title: 353_Wang_HiC_BWX4515_1mM_120m

description: genomic DNA

value: parS{delta}9 no a.b., -91deg parS (loxP-kan-loxP), yhdG::Phyperspank-(optRBS)-sirA (phleo)


title: RNA0288_APC74_Plate_1_26

status: Public on Jun 10 2021

type: SRA

city: Singapore

first: Florent

last: Ginhoux

address: 8A Biomedical Grove, Immunos Building, Level 3

country: Singapore

institute: Singapore Immunology Network (SIgN), A*STAR

description: Human Skin RNA-seq

library_source: transcriptomic

data_processing:
Raw reads were aligned to the human reference genome GRCh38 from GENCODE using RSEM program version 1.3.0 with default parameters. Gene expression values in transcripts per million (TPM) were calculated using the same RSEM program and the human GENCODE annotation version 25.
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Human Skin

extract_protocol:
We index-sorted cutaneous DC and monocyte-macrophages using flow cytometry based on expression of characteristic patterns of surface markers/proteins into 96 well plates containing Lysis buffer.
Single-cell cDNA libraries were prepared using the Smart-seq v2 protocol with the following modifications: (i) 1 mg/mL BSA Lysis buffer (Ambion Thermo Fisher Scientific, Waltham, MA, USA); and (ii) 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit. The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip. All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq 4000 system for about 1 million reads per sample.

tag: tissue

value: Skin

tag: donor

tag: condition

value: PSO


title: RNA0288_APC74_Plate_1_25

description: Human Skin RNA-seq


title: 367_Wang_ChIPSMC_BWX5066rep2_1mM_060m

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

country: USA

institute: Indiana University at Bloomington

description: ChIP using anti-SMC antibodies

library_source: genomic

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.  For ChIP-seq, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) genome was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of Bacillus subtilis (PY79) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: NC_022898.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. 10kb bins of B. subtilis genome. normalized Hi-C interaction scores.
Supplementary_files_format_and_content: Files ending with .csv: comma-separated values files of ChIP-seq results. genome position; reads at each position.

molecule: genomic DNA

organism: Bacillus subtilis PY79

source_name: Bacillus subtilis PY79

growth_protocol: Bacillus subtilis strains were derived from the prototrophic strain PY79 (Youngman et al 1983, PMID: 6300908). Cells were grown in defined rich medium (CH) (Harwood and Cutting 1990, Molecular Biological Methods for Bacillus) at specified temperature.

extract_protocol:
Hi-C experiments were performed using HindIII according to previous publications (Le et al, 2013, PMID: 24158908; Wang et al 2015, PMID: 26253537). ChIP-seq experiments were performed using anti-SMC antibodies according to previous publication (Graham et al 2014, PMID: 24829297).
Standard library construction protocol was used for Illumina Nextseq550 sequencing platforms. Illumina Truseq indexes were used.

treatment_protocol:
Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 60 min, fixed by 3% formaldehyde for 30min at room temperature
None

tag: growth

value: CH, 37 C, 1mM IPTG for 60 min

tag: genotype

value: parS{delta}9 no a.b., -27deg parS, -59deg parS no a.b., -91deg parS (loxP-kan-loxP), yhdG::Phyperspank-(optRBS)-sirA (phleo)


title: RNA0288_APC74_Plate_1_09

description: Human Skin RNA-seq


title: RNA0288_APC74_Plate_1_08

description: Human Skin RNA-seq


title: 363_Wang_HiC_BWX4359_1mM_060m

description: genomic DNA

value: yhdG::Phyperspank-(optRBS)-sirA (phleo)


title: RNA0288_APC74_Plate_1_14

description: Human Skin RNA-seq


title: RNA0288_APC74_Plate_1_22

description: Human Skin RNA-seq


title: RNA0288_APC74_Plate_1_07

description: Human Skin RNA-seq


title: 349_Wang_HiC_BWX4475_1mM_090m

description: genomic DNA

treatment_protocol:
Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 90 min, fixed by 3% formaldehyde for 30min at room temperature
None

value: CH, 37 C, 1mM IPTG for 90 min

value: parS{delta}9 no a.b., -59deg parS (loxP-kan-loxP), yhdG::Phyperspank-(optRBS)-sirA (phleo)


title: RNA0288_APC74_Plate_1_03

description: Human Skin RNA-seq


title: RNA0288_APC74_Plate_1_02

description: Human Skin RNA-seq


title: 346_Wang_HiC_BWX4885

description: genomic DNA

treatment_protocol:
Cells were growing in CH medium at 37˚C, fixed by 3% formaldehyde for 30min at room temperature
None

value: CH, 37 C

value: parS{delta}9 no a.b., -91deg parS no a.b. , -117deg parS (loxP-kan-loxP)


title: 360_Wang_HiC_BWX5132_1mM_120m

description: genomic DNA

treatment_protocol:
Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 120 min, fixed by 3% formaldehyde for 30min at room temperature
None

value: CH, 37 C, 1mM IPTG for 120 min

value: parS{delta}9 no a.b., -27deg parS, -59deg parS (loxP-kan-loxP), amyE::Phyperspank-(optRBS)-smc (spec), yhdG::Phyperspank-(optRBS)-scpAB (phleo), yvbJ::Phyperspank-(optRBS)-sirA (erm)


title: RNA0288_APC74_Plate_1_18

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_96

description: Human Skin RNA-seq

value: AD


title: 344_Wang_HiC_BWX4870

description: genomic DNA

value: parS{delta}9 no a.b., -59deg parS no a.b., -91deg parS (loxP-kan-loxP)


title: RNA0288_APC74_Plate_1_17

description: Human Skin RNA-seq


title: 358_Wang_HiC_BWX5132_1mM_060m

description: genomic DNA


title: 342_Wang_HiC_BWX4424

description: genomic DNA

value: parS{delta}9 no a.b., -27deg parS, -117deg parS (loxP-kan-loxP)


title: RNA0288_APC74_Plate_1_05

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_94

description: Human Skin RNA-seq


title: 357_Wang_HiC_BWX4892_1mM_120m

description: genomic DNA

value: parS{delta}9 no a.b., -91deg parS no a.b. , -117deg parS (loxP-kan-loxP), yhdG::Phyperspank-(optRBS)-sirA (phleo)


title: 356_Wang_HiC_BWX4892_1mM_090m

description: genomic DNA


title: 364_Wang_HiC_BWX4359_1mM_090m

description: genomic DNA


title: RNA0288_APC74_Plate_1_23

description: Human Skin RNA-seq


title: 340_Wang_HiC_BWX4422

description: genomic DNA

value: parS{delta}9 no a.b., -27deg parS, -59deg parS (loxP-kan-loxP)


title: RNA0288_APC73_Plate_7_90

description: Human Skin RNA-seq


title: 343_Wang_HiC_BWX4425

description: genomic DNA

value: parS{delta}9 no a.b., -27deg parS, -153deg parS (loxP-kan-loxP)


title: 362_Wang_HiC_BWX5066_1mM_120m

description: genomic DNA


title: 338_Wang_input_BWX4462_1mM_120m

description: genomic DNA, input sample (no antibodies)

value: parS{delta}9 no a.b., -27deg parS, -59deg parS (loxP-kan-loxP), yhdG::Phyperspank-(optRBS)-sirA (phleo)

tag: restriction enzyme


title: RNA0288_APC73_Plate_7_86

description: Human Skin RNA-seq

value: Skin


title: 351_Wang_HiC_BWX4515_1mM_060m

description: genomic DNA

value: CH, 37 C, 1mM IPTG for 60 min

value: parS{delta}9 no a.b., -91deg parS (loxP-kan-loxP), yhdG::Phyperspank-(optRBS)-sirA (phleo)


title: RNA0288_APC73_Plate_7_85

description: Human Skin RNA-seq


title: RNA0288_APC74_Plate_1_15

description: Human Skin RNA-seq

value: PSO


title: 350_Wang_HiC_BWX4475_1mM_120m

description: genomic DNA


title: 333_Wang_ChIPSMC_BWX4462_1mM_060m

description: ChIP using anti-SMC antibodies


title: RNA0288_APC73_Plate_7_80

description: Human Skin RNA-seq


title: 352_Wang_HiC_BWX4515_1mM_090m

description: genomic DNA

value: CH, 37 C, 1mM IPTG for 90 min


title: RNA0288_APC74_Plate_1_04

description: Human Skin RNA-seq


title: 348_Wang_HiC_BWX5066_0IPTG

description: genomic DNA

value: parS{delta}9 no a.b., -27deg parS, -59deg parS no a.b., -91deg parS (loxP-kan-loxP), yhdG::Phyperspank-(optRBS)-sirA (phleo)


title: 347_Wang_HiC_BWX4891

description: genomic DNA

value: CH, 37 C

value: parS{delta}9 no a.b., -59deg parS no a.b., -91deg parS no a.b., -117deg parS (loxP-kan-loxP)


title: 345_Wang_HiC_BWX4429

description: genomic DNA

value: parS{delta}9 no a.b., -59deg parS no a.b., -117deg parS (loxP-kan-loxP)


title: RNA0288_APC74_Plate_1_01

description: Human Skin RNA-seq


title: 329_Wang_HiC_BWX4927_1mM_060m

description: genomic DNA

value: parS{delta}9 no a.b., -59deg parS no a.b., -91deg parS no a.b., -117deg parS (loxP-kan-loxP), yhdG::Phyperspank-(optRBS)-sirA (phleo)


title: RNA0288_APC73_Plate_7_95

description: Human Skin RNA-seq

value: AD


title: 327_Wang_HiC_BWX4482_1mM_060m

description: genomic DNA

value: parS{delta}9 no a.b., -59deg parS no a.b., -117deg parS (loxP-kan-loxP), yhdG::Phyperspank-(optRBS)-sirA (phleo)


title: 339_Wang_HiC_BWX4428

description: genomic DNA

value: parS{delta}9 no a.b., -59deg parS no a.b., -94deg parS (loxP-kan-loxP)


title: RNA0288_APC73_Plate_7_89

description: Human Skin RNA-seq


title: 337_Wang_input_BWX4462_1mM_090m


title: 330_Wang_HiC_BWX5066_1mM_060m

description: genomic DNA


title: 326_Wang_HiC_BWX4883_1mM_060m

description: genomic DNA

value: parS{delta}9 no a.b., -59deg parS no a.b., -91deg parS (loxP-kan-loxP), yhdG::Phyperspank-(optRBS)-sirA (phleo)


title: 325_Wang_HiC_BWX4481_1mM_060m

description: genomic DNA

value: parS{delta}9 no a.b., -27deg parS, -153deg parS (loxP-kan-loxP), yhdG::Phyperspank-(optRBS)-sirA (phleo)


title: 341_Wang_HiC_BWX4423

description: genomic DNA

value: parS{delta}9 no a.b., -27deg parS, -94deg parS (loxP-kan-loxP)


title: RNA0288_APC73_Plate_7_76

description: Human Skin RNA-seq


title: 336_Wang_input_BWX4462_1mM_060m

value: parS{delta}9 no a.b., -27deg parS, -59deg parS (loxP-kan-loxP), yhdG::Phyperspank-(optRBS)-sirA (phleo)


title: RNA0288_APC73_Plate_7_93

description: Human Skin RNA-seq

value: Skin


title: RNA0288_APC73_Plate_7_71

description: Human Skin RNA-seq


title: 335_Wang_ChIPSMC_BWX4462_1mM_120m

description: ChIP using anti-SMC antibodies

value: CH, 37 C, 1mM IPTG for 120 min


title: RNA0288_APC73_Plate_7_82

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_67

description: Human Skin RNA-seq


title: 322_Wang_HiC_BWX4462_1mM_060m

description: genomic DNA

value: CH, 37 C, 1mM IPTG for 60 min


title: 321_Wang_HiC_BWX4492_xyl30m_1mM_30m

description: genomic DNA

treatment_protocol:
Cells were growing in CH medium at 37˚C, xylose was added to 0.5% final concentration for 30 min, then IPTG was added to 1mM final concentration for 30 min, fixed by 3% formaldehyde for 30min at room temperature
None

value: CH, 37 C, 0.5% xylose for 30 min, then 1mM IPTG for 30 min

value: parS{delta}9 no a.b., -94deg parS no a.b., {delta}parB({delta}parS) (loxP-spec-loxP), yvbJ::Pspank-(optRBS)-parB({delta}parS) (cat), yhdG::Pxyl-(optRBS)-sirA (phleo)


title: RNA0288_APC73_Plate_7_91

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_64

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_81

description: Human Skin RNA-seq


title: 332_Wang_HiC_BWX4462_1mM_120m

description: genomic DNA


title: 334_Wang_ChIPSMC_BWX4462_1mM_090m

description: ChIP using anti-SMC antibodies

value: CH, 37 C, 1mM IPTG for 90 min


title: RNA0288_APC73_Plate_7_79

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_77

description: Human Skin RNA-seq


title: 331_Wang_HiC_BWX4462_1mM_090m

description: genomic DNA


title: RNA0288_APC73_Plate_7_62

description: Human Skin RNA-seq


title: 328_Wang_HiC_BWX4892_1mM_060m

description: genomic DNA

value: parS{delta}9 no a.b., -91deg parS no a.b. , -117deg parS (loxP-kan-loxP), yhdG::Phyperspank-(optRBS)-sirA (phleo)


title: RNA0288_APC73_Plate_7_61

description: Human Skin RNA-seq


title: 316_Wang_HiC_BWX4492_xyl30m_1mM_00m

description: genomic DNA

treatment_protocol:
Cells were growing in CH medium at 37˚C, xylose was added to 0.5% final concentration for 30 min, fixed by 3% formaldehyde for 30min at room temperature
None

value: CH, 37 C, 0.5% xylose for 30 min

value: HindIII


title: RNA0288_APC73_Plate_7_74

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_73

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_72

description: Human Skin RNA-seq


title: 324_Wang_HiC_BWX4480_1mM_060m

description: genomic DNA

value: parS{delta}9 no a.b., -27deg parS, -117deg parS (loxP-kan-loxP), yhdG::Phyperspank-(optRBS)-sirA (phleo)


title: RNA0288_APC73_Plate_7_75

description: Human Skin RNA-seq

value: AD


title: RNA0288_APC73_Plate_7_56

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_70

description: Human Skin RNA-seq


title: 319_Wang_HiC_BWX4492_xyl30m_1mM_20m

description: genomic DNA

treatment_protocol:
Cells were growing in CH medium at 37˚C, xylose was added to 0.5% final concentration for 30 min, then IPTG was added to 1mM final concentration for 20 min, fixed by 3% formaldehyde for 30min at room temperature
None

value: CH, 37 C, 0.5% xylose for 30 min, then 1mM IPTG for 20 min


title: 311_Wang_HiC_BWX4491_xyl30m_1mM_10m

description: genomic DNA

treatment_protocol:
Cells were growing in CH medium at 37˚C, xylose was added to 0.5% final concentration for 30 min, then IPTG was added to 1mM final concentration for 10 min, fixed by 3% formaldehyde for 30min at room temperature
None

value: CH, 37 C, 0.5% xylose for 30 min, then 1mM IPTG for 10 min

value: parS{delta}9 no a.b., -59deg parS no a.b., {delta}parB({delta}parS) (loxP-spec-loxP), yvbJ::Pspank-(optRBS)-parB({delta}parS) (cat), yhdG::Pxyl-(optRBS)-sirA (phleo)


title: RNA0288_APC73_Plate_7_50

description: Human Skin RNA-seq


title: 310_Wang_HiC_BWX4491_xyl30m_1mM_00m

description: genomic DNA


title: 323_Wang_HiC_BWX4479_1mM_060m

description: genomic DNA

value: parS{delta}9 no a.b., -27deg parS, -94deg parS (loxP-kan-loxP), yhdG::Phyperspank-(optRBS)-sirA (phleo)


title: RNA0288_APC73_Plate_7_48

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_51

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_63

description: Human Skin RNA-seq


title: 317_Wang_HiC_BWX4492_xyl30m_1mM_10m

description: genomic DNA


title: 308_Wang_HiC_BWX4493_xyl30m_1mM_25m

description: genomic DNA

treatment_protocol:
Cells were growing in CH medium at 37˚C, xylose was added to 0.5% final concentration for 30 min, then IPTG was added to 1mM final concentration for 25 min, fixed by 3% formaldehyde for 30min at room temperature
None

value: CH, 37 C, 0.5% xylose for 30 min, then 1mM IPTG for 25 min

value: parS{delta}9 no a.b., -59deg parS no a.b., -94deg parS (loxP-kan-loxP), {delta}parB({delta}parS) (loxP-spec-loxP), yvbJ::Pspank-(optRBS)-parB({delta}parS) (cat), yhdG::Pxyl-(optRBS)-sirA (phleo)


title: 318_Wang_HiC_BWX4492_xyl30m_1mM_15m

description: genomic DNA

treatment_protocol:
Cells were growing in CH medium at 37˚C, xylose was added to 0.5% final concentration for 30 min, then IPTG was added to 1mM final concentration for 15 min, fixed by 3% formaldehyde for 30min at room temperature
None

value: CH, 37 C, 0.5% xylose for 30 min, then 1mM IPTG for 15 min


title: 320_Wang_HiC_BWX4492_xyl30m_1mM_25m

description: genomic DNA


title: RNA0288_APC73_Plate_7_60

description: Human Skin RNA-seq

value: Skin


title: RNA0288_APC73_Plate_7_58

description: Human Skin RNA-seq


title: 312_Wang_HiC_BWX4491_xyl30m_1mM_15m

description: genomic DNA


title: RNA0288_APC73_Plate_7_68

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_44

description: Human Skin RNA-seq


title: 307_Wang_HiC_BWX4493_xyl30m_1mM_20m

description: genomic DNA


title: 314_Wang_HiC_BWX4491_xyl30m_1mM_25m

description: genomic DNA


title: 302_Wang_HiC_BWX4475_1mM_060m

description: genomic DNA

value: CH, 37 C, 1mM IPTG for 60 min

value: parS{delta}9 no a.b., -59deg parS (loxP-kan-loxP), yhdG::Phyperspank-(optRBS)-sirA (phleo)


title: 313_Wang_HiC_BWX4491_xyl30m_1mM_20m

description: genomic DNA


title: RNA0288_APC73_Plate_7_54

description: Human Skin RNA-seq


title: 315_Wang_HiC_BWX4491_xyl30m_1mM_30m

description: genomic DNA

value: CH, 37 C, 0.5% xylose for 30 min, then 1mM IPTG for 30 min


title: RNA0288_APC73_Plate_7_55

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_37

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_39

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_53

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_35

description: Human Skin RNA-seq


title: 309_Wang_HiC_BWX4493_xyl30m_1mM_30m

description: genomic DNA


title: RNA0288_APC73_Plate_7_46

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_32

description: Human Skin RNA-seq


title: 590043

type: RNA

city: San Francisco

first: Denise

middle: M

last: Wolf

state: CA

address: 2340 Sutter st

institute: University of California, San Francisco

hyb_protocol: Performed by Agendia Inc (Irvine, CA)

scan_protocol: Performed by Agendia Inc (Irvine, CA)

data_processing: gNormalizedSignal  (log2)  data, as provided in the raw files on each patient by Agendia, was extracted.  All values indicated for non-confirmity, as indicated by the 'gIsFeatNonUnifOL' column in the raw files, are NA'd out. Probeset level data per array were mean-collapsed to the gene level. Gene level data was used in the analysis.

source_name: Breast cancer biopsy (pre-treatment)

label_protocol: Performed by Agendia Inc (Irvine, CA)

extract_protocol: Performed by Agendia Inc (Irvine, CA)

value: breast cancer

tag: hr

tag: pcr

tag: mp

tag: arm

value: durvalumab/olaparib


title: RNA0288_APC73_Plate_7_45

description: Human Skin RNA-seq


title: 306_Wang_HiC_BWX4493_xyl30m_1mM_15m

description: genomic DNA


title: RNA0288_APC73_Plate_7_29

description: Human Skin RNA-seq


title: 472589

value: control


title: 305_Wang_HiC_BWX4493_xyl30m_1mM_10m

description: genomic DNA

value: HindIII


title: RNA0288_APC73_Plate_7_43

description: Human Skin RNA-seq


title: 304_Wang_HiC_BWX4493_xyl30m_1mM_00m

description: genomic DNA

value: CH, 37 C, 0.5% xylose for 30 min


title: RNA0288_APC73_Plate_7_41

description: Human Skin RNA-seq

value: AD


title: RNA0288_APC73_Plate_7_24

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_30

description: Human Skin RNA-seq


title: 303_Wang_HiC_BWX4463_1mM_060m

description: genomic DNA

value: parS{delta}9 no a.b., -59deg parS no a.b., -94deg parS (loxP-kan-loxP), yhdG::Phyperspank-(optRBS)-sirA (phleo)


title: 425827


title: RNA0288_APC73_Plate_7_38

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_23

description: Human Skin RNA-seq


title: 301_Wang_HiC_BWX4476_1mM_060m

description: genomic DNA

value: parS{delta}9 no a.b., -94deg parS no a.b., yhdG::Phyperspank-(optRBS)-sirA (phleo)


title: RNA0288_APC73_Plate_7_36

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_20

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_25

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_34

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_33

description: Human Skin RNA-seq


title: 216384


title: 979809


title: 393548


title: 248319


title: RNA0288_APC73_Plate_7_19

description: Human Skin RNA-seq


title: 904801


title: RNA0288_APC73_Plate_7_18

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_31

description: Human Skin RNA-seq


title: 123591


title: RNA0288_APC73_Plate_7_28

description: Human Skin RNA-seq


title: 689881


title: RNA0288_APC73_Plate_7_15

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_14

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_26

description: Human Skin RNA-seq


title: 843965


title: 503905


title: RNA0288_APC73_Plate_7_12

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_10

description: Human Skin RNA-seq


title: 746954


title: RNA0288_APC73_Plate_7_08

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_07

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_22

description: Human Skin RNA-seq


title: 158712


title: 989123


title: 549018


title: 664615


title: RNA0288_APC73_Plate_7_21

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_05

description: Human Skin RNA-seq


title: 594563


title: 194365


title: 270166


title: RNA0288_APC73_Plate_7_17

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_6_45

description: Human Skin RNA-seq


title: 639629


title: RNA0288_APC73_Plate_7_16

description: Human Skin RNA-seq


title: 795270


title: 901843


title: 496973


title: RNA0288_APC73_Plate_7_09

description: Human Skin RNA-seq


title: 366264


title: 596447


title: 446038


title: RNA0288_APC73_Plate_6_40

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_7_03

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_6_54

description: Human Skin RNA-seq


title: 872208


title: 255981


title: 333236


title: RNA0288_APC73_Plate_6_46

description: Human Skin RNA-seq


title: 965961


title: 189829


title: 925619


title: RNA0288_APC73_Plate_6_42

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_6_44

description: Human Skin RNA-seq


title: 944184


title: RNA0288_APC73_Plate_6_29

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_6_41

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_6_22

description: Human Skin RNA-seq


title: 228494


title: 671271


title: RNA0288_APC73_Plate_6_39

description: Human Skin RNA-seq


title: 651891


title: RNA0288_APC73_Plate_6_35

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_6_32

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_6_26

description: Human Skin RNA-seq


title: 751468


title: RNA0288_APC73_Plate_6_16

description: Human Skin RNA-seq


title: 384454


title: 450178


title: RNA0288_APC73_Plate_6_19

description: Human Skin RNA-seq


title: 134956


title: 859920


title: 490036


title: RNA0288_APC73_Plate_6_02

description: Human Skin RNA-seq


title: 291295


title: RNA0288_APC73_Plate_6_01

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_6_17

description: Human Skin RNA-seq


title: 151964


title: RNA0288_APC73_Plate_6_08

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_6_10

description: Human Skin RNA-seq


title: 652071


title: RNA0288_APC73_Plate_6_21

description: Human Skin RNA-seq


title: 641103


title: 276279


title: RNA0288_APC73_Plate_6_04

description: Human Skin RNA-seq


title: 406818


title: 862614


title: 646371


title: RNA0288_APC73_Plate_5_95

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_88

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_81

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_94

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_6_07

description: Human Skin RNA-seq


title: 226347


title: RNA0288_APC73_Plate_5_93

description: Human Skin RNA-seq


title: 711834


title: RNA0288_APC73_Plate_5_77

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_92

description: Human Skin RNA-seq


title: 824200


title: 337915


title: RNA0288_APC73_Plate_5_73

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_75

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_79

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_76

description: Human Skin RNA-seq


title: 111922


title: 367928


title: 476800


title: RNA0288_APC73_Plate_5_72

description: Human Skin RNA-seq


title: 795775


title: 102596


title: 486129


title: 519057


title: RNA0288_APC73_Plate_5_70

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_61

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_62

description: Human Skin RNA-seq


title: 186391


title: RNA0288_APC73_Plate_5_59

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_64

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_63

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_58

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_43

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_51

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_39

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_38

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_28

description: Human Skin RNA-seq


title: 307150


title: RNA0288_APC73_Plate_5_35

description: Human Skin RNA-seq


title: 562033


title: 358563


title: 273705


title: RNA0288_APC73_Plate_5_25

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_27

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_16

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_18

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_21

description: Human Skin RNA-seq


title: 386299


title: 479488


title: 437689


title: 636524


title: 802319


title: 770991


title: 115724


title: 377798


title: 901539


title: 577470


title: 254429


title: 351319


title: 932933


title: 186848


title: RNA0288_APC73_Plate_5_36

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_13

description: Human Skin RNA-seq


title: 436924


title: RNA0288_APC73_Plate_6_38

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_12

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_10

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_08

description: Human Skin RNA-seq


title: 319218


title: RNA0288_APC73_Plate_5_07

description: Human Skin RNA-seq


title: 174495


title: 422525


title: 999675


title: 921568


title: RNA0288_APC73_Plate_5_11

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_4_95

description: Human Skin RNA-seq


title: 941319


title: 602758


title: 670384


title: RNA0288_APC73_Plate_4_84

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_4_94

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_4_91

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_4_90

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_5_05

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_4_88

description: Human Skin RNA-seq


title: 553111


title: 265106


title: 360860


title: RNA0288_APC73_Plate_4_86

description: Human Skin RNA-seq


title: 252681


title: 624668


title: RNA0288_APC73_Plate_4_89

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_4_87

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_4_83

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_4_79

description: Human Skin RNA-seq


title: 623922


title: 689692


title: RNA0288_APC73_Plate_4_75

description: Human Skin RNA-seq


title: PR-4-pretreatment

city: Beijing

first: chong

last: wei

address: Dongdan

country: China

institute: Peking Union Medical College Hospital

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.1.0 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: human PD-1(+) cell

growth_protocol: the PD-1(+) cells were isolated from peripheral blood of PTCL patients

extract_protocol:
Total RNA was extracted from PD-1(+) cells by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
Hiseq Sequencing Protocol

treatment_protocol: Blood samples were collected both at baseline and at the end of first-line treatment. Flow cytometry analysis was performed to ensure that there were no tumor cells in the peripheral blood. Peripheral blood mononuclear cells (PBMCs) were isolated from blood samples using the Ficoll-Hypaque density centrifugation method. PD-1(+) cells were isolated from PBMCs using the magnetic-activated cell sorting (MACS) method according to the manufacturer’s instructions (Miltenyi Biotech, Germany). Briefly, PBMCs were first incubated with 20 µL anti-CD279-PE antibodies (Miltenyi Biotech, Germany; 130-117-384) at 4°C for 20 min. After washing and centrifugation, the cells were incubated with anti-PE microbeads (Miltenyi Biotech, Germany; 130‐048‐801). The labeled cell suspension was then filled into the reservoir of a large-volume separation column (Miltenyi Biotech, Germany) placed in a magnetic field. After removing the column from the magnetic field, PD-1(+) cells were eluted by flushing the column with PBS buffer. The collected PD-1(+) cell suspension was counted and prepared for mRNA extraction.

tag: treatment

value: pretreatment

tag: cell type

value: peripheral blood PD-1(+) cells

tag: patient diagnosis

value: Peripheral T‐cell lymphoma

tag: remission group

value: incomplete remission


title: RNA0288_APC73_Plate_4_85

description: Human Skin RNA-seq


title: PR-3-postreatment

value: postreatment


title: 437918


title: RNA0288_APC73_Plate_4_73

description: Human Skin RNA-seq

value: Skin


title: RNA0288_APC73_Plate_4_80

description: Human Skin RNA-seq


title: 143063


title: 342844


title: RNA0288_APC73_Plate_4_82

description: Human Skin RNA-seq


title: 679271


title: PR-4-postreatment


title: RNA0288_APC73_Plate_4_63

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_4_68

description: Human Skin RNA-seq


title: 178297


title: RNA0288_APC73_Plate_4_76

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_4_78

description: Human Skin RNA-seq


title: PR-3-pretreatment


title: CR-5-postreatment

value: complete remission


title: PR-2-postreatment


title: RNA0288_APC73_Plate_4_54

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_4_56

description: Human Skin RNA-seq


title: CR-5-pretreatment


title: 856496


title: PR-2-pretreatment


title: PR-1-postreatment


title: 524763


title: PR-1-pretreatment


title: CR-4-postreatment


title: RNA0288_APC73_Plate_4_53

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_4_44

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_4_74

description: Human Skin RNA-seq


title: CR-3-pretreatment


title: RNA0288_APC73_Plate_4_51

description: Human Skin RNA-seq


title: CR-1-postreatment


title: RNA0288_APC73_Plate_4_48

description: Human Skin RNA-seq


title: CR-1-pretreatment


title: CR-4-pretreatment


title: CR-2-pretreatment


title: RNA0288_APC73_Plate_4_41

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_4_33

description: Human Skin RNA-seq


title: TG-3

city: New York

first: Thomas

last: Zwaka

state: NY

address: 1425 Madison Ave

department: CDRB

institute: Icahn School of Medicine

description:
TG-3
L7-Ronin  Replicate 3: Gene expression data of cerebellum overexpressing L7-Ronin transgene

data_processing:
[Read generation]  42-nt sequence reads were generated using Illumina NextSeq 500.
[Mapping]  Fragments were mapped to the genome using the STAR algorithm with default settings. Fragments were assigned to overlapping predefined genomic features of interest (e.g. genes). Only read pairs that have both ends aligned were counted. Read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands were discarded.  At least 25 bp overlapping bases were required in a fragment for read assignment. The gene annotations were obtained from the Subread package. These annotations were originally from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene. Genes with the same Entrez gene identifiers were also merged into one gene..
[Normalization]  Data were normalized correcting for library size using the median-of-ratios method. Multiple testing adjustment and independent filtering were performed to filter out genes with low counts.  Average counts of each gene (i.e. baseMean), across all samples, are used as filter criterion, and all genes with average normalized counts below a filtering threshold from multiple testing adjustment are omitted. This filtering threshold was automatically determined to maximize detection power (i.e. maximize the number of differential genes detected) at a specified FDR.
[Differential analysis]  Differential genes were detected by DESeq2 at 0.1 (or 10%) FDR (i.e. adjusted p-value). Otherwise, differential genes were defined using shrunkenLog2FC (default cutoff is 0.3) when there is no replication data.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited txt file with DESeq2 normalized counts for all genes: Column 1 is the Entrez gene id, column 2 is the gene symbol. Columns 3-6: used for assigning gene counts (Chromosome, Start, End, Strand), Column 7: total number of non-overlapping bases included in all exons belonging to the same gene,  Columns  8-13: Normalized reads for samples as indicated. Column 14 and 15: averages of normalized counts for each group of replicates. column 16: average of normalized counts across all samples; column 17 and 18: log2 fold changes (i.e. log2 FC) before and after DESeq2’s shrinkage (i.e. rawLog2FC and shrunkenLog2FC). To avoid division by zero, we added a pseudo count “one” to the averages of normalized counts of the two comparison groups to generate the raw log2 fold changes (i.e. rawLog2FC); column 19-22: the DESeq2’s test statistics – including standard errors, test statistics, p-values and adjusted p-values after multiple-test adjustment.

organism: Mus musculus

source_name: cerebellum

extract_protocol:
Qiagen RNeasy
Illumnina TruSeq Stranded mRNA Library kit

value: L7-Ronin transgene

value: cerebellum


title: RNA0288_APC73_Plate_4_30

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_4_32

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_4_27

description: Human Skin RNA-seq


title: TG-2

description:
TG-2
L7-Ronin  Replicate 2: Gene expression data of cerebellum overexpressing L7-Ronin transgene


title: TG-1

description:
TG-1
L7-Ronin  Replicate 1: Gene expression data of cerebellum overexpressing L7-Ronin transgene


title: RNA0288_APC73_Plate_4_26

description: Human Skin RNA-seq


title: WT-3

description:
WT-3
Wildtype Replicate 3: Gene expression data of wildtype cerebellum

value: wildtype


title: CR-3-postreatment


title: RNA0288_APC73_Plate_4_23

description: Human Skin RNA-seq


title: WT-2

description:
WT-2
Wildtype Replicate 2: Gene expression data of wildtype cerebellum


title: RNA0288_APC73_Plate_4_22

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_4_16

description: Human Skin RNA-seq


title: CR-2-postreatment


title: RNA0288_APC73_Plate_4_21

description: Human Skin RNA-seq


title: WT-1

description:
WT-1
Wildtype Replicate 1: Gene expression data of wildtype cerebellum


title: RNA0288_APC73_Plate_4_13

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_4_14

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_4_15

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_4_08

description: Human Skin RNA-seq


title: M6 Tumor

city: Birmingham

first: Nilesh

last: Kumar

state: Alabama

address: 1331 14th Ave S Apt 10

institute: University of Alabama at Birmingham

data_processing:
The RAW sequences were trimmed using Trimmomatic 0.38 and low-quality reads were removed.
The quantification of the expression of transcripts of preprocessed sequences was using salmon 1.4.0 and mm10 mouse reference genome.
The quant (transcript abundance estimates) values were utilized for the differential expression analysis.
Differential gene expression analysis was done using DESeq2 and for downstream analysis and visualization python (v.3.8) and Bash scripting were used.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: Tumor

extract_protocol:
Per manufacturer's protocol, Qiagen 74134
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Tumor

tag: Sex

value: Male


title: NI1 Normal Islet

source_name: beta islets

value: beta islets


title: NI3 Normal Islet


title: M4 Tumor


title: M5 Tumor


title: M2 Tumor Inulin

value: Female


title: NI2 Normal Islet


title: M3 Tumor Inulin


title: RNA0288_APC73_Plate_4_07

description: Human Skin RNA-seq

value: AD


title: M1 Tumor Inulin


title: WT3

city: London

first: Esteban

middle: Alberto

last: Gomez Cifuentes

address: Charterhouse Square

department: William Harvey Research Institute

country: United Kingdom

institute: Queen Mary University of London

description: Differential Gene Expression analysis were made to compare transcriptomic profiles between Tregs from WT and KO mices.

data_processing:
Illumina NextSeq 500
TrueQuant SmallRNA-Seq: SmallRNA library.
omiRAS tool: Trimming and reads aligment (Bowtie)
Filtering: genes were considered to be expressed at a reasonable level if two or more counts per each million mapped reads were identified per sample, in at least half of the samples.
Differential Gene Expression Analysis between Alox15-/- Treg vs WT Treg: quasi-likelihood method of the Bioconductor R package “edgeR” (adjust p value < 0.05 using BH correction)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include gene read counts for each sample.

source_name: WT_CD4+ T lymphocytes

extract_protocol:
Spleens were preserved in RLT Buffer at -80°C until analysis. The samples were processed and analysed by GenXPro GmbH (Goethe University, Frankfurt, Germany). RNA of the Treg was extracted using Zymo IC columns (Zymo), as described by the manufacturer. DNAse digestion was performed using DNAseI (NEB) and the RNA was purified using the “Zymo RNA Clean & Concentrator Kit” (Zymo).
SmallRNA libraries were prepared using the “TrueQuant SmallRNA-Seq” kit (GenXPro) according to the manufacturer’s instructions.

tag: strain background

tag: genotype/variation

value: wild type

value: Spleen

value: CD4+ T lymphocytes

tag: cell subtype

value: Tregs

tag: pre-analysis test

value: Raw seq were cleaned and trimmed


title: RNA0288_APC73_Plate_4_58

description: Human Skin RNA-seq

tag: tissue

tag: donor

tag: condition


title: RNA0288_APC73_Plate_3_95

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_94

description: Human Skin RNA-seq


title: WT1


title: RNA0288_APC73_Plate_3_91

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_85

description: Human Skin RNA-seq


title: WT2


title: RNA0288_APC73_Plate_3_87

description: Human Skin RNA-seq


title: KO4

source_name: KO_CD4+ T lymphocytes


title: KO3


title: RNA0288_APC73_Plate_4_12

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_4_10

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_79

description: Human Skin RNA-seq


title: KO2


title: RNA0288_APC73_Plate_3_78

description: Human Skin RNA-seq


title: KO1


title: RNA0288_APC73_Plate_3_77

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_96

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_73

description: Human Skin RNA-seq


title: WT4


title: RNA0288_APC73_Plate_3_76

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_75

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_74

description: Human Skin RNA-seq


title: L11_ROI190_Tumor [ICP20th-L11-ICPKilo-ROI190-Tumor-H11]

city: Seattle

first: Patrick

last: Danaher

state: WA

address: 530 Fairview Ave N

institute: NanoString Technologies, Inc.

data_processing:
Library strategy: GeoMx-Seq
Adapter trimming with trim galore,  trimGaloreOpts = " --hardtrim5 26 --dont_gzip"
If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts = " -m 26 -e 26 -f 26 -s 1 -r 27"
Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1"
Genome_build: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform
Supplementary_files_format_and_content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary_files_format_and_content: Values represented in the collapsed target counts tab are the geometric mean of the probes for a given, removing any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments.

source_name: NSCLC tumor

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

value: ICPKilo

tag: roi

value: PanCK

value: grid/seg

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: uid

tag: normfactorhk

tag: roi x position

tag: roi y position

tag: nuclei


title: L11_ROI190_TME [ICP20th-L11-ICPKilo-ROI190-TME-H12]

value: TME


title: L11_ROI188_TME [ICP20th-L11-ICPKilo-ROI188-TME-H08]


title: L11_ROI189_Tumor [ICP20th-L11-ICPKilo-ROI189-Tumor-H09]


title: L11_ROI189_TME [ICP20th-L11-ICPKilo-ROI189-TME-H10]


title: RNA0288_APC73_Plate_3_69

description: Human Skin RNA-seq

value: Skin


title: RNA0288_APC73_Plate_3_62

description: Human Skin RNA-seq


title: L11_ROI187_TME [ICP20th-L11-ICPKilo-ROI187-TME-H06]


title: L11_ROI187_Tumor [ICP20th-L11-ICPKilo-ROI187-Tumor-H05]


title: RNA0288_APC73_Plate_3_56

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_55

description: Human Skin RNA-seq


title: L11_ROI186_TME [ICP20th-L11-ICPKilo-ROI186-TME-H04]


title: L11_ROI186_Tumor [ICP20th-L11-ICPKilo-ROI186-Tumor-H03]


title: L11_ROI185_TME [ICP20th-L11-ICPKilo-ROI185-TME-H02]


title: 873784

value: breast cancer

tag: hr

tag: pcr

tag: mp

tag: arm

value: durvalumab/olaparib


title: L11_ROI184_Tumor [ICP20th-L11-ICPKilo-ROI184-Tumor-G11]

tag: tissue

value: Tumor


title: L11_ROI184_TME [ICP20th-L11-ICPKilo-ROI184-TME-G12]

tag: roi


title: L11_ROI188_Tumor [ICP20th-L11-ICPKilo-ROI188-Tumor-H07]

tag: rawreads


title: RNA0288_APC73_Plate_3_44

description: Human Skin RNA-seq

tag: donor

tag: condition


title: RNA0288_APC73_Plate_3_36

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_45

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_34

description: Human Skin RNA-seq


title: L11_ROI183_TME [ICP20th-L11-ICPKilo-ROI183-TME-G10]

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: RNA0288_APC73_Plate_3_51

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_32

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_35

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_46

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_53

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_59

description: Human Skin RNA-seq


title: L11_ROI181_TME [ICP20th-L11-ICPKilo-ROI181-TME-G06]

tag: deduplicatedreads

tag: sequencingsaturation

tag: uid


title: L11_ROI183_Tumor [ICP20th-L11-ICPKilo-ROI183-Tumor-G09]

tag: normfactorhk

tag: roi x position

tag: roi y position


title: L11_ROI182_Tumor [ICP20th-L11-ICPKilo-ROI182-Tumor-G07]

tag: nuclei


title: L11_ROI181_Tumor [ICP20th-L11-ICPKilo-ROI181-Tumor-G05]


title: L11_ROI180_Tumor [ICP20th-L11-ICPKilo-ROI180-Tumor-G03]


title: L11_ROI185_Tumor [ICP20th-L11-ICPKilo-ROI185-Tumor-H01]


title: L11_ROI180_TME [ICP20th-L11-ICPKilo-ROI180-TME-G04]


title: L11_ROI179_TME [ICP20th-L11-ICPKilo-ROI179-TME-G02]


title: L11_ROI179_Tumor [ICP20th-L11-ICPKilo-ROI179-Tumor-G01]


title: L11_ROI182_TME [ICP20th-L11-ICPKilo-ROI182-TME-G08]


title: L11_ROI177_TME [ICP20th-L11-ICPKilo-ROI177-TME-F10]


title: L11_ROI178_TME [ICP20th-L11-ICPKilo-ROI178-TME-F12]


title: L11_ROI178_Tumor [ICP20th-L11-ICPKilo-ROI178-Tumor-F11]


title: L11_ROI177_Tumor [ICP20th-L11-ICPKilo-ROI177-Tumor-F09]


title: L11_ROI176_TME [ICP20th-L11-ICPKilo-ROI176-TME-F08]


title: L11_ROI176_Tumor [ICP20th-L11-ICPKilo-ROI176-Tumor-F07]


title: RNA0288_APC73_Plate_3_23

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_30

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_19

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_16

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_22

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_26

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_27

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_31

description: Human Skin RNA-seq


title: L11_ROI175_TME [ICP20th-L11-ICPKilo-ROI175-TME-F06]


title: RNA0288_APC73_Plate_3_24

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_08

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_15

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_3_06

description: Human Skin RNA-seq


title: L11_ROI175_Tumor [ICP20th-L11-ICPKilo-ROI175-Tumor-F05]


title: RNA0288_APC73_Plate_3_12

description: Human Skin RNA-seq


title: L11_ROI174_TME [ICP20th-L11-ICPKilo-ROI174-TME-F04]


title: RNA0288_APC73_Plate_3_05

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_2_94

description: Human Skin RNA-seq


title: L11_ROI173_TME [ICP20th-L11-ICPKilo-ROI173-TME-F02]


title: RNA0288_APC73_Plate_2_96

description: Human Skin RNA-seq


title: L11_ROI174_Tumor [ICP20th-L11-ICPKilo-ROI174-Tumor-F03]


title: RNA0288_APC73_Plate_2_91

description: Human Skin RNA-seq


title: L11_ROI173_Tumor [ICP20th-L11-ICPKilo-ROI173-Tumor-F01]


title: RNA0288_APC73_Plate_3_13

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_2_90

description: Human Skin RNA-seq


title: L11_ROI172_TME [ICP20th-L11-ICPKilo-ROI172-TME-E12]


title: L11_ROI172_Tumor [ICP20th-L11-ICPKilo-ROI172-Tumor-E11]


title: RNA0288_APC73_Plate_2_84

description: Human Skin RNA-seq


title: L11_ROI171_TME [ICP20th-L11-ICPKilo-ROI171-TME-E10]


title: RNA0288_APC73_Plate_2_83

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_2_81

description: Human Skin RNA-seq


title: L11_ROI170_TME [ICP20th-L11-ICPKilo-ROI170-TME-E08]


title: RNA0288_APC73_Plate_2_70

description: Human Skin RNA-seq


title: L11_ROI170_Tumor [ICP20th-L11-ICPKilo-ROI170-Tumor-E07]


title: RNA0288_APC73_Plate_2_76

description: Human Skin RNA-seq


title: L11_ROI169_Tumor [ICP20th-L11-ICPKilo-ROI169-Tumor-E05]


title: L11_ROI171_Tumor [ICP20th-L11-ICPKilo-ROI171-Tumor-E09]


title: L11_ROI169_TME [ICP20th-L11-ICPKilo-ROI169-TME-E06]


title: RNA0288_APC73_Plate_2_78

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_2_67

description: Human Skin RNA-seq


title: L11_ROI168_Tumor [ICP20th-L11-ICPKilo-ROI168-Tumor-E03]


title: L11_ROI167_TME [ICP20th-L11-ICPKilo-ROI167-TME-E02]


title: L11_ROI168_TME [ICP20th-L11-ICPKilo-ROI168-TME-E04]


title: RNA0288_APC73_Plate_2_63

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_2_66

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_2_62

description: Human Skin RNA-seq


title: L11_ROI167_Tumor [ICP20th-L11-ICPKilo-ROI167-Tumor-E01]


title: L11_ROI166_Tumor [ICP20th-L11-ICPKilo-ROI166-Tumor-D11]


title: L11_ROI166_TME [ICP20th-L11-ICPKilo-ROI166-TME-D12]


title: RNA0288_APC73_Plate_2_59

description: Human Skin RNA-seq


title: L11_ROI165_TME [ICP20th-L11-ICPKilo-ROI165-TME-D10]


title: RNA0288_APC73_Plate_2_54

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_2_57

description: Human Skin RNA-seq


title: L11_ROI165_Tumor [ICP20th-L11-ICPKilo-ROI165-Tumor-D09]


title: L11_ROI164_TME [ICP20th-L11-ICPKilo-ROI164-TME-D08]


title: RNA0288_APC73_Plate_2_77

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_2_69

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_2_44

description: Human Skin RNA-seq


title: L11_ROI164_Tumor [ICP20th-L11-ICPKilo-ROI164-Tumor-D07]


title: RNA0288_APC73_Plate_2_41

description: Human Skin RNA-seq


title: L11_ROI163_TME [ICP20th-L11-ICPKilo-ROI163-TME-D06]


title: RNA0288_APC73_Plate_2_38

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_2_34

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_2_37

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_2_35

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_2_36

description: Human Skin RNA-seq


title: L11_ROI163_Tumor [ICP20th-L11-ICPKilo-ROI163-Tumor-D05]


title: L11_ROI161_TME [ICP20th-L11-ICPKilo-ROI161-TME-D02]


title: L11_ROI161_Tumor [ICP20th-L11-ICPKilo-ROI161-Tumor-D01]


title: L11_ROI162_TME [ICP20th-L11-ICPKilo-ROI162-TME-D04]


title: RNA0288_APC73_Plate_2_32

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_2_31

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_2_30

description: Human Skin RNA-seq


title: L11_ROI160_TME [ICP20th-L11-ICPKilo-ROI160-TME-C12]


title: RNA0288_APC73_Plate_2_26

description: Human Skin RNA-seq


title: L11_ROI159_Tumor [ICP20th-L11-ICPKilo-ROI159-Tumor-C09]


title: RNA0288_APC73_Plate_2_25

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_2_23

description: Human Skin RNA-seq


title: L11_ROI160_Tumor [ICP20th-L11-ICPKilo-ROI160-Tumor-C11]


title: RNA0288_APC73_Plate_2_22

description: Human Skin RNA-seq


title: L11_ROI158_Tumor [ICP20th-L11-ICPKilo-ROI158-Tumor-C07]


title: L11_ROI157_TME [ICP20th-L11-ICPKilo-ROI157-TME-C06]


title: L11_ROI158_TME [ICP20th-L11-ICPKilo-ROI158-TME-C08]


title: RNA0288_APC73_Plate_2_18

description: Human Skin RNA-seq


title: L11_ROI162_Tumor [ICP20th-L11-ICPKilo-ROI162-Tumor-D03]


title: L11_ROI157_Tumor [ICP20th-L11-ICPKilo-ROI157-Tumor-C05]


title: RNA0288_APC73_Plate_2_17

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_2_16

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_2_12

description: Human Skin RNA-seq


title: L11_ROI155_TME [ICP20th-L11-ICPKilo-ROI155-TME-C02]


title: L11_ROI159_TME [ICP20th-L11-ICPKilo-ROI159-TME-C10]


title: RNA0288_APC73_Plate_2_05

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_2_03

description: Human Skin RNA-seq


title: L11_ROI156_TME [ICP20th-L11-ICPKilo-ROI156-TME-C04]


title: RNA0288_APC73_Plate_1_87

description: Human Skin RNA-seq


title: L11_ROI154_TME [ICP20th-L11-ICPKilo-ROI154-TME-B12]


title: L11_ROI155_Tumor [ICP20th-L11-ICPKilo-ROI155-Tumor-C01]


title: L11_ROI153_Tumor [ICP20th-L11-ICPKilo-ROI153-Tumor-B09]


title: RNA0288_APC73_Plate_1_92

description: Human Skin RNA-seq


title: L11_ROI153_TME [ICP20th-L11-ICPKilo-ROI153-TME-B10]


title: RNA0288_APC73_Plate_1_86

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_83

description: Human Skin RNA-seq


title: L11_ROI152_Tumor [ICP20th-L11-ICPKilo-ROI152-Tumor-B07]


title: RNA0288_APC73_Plate_1_85

description: Human Skin RNA-seq


title: L11_ROI152_TME [ICP20th-L11-ICPKilo-ROI152-TME-B08]


title: L11_ROI151_TME [ICP20th-L11-ICPKilo-ROI151-TME-B06]


title: RNA0288_APC73_Plate_1_79

description: Human Skin RNA-seq


title: L11_ROI156_Tumor [ICP20th-L11-ICPKilo-ROI156-Tumor-C03]


title: L11_ROI151_Tumor [ICP20th-L11-ICPKilo-ROI151-Tumor-B05]


title: RNA0288_APC73_Plate_1_80

description: Human Skin RNA-seq


title: L11_ROI149_TME [ICP20th-L11-ICPKilo-ROI149-TME-B02]


title: L11_ROI150_Tumor [ICP20th-L11-ICPKilo-ROI150-Tumor-B03]


title: RNA0288_APC73_Plate_1_82

description: Human Skin RNA-seq


title: L11_ROI154_Tumor [ICP20th-L11-ICPKilo-ROI154-Tumor-B11]


title: RNA0288_APC73_Plate_1_96

description: Human Skin RNA-seq


title: L11_ROI148_TME [ICP20th-L11-ICPKilo-ROI148-TME-A12]


title: RNA0288_APC73_Plate_1_77

description: Human Skin RNA-seq


title: L11_ROI150_TME [ICP20th-L11-ICPKilo-ROI150-TME-B04]


title: L11_ROI147_Tumor [ICP20th-L11-ICPKilo-ROI147-Tumor-A09]


title: L11_ROI148_Tumor [ICP20th-L11-ICPKilo-ROI148-Tumor-A11]


title: RNA0288_APC73_Plate_1_81

description: Human Skin RNA-seq


title: L11_ROI146_TME [ICP20th-L11-ICPKilo-ROI146-TME-A08]


title: RNA0288_APC73_Plate_1_70

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_72

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_73

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_74

description: Human Skin RNA-seq


title: L11_ROI146_Tumor [ICP20th-L11-ICPKilo-ROI146-Tumor-A07]


title: RNA0288_APC73_Plate_1_68

description: Human Skin RNA-seq


title: L11_ROI147_TME [ICP20th-L11-ICPKilo-ROI147-TME-A10]


title: RNA0288_APC73_Plate_1_69

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_65

description: Human Skin RNA-seq


title: L11_ROI144_TME [ICP20th-L11-ICPKilo-ROI144-TME-A04]


title: RNA0288_APC73_Plate_1_64

description: Human Skin RNA-seq


title: L11_ROI145_TME [ICP20th-L11-ICPKilo-ROI145-TME-A06]


title: L11_ROI144_Tumor [ICP20th-L11-ICPKilo-ROI144-Tumor-A03]


title: L11_ROI145_Tumor [ICP20th-L11-ICPKilo-ROI145-Tumor-A05]


title: L11_ROI143_TME [ICP20th-L11-ICPKilo-ROI143-TME-A02]


title: RNA0288_APC73_Plate_1_62

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_60

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_61

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_56

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_54

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_58

description: Human Skin RNA-seq


title: L11_ROI191_TME [ICP20th-L11-ICPKilo-ROI191-TME-A03]


title: RNA0288_APC73_Plate_1_53

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_51

description: Human Skin RNA-seq


title: L11_ROI142_Tumor [ICP20th-L11-ICPKilo-ROI142-Tumor-H10]


title: L11_ROI142_TME [ICP20th-L11-ICPKilo-ROI142-TME-H11]


title: L11_ROI140_TME [ICP20th-L11-ICPKilo-ROI140-TME-H07]


title: L11_ROI141_Tumor [ICP20th-L11-ICPKilo-ROI141-Tumor-H08]


title: L11_ROI140_Tumor [ICP20th-L11-ICPKilo-ROI140-Tumor-H06]


title: RNA0288_APC73_Plate_1_46

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_50

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_44

description: Human Skin RNA-seq


title: L11_ROI139_Tumor [ICP20th-L11-ICPKilo-ROI139-Tumor-H04]


title: RNA0288_APC73_Plate_1_43

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_38

description: Human Skin RNA-seq


title: L11_ROI138_TME [ICP20th-L11-ICPKilo-ROI138-TME-H03]


title: L11_ROI137_TME [ICP20th-L11-ICPKilo-ROI137-TME-H01]


title: RNA0288_APC73_Plate_1_37

description: Human Skin RNA-seq


title: L11_ROI143_Tumor [ICP20th-L11-ICPKilo-ROI143-Tumor-H12]


title: L11_ROI136_TME [ICP20th-L11-ICPKilo-ROI136-TME-G11]


title: L11_ROI137_Tumor [ICP20th-L11-ICPKilo-ROI137-Tumor-G12]


title: RNA0288_APC73_Plate_1_34

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_36

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_45

description: Human Skin RNA-seq


title: L11_ROI135_TME [ICP20th-L11-ICPKilo-ROI135-TME-G09]


title: L11_ROI138_Tumor [ICP20th-L11-ICPKilo-ROI138-Tumor-H02]


title: L11_ROI136_Tumor [ICP20th-L11-ICPKilo-ROI136-Tumor-G10]


title: L11_ROI139_TME [ICP20th-L11-ICPKilo-ROI139-TME-H05]


title: RNA0288_APC73_Plate_1_32

description: Human Skin RNA-seq


title: L11_ROI141_TME [ICP20th-L11-ICPKilo-ROI141-TME-H09]


title: RNA0288_APC73_Plate_1_25

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_27

description: Human Skin RNA-seq


title: L11_ROI135_Tumor [ICP20th-L11-ICPKilo-ROI135-Tumor-G08]


title: RNA0288_APC73_Plate_1_22

description: Human Skin RNA-seq


title: L11_ROI133_Tumor [ICP20th-L11-ICPKilo-ROI133-Tumor-G04]


title: L11_ROI133_TME [ICP20th-L11-ICPKilo-ROI133-TME-G05]


title: RNA0288_APC73_Plate_1_28

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_20

description: Human Skin RNA-seq


title: L11_ROI132_Tumor [ICP20th-L11-ICPKilo-ROI132-Tumor-G02]


title: L11_ROI131_TME [ICP20th-L11-ICPKilo-ROI131-TME-G01]


title: RNA0288_APC73_Plate_1_40

description: Human Skin RNA-seq


title: L11_ROI131_Tumor [ICP20th-L11-ICPKilo-ROI131-Tumor-F12]


title: RNA0288_APC73_Plate_1_18

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_16

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_13

description: Human Skin RNA-seq


title: L11_ROI130_Tumor [ICP20th-L11-ICPKilo-ROI130-Tumor-F10]


title: RNA0288_APC73_Plate_1_12

description: Human Skin RNA-seq


title: L11_ROI134_TME [ICP20th-L11-ICPKilo-ROI134-TME-G07]


title: L11_ROI129_Tumor [ICP20th-L11-ICPKilo-ROI129-Tumor-F08]


title: RNA0288_APC73_Plate_1_30

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_11

description: Human Skin RNA-seq


title: L11_ROI128_TME [ICP20th-L11-ICPKilo-ROI128-TME-F07]


title: L11_ROI132_TME [ICP20th-L11-ICPKilo-ROI132-TME-G03]


title: L11_ROI128_Tumor [ICP20th-L11-ICPKilo-ROI128-Tumor-F06]


title: RNA0288_APC73_Plate_1_10

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_05

description: Human Skin RNA-seq


title: RNA0288_APC73_Plate_1_02

description: Human Skin RNA-seq


title: L11_ROI127_TME [ICP20th-L11-ICPKilo-ROI127-TME-F05]


title: Input WT hESCs

city: Indianapolis

first: Lei

last: Yang

state: Indiana

address: 1044 W. Walnut St.

department: Department of Pediatrics

institute: Indiana University School of Medicine

description: 1 1% Input

data_processing:
Base calling and quality scoring were performed in Illumina  HiSeq 4000
The reads were mapped to the human genome (UCSC hg38) using Bowtie2 (v2.3.2), PICARD (v2.10.7) function MarkDuplicates was used to identify duplicate reads
MACS2 (v 2.1.2) were used to call peaks using Input as control at FDR cut off of less than 1e-2
The signal at each base was normalized by per 10 million reads
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig file showing the normalized read signal, narrowpeak file showing the peaks

source_name: hESCs

growth_protocol: hESCs were routinely cultured in mTesR medium (typically 1× 106 - 1×107 cells in a matrigel-coated P10 plate).

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.

treatment_protocol: Briefly, hESCs were fixed with methanol-free formaldehyde provided by truChIP™ Chromatin Shearing Kit (Covaris, PN 520154). Chromatin of cell lysis was sheared using truChIP™ Chromatin Shearing Kit according its manual by ME220 Focused-ultrasonicator (Covaris). The sheared chromatin was then incubated with antibody and purified by using EZ-Magna ChIP™ A/G Chromatin Immunoprecipitation Kit (Millipore, 17-10086). Chromatin DNAs quality was assessed by 2100 Bioanalyzer (Agilent Technologies).

tag: cell type

value: hESCs

tag: genotype

value: WT

tag: chip antibody

value: no antibody, input


title: RNA0288_APC73_Plate_1_21

description: Human Skin RNA-seq

tag: tissue

value: AD


title: L11_ROI126_Tumor [ICP20th-L11-ICPKilo-ROI126-Tumor-F02]

tag: roi

tag: rawreads


title: RNA0288_APC73_Plate_1_04

description: Human Skin RNA-seq

tag: donor

tag: condition


title: EED ChIP-seq in JARID2 KO hESCs

description: 3-2 EED

value: JARID2 KO

value: EED antibody, Active motif, RRID:AB_2615071, Catalog No:61203


title: L11_ROI125_Tumor [ICP20th-L11-ICPKilo-ROI125-Tumor-E12]

tag: trimmedreads

tag: stitchedreads


title: L11_ROI124_TME [ICP20th-L11-ICPKilo-ROI124-TME-E11]

tag: alignedreads

tag: deduplicatedreads


title: L11_ROI125_TME [ICP20th-L11-ICPKilo-ROI125-TME-F01]

tag: sequencingsaturation

tag: uid


title: L11_ROI129_TME [ICP20th-L11-ICPKilo-ROI129-TME-F09]

tag: normfactorhk

tag: roi x position


title: EED ChIP-seq in WT hESCs

description: 1-2 EED


title: L11_ROI124_Tumor [ICP20th-L11-ICPKilo-ROI124-Tumor-E10]

tag: roi y position

tag: nuclei


title: L11_ROI127_Tumor [ICP20th-L11-ICPKilo-ROI127-Tumor-F04]


title: L11_ROI126_TME [ICP20th-L11-ICPKilo-ROI126-TME-F03]


title: WT hiPSCs

description: 1% Input

data_processing:
Base calling and quality scoring were performed in Illumina HiSeq 4000
The reads were mapped to the human genome (UCSC hg38) using Bowtie2 (v2.3.2), PICARD (v2.10.7) function MarkDuplicates was used to identify duplicate reads
MACS2 (v 2.1.2) were used to call peaks using Input as control at FDR cut off of less than 1e-2
The signal at each base was normalized by per 10 million reads
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig file showing the normalized read signal, narrowpeak file showing the peaks

source_name: hiPSCs

growth_protocol: hiPSCs were routinely cultured in mTesR medium (typically 1× 106 - 1×10e7 cells in a matrigel-coated P10 plate).

treatment_protocol: Briefly, hiPSCs were fixed with methanol-free formaldehyde provided by truChIP™ Chromatin Shearing Kit (Covaris, PN 520154). Chromatin of cell lysis was sheared using truChIP™ Chromatin Shearing Kit according its manual by ME220 Focused-ultrasonicator (Covaris). The sheared chromatin was then incubated with antibody and purified by using EZ-Magna ChIP™ A/G Chromatin Immunoprecipitation Kit (Millipore, 17-10086). Chromatin DNAs quality was assessed by 2100 Bioanalyzer (Agilent Technologies).

tag: cell type

value: hiPSCs

tag: genotype


title: L11_ROI123_Tumor [ICP20th-L11-ICPKilo-ROI123-Tumor-E08]

tag: tissue


title: H3K27me3 ChIP-seq in HBL1KO #150 hiPSCs

description: 3-3 H3K27me3

value: HBL1 KO

tag: chip antibody

value: H3K27me3 antibody, millipore, 07-449 RRID:AB_310624


title: H3K27me3 ChIP-seq in WT hiPSCs

description: 1-3 H3K27me3


title: H3K27me3 ChIP-seq in HBL1KO #22 hiPSCs

description: 2-3 H3K27me3


title: EED ChIP-seq in HBL1KO #150 hiPSCs

description: 3-2 EED


title: EED ChIP-seq in HBL1KO #22 hiPSCs

description: 2-2 EED


title: L11_ROI122_Tumor [ICP20th-L11-ICPKilo-ROI122-Tumor-E06]

value: ICPKilo

tag: roi

tag: rawreads


title: EED ChIP-seq in WT hiPSCs

description: 1-2 EED


title: L11_ROI121_TME [ICP20th-L11-ICPKilo-ROI121-TME-E05]


title: WT hPSCs

source_name: hPSCs

growth_protocol: hPSCs were routinely cultured in mTesR medium (typically 1× 106 - 1×107 cells in a matrigel-coated P10 plate).

treatment_protocol: Briefly, hPSCs were fixed with methanol-free formaldehyde provided by truChIP™ Chromatin Shearing Kit (Covaris, PN 520154). Chromatin of cell lysis was sheared using truChIP™ Chromatin Shearing Kit according its manual by ME220 Focused-ultrasonicator (Covaris). The sheared chromatin was then incubated with antibody and purified by using EZ-Magna ChIP™ A/G Chromatin Immunoprecipitation Kit (Millipore, 17-10086). Chromatin DNAs quality was assessed by 2100 Bioanalyzer (Agilent Technologies).

value: hPSCs

tag: antibody


title: L11_ROI123_TME [ICP20th-L11-ICPKilo-ROI123-TME-E09]

value: grid/seg

tag: trimmedreads


title: L11_ROI121_Tumor [ICP20th-L11-ICPKilo-ROI121-Tumor-E04]

value: PanCK

tag: stitchedreads


title: JARID2 ChIP-seq in WT hPSCs

value: JARID2 antibody, cell signaling technology, 13594S, RRID:AB_2798269


title: JARID2 ChIP-seq in HBL1KO #150 hPSCs


title: L11_ROI120_Tumor [ICP20th-L11-ICPKilo-ROI120-Tumor-E02]

tag: alignedreads


title: L11_ROI119_TME [ICP20th-L11-ICPKilo-ROI119-TME-E01]

value: TME

tag: deduplicatedreads


title: SMInput

city: Nakhon Pathom

first: Opas

last: Choksupmanee

address: 25/25 Phuttamonthon 4 Rd., Salaya, Phuttamonthon

country: Thailand

institute: Institute of Molecular Biosciences, Mahidol University

data_processing:
PolyA triming and Q20 quality triming with Fastp version 0.20.0
Perform repetitive element (Repbase) mapping using STAR version 2.6.1d
Extract non-repeat mapped reads then perform reads alignment on human genome (GRCh38) with STAR version 2.6.1d
Collapse PCR duplication with picard version 2.21.6
Read counting on gene region with htseq-count version 0.11.2
Gene expression analysis with DESeq2 version 1.26.0
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV file contain gene expression analysis result between infected versus non-infected sample
PolyA triming and Q20 quality triming with Fastp version 0.20.0
Collapse exact PCR duplication with fastq2collapse.pl from CTK version 1.1.3
Perfrom reads alignment on human genome (GRCh38) with BWA version 0.7.17. Using aln command to create suffix array index and samse command to perform reference mapping.
Extract unmapped reads then perform reads alignment on DENV-2 (1668) with BWA version 0.7.17 by using the same set of command from previous step.
Collapse PCR duplication with tag2collapse.pl from CTK version 1.1.3 on unique mapped reads
Merge biological replicate by using bed2rgb.pl to add color tag to each replicate then concatenate every replicate into single file with cat command.
Perfom peak calling by using tag2peak.pl from CTK version 1.1.3. Perform convert peak calling reslut and alignment information into bedgraph format.
In house python script has been use to perform fold change calculation and Fisher's exact test to indicate significant peak.
Genome_build: GRCh38 and DENV-2 (1668)
Supplementary_files_format_and_content: Tab-dilimitted file for infected and no infected sample which contain peak id, start position, stop position, log2FoldChange Odds_ratio, p value.

growth_protocol: HuH-7 cells  were grown in completed DMEM (DMEM suplemented with 10%FBS and penicillin-streptomycin) (typically 15 × 106 cells into a 150 mm dish)

extract_protocol:
HuH-7 cells with or without DENV-2 infection (MOI = 5) were first irradiated by UV254 nm at 400 mJ/cm2 and lysed prior to perform DNase I treatment (NEB, #M0303L) at 37°C for 5 min. Cell lysates were clarified by centrifugation and performed DDX6 pull-down at 4°C for overnight. The RNA fragmentation was performed directly on beads by utilizing 4 U of ShortCut® RNase III (NEB, #M0245S) at 37°C for 4 min. Subsequently, 3´ end of shortened RNA was ligated with 5´ pre-adenylated linkers using T4 RNA ligase 2, truncated KQ (NEB, #M0373L) activity. For excess linkers removal, deadenylase (NEB, #M0331S)] and Terminator™ 5´-Phosphate-Dependent Exonuclease (Epicentre, #TER51020)] were used. Proteinase K (NEB, #P8107S) and Quick-RNA™ MicroPrep (Zymo Research, #R1051) were utilized to extracted the RNAs.
Reverse transcription (RT) with SuperScript™ IV Reverse Transcriptase (Thermo Fisher Scientific, 18090050) was performed at 42°C for 20 min and 50°C for 20 min. The cDNAs were cleaned and poly-A tailed by exonuclease I (NEB, #M0293S) and terminal transferase (NEB, #M0315S), respectively. cDNA libraries were amplified with specific primers containing Illumina compatible sequences, and KAPA HiFi HotStart DNA polymerase (KAPA Biosystems, #KK2501) at 98°C for 3 min, 40°C for 1 min and 72°C for 1 min. The size of libraries that larger than 130 bp of self-annealing primers, were further purified in 2 steps by using QIAquick PCR purification kit (QIAGEN, #28106) and AMPure® XP magnetic beads (Beckman Coulter, #A63881), respectively. The concentration and size of cDNA libraries were verified by utilizing Qubit™ fluorometric quantitation [Quant-iT™ PicoGreen® dsDNA Reagent and Kits (Thermo Fisher Scientific, #P7589)] and Bioanalyzer. Finally, cDNA libraries were performed paired-end sequencing on Illumina HiSeq 4000.

treatment_protocol: 80% confluency of HuH-7 cells were infected with dengue virus serotype 2 (16681) (MOI5) for 48 h

tag: cell line

tag: infection

tag: experiment

value: input


title: L11_ROI118_TME [ICP20th-L11-ICPKilo-ROI118-TME-D11]

tag: sequencingsaturation

tag: uid

tag: normfactorhk

tag: roi x position


title: SMInput + DENV2

source_name: DENV-2 infected HuH-7

value: DENV-2 strain 16681


title: L11_ROI122_TME [ICP20th-L11-ICPKilo-ROI122-TME-E07]

tag: roi y position

tag: nuclei


title: DDX6 CLIP-seq + DENV2 Rep3

value: CLIP-Seq


title: DDX6 CLIP-seq Rep3


title: L11_ROI118_Tumor [ICP20th-L11-ICPKilo-ROI118-Tumor-D10]

tag: tissue

value: Tumor


title: DDX6 CLIP-seq + DENV2 Rep2


title: DDX6 CLIP-seq Rep2


title: L11_ROI117_TME [ICP20th-L11-ICPKilo-ROI117-TME-D09]

tag: roi


title: L11_ROI116_TME [ICP20th-L11-ICPKilo-ROI116-TME-D07]

tag: rawreads


title: L11_ROI116_Tumor [ICP20th-L11-ICPKilo-ROI116-Tumor-D06]


title: L11_ROI120_TME [ICP20th-L11-ICPKilo-ROI120-TME-E03]


title: DDX6 CLIP-seq Rep1


title: L11_ROI114_Tumor [ICP20th-L11-ICPKilo-ROI114-Tumor-D02]


title: L11_ROI115_TME [ICP20th-L11-ICPKilo-ROI115-TME-D05]


title: L11_ROI114_TME [ICP20th-L11-ICPKilo-ROI114-TME-D03]


title: L11_ROI117_Tumor [ICP20th-L11-ICPKilo-ROI117-Tumor-D08]


title: L11_ROI113_TME [ICP20th-L11-ICPKilo-ROI113-TME-D01]


title: Sparcl1-1_sequence

city: Lianyungang City

first: bin

last: liu

state: Jiangsu Province

institute: Jiangsu Ocean University

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions.
Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).
Library sequencing was performed on an illumina Hiseq instrument with 150bp paired end reads. Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC mm10) with hisat2 software (v2.0.4).
Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and P value were calculated based on FPKM, differentially expressed mRNA were identified.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: liver

extract_protocol:
Total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For NASH diet feeding, C57BL/6J mice were fed a diet containing 40% fat, 22% fructose, and 2% cholesterol (D09100310, Research Diets Inc.) for 12 or 28 weeks. Mice were intraperitoneal injected with saline or recombinant Sparcl1 protein (0.2mg/kg) every other day for 3 weeks

tag: strain

value: liver

tag: genotype

value: wild type

tag: treatment


title: DDX6 CLIP-seq + DENV2 Rep1


title: Sparcl1-3_sequence


title: L11_ROI113_Tumor [ICP20th-L11-ICPKilo-ROI113-Tumor-C12]

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: Saline-1_sequence

value: saline


title: L11_ROI119_Tumor [ICP20th-L11-ICPKilo-ROI119-Tumor-D12]

tag: deduplicatedreads


title: 10.14-eWAT-M4

source_name: eWAT

value: eWAT

value: HFHC diet for 28 weeks


title: L11_ROI112_TME [ICP20th-L11-ICPKilo-ROI112-TME-C11]


title: L11_ROI112_Tumor [ICP20th-L11-ICPKilo-ROI112-Tumor-C10]


title: 10.14-eWAT-M3


title: 10.14-eWAT-M2


title: L11_ROI111_Tumor [ICP20th-L11-ICPKilo-ROI111-Tumor-C08]


title: L11_ROI111_TME [ICP20th-L11-ICPKilo-ROI111-TME-C09]


title: Sparcl1-2_sequence


title: Saline-3_sequence


title: 10.14-eWAT-C4

value: normal chow diet for 28 weeks


title: 10.14-eWAT-C3


title: L11_ROI109_TME [ICP20th-L11-ICPKilo-ROI109-TME-C05]


title: L11_ROI110_TME [ICP20th-L11-ICPKilo-ROI110-TME-C07]


title: 10.14-eWAT-C1


title: 6.10-eWAT-M3

value: HFHC diet for 12 weeks


title: L11_ROI108_Tumor [ICP20th-L11-ICPKilo-ROI108-Tumor-C02]

value: ICPKilo


title: 6.10-eWAT-M4


title: L11_ROI107_TME [ICP20th-L11-ICPKilo-ROI107-TME-C01]


title: L11_ROI107_Tumor [ICP20th-L11-ICPKilo-ROI107-Tumor-B12]


title: L11_ROI108_TME [ICP20th-L11-ICPKilo-ROI108-TME-C03]


title: 6.10-eWAT-M2


title: L11_ROI106_Tumor [ICP20th-L11-ICPKilo-ROI106-Tumor-B10]


title: L11_ROI106_TME [ICP20th-L11-ICPKilo-ROI106-TME-B11]


title: 6.10-eWAT-C8

value: normal chow diet for 12 weeks


title: L11_ROI105_TME [ICP20th-L11-ICPKilo-ROI105-TME-B09]

value: grid/seg


title: 6.10-eWAT-C7


title: RNA Pol II ChIP-seq IP rep2

city: Boston

first: Hu

last: Jin

state: MA

address: 10 Shattuck St

department: Biomedical Informatics

institute: Harvard Medical School

data_processing:
ChIP-seq and DSB-seq reads were mapped to the mm9 genome using Bowtie2 [pubmed/22388286] with the options --end-to-end --sensitive --score-min L,-1.5,-0.3. Reads with mapping quality smaller than 13 were filtered out. PCR duplicates were removed by keeping at most one mapped read at each genomic position. Biological replicates were then combined. Read coverage profiles were generated using bedtools [pubmed/20110278] after extending the mapped reads from 5’ to 3’ end to 200 bp.
DSB-seq peaks were called using MACS2 [pubmed/18798982] with the options --shift 0 --nomodel --extsize 200 -g mm and default q-value cutoff 0.05. 5903 and 183 peaks were identified for Chd1 KO and WT cells, respectively. After filtering out peaks overlapping with blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm9-mouse/mm9-blacklist.bed.gz), 5671 and 54 peaks were retained for Chd1 KO and WT cells, respectively.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files and narrowPeak files

source_name: mouse embryonic stem cells

growth_protocol: Cells were grown in DMEM GlutaMAX with 15% FBS (Atlanta Biologicals), 0.1 mM non-essential amino acids, 50 U/ml Penicillin/Streptomycin (UCSF Cell Culture Facility), 0.1 mM EmbryoMax 2-Mercaptoethanol (Millipore) and 2000 U/ml ESGRO supplement (LIF, Millipore or Gemini) under ambient air with 5% CO2. Cells tested negative for mycoplasma contamination.

extract_protocol: Chd1fl/D and Chd1D/D (7 days post-KO) ES cells were used. ChIP was performed as described before (pubmed/22305566). After aspiration of culture medium, cells were washed with PBS and fixed on the culture dish using 1% formaldehyde in PBS for 10 minutes at room temperature (RT). Glycine was added to a final concentration of 125 mM to quench formaldehyde for 5 minutes at RT. Cells were washed twice with ice-cold PBS, incubated in Swelling Buffer (25 mM HEPES pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.1% NP-40 with 1x Halt protease inhibitor cocktail (Thermo Fisher Scientific, 78425), 1 mM PMSF, 5 mM NaF and 1 mM NaVO4) for 10 minutes, scraped, passed through an 18Gx11/2” needle (5x) and spun down at 3,000g, 4oC, 5 minutes. Nuclei were resuspended in Sonication Buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate 0.1% SDS with 1x Halt protease inhibitor cocktail, 1 mM PMSF, 5 mM NaF and 1 mM NaVO4) and sonicated using a Covaris S2 sonicator with settings 5% duty cycle, intensity 4, cycles per burst 200, frequency sweeping. 20 ml chromatin was incubated sequentially with 1 ml RNaseA and 5 ml proteinase K in 100 ml total volume at 37oC for 30 min and 65oC for 1h, purified using a Qiagen PCR purification kit and DNA content was quantified using a NanoDrop. Fragment size distribution was checked on a 1% agarose gel. Chromatin was snap frozen if not immediately used for IP. Chromatin volume equivalent to 25 mg DNA was used for each IP. Chromatin was immunoprecipitated in the presence of 20 ml pre-washed Protein A or G Dynabeads (Thermo Fisher Scientific, 1002D or 1004D) and the following antibodies: Flag (Sigma, F1804), Kap1 (Abcam, ab22553), phospho S824 Kap1 (Abcam, ab70369), gH2A.X (Abcam, ab2893), H2A.X (Abcam, ab11175), H1 (Thermo Fisher Scientific, PA128374), Polr1a (Cell Signaling, D6S6S), Atm (Genetex, GTX10701). Beads were washed in sonication buffer (2 times), wash buffer A (sonication buffer with 500 mM NaCl) and TE buffer (10 mM Tris pH 8.0, 1 mM EDTA), and resuspended in elution buffer (50 mM Tris pH 7.5, 1 mM EDTA, 1% SDS) with 1 ml RNaseA and 5 ml proteinase K in 100 ml total volume. After incubation at 37oC for 30 min and 65oC for 2h to overnight, DNA was purified using a Qiagen PCR purification kit. qPCR was performed with KAPA SYBR FAST qPCR Master Mix (Kapa Biosystems) and amplified on a 7900HT Real-time PCR machine (Applied Biosystems). For sequencing, libraries were prepared using the NEBNext ChIP-seq Library Prep for Illumina kit. Library quality and quantity were analyzed using Bioanalyzer (Agilent). Samples were sequenced on a HiSeq 2500 using single-end 50 bp sequencing reads in rapid mode.

tag: cell type

value: mouse embryonic stem cells


title: L11_ROI103_TME [ICP20th-L11-ICPKilo-ROI103-TME-B05]

tag: sequencingsaturation


title: L11_ROI105_Tumor [ICP20th-L11-ICPKilo-ROI105-Tumor-B08]

value: PanCK

tag: uid


title: L11_ROI104_Tumor [ICP20th-L11-ICPKilo-ROI104-Tumor-B06]

tag: normfactorhk


title: RNA Pol II ChIP-seq IP rep1


title: Saline-2_sequence


title: L11_ROI104_TME [ICP20th-L11-ICPKilo-ROI104-TME-B07]

value: TME

tag: roi x position


title: Chd1 KO DSB-seq rep2

description:
DSB.KO_merged.bw
DSB.KO_merged.peaks.filtered.narrowPeak

data_processing:
Library strategy: DSB-seq
ChIP-seq and DSB-seq reads were mapped to the mm9 genome using Bowtie2 [pubmed/22388286] with the options --end-to-end --sensitive --score-min L,-1.5,-0.3. Reads with mapping quality smaller than 13 were filtered out. PCR duplicates were removed by keeping at most one mapped read at each genomic position. Biological replicates were then combined. Read coverage profiles were generated using bedtools [pubmed/20110278] after extending the mapped reads from 5’ to 3’ end to 200 bp.
DSB-seq peaks were called using MACS2 [pubmed/18798982] with the options --shift 0 --nomodel --extsize 200 -g mm and default q-value cutoff 0.05. 5903 and 183 peaks were identified for Chd1 KO and WT cells, respectively. After filtering out peaks overlapping with blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm9-mouse/mm9-blacklist.bed.gz), 5671 and 54 peaks were retained for Chd1 KO and WT cells, respectively.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files and narrowPeak files

extract_protocol: Chd1fl/D and Chd1D/D (established) ES cells were used. For detection of double stranded DNA breaks, we combined the Baranello et al (pubmed/25056547) and BLESS (pubmed/23503052) protocols to achieve end labeling in situ. 1.5x108 cells were fixed in 2% formaldehyde suspension for 30 min at room temperature, followed by quenching in 0.25M glycine for 5 min. Cells were centrifuged, washed twice in PBS, and incubated in 25 ml lysis buffer (10 mM Tris pH 8.0, 10 mM NaCl, 1 mM EDTA, 1 mM EGTA, 0.2% NP-40) for 1 h at 4oC. Pellets were resuspended in nucleus break buffer (10 mM Tris pH 8.0, 150 mM NaCl, 1 mM EDTA, 1 mM EGTA, 0.3% SDS, 1mM DTT) and incubated for 45 min at 37C. After centrifugation, nuclei were resuspended in 1x NEB buffer 2 on ice. 10 ml Proteinase K (20 mg/ml) was added, digestion was performed for 4 min at 37C, and samples were immediately returned to ice and 25 ml PMSF was added. Nuclei were centrifuged, and resuspended in 5 ml 1x NEB Buffer 2 + 15 ml Triton X-100, and centrifuged again at 200g for 10 min at 4oC. Nuclei were washed once in water, and divided into two tubes for end labeling and control reactions. Nuclei were resuspended in 625 ml 1x TdT buffer with 2.5 ml TdT (Promega, M1871) and 2 ml biotin-16-dUTP (Roche 11093070910), and were incubated at 37oC for 1 hour. Control reaction was assembled the same way without TdT. 1:50 volume of 0.5M EDTA was added to stop the reaction. Proteins were digested with 5 ml Proteinase K (20 mg/ml) at 2h to overnight at 65oC. Labeled DNA was precipitated using sodium acetate (70 ml) and isopropanol (700 ml), centrifuged, washed with 70% ethanol and resuspended in water. Genomic DNA was sonicated using a Covaris S2 sonicator with settings 5% duty cycle, intensity 4, cycles per burst 200, frequency sweeping for 4.5 cycles. DNA amount was quantified on a NanoDrop. Size distribution was checked on a 1% agarose gel. For biotinylated DNA pull-down, 20 mg DNA was adjusted to 600 ml final volume in W&B buffer (10 mM Tris pH 7.5, 1 mM EDTA, 1 M NaCl). 10 ml Dynabeads MyOne C1 was washed twice with W&B buffer and added to DNA. Sample was incubated for 1 hour at 4oC. Beads were washed twice in W&B buffer, and resuspended in 100 ml elution buffer (95% v/v formamide, 10 mM EDTA). After incubation at 65oC for 5 min, DNA was purified using a Qiagen PCR purification column. For sequencing, biotinylated overhangs were removed using S1 nuclease. Sequencing libraries were prepared using the NEBNext ChIP-seq Library Prep for Illumina kit. Library quality and quantity were analyzed using Bioanalyzer (Agilent). Samples were sequenced on a HiSeq 4000 using single-end 50 bp sequencing reads.


title: Chd1 WT DSB-seq rep1

description:
DSB.WT_merged.bw
DSB.WT_merged.peaks.filtered.narrowPeak


title: Chd1 WT DSB-seq rep2


title: L11_ROI103_Tumor [ICP20th-L11-ICPKilo-ROI103-Tumor-B04]

tag: roi y position


title: L11_ROI102_TME [ICP20th-L11-ICPKilo-ROI102-TME-B03]

tag: nuclei


title: L11_ROI102_Tumor [ICP20th-L11-ICPKilo-ROI102-Tumor-B02]

tag: tissue


title: L11_ROI100_TME [ICP20th-L11-ICPKilo-ROI100-TME-A11]

tag: roi


title: 6.10-eWAT-C4


title: L11_ROI101_Tumor [ICP20th-L11-ICPKilo-ROI101-Tumor-A12]

tag: rawreads


title: Chd1 KO DSB-seq rep1


title: L11_ROI101_TME [ICP20th-L11-ICPKilo-ROI101-TME-B01]


title: HeLa 4 hr SeV

first: Aubhishek

last: Zaman

state: CALIFORNIA

address: 600 16th St. Genentech hall N216.R, The Bivona laboratory

institute: UCSF

data_processing:
Illumina Casava1.7 software used for basecalling.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: HeLa cells

growth_protocol: Grown on DMEM +10% FBS

extract_protocol:
mRNA was isolated using RNeasy Kit (Qiagen)
Samples are run on the Agilent 2100 Bioanalyzer to determine level of degradation thus ensuring only high quality RNA is used (RIN Score 8 or higher). The Qubit fluorometer is used to determine the concentration prior to staring library prep. 4 µg of total DNAse treated RNA are then prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina. Poly-A RNA is purified and fragmented before strand specific cDNA synthesis. cDNA are then a-tailed and indexed adapters are ligated. After adapter ligation, samples are PCR amplified and purified with Ampure XP beads, then validated again on the Agilent 2100 Bioanalyzer. Samples are quantified by Qubit before being normalized and pooled, then run on the Illumina HiSeq 2500 using SBS v3 reagents.

treatment_protocol: pI:C= 2µg/ml, SeV= 50HA/mL

value: cervical cancer cell

tag: cell line

value: HeLa

tag: agent

value: Sendai virus


title: HeLa 0 hr pI:C or SeV


title: L11_ROI99_Tumor [ICP20th-L11-ICPKilo-ROI99-Tumor-A08]

value: Tumor


title: L11_ROI100_Tumor [ICP20th-L11-ICPKilo-ROI100-Tumor-A10]


title: HeLa 4 hr pI:C


title: Chd1 Flag ChIP-seq IP

tag: genotype


title: Chd1 Flag ChIP-seq input


title: L11_ROI98_TME [ICP20th-L11-ICPKilo-ROI98-TME-A07]

tag: trimmedreads


title: L11_ROI98_Tumor [ICP20th-L11-ICPKilo-ROI98-Tumor-A06]

tag: stitchedreads


title: L11_ROI97_TME [ICP20th-L11-ICPKilo-ROI97-TME-A05]

tag: alignedreads


title: L11_ROI97_Tumor [ICP20th-L11-ICPKilo-ROI97-Tumor-A04]

tag: deduplicatedreads


title: L11_ROI96_Tumor [ICP20th-L11-ICPKilo-ROI96-Tumor-A02]


title: L11_ROI191_Tumor [ICP20th-L11-ICPKilo-ROI191-Tumor-A02]


title: L11_ROI94_Tumor [ICP20th-L11-ICPKilo-ROI94-Tumor-H09]


title: L11_ROI94_TME [ICP20th-L11-ICPKilo-ROI94-TME-H10]


title: L11_ROI95_Tumor [ICP20th-L11-ICPKilo-ROI95-Tumor-H11]


title: L11_ROI93_Tumor [ICP20th-L11-ICPKilo-ROI93-Tumor-H07]


title: L11_ROI93_TME [ICP20th-L11-ICPKilo-ROI93-TME-H08]


title: L11_ROI92_Tumor [ICP20th-L11-ICPKilo-ROI92-Tumor-H05]


title: L11_ROI91_TME [ICP20th-L11-ICPKilo-ROI91-TME-H04]


title: L11_ROI92_TME [ICP20th-L11-ICPKilo-ROI92-TME-H06]


title: L11_ROI91_Tumor [ICP20th-L11-ICPKilo-ROI91-Tumor-H03]


title: L11_ROI96_TME [ICP20th-L11-ICPKilo-ROI96-TME-A03]


title: L11_ROI99_TME [ICP20th-L11-ICPKilo-ROI99-TME-A09]


title: L11_ROI90_TME [ICP20th-L11-ICPKilo-ROI90-TME-H02]


title: L11_ROI90_Tumor [ICP20th-L11-ICPKilo-ROI90-Tumor-H01]


title: L11_ROI89_Tumor [ICP20th-L11-ICPKilo-ROI89-Tumor-G11]


title: L11_ROI89_TME [ICP20th-L11-ICPKilo-ROI89-TME-G12]


title: L11_ROI87_TME [ICP20th-L11-ICPKilo-ROI87-TME-G08]


title: L11_ROI88_TME [ICP20th-L11-ICPKilo-ROI88-TME-G10]


title: L11_ROI88_Tumor [ICP20th-L11-ICPKilo-ROI88-Tumor-G09]


title: L11_ROI86_TME [ICP20th-L11-ICPKilo-ROI86-TME-G06]


title: L11_ROI85_TME [ICP20th-L11-ICPKilo-ROI85-TME-G04]


title: L11_ROI84_TME [ICP20th-L11-ICPKilo-ROI84-TME-G02]


title: L11_ROI84_Tumor [ICP20th-L11-ICPKilo-ROI84-Tumor-G01]


title: L11_ROI95_TME [ICP20th-L11-ICPKilo-ROI95-TME-H12]


title: L11_ROI86_Tumor [ICP20th-L11-ICPKilo-ROI86-Tumor-G05]


title: L11_ROI83_TME [ICP20th-L11-ICPKilo-ROI83-TME-F12]


title: L11_ROI83_Tumor [ICP20th-L11-ICPKilo-ROI83-Tumor-F11]


title: L11_ROI81_Tumor [ICP20th-L11-ICPKilo-ROI81-Tumor-F07]


title: L11_ROI80_TME [ICP20th-L11-ICPKilo-ROI80-TME-F06]


title: L11_ROI82_TME [ICP20th-L11-ICPKilo-ROI82-TME-F10]


title: L11_ROI78_Tumor [ICP20th-L11-ICPKilo-ROI78-Tumor-F01]


title: L11_ROI82_Tumor [ICP20th-L11-ICPKilo-ROI82-Tumor-F09]


title: L11_ROI79_Tumor [ICP20th-L11-ICPKilo-ROI79-Tumor-F03]


title: L11_ROI80_Tumor [ICP20th-L11-ICPKilo-ROI80-Tumor-F05]


title: L11_ROI76_TME [ICP20th-L11-ICPKilo-ROI76-TME-E10]


title: L11_ROI77_Tumor [ICP20th-L11-ICPKilo-ROI77-Tumor-E11]


title: L11_ROI79_TME [ICP20th-L11-ICPKilo-ROI79-TME-F04]


title: L11_ROI87_Tumor [ICP20th-L11-ICPKilo-ROI87-Tumor-G07]


title: L11_ROI76_Tumor [ICP20th-L11-ICPKilo-ROI76-Tumor-E09]


title: L11_ROI77_TME [ICP20th-L11-ICPKilo-ROI77-TME-E12]


title: L11_ROI75_TME [ICP20th-L11-ICPKilo-ROI75-TME-E08]


title: L11_ROI75_Tumor [ICP20th-L11-ICPKilo-ROI75-Tumor-E07]


title: L11_ROI73_Tumor [ICP20th-L11-ICPKilo-ROI73-Tumor-E03]


title: L11_ROI73_TME [ICP20th-L11-ICPKilo-ROI73-TME-E04]


title: L11_ROI74_TME [ICP20th-L11-ICPKilo-ROI74-TME-E06]


title: L11_ROI74_Tumor [ICP20th-L11-ICPKilo-ROI74-Tumor-E05]


title: L11_ROI72_Tumor [ICP20th-L11-ICPKilo-ROI72-Tumor-E01]


title: L11_ROI72_TME [ICP20th-L11-ICPKilo-ROI72-TME-E02]


title: L11_ROI70_Tumor [ICP20th-L11-ICPKilo-ROI70-Tumor-D09]


title: L11_ROI71_TME [ICP20th-L11-ICPKilo-ROI71-TME-D12]


title: L11_ROI69_TME [ICP20th-L11-ICPKilo-ROI69-TME-D08]


title: L11_ROI70_TME [ICP20th-L11-ICPKilo-ROI70-TME-D10]


title: L11_ROI81_TME [ICP20th-L11-ICPKilo-ROI81-TME-F08]


title: L11_ROI71_Tumor [ICP20th-L11-ICPKilo-ROI71-Tumor-D11]


title: L11_ROI69_Tumor [ICP20th-L11-ICPKilo-ROI69-Tumor-D07]


title: L11_ROI68_TME [ICP20th-L11-ICPKilo-ROI68-TME-D06]


title: L11_ROI67_Tumor [ICP20th-L11-ICPKilo-ROI67-Tumor-D03]


title: L11_ROI68_Tumor [ICP20th-L11-ICPKilo-ROI68-Tumor-D05]


title: L11_ROI64_Tumor [ICP20th-L11-ICPKilo-ROI64-Tumor-C09]


title: L11_ROI65_Tumor [ICP20th-L11-ICPKilo-ROI65-Tumor-C11]


title: L11_ROI66_Tumor [ICP20th-L11-ICPKilo-ROI66-Tumor-D01]


title: L11_ROI66_TME [ICP20th-L11-ICPKilo-ROI66-TME-D02]


title: L11_ROI67_TME [ICP20th-L11-ICPKilo-ROI67-TME-D04]


title: L11_ROI64_TME [ICP20th-L11-ICPKilo-ROI64-TME-C10]


title: L11_ROI63_TME [ICP20th-L11-ICPKilo-ROI63-TME-C08]


title: L11_ROI65_TME [ICP20th-L11-ICPKilo-ROI65-TME-C12]


title: L11_ROI62_TME [ICP20th-L11-ICPKilo-ROI62-TME-C06]


title: L11_ROI63_Tumor [ICP20th-L11-ICPKilo-ROI63-Tumor-C07]


title: L11_ROI61_Tumor [ICP20th-L11-ICPKilo-ROI61-Tumor-C03]


title: L11_ROI62_Tumor [ICP20th-L11-ICPKilo-ROI62-Tumor-C05]


title: L11_ROI78_TME [ICP20th-L11-ICPKilo-ROI78-TME-F02]


title: L11_ROI59_TME [ICP20th-L11-ICPKilo-ROI59-TME-B12]


title: L11_ROI61_TME [ICP20th-L11-ICPKilo-ROI61-TME-C04]


title: L11_ROI59_Tumor [ICP20th-L11-ICPKilo-ROI59-Tumor-B11]


title: L11_ROI58_TME [ICP20th-L11-ICPKilo-ROI58-TME-B10]


title: L11_ROI58_Tumor [ICP20th-L11-ICPKilo-ROI58-Tumor-B09]


title: L11_ROI57_Tumor [ICP20th-L11-ICPKilo-ROI57-Tumor-B07]


title: L11_ROI56_TME [ICP20th-L11-ICPKilo-ROI56-TME-B06]


title: L11_ROI56_Tumor [ICP20th-L11-ICPKilo-ROI56-Tumor-B05]


title: L11_ROI55_TME [ICP20th-L11-ICPKilo-ROI55-TME-B04]


title: L11_ROI54_Tumor [ICP20th-L11-ICPKilo-ROI54-Tumor-B01]


title: L11_ROI55_Tumor [ICP20th-L11-ICPKilo-ROI55-Tumor-B03]


title: L11_ROI54_TME [ICP20th-L11-ICPKilo-ROI54-TME-B02]


title: L11_ROI53_Tumor [ICP20th-L11-ICPKilo-ROI53-Tumor-A11]


title: L11_ROI52_Tumor [ICP20th-L11-ICPKilo-ROI52-Tumor-A09]


title: L11_ROI51_Tumor [ICP20th-L11-ICPKilo-ROI51-Tumor-A07]


title: L11_ROI52_TME [ICP20th-L11-ICPKilo-ROI52-TME-A10]


title: L11_ROI50_TME [ICP20th-L11-ICPKilo-ROI50-TME-A06]


title: L11_ROI53_TME [ICP20th-L11-ICPKilo-ROI53-TME-A12]


title: L11_ROI50_Tumor [ICP20th-L11-ICPKilo-ROI50-Tumor-A05]


title: L11_ROI49_Tumor [ICP20th-L11-ICPKilo-ROI49-Tumor-A03]


title: L11_ROI48_TME [ICP20th-L11-ICPKilo-ROI48-TME-A02]


title: L11_ROI51_TME [ICP20th-L11-ICPKilo-ROI51-TME-A08]


title: L11_ROI60_TME [ICP20th-L11-ICPKilo-ROI60-TME-C02]


title: L11_ROI48_Tumor [ICP20th-L11-ICPKilo-ROI48-Tumor-H12]


title: L11_ROI47_TME [ICP20th-L11-ICPKilo-ROI47-TME-H11]


title: L11_ROI49_TME [ICP20th-L11-ICPKilo-ROI49-TME-A04]


title: L11_ROI60_Tumor [ICP20th-L11-ICPKilo-ROI60-Tumor-C01]


title: L11_ROI45_TME [ICP20th-L11-ICPKilo-ROI45-TME-H07]


title: L11_ROI46_Tumor [ICP20th-L11-ICPKilo-ROI46-Tumor-H08]


title: L11_ROI46_TME [ICP20th-L11-ICPKilo-ROI46-TME-H09]


title: L11_ROI45_Tumor [ICP20th-L11-ICPKilo-ROI45-Tumor-H06]


title: L11_ROI44_TME [ICP20th-L11-ICPKilo-ROI44-TME-H05]


title: L11_ROI44_Tumor [ICP20th-L11-ICPKilo-ROI44-Tumor-H04]


title: L11_ROI57_TME [ICP20th-L11-ICPKilo-ROI57-TME-B08]


title: L11_ROI43_Tumor [ICP20th-L11-ICPKilo-ROI43-Tumor-H02]


title: L11_ROI43_TME [ICP20th-L11-ICPKilo-ROI43-TME-H03]


title: L11_ROI42_Tumor [ICP20th-L11-ICPKilo-ROI42-Tumor-G12]


title: L11_ROI41_TME [ICP20th-L11-ICPKilo-ROI41-TME-G11]


title: L11_ROI40_TME [ICP20th-L11-ICPKilo-ROI40-TME-G09]


title: L11_ROI39_TME [ICP20th-L11-ICPKilo-ROI39-TME-G07]


title: L11_ROI39_Tumor [ICP20th-L11-ICPKilo-ROI39-Tumor-G06]


title: L11_ROI38_TME [ICP20th-L11-ICPKilo-ROI38-TME-G05]


title: L11_ROI47_Tumor [ICP20th-L11-ICPKilo-ROI47-Tumor-H10]


title: L11_ROI40_Tumor [ICP20th-L11-ICPKilo-ROI40-Tumor-G08]


title: L11_ROI35_TME [ICP20th-L11-ICPKilo-ROI35-TME-F11]


title: L11_ROI36_Tumor [ICP20th-L11-ICPKilo-ROI36-Tumor-F12]


title: L11_ROI35_Tumor [ICP20th-L11-ICPKilo-ROI35-Tumor-F10]


title: L11_ROI36_TME [ICP20th-L11-ICPKilo-ROI36-TME-G01]


title: L11_ROI41_Tumor [ICP20th-L11-ICPKilo-ROI41-Tumor-G10]


title: L11_ROI38_Tumor [ICP20th-L11-ICPKilo-ROI38-Tumor-G04]


title: L11_ROI37_Tumor [ICP20th-L11-ICPKilo-ROI37-Tumor-G02]


title: L11_ROI34_TME [ICP20th-L11-ICPKilo-ROI34-TME-F09]


title: L11_ROI37_TME [ICP20th-L11-ICPKilo-ROI37-TME-G03]


title: L11_ROI33_Tumor [ICP20th-L11-ICPKilo-ROI33-Tumor-F06]


title: L11_ROI33_TME [ICP20th-L11-ICPKilo-ROI33-TME-F07]


title: L11_ROI34_Tumor [ICP20th-L11-ICPKilo-ROI34-Tumor-F08]


title: L11_ROI31_Tumor [ICP20th-L11-ICPKilo-ROI31-Tumor-F02]


title: L11_ROI29_TME [ICP20th-L11-ICPKilo-ROI29-TME-E11]


title: L11_ROI32_TME [ICP20th-L11-ICPKilo-ROI32-TME-F05]


title: L11_ROI30_Tumor [ICP20th-L11-ICPKilo-ROI30-Tumor-E12]


title: L11_ROI32_Tumor [ICP20th-L11-ICPKilo-ROI32-Tumor-F04]


title: L11_ROI30_TME [ICP20th-L11-ICPKilo-ROI30-TME-F01]


title: L11_ROI31_TME [ICP20th-L11-ICPKilo-ROI31-TME-F03]


title: L11_ROI42_TME [ICP20th-L11-ICPKilo-ROI42-TME-H01]


title: L11_ROI27_TME [ICP20th-L11-ICPKilo-ROI27-TME-E07]


title: L11_ROI28_Tumor [ICP20th-L11-ICPKilo-ROI28-Tumor-E08]


title: L11_ROI29_Tumor [ICP20th-L11-ICPKilo-ROI29-Tumor-E10]


title: L11_ROI27_Tumor [ICP20th-L11-ICPKilo-ROI27-Tumor-E06]


title: L11_ROI26_TME [ICP20th-L11-ICPKilo-ROI26-TME-E05]


title: L11_ROI24_Tumor [ICP20th-L11-ICPKilo-ROI24-Tumor-D12]


title: L11_ROI24_TME [ICP20th-L11-ICPKilo-ROI24-TME-E01]


title: L11_ROI23_TME [ICP20th-L11-ICPKilo-ROI23-TME-D11]


title: L11_ROI26_Tumor [ICP20th-L11-ICPKilo-ROI26-Tumor-E04]


title: L11_ROI21_TME [ICP20th-L11-ICPKilo-ROI21-TME-D07]


title: L11_ROI25_TME [ICP20th-L11-ICPKilo-ROI25-TME-E03]


title: L11_ROI28_TME [ICP20th-L11-ICPKilo-ROI28-TME-E09]


title: L11_ROI23_Tumor [ICP20th-L11-ICPKilo-ROI23-Tumor-D10]


title: L11_ROI21_Tumor [ICP20th-L11-ICPKilo-ROI21-Tumor-D06]


title: L11_ROI20_TME [ICP20th-L11-ICPKilo-ROI20-TME-D05]


title: L11_ROI19_TME [ICP20th-L11-ICPKilo-ROI19-TME-D03]


title: L11_ROI20_Tumor [ICP20th-L11-ICPKilo-ROI20-Tumor-D04]


title: L11_ROI18_Tumor [ICP20th-L11-ICPKilo-ROI18-Tumor-C12]


title: L11_ROI18_TME [ICP20th-L11-ICPKilo-ROI18-TME-D01]


title: L11_ROI19_Tumor [ICP20th-L11-ICPKilo-ROI19-Tumor-D02]


title: L11_ROI17_Tumor [ICP20th-L11-ICPKilo-ROI17-Tumor-C10]


title: L11_ROI17_TME [ICP20th-L11-ICPKilo-ROI17-TME-C11]


title: L11_ROI16_TME [ICP20th-L11-ICPKilo-ROI16-TME-C09]


title: L11_ROI16_Tumor [ICP20th-L11-ICPKilo-ROI16-Tumor-C08]


title: L11_ROI15_Tumor [ICP20th-L11-ICPKilo-ROI15-Tumor-C06]


title: L11_ROI25_Tumor [ICP20th-L11-ICPKilo-ROI25-Tumor-E02]


title: L11_ROI14_Tumor [ICP20th-L11-ICPKilo-ROI14-Tumor-C04]


title: L11_ROI15_TME [ICP20th-L11-ICPKilo-ROI15-TME-C07]


title: L11_ROI11_TME [ICP20th-L11-ICPKilo-ROI11-TME-B11]


title: L11_ROI12_Tumor [ICP20th-L11-ICPKilo-ROI12-Tumor-B12]


title: L11_ROI11_Tumor [ICP20th-L11-ICPKilo-ROI11-Tumor-B10]


title: L11_ROI12_TME [ICP20th-L11-ICPKilo-ROI12-TME-C01]


title: L11_ROI22_Tumor [ICP20th-L11-ICPKilo-ROI22-Tumor-D08]


title: L11_ROI14_TME [ICP20th-L11-ICPKilo-ROI14-TME-C05]


title: L11_ROI22_TME [ICP20th-L11-ICPKilo-ROI22-TME-D09]


title: L11_ROI13_Tumor [ICP20th-L11-ICPKilo-ROI13-Tumor-C02]


title: L11_ROI09_TME [ICP20th-L11-ICPKilo-ROI09-TME-B07]


title: L11_ROI09_Tumor [ICP20th-L11-ICPKilo-ROI09-Tumor-B06]


title: L11_ROI07_Tumor [ICP20th-L11-ICPKilo-ROI07-Tumor-B02]


title: L11_ROI08_Tumor [ICP20th-L11-ICPKilo-ROI08-Tumor-B04]


title: L11_ROI07_TME [ICP20th-L11-ICPKilo-ROI07-TME-B03]


title: L11_ROI05_TME [ICP20th-L11-ICPKilo-ROI05-TME-A11]


title: L11_ROI04_TME [ICP20th-L11-ICPKilo-ROI04-TME-A09]


title: L11_ROI06_Tumor [ICP20th-L11-ICPKilo-ROI06-Tumor-A12]


title: L11_ROI13_TME [ICP20th-L11-ICPKilo-ROI13-TME-C03]


title: L11_ROI06_TME [ICP20th-L11-ICPKilo-ROI06-TME-B01]


title: L11_ROI04_Tumor [ICP20th-L11-ICPKilo-ROI04-Tumor-A08]


title: L11_ROI03_Tumor [ICP20th-L11-ICPKilo-ROI03-Tumor-A06]


title: L11_ROI03_TME [ICP20th-L11-ICPKilo-ROI03-TME-A07]


title: L11_ROI02_TME [ICP20th-L11-ICPKilo-ROI02-TME-A05]


title: L11_ROI08_TME [ICP20th-L11-ICPKilo-ROI08-TME-B05]


title: L11_ROI10_Tumor [ICP20th-L11-ICPKilo-ROI10-Tumor-B08]


title: L11_ROI01_TME [ICP20th-L11-ICPKilo-ROI01-TME-A03]


title: 5% HEK293T [ZZ203-PP04-G07]

description:
photocleaved oligonucleotide barcodes
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation

source_name: HEK293T/CCRM-CEM mixture

tag: x

tag: panel

value: broad

tag: construct

value: directPCR

value: NEXTSEQ

value: CATATGTT

value: CGAATGAT

value: Giang CPA

value: solid

value: mixed cell line

tag: notes

value: CCRF-CEM

tag: mixprop

tag: hkfactor

tag: bgmean


title: L11_ROI10_TME [ICP20th-L11-ICPKilo-ROI10-TME-B09]

tag: tissue

value: ICPKilo

value: grid/seg

tag: sequencingsaturation

tag: uid

tag: normfactorhk

tag: roi x position

tag: roi y position

tag: nuclei