title: Block_7_005

description: In-situ hybridization

extract_protocol:
Barcoded, UMI-labelled probes targeting specific mRNA were hybridized to formalin-fixed, paraffin-embedded tissues and acquired at Nanostring (Seattle, WA) or the University of Colorado Anschutz Medical Campus (Aurora, CO).
A commercially available protocol was followed  (Nanostring, Seattle, WA).

tag: cell line

tag: batch

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

tag: genedetectionrate

tag: age

tag: Sex

value: Non-hispanic

value: White

tag: smoking

value: Former


title: Block_7_006

status: Public on Jul 29 2024

type: SRA

city: Aurora

first: Ivana

last: Yang

state: CO

address: 1635 Aurora Ct

country: USA

institute: University of Colorado

description: In-situ hybridization

library_source: transcriptomic

data_processing:
Samples were acquired on a Nanostring GeoMx DSP instrument using standard protocols.
Barcoded UMIs from regions of interest were acquired via a photoactivatable linker, sequenced, demuliplexed, and quantified using the R software package "GeoMxWorkflows" according to the vignette (https://bioconductor.org/packages/devel/workflows/vignettes/GeoMxWorkflows/inst/doc/GeomxTools_RNA-NGS_Analysis.html). Raw counts and segments were filtered according to the default quality control thresholds in the vignette, with the modification that segments from which less than 2% of genes in the genome were detected were excluded. Raw counts were normalized using the variant stabilizing transformation function from the DESeq package (https://github.com/thelovelab/DESeq2). Covariates, including donor ("Tissue_ID"), batch, aquisition area ("rounded_area"), region of interest ("Segment"), diagnosis ("Disease"), and MUC5B promoter genotype according to a dominant model (either "G" for GG homozygotes, or "T" for heerozygous or homozygous variants, "Geno"). Downstream analysis used linear mixed effects modeling including region of interest area and batch as fixed effects and donor as a random effect for specimens with multiple regions from the same donor using the "lme4" wrapper, "lmerSeq" (https://github.com/stop-pre16/lmerSeq).
Supplementary files format and content: Variance stabilizing transformed count values.
Supplementary files format and content: dcc

molecule: total RNA

organism: Homo sapiens

growth_protocol: Formalin-fixed, paraffin-embedded tissues were obtained from the Lung Tissue Research Consortum or from patients undergoing lung transplant at the University of Colorado (Colorado Multi-Institutional Review Board protocol #15-1147).

treatment_protocol: Formalin-fixed, paraffin-embedded lung tissues from 75 age-matched donors who were either unaffected (21) or had IPF (54) were arranged into tissue macroarray blocks at National Jewish Health by our histopathologist (D.H.). 310 regions were acquired which fell into one of five categories: Airway, alveolus, transition zones characterized by fibroblastic foci, dense fibrosis, or honeycomb cysts guided by our pathologist (C.D.C.). Specimens were genotyped for the IPF risk variant in the promoter for the MUC5B gene, rs35705950 G:T, with 7 control specimens and 31 IPF specimens containing at least one copy of the variant allele.

tag: origin

value: LTRC

tag: roi area

tag: negative probe_geometric_mean

value: Male

tag: ethnicity

tag: race

tag: muc5b rs35705950_genotype

value: GT

tag: disease

value: IPF

tag: segment roi_morphology

value: HC


title: Block_7_003

description: In-situ hybridization

tag: cell line

value: dense


title: p22rv1-Replicate 2 hypoxia (0.5%O2)

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

data_processing:
Single-end sequencing of 50 bases of each cDNA
Real-time analysis, base calling, adapter clipping and filtering of low quality reads performed by Illumina software according to standard protocols.
Quality assessment was based on the reads using the FASTQC quality control
Read alignment software: miRDeep2 v.2.0.0.5 with mirBase v.21 for annotation of mature miRNAs
Assembly: Hg19
Supplementary files format and content: Cellines_miRNAcounts_unnorm_matrix: matrix with raw counts for every miRNA in every sample . In cases when mature miRNA IDs had duplicates, the duplicate with the highest mean expression was kept.
Supplementary files format and content: Cellines_miRNA_TMMnorm_matrix: matrix with normalized counts (RPM) for every miRNA in every sample. In cases when mature miRNA IDs had duplicates, the duplicate with the highest mean expression was kept.

source_name: Prostate cancer cell line

growth_protocol: The cells were kept in RPMI-1640 medium supplemented with 10% fetal bovine serum, 1% penicillin–streptomycin and 1% L-glutamine.

extract_protocol:
Total RNA was isolated using miRNeasy MiniKit, according to the information given for each sample.
Small RNA preparation for sequencing was performed according to Illumina TruSeq Small RNA library protocols. Briefly, indexed 3’- and 5’end RNA adapters were ligated to 1 ug of isolated total RNA per sample followed by reverse transcription and library amplification. The cDNA was purified on a PAGE gel by cutting out bands corresponding to 140-160 bp (length of miRNA + adapter and index sequences), pooled and ethanol precipitated.

treatment_protocol: Hypoxia treatment (0%, 0.2%, 0.5%, 1%, 2% or 5% O2) of exponentially growing cells was carried out at 60-70% cell confluence in an In Vivo2 200 chamber for 24 hours at 37°C. All hypoxia treatments were performed in duplicate.

tag: tissue

value: Prostate cancer cell line

value: Primary, from xenograft CWR22R subline

tag: treatment

value: Hypoxia


title: Block_7_002

description: In-situ hybridization

tag: batch

tag: negative probe_standard_deviation

tag: limit of_quantification


title: p22rv1-Replicate 2 normoxia (control for 0.5%O2)

value: Normoxia


title: Block_7_007

description: In-situ hybridization

tag: genesdetected

tag: genedetectionrate

tag: age

value: transition


title: Htz1 WT rep2

city: Ithaca

first: Justin

middle: Sungsoo

last: Cha

state: NY

address: 526 Campus Rd

department: Computational Biology

institute: Cornell University

library_source: genomic

data_processing:
ChIP-exo reads were aligned using bwa-mem with the following settings: -v (1)  -T (30) -h (5)
Remove duplicate reads and generate a deduplicated BAM file using picard MarkDuplicates and samtools
Generate forward and reverse BIGWIG files from deduplicated BAM file using deeptools bamCoverage (forward: --binSize 1 --Offset 1 --samFlagInclude 64 --samFlagExclude 16, reverse: --binSize 1 --Offset 1 --samFlagInclude 80 --samFlagExclude 0)
Assembly: sacCer3
Supplementary files format and content: Bigwig for forward strand -- coverage of 5' end of Read 1 across the genome
Supplementary files format and content: Bigwig for reverse strand -- coverage of 5' end of Read 1 across the genome

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: S. Cerevisiae cells

growth_protocol: S. cerevisiae strains containing FLAG-tagged H2A.Z or TAP-tagged Swr1 in WT or mutants were grown in YPD media to an O.D600 of 0.6-0.8 at 25˚C

extract_protocol:
50 mL cell pellets were resuspended in 750 uL FA lysis buffer (50 mM HEPES-KOH, pH7.5, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate and complete protease inhibitor (Roche) along with 1 ml of 0.5 mm acid washed zirconia beads. Lysis was performed by bead beating for 4 cycles of 3 min on and 7 min off in a Mini-Beadbeater-96 machine (Biospec). Whole cell lysates were centrifuged at 14,000 rpm for 3 min at 4 ˚C. Cytoplasmic supernatants were discarded and nuclear pellets were resuspended in 200 uL FA lysis buffer supplemented with 0.1% SDS and 75 uL 0.1 mm zirconia beads. Nuclear samples were sonicated in a Bioruptor (Diagenode) for 4 cycles of 30 sec on and 30 sec off. Samples were centrifuged at 14,000 rpm for 10 min to collect sonicated chromatin fraction which was predominantly enriched with DNA fragments in a range of 100-500 bp in size (verified on agarose gels). Following antibodies were used according to the manufacturer’s instructions to prepare ChIP-exo libraries: anti-FLAG (Sigma, M8823), anti-IgG (Sigma, i5006). Chromatin obtained from 50 mL culture was used for a single ChIP experiment. Appropriate antibodies (3-5 ug per ChIP) were conjugated to protein A/G magnetic Sepharose resin (GE Healthcare Life Sciences) at 4 ˚C for 6-8 hr. Unconjugated antibody was removed, then chromatin sample were immunoprecipitated overnight (12-16 hr) at 4 ˚C. For TAP-tagged samples, 40 uL IgG-Dynabeads slurry was used per sample. Subsequent steps were performed as described previously (Rossi et al., 2018).
ChIP-exo libraries were gel purified and were sequenced in a paired-end mode with NextSeq 500 (Read_1 40 cycles, Read_2 36 cycles).

