title: ChIA-PET from endothelial cell of umbilical vein (ENCLB995LGU)

description:
https://www.encodeproject.org/experiments/ENCSR080OMN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in HUVEC
experiment encode accession: ENCSR080OMN
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR049NDZ
encode release date: 2021-04-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB995LGU
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: endothelial cell of umbilical vein

value: primary cell

value: not collected

value: newborn

value: Lonza

value: ENCBS046NPX at ENCODE; https://www.encodeproject.org/ENCBS046NPX/

value: Derived from ENCODE donor ENCDO000AAS; https://www.encodeproject.org/ENCDO000AAS/


title: ChIA-PET from HCT116 (ENCLB610CWY)

status: Public on Jun 15 2021

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR278IZK/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in HCT116
experiment encode accession: ENCSR278IZK
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR012LAX
encode release date: 2021-04-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB610CWY
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens HCT116 cell line

tag: antibody

value: CTCF

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: male

tag: health state

value: colorectal carcinoma

tag: dev stage

value: adult

tag: age

value: 48 year

tag: lab

value: Yijun Ruan, JAX

tag: source

value: ATCC

tag: link

value: ENCBS801HHZ at ENCODE; https://www.encodeproject.org/ENCBS801HHZ/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: ChIA-PET from MCF-7 (ENCLB154ZTB)

description:
https://www.encodeproject.org/experiments/ENCSR059HDE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in MCF7
experiment encode accession: ENCSR059HDE
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2020-12-16
lab: Yijun Ruan, JAX
library encode accession: ENCLB154ZTB
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens MCF-7 cell line

extract_protocol:
general protocol: https://www.encodeproject.org/documents/f7779792-9403-4396-9ff6-8e859edd608c/@@download/attachment/In-situ%20chiapet_Ruan%20Lab_final.pdf
extraction method: SDS

tag: description

value: Breast cancer derived from metastatic site. The MCF7 line retains several characteristics of differentiated mammary epithelium including ability to process estradiol via cytoplasmic estrogen receptors and the capability of forming domes. The cells express the WNT7B oncogene.

value: female

value: breast cancer (adenocarcinoma)

value: 69 year

value: ENCBS734CYW at ENCODE; https://www.encodeproject.org/ENCBS734CYW/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/


title: ChIA-PET from MCF 10A (ENCLB137PZC)

description:
https://www.encodeproject.org/experiments/ENCSR403ZYJ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET with MCF10A cell
experiment encode accession: ENCSR403ZYJ
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR775RVY
encode release date: 2021-01-25
lab: Yijun Ruan, JAX
library encode accession: ENCLB137PZC
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens MCF 10A cell line

value: MCF 10A

value: The MCF 10A cell line is a non-tumorigenic epithelial cell line. The cells are positive for epithelial sialomucins, cytokeratins and milk fat globule antigen.

value: fibrocystic disease

value: 36 year

value: ENCBS283FQS at ENCODE; https://www.encodeproject.org/ENCBS283FQS/

value: Derived from ENCODE donor ENCDO000AAP; https://www.encodeproject.org/ENCDO000AAP/


title: ChIA-PET from RWPE1 (ENCLB486MDS)

description:
https://www.encodeproject.org/experiments/ENCSR030KAB/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in RWPE1
experiment encode accession: ENCSR030KAB
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-01-25
lab: Yijun Ruan, JAX
library encode accession: ENCLB486MDS
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens RWPE1 cell line

value: CTCF

value: cell line

value: prostate epithelial transformed by HPV

value: male

value: normal

value: adult

value: 54 year

value: ENCBS299YNR at ENCODE; https://www.encodeproject.org/ENCBS299YNR/

value: Derived from ENCODE donor ENCDO000ADM; https://www.encodeproject.org/ENCDO000ADM/


title: ChIA-PET from MCF-7 (ENCLB221UOT)

description:
https://www.encodeproject.org/experiments/ENCSR200VHL/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in MCF7
experiment encode accession: ENCSR200VHL
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-01-25
lab: Yijun Ruan, JAX
library encode accession: ENCLB221UOT
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: Breast cancer derived from metastatic site. The MCF7 line retains several characteristics of differentiated mammary epithelium including ability to process estradiol via cytoplasmic estrogen receptors and the capability of forming domes. The cells express the WNT7B oncogene.

value: female

value: breast cancer (adenocarcinoma)

value: 69 year

value: Yijun Ruan, JAX

value: ATCC

value: ENCBS581IOB at ENCODE; https://www.encodeproject.org/ENCBS581IOB/


title: ChIA-PET from MCF-7 (ENCLB357XCL)

description:
https://www.encodeproject.org/experiments/ENCSR059HDE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in MCF7
experiment encode accession: ENCSR059HDE
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2020-12-16
lab: Yijun Ruan, JAX
library encode accession: ENCLB357XCL
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/


title: ChIA-PET from HCT116 (ENCLB557QDS)

description:
https://www.encodeproject.org/experiments/ENCSR278IZK/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in HCT116
experiment encode accession: ENCSR278IZK
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR012LAX
encode release date: 2021-04-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB557QDS
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: CTCF

value: colorectal carcinoma

value: 48 year

value: ENCBS855FZN at ENCODE; https://www.encodeproject.org/ENCBS855FZN/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: ChIA-PET from BJ (ENCLB445PAR)

description:
https://www.encodeproject.org/experiments/ENCSR573PZV/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in BJ
experiment encode accession: ENCSR573PZV
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-01-26
lab: Yijun Ruan, JAX
library encode accession: ENCLB445PAR
size range: 350-600

source_name: Homo sapiens BJ cell line

value: BJ

value: cell line

value: skin fibroblast, The line was established from skin taken from normal foreskin. - ATCC.

value: male

value: normal

value: newborn

value: not collected

value: ENCBS116BPR at ENCODE; https://www.encodeproject.org/ENCBS116BPR/

value: Derived from ENCODE donor ENCDO000AAG; https://www.encodeproject.org/ENCDO000AAG/


title: ChIA-PET from RWPE1 (ENCLB492KKV)

description:
https://www.encodeproject.org/experiments/ENCSR030KAB/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in RWPE1
experiment encode accession: ENCSR030KAB
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-01-25
lab: Yijun Ruan, JAX
library encode accession: ENCLB492KKV
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: prostate epithelial transformed by HPV

value: adult

value: 54 year

value: Yijun Ruan, JAX

value: ATCC

value: ENCBS685IEZ at ENCODE; https://www.encodeproject.org/ENCBS685IEZ/

value: Derived from ENCODE donor ENCDO000ADM; https://www.encodeproject.org/ENCDO000ADM/


title: ChIA-PET from A549 (ENCLB430DDY)

description:
https://www.encodeproject.org/experiments/ENCSR138NSW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in A549
experiment encode accession: ENCSR138NSW
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR414IDX
encode release date: 2021-01-12
lab: Yijun Ruan, JAX
library encode accession: ENCLB430DDY
size range: 350-600

source_name: Homo sapiens A549 cell line

value: human epithelial cell line derived from a lung carcinoma tissue. The cells are adherent in culture. The karyotype is hypotriploid male with a modal chromosome number of 12. There are numerous chromosome abnormalities and marker chromosomes.

value: 58 year

value: ENCBS744PGM at ENCODE; https://www.encodeproject.org/ENCBS744PGM/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIA-PET from SK-N-SH (ENCLB769KWJ)

description:
https://www.encodeproject.org/experiments/ENCSR130BTG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in SK-N-SH
experiment encode accession: ENCSR130BTG
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2020-12-18
lab: Yijun Ruan, JAX
library encode accession: ENCLB769KWJ
size range: 350-600

source_name: Homo sapiens SK-N-SH cell line

value: SK-N-SH

value: cell line

value: neuroblastoma, newly promoted to tier 2:not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

value: female

value: Metastatic neuroblastoma from bone marrow

value: child

value: 4 year

value: ENCBS210ZQV at ENCODE; https://www.encodeproject.org/ENCBS210ZQV/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/


title: ChIA-PET from AG04450 (ENCLB445BGB)

description:
https://www.encodeproject.org/experiments/ENCSR514BNX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in AG04450
experiment encode accession: ENCSR514BNX
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-02-23
lab: Yijun Ruan, JAX
library encode accession: ENCLB445BGB
size range: 350-600

source_name: Homo sapiens AG04450 cell line

value: male

value: apparently healthy

value: embryonic

value: 12 week

value: Yijun Ruan, JAX

value: Coriell

value: ENCBS452VFY at ENCODE; https://www.encodeproject.org/ENCBS452VFY/

value: Derived from ENCODE donor ENCDO001AAA; https://www.encodeproject.org/ENCDO001AAA/


title: ChIA-PET from SK-N-SH (ENCLB071SGG)

description:
https://www.encodeproject.org/experiments/ENCSR130BTG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in SK-N-SH
experiment encode accession: ENCSR130BTG
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2020-12-18
lab: Yijun Ruan, JAX
library encode accession: ENCLB071SGG
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: SK-N-SH

value: ATCC

value: ENCBS128XPF at ENCODE; https://www.encodeproject.org/ENCBS128XPF/


title: ChIA-PET from endothelial cell of umbilical vein (ENCLB444ZUY)

description:
https://www.encodeproject.org/experiments/ENCSR080OMN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in HUVEC
experiment encode accession: ENCSR080OMN
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR049NDZ
encode release date: 2021-04-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB444ZUY
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens newborn endothelial of umbilical vein primary cell

value: endothelial cell of umbilical vein

value: primary cell

value: not collected

value: unknown

value: newborn

value: Lonza

value: ENCBS519IYJ at ENCODE; https://www.encodeproject.org/ENCBS519IYJ/

value: Derived from ENCODE donor ENCDO000AAS; https://www.encodeproject.org/ENCDO000AAS/


title: ChIA-PET from A549 (ENCLB877LSQ)

description:
https://www.encodeproject.org/experiments/ENCSR138NSW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in A549
experiment encode accession: ENCSR138NSW
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR414IDX
encode release date: 2021-01-12
lab: Yijun Ruan, JAX
library encode accession: ENCLB877LSQ
size range: 350-600

value: cell line

value: human epithelial cell line derived from a lung carcinoma tissue. The cells are adherent in culture. The karyotype is hypotriploid male with a modal chromosome number of 12. There are numerous chromosome abnormalities and marker chromosomes.

value: male

value: adult

value: 58 year

value: ENCBS085MQM at ENCODE; https://www.encodeproject.org/ENCBS085MQM/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: PFC high performer #2 [13_pfc_88_ACTGAT]

status: Public on Oct 01 2020

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

library_source: transcriptomic

data_processing:
RNA-seq samples were aligned using STAR, quantified using Salmon, and normalized counts were determined using DESeq2
Genome_build: m38.p4
Supplementary_files_format_and_content: Normalized counts files are comma separated value matrices containing the DESeq2 normalized counts for each of the samples.

molecule: total RNA

organism: Mus musculus

source_name: PFC high performer

extract_protocol: Libraries were prepared according to the Illumina TruSeq stranded mRNA LT sample preparation kit.

tag: mouse group

value: high performing mouse

tag: tissue

value: prefrontal cortex (PFC)


title: MDTH high performer #2 [8_mdth_88_AGTTCC]

source_name: MDTH high performer

value: mouse MDTH


title: ChIA-PET from SK-N-SH (ENCLB363ZIK)

description:
https://www.encodeproject.org/experiments/ENCSR514HBO/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in SK-N-SH
experiment encode accession: ENCSR514HBO
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-01-25
lab: Yijun Ruan, JAX
library encode accession: ENCLB363ZIK
size range: 350-600

value: CTCF

value: SK-N-SH

value: neuroblastoma, newly promoted to tier 2:not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

value: female

value: Metastatic neuroblastoma from bone marrow

value: child

value: 4 year

value: Yijun Ruan, JAX

value: ATCC

value: ENCBS128XPF at ENCODE; https://www.encodeproject.org/ENCBS128XPF/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/


title: Egr2fl/fl unstimulated BMDM ATAC-seq replicate 1

status: Public on Sep 15 2020

city: New York

first: Laszlo

last: Halasz

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

data_processing:
RNA-seq: Reads were aligned to the mouse reference genome (mm10) using the default parameters of HISAT2. Rsubread’s featureCounts function was used to quantify the reference transcriptome (Gencode: M21) and generate raw count table (useMetaFeatures=TRUE and allowMultiOverlap=TRUE).
The primary analysis of ATAC-seq and ChIP-seq reads were carried out using ChIP-seq command line pipeline [Barta, 2011]. Briefly, reads were mapped to the mouse reference genome (mm10) using the default parameters of BWA MEM aligner. Low mapping quality reads (MAPQ<10), reads mapping to ENCODE mouse blacklisted [ref] regions and duplicated reads are discarded from downstream analysis, using samtools rmdup and bedtools intersectBed. Open chromatin regions or putative binding sites were determined using MACS2 at 5% false discovery rate (FDR). Coverage profiles were calculated using deeptools2 bamCoverage (--binSize 10 --smoothLength 40 --normalizeUsing RPGC –effectiveGenomeSize 2652783500).
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: Raw and normalized (edgeR, cpm) count matrices. ChIP-seq, ATAC-seq: Normalized coverage files (deeptools2, bigwigs).

source_name: Bone marrow derived macrophages

growth_protocol: Isolated bone marrow-derived cells were differentiated for 6 days in the presence of L929 supernatant. Cells were either exposed to IL-4 (5ng/ml) during the whole differentiation process or polarized on the 6th day of the differentiation with IL-4 (20ng/ml) for the indicated period of time.

extract_protocol:
For RNA-seq, wild type and Egr2fl/fl macrophages were differentiated in the presence of M-CSF using L929 cell supernatants for 6 days. On the 6th day cells were re-plated and treated with IL-4 (20ng/ml) for 24 hours or left untreated. Poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single ‘A’ base addition and ligation of barcode-indexed adaptors to the DNA fragments. ChIP was performed essentially as previously described (Daniel et al., 2014b), (Daniel et al., 2014a). ATAC-seq was carried out as described earlier with minor modification (Buenrostro et al., 2013).
For RNA-seq adapter-specific PCRs were performed to generate sequencing libraries. Approximately 2.5ug was used for library preparation with TruSeq RNA Sample Preparation Kit (Illumina). Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.

treatment_protocol: ATAC-seq, ChIP-seq and gene expression measurements were performed in macrophages differentiated with M-CSF, on the 6th day cells were exposed to IL-4 (20ng/ul) for the indicated period of time.

tag: strain

value: Bone marrow

tag: cell type

value: Bone marrow derived macrophages (BMDM)

tag: genotype

tag: treatment

value: CTRL


title: Egr2fl/fl 24-h IL-4 treated BMDM ATAC-seq replicate 1

tag: time


title: Wild-type IL-4 24h BMDM ATAC-seq replicate 2


title: Wild-type IL-4 24h BMDM ATAC-seq replicate 1


title: Egr2fl/fl 24-h IL-4 treated BMDM RNAPIIpS2 ChIP-seq replicate 2

description: mm_BMDM_ChIPseq_Egr2KO_RNAPIIpS2_IL4_24h_rep2

tag: chip antibody


title: Egr2fl/fl 24-h IL-4 treated BMDM RNAPIIpS2 ChIP-seq replicate 1

description: mm_BMDM_ChIPseq_Egr2KO_RNAPIIpS2_IL4_24h_rep1


title: Wild-type unstimulated BMDM ATAC-seq replicate 1


title: Egr2fl/fl unstimulated BMDM ATAC-seq replicate 2


title: Egr2fl/fl unstimulated BMDM RNAPIIpS2 ChIP-seq replicate 2

description: mm_BMDM_ChIPseq_Egr2KO_RNAPIIpS2_CTRL_rep2


title: Wild-type unstimulated BMDM RNAPIIpS2 ChIP-seq replicate 2

description: mm_BMDM_ChIPseq_Egr2WT_RNAPIIpS2_CTRL_rep2


title: Wild-type IL-4 24h BMDM RNAPIIpS2 ChIP-seq replicate 1

description: mm_BMDM_ChIPseq_Egr2WT_RNAPIIpS2_IL4_24h_rep1


title: Wild-type unstimulated BMDM RNAPIIpS2 ChIP-seq replicate 1

description: mm_BMDM_ChIPseq_Egr2WT_RNAPIIpS2_CTRL_rep1


title: Wild-type IL-4 24h BMDM RNAPIIpS2 ChIP-seq replicate 2

description: mm_BMDM_ChIPseq_Egr2WT_RNAPIIpS2_IL4_24h_rep2


title: Egr2fl/fl unstimulated BMDM BRM ChIP-seq replicate 2

value: BRM


title: ChIA-PET from HCT116 (ENCLB512JGR)

description:
https://www.encodeproject.org/experiments/ENCSR035PVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116
experiment encode accession: ENCSR035PVZ
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR012LAX
encode release date: 2021-04-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB512JGR
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: ENCBS801HHZ at ENCODE; https://www.encodeproject.org/ENCBS801HHZ/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: Egr2fl/fl 24-h IL-4 treated BMDM BRM ChIP-seq replicate 2


title: Egr2fl/fl 24-h IL-4 treated BMDM BRM ChIP-seq replicate 1


title: Egr2fl/fl unstimulated BMDM BRM ChIP-seq replicate 1


title: Wild-type IL-4 24h BMDM BRM ChIP-seq replicate 2


title: Egr2fl/fl 24-h IL-4 treated BMDM ATAC-seq replicate 2


title: Wild-type unstimulated BMDM BRM ChIP-seq replicate 1


title: ChIA-PET from HCT116 (ENCLB488ZZW)

description:
https://www.encodeproject.org/experiments/ENCSR035PVZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116
experiment encode accession: ENCSR035PVZ
assay title: ChIA-PET
assembly: GRCh38
possible controls: ENCSR012LAX
encode release date: 2021-04-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB488ZZW
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

tag: Sex

tag: health state

tag: dev stage

value: ENCBS855FZN at ENCODE; https://www.encodeproject.org/ENCBS855FZN/


title: Egr2fl/fl 24-h IL-4 treated BMDM BRD4 ChIP-seq replicate 2

description: mm_BMDM_ChIPseq_Egr2KO_BRD4_IL4_24h_rep2


title: Wild-type unstimulated BMDM BRM ChIP-seq replicate 2


title: Wild-type unstimulated BMDM ATAC-seq replicate 2


title: Egr2fl/fl 24-h IL-4 treated BMDM BRD4 ChIP-seq replicate 1

description: mm_BMDM_ChIPseq_Egr2KO_BRD4_IL4_24h_rep1


title: Egr2fl/fl unstimulated BMDM BRD4 ChIP-seq replicate 2


title: Egr2fl/fl unstimulated BMDM BRD4 ChIP-seq replicate 1


title: Egr2fl/fl unstimulated BMDM RNAPIIpS2 ChIP-seq replicate 1

description: mm_BMDM_ChIPseq_Egr2KO_RNAPIIpS2_CTRL_rep1


title: Wild-type unstimulated BMDM BRD4 ChIP-seq replicate 2


title: Wild-type unstimulated BMDM BRD4 ChIP-seq replicate 1


title: Egr2fl/fl 24-h IL-4 treated BMDM H3K27ac ChIP-seq replicate 2

description: mm_BMDM_ChIPseq_Egr2KO_H3K27ac_IL4_24h_rep2


title: Egr2fl/fl unstimulated BMDM H3K27ac ChIP-seq replicate 2

description: mm_BMDM_ChIPseq_Egr2KO_H3K27ac_CTRL_rep2


title: Egr2fl/fl 24-h IL-4 treated BMDM H3K27ac ChIP-seq replicate 1

description: mm_BMDM_ChIPseq_Egr2KO_H3K27ac_IL4_24h_rep1


title: Egr2fl/fl unstimulated BMDM H3K27ac ChIP-seq replicate 1

description: mm_BMDM_ChIPseq_Egr2KO_H3K27ac_CTRL_rep1


title: Wild-type IL-4 24h BMDM BRM ChIP-seq replicate 1


title: Wild-type IL-4 24h BMDM H3K27ac ChIP-seq replicate 2

description: mm_BMDM_ChIPseq_Egr2WT_H3K27ac_IL4_24h_rep2


title: Wild-type unstimulated BMDM H3K27ac ChIP-seq replicate 1

description: mm_BMDM_ChIPseq_Egr2WT_H3K27ac_CTRL_rep1


title: Wild-type IL-4 24h BMDM P300 ChIP-seq replicate 1

description: mm_BMDM_ChIPseq_Egr2WT_P300_IL4_24h_rep1


title: Wild-type IL-4 24h BMDM P300 ChIP-seq replicate 2

description: mm_BMDM_ChIPseq_Egr2WT_P300_IL4_24h_rep2


title: Wild-type unstimulated BMDM H3K27ac ChIP-seq replicate 2

description: mm_BMDM_ChIPseq_Egr2WT_H3K27ac_CTRL_rep2


title: Wild-type IL-4 24h BMDM H3K27ac ChIP-seq replicate 1

description: mm_BMDM_ChIPseq_Egr2WT_H3K27ac_IL4_24h_rep1


title: Wild-type unstimulated BMDM P300 ChIP-seq replicate 2


title: Egr2fl/fl unstimulated BMDM P300 ChIP-seq replicate 2


title: WT IL-4 24h BMDM P300 ChIP-seq replicate 2

value: WT


title: Wild-type unstimulated BMDM P300 ChIP-seq replicate 1


title: WT IL-4 24h BMDM P300 ChIP-seq replicate 1


title: WT IL-4 1h BMDM P300 ChIP-seq replicate 1


title: WT IL-4 1h BMDM P300 ChIP-seq replicate 2


title: WT unstimulated BMDM P300 ChIP-seq replicate 2


title: WT unstimulated BMDM P300 ChIP-seq replicate 1


title: WT IL-4 24h BMDM Egr2 ChIP-seq replicate 1


title: Wild-type IL-4 24h BMDM BRD4 ChIP-seq replicate 1

description: mm_BMDM_ChIPseq_Egr2WT_BRD4_IL4_24h_rep1


title: WT IL-4 1h BMDM Egr2 ChIP-seq replicate 1


title: Egr2fl/fl 24-h IL-4 treated BMDM P300 ChIP-seq replicate 2

description: mm_BMDM_ChIPseq_Egr2KO_P300_IL4_24h_rep2


title: Egr2fl/fl unstimulated BMDM P300 ChIP-seq replicate 1


title: Egr2fl/fl 24-h IL-4 treated BMDM P300 ChIP-seq replicate 1

description: mm_BMDM_ChIPseq_Egr2KO_P300_IL4_24h_rep1


title: Egr2fl/fl 24-h IL-4 treated BMDM RNA-seq replicate 1

description:
mm_BMDM_RNAseq_Egr2KO_IL4_24h_rep1
mm_BMDM_Egr2_RNAseq_raw_counts.txt
mm_BMDM_Egr2_RNAseq_CPM_counts.txt

molecule: polyA RNA


title: WT unstimulated BMDM Egr2 ChIP-seq replicate 1


title: Egr2fl/fl unstimulated BMDM RNA-seq replicate 2

description:
mm_BMDM_RNAseq_Egr2KO_ctrl_24h_rep2
mm_BMDM_Egr2_RNAseq_raw_counts.txt
mm_BMDM_Egr2_RNAseq_CPM_counts.txt

value: ctrl


title: Egr2fl/fl unstimulated BMDM RNA-seq replicate 3

description:
mm_BMDM_RNAseq_Egr2KO_ctrl_24h_rep3
mm_BMDM_Egr2_RNAseq_raw_counts.txt
mm_BMDM_Egr2_RNAseq_CPM_counts.txt


title: Egr2fl/fl 24-h IL-4 treated BMDM RNA-seq replicate 2

description:
mm_BMDM_RNAseq_Egr2KO_IL4_24h_rep2
mm_BMDM_Egr2_RNAseq_raw_counts.txt
mm_BMDM_Egr2_RNAseq_CPM_counts.txt


title: Egr2fl/fl 24-h IL-4 treated BMDM RNA-seq replicate 3

description:
mm_BMDM_RNAseq_Egr2KO_IL4_24h_rep3
mm_BMDM_Egr2_RNAseq_raw_counts.txt
mm_BMDM_Egr2_RNAseq_CPM_counts.txt


title: WT IL-4 24h BMDM Egr2 ChIP-seq replicate 2


title: Egr2fl/fl unstimulated BMDM RNA-seq replicate 1

description:
mm_BMDM_RNAseq_Egr2KO_ctrl_24h_rep1
mm_BMDM_Egr2_RNAseq_raw_counts.txt
mm_BMDM_Egr2_RNAseq_CPM_counts.txt


title: Wild-type 24-h IL-4 treated BMDM RNA-seq replicate 2

description:
mm_BMDM_RNAseq_Egr2WT_IL4_24h_rep2
mm_BMDM_Egr2_RNAseq_raw_counts.txt
mm_BMDM_Egr2_RNAseq_CPM_counts.txt


title: Wild-type 24-h IL-4 treated BMDM RNA-seq replicate 3

description:
mm_BMDM_RNAseq_Egr2WT_IL4_24h_rep3
mm_BMDM_Egr2_RNAseq_raw_counts.txt
mm_BMDM_Egr2_RNAseq_CPM_counts.txt


title: Wild-type 24-h IL-4 treated BMDM RNA-seq replicate 1

description:
mm_BMDM_RNAseq_Egr2WT_IL4_24h_rep1
mm_BMDM_Egr2_RNAseq_raw_counts.txt
mm_BMDM_Egr2_RNAseq_CPM_counts.txt


title: Wild-type unstimulated BMDM RNA-seq replicate 1

description:
mm_BMDM_RNAseq_Egr2WT_ctrl_24h_rep1
mm_BMDM_Egr2_RNAseq_raw_counts.txt
mm_BMDM_Egr2_RNAseq_CPM_counts.txt


title: Wild-type unstimulated BMDM RNA-seq replicate 2

description:
mm_BMDM_RNAseq_Egr2WT_ctrl_24h_rep2
mm_BMDM_Egr2_RNAseq_raw_counts.txt
mm_BMDM_Egr2_RNAseq_CPM_counts.txt


title: Wild-type IL-4 24h BMDM BRD4 ChIP-seq replicate 2

description: mm_BMDM_ChIPseq_Egr2WT_BRD4_IL4_24h_rep2


title: WT IL-4 1h BMDM Egr2 ChIP-seq replicate 2


title: WT unstimulated BMDM Egr2 ChIP-seq replicate 2


title: HUVECs, W-1-4_Hi-C

status: Public on Jul 15 2020

city: Beijing

first: Jingxue

last: Xin

address: 55 Zhong Guan Cun East Road

department: Academy of Mathematics and Systems Science

country: China

institute: Chinese Academy of Sciences

description: Han-1 hypoxia 3d

data_processing:
We used TopHat to map sequencing reads to human reference genome hg19.
We used Cufflinks to call FPKM values as gene expression measurement.
ATAC-seq pair-end reads were trimmed for Illumina adaptor sequences and transposase sequences.
We mapped the reads to reference human genome hg19 with Bowtie v1.0.0. Duplicate reads were removed with Samtools.v0.1.19.  Only uniquely aligned reads were used for peak calling with Hotspot using default parameters
HiC-Pro was used to process Hi-C data from raw sequencing reads to normalized contact matrix.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Supplementary_files_format_and_content: Peaks calling by hotspot. The score in the 5th column of the hotspot files are the z-scores that come from the binomial model for scoring hotspots.

source_name: Human Umbilical Vein Endothelial Cells

growth_protocol: HUVECs were cultured on flasks coated with 0.1% gelatin. The cells were grown in complete medium (Medium199 supplemented with 10% FBS, 20 mmol/l HEPES (pH 7.4), 1 ng/ml recombinant human fibroblast growth factor (bFGF), 1 ng/ml endothelial growth factors (EGF), and 100 units/ml penicillin, 0.1 mg/ml streptomycin) (Gibco) at 37C in 5% CO2, and the medium was changed every 2–3 days. About 7 to 10 days, the primary culture cells were confluent in the flask. For subculture, cells were detached and harvested with 0.05% trypsin-EDTA solution, then neutralized with FBS (Gibco). When the cells were cultured to passage-3, they were cryopreserved with cell freezing medium (NCS + 10% DMSO) in liquid nitrogen.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Ambion).
Libraries from the resulting total RNA were prepared using the TruSeq paired-end mRNASeq kit.
We used the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) to prepare the ready-to-use DNA library for ATAC-Seq
Hi-C library was performed as described in Belaghzal H et al, 2017.

treatment_protocol: Cells were placed in a conventional 37° C humidified incubator (Thermo-Forma, Model 3141) with automated gas control of 1% O2, 5% CO2, balanced with N2. The oxygen concentration of the hypoxic incubator was constantly monitored by a real-time O2 sensor with 0.1% sensitivity.

value: HUVEC

tag: individual

tag: stress

value: hypoxia


title: HUVECs, W-3-4_Hi-C

description: Han-3 hypoxia 3d


title: HUVECs, A-3-1_Hi-C

description: Tibetan-3 normoxia 0h

value: normoxia


title: HUVECs, A-1-4_Hi-C

description: Tibetan-1 hypoxia 3d


title: HUVECs, W-3-1_Hi-C

description: Han-3 normoxia 0h


title: HUVECs, W-1-1_Hi-C

description: Han-1 normoxia 0h


title: HUVECs, A-3-4_Hi-C

description: Tibetan-3 hypoxia 3d


title: HUVECs, A-1-1_Hi-C

description: Tibetan-1 normoxia 0h


title: Arabidopsis root cells - tnw2

status: Public on Jul 02 2020

city: Durham

first: Philip

middle: N.

last: Benfey

state: North Carolina

address: 130 Science Drive

department: Biology

institute: Duke University

description:
Arabidopsis root cells - Benfey Lab
Single-cell RNA-seq

data_processing:
Processed by COPILOT (https://github.com/Hsu-Che-Wei/COPILOT).
Genome_build: TAIR10
Supplementary_files_format_and_content: *_mtx.tar: Include gene-by-cell count matrices.
Supplementary_files_format_and_content: *_COPILOT.rds: Seurat objects.

organism: Arabidopsis thaliana

source_name: Arabidopsis root cells

growth_protocol: Seeds from wildtype Arabidopsis thaliana ecotype Columbia (Col-0), shortroot-2 (Col-0 background), and scarecrow-4 (Landsberg background backcrossed to Col-0 at least 5 times) were surface sterilized with a 50% (v/v) bleach, 0.05% (v/v) Tween-20 solution for 10 minutes and subsequently stratified for 48 hours at 4°C. Seeds were sown at a density of ~150-300 seeds/row on 1X Linsmaier and Skoog (LSP03-1LT, Caisson Labs; pH 5.7), 1% sucrose media covered by 100/ 47 µm mesh. Plates were placed vertically in a Percival chamber programmed to 16h light, 8h dark conditions at 22°C.

extract_protocol: Chromium Single Cell 3ʹ GEM Kit v3.

tag: ecotype/background

value: Wild type

value: Root

tag: use for atlas

value: Yes


title: Arabidopsis root cells - tnw1

tag: tissue


title: Arabidopsis root cells - sc_37


title: Wild-type unstimulated BMDM RNA-seq replicate 3

description:
mm_BMDM_RNAseq_Egr2WT_ctrl_24h_rep3
mm_BMDM_Egr2_RNAseq_raw_counts.txt
mm_BMDM_Egr2_RNAseq_CPM_counts.txt

tag: strain

value: Bone marrow

value: Bone marrow derived macrophages (BMDM)


title: Hi-C_shTopors-2

status: Public on Jun 24 2020

city: Shanghai

first: Luzhang

last: Ji

address: 1239 Siping Rd.

institute: Tongji University

data_processing:
Raw HiC data were processed through the HiC-Pro pipeline (Servant et al., 2015) (including read mapping/binning/ICE correction).
hic files were generated using HiC-Pro script: hicpro2juicebox.sh
Genome_build: mm9
Supplementary_files_format_and_content: hic files contain the HiC contact matrix at different resolution.

source_name: shTopors

growth_protocol: AML12 cells were cultured in  DMEM/F12 supplemented with 10% fetal bovine serum,  ITS Liquid Media Supplement, and 0.1μM dexamethasone at 37 °C and 5% CO2.

extract_protocol:
We generated in situ Hi-C libraries following the protocol as described (Rao et al., 2014) after isolating G0G1 cells (Bonev et al., 2017).
Illumina sequencing library were prepared according to the standard Illumina protocol.

treatment_protocol: The shRNA lentiviruses were prepared as previously described (Fu et al., 2015). Then AML12 cells were infected with 200 μl of virus concentrate in a well of six-well-plates. Medium was changed 24 hours after transfection, and then collect cells 5 days after transfection.

tag: cell line

value: AML12 cells

tag: genotype/variation

value: shTopors


title: Hi-C_shTopors-1


title: Hi-C_shCtrl-2

source_name: shCtrl

value: shCtrl


title: Arabidopsis root cells - sc_40

tag: genotype


title: HiC_GES1_EBVi

status: Public on May 23 2020

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
BCL2FASTQ version1.8.4 software was used for basecalling.
Hi-C reads were processed using HiC-Pro or Juicer
Genome_build: hg19+NC007605.1
Supplementary_files_format_and_content: .hic

growth_protocol: These cells were cultured in RPMI 1640 (Wako, Tokyo, Japan) with 10% fetal bovine serum (FBS) (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO) at 37 °C in 5% CO2 incubator.

extract_protocol: Hi-C experiment were conducted in biological replicates using NlaIII, according to the protocol published by Suhas S.P. Rao et al. Cell 2014 (PMID: 25497547).  DNA libraries were prepared during Hi-C protocol according to experimental procedures described in Suhas S.P. Rao et al. Cell 2014 (PMID: 25497547).

value: GES

tag: cell type

value: Normal gastric epithelial cell line

tag: treatment

value: EBV infected cell


title: HiC_GES1_WT

value: uninfected control cell


title: HiC_SNU1967

source_name: Gastric cancer cell line

value: Gastric cancer cell line SNU1967


title: HiC_SNU1750

value: Gastric cancer cell line SNU1750


title: HiC_SNU484

value: Gastric cancer cell line SNU484


title: HiC_21080055T

source_name: primary EBV(+) GC tissue

value: primary gastric cancer tissue


title: Hi-C_shCtrl-1


title: HiC_SNU16

value: Gastric cancer cell line SNU16


title: HiC_OCUM1

value: Gastric cancer cell line OCUM1


title: HiC_NCC59

value: Gastric cancer cell line NCC59


title: HiC_SNU719

value: Gastric cancer cell line SNU719


title: HiC_NUGC3

value: Gastric cancer cell line NUGC3


title: HiC_NCC19

value: Gastric cancer cell line NCC19


title: HiC_MKN7

value: Gastric cancer cell line MKN7


title: HiC_MKN1

value: Gastric cancer cell line MKN1


title: HiC_NCC24

value: Gastric cancer cell line NCC24


title: HiC_HFE145

source_name: Normal gastric epithelial cell

value: Normal gastric epithelial cell line HFE145


title: HiC_IM95

value: Gastric cancer cell line IM95


title: HiC_GES-1

value: Normal gastric epithelial cell line GES-1


title: HiC_YCC10

value: Gastric cancer cell line YCC10


title: RNA-seq_HC8_mouse_proB_REP4

status: Public on Mar 23 2020

city: Boston

first: Scott

last: Armstrong

state: MA

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

data_processing:
STAR (Version 2.5.1)
--genomeDir <path to reference data (mm10)>
--readFilesIn ${ID}.fastq
--runThreadN 20
--outFilterMultimapScoreRange 1
--outFilterMultimapNmax 20
--outFilterMismatchNmax 10
--alignIntronMax 500000
--alignMatesGapMax 1000000
--sjdbScore 2
--alignSJDBoverhangMin 1
--genomeLoad NoSharedMemory
--limitBAMsortRAM 0
--readFilesCommand <bzcat|cat|zcat>
--outFilterMatchNminOverLread 0.33
--outFilterScoreMinOverLread 0.33
--sjdbOverhang 100
--outSAMstrandField intronMotif
--outSAMattributes NH HI NM MD AS XS
--outSAMunmapped Within
--outSAMtype BAM SortedByCoordinate
--outSAMheaderHD @HD VN:1.4
--outSAMattrRGline <formatted RG line provided by wrapper>
TRUST (Version 3.0.1)
trust -f [PATH]$FILENAME.bam -g mm10 -B -c -o [PATH]BCR_H/
trust -f [PATH]$FILENAME.bam -g mm10 -B -L -c -o [PATH]BCR_L/
Genome_build: mm10
Supplementary_files_format_and_content: TXT of TRUST output of assembled CDR3s for heavy and light chain locus

source_name: mouse proB cells

growth_protocol: proB cells were sorted from bone marrow of 8 week old mice

extract_protocol:
For RNA isolation, cells were lysed in 350 µl of RLT buffer and RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturers instructions.
Poly-A tail selection and library preparation were performed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA).
Sequencing was done using the Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) with 75bp, single-end reads.

treatment_protocol: no treatment

value: primary proB cells

tag: timepoint

value: 8 weeks

value: no treatment

tag: genetic alteration

value: control

tag: seqbatch


title: Mouse 1432 Igheavy chain Variable family Q52 amplicon

description:
Q1432_Q52
kept.cdr3s.csv

data_processing:
MiXCR Version: 2.1.11; built=Fri Jun 15 06:30:50 CST 2018; rev=45d8571; lib=repseqio.v1.5
Command line arguments: align -s mmu -p rna-seq -OallowPartialAlignments=true -OvParameters.parameters.maxHits=1 -OdParameters.maxHits=1 -OjParameters.parameters.maxHits=1 -OvParameters.geneFeatureToAlign=VGeneWithP -OdParameters.geneFeatureToAlign=DRegionWithP -OjParameters.geneFeatureToAlign=JRegionWithP --report filname.log -f filename.r1.fq filename.r2.fq alignments.vdjca
Command line arguments: assemblePartial --report filename.log -f alignments.vdjca alignments_rescued_1.vdjca
Command line arguments: assemblePartial --report filename.log -f alignments_rescued_1.vdjca alignments_rescued_2.vdjca
Command line arguments: assemble --report filename.log -f alignments_rescued_2.vdjca clones.clns
Genome_build: None
Supplementary_files_format_and_content: [kept.cdr3s.csv]  CSV of MiXCR output for all unique detected CDR3 clones, heavy chain locus, alignment scores
Supplementary_files_format_and_content: [clones.txt]  TXT of detected clones per sample
Supplementary_files_format_and_content: https://mixcr.readthedocs.io/en/master/export.html#available-fields

extract_protocol:
Genomic DNA was isolated using the Invitrogen PureLink Genomic DNA Kit and PCR was conducted.  A 500bp fragment corresponding to Variable gene to JH4 Product was gel extracted with Qiagen gel extraction kit.
Poly-A tail selection and library preparation were performed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA). platform (Illumina, San Diego, CA) with 150bp, paired-end reads.
Sequencing was done using the Illumina MiSeq, utilizing V2 chemistry.

value: WT

tag: pcr primer


title: Mouse 1485 Igheavy chain Variable family Q52 amplicon

description:
Q1485_Q52
kept.cdr3s.csv


title: Mouse 1536 Igheavy chain Variable family Q52 amplicon

description:
Q1536_Q52
kept.cdr3s.csv


title: Mouse 1464 Igheavy chain Variable family Q52 amplicon

description:
Q1464_Q52
kept.cdr3s.csv

value: KO


title: Mouse 1500 Igheavy chain Variable family Q52 amplicon

description:
Q1500_Q52
kept.cdr3s.csv


title: RNA-seq_HC6_mouse_proB_REP3


title: RNA-seq_HC7_mouse_proB-Setd2-ko_REP4

value: Setd2 knockout


title: RNA-seq_HC2_mouse_proB-Setd2-ko_REP1


title: RNA-seq_HC4_mouse_proB_REP2


title: Mouse 1487 Igheavy chain Variable family Q52 amplicon

description:
Q1487_Q52
kept.cdr3s.csv


title: RNA-seq_HC3_mouse_proB-Setd2-ko_REP2


title: RNA-seq_HC5_mouse_proB-Setd2-ko_REP3


title: Mouse 1484 Igheavy chain Variable family Q52 amplicon

description:
Q1484_Q52
kept.cdr3s.csv


title: Mouse 1487 Igheavy chain Variable family 7183 amplicon

description:
1487_V7183
kept.cdr3s.csv


title: RNA-seq_HC1_mouse_proB_REP1


title: Mouse 1485 Igheavy chain Variable family 7183 amplicon

description:
1485_V7183
kept.cdr3s.csv


title: Mouse 1484 Igheavy chain Variable family 7183 amplicon

description:
1484_V7183
kept.cdr3s.csv


title: Mouse 1536 Igheavy chain Variable family 7183 amplicon

description:
1536_V7183
kept.cdr3s.csv


title: Mouse 1421 Igheavy chain Variable family Q52 amplicon

description:
Q1421_Q52
kept.cdr3s.csv


title: Mouse 1418 Igheavy chain Variable family Q52 amplicon

description:
Q1418_Q52
kept.cdr3s.csv


title: Mouse 1500 Igheavy chain Variable family 7183 amplicon

description:
1500_V7183
kept.cdr3s.csv


title: Mouse 1464 Igheavy chain Variable family 7183 amplicon

description:
1464_V7183
kept.cdr3s.csv


title: Mouse 1418 Igheavy chain Variable family 7183 amplicon

description:
1418_V7183
kept.cdr3s.csv


title: Mouse 1423 Igheavy chain Variable family 7183 amplicon

description:
1423_V7183
kept.cdr3s.csv


title: Mouse 1423 Igheavy chain Variable family 558 amplicon replicate

description:
1423_V558
kept.cdr3s.csv


title: Mouse 1536 Igheavy chain Variable family 558 amplicon replicate

description:
1536_V558
kept.cdr3s.csv


title: Mouse 1421 Igheavy chain Variable family 558 amplicon replicate

description:
1421_V558
kept.cdr3s.csv


title: Mouse 1421 Igheavy chain Variable family 7183 amplicon

description:
1421_V7183
kept.cdr3s.csv


title: Mouse 1432 Igheavy chain Variable family 7183 amplicon

description:
1432_V7183
kept.cdr3s.csv


title: Mouse 1418 Igheavy chain Variable family 558 amplicon replicate

description:
1418_V558
kept.cdr3s.csv


title: Mouse 1485 Igheavy chain Variable family 558 amplicon

description:
1485_V558
kept.cdr3s.csv


title: Mouse 1500 Igheavy chain Variable family 558 amplicon

description:
1500_V558
kept.cdr3s.csv


title: Mouse 1432 Igheavy chain Variable family 558 amplicon

description:
1432 V558
kept.cdr3s.csv


title: Mouse 1534 Igheavy chain Variable family 558 amplicon

description:
1534_V558
kept.cdr3s.csv
SRR9107707 corresponds to processed data file 1534_1534_296841w_NE4.clones.txt.
SRR9107708 corresponds to processed data file 1534_1534_298140w_BB3.clones.txt.


title: Mouse 1464 Igheavy chain Variable family 558 amplicon

description:
1464_V558
kept.cdr3s.csv


title: Mouse 1423 Igheavy chain Variable family 558 amplicon

description:
S1423_V558
kept.cdr3s.csv


title: Mouse 1421 Igheavy chain Variable family 558 amplicon

description:
S1421_V558
kept.cdr3s.csv


title: mouse_GMP_RNA_wt_REP3_190109_ATGTCA_S15

status: Public on Feb 11 2020

description:
Table_S1_RNAseq.xlsx
consolidated_counts_sorted_rmdup-190109.txt

data_processing:
Raw Illumina sequencing output was converted to FASTQ format using bcl2fastq (v2.17). Reads (37- or 75-mers) were trimmed for quality using trimmomatic (v0.36; minimum trimmed length 34bp).
Reads were aligned to the human or mouse genome (GRCh37/hg19 or mm10) and associated human RefSeq transcript reference (180625 samples only) or Trinity CTAT gene Ensembl GTF reference (GRCh37_v19_CTAT_lib_Feb092018 or Mouse_M16_CTAT_lib_Feb092018, respectively, with External RNA Controls Consortium [ERCC] spike-in sequence references appended, as appropriate) using STAR (v2.6.1b).
Aligned reads were sorted and duplicates marked/removed with picard pipeline tools (v2.9.4). Final “deduped” BAM files were indexed using SAMtools (v1.2).
Raw per-gene counts calculated with HTSeq (htseq-count, v0.6.1pl).
Differential RNA-seq expression was calculated using the BioConductor DESeq2 package (v1.22.1), using raw unnormalized per-gene counts from deduplicated BAMs.
Genome_build: GRCh37/mm10
Supplementary_files_format_and_content: XLSX of log2 expression fold changes (treatment vs control for individual cell lines/types)
consolidated_counts_sorted_rmdup-171124.txt (TXT of raw unnormalized per-gene counts (Ensembl GRCh37 reference)_
consolidated_counts_sorted_rmdup-171220.txt (TXT of raw unnormalized per-gene counts (Ensembl GRCh37 reference)_
consolidated_counts_sorted_rmdup-180625.txt (TXT of raw unnormalized per-tx counts (RefSeq GRCh37 reference)_
consolidated_counts_sorted_rmdup-181003.txt (TXT of raw unnormalized per-gene counts (Ensembl GRCh37 reference)_
consolidated_counts_sorted_rmdup-181112.txt (TXT of raw unnormalized per-gene counts (Ensembl GRCh37 reference)_
consolidated_counts_sorted_rmdup-190109.txt (TXT of raw unnormalized per-gene counts (Ensembl GRCh37 reference)_

source_name: mouse GMP cells

growth_protocol: Mouse cell lines were grown in myeloid medium (IMDM, supplemented with 15% FBS, mIl6 mSCF and mIl3), Human cell lines were cultured in RPMI with 10% FBS.

treatment_protocol: Treatment regimens indicated for each sample.

value: mouse GMP cells


title: mouse_GMP_RNA_wt_REP2_190109_AGTTCC_S14


title: SIIIL12_RNA_MSCVMeis1_VTP_30nM_d3_REP2_190109_GGCTAC_S11

source_name: mouse MIG-Cre NPM1c/DNMT3a cell line

value: MIG-Cre NPM1c/DNMT3a

value: day 3

tag: manipulation

value: MSCV Meis1

value: NPM1c/DNMT3a double knockin


title: mouse_LSKder_L-GMP_RNA_MIG-CreNPM1cDNMT3a_REP2_190109_GTCCGC_S17

source_name: mouse LSK-derived GMP-like cells

value: mouse LSK-derived GMP-like cells


title: mouse_LSKder_L-GMP_RNA_MIG-CreNPM1cDNMT3a_REP3_190109_CGTACG_S21

source_name: mouse GMP-derived GMP-like cells

value: mouse GMP-derived GMP-like cells


title: mouse_LSKder_L-GMP_RNA_MIG-CreNPM1cDNMT3a_REP2_190109_GTTTCG_S20


title: mouse_LSKder_L-GMP_RNA_MIG-CreNPM1cDNMT3a_REP1_190109_GTGGCC_S19


title: mouse_LSKder_L-GMP_RNA_MIG-CreNPM1cDNMT3a_REP3_190109_GTGAAA_S18


title: SIIIL12_RNA_MSCVMeis1_DMSO_d3_REP3_190109_GATCAG_S9


title: SIIIL12_RNA_MSCVMeis1_DMSO_d3_REP2_190109_ACTTGA_S8


title: SIIIL12_RNA_MSCV_VTP_30nM_d3_REP3_190109_GCCAAT_S6

value: MSCV-PURO


title: SIIIL12_RNA_MSCV_DMSO_d3_REP3_190109_TTAGGC_S3


title: SIIIL12_RNA_MSCV_DMSO_d3_REP2_190109_CGATGT_S2


title: SIIIL12_RNA_MSCV_VTP_30nM_d3_REP1_190109_TGACCA_S4


title: SIIIL12_RNA_MSCV_VTP_30nM_d3_REP2_190109_ACAGTG_S5


title: SIIIL12_RNA_MSCVMeis1_DMSO_d3_REP1_190109_CAGATC_S7


title: Mouse 1418 Igheavy chain Variable family 558 amplicon

description:
S1418_V558
kept.cdr3s.csv


title: SIIIL12_RNA_MSCV_DMSO_d3_REP1_190109_ATCACG_S1


title: mouse_GMP_RNA_wt_REP1_190109_AGTCAA_S13


title: mouse_LSKder_L-GMP_RNA_MIG-CreNPM1cDNMT3a_REP1_190109_CCGTCC_S16


title: mouse_GMP_RNA_wt_VTP_d5_REP2_181003_GTTTCG_S19

description:
Table_S1_RNAseq.xlsx
consolidated_counts_sorted_rmdup-181003.txt

value: day 5

value: 1% VTP50469 chow


title: Mouse 1536 Igheavy chain Variable family 558 amplicon

description:
1536_V558
kept.cdr3s.csv

value: primary proB cells


title: mouse_GMP_RNA_wt_VTP_d5_REP1_181003_GTGGCC_S18


title: SIIIL12_RNA_MSCVMeis1_VTP_30nM_d3_REP3_190109_CTTGTA_S12


title: mouse_GMP_RNA_wt_VTP_d5_REP3_181003_CGTACG_S20


title: mouse_GMP_RNA_wt_untreated_d5_REP3_181003_GTGAAA_S17


title: SIIIL12_RNA_MSCVMeis1_VTP_30nM_d3_REP1_190109_TAGCTT_S10


title: mouse_GMP_RNA_wt_untreated_d5_REP2_181003_GTCCGC_S16


title: mouse_LSK_RNA_wt_VTP_d5_REP3_181003_AGTTCC_S14

source_name: mouse LSK cells

value: mouse LSK cells


title: mouse_GMP_RNA_wt_untreated_d5_REP1_181003_CCGTCC_S15


title: mouse_LSK_RNA_wt_VTP_d5_REP2_181003_AGTCAA_S13


title: mouse_LSK_RNA_wt_untreated_d5_REP2_181003_TAGCTT_S10


title: mouse_ltGMPder_GMP_RNA_MxCreNPM1cDNMT3a_control_d5_REP3_181003_CAGATC_S7

source_name: mouse long-term GMP-derived GMP cells

value: mouse long-term GMP-derived GMP cells

value: MxCre NPM1c/DNMT3a


title: mouse_ltGMPder_GMP_RNA_MxCreNPM1cDNMT3a_control_d5_REP4_181003_ACTTGA_S8


title: mouse_LSK_RNA_wt_untreated_d5_REP1_181003_GATCAG_S9


title: mouse_ltGMPder_GMP_RNA_MxCreNPM1cDNMT3a_VTP_d5_REP3_181003_ACAGTG_S5


title: mouse_ltGMPder_GMP_RNA_MxCreNPM1cDNMT3a_VTP_d5_REP2_181003_TGACCA_S4


title: mouse_LSK_RNA_wt_VTP_d5_REP1_181003_CTTGTA_S12


title: mouse_ltGMPder_GMP_RNA_MxCreNPM1cDNMT3a_VTP_d5_REP1_181003_TTAGGC_S3


title: mouse_ltGMPder_GMP_RNA_MxCreNPM1cDNMT3a_control_d5_REP2_181003_CGATGT_S2


title: mouse_ltGMPder_GMP_RNA_MxCreNPM1c_VTP_d5_REP3_180625_CGTACG_S19

description:
Table_S1_RNAseq.xlsx
consolidated_counts_sorted_rmdup-180625.txt

value: Mx1-Cre NPM1c

value: NPM1c knockin


title: mouse_ltGMPder_GMP_RNA_MxCreNPM1c_VTP_d5_REP2_180625_GTTTCG_S18


title: mouse_ltGMPder_GMP_RNA_MxCreNPM1c_VTP_d5_REP1_180625_GTGGCC_S17


title: mouse_ltGMPder_GMP_RNA_MxCreNPM1cDNMT3a_control_d5_REP1_181003_ATCACG_S1


title: mouse_ltGMPder_GMP_RNA_MxCreNPM1c_control_d5_REP3_180625_GTGAAA_S16


title: mouse_GMP_RNA_MIG-CreDNMT3a_d3_REP2_180625_AGTTCC_S13

value: 3 days post induction of NPM1c

value: MIG-Cre DNMT3a

value: DNMT3a knockin


title: mouse_ltGMPder_GMP_RNA_MxCreNPM1c_control_d5_REP1_180625_CCGTCC_S14


title: mouse_ltGMPder_GMP_RNA_MxCreNPM1c_control_d5_REP2_180625_GTCCGC_S15


title: mouse_GMP_RNA_MIG-CreWT_d3_REP4_180625_GGCTAC_S11

value: mouse GMP cells

value: MIG-Cre


title: mouse_GMP_RNA_MIG-CreNPM1cDNMT3a_d3_REP2_180625_ACTTGA_S9

value: MIG-Cre NPM1c/DNMT3a

value: NPM1c/DNMT3a double knockin


title: mouse_ltGMPder_GMP_RNA_MxCreNPM1cDNMT3a_VTP_d5_REP4_181003_GCCAAT_S6


title: mouse_GMP_RNA_MIG-CreNPM1cDNMT3a_d3_REP1_180625_CAGATC_S8


title: mouse_GMP_RNA_MIG-CreNPM1c_d3_REP1_180625_TGACCA_S5

value: MIG-Cre NPM1c


title: mouse_GMP_RNA_MIG-CreNPM1c_d3_REP3_180625_GCCAAT_S7


title: mouse_GMP_RNA_MIG-CreNPM1c_d3_REP4_180625_CTTGTA_S12


title: mouse_GMP_RNA_MIG-CreNPM1cDNMT3a_d3_REP3_180625_TAGCTT_S10


title: mouse_GMP_RNA_MIG-CreNPM1c_d3_REP2_180625_ACAGTG_S6


title: mouse_GMP_RNA_MIG-CreWT_d3_REP1_180625_AGTCAA_S1


title: mouse_GMPder-GMP_RNA_MIG-CreNPM1cDNMT3a_9mTx_REP1_171220_ACTTGA_S8

description:
Table_S1_RNAseq.xlsx
consolidated_counts_sorted_rmdup-171220.txt

source_name: mouse GMP-derived GMP cells

value: mouse GMP-derived GMP cells

value: 9 months post transplant


title: mouse_LSK_RNA_wt_untreated_d5_REP3_181003_GGCTAC_S11

value: day 5


title: mouse_GMP_RNA_MIG-CreDNMT3a_d3_REP1_180625_TTAGGC_S4


title: mouse_LSKder-LSK_RNA_MIG-CreNPM1cDNMT3a_9mTx_REP1_171220_GATCAG_S9

source_name: mouse LSK-derived LSK cells

value: mouse LSK-derived LSK cells


title: mouse_GMP_RNA_wt_REP3_171220_GCCAAT_S6


title: mouse_LSKder-GMP_RNA_MIG-CreNPM1cDNMT3a_9mTx_REP1_171220_CAGATC_S7

source_name: mouse LSK-derived GMP cells

value: mouse LSK-derived GMP cells


title: mouse_GMP_RNA_MIG-CreWT_d3_REP2_180625_ATCACG_S2


title: mouse_GMP_RNA_wt_REP2_171220_ACAGTG_S5


title: mouse_LSK_RNA_wt_REP3_171220_TTAGGC_S3

value: mouse LSK cells


title: mouse_LSK_RNA_wt_REP2_171220_CGATGT_S2


title: mouse_LSK_RNA_wt_REP1_171220_ATCACG_S1


title: mouse_GMP_RNA_MxCreNPM1c_REP3_171124_GTTTCG_S20

description:
Table_S1_RNAseq.xlsx
consolidated_counts_sorted_rmdup-171124.txt

value: 4 weeks

value: pIpC induction


title: mouse_GMP_RNA_wt_REP3_171124_GTCCGC_S17


title: mouse_GMP_RNA_MxCreNPM1c_REP1_171124_GTGAAA_S18

value: Mx1-Cre NPM1c

value: NPM1c knockin


title: mouse_GMP_RNA_MIG-CreWT_d3_REP3_180625_CGATGT_S3

value: 3 days post induction of NPM1c


title: mouse_GMPder-LSK_RNA_MIG-CreNPM1cDNMT3a_9mTx_REP1_171220_TAGCTT_S10

source_name: mouse GMP-derived LSK cells

value: mouse GMP-derived LSK cells


title: mouse_LSK_RNA_MxCreNPM1c_REP3_171124_AGTTCC_S14


title: mouse_LSK_RNA_MxCreNPM1c_REP2_171124_AGTCAA_S13


title: mouse_GMP_RNA_wt_REP2_171124_CCGTCC_S16

value: mouse GMP cells


title: mouse_LSK_RNA_MxCreNPM1c_REP1_171124_CTTGTA_S12


title: mouse_LSK_RNA_wt_REP2_171124_TAGCTT_S10


title: mouse_LSK_RNA_wt_REP1_171124_GATCAG_S9


title: mouse_GMP_RNA_wt_REP1_171220_TGACCA_S4


title: mouse_LSK_RNA_wt_REP3_171124_GGCTAC_S11


title: IMSM2_RNA_DMSO_d7_REP2_181121_ACTTGA

description:
processed data file:
Table_S1_RNAseq.xlsx
consolidated_counts_sorted_rmdup-181121.txt

data_processing:
Raw Illumina sequencing output was converted to FASTQ format using bcl2fastq (v2.17). Reads (37- or 75-mers) were trimmed for quality using trimmomatic (v0.36; minimum trimmed length 34bp).
Reads were aligned to the human or genome (GRCh37/hg19) and Trinity CTAT gene Ensembl GTF reference (GRCh37_v19_CTAT_lib_Feb092018, with External RNA Controls Consortium [ERCC] spike-in sequence references appended) using STAR (v2.6.1b).
Aligned reads were sorted and duplicates marked/removed with picard pipeline tools (v2.9.4). Final “deduped” BAM files were indexed using SAMtools (v1.2).
Raw per-gene counts calculated with HTSeq (htseq-count, v0.6.1pl).
Differential RNA-seq expression was calculated using the BioConductor DESeq2 package (v1.22.1), using raw unnormalized per-gene counts from deduplicated BAMs.
Genome_build: Ensembl GRCh37 reference/mm10
Supplementary_files_format_and_content: TXT of raw unnormalized per-gene counts; XLSX of log2 expression fold changes (treatment vs control for individual cell lines/types)

source_name: IMS-M2 cultured cells

growth_protocol: Human cell lines were cultured in RPMI with 10% FBS.

value: day 7


title: IMSM2_RNA_DMSO_d7_REP3_181121_GATCAG


title: IMSM2_RNA_VTP_330nM_d7_REP2_181121_GGCTAC


title: OCIAML3_RNA_VTP_330nM_d7_REP1_181121_TGACCA

source_name: OCI-AML-3 cultured cells


title: IMSM2_RNA_VTP_330nM_d7_REP1_181121_TAGCTT


title: OCIAML3_RNA_VTP_330nM_d7_REP2_181121_ACAGTG


title: IMSM2_RNA_DMSO_d7_REP1_181121_CAGATC


title: IMSM2_RNA_VTP_330nM_d7_REP3_181121_CTTGTA


title: OCIAML3_RNA_DMSO_d7_REP1_181121_ATCACG


title: IMSM2_RNA_VTP_330nM_d5_REP1_181112_GAGTGG_S22

description:
Table_S1_RNAseq.xlsx
consolidated_counts_sorted_rmdup-181112.txt


title: OCIAML3_RNA_DMSO_d7_REP2_181121_CGATGT


title: IMSM2_RNA_VTP_330nM_d5_REP3_181112_ATTCCT_S24


title: OCIAML3_RNA_DMSO_d7_REP3_181121_TTAGGC


title: IMSM2_RNA_DMSO_d5_REP3_181112_CGTACG_S21


title: IMSM2_RNA_DMSO_d5_REP1_181112_GTGGCC_S19


title: mouse_GMP_RNA_MxCreNPM1c_REP2_171124_GTGGCC_S19


title: IMSM2_RNA_VTP_330nM_d5_REP2_181112_ACTGAT_S23


title: OCIAML3_RNA_VTP_330nM_d5_REP3_181112_GTGAAA_S18


title: IMSM2_RNA_DMSO_d5_REP2_181112_GTTTCG_S20


title: OCIAML3_RNA_DMSO_d5_REP3_181112_ATGTCA_S15


title: OCIAML3_RNA_VTP_330nM_d5_REP1_181112_CCGTCC_S16


title: OCIAML3_RNA_DMSO_d5_REP1_181112_AGTCAA_S13


title: OCIAML3_RNA_DMSO_d5_REP2_181112_AGTTCC_S14


title: IMSM2_RNA_VTP_330nM_d3_REP3_181112_CTTGTA_S12

value: day 3


title: mouse_GMP_RNA_wt_REP1_171124_ATGTCA_S15


title: OCIAML3_RNA_VTP_330nM_d5_REP2_181112_GTCCGC_S17


title: IMSM2_RNA_VTP_330nM_d3_REP2_181112_GGCTAC_S11


title: IMSM2_RNA_VTP_330nM_d3_REP1_181112_TAGCTT_S10


title: IMSM2_RNA_DMSO_d3_REP3_181112_GATCAG_S9


title: IMSM2_RNA_DMSO_d3_REP2_181112_ACTTGA_S8


title: IMSM2_RNA_DMSO_d3_REP1_181112_CAGATC_S7


title: OCIAML3_RNA_VTP_330nM_d3_REP2_181112_ACAGTG_S5


title: OCIAML3_RNA_VTP_330nM_d3_REP1_181112_TGACCA_S4


title: OCIAML3_RNA_DMSO_d3_REP3_181112_TTAGGC_S3


title: OCIAML3_RNA_VTP_330nM_d3_REP3_181112_GCCAAT_S6


title: OCIAML3_RNA_DMSO_d3_REP2_181112_CGATGT_S2


title: OCIAML3_RNA_DMSO_d3_REP1_181112_ATCACG_S1


title: OCIAML3_RNA_VTP_330nM_d7_REP3_181121_GCCAAT


title: IMSM2_ChIP_MLL_DMSO_d4_REP1_180919_TCCAGTCG

description:
IMSM2_OCIAML3_ChIPseq_CEAS_TSS_1000u_3000d_res200_signal.xlsx
Table_S2_ChIPseq.xlsx

data_processing:
Raw Illumina sequencing output was converted to FASTQ format using bcl2fastq (v2.17). Reads (37- or 75-mers) were trimmed for quality using trimmomatic (v0.36; minimum trimmed length 34bp).
Reads were aligned to the human genome (GRCh37/hg19) using STAR (v2.6.1b), sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Aligned reads were sorted and duplicates marked/removed with picard pipeline tools (v2.9.4). Final “deduped” BAM files were indexed using SAMtools (v1.2).
Total ChIP-seq signal was assessed around transcription start site (TSS) regions using the sitepro tool from the CEAS (Cis-regulatory Element Annotation System) package (using 4kb windows off-centered around TSS regions [1kb upstream, 3kb into gene bodies] with 200bp tiling and input-subtracted signal summed across each TSS window), based on signal from WIG files generated using IGVtools (v2.3.98).
ChIP-seq data visualizations were produced using IGVtools (TDF signal pileups) and ngs.plot (pileup heatmaps).
Genome_build: GRCh37
Supplementary_files_format_and_content: Table_S2_ChIPseq.xlsx [TSS region differential occupancy for all genes]
IMSM2_OCIAML3_ChIPseq_CEAS_TSS_1000u_3000d_res200_signal.xlsx [TSS region occupancy signal for all samples]

growth_protocol: Human cell lines were cultured in RPMI with 10% FBS and 330nM VTP-50469 or DMSO control for 4 days.

extract_protocol:
DMSO or VTP-50469 treated cells were crosslinked with 1% methanol-free formaldehyde (ThermoFisher) for 7-10 min at room temperature, followed by quenching with 100 mM Tris pH8.0 and 25 mM Glycine, and the cells were lysed in SDS buffer. Cytoplasm was lysed using 50 mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM EDTA, 1% SDS for 10 min and nuclei were precipitated by centrifugation at 10,000´g. Nuclei were resuspended in 66 mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM EDTA, 1.7% Triton X-100, 0.5% SDS and sheared using E100S (Covaris) to chromatin fragments of 200-400 base-pair DNA size.
1-10 ng of DNA was used in preparation of Illumina-compatible libraries using ThruPlex DNA kit (Rubicon Genomics)
Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) was used to obtain 1-5´107 unique sequencing paired-end tags

value: 4 days

value: DMSO

tag: chip target

value: MLL

tag: chip antibody

value: anti-MLL1n (A300-086A, Bethyl)


title: OCIAML3_ChIP_Input_DMSO_d4_REP1_TAGTCTTG


title: IMSM2_ChIP_MENIN_VTP50469_330nM_d4_REP1_180919_TCTCACGG

value: Menin

value: anti-Menin (A300-105A, Bethyl)


title: IMSM2_ChIP_MLL_VTP50469_330nM_d4_REP1_180919_TGTATGCG


title: OCIAML3_ChIP_MENIN_DMSO_d4_REP1_181004_TGCGATCT


title: OCIAML3_ChIP_Input_VTP50469_330nM_d4_REP1_TTCCATTG


title: IMSM2_ChIP_Input_VTP50469_330nM_d4_REP1_180919_TGGCTCAG


title: IMSM2_ChIP_MENIN_DMSO_d4_REP1_180919_GGCACAAC


title: OCIAML3_ChIP_MLL_VTP50469_330nM_d4_REP1_181004_TGTGGTTG


title: IMSM2_ChIP_Input_DMSO_d4_REP1_180919_TCATTGAG


title: NT_Rep3_S6/G2/M

status: Public on Dec 29 2019

city: Paris

first: Chunlong

last: Chen

address: 26 rue d’Ulm

country: France

institute: Institut Curie

description: Enrichement of BrdU labelled DNA (Replicate 3)

data_processing:
Library strategy: Repli-seq
The sequencing data were demultiplexed using the distribution of CASAVA software (CASAVA-1.8.2 bcl2fastq2 v2.18.12)
Illumina adapters were removed using Cutadapt-1.15, keeping only reads with a minimal length of 10 nucleotides.
The reads were mapped on the human genome (Hg19), the chicken genome (galGal4, BrdU label DNA as positive control) and the salmon genome (GCF_000233375.1_ICSASG_v2, unlabelled DNA as negative control) using bwa-0.6.2-r126.
The PCR duplicates were removed by Picard tools (http://broadinstitute.github.io/picard).
The sequence reads located within the regions likely resulted from the sequencing hotspots (defined as the 0,5% windows with the highest amount of reads within 200bp windows) were also removed.
The read density was them computed for each 50 kb nonoverlapping windows (w) for each sample Si corresponding to different S phase fractions (i = 1–6).
The background levels were them estimated and the density profiles were normalized as described in previous study (Chen Genome Res 2010).
A Replication Index (RI), measuring the difference between the Aph and NT signals summed over the six periods, was defined as the Z-score computed on the delta(Aph – NT) by using all 50 kb window along the human genome.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files on sample records are for individual replicates, bigwig files on the series records are replicate means, scores represent the Replicaton Index (RI) or the normalized Repli-Seq signal

source_name: human lymphoblastoid cells

growth_protocol: Epstein–Barr-virus-immortalized human B lymphocytes (JEFF cells) were grown in RPMI-1640 plus GlutaMAX-I medium (GIBCO) with 10% fetal calf serum (PAN-Biotech GmbH), 100 µg/ml of penicillin and streptomycin (GIBCO).

extract_protocol:
Cells were incubated overnight in lysis buffer (50 mM Tris-HCl pH8, 10 mM EDTA, 0.1% SDS, 50 ug/mL RNAse A, 100 ug/mL Proteinase K). DNA was purified from the lysates by phenol extraction.
Four µg of genomic DNA was fragmented to a mean size of 500 bp on a Covaris S220 intrument (peak power: 140, duty factor: 10%, cycle/burst: 200, time: 80 seconds). Fragmented DNA was treated with the End-Repair module (New England BioLabs, E6050) and the A-Tailing module (New England BioLabs, E6053), according to the manufacturer recommendations. Illumina Truseq indexed adapters were ligated on the resulting fragments, using the Quick Ligation module (New England BioLabs, E6056), according to the manufacturer recommendations. Following heat denaturation, BrdU-DNA was isolated by immunoprecipitation using an anti-BrdU monoclonal antibody (BD Biosciences, 347580). Immunoprecipitated fragments were amplified for 10 cycles using the KAPA Hifi DNA polymerase (KAPABiosystems, KK2502) and the resulting libraries were purified with AMPure XP beads (Beckman Coulter, A63881). Illumina libraries were pooled and sequenced on a NextSeq500 instrument on Paired-end 2x43 bp runs, using a NextSeq 500/550 High Output Kit v2 (75 cycles) kit.

treatment_protocol: Exponentially growing lymphoblastoid cells (~200x106), were pulse-labelled with 50 µM BrdU (Merck, B-5002) prior to recovery. Untreated cells were pulse labeled for 1 h and Aph treated cells (600 nM, for a total of 16 h) were labeled for the last 3 h. Cells were then fixed in 70% ethanol and incubated overnight at 4°C in the presence of 15 µg/ml Hoescht 33342 (ThermoFisher Scientific, H3570). Cells were re-suspended in 1X PBS and sorted in six fractions at a time by flow cytometry based on their DNA content using a BD Biosciences INFLUX cell sorter. The first fraction contains cells in the second half of the G1 phase plus very early S (called G1/S1); the rest of the S phase was divided into four fractions (S2 to S5); and the last fraction contains cells in very late S, G2 and M phases (S6/G2/M).

value: JEFF cells

value: Epstein-Barr-virus-immortalized human B lymphocytes

value: Non-Treated

tag: s phase


title: NT_Rep2_S6/G2/M

description: Enrichement of BrdU labelled DNA (Replicate 2)


title: DPY27_HiChIP_hermaphrodites_rep1

status: Public on Feb 04 2020

city: Omaha

first: M

middle: Jordan

last: Rowley

state: NE

address: 601 S Saddle Creek Rd

department: GCBA

institute: Univ of Nebraska Medical Center

description: DPY27 HiChIP Rep1

data_processing:
Library strategy: HiChIP
Both Hi-C and HiChIP data were mapped and processed using Juicer with DPNII restriction genomic sites.
Genome_build: CE10
Supplementary_files_format_and_content: Juicebox .hic files with interactions in multiple bin sizes and normalization schemes

organism: Caenorhabditis elegans

source_name: hermaphordite late embryos

growth_protocol: N2 strain was cultured under standard conditions on NG agar plates with E. coli (OP50) as a food source.

extract_protocol:
Embryos were crosslinked with 1.1% formaldehyde. Nuclei were isolate in a dounce and recrosslinked with 1% formaldehyde for 10 minutes.Chromatin was digested by DpnII, filled in with biotin-dCTP, and ligated. DNA was then isolated for Hi-C library prep. For HiChIP, ligated chromatin was sonicated and precleared with Protein A and G Dynabeads at 4°C for 2 hours, then precipitated using anti-DPY27 antibody overnight. Isolated chromatin was washed, eluted, reverse crosslinked and purified by standard methods, after which ligation events were enriched by streptavidin precipitation.
Libraries were constructed using the standard protocol or using a Tn5 library prepartion protocol. Genomic fragments were end repaired, A-tailed by adding  adenosine to  the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs), and adaptors were ligatedat room temperature for 1 hr with T4 DNA ligase (New England Biolabs). For Tn5 protocol, samples were incubated with Tn5 transposase in the presence of adaptors. Libraries were amplified with Illumina primers using the KAPA SYBR FAST qPCR Master Mix.

tag: developmental stage

value: late embryos

tag: Sex

value: hermaphrodite


title: HiC_hermaphrodites_rep2

description: Hi-C Rep2

data_processing:
Both Hi-C and HiChIP data were mapped and processed using Juicer with DPNII restriction genomic sites.
Genome_build: CE10
Supplementary_files_format_and_content: Juicebox .hic files with interactions in multiple bin sizes and normalization schemes


title: DPY27_HiChIP_hermaphrodites_rep2

description: DPY27 HiChIP Rep2


title: MOLM13-Cas9_CUTRUN_MLL1_sgNull_d6_REP2_190710_CGATGT_S2

status: Public on Nov 06 2019

data_processing:
Library strategy: Cut&Run-Seq
Raw Illumina NextSeq BCL files converted to FASTQs using Illumina bcl2fastq v02.14.01.07.
FASTQ files processed using a version of published CUT&RUNTools suite, modified to run on a local HPC cluster. (Briefly, the relevant steps include: reads trimmed using trimmomatic, aligned to genome with Bowtie 2, BAMs sorted and filtered for fragments < 120bp with samtools, peaks called with MACS2.)
WIG and TDF files produced from CUT&RUNTools BAM file outputs (duplicate reads marked but not removed) using IGVTools (v2.3.98).
Total signal was assessed around transcription start site (TSS) regions using the sitepro tool (v0.6.6) from the CEAS (Cis-regulatory Element Annotation System) package (using signal windows from TSS extending 10kb into the gene body with 100bp tiling and signal summed across each window), based on signal from WIG files generated above.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Sample signal files for visualization in IGV (.tdf) and wiggle txt format (.wig)

source_name: MOLM13-Cas9 cultured cells

growth_protocol: MOLM13 cells expressing Cas9 were cultured in PRMI1640 media supplemented with 10% Fetal bovine serum (v/v) (Gibco), 1x penicillin/streptomycin (Gibco), plasmocin (ThermoFisher).

extract_protocol:
The cells were collected and washed twice in ice-cold PBS. The cells were immobilized on Concavaline-A magnetic beads; followed by permealization pf cells with Triton-X100. Immobilized cells were incubated with anti-MLL1n antibody for 2 hours, washed, and incubated with ProteinA-MNase conjugate for 4 hours. After two washes MNase was activated by addition of 2mM CaCl2 for 30 min. Released DNA fragments were collected in supernatant and purified using AmpureXP beads
1-10 ng of ChIP'ed DNA was used for Illumina compatibl library generation using NEB Ultra II kit with 12 cycles of amplification with single end barcodes
Cut&Run-seq using NEB Ultra II protocol

treatment_protocol: infection with control or MEN1 sgRNA for 6 days

tag: antibody

value: anti-MLL1n (Bethyl #A300-086A)

value: 6 days

value: infection with control sgRNA


title: MOLM13-Cas9_CUTRUN_MLL1_sgNull_d6_REP1_190710_ATCACG_S1


title: HiC_hermaphrodites_rep1

description: Hi-C Rep1

tag: strain


title: MOLM13-Cas9_CUTRUN_MLL1_sgMEN1-1_sgMEN1-2_d6_REP2_190710_TGACCA_S4

tag: cell line

value: infection with MEN1 sgRNA


title: MOLM13-Cas9_RNA_sgMEN1-2_d6i_d4s_AAGCTC_S9_R1_merged.fastq.gz

data_processing:
Raw Illumina NextSeq BCL files converted to FASTQs using Illumina bcl2fastq v02.14.01.07 and reads trimmed using Trimmomatic v0.36 (phred quality threshold 33).
Reads aligned using STAR (v2.6.1b) and UCSC hg19 genome, gene and transcriptome references from Illumina iGenomes resource.
Aligned BAM files indexed with samtools v1.2; sorted, duplicate reads marked and removed (in cell line samples) using Broad picard tools v.2.9.4; and deduplicated BAMs indexed using samtools.
Read counts per gene calculated using HTSeq v0.11 htseq-count with hg19 gene reference from Illumina iGenomes and differential expression calculated using Bioconductor DESeq2 package.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Summary of raw counts per gene per sample (.txt)

growth_protocol: MOLM13 cells expressing Cas9 were cultured in PRMI1640 media supplemented with 10% Fetal bovine serum (v/v) (Gibco), 1x penicillin/streptomycin (Gibco), plasmocin (ThermoFisher). The cells were spinfected with lentiviruses carrying sgRNA for MEN1

extract_protocol:
Cell Lines: The cells were collected and washed twice in ice-cold PBS followed by lysis and RNA extraction using RNEasy (Qiagen) kit.  Quality of RNA was tested using RNA TAPE and samples qith RIN >7 were used for library preparation.
10-100 ng of total RNA converted to illumina compatible sequencing libraries using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina

treatment_protocol: CRISPR based knock out of MEN1 using 3 independent sgRNA for 6 days post infection

value: 6 days post infection

value: CRISPR based knock out of MEN1


title: MOLM13-Cas9_RNA_sgMEN1-1_d6i_d4s_GACGAT_S6_R1_merged.fastq.gz


title: MOLM13-Cas9_RNA_control_REP3_TCTTAA_S3_R1_merged.fastq.gz

value: control


title: OCIAML3_ChIP_MENIN_VTP50469_330nM_d4_REP1_181004_TTCCTGCT

value: 4 days


title: MOLM13-Cas9_RNA_control_REP1_CAGCGT_S1_R1_merged.fastq.gz


title: MOLM13-Cas9_CUTRUN_MLL1_sgMEN1-1_sgMEN1-2_d6_REP1_190710_TTAGGC_S3


title: RS411_ChIP_input_DMSO_d3_180110_ATTCAGAA_AGGCTATA

description: processed data file: ML2_MOLM13_RS411_ROSE_TSS-associated_DOT1L_MENIN_MLL1_ChIPseq_signal.txt

data_processing:
Raw Illumina NextSeq BCL files converted to FASTQs using Illumina bcl2fastq v02.14.01.07 and reads trimmed using Trimmomatic v0.36 (phred quality threshold 33).
Reads aligned to human GRCh37/hg19 genome using bowtie2 v2.1 (params: -q -p 11 --phred33 -N 1 --very-sensitive ) or STAR 2.6.1b (181116 samples; params: --twopassMode Basic --outReadsUnmapped None --runThreadN 4 --limitBAMsortRAM 12000000000 --outSAMstrandField intronMotif --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat).
The 181116 samples also contain Drosophila spike-in chromatin as described; these samples were additionally aligned to dm6 as above. Global differences in fly-human chromatin ratios were found to be small, so no additional spike-in normalization was performed in analysis of these samples.
Aligned BAM files sorted, duplicate reads marked and removed, and deduplicated BAMs indexed using Broad picard tools v2.9.4.
Alternative TSS-associated signal was calculated using the ROSE (Ranking Of SuperEnhancer) package v2 with 6kb windows centered around annotated RefGene TSS coordinates, input samples matched by cell line and stitching distance set to 0b. Input-subtracted signal within ROSE-calculated regions were used for comparisons.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Sample signal files for visualization in IGV (.tdf).
Supplementary_files_format_and_content: Summary ROSE TSS signal output (for all samples excluding H3K79me2) (.txt).

source_name: RS411 cultured cells

growth_protocol: MOLM13, RS4;11 and ml-2 cells were cultured in RPMI1640 media supplemented with 10% Fetal bovine serum (v/v) (Gibco), 1x penicillin/streptomycin (Gibco), plasmocin (ThermoFisher). For the treatment the cells were plated at 2x10^5 cells/ml in T75 tissue culture treated flasks. DMSO or VTP-50469 were added at 1:3000 dilution.

extract_protocol:
The cells were collected and washed twice in ice-cold PBS followed by crosslinking in 1% formaldehyde (methanol free) for 5 minutes. Excess of formaldehyde was quenched by addition of Tris pH 8.0 to 100nM final and Glycine 125 mM final. Chromatin was sheared using Covaris E220 for 20 min with power 140; duty 5; bursts 200/sec. We then used 5ul aliquot of sheared chromatin to decrosslink in order to test completeness of shearing. Chromatin was considered passed QC if fragments 100-600bp were >90%. For immunoprecipitation we used approximately chromatin from 1-10x10^6 cells, 5-10ug of specific antibody and 10-20ul of Protein-A/G magnetic beads (Dynal). In 16 hours the immune complexes were washed in Mixed Micelle Buffer, buffer 500, LiCl/detergent solution and TE buffers. DNA was eluted from the beads using 100mM NaHCO3 100mM NaCl 1% SDS and purified using AmpureXP beads.
1-10 ng of ChIP'ed DNA was used for Illumina compatible library generation using ThruPlex DNA-seq kit with 10 to 14 cycles of amplification with single or paired end barcodes.

treatment_protocol: DMSO or VTP-50469 (in DMSO) were added at 1:3000 dilution, for final concentration of DMSO 0.33% and VTP-50469 100 to 330nM.

value: 3 days


title: RS411_ChIP_H3K79me2-CST_VTP_330nM_d3_181213_TACTAGTC

value: anti-H3K79me2 (Cell signaling #5427 lot:4)


title: OCIAML3_ChIP_MLL_DMSO_d4_REP1_181004_TCCTCAAT

value: DMSO

value: MLL

value: anti-MLL1n (A300-086A, Bethyl)


title: RS411_ChIP_MLL1n_VTP_d3_180402_TTCAGCTC

value: anti-MLL1n (Bethyl #A300-086A lots:5 or 6)


title: RS411_ChIP_H3K79me2-CST_DMSO_d3_181213_TCAGATTC


title: RS411_ChIP_MLL1n_DMSO_d3_180402_TACTAGTC


title: RS411_ChIP_MENIN_VTP_d3_180110_TCCGGAGA_TCAGAGCC

value: MENIN

value: anti-Menin (Bethyl #A300-105A Lot:8)


title: RS411_ChIP_MENIN_DMSO_d3_180110_TCCGGAGA_AGGATAGG


title: MOLM13_ChIP_input_VTP_180209_TTCTGTGT

source_name: MOLM13 cultured cells


title: RS411_ChIP_DOT1L_DMSO_d3_180110_TCCGGAGA_CTTCGCCT

value: anti-DOT1L (Cell signaling #77087S clone 1W4Z lot 0)


title: MOLM13_ChIP_input_DMSO_d3_180110_CGCTCATT_AGGCTATA


title: MOLM13_ChIP_H3K79me2_DMSO_d3_190211_TGCGATCT


title: MOLM13_ChIP_H3K79me2_VTP_d3_190211_TTCCTGCT


title: MOLM13_ChIP_MLL1n_VTP_d3_180110_ATTACTCG_CTTCGCCT


title: MOLM13_ChIP_MLL1n_DMSO_d3_180110_ATTACTCG_TCAGAGCC


title: MOLM13_ChIP_MENIN_DMSO_d4_180919_TTAGGCAT


title: MOLM13_ChIP_DOT1L_DMSO_d3_180110_ATTACTCG_TAAGATTA


title: MOLM13_ChIP_MENIN_VTP_330nM_d4_180919_TGACCACT


title: ML2_ChIP_input_DMSO_180619_ATCACGTT

source_name: ML2 cultured cells


title: MOLM13_ChIP_DOT1L_VTP_d3_180110_ATTACTCG_ACGTCCTG


title: ML2_ChIP_MENIN_VTP_180619_CAGATCTG


title: ML2_ChIP_DOT1L_VTP_180726_TGTACCTT


title: ML2_ChIP_MENIN_DMSO_180619_ACAGTGGT


title: ML2_ChIP_DOT1L_DMSO_180726_TGGTTGTT


title: m819BM_PDX-CBAB22694_RNA_control_d28_171121_AATCCG

description:
3'-end RNA-seq
processed data file: CBAB22694_PDX_VTP50469_control_d28_htseq_counts_sorted.txt

data_processing:
Raw Illumina NextSeq BCL files converted to FASTQs using Illumina bcl2fastq v02.14.01.07 and reads trimmed using Trimmomatic v0.36 (phred quality threshold 33).
Reads uniquely aligned using Tophat v2.1.0 (params: -g 1 -x 1) and UCSC hg19 genome, gene and transcriptome references from Illumina iGenomes resource.
Aligned BAM files sorted, duplicate reads marked and removed (in cell line samples), and deduplicated BAMs indexed using Broad picard tools v2.9.4.
Read counts per gene calculated using HTSeq v0.11 htseq-count with hg19 gene reference from Illumina iGenomes.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Summary of raw counts per gene per sample (.txt).

source_name: PDX-CBAB22694 implanted in mouse 819

growth_protocol: MOLM13 and RS4;11 cells were cultured in RPMI1640 media supplemented with 10% Fetal bovine serum (v/v) (Gibco), 1x penicillin/streptomycin (Gibco), plasmocin (ThermoFisher). For the treatment the cells were plated at 2x10^5 cells/ml in T75 tissue culture treated flasks. DMSO or VTP-50469 were added at 1:3000 dilution.

extract_protocol:
Cell Lines: The cells were collected and washed twice in ice-cold PBS followed by lysis and RNA extraction using RNeasy (Qiagen) kit. PDX: The mice transplanted with MLL-r B-ALL PDX were fed for 28 days with either control or 0.1% VTP-50469 diet. After 28 days the mice were sacrificed and bone marrow collected. The bone marrow containing both mouse and human cells was labeled with mouse CD45-FITC TER119-FITC and human CD45-APC antibody and subjected to cell sorting. We collected hCD45+ cells which were used for total RNA isolation using RNeasy (Qiagen) kit. Quality of RNA was tested using RNA TAPE and samples with RIN >7 were used for library preparation.
10-100 ng of total RNA converted to Illumina compatible sequencing libraries using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina.

value: 28 days


title: m818BM_PDX-CBAB22694_RNA_control_d28_171121_CCTAAG

source_name: PDX-CBAB22694 implanted in mouse 818


title: m815BM_PDX-CBAB22694_RNA_VTP50469_d28_171121_ATGAAC

source_name: PDX-CBAB22694 implanted in mouse 815

value: 1% VTP50469 chow


title: m814BM_PDX-CBAB22694_RNA_VTP50469_d28_171121_TTAACT

source_name: PDX-CBAB22694 implanted in mouse 814


title: m812BM_PDX-CBAB22694_RNA_VTP50469_d28_171121_TCAGGA

source_name: PDX-CBAB22694 implanted in mouse 812


title: RS411_RNA_EPZ5676_1uM_d7_REP2_180927_GATTGT

description:
3'-end RNA-seq
processed data file: MOLM13_RS411_EPZ5676_VTP50469_d2_d7_180927_htseq_counts_rmdup.txt

value: 7 days

value: 1uM EPZ5676


title: RS411_RNA_EPZ5676_1uM_d7_REP1_180927_CGAAGG


title: RS411_RNA_VTP50469_330nM_d7_REP1_180927_TGTGCA


title: RS411_RNA_VTP50469_330nM_d7_REP3_180927_CCGCAA


title: RS411_RNA_DMSO_d7_REP3_180927_AGGCAT


title: RS411_RNA_DMSO_d7_REP2_180927_GGCCAA


title: RS411_RNA_VTP50469_330nM_d7_REP2_180927_TACCTT


title: RS411_RNA_EPZ5676_1uM_d2_REP3_180927_CAGATG

value: 2 days


title: ML2_ChIP_MLL1n_VTP_d3_180402_CGATGTTT


title: RS411_RNA_EPZ5676_1uM_d2_REP1_180927_ACAACG


title: RS411_RNA_EPZ5676_1uM_d7_REP3_180927_AATAGC


title: RS411_RNA_DMSO_d7_REP1_180927_CATCTA


title: RS411_RNA_VTP50469_330nM_d2_REP3_180927_GCATGG


title: RS411_RNA_EPZ5676_1uM_d2_REP2_180927_ACGTCT


title: RS411_RNA_VTP50469_330nM_d2_REP2_180927_CAACAG


title: RS411_RNA_VTP50469_330nM_d2_REP1_180927_ACCTAC


title: RS411_RNA_DMSO_d2_REP1_180927_CTAGTC


title: MOLM13-Cas9_RNA_control_REP2_TCAGGA_S2_R1_merged.fastq.gz

value: 6 days post infection


title: RS411_RNA_DMSO_d2_REP2_180927_GGCTGC


title: ML2_ChIP_MLL1n_DMSO_d3_180402_ATCACGTT


title: m813BM_PDX-CBAB22694_RNA_control_d28_171121_CGGTTA

source_name: PDX-CBAB22694 implanted in mouse 813


title: MOLM13_RNA_VTP50469_330nM_d7_REP3_180927_GAGTCC


title: RS411_RNA_DMSO_d2_REP3_180927_CACACT


title: MOLM13_RNA_EPZ5676_1uM_d7_REP1_180927_GCGAAT


title: MOLM13_RNA_EPZ5676_1uM_d7_REP3_180927_TAGGCT


title: MOLM13_RNA_VTP50469_330nM_d7_REP2_180927_CCTAAG


title: MOLM13_RNA_VTP50469_330nM_d7_REP1_180927_ACATTA


title: MOLM13_RNA_DMSO_d7_REP3_180927_GAACCT


title: MOLM13_RNA_DMSO_d7_REP2_180927_AAGTGG


title: MOLM13_RNA_EPZ5676_1uM_d2_REP3_180927_CCAATT


title: MOLM13_RNA_EPZ5676_1uM_d2_REP2_180927_TTCCGC


title: MOLM13_RNA_DMSO_d7_REP1_180927_ATGGCG


title: MOLM13_RNA_EPZ5676_1uM_d2_REP1_180927_GGTATA


title: MOLM13_RNA_VTP50469_330nM_d2_REP3_180927_ACAGAT


title: MOLM13_RNA_VTP50469_330nM_d2_REP2_180927_CGCAAC


title: MOLM13_RNA_DMSO_d2_REP2_180927_ATGAAC


title: MOLM13_RNA_VTP50469_330nM_d2_REP1_180927_GCTCGA


title: MOLM13_RNA_DMSO_d2_REP3_180927_TATGTC


title: MOLM13_RNA_DMSO_d2_REP1_180927_TGCACG


title: MOLM13_RNA_EPZ5676_1uM_d7_REP2_180927_TGGCGA


title: Aged adult OPCs rep 2

status: Public on Nov 01 2019

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

description: RNA depleted from ribosomal RNA

data_processing:
Reads were quality-trimmed using 'TrimGalore!'.
Trimmed reads were aligned to the rat reference genome (Rnor_6.0/rn6) using 'tophat2' with paramers "--no-coverage-search --read-mismatch 2 --max-multihits 1 --b2-sensitive", allowing for two mismatches and considering uniquely mapping reads only.
Read counts per ENSEMBL 92 transcripts were obtained using featureCounts' with options '-p -O -C --minOverlap 10'
Genome_build: RGSC Rnor_6.0/rn6
Supplementary_files_format_and_content: Read counts per ENSEMBL 92 obtained by 'featureCounts'.

organism: Rattus norvegicus

source_name: A2B5 positive brain cells

growth_protocol: All cells were isolated from female Sprague Dawley rats that were housed under standard laboratory conditions on a 12 h light/dark cycle with constant access to food and water. All animals were housed in pairs or groups of up to 4 animals.

extract_protocol:
Adult male and female rats (2-24 months) were decapitated after lethal injection with phenobarbital. The brains were removed quickly and placed into ice-cold isolation medium (SI Tab. 3, alternatively Hibernate A Brainbits). The telencephalon and cerebellum were dissected in isolation medium; meninges, and the olfactory bulb were mechanically removed and the brain tissue was mechanically minced into 1mm3 pieces. The tissue pieces were spun down at 100g for 1min at RT and the tissue was washed in HBSS- (no Mg2+ and Ca2+, Gibco). Each half of the brain was mixed with 5ml of dissociation solution (34U/ml papain (Worthington), 20μg/ml DNAse Type IV (Gibco) in isolation medium). The brain tissue was dissociated on a shaker (50rpm) for 40 min at 35ºC. The digestion was stopped by addition of ice cold HBSS-. The tissue was centrifuged (200g, 3 min, RT), the supernatant completely aspirated and the tissue resuspended in isolation medium supplemented with 2% B27 and 2mM sodium-pyruvate (trituration solution). The tissue was allowed to sit in this solution for 5min. To obtain a single cell suspension the tissue suspension was triturated 10 times using first a 5ml serological pipette and subsequently three fire polished glass pipettes (opening diameter >0.5mm). After each trituration step the tissue suspension was allowed to sediment (approximately 1-2 min) and the supernatant (approximately 2ml), containing the cells, was transferred into a fresh tube. After each round of trituration 2ml of fresh trituration solution were added. To remove accidentally transferred undigested tissue bits, the collected supernatant was filtered through 70μm cell strainers into tubes that contained 90% isotonic Percoll (GE Healthcare, 17-0891-01, in 10xPBS pH7.2 (Lifetech). The final volume was topped up with phenol-red free DMEM/F12 with HEPES (Gibco) and mixed to yield a homogenous suspension with a final Percoll concentration of 22.5%. The single cell suspension was separated from remaining debris particles by gradient density centrifugation (800g, 20min, RT, without break). The myelin debris and all layers without cells were discarded and the brain cell containing phase (last 2ml) and cell pellet were resuspended in HBSS+ and combined in a fresh 15ml tubes and centrifuged (300g, 5min, RT). The cell pellet was resuspended in red blood cell lysis buffer (Sigma, R7757) and incubated for 1min at RT to remove red blood cells. 10ml of HBSS+ were added to this cell suspension and spun down (300g, 5min, RT). The cell pellets were resuspended in 0.5ml modified Milteny washing buffer (MWB, 2mM EDTA, 2mM Na-Pyruvate, 0.5% BSA in PBS, pH 7.3) supplemented with 10ng/ml human recombinant insulin (Gibco). To this cell suspension 2.5µg mouse-anti-rat-A2B5-IgM antibody (Millipore, Extended data Tab. 4) were added for every 10 million cells. After 25 min incubation, gently shaking at 4ºC, 7ml of MWB were added. The solution was centrifuged (300g, 5min, RT) and the pellet resuspended in 80μl MWB supplemented with 20μl rat-anti-mouse-IgM antibody (Milteny, 130-047-302) per 10 million cells. The cells were incubated for 15 min, slowly shaking at 4ºC. The secondary antibody was again washed out with 7ml MWB and the sample was centrifuged (300g, 5min, RT). The cell pellet was resuspended in 0.5ml and MACS was performed according to the recommendations of the supplier. Briefly, a MS column (Milteny, 130-042-201) were inserted into MiniMACS Separator (Miltenyi; 130-042-102) and pre-wet with 0.5ml MWB. Resuspended cells were put onto one MS column. Subsequently the column was washed three times using 500μl MWB for each wash. Finally, A2B5 positive cells were flushed out the column with 1ml MWB. The cells were pelleted by centrifugation and the RNA was isolated using the Qiagen RNAeasy micro kit (Qiagen).
Purification of polyA+ mRNA

value: Oligodendrocyte progenitor cells

tag: age

value: 20-24 months

value: Sprague Dawley

tag: gender

value: female


title: Young adult OPCs rep 1

description: RNA depleted from ribosomal RNA

tag: cell type

value: 2-3 months


title: Aged adult OPCs rep 3

description: RNA depleted from ribosomal RNA


title: ADAR1 WT ADAR2 KO Adult Brain  - Whole. Replicate 2 (510) A2KOr2

status: Public on Oct 27 2019

city: Meblourne

first: Alistair

middle: Morgan

last: Chalk

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: WEHI

description:
ADAR1 WT ADAR2 KO Adult Brain  - Whole. Replicate 2 (510)
Adar2KO_510
S4_Adar1_+_+_Ifih_-_-_Adar2_-_-_Gria2_RR

data_processing:
Illumina Casava1.7 software used for basecalling.
Preprocessing: Sequenced reads (150bp) were trimmed for adaptor sequence and low quality reads using fastp (v 0.19.5, Shifu Chen, fastp: A fast FASTQ preprocessor with full features, (2017), GitHub repository, https://github.com/OpenGene/fastp ). Command line used: fastp  --trim_front1 10 --trim_front2 10
Preprocessing: Sequenced reads (75bp) from GSE94387 were trimmed for adaptor sequence and low quality reads using fastp (v 0.19.5, Shifu Chen, fastp: A fast FASTQ preprocessor with full features, (2017), GitHub repository, https://github.com/OpenGene/fastp ). Command line used: fastp  --trim_front1 10 --trim_front2 10 --trim_tail1 1 --trim_tail2 1
Preprocessing: Reads mapping to rRNA were removed using Bbmap . Command line used: bbsplit.sh minratio=0.56 minhits=1 maxindel=16000
RNA Editing: Editing calling of known sites (RNA vs mm10) was performed using JACUSA 2.0.0-RC540 (https://github.com/dieterich-lab/JACUSA): parameters used: -F 1024 -filterNH_ 99,  -filterNM_ 99, -c 3 -P RF-FIRSTSTRAND.
RNA Editing: Calling of differential editing in known sites (RNA genotype vs RNA genotype) was performed using JACUSA 2.0.0-RC540. Briefly, call-2 was used to determine the difference in editing level for all known sites (all replicates of genotype A vs all replicates of genotype B). Duplicate reads were removed.
Gene expression: Trimmeds reads were aligned using Salmon (version v0.11.3) against mm10 (Annotation: gencode.mm10.vM14.annotation.gtf).
Gene expression: Data was normalised in Degust (http://victorian-bioinformatics-consortium.github.io/degust/) using EdgeR (McCarthy, J. D, Chen, Yunshun, Smyth and K. G (2012). “Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.” Nucleic Acids Research, 40(10), pp. -9.). Genes with count >1 and CPM > 1 in at least 3/3 samples of a given genotype were considered for further analysis. Each comparison (E861A vs WT, A2KO vs Het, DKO vs Het) was performed seperately. Differential expression was performed in Degust using EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: count

source_name: ADAR1 WT ADAR2 KO Adult Brain

growth_protocol: RNA was harvested from Single cell suspensions of whole feotal brain using Trizol reagent . >2.5 ug of total RNA was used for the construction of sequencing libraries.

extract_protocol:
[75bp] Post ribosome depleted RNA was purified and subjected to indexing and library preparation using the Kapa Stranded RNA-seq Library Preparation Kit for Illumina Platforms (Kapa Biosystems). Library amplification was performed for 9 cycles of PCR. The resultant libraries were pooled and sequenced on a single run using the Illumina NextSeq500 with 75bp paired end reads at the Ramaciotti Centre for Genomics (UNSW, Australia).
[150bp] Total RNA was isolated from the whole brain from 12-week-old males Adar1E861A/+Ifih1-/-Adar2+/-Gria2R/R (dHet), Adar1+/+Ifih1-/-Adar2-/-Gria2R/R (Adar2-/-) and Adar1E861A/E861AIfih1-/- Adar2-/-Gria2R/R (Quad) mice (n= 3/genotype). Whole brain was lysed in Trisure and purified using DirectZol columns. Post ribosome-depleted RNA was purified and subjected to indexing and library preparation using the Kapa Stranded RNA-seq Library Preparation Kit (Kapa Biosystems) and sequenced at PE150bp on the Illumina platform by the Novogene (Hong Kong).

tag: strain background

value: 12 week old; adult

value: male

tag: adar1 genotype

value: WT

tag: adar2 genotype

tag: gria2 genotype

value: R/R

tag: ifih1 genotype

tag: tissue

value: Adult Brain

tag: replicate


title: ADAR1 WT ADAR2 KO Adult Brain  - Whole. Replicate 1 (502) A2KOr1

description:
ADAR1 WT ADAR2 KO Adult Brain  - Whole. Replicate 1 (502)
Adar2KO_502
S1_Adar1_+_+_Ifih_-_-_Adar2_-_-_Gria2_RR


title: ADAR1 Het ADAR2 Het Adult Brain  - Whole. Replicate 3 (547) Hetr3

description:
ADAR1 Het ADAR2 Het Adult Brain  - Whole. Replicate 3 (547)
Adar1_Adar2_Het_547
S9_Adar1_E861A_+_Ifih_-_-_Adar2_+_-_Gria2_RR

source_name: ADAR1 Het ADAR2 Het Adult Brain

value: WT/-


title: ADAR1 Het ADAR2 Het Adult Brain  - Whole. Replicate 2 (515) Hetr2

description:
ADAR1 Het ADAR2 Het Adult Brain  - Whole. Replicate 2 (515)
Adar1_Adar2_Het_515
S5_Adar1_E861A_+_Ifih_-_-_Adar2_+_-_Gria2_RR


title: ADAR1 WT ADAR2 KO Adult Brain  - Whole. Replicate 3 (521) A2KOr3

description:
ADAR1 WT ADAR2 KO Adult Brain  - Whole. Replicate 3 (521)
Adar2KO_521
S7_Adar1_+_+_Ifih_-_-_Adar2_-_-_Gria2_RR


title: ADAR1 WT MDA5 knockout Adult Brain - Whole. Replicate 3 (84B) WTr3 [re-analysis]

description:
This is duplicated sample record of GSM2474529 for the convenient retrieval of the complete raw data from SRA
ADAR1 WT MDA5 knockout Adult Brain - Whole. Replicate 1 (84B)
MDA5_KO_84B
ADAR_DKO_ADARwt_MDA5ko_RAdar84B

source_name: ADAR1 WT MDA5 knockout Adult Brain


title: ADAR1 WT MDA5 knockout Adult Brain - Whole. Replicate 1 (75B) WTr1 [re-analysis]

description:
This is duplicated sample record of GSM2474527 for the convenient retrieval of the complete raw data from SRA
ADAR1 WT MDA5 knockout Adult Brain - Whole. Replicate 1 (75B)
MDA5_KO_75B
ADAR_DKO_ADARwt_MDA5ko_RAdar75B


title: ADAR1 Het ADAR2 Het Adult Brain  - Whole. Replicate 1 (510) Hetr1

description:
ADAR1 Het ADAR2 Het Adult Brain  - Whole. Replicate 1 (510)
Adar1_Adar2_Het_510
S2_Adar1_E861A_+_Ifih_-_-_Adar2_+_-_Gria2_RR


title: Young adult OPCs rep 2

description: RNA depleted from ribosomal RNA


title: ADAR1 E861A MDA5 knockout Adult Brain - Whole. Replicate 2 (411B) E861Ar2 [re-analysis]

description:
This is duplicated sample record of GSM2474525 for the convenient retrieval of the complete raw data from SRA
ADAR1 E861A MDA5 knockout Adult Brain - Whole. Replicate 1 (411B)
E861A_MDA5_DKO_411B
ADAR_DKO_ADAR_E861A_MDA5ko_RAdar411B

source_name: ADAR1 E861A MDA5 knockout Adult Brain


title: Aged adult OPCs rep 1

description: RNA depleted from ribosomal RNA


title: ADAR1 E861A ADAR2 KO Adult Brain  - Whole. Replicate 1 (511) DKOr1

description:
ADAR1 E861A ADAR2 KO Adult Brain  - Whole. Replicate 1 (511)
Adar1_Adar2_DKO_511
S3_Adar1_E861A_E861A_Ifih_-_-_Adar2_-_-_Gria2_RR

source_name: ADAR1 E861A ADAR2 KO Adult Brain


title: ADAR1 E861A MDA5 knockout Adult Brain - Whole. Replicate 3 (413B) E861Ar3 [re-analysis]

description:
This is duplicated sample record of GSM2474526 for the convenient retrieval of the complete raw data from SRA
ADAR1 E861A MDA5 knockout Adult Brain - Whole. Replicate 1 (413B)
E861A_MDA5_DKO_413B
ADAR_DKO_ADAR_E861A_MDA5ko_RAdar413B


title: Polysome_Kn [S2_L1]

status: Public on May 28 2019

first: Manoj

last: Bhasin

address: 99 Brookline Ave

institute: BIDMC

data_processing:
fastq
Quality control checks done on fastq files using fastqc and fastx.
trimmoatic and cutadapt used for trimming the adaptors and poor quality reads.
tophat2 alignment with hg19.
htseq-count for counting the reads.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_L1_sn.count.txt: Tab-delimited text files include counts.

source_name: human keratinocytes (YBX1_RNAi)

growth_protocol: Primary adult keratinocytes were isolated from human skin tissue samples obtained during abdominoplasty procedures at Massachusetts General Hospital, Boston, MA with IRB (Institutional Review Board) approval for discarded human tissue. Primary cultures from donors were isolated following the protocol developed by CELLnTEC Advanced Cell Systems AG and described in details here: http://cellntec.com/products/resources/protocols/isolation/ , (CELLnTEC Advanced Cell Systems AG, Bern, Switzerland). Cultures were maintained at 37oC in 5% CO2. Cells were passaged around 70% and split 1:3 by using TrypLETM (Thermo Scientific). HKC cultures were used between passages 1 and 3.

extract_protocol:
4 days after siRNA transfection, total mRNA and polysomaly associated mRNAs were extracted using sucrose density gradient sedimentation.
Libraries were generated from double-stranded cDNA using the Illumina TruSeq kit according to the manufacturer’s protocol. Library quality control was checked using the Agilent DNA High Sensitivity Chip.

treatment_protocol: Predesigned siRNAs for human YBX1 and control siRNAs were purchased from Invitrogen, Carlsbad, CA (Cat. No: s9732, s9733 and 4390843). Pooled from different donors primary human keratinocytes cultures were transfected with control or YBX1 siRNAs by electroporation.

value: Proliferating epidermal progenitors

tag: tissue origin

value: adult human epidermis

tag: passages

tag: sirna

tag: rna

value: Polysomal mRNA


title: ADAR1 E861A ADAR2 KO Adult Brain  - Whole. Replicate 2 (520) DKOr2

description:
ADAR1 E861A ADAR2 KO Adult Brain  - Whole. Replicate 2 (520)
Adar1_Adar2_DKO_520
S6_Adar1_E861A_E861A_Ifih_-_-_Adar2_-_-_Gria2_RR

tag: Sex


title: Polysome_Kn [S1_L1]


title: T_Kn [S11_L1]

value: Total mRNA


title: Young adult OPCs rep 3

description: RNA depleted from ribosomal RNA

tag: strain


title: Polysome_Wild [C2_L1]

source_name: human keratinocytes (contr_RNAi)

value: control


title: T_Wild [C11_L1]


title: Polysome_Wild [C1_L1]


title: ADAR1 WT MDA5 knockout Adult Brain - Whole. Replicate 2 (82B) WTr2 [re-analysis]

description:
This is duplicated sample record of GSM2474528 for the convenient retrieval of the complete raw data from SRA
ADAR1 WT MDA5 knockout Adult Brain - Whole. Replicate 1 (82B)
MDA5_KO_82B
ADAR_DKO_ADARwt_MDA5ko_RAdar82B


title: A2

status: Public on Jul 06 2019

city: Cambridge

first: Kevin

last: Chalut

address: Tennis Court Road

department: Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
1. Trimmomatic adaptor clipping for TruSeq-HT adapters.
2. Hisat2 alignment to rat genome Rn6 paired end
3. Stringtie
4. Bowtie
Genome_build: RN6
Supplementary_files_format_and_content: All processed data files are supplied in the GTF format.

source_name: primary MACs sorted OPC

growth_protocol: MACs sorted OPCs cultured  in FGF and PDGF

extract_protocol:
Zymo Directzol RNA microkit
SMARTer Stranded Total RNA-pico Input Mammalian Kit

treatment_protocol: OPCs were cultured on laminin coated hydrogels of differing stiffness

value: primary MACs sorted OPC


title: A3


title: A1


title: VWN3

status: Public on Oct 03 2018

city: Sheffield

first: Ian

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

institute: University of Sheffield

data_processing:
Nine nucleotides were removed from read 1 fastq files, and six were removed from read 2, as suggested by the Lexogen SENSE library preparation manual using the cutadapt tool. Samples split across two lanes were merged into a single fastq file.
Transcript abundances were estimated using salmon with Ensembl v75 annotation. Abundances were then aggregated to gene level using tximport.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample; salmon quantifications

source_name: HEK293_Virilizer/WTAP RNAi_Nuclear

extract_protocol:
The RNA content from each fraction was extracted using TRIzol, following the manufacturer’s guidelines. All RNA samples were DNase-treated (TurboDNase, Ambion), phenol/chlorophorm extracted, ethanol precipitated, and resuspended in RNases-free water (Sigma). Fractionations were assessed by western blot analysis, using histone H3, as a chromatin marker, Alyref or Ssrp1 as nuclear markers, and Tubulin as a cytoplasmic marker.
Libraries for sequencing were prepared using the Lexogen SENSE mRNA-Seq Library Prep according to the manufacturer’s instructions and sequenced using a Hiseq 2500.

tag: cell line

tag: condition

value: Virilizer/WTAP RNAi

tag: cellular fraction

value: Nuclear

value: Replicate 3


title: VWN1

value: Replicate 1


title: VWN2

value: Replicate 2


title: VWC2

source_name: HEK293_Virilizer/WTAP RNAi_Cytoplasms

value: Cytoplasms


title: VWC1


title: ADAR1 E861A ADAR2 KO Adult Brain  - Whole. Replicate 3 (546) DKOr3

description:
ADAR1 E861A ADAR2 KO Adult Brain  - Whole. Replicate 3 (546)
Adar1_Adar2_DKO_546
S8_Adar1_E861A_E861A_Ifih_-_-_Adar2_-_-_Gria2_RR

tag: age

value: 12 week old; adult

value: male


title: VWC3


title: CN3

value: Control


title: CN2


title: CN1


title: ADAR1 E861A MDA5 knockout Adult Brain - Whole. Replicate 1 (401B) E861Ar1 [re-analysis]

description:
This is duplicated sample record of GSM2474524 for the convenient retrieval of the complete raw data from SRA
ADAR1 E861A MDA5 knockout Adult Brain - Whole. Replicate 1 (401B)
E861A_MDA5_DKO_401B
ADAR_DKO_ADAR_E861A_MDA5ko_RAdar401B

tag: strain background

value: WT

value: Adult Brain


title: RS411_ChIP_DOT1L_VTP_d3_180110_TCCGGAGA_TAAGATTA

description: processed data file: ML2_MOLM13_RS411_ROSE_TSS-associated_DOT1L_MENIN_MLL1_ChIPseq_signal.txt

source_name: RS411 cultured cells

tag: chip target

tag: antibody

value: anti-DOT1L (Cell signaling #77087S clone 1W4Z lot 0)

tag: timepoint

value: 3 days

tag: treatment


title: CC2