title: HeLa Mitotic Cell Cut&Run no antibody control 10 min R1T1 (match with CTCF R1)

description:
MOCR-HeLa-MC-NoAb-10min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run no antibody control 10 min R1T1 (match with CTCF R1, processed files combine replicates R1 and R2 for CTCF)


title: T47D-shTRPS1

status: Public on Nov 19 2018

type: RNA

city: Jinan

first: Jing

last: Hu

address: Wenhua xi road

department: Department of Pathology

country: China

institute: Shandong University

description: This sample is of T47D transfected with lentivirus of shTRPS1.

hyb_protocol: Microarray hybridization was performed at 65°C for 17 hours on NimbleGen 12x135k Whole Human Genome Oligonucleotide Microarray (HG18) in NimbleGen Hybridization System.

scan_protocol: After being washed in an ozone-free environment, image capture was performed with Axon GenePix 4000B (Molecular Devices) and uploaded into NimbleScan (v2.5), and Cy3 label intensities determined.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

molecule: total RNA

organism: Homo sapiens

label_protocol: cDNA samples were amplified, Cy3-labeled with NimbleGen one-color DNA labeling kit following manufacturer’s protocol. Microarray hybridization was performed at 65°C for 17 hours to NimbleGen whole human genome 12x135K microarrays in NimbleGen Hybridization System.

growth_protocol: Cells were maintained in DMEM medium supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin and streptomycin. Cell cultures were held in a humid, 37o C and 5% CO2 cell culture incubator.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: T47D cells transfected with lentivirus are referred as T47D-NC and T47D-shTRPS1.

tag: cell line

value: breast cancer cell line T47D


title: HeLa non sync cell Cut&Run no antibody control 0 sec control R1T1 (match with CTCF R1)

type: SRA

city: München

first: Marlies

middle: E

last: Oomen

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

description:
MOCR-HeLa-NS-NoAb-0sec-R1T1S1.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run no antibody control 0 sec control R1T1 (match with CTCF R1, processed files combine replicates R1 and R2 for CTCF)

library_source: genomic

data_processing:
Library strategy: CUT&RUN (Cleavage under targets and Release using nuclease)
Reads were mapped to hg19 using bowtie2. For more details see https://github.com/dekkerlab/CTCF_in_mitosis_GR_2018
PCR duplicates, ChrM etc were removed to obtain bam files of valid reads. For more details see https://github.com/dekkerlab/CTCF_in_mitosis_GR_2018
Bam files of valid reads were converted to bed files and separated by reads longer than 120bp and smaller than 120bp for further downstream analysis using HOMER. For more details see https://github.com/dekkerlab/CTCF_in_mitosis_GR_2018
These cut and run bed files were only used to make signal aggregation plots on functional elements using HOMER.
For correct use of no antibody control files, files should be match to the cut&run experiment done at the same time. CTCF matches with NoAb R1 and R2, H2A.Z matches with NoAb R2 and R3 and H3K4Me1 and Me3 match with NoAb R3 and R4.
Genome_build: hg19
Supplementary_files_format_and_content: bed files of all valid reads of combined replicates for further processing using HOMER

molecule: genomic DNA

source_name: HeLa-S3 cells

growth_protocol: HeLa-S3 cells were cultured glutamax DMEM supplemented with 10% heat-inactivated FBS and penicillin-streptomycin.

extract_protocol:
For each CUT&RUN library 500,000 cells were used
CUT&RUN was performed according to published protocol (Skene and Henikoff, Elife, 2017), with minor changes. See supplemental methods in Oomen et al 2018 for more information

treatment_protocol: Cells were harvested as non-synchrous without treatment or arrested in mitosis using Thymidine treatment and Nocodazole (mitotic cells). See supplemental methods for more information

tag: protocol

value: CUT&RUN

tag: enzyme

value: MNase

tag: cell type

value: Human adenocarcinoma cells

value: HeLa-S3 (CCL-2.2)


description:
MOCR-HeLa-MC-CTCF-0sec-R1T1S1.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on CTCF 0 sec control R2T1


description:
MOCR-HeLa-MC-CTCF-10min-combined_R1_R2.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on CTCF 10 min R2T1


description:
MOCR-HeLa-NS-CTCF-0sec-R1T1S1.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on CTCF 0 sec control R1T1


description:
MOCR-HeLa-NS-CTCF-10min-combined_R1_R2.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on CTCF 10 min R2T1


title: HeLa non sync cell Cut&Run no antibody control 10 sec R1T1 (match with CTCF R1)

description:
MOCR-HeLa-NS-NoAb-10sec-R1T1S1.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run no antibody control 10 sec R1T1 (match with CTCF R1, processed files combine replicates R1 and R2 for CTCF)


description:
MOCR-HeLa-NS-H2Az-5min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on H2A.Z 5 min R1T1


description:
MOCR-HeLa-NS-H2Az-10min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on H2A.Z 10 min R1T1


description:
MOCR-HeLa-NS-H2Az-30min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on H2A.Z 30 min R1T1


description:
MOCR-HeLa-MC-H2Az-5min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on H2A.Z 5 min R1T1


description:
MOCR-HeLa-MC-H2Az-30min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on H2A.Z 30 min R1T1


title: HeLa non sync cell Cut&Run no antibody control 5 min R2T1 (matched with H2A.Z R1 and CTCF R2)

description:
MOCR-HeLa-NS-NoAb-5min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run no antibody control 5 min R2T1 (matched with H2A.Z R1 and CTCF R2, processed files combine replicates R2 and R3 for H2A.Z and R1 and R2 for CTCF)


description:
MOCR-HeLa-MC-H2Az-10min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on H2A.Z 10 min R1T1


title: HeLa Mitotic Cell Cut&Run no antibody control 5 min R2T1 (matched with H2A.Z R1 and CTCF R2)

description:
MOCR-HeLa-MC-NoAb-5min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run no antibody control 5 min R2T1 (matched with H2A.Z R1 and CTCF R2, processed files combine replicates R2 and R3 for H2A.Z and R1 and R2 for CTCF)


title: HeLa non sync cell Cut&Run no antibody control 10 min R2T1 (matched with H2A.Z R1 and CTCF R2)

description:
MOCR-HeLa-NS-NoAb-10min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run no antibody control 10 min R2T1 (matched with H2A.Z R1 and CTCF R2, processed files combine replicates R2 and R3 for H2A.Z and R1 and R2 for CTCF)


title: HeLa non sync cell Cut&Run no antibody control 30 min R2T1 (matched with H2A.Z R1 and CTCF R2)

description:
MOCR-HeLa-NS-NoAb-30min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run no antibody control 30 min R2T1 (matched with H2A.Z R1 and CTCF R2, processed files combine replicates R2 and R3 for H2A.Z and R1 and R2 for CTCF)


title: HeLa Mitotic Cell Cut&Run no antibody control 10 min R2T1 (matched with H2A.Z R1 and CTCF R2)

description:
MOCR-HeLa-MC-NoAb-10min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run no antibody control 10 min R2T1 (matched with H2A.Z R1 and CTCF R2, processed files combine replicates R2 and R3 for H2A.Z and R1 and R2 for CTCF)


description:
MOCR-HeLa-MC-H2Az-10min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on H2A.Z 10 min R2T1


title: HeLa Mitotic Cell Cut&Run no antibody control 30 min R2T1 (matched with H2A.Z R1 and CTCF R2)

description:
MOCR-HeLa-MC-NoAb-30min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run no antibody control 30 min R2T1 (matched with H2A.Z R1 and CTCF R2, processed files combine replicates R2 and R3 for H2A.Z and R1 and R2 for CTCF)


description:
MOCR-HeLa-MC-H3K4me1-10min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on H3K4Me1 10 min R1T1


description:
MOCR-HeLa-MC-H3K4me1-5min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on H3K4Me1 5 min R1T1


description:
MOCR-HeLa-MC-H2Az-30min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on H2A.Z 30 min R2T1


description:
MOCR-HeLa-MC-H3K4me1-30min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on H3K4Me1 30 min R1T1


description:
MOCR-HeLa-MC-H3K4me3-5min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on H3K4Me3 5 min R1T1


title: HeLa Mitotic Cell Cut&Run no antibody control 30 min R3T1 (matched with H3K4Me1 and Me3 R1 and H2A.Z R2)

description:
MOCR-HeLa-MC-NoAb-30min-R2_R3.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run no antibody control 30 min R3T1 (matched with H3K4Me1 and Me3 R1 and H2A.Z R2, processed files combine replicates R3 and R4 for H3K4me3 and H3K4me1 and replicates R2 and R3 for H2A.Z)


title: HeLa Mitotic Cell Cut&Run no antibody control 10 min R3T1 (matched with H3K4Me1 and Me3 R1 and H2A.Z R2)

description:
MOCR-HeLa-MC-NoAb-10min-R2_R3.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run no antibody control 10 min R3T1 (matched with H3K4Me1 and Me3 R1 and H2A.Z R2, processed files combine replicates R3 and R4 for H3K4me3 and H3K4me1 and replicates R2 and R3 for H2A.Z)


description:
MOCR-HeLa-MC-H3K4me3-10min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on H3K4Me3 10 min R1T1


description:
MOCR-HeLa-MC-H3K4me3-30min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on H3K4Me3 30 min R1T1


description:
MOCR-HeLa-NS-H2Az-30min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on H2A.Z 30 min R2T1


description:
MOCR-HeLa-NS-H2Az-5min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on H2A.Z 5 min R2T1


description:
MOCR-HeLa-NS-H3K4me1-5min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on H3K4Me1 5 min R1T1


title: HeLa Mitotic Cell Cut&Run no antibody control 5 min R3T1 (matched with H3K4Me1 and Me3 R1 and H2A.Z R2)

description:
MOCR-HeLa-MC-NoAb-5min-R2_R3.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run no antibody control 5 min R3T1 (matched with H3K4Me1 and Me3 R1 and H2A.Z R2, processed files combine replicates R3 and R4 for H3K4me3 and H3K4me1 and replicates R2 and R3 for H2A.Z)


description:
MOCR-HeLa-NS-H3K4me1-30min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on H3K4Me1 30 min R1T1


description:
MOCR-HeLa-NS-H3K4me3-10min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on H3K4Me3 10 min R1T1


description:
MOCR-HeLa-NS-H3K4me3-5min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on H3K4Me3 5 min R1T1


title: HeLa non sync cell Cut&Run no antibody control 10 min R3T1 (matched with H3K4Me1 and Me3 R1 and H2A.Z R2)

description:
MOCR-HeLa-NS-NoAb-10min-R2_R3.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run no antibody control 10 min R3T1 (matched with H3K4Me1 and Me3 R1 and H2A.Z R2, processed files combine replicates R3 and R4 for H3K4me3 and H3K4me1 and replicates R2 and R3 for H2A.Z)


description:
MOCR-HeLa-MC-H2Az-5min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on H2A.Z 5 min R2T1


title: HeLa non sync cell Cut&Run no antibody control 10 min R4T1 (matched with H3K4Me1 and Me3 R2)

description:
MOCR-HeLa-NS-NoAb-10min-R3_R4.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run no antibody control 10 min R4T1 (matched with H3K4Me1 and Me3 R2,, processed files combine replicates R3 and R4 for H3K4me3 and H3K4me1)


description:
MOCR-HeLa-NS-H3K4me3-30min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on H3K4Me3 30 min R1T1


description:
MOCR-HeLa-NS-H3K4me1-5min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on H3K4Me1 5 min R2T1


description:
MOCR-HeLa-NS-H3K4me1-30min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on H3K4Me1 30 min R2T1


title: HeLa non sync cell Cut&Run no antibody control 5 min R3T1 (matched with H3K4Me1 and Me3 R1 and H2A.Z R2)

description:
MOCR-HeLa-NS-NoAb-5min-R2_R3.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run no antibody control 5 min R3T1 (matched with H3K4Me1 and Me3 R1 and H2A.Z R2, processed files combine replicates R3 and R4 for H3K4me3 and H3K4me1 and replicates R2 and R3 for H2A.Z)


title: HeLa non sync cell Cut&Run no antibody control 5 min R4T1 (matched with H3K4Me1 and Me3 R2)

description:
MOCR-HeLa-NS-NoAb-5min-R3_R4.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run no antibody control 5 min R4T1 (matched with H3K4Me1 and Me3 R2, processed files combine replicates R3 and R4 for H3K4me3 and H3K4me1)


title: HeLa non sync cell Cut&Run no antibody control 30 min R3T1 (matched with H3K4Me1 and Me3 R1 and H2A.Z R2)

description:
MOCR-HeLa-NS-NoAb-30min-R2_R3.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run no antibody control 30 min R3T1 (matched with H3K4Me1 and Me3 R1 and H2A.Z R2, processed files combine replicates R3 and R4 for H3K4me3 and H3K4me1 and replicates R2 and R3 for H2A.Z)


description:
MOCR-HeLa-NS-H3K4me3-10min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on H3K4Me3 10 min R2T1


description:
MOCR-HeLa-NS-H3K4me3-30min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on H3K4Me3 30 min R2T1


description:
MOCR-HeLa-NS-H3K4me3-5min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on H3K4Me3 5 min R2T1


title: HeLa Mitotic Cell Cut&Run no antibody control 10 min R4T1 (matched with H3K4Me1 and Me3 R2)

description:
MOCR-HeLa-MC-NoAb-10min-R3_R4.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run no antibody control 10 min R4T1 (matched with H3K4Me1 and Me3 R2, processed files combine replicates R3 and R4 for H3K4me3 and H3K4me1)


description:
MOCR-HeLa-NS-H2Az-10min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on H2A.Z 10 min R2T1


description:
MOCR-HeLa-NS-H3K4me1-10min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on H3K4Me1 10 min R1T1


title: HeLa non sync cell Cut&Run no antibody control 30 min R4T1 (matched with H3K4Me1 and Me3 R2)

description:
MOCR-HeLa-NS-NoAb-30min-R3_R4.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run no antibody control 30 min R4T1 (matched with H3K4Me1 and Me3 R2, processed files combine replicates R3 and R4 for H3K4me3 and H3K4me1)


title: HeLa Mitotic Cell Cut&Run no antibody control 5 min R4T1 (matched with H3K4Me1 and Me3 R2)

description:
MOCR-HeLa-MC-NoAb-5min-R3_R4.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run no antibody control 5 min R4T1 (matched with H3K4Me1 and Me3 R2, processed files combine replicates R3 and R4 for H3K4me3 and H3K4me1)


description:
MOCR-HeLa-MC-H3K4me1-5min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on H3K4Me1 5 min R2T1


title: HeLa Mitotic Cell Cut&Run no antibody control 30 min R4T1 (matched with H3K4Me1 and Me3 R2)

description:
MOCR-HeLa-MC-NoAb-30min-R3_R4.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run no antibody control 30 min R4T1 (matched with H3K4Me1 and Me3 R2, processed files combine replicates R3 and R4 for H3K4me3 and H3K4me1)


description:
MOCR-HeLa-NS-H3K4me1-10min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on H3K4Me1 10 min R2T1


description:
MOCR-HeLa-MC-H3K4me1-30min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on H3K4Me1 30 min R2T1


description:
MOCR-HeLa-MC-H3K4me1-10min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on H3K4Me1 10 min R2T1


description:
MOCR-HeLa-MC-H3K4me3-10min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on H3K4Me3 10 min R2T1


description:
MOCR-HeLa-MC-H3K4me3-5min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on H3K4Me3 5 min R2T1


description:
MOCR-HeLa-MC-H3K4me3-30min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on H3K4Me3 30 min R2T1


title: B2H_rep0

city: Durham

first: Sudarshan

last: Rajagopal

state: North Carolina

address: 303 Research Drive

department: Department of Medicine

country: USA

institute: Duke University Medical Center

description: β-arrestin 2 -/-

library_source: transcriptomic

data_processing:
Six libraries with different indices were pooled in a lane and sequenced (50bp single end read) by Illumina HiSeq 2000/2500 platform.
Raw reads of RNAseq were filtered. Read quality was checked for each sample using FastQC. Clean reads were aligned to the mouse genome (mm10) by web-based Galaxy platform using TopHat (Genomics Virtual Lab).
Differential gene expression was analyzed by CuffDiff.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized_FPKM

organism: Mus musculus

source_name: Lung

extract_protocol:
Total RNA was extracted from ~30 mg of fresh frozen lung tissue by using the RNeasy Mini plus Kit (Qiagen, Cat # 74134). RNA quality was analyzed with an Agilent 2100 Bioanalyzer (Agilent Technologies).
Enrichment of mRNA was performed by NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat # E7490S) from 1 ug of mRNA. cDNA libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (Cat # E7530S).

treatment_protocol: Eight to twelve weeks old male mice were kept at normal altitude (normoxia, PAO2 ~ 150 mmHg) or a pressure corresponding to 18000 feet (hypoxia, PAO2 ~ 70 mmHg) for 4 weeks.

tag: strain

tag: genotype

value: beta-arrestin 2 -/-

tag: tissue

value: Lung

tag: treatment

value: Hypoxia (H)

tag: age

value: 12-16 weeks


title: B2H_rep1

description: β-arrestin 2 -/-


title: B2H_rep2

description: β-arrestin 2 -/-


title: B2N_rep2

description: β-arrestin 2 -/-

value: Normoxia (N)


title: B2N_rep0

description: β-arrestin 2 -/-


title: B1H_rep2

description: β-arrestin 1 -/-

value: beta-arrestin 1 -/-


title: B1H_rep0

description: β-arrestin 1 -/-


title: B2N_rep1

description: β-arrestin 2 -/-


title: B1H_rep1

description: β-arrestin 1 -/-


title: B1N_rep2

description: β-arrestin 1 -/-


title: B1N_rep1

description: β-arrestin 1 -/-


title: WTH_rep1

value: wild type


title: WTH_rep2


title: B1N_rep0

description: β-arrestin 1 -/-


title: WTH_rep0


title: WTN_rep0


title: WTN_rep2


title: WTN_rep1


title: 3D-CCM2-6hrs

city: Atlanta

first: Denis

last: Tsygankov

state: GA

address: North Ave NW

department: Biomedical Engineering

institute: Georgia Institute of Technology

data_processing:
Quality control and adapter trimming: BBDuk, BBTools package Version 35.92. Values of parameters: ktrim=r k=27 hdist=1 edist=0 mink=4 qtrim=rl trimq=30 minlength=50 qin=33
Transcriptome alignment: TopHat2 v2.1.1 (human genome build GRCh38). Values of parameters: --no-coverage-search --b2-very-sensitive --no-novel-juncs
Reads counting and ranking of differentially expressed genes: GFOLD. Cutoff for generalized fold change: 0.3. Comand for reads counting: gfold count -ann [genome annotation] -tag [SAM file with mapped reads] -o [output file]. Command for identification of differentially expressed genes: gfold diff -s1 [reads counts for sample 1] -s2 [reads counts for sample 2] -suf .read_cnt -o [output_file.diff]
Genome_build: Human genome GRCh38
Supplementary_files_format_and_content: Tab-delimited text files generated by GFOLD, include GeneSymbols, GeneNames, GFOLD values, RPKM values and other information

growth_protocol: Human umbilical cord endothelial cells (HUVEC) were maintained in EGM-2 medium at 37°C/5% CO2 and passaged every 3 to 4 days for up to 6 passages at a 1:5 sub-culturing ratio.  For tube formation experiments, 4.5-5x103 cells were plated into each well of angiogenesis µ-slides coated with 10 µl of growth factor reduced phenol red-free Matrigel, and incubated for up to 18 hrs.

extract_protocol:
Total RNA was extracted using RNeasy extraction kit (Qiagen, Valencia, CA, USA) following the manufacturer’s protocol. RNA was reverse-transcribed using the high-capacity cDNA kit (Life Technologies, Carlsbad, CA, USA). The analysis was done StepOnePlus™ Real-Time PCR System (Applied Biosystems, Foster City, CA), and the level of transcripts was quantified using TaqMan probes (Applied Biosystems): KRIT1 Hs01090981_m1; CCM2 Hs01123856_m1; PDCD10 Hs00200578_m1; TBP Hs00427620_m1. Fold change in gene expression was determined using ΔΔCt algorithm.
HUVEC cells were transfected with non-targeting siRNA or siRNA against krit1, ccm2, and pdcd10 genes as described above. 48 hrs after transfection cells were plated on growth factor reduced Matrigel, and incubated for 2 hrs (initial stages of endothelial tubule formation) or 6 hrs (advanced stages of tubule formation). Total RNA was isolated from each culture (control, and siRNA against krit1, ccm2, and pdcd10) cells cultured on the 2D (Matrigel-coated plastic), and in 3D (Matrigel) substrate, using RNAeasy kit (Qiagen, Valencia, CA, USA) per the manufacturer’s instructions. RNA quality control was performed by studying the relative intensity of 18s and 28s rRNA bands using an Agilent 2100 Bioanalyzer and RNA6000 Pico LabChip Kit (Agilent Technologies). Between 200ng and 1ug of RNA were used directly in the TruSeq mRNA stranded kit (Illumina, San Diego, CA) for isolation of mRNA from total RNA, generation of ds cDNA and preparation of libraries. The cDNA was quantified using the Qubit HS DNA kit (Thermo Fisher Scientific, Rockford, IL), and cDNA libraries were prepared using a TruSeq Stranded mRNA library prep kit (Illumina, San Diego, CA). The samples were run on a NextSeq 500 instrument (Illumina, San Diego, CA) with a read length of PE75bp.

treatment_protocol: Cells were transfected with 50 nM siRNA against human krit1 (LQ-003825-00), ccm2 (LG-014728-01), and pdcd10 (LQ-004436-00), or control non-targeting siRNA (D-001810-01-05), using DharmaFECT 4 transfection reagent. Gene expression was analyzed at 48 hrs, protein expression at 72 hrs after transfection, and phenotypic studies were conducted 60-72 hrs after transfection.

value: HUVEC

tag: sirna for gene knockdown

tag: substrate for cultivation

value: Matrigel

tag: time of incubation

value: 6 hours


title: 1001702104_K23

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

country: Australia

institute: University of New South Wales

data_processing:
bcl2fastq demux
STAR mapping
Htseq-count 0.7+ gene counting
Stampy virus mapping
Custom script for filtering virus reads
Genome_build: grch38
Supplementary_files_format_and_content: One TSV for each sample containing the counts of gene expression.

source_name: blood (PBMCs)

extract_protocol:
No extraction, single cells are sorted into 0.4ul lysis buffer
Cells are lysed in lysis buffer containing Triton X-100, then RT using template switching oligo and preamplification for 21 cycles as in SmartSeq2 is performed. Cells with different levels of intracellular virus are cherry picked and sequencing libraries are made using illumina’s Nextera XT kit.

value: blood

tag: patient id

value: monocyte

tag: Sex

value: F

tag: diseaseseverity

value: severe dengue

tag: numberhumanuniquelymappedreads

tag: numbervirusreads


title: 1001702104_K5

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title: 1001702104_J13

value: cDC


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