODN DNA replicate 2 and ZSCAN2 CDKN2A-ON A3B dCas9 Indel DNA replicate2 and ZSCAN2 RAG1-ON A3B dCas9 Indel DNA replicate2 and ZSCAN2 VEGFA-ON A3B dCas9 Indel DNA replicate2


title: T_cell_RNA4_HDR_NT_2 T_cell_RNA4_dn_HDR_dsODN_siA3_2

description: T cell RNA4 HDR Non-transfected DNA replicate 2 and T cell RNA4 downstream HDR dsODN siA3 DNA replicate 2


title: RNA4_up_HDR_A3Bm_ssODN_2 ZSCAN2_CDKN2A-ON_A3B_Cas9_1 ZSCAN2_RAG1-ON_A3B_Cas9_1 ZSCAN2_VEGFA-ON_A3B_Cas9_1

description: RNA4 upstream HDR A3Bm ssODN DNA replicate 2 and ZSCAN2 CDKN2A-ON A3B Cas9 Indel DNA replicate1 and ZSCAN2 RAG1-ON A3B Cas9 Indel DNA replicate1 and ZSCAN2 VEGFA-ON A3B Cas9 Indel DNA replicate1


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_ctrl_rep2)


title: RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_ctrl_rep1)

data_processing:
Samples were aligned with TopHat v2.0.7 using default parameters.
RPKM values were calculated by cufflinks v2.0.2 using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: table (tsv) of fpkm values


title: RNA4_dn_HDR_A3B_ssODN_2 VEGFA_A3B_dC9_2 EMX1_EMX1_SMUG1_KO_UDG_KO_D10A_2

description: RNA4 downstream HDR A3B ssODN DNA replicate 2 and VEGFA A3B dCas9 Indel DNA replicate2 and EMX1 EMX1 SMUG1 KO UDG KO D10A Indel DNA replicate2


title: YT

city: Helsinki

first: Olli

last: Dufva

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
YT cell line
Sample_10

data_processing:
Basecalls performed using standard Illumina base-caller
RNA-seq reads were pre-processed using Trimmomatics v0.32 with the following configurations ILLUMINACLIP:TruSeqAdapters-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Pre-processed RNA-seq reads were aligned to the hg38 genome assembly (EnsEMBL v82) using the STAR per-sample 2-pass mapping strategy. STAR v2.3.0e aligner was used with the following configurations --outSAMattributes All --outSAMunmapped Within. The STAR indexes were build from primary assembly sequences and by taking into account transcript annotations.
PCR duplicates were marked with the MarkDuplicates tool of PICARD v1.63 with the following configurations CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT
Counts were calculated using subreadR as implemented in the statistical environment R (v.3.3.0).
Genome_build: hg38 genome assembly, EnsEMBL v82
Supplementary_files_format_and_content: Tab-delimited text file (.txt). Columns: 1) element's row number, 2) EnsEMBL gene id, 3) gene model's start coordinate, 4) gene model's stop coordinate, 5) gene model's chromosome, 6) gene name, 7) biotype information, 8) raw count value

source_name: natural killer cell line

growth_protocol: Cells were seeded at 5x10^5 cells/ml and cultured for 72 h in  RPMI-1640 (Lonza) with 10% FBS, 2 mM L-glutamine, 100 U/mL penicillin, and 100 µg/mL streptomycin supplemented with 2.5 ng/ml IL-2 (Peprotech, 20 ng/ml for IMC-1) prior to harvesting for extraction.

extract_protocol:
RNA was extracted using miRNeasy Mini Kit (Qiagen). Agilent Bioanalyzer RNApico chip (Agilent) was used to evaluate the integrity of RNA and Qubit RNA kit (Life Technologies) to quantitate RNA in samples. 1.5 µg of total RNA was used for ScriptSeq v2™ Complete kit for human/mouse/rat (Illumina) to ribodeplete rRNA and further for RNA-seq library preparation. SPRI beads (Agencourt AMPure XP, Beckman Coulter) were used for purification of RNAseq libraries. The library QC was evaluated on High Sensitivity chips by Agilent Bioanalyzer (Agilent). Sequencing libraries were sequenced using paired end 100 bp read format on an Illumina HiSeq 2000 instrument (Illumina).
Ribo depletion RNA-Seq: Agilent Bioanalyzer RNApico chip (Agilent) was used to evaluate the integrity of RNA and Qubit RNA kit (Life Technologies) to quantitate RNA in samples. 1.5 µg of total RNA was used for ScriptSeq v2™ Complete kit for human/mouse/rat (Illumina) to ribodeplete rRNA and further for RNA-seq library preparation. SPRI beads (Agencourt AMPure XP, Beckman Coulter) were used for purification of RNAseq libraries. The library QC was evaluated on High Sensitivity chips by Agilent Bioanalyzer (Agilent). Sequencing libraries were sequenced using paired end 100 bp read format on an Illumina HiSeq 2000 instrument (Illumina).

value: YT

tag: cancer type

value: acute lymphoblastic leukemia with thymoma

value: natural killer cell line


title: RNA4_up_HDR_A3B_ssODN_3 FANCF_CDKN2A-ON_A3B_H8A_2 FANCF_RAG1-ON_A3B_H8A_2 FANCF_VEGFA-ON_A3B_H8A_2

description: RNA4 upstream HDR A3B ssODN DNA replicate 3 and FANCF CDKN2A-ON A3B H840A Indel DNA replicate2 and FANCF RAG1-ON A3B H840A Indel DNA replicate2 and FANCF VEGFA-ON A3B H840A Indel DNA replicate2


title: SNK-6

description:
SNK-6 cell line
Sample_09

value: extranodal natural killer/T cell lymphoma, nasal type


title: NK-YS

description:
NK-YS cell line
Sample_07

value: NK-YS


title: NKL

description:
NKL cell line
Sample_08

value: NKL

value: natural killer-cell large granular lymphocytic leukemia


title: NK-92

description:
NK-92 cell line
Sample_06

value: aggressive natural killer-cell leukemia


title: FANCF_up_HDR_A3B_ssODN_1 RNA4_up_HDR_A3B_ssODN_1

description: FANCF upstream HDR A3B ssODN DNA replicate 1 and RNA4 upstream HDR A3B ssODN DNA replicate 1

source_name: FANCF downstream HDR A3B ssODN DNA replicate 1 and RNA4 upstream HDR A3B ssODN DNA replicate 1


title: RNA4_up_HDR_ssODN_3 FANCF_CDKN2A-ON_A3B_Cas9_2 FANCF_RAG1-ON_A3B_Cas9_2 FANCF_VEGFA-ON_A3B_Cas9_2

description: RNA4 upstream HDR ssODN DNA replicate 3 and FANCF CDKN2A-ON A3B Cas9 Indel DNA replicate2 and FANCF RAG1-ON A3B Cas9 Indel DNA replicate2 and FANCF VEGFA-ON A3B Cas9 Indel DNA replicate2

source_name: RNA4 upstream HDR ssODN DNA replicate 3


title: KHYG-1

description:
KHYG-1 cell line
Sample_05


title: FANCF_dn_HDR_ssODN_3

description: FANCF downstream HDR ssODN DNA replicate 3


title: KAI3

description:
KAI3 cell line
Sample_04

value: chronic active EBV infection


title: RNA4_dn_HDR_ssODN_2 FANCF_dn_HDR_ssODN_3 VEGFA_A3B_H8A_2 EMX1_EMX1_SMUG1_KO_UDG_KO_Cas9_2

description: RNA4 downstream HDR ssODN DNA replicate 2 and FANCF downstream HDR ssODN DNA replicate 3 and VEGFA A3B H840A Indel DNA replicate2 and EMX1 EMX1 SMUG1 KO UDG KO Cas9 Indel DNA replicate2


title: DERL-7

description:
DERL-7 cell line
Sample_02

source_name: NK cell characteristics

value: hepatosplenic gammadelta cell lymphoma

value: NK cell characteristics


title: RNA4_up_HDR_ssODN_2 FANCF_CDKN2A-ON_A3B_Cas9_1 FANCF_RAG1-ON_A3B_Cas9_1 FANCF_VEGFA-ON_A3B_Cas9_1

description: RNA4 upstream HDR ssODN DNA replicate 2 and FANCF CDKN2A-ON A3B Cas9 Indel DNA replicate1 and FANCF RAG1-ON A3B Cas9 Indel DNA replicate1 and FANCF VEGFA-ON A3B Cas9 Indel DNA replicate1

source_name: RNA4 upstream HDR ssODN DNA replicate 2


title: FANCF_dn_HDR_ssODN_2 EMX1_EMX1_SMUG1_KO_UDG_KO_dC9_1

description: FANCF downstream HDR ssODN DNA replicate 2 and EMX1 EMX1 SMUG1 KO UDG KO dCas9 Indel DNA replicate1


title: DERL-2

description:
DERL-2 cell line
Sample_01

source_name: gammadelta T cell line

value: gammadelta T cell line


title: IMC-1

description:
IMC-1 cell line
Sample_03


title: FANCF_up_HDR_ssODN_2 RNA4_dn_HDR_ssODN_3 VEGFA_A3B_H8A_3 EMX1_EMX1_SMUG1_KO_UDG_KO_Cas9_3

description: FANCF upstream HDR ssODN DNA replicate 2 and RNA4 downstream HDR ssODN DNA replicate 3 and VEGFA A3B H840A Indel DNA replicate3 and EMX1 EMX1 SMUG1 KO UDG KO Cas9 Indel DNA replicate3


title: FANCF_up_HDR_ssODN_1 RNA4_up_HDR_ssODN_1

description: FANCF upstream HDR ssODN DNA replicate 1 and RNA4 upstream HDR ssODN DNA replicate 1

source_name: FANCF downstream HDR ssODN DNA replicate 1 and RNA4 upstream HDR ssODN DNA replicate 1


title: FANCF_dn_HDR_ssODN_1 RNA4_dn_HDR_ssODN_1

description: FANCF downstream HDR ssODN DNA replicate 1 and RNA4 downstream HDR ssODN DNA replicate 1

source_name: FANCF upstream HDR ssODN DNA replicate 1


title: FANCF_dn_HDR_A3B_ssODN_1 RNA4_dn_HDR_A3B_ssODN_1

description: FANCF downstream HDR A3B ssODN DNA replicate 1 and RNA4 downstream HDR A3B ssODN DNA replicate 1

source_name: RNA4 downstream HDR ssODN DNA replicate 1 and FANCF upstream HDR A3B ssODN DNA replicate 1 and RNA4 downstream HDR A3B ssODN DNA replicate 1


title: D2

city: Guangzhou

first: Yizhao

last: Luan

state: Guangdong

address: Xianlie South Rd. 54, Yuexiu Dist

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat v2.0.11 with parameters --mate-inner--dist 200, other default
Aligned reads were counted using HTSeq v0.6.1 with parameter -q -m union -s no -a 20 -t exon -I gene_id
Differential expression analysis using DESeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw gene count values for each Sample

source_name: brain glioma, 6 hour dbcAMP treatment

extract_protocol:
Total RNA was isolated from cultured cell lines.
Beads containing oligo (dT) were used to isolate poly(A) mRNA from total RNA. Purified mRNA was then fragmented in fragmentation buffer. Using these short fragments as templates, random hexamer-primers  ere used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I. Short double-stranded cDNA fragments were purified with a QIAquick PCR extraction kit (vendor) and eluted with EB buffer for end repair and the addition of an ‘A’ base. Next, the short fragments were ligated to Illumina sequencing adaptors. DNA fragments of a selected size were gel-purified and amplified by PCR. The amplified library was sequenced using Illumina HiSeq 2000.

treatment_protocol: DBTRG-05MG cell lines were maintained at 37°C under 5% CO2 in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum (Gibco) and penicillin/streptomycin.

value: Brain glioma


title: D3

source_name: brain glioma, 12 hour dbcAMP treatment


title: D5

source_name: brain glioma, 48 hour dbcAMP treatment


title: RNA4_up_HDR_A3B_ssODN_2 FANCF_CDKN2A-ON_A3B_H8A_1 FANCF_RAG1-ON_A3B_H8A_1 FANCF_VEGFA-ON_A3B_H8A_1

description: RNA4 upstream HDR A3B ssODN DNA replicate 2 and FANCF CDKN2A-ON A3B H840A Indel DNA replicate1 and FANCF RAG1-ON A3B H840A Indel DNA replicate1 and FANCF VEGFA-ON A3B H840A Indel DNA replicate1


title: FANCF_up_HDR_A3B_ssODN_2 VEGFA_A3B_dC9_3 EMX1_EMX1_SMUG1_KO_UDG_KO_D10A_3

description: FANCF upstream HDR A3B ssODN DNA replicate 2 and VEGFA A3B dCas9 Indel DNA replicate3 and EMX1 EMX1 SMUG1 KO UDG KO D10A Indel DNA replicate3


title: D1

source_name: brain glioma, 0 hour dbcAMP treatment


title: D4

source_name: brain glioma, 24 hour dbcAMP treatment


title: RNA4_HDR_NT_3

description: RNA4 HDR Non-transfected DNA replicate 3


title: FANCF_HDR_NT_3 VEGFA_NT_Indel_3

description: FANCF HDR Non-transfected DNA replicate 3 and VEGFA NT Indel DNA replicate 3


title: RNA4_HDR_NT_2

description: RNA4 HDR Non-transfected DNA replicate 2


title: FANCF_HDR_NT_2 RNA4_HDR_NT_1 EMX1_NT_3 FANCF_NT_3 RNA4_NT_3 ZSCAN2_NT_3 VEGFA_NT_2

description: FANCF HDR Non-transfected DNA replicate 2 and RNA4 HDR Non-transfected DNA replicate 1 and EMX1 NT Indel DNA replicate3 and FANCF NT Indel DNA replicate3 and RNA4 NT Indel DNA replicate3 and ZSCAN2 NT Indel DNA replicate3 and VEGFA NT Indel DNA replicate2