tag: cell type

value: S. Cerevisiae cells

tag: base strain

tag: genetic modification

value: WT

tag: epitope tag

tag: antibody

tag: growth media

value: YPDad


title: Block_6_027

description: In-situ hybridization

tag: origin

value: University of Colorado

tag: roi area

tag: negative probe_geometric_mean

tag: Sex

tag: ethnicity

value: Non-hispanic

tag: race

tag: smoking

tag: muc5b rs35705950_genotype

tag: disease


title: p22rv1-Replicate 2 hypoxia (1%O2)

tag: tissue

tag: treatment


title: Block_6_026

description: In-situ hybridization

tag: cell line

tag: batch

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

tag: genedetectionrate

tag: age

value: White

value: Former

tag: segment roi_morphology


title: p22rv1-Replicate 2 normoxia (control for 0%O2)

tag: origin


title: p22rv1-Replicate 2 hypoxia (2%O2)


title: Block_7_009

description: In-situ hybridization

value: LTRC

tag: roi area

tag: negative probe_geometric_mean

tag: Sex

value: Male

value: Never


title: p22rv1-Replicate 2 normoxia (control for 2%O2)


title: Block_6_023

description: In-situ hybridization

tag: ethnicity

tag: race

tag: smoking

value: GG

value: IPF

value: airway


title: p22rv1-Replicate 2 normoxia (control for 5%O2)

tag: tissue

value: Prostate cancer cell line

value: Primary, from xenograft CWR22R subline


title: Block_6_022

description: In-situ hybridization

tag: muc5b rs35705950_genotype

tag: disease

value: dense


title: p22rv1-Replicate 2 normoxia (control for 1%O2)

tag: treatment

value: Normoxia


title: Block_6_021

description: In-situ hybridization

tag: cell line

tag: batch

tag: negative probe_standard_deviation

value: transition


title: p22rv1-Replicate 2 hypoxia (5%O2)

value: Hypoxia


title: p22rv1-Replicate 2 hypoxia (0%O2)


title: Block_7_004

description: In-situ hybridization

tag: limit of_quantification

tag: genesdetected

tag: genedetectionrate

value: Female

value: control

value: alveolar


title: p22rv1-Replicate 1 normoxia (control for 0%O2)

tag: origin


title: Block_6_020

description: In-situ hybridization

value: University of Colorado

tag: roi area

tag: age

value: Non-hispanic

value: White

tag: segment roi_morphology

value: HC


title: p22rv1-Replicate 1 hypoxia (0%O2)


title: Block_6_019

description: In-situ hybridization

tag: negative probe_geometric_mean

tag: Sex

value: Male

tag: ethnicity

value: Unk

value: Current


title: Block_6_018

description: In-situ hybridization

tag: race

tag: smoking

value: GG

value: airway


title: p22rv1-Replicate 1 hypoxia (0.2%O2)

tag: tissue

value: Prostate cancer cell line

value: Primary, from xenograft CWR22R subline


title: Block_6_017

description: In-situ hybridization

value: American Indian

value: Never

tag: muc5b rs35705950_genotype

tag: disease

value: IPF


title: Block_7_001

description: In-situ hybridization

tag: cell line

value: LTRC

tag: batch

value: Former

value: GT


title: Block_6_016

description: In-situ hybridization

value: University of Colorado

tag: negative probe_standard_deviation

tag: limit of_quantification

value: transition


title: p22rv1-Replicate 1 normoxia (control for 0.5%O2)

tag: treatment

value: Normoxia


title: Block_6_015

description: In-situ hybridization

tag: origin

tag: genesdetected

tag: genedetectionrate

value: Non-hispanic

value: White

value: alveolar


title: p22rv1-Replicate 1 hypoxia (0.5%O2)

value: Hypoxia


title: p22rv1-Replicate 1 normoxia (control for 1%O2)


title: Block_6_014

description: In-situ hybridization

tag: roi area

tag: age

value: Male

tag: segment roi_morphology


title: p22rv1-Replicate 1 hypoxia (1%O2)


title: Block_6_013

description: In-situ hybridization

tag: negative probe_geometric_mean

tag: Sex

value: Female

tag: ethnicity

value: GG

value: HC


title: p22rv1-Replicate 1 normoxia (control for 2%O2)

tag: tissue

value: Prostate cancer cell line

value: Primary, from xenograft CWR22R subline


title: Block_6_012

description: In-situ hybridization

tag: race

tag: smoking

tag: muc5b rs35705950_genotype

value: IPF


title: p22rv1-Replicate 1 hypoxia (2%O2)


title: Block_6_010

description: In-situ hybridization

tag: cell line

value: LTRC

tag: batch

value: Unk

tag: disease

value: dense


title: Block_6_009

description: In-situ hybridization

tag: negative probe_standard_deviation

tag: limit of_quantification

value: Former

value: airway


title: p22rv1-Replicate 1 normoxia (control for 5%O2)

tag: origin

tag: treatment

value: Normoxia


title: PC3-Replicate 2 normoxia (control for 0%O2)

value: Bone metastasis


title: p22rv1-Replicate 1 hypoxia (5%O2)


title: Block_6_011

description: In-situ hybridization

tag: roi area

tag: genesdetected

tag: genedetectionrate

value: White

value: transition


title: Block_6_008

description: In-situ hybridization

tag: negative probe_geometric_mean

tag: age

tag: segment roi_morphology

value: alveolar


title: Block_6_007

description: In-situ hybridization

value: University of Colorado

tag: Sex

value: Male

tag: ethnicity

value: Non-hispanic

value: Never


title: Block_6_006

description: In-situ hybridization

tag: race

tag: smoking

value: GG


title: p22rv1-Replicate 1 normoxia (control for 0.2%O2)

tag: tissue

value: Prostate cancer cell line

value: Primary, from xenograft CWR22R subline


title: PC3-Replicate 2 hypoxia (0.2%O2)

value: Hypoxia


title: PC3-Replicate 2 hypoxia (0%O2)


title: PC3-Replicate 2 normoxia (control for 0.5%O2)


title: Block_6_005

description: In-situ hybridization

tag: cell line

tag: batch

tag: muc5b rs35705950_genotype

value: IPF


title: PC3-Replicate 2 normoxia (control for 0.2%O2)


title: PC3-Replicate 2 hypoxia (0.5%O2)


title: Block_6_002

description: In-situ hybridization

tag: negative probe_standard_deviation

tag: limit of_quantification

value: Unk

tag: disease

value: control


title: PC3-Replicate 2 normoxia (control for 1%O2)

tag: origin

tag: treatment


title: Block_4-2_059

description: In-situ hybridization

value: LTRC

tag: roi area

tag: genesdetected

tag: genedetectionrate

value: Not Hispanic or Latino

value: Caucasian

value: nonsmoker


title: PC3-Replicate 2 normoxia (control for 2%O2)

value: Bone metastasis

value: Normoxia


title: Block_4-2_057

description: In-situ hybridization

tag: negative probe_geometric_mean

tag: age

value: Female

value: GT

tag: segment roi_morphology

value: alveolar


title: Block_4-2_056

description: In-situ hybridization

tag: Sex

tag: ethnicity

tag: race


title: Block_4-2_055

description: In-situ hybridization

tag: cell line

tag: smoking

value: former

value: airway


title: Block_4-2_054

description: In-situ hybridization

tag: batch

tag: muc5b rs35705950_genotype

value: GG


title: PC3-Replicate 2 hypoxia (1%O2)

tag: tissue

value: Prostate cancer cell line


title: PC3-Replicate 2 normoxia (control for 5%O2)


title: Block_4-2_053

description: In-situ hybridization

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: disease


title: Block_6_004

description: In-situ hybridization

tag: origin

value: University of Colorado

tag: roi area

value: Male

value: Non-hispanic

value: White

value: Never


title: PC3-Replicate 2 hypoxia (5%O2)

tag: treatment

value: Hypoxia


title: PC3-Replicate 1 normoxia (control for 0%O2)


title: Block_6_003

description: In-situ hybridization

tag: negative probe_geometric_mean

tag: genesdetected

tag: genedetectionrate

value: IPF

value: HC


title: Block_4-2_052

description: In-situ hybridization

tag: age

tag: Sex

value: non-hispanic

value: white

value: TT

tag: segment roi_morphology


title: Block_6_001

description: In-situ hybridization

tag: cell line

tag: ethnicity

value: Unk

tag: race

value: control


title: Block_4-2_050

description: In-situ hybridization

tag: batch

tag: smoking

tag: muc5b rs35705950_genotype

value: transition


title: ICH_CONTROL 1

type: RNA

city: BORDEAUX

first: Estibaliz

last: LAZARO

address: Avenue Magellan

country: France

institute: Bordeaux Hospital University

description: CONTROL 1

data_processing:
Gene-level counts were determined using featureCounts packgae
Raw counts were analyzed for differential expression
Standard normalization applies a sample-specific correction factor to all the target probes. It uses a combination of Positive Control Normalization, which uses synthetic positive control targets, and CodeSet Content Normalization, which uses housekeeping genes.
fold_change.txt = the ratio of each value between the patient and the median of the controls.
log2.txt = each value using the value of the logarithm function with base two.

label: not provided

source_name: placental tissue

extract_protocol: RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).

tag: group

value: Control

tag: tissue

value: placental tissue

tag: age (years)

tag: gestational age (years)

value: Caucasian

tag: bmi (kg/m2)

tag: active smoking

value: Yes

tag: chi history

value: No

tag: chi grade

value: no CHI

tag: ongoing treatment (when analysis was performed)

value: No treatment

tag: cesarean section

tag: birth weight

tag: newborn sex

value: female


title: ICH_CONTROL 2

description: CONTROL 2


title: ICH_CONTROL 4

description: CONTROL 4

value: male


title: ICH_CONTROL 5

description: CONTROL 5


title: ICH_CONTROL 6

description: CONTROL 6


title: Block_4-2_049

description: In-situ hybridization

tag: cell line

tag: origin

value: University of Colorado

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

tag: genedetectionrate

tag: age

tag: Sex

value: Male

tag: ethnicity

value: Never

tag: disease

value: IPF

tag: segment roi_morphology


title: ICH_CONTROL 3

description: CONTROL 3

tag: group

tag: tissue

tag: age (years)

tag: gestational age (years)

tag: race

tag: bmi (kg/m2)

tag: active smoking

tag: chi history

tag: chi grade


title: Block_4-2_060

description: In-situ hybridization

tag: cell line

tag: origin

value: LTRC

tag: batch

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: limit of_quantification

value: Not Hispanic or Latino

tag: smoking

value: nonsmoker

tag: muc5b rs35705950_genotype

value: GG

value: alveolar


title: Block_4-2_061

description: In-situ hybridization

tag: genesdetected

tag: genedetectionrate

tag: age

tag: Sex

tag: ethnicity

tag: disease

value: control

tag: segment roi_morphology

value: airway


title: ICH_SAMPLE 18

description: SAMPLE 18

tag: group

value: Test

tag: tissue

value: placental tissue

tag: age (years)

tag: gestational age (years)

tag: race

value: Caucasian

tag: bmi (kg/m2)

tag: active smoking

value: Yes

tag: chi history

tag: chi grade

tag: ongoing treatment (when analysis was performed)

tag: cesarean section

tag: birth weight

tag: newborn sex


title: ICH_SAMPLE 17

description: SAMPLE 17

value: No

value: No treatment

value: female


title: Block_4-2_058

description: In-situ hybridization

tag: cell line

tag: origin

tag: batch

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

tag: genedetectionrate

tag: age

tag: Sex

value: Female

tag: smoking

tag: muc5b rs35705950_genotype

value: GT


title: Block_4-2_044

description: In-situ hybridization

value: University of Colorado

value: Male

tag: ethnicity

value: non-hispanic

tag: race

value: white

value: Never

tag: disease

value: IPF

tag: segment roi_morphology

value: transition


title: PC3-Replicate 2 hypoxia (2%O2)

tag: tissue

value: Prostate cancer cell line

value: Bone metastasis

tag: treatment

value: Hypoxia


title: PC3-Replicate 1 normoxia (control for 0.2%O2)

tag: origin

value: Normoxia


title: Block_4-2_046

description: In-situ hybridization

tag: cell line

tag: batch

tag: roi area

value: HC


title: Block_4-2_045

description: In-situ hybridization

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: limit of_quantification


title: Block_4-2_047

description: In-situ hybridization

tag: genesdetected

tag: genedetectionrate

tag: age

value: TT

value: dense


title: Block_4-2_043

description: In-situ hybridization

tag: Sex

tag: smoking

tag: muc5b rs35705950_genotype


title: PC3-Replicate 1 hypoxia (0%O2)


title: PC3-Replicate 1 hypoxia (0.2%O2)


title: Block_4-2_021

description: In-situ hybridization

value: LTRC

tag: ethnicity

value: Not Hispanic or Latino

tag: race

value: African-American

value: former

value: GG

tag: disease


title: Block_4-2_041

description: In-situ hybridization

value: University of Colorado

value: Male

value: non-hispanic

value: GT

tag: segment roi_morphology

value: airway


title: Block_4-2_020

description: In-situ hybridization

tag: origin

value: Female

value: IPF


title: ICH_SAMPLE 16

description: SAMPLE 16

tag: group

value: Test

tag: tissue

value: placental tissue

tag: age (years)

tag: gestational age (years)

value: Caucasian

tag: bmi (kg/m2)

tag: active smoking

value: No

tag: chi history

tag: chi grade

tag: ongoing treatment (when analysis was performed)

value: No treatment

tag: cesarean section

value: Yes

tag: birth weight

tag: newborn sex

value: female


title: ICH_SAMPLE 15

description: SAMPLE 15

value: Black

value: LDA + low molecular weight heparin + Immunoglobulins + hydroxychlorquine


title: PC3-Replicate 1 normoxia (control for 0.5%O2)

value: Prostate cancer cell line

value: Bone metastasis

tag: treatment

value: Normoxia


title: Block_4-2_051

description: In-situ hybridization

tag: cell line

value: University of Colorado

tag: batch

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

tag: genedetectionrate

tag: age

tag: Sex

value: Male

tag: ethnicity

value: non-hispanic

tag: race

value: white

tag: smoking

value: Never

tag: muc5b rs35705950_genotype

value: TT

value: transition


title: Block_4-2_017

description: In-situ hybridization

tag: origin

value: LTRC

value: Female

value: Not Hispanic or Latino

value: African-American

value: former

value: GG

tag: disease

value: IPF

tag: segment roi_morphology


title: ICH_SAMPLE 11

description: SAMPLE 11

tag: group

value: Test

tag: tissue

value: placental tissue

tag: age (years)

value: Black

tag: bmi (kg/m2)

tag: active smoking

tag: chi history

tag: chi grade

tag: ongoing treatment (when analysis was performed)

tag: cesarean section

value: No

tag: birth weight

tag: newborn sex

value: male


title: Block_4-2_019

description: In-situ hybridization

tag: cell line

tag: batch

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

tag: genedetectionrate

tag: age

tag: Sex

tag: ethnicity

tag: race

value: dense


title: PC3-Replicate 1 hypoxia (0.5%O2)

tag: tissue

value: Prostate cancer cell line

tag: origin

value: Bone metastasis

tag: treatment

value: Hypoxia


title: PC3-Replicate 1 normoxia (control for 1%O2)

value: Normoxia


title: Block_4-2_018

description: In-situ hybridization

value: LTRC

tag: smoking

tag: muc5b rs35705950_genotype

tag: disease

tag: segment roi_morphology

value: transition


title: PC3-Replicate 1 hypoxia (1%O2)


title: ICH_SAMPLE 12

description: SAMPLE 12

tag: group

tag: age (years)

tag: bmi (kg/m2)

tag: active smoking

tag: chi history

tag: chi grade

tag: ongoing treatment (when analysis was performed)

tag: cesarean section

tag: birth weight

tag: newborn sex

value: female


title: ICH_SAMPLE 13

description: SAMPLE 13

tag: tissue

tag: gestational age (years)

tag: race

value: Caucasian

value: No treatment

value: Yes


title: Block_4-2_016

description: In-situ hybridization

tag: cell line

tag: origin

tag: batch

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

tag: genedetectionrate

tag: age

tag: Sex

value: Female

tag: ethnicity

value: Not Hispanic or Latino

value: African-American

tag: smoking

value: former

value: GG

value: IPF

value: airway


title: Block_4-2_015

description: In-situ hybridization

value: Male

tag: muc5b rs35705950_genotype

tag: disease

tag: segment roi_morphology

value: alveolar


title: PC3-Replicate 1 normoxia (control for 2%O2)

tag: tissue

value: Prostate cancer cell line

value: Bone metastasis

tag: treatment


title: Block_4-2_013

description: In-situ hybridization

tag: cell line

tag: origin

value: LTRC

tag: race


title: Block_4-2_011

description: In-situ hybridization

tag: batch

tag: roi area

tag: negative probe_geometric_mean

value: dense


title: ICH_SAMPLE 10

description: SAMPLE 10

tag: group

value: Test

value: placental tissue

tag: age (years)

value: Black

tag: bmi (kg/m2)

tag: active smoking

tag: chi history

tag: chi grade

tag: ongoing treatment (when analysis was performed)

tag: cesarean section

tag: birth weight

tag: newborn sex

value: female


title: Block_4-2_008

description: In-situ hybridization

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

tag: genedetectionrate

tag: age

tag: Sex

tag: ethnicity

value: White

tag: smoking

tag: muc5b rs35705950_genotype

tag: disease

tag: segment roi_morphology


title: ICH_SAMPLE 8

description: SAMPLE 8

tag: group

tag: tissue

tag: age (years)

tag: gestational age (years)

tag: race

value: Caucasian

tag: bmi (kg/m2)

tag: active smoking

value: Yes

tag: chi history

value: No

value: No treatment

value: male


title: Block_4-2_009

description: In-situ hybridization

tag: cell line

tag: origin

tag: batch

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

value: Not Hispanic or Latino

value: former

value: GG

value: IPF

value: transition


title: Block_4-2_014

description: In-situ hybridization

value: LTRC

tag: genedetectionrate

tag: age

tag: Sex

value: Male

tag: ethnicity

value: African-American

tag: smoking

tag: muc5b rs35705950_genotype

tag: disease

tag: segment roi_morphology

value: alveolar


title: PC3-Replicate 1 hypoxia (5%O2)

tag: tissue

value: Prostate cancer cell line

value: Bone metastasis

tag: treatment

value: Hypoxia


title: Block_4-2_007

description: In-situ hybridization

tag: cell line

tag: origin

tag: race

value: White


title: Block_4-2_040

description: In-situ hybridization

value: University of Colorado

tag: batch

tag: roi area

tag: negative probe_geometric_mean

value: non-hispanic

value: white

value: Never

value: GT


title: ICH_SAMPLE 7

description: SAMPLE 7

tag: group

value: Test

value: placental tissue

tag: age (years)

tag: gestational age (years)

value: Caucasian

tag: bmi (kg/m2)

tag: active smoking

value: Yes

tag: chi history

value: No

tag: chi grade

tag: ongoing treatment (when analysis was performed)

value: No treatment

tag: cesarean section

tag: birth weight

tag: newborn sex

value: male


title: Block_4-2_006

description: In-situ hybridization

tag: cell line

value: LTRC

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

tag: genedetectionrate

tag: age

tag: Sex

value: Male

tag: ethnicity

value: Not Hispanic or Latino

tag: smoking

value: former

tag: muc5b rs35705950_genotype

value: GG

tag: disease

value: IPF

tag: segment roi_morphology

value: dense


title: PC3-Replicate 1 hypoxia (2%O2)

tag: tissue

value: Prostate cancer cell line

tag: origin

value: Bone metastasis

tag: treatment

value: Hypoxia


title: ICH_SAMPLE 14

description: SAMPLE 14

tag: group

value: Test

tag: age (years)

tag: gestational age (years)

tag: race

value: Black

tag: bmi (kg/m2)

tag: active smoking

tag: chi history

tag: chi grade

tag: ongoing treatment (when analysis was performed)

value: LDA

tag: cesarean section

tag: birth weight


title: ICH_SAMPLE 9

description: SAMPLE 9

value: placental tissue

value: Yes

tag: newborn sex

value: female


title: ICH_SAMPLE 5

description: SAMPLE 5

value: No

value: No treatment


title: Block_4-2_005

description: In-situ hybridization

tag: cell line

value: LTRC

tag: batch

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

tag: genedetectionrate

tag: age

tag: Sex

value: Male

tag: ethnicity

value: White

tag: smoking

tag: muc5b rs35705950_genotype

tag: disease

value: HC


title: PC3-Replicate 1 normoxia (control for 5%O2)

tag: tissue

tag: origin

tag: treatment

value: Normoxia


title: Tumor biopsy 91

data_processing:
Single-end sequencing of 50 bases of each cDNA
Real-time analysis, base calling, adapter clipping and filtering of low quality reads performed by Illumina software according to standard protocols.
Quality assessment was based on the reads using the FASTQC quality control
Read alignment software: miRDeep2 v.2.0.0.5 with mirBase v.21 for annotation of mature miRNAs
Assembly: Hg19
Supplementary files format and content: Funcprost_miRNAcounts_unnorm_matrix: matrix with raw counts for every miRNA in every sample . In cases when mature miRNA IDs had duplicates, the duplicate with the highest mean expression was kept.
Supplementary files format and content: Funcprost_miRNA_TMMnorm_matrix: matrix with normalized counts (RPM) for every miRNA in every sample. In cases when mature miRNA IDs had duplicates, the duplicate with the highest mean expression was kept.

source_name: Prostate tumor

growth_protocol: 1-2 punch biopsies (T1 and/or T2) were collected from each patient at the time of surgery

extract_protocol:
Total RNA was isolated from a piece of each biopsy (10 slices x 20μm), using miRNeasy MiniKit (Qiagen, Hilden, Germany), according to the information given for each sample. All samples had an RNA integrity number (RIN) of 6 or above, as assessed by the Agilent 2100 Bioanalyzer (Agilent Technology, Santa Clara, CA, USA).
Small RNA preparation for sequencing was performed according to Illumina TruSeq Small RNA library protocols. Briefly, indexed 3’- and 5’end RNA adapters were ligated to 1 ug of isolated total RNA per sample followed by reverse transcription and library amplification. The cDNA was purified on a PAGE gel by cutting out bands corresponding to 140-160 bp (length of miRNA + adapter and index sequences), pooled and ethanol precipitated.

treatment_protocol: The samples were immediately snap-frozen in liquid nitrogen and stored at -80 C until used for analysis. Biopsies with more than 75% malignant glands and less than 50% stroma in HE stained sections from the specimen were used further.

value: Prostate tumor

tag: histology

value: Adeno carcinoma

tag: d'amico risk_classification

tag: tumor gleason_score_pathology

tag: tumor isup_grade_group

tag: pathological tumor_stage_(2vs3vs4)

tag: lymph node_status


title: Block_4-2_010

description: In-situ hybridization

tag: cell line

tag: batch

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

value: Not Hispanic or Latino

tag: race

value: African-American

value: GG

value: IPF

tag: segment roi_morphology

value: airway


title: Tumor biopsy 90

tag: tissue


title: Block_4-2_004

description: In-situ hybridization

tag: origin

tag: genedetectionrate

tag: age

tag: Sex

tag: ethnicity

tag: smoking

value: former

tag: muc5b rs35705950_genotype

tag: disease


title: ICH_SAMPLE 3

description: SAMPLE 3

tag: group

value: Test

value: placental tissue

tag: age (years)

tag: gestational age (years)

value: Caucasian

tag: bmi (kg/m2)

tag: active smoking

value: Yes

tag: chi history

tag: chi grade

tag: ongoing treatment (when analysis was performed)

tag: cesarean section

tag: birth weight

tag: newborn sex


title: Block_3-2_014

description: In-situ hybridization

tag: cell line

tag: origin

value: LTRC

tag: batch

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

tag: genedetectionrate

tag: age

tag: race

value: control

tag: segment roi_morphology


title: Tumor biopsy 89

tag: tissue

tag: histology

tag: d'amico risk_classification

tag: tumor gleason_score_pathology

tag: tumor isup_grade_group

tag: pathological tumor_stage_(2vs3vs4)

tag: lymph node_status


title: ICH_SAMPLE 6

description: SAMPLE 6

tag: group

tag: age (years)

tag: gestational age (years)

value: Black

tag: bmi (kg/m2)

tag: active smoking

value: No

tag: chi history

tag: chi grade

tag: ongoing treatment (when analysis was performed)

value: No treatment

tag: cesarean section

tag: birth weight

tag: newborn sex

value: male


title: Block_4-2_003

description: In-situ hybridization

tag: cell line

tag: origin

tag: batch

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

tag: genedetectionrate

tag: age

tag: Sex

value: Female

tag: ethnicity

tag: race

value: White

tag: smoking

tag: muc5b rs35705950_genotype

value: GT

tag: disease

tag: segment roi_morphology

value: alveolar


title: Block_3-2_013

description: In-situ hybridization

tag: cell line

value: Male

value: Not Hispanic or Latino

value: GG


title: Tumor biopsy 87

tag: tissue

value: Prostate tumor

tag: histology

value: Adeno carcinoma

tag: d'amico risk_classification

tag: tumor gleason_score_pathology

tag: tumor isup_grade_group

tag: pathological tumor_stage_(2vs3vs4)

tag: lymph node_status


title: Block_3-2_011

description: In-situ hybridization

tag: origin

tag: batch

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

tag: genedetectionrate

value: Caucasian

value: former

value: airway


title: ICH_SAMPLE 4

description: SAMPLE 4

tag: group

value: Test

value: placental tissue

tag: age (years)

tag: gestational age (years)

tag: race

tag: bmi (kg/m2)

tag: active smoking

value: Yes

tag: chi history

tag: chi grade

tag: ongoing treatment (when analysis was performed)

tag: cesarean section

tag: birth weight

tag: newborn sex

value: female


title: Block_3-2_009

description: In-situ hybridization

tag: cell line

tag: origin

value: LTRC

tag: batch

tag: roi area

tag: negative probe_geometric_mean

tag: age

tag: Sex

tag: ethnicity

tag: smoking

tag: muc5b rs35705950_genotype

tag: disease

value: control

tag: segment roi_morphology


title: ICH_SAMPLE 2

description: SAMPLE 2

tag: group

tag: tissue

tag: age (years)

tag: gestational age (years)

tag: race

tag: bmi (kg/m2)

tag: active smoking

value: No

tag: chi history

tag: chi grade

value: No treatment

value: male


title: Block_3-2_012

description: In-situ hybridization

tag: cell line

tag: origin

tag: batch

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

tag: genedetectionrate

value: Male

value: alveolar


title: T. brucei 427-060RS_C

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description: 060_TLF Revertant_C

data_processing:
Raw reads were trimmed with the default settings of fastp (v0.19.5)
alignment: Bowtie2 v2.3.4.1 using sensitive local alignment mode
sorting: Samtools v1.2 using default parameters
expression levels: DESeq2 variance stabilized counts
Assembly: Trypanosoma brucei Lister 427 (v9.0 from TriTrypDB.org)
Supplementary files format and content: tab-delimited text file, see metafile for column headers

molecule: polyA RNA

organism: Trypanosoma brucei

source_name: Tb Lister 427-221

growth_protocol: Bloodstream form T. brucei cells were grown as described in Hirumi et al. (1980).  Parasitology 80, 371–382.

extract_protocol:
Total RNA was isolated from T. brucei cultures using TriPure, according to the manufacturer’s instructions. 5x107 cells were used for each prep.
Schmitz lab

treatment_protocol: WT cells were treated with TLF for four months and resistant cells generated as described in Kieft et al. (2010) PNAS 107,16137-16141. Removal of TLF pressure for two weeks led to generation of TLF sensitive (Revertant) cells also as previoulsy described.

tag: tissue

value: Lister 427 Blood Stream Form


title: Block_4-2_002

description: In-situ hybridization

tag: age

tag: Sex

value: Female

tag: ethnicity

value: Not Hispanic or Latino

value: White

tag: smoking

tag: muc5b rs35705950_genotype

value: GT

tag: disease

tag: segment roi_morphology


title: Block_4-2_001

description: In-situ hybridization

tag: cell line

tag: race

value: former

value: airway


title: T. brucei 427-060RS_B

description: 060_TLF Revertant_B


title: ICH_SAMPLE 1

description: SAMPLE 1

tag: group

value: Test

value: placental tissue

tag: age (years)

tag: gestational age (years)

tag: bmi (kg/m2)

tag: active smoking

tag: chi history

tag: chi grade

tag: ongoing treatment (when analysis was performed)

value: Low dose aspirine (LDA)

tag: cesarean section

tag: birth weight

tag: newborn sex


title: Tumor biopsy 88

tag: tissue

value: Prostate tumor

tag: histology

value: Adeno carcinoma

tag: d'amico risk_classification

tag: tumor gleason_score_pathology

tag: tumor isup_grade_group

tag: pathological tumor_stage_(2vs3vs4)

tag: lymph node_status


title: Block_4-2_012

description: In-situ hybridization

tag: cell line

tag: origin

value: LTRC

tag: batch

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

tag: genedetectionrate

tag: age

tag: Sex

tag: ethnicity

tag: race

value: African-American

tag: smoking

tag: muc5b rs35705950_genotype

value: GG

tag: disease

value: IPF

tag: segment roi_morphology

value: transition


title: Tumor biopsy 86

tag: tissue

tag: histology

tag: d'amico risk_classification

tag: tumor gleason_score_pathology

tag: tumor isup_grade_group

tag: pathological tumor_stage_(2vs3vs4)

tag: lymph node_status


title: Block_3-2_005

description: In-situ hybridization

tag: cell line

tag: origin

value: University of Colorado

tag: batch

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

value: Male

value: non-hispanic

value: white

value: Never


title: Block_3-2_010

description: In-situ hybridization

tag: genedetectionrate

tag: age

tag: Sex

tag: ethnicity

value: Not Hispanic or Latino

tag: race

value: Caucasian

tag: smoking

value: former

tag: muc5b rs35705950_genotype

value: GT

tag: disease

value: control

value: alveolar


title: Block_3-2_006

description: In-situ hybridization

tag: segment roi_morphology

value: airway


title: Tumor biopsy 85

tag: tissue

value: Prostate tumor

tag: histology

value: Adeno carcinoma

tag: d'amico risk_classification

tag: tumor gleason_score_pathology

tag: tumor isup_grade_group

tag: pathological tumor_stage_(2vs3vs4)

tag: lymph node_status


title: Block_3-2_003

description: In-situ hybridization

tag: cell line

tag: origin

tag: batch

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

value: dense


title: Block_3-2_002

description: In-situ hybridization

tag: genedetectionrate

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: smoking

tag: muc5b rs35705950_genotype

tag: disease

value: IPF


title: T. brucei 427-060RS_A

description: 060_TLF Revertant_A

tag: tissue

value: Lister 427 Blood Stream Form


title: Block_3-2_004

description: In-situ hybridization

tag: cell line

value: University of Colorado

tag: segment roi_morphology

value: transition


title: Tumor biopsy 84

tag: histology

tag: d'amico risk_classification

tag: tumor gleason_score_pathology

tag: tumor isup_grade_group

tag: pathological tumor_stage_(2vs3vs4)

tag: lymph node_status


title: Tumor biopsy 83


title: Block_3-2_001

description: In-situ hybridization

tag: origin

tag: batch

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

tag: genedetectionrate

value: Female

value: non-hispanic

value: Former-3 pack years


title: T. brucei 427-060R_C

description: 060_TLF Resistant_C

tag: tissue


title: Tumor biopsy 82


title: Tumor biopsy 81


title: GCA212-Severe-TI-Surgical-Rep3

city: nashville

first: Qi

last: Liu

state: TN

address: 2525 West End Ave

institute: Vanderbilt univeristy medical center

description:
7564-YX-17_S1_L005
Raw_counts_TI_Surgical.txt.gz
Annotation_TI_surgical.txt.gz

library_source: transcriptomic single cell

data_processing:
Single-cell RNAseq reads were filtered, demultiplexed, and quantified by dropEst to generate cell-by-gene count matrices. Specifically, reads with expected structure were kept, and cell barcodes and UMI were extracted by dropTag.
Assembly: Demultiplexed reads were aligned to the human reference transcriptome GRCh38 using STAR
Supplementary files format and content: Processed data includes raw count and meta data with annotation for each cell.

source_name: Terminal Ileum

extract_protocol:
Tissues were incubated in a chelating buffer (0.5M EDTA, 0.1M DTT in DPBS) for 1.25hrs, and then transferred to cold active protease (5 mg/ml Protease from Bacillus licheniformis, 2.5 mg/mL DNase in PBS) for 25 minutes at 4˚c. Tissues were then pipetted 10-20 times to yield single cells. Cell suspensions were filtered, washed, and inspected for count and quality before loading onto inDrops for microfluidic capture.
TruDrop libraries, at a 2 nM standard loading concentration, were pooled with other Illumina compatible libraries, and sequenced to various target depths (50–500 million reads)

value: Terminal Ileum

tag: patient

value: Severe


title: T. brucei 427-060R_B

description: 060_TLF Resistant_B


title: GCA212-Severe-TI-Surgical-Rep1

description:
7564-YX-15_S1_L005
Raw_counts_TI_Surgical.txt.gz
Annotation_TI_surgical.txt.gz


title: GCA212-Normal_CD-AC-Surgical-Rep2

description:
7564-YX-16_S1_L005
Raw_counts_AC_Surgical.txt.gz
Annotation_AC_surgical.txt.gz

source_name: Ascending Colon

value: Ascending Colon


title: Tumor biopsy 80


title: T. brucei 427-060R_A

description: 060_TLF Resistant_A


title: GCA211-Control-AC-Surgical-Rep5

description:
7564-YX-14_S1_L005
Raw_counts_AC_Surgical.txt.gz
Annotation_AC_surgical.txt.gz

value: Control


title: T. brucei WT 427_C


title: T. brucei WT 427_B


title: GCA211-Control-AC-Surgical-Rep3

description:
7564-YX-12_S1_L005
Raw_counts_AC_Surgical.txt.gz
Annotation_AC_surgical.txt.gz


title: Tumor biopsy 78


title: GCA211-Control-AC-Surgical-Rep1

description:
7564-YX-10_S1_L005
Raw_counts_AC_Surgical.txt.gz
Annotation_AC_surgical.txt.gz


title: Tumor biopsy 79


title: GCA211-Control-AC-Surgical-Rep2

description:
7564-YX-11_S1_L005
Raw_counts_AC_Surgical.txt.gz
Annotation_AC_surgical.txt.gz


title: GCA211-Control-TI-Surgical-Rep1

description:
7564-YX-7_S1_L005
Raw_counts_TI_Surgical.txt.gz
Annotation_TI_surgical.txt.gz


title: GCA211-Control-TI-Surgical-Rep3

description:
7564-YX-9_S1_L005
Raw_counts_TI_Surgical.txt.gz
Annotation_TI_surgical.txt.gz


title: GCA211-Control-TI-Surgical-Rep2

description:
7564-YX-8_S1_L005
Raw_counts_TI_Surgical.txt.gz
Annotation_TI_surgical.txt.gz


title: T. brucei WT 427_A


title: Tumor biopsy 76


title: Tumor biopsy 77


title: GCA210-Normal_CD-AC-Surgical-Rep2

description:
7564-YX-4_S1_L005
Raw_counts_AC_Surgical.txt.gz
Annotation_AC_surgical.txt.gz


title: Tumor biopsy 75


title: GCA210-Normal_CD-AC-Surgical-Rep1

description:
7564-YX-2_S1_L005
Raw_counts_AC_Surgical.txt.gz
Annotation_AC_surgical.txt.gz


title: GCA210-Mild-TI-Surgical-Rep2

description:
7564-YX-3_S1_L005
Raw_counts_TI_Surgical.txt.gz
Annotation_TI_surgical.txt.gz

value: Mild


title: PBMC_COVID_nonsurvivor_66_Day 7

city: COLUMBUS

first: Joseph

middle: S

last: Bednash

state: OH

address: 473 W 12th Avenue, DHLRI 509

department: Medicine

institute: Ohio State University

data_processing:
fastq files from each samples were sequenced in replicate and concatenated for each sample.
HiSAT2 (v2.1.0) was used to align reads to the hg GRCh38.96 reference genome and obtain feature counts.
DESeq2 was used to perform differential expression analysis.
Assembly: human genome GRCh38.96 (GCF_000001405.26)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Blood - PBMCs

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Miniprep Plus kit (Zymo Research) followed in tube DNaseI treatment and RNA cleanup with the Monarch RNA Cleanup Kit (New England BioLabs), per the manufacturer’s protocols.
RNA-seq libraries were generated using 100ng total RNA and the following kits and conditions: NEBNExt Ultra II Directional (stranded) RNA Library Prep Kit for Illumina, NEBNext rRNA Depletion Kit, and NEBNExt Multiplex Oligos for Illumina Unique Dual Index Primer Pairs (All New England BioLabs).

value: Blood - PBMCs

tag: disease status

tag: subject

tag: time

value: Day 7


title: GCA210-Mild-TI-Surgical-Rep1

description:
7564-YX-1_S1_L005
Raw_counts_TI_Surgical.txt.gz
Annotation_TI_surgical.txt.gz


title: PBMC_COVID_nonsurvivor_66_Day 3

value: Day 3


title: GCA211-Control-AC-Surgical-Rep4

description:
7564-YX-13_S1_L005
Raw_counts_AC_Surgical.txt.gz
Annotation_AC_surgical.txt.gz


title: Tumor biopsy 74

value: Prostate tumor

tag: histology

value: Adeno carcinoma

tag: d'amico risk_classification

tag: tumor gleason_score_pathology


title: GCA209-Quiescent-AC-Surgical-Rep2

description:
7408-YX-17_S1_L005
Raw_counts_AC_Surgical.txt.gz
Annotation_AC_surgical.txt.gz

value: Quiescent


title: Tumor biopsy 73

tag: tumor isup_grade_group

tag: pathological tumor_stage_(2vs3vs4)

tag: lymph node_status


title: PBMC_COVID_nonsurvivor_54_Day 7


title: GCA209-Mild-TI-Surgical-Rep1

description:
7408-YX-14_S1_L005
Raw_counts_TI_Surgical.txt.gz
Annotation_TI_surgical.txt.gz


title: GCA208-Quiescent-TI-Surgical

description:
7408-YX-10_S1_L005
Raw_counts_TI_Surgical.txt.gz
Annotation_TI_surgical.txt.gz


title: GCA208-Normal_CD-AC-Surgical

description:
7408-YX-9_S1_L005
Raw_counts_AC_Surgical.txt.gz
Annotation_AC_surgical.txt.gz


title: PBMC_COVID_nonsurvivor_66_Day 10

value: Day 10


title: Tumor biopsy 71


title: Tumor biopsy 72


title: PBMC_COVID_nonsurvivor_54_Day 1

value: Day 1


title: PBMC_COVID_nonsurvivor_54_Day 3


title: GCA205-Normal_CD-TI-Surgical

description:
6985-YX-18_S1_L005
Raw_counts_TI_Surgical.txt.gz
Annotation_TI_surgical.txt.gz


title: GCA207-Severe-TI-Surgical-Rep2

description:
6985-YX-24_S1_L005
Raw_counts_TI_Surgical.txt.gz
Annotation_TI_surgical.txt.gz


title: GCA207-Mild-AC-Surgical

description:
6985-YX-23_S1_L005
Raw_counts_AC_Surgical.txt.gz
Annotation_AC_surgical.txt.gz


title: Tumor biopsy 70


title: GCA207-Severe-TI-Surgical-Rep1

description:
6985-YX-22_S1_L005
Raw_counts_TI_Surgical.txt.gz
Annotation_TI_surgical.txt.gz


title: PBMC_COVID_nonsurvivor_48_Day 10


title: GCA204-Severe-TI-Surgical

description:
6985-YX-16_S1_L005
Raw_counts_TI_Surgical.txt.gz
Annotation_TI_surgical.txt.gz


title: Tumor biopsy 69


title: GCA204-Mild-AC-Surgical

description:
6985-YX-17_S1_L005
Raw_counts_AC_Surgical.txt.gz
Annotation_AC_surgical.txt.gz


title: GCA203-Normal_CD-AC-Surgical

description:
6985-YX-15_S1_L005
Raw_counts_AC_Surgical.txt.gz
Annotation_AC_surgical.txt.gz


title: PBMC_COVID_nonsurvivor_66_Day 1


title: GCA209-Quiescent-AC-Surgical-Rep1

description:
7408-YX-15_S1_L005
Raw_counts_AC_Surgical.txt.gz
Annotation_AC_surgical.txt.gz


title: PBMC_COVID_nonsurvivor_48_Day 7


title: Tumor biopsy 68


title: GCA209-Mild-TI-Surgical-Rep2

description:
7408-YX-16_S1_L005
Raw_counts_TI_Surgical.txt.gz
Annotation_TI_surgical.txt.gz


title: PBMC_COVID_nonsurvivor_48_Day 3


title: GCA203-Mild-TI-Surgical

description:
6985-YX-14_S1_L005
Raw_counts_TI_Surgical.txt.gz
Annotation_TI_surgical.txt.gz


title: GCA202-Control-AC-Surgical-Rep4

description:
6199-YX-6_S1_L005
Raw_counts_AC_Surgical.txt.gz
Annotation_AC_surgical.txt.gz


title: PBMC_COVID_nonsurvivor_48_Day 1


title: PBMC_COVID_nonsurvivor_20_Day 10


title: GCA202-Control-TI-Surgical-Rep1

description:
6199-YX-4_S1_L005
Raw_counts_TI_Surgical.txt.gz
Annotation_TI_surgical.txt.gz


title: GCA202-Control-TI-Surgical-Rep2

description:
6199-YX-7_S1_L005
Raw_counts_TI_Surgical.txt.gz
Annotation_TI_surgical.txt.gz


title: GCA202-Control-AC-Surgical-Rep1

description:
6199-YX-1_S1_L005
Raw_counts_AC_Surgical.txt.gz
Annotation_AC_surgical.txt.gz


title: Tumor biopsy 66


title: GCA201-Normal_CD-AC-Surgical

description:
5314-YX-11_S1_L005
Raw_counts_AC_Surgical.txt.gz
Annotation_AC_surgical.txt.gz


title: Tumor biopsy 67


title: GCA202-Control-AC-Surgical-Rep2

description:
6199-YX-2_S1_L005
Raw_counts_AC_Surgical.txt.gz
Annotation_AC_surgical.txt.gz


title: GCA200-Normal_CD-AC-Surgical

description:
5314-YX-7_S1_L005
Raw_counts_AC_Surgical.txt.gz
Annotation_AC_surgical.txt.gz


title: PBMC_COVID_nonsurvivor_20_Day 7


title: GCA201-Severe-TI-Surgical

description:
5314-YX-10_S1_L005
Raw_counts_TI_Surgical.txt.gz
Annotation_TI_surgical.txt.gz


title: PBMC_COVID_nonsurvivor_20_Day 3


title: GCA119-Moderate-AC-Endoscopy-Rep2

description:
7796-YX-6_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz

value: Moderate


title: Tumor biopsy 62


title: GCA202-Control-AC-Surgical-Rep3

description:
6199-YX-5_S1_L005
Raw_counts_AC_Surgical.txt.gz
Annotation_AC_surgical.txt.gz


title: GCA119-Moderate-AC-Endoscopy-Rep1

description:
7796-YX-5_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: Tumor biopsy 60


title: GCA117-Quiescent-TI-Endoscopy

description:
7564-YX-24_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: Tumor biopsy 63


title: GCA200-Severe-TI-Surgical-Rep2

description:
5314-YX-6_S1_L005
Raw_counts_TI_Surgical.txt.gz
Annotation_TI_surgical.txt.gz


title: Tumor biopsy 61


title: Tumor biopsy 65


title: PBMC_COVID_nonsurvivor_11_Day 7


title: PBMC_COVID_nonsurvivor_11_Day 10


title: GCA116-Normal_CD-TI-Endoscopy

description:
7796-YX-2_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: GCA118-Mild-TI-Endoscopy

description:
7796-YX-3_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: Tumor biopsy 58


title: Tumor biopsy 64


title: PBMC_COVID_nonsurvivor_11_Day 3


title: PBMC_COVID_nonsurvivor_11_Day 1


title: Tumor biopsy 57


title: GCA116-Quiescent-AC-Endoscopy

description:
7796-YX-1_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: GCA115-Normal_CD-AC-Endoscopy

description:
7564-YX-23_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: Tumor biopsy 59


title: GCA115-Mild-TI-Endoscopy

description:
7564-YX-22_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: PBMC_COVID_survivor_41_Day 7


title: Tumor biopsy 56


title: PBMC_COVID_nonsurvivor_20_Day 1


title: GCA200-Severe-TI-Surgical-Rep1

description:
5314-YX-5_S1_L005
Raw_counts_TI_Surgical.txt.gz
Annotation_TI_surgical.txt.gz


title: GCA114-Normal_CD-TI-Endoscopy

description:
7564-YX-21_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: GCA112-Normal_CD-AC-Endoscopy

description:
7408-YX-23_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: PBMC_COVID_survivor_41_Day 1


title: PBMC_COVID_survivor_41_Day 3


title: GCA112-Moderate-TI-Endoscopy

description:
7408-YX-22_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: GCA111-Normal_CD-AC-Endoscopy

description:
7408-YX-20_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: GCA118-Normal_CD-AC-Endoscopy

description:
7796-YX-4_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: GCA110-Normal_CD-TI-Endoscopy

description:
7408-YX-18_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: GCA113-Mild-AC-Endoscopy

description:
7564-YX-19_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: Tumor biopsy 53


title: Tumor biopsy 55


title: PBMC_COVID_survivor_40_Day 10


title: Tumor biopsy 54


title: Tumor biopsy 52


title: PBMC_COVID_survivor_40_Day 7


title: GCA108-Quiescent-TI-Endoscopy

description:
7408-YX-13_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: PBMC_COVID_survivor_40_Day 3


title: GCA109-Mild-TI-Endoscopy

description:
7564-YX-5_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: Tumor biopsy 51


title: GCA105-Mild-AC-Endoscopy

description:
7408-YX-11_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: GCA104-Normal_CD-AC-Endoscopy

description:
7408-YX-8_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: Tumor biopsy 49


title: GCA104-Quiescent-TI-Endoscopy

description:
7408-YX-7_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: GCA113-Mild-TI-Endoscopy

description:
7564-YX-18_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: GCA108-Normal_CD-AC-Endoscopy

description:
7408-YX-12_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: PBMC_COVID_survivor_40_Day 1


title: GCA101-Normal_CD-TI-Endoscopy

description:
7408-YX-1_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: PBMC_COVID_survivor_23_Day 10


title: PBMC_COVID_survivor_38_Day 3


title: Tumor biopsy 50


title: GCA103-Normal_CD-AC-Endoscopy

description:
7408-YX-6_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: PBMC_COVID_survivor_38_Day 7


title: PBMC_COVID_survivor_23_Day 7


title: GCA101-Normal_CD-AC-Endoscopy

description:
7408-YX-2_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: GCA102-Normal_CD-TI-Endoscopy

description:
7408-YX-3_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: Tumor biopsy 46


title: GCA100-Normal_CD-TI-Endoscopy

description:
6778-YX-5_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: PBMC_COVID_survivor_23_Day 3


title: PBMC_COVID_survivor_38_Day 1


title: GCA099-Severe-AC-Endoscopy

description:
6985-YX-12_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: GCA110-Normal_CD-AC-Endoscopy

description:
7408-YX-19_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: GCA111-Normal_CD-TI-Endoscopy

description:
7408-YX-21_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: GCA102-Quiescent-AC-Endoscopy

description:
7408-YX-4_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: GCA098-Normal_CD-AC-Endoscopy

description:
6778-YX-4_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: Tumor biopsy 48


title: PBMC_COVID_survivor_23_Day 1


title: GCA109-Mild-AC-Endoscopy

description:
7564-YX-6_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: Tumor biopsy 47


title: PBMC_ARDS_CON_83_Day 10


title: GCA095-Normal_CD-TI-Endoscopy

description:
6778-YX-1_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: GCA100-Normal_CD-AC-Endoscopy

description:
6778-YX-6_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: GCA098-Normal_CD-TI-Endoscopy

description:
6778-YX-3_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: GCA095-Normal_CD-AC-Endoscopy

description:
6778-YX-2_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: PBMC_ARDS_CON_83_Day 7


title: Tumor biopsy 44


title: GCA097-Normal_CD-TI-Endoscopy

description:
6778-YX-21_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: GCA093-Severe-TI-Endoscopy

description:
6985-YX-8_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: PBMC_ARDS_CON_83_Day 3


title: GCA099-Moderate-TI-Endoscopy

description:
6985-YX-13_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: GCA091-Normal_CD-AC-Endoscopy

description:
6985-YX-21_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: PBMC_ARDS_CON_83_Day 1


title: Tumor biopsy 40


title: PBMC_ARDS_CON_79_Day 10


title: GCA091-Normal_CD-TI-Endoscopy

description:
6985-YX-20_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: GCA090-Control-AC-Endoscopy

description:
6778-YX-12_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: GCA094-Moderate-AC-Endoscopy

description:
6985-YX-10_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: Tumor biopsy 38


title: Tumor biopsy 42


title: Tumor biopsy 43


title: GCA090-Control-TI-Endoscopy

description:
6778-YX-11_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: Tumor biopsy 45


title: GCA092-Mild-TI-Endoscopy

description:
6985-YX-6_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: GCA093-Normal_CD-AC-Endoscopy

description:
6985-YX-9_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: myd88_3

city: Bad Nauheim

first: Noah

last: Knoppik

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max-Planck-Institute for Heart and Lung Research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl zebrafish genome version danRer11 (Ensembl release 109) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.0.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: danRer11
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized gene counts.

organism: Danio rerio

source_name: endocardial

extract_protocol:
RNA was isolated from FACS-sorted endocardial cells from a pool of 4 ET(krt4:EGFP); myd88+/+ and 4 ET(krt4:EGFP); myd88-/- ventricles for each sample using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-free DNase set, Qiagen) to avoid contamination by genomic DNA.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

tag: cell type

value: endocardial

tag: genotype

value: 96 hpci


title: Tumor biopsy 41


title: GCA092-Mild-AC-Endoscopy

description:
6985-YX-7_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: GCA089-Mild-AC-Endoscopy

description:
6985-YX-5_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: Tumor biopsy 37


title: Tumor biopsy 36


title: myd88_1


title: Tumor biopsy 39


title: PBMC_ARDS_CON_79_Day 3


title: myd88_2


title: GCA088-Control-AC-Endoscopy

description:
6778-YX-8_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: PBMC_ARDS_CON_63_Day 10


title: Tumor biopsy 35


title: GCA088-Control-TI-Endoscopy

description:
6778-YX-7_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: WT_3


title: PBMC_ARDS_CON_63_Day 7


title: WT_2


title: GCA087-Control-TI-Endoscopy

description:
6778-YX-9_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: Tumor biopsy 34


title: PBMC_ARDS_CON_63_Day 3


title: GCA087-Control-AC-Endoscopy

description:
6778-YX-10_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: PBMC_ARDS_CON_79_Day 7


title: Tumor biopsy 33


title: PBMC_ARDS_CON_63_Day 1


title: WT_1


title: GCA086-Control-TI-Endoscopy

description:
7796-YX-11_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: D5-PATZ1-GTF2i

city: New York

first: Prashant

last: Rajbhandari

state: New York

address: 1468 Madison Ave, Annenberg 18-10

institute: Icahn School of Medicine at Mount Sinai

data_processing:
ChIP-seq pipeline paired_end FASTQ files were processed using the nf-core-chipseq pipeline (v2.0.0). Adapter sequences were removed with Trim Galore. Reads were aligned with Bowtie to GRCm38 (NCBI, p.6, release 108, updated annotations) and duplicates were marked and removed from all samples with picard. Generally speaking, "peaks" refer to regions where at least one of the target samples significantly exceeds its matched control for a given genomic region. Here, peaks were called with macs26 (peak mode: narrow) using a p-value threshold of 0.01 and an effective genome size of 2,650,000,000. Consensus peaks were merged across all samples using BEDTools and annotated to the nearest gene transcriptional start site using HOMER. Peak counts were generated using featureCounts. Analysis performed using Pluto Biosciences (http://pluto.bio)
Assembly: mm10 (GRCm38)
Supplementary files format and content: BigWig

organism: Mus musculus

extract_protocol:
ChIP experiments were performed according to standard protocols (78, 79). Lysed cells were sonicated using a Bioruptor (Diagenode) according to the manufacturer’s protocol, and chromatin was immunoprecipitated with antibodies against PATZ1 (sc-390577, Santa Cruz Biotechnology) for D0 and D5, sequential PATZ1 and GTF2I (PA5-17642, Thermo Fisher) for ChIP-reChip seq, PATZ1 (A10053,Abclonal) for D-2, D0, D5, D8, and IgG (PP64, Millipore) overnight at 4°C in the presence of Protein A beads (GE Healthcare).
ChIP-Seq libraries were prepared using the Kapa LTP Library Preparation Kit (Kapa Biosystems). The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. cDNA libraries were single-end sequenced (50bp) on an Illumina Novaseq.

tag: treatment


title: PBMC_ARDS_CON_30_Day 10


title: Tumor biopsy 32


title: PBMC_ARDS_CON_79_Day 1


title: D0-PATZ1-GTF2i


title: Tumor biopsy 31


title: PBMC_ARDS_CON_30_Day 7


title: GCA085-Normal_CD-TI-Endoscopy

description:
6985-YX-3_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: Tumor biopsy 30


title: PBMC_ARDS_CON_30_Day 3


title: 10T-WATdiff-Day8

data_processing:
ChIP-seq pipeline paired_end FASTQ files were processed using the nf-core-chipseq pipeline (v2.0.0). Adapter sequences were removed with Trim Galore. Reads were aligned with Bowtie to GRCm38 (NCBI, p.6, release 108, updated annotations) and duplicates were marked and removed from all samples with picard. Generally speaking, "peaks" refer to regions where at least one of the target samples significantly exceeds its matched control for a given genomic region. Here, peaks were called with macs26 (peak mode: narrow) using a p-value threshold of 0.01 and an effective genome size of 2,650,000,000. Consensus peaks were merged across all samples using BEDTools and annotated to the nearest gene transcriptional start site using HOMER. Peak counts were generated using featureCounts
Assembly: mm10 GRCm38 (NCBI, p.6, release 108, updated annotations)
Supplementary files format and content: BigWig

extract_protocol:
ChIP experiments were performed according to standard protocols (78, 79). Lysed cells were sonicated using a Bioruptor (Diagenode) according to the manufacturer’s protocol, and chromatin was immunoprecipitated with antibodies against PATZ1 (sc-390577, Santa Cruz Biotechnology) for D0 and D5, sequential PATZ1 and GTF2I (PA5-17642, Thermo Fisher) for ChIP-reChip seq, PATZ1 (A10053,Abclonal) for D-2, D0, D5, D8, and IgG (PP64, Millipore) overnight at 4°C in the presence of Protein A beads (GE Healthcare).
ChIP-Seq libraries were prepared using the Kapa LTP Library Preparation Kit (Kapa Biosystems). The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. cDNA libraries were single-end sequenced (50bp) on an Illumina NOVAseq


title: Input


title: GCA084-Normal_CD-AC-Endoscopy

description:
6985-YX-2_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: Tumor biopsy 29


title: Tumor biopsy 28


title: PBMC_ARDS_CON_30_Day 1


title: GCA083-Normal_CD-AC-Endoscopy

description:
6778-YX-18_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: 10T-WATdiff-Day5


title: 10T-WATdiff-Day0


title: 10T-WATdiff-Day-2


title: Tumor biopsy 26


title: GCA086-Control-AC-Endoscopy

description:
7796-YX-12_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: HLC differentiated day 17 Rep 2

city: Heidelberg

first: Viet Loan

last: Dao Thi

address: Im Neuenheimer Feld 344

department: Virology

institute: Heidelberg University

data_processing:
Sequencing reads were trimmed for low-quality/adapter sequence and mapped to the reference human transcriptome assembly GRCh38 release 95 (also known as hg38).
Read mapping and transcript quantification was performed using Salmon (version 0.15.2; parameters --validateMappings, --gcBias, --numGibbsSamples: 20).
Assembly: GRCh38 release 95 (hg38)
Supplementary files format and content: Comma-separated text file includes raw counts for each sample

source_name: Liver

growth_protocol: hPSC H9 cells were differentiated to hepatocyte-like cells as described in the manuscript

extract_protocol:
RNA was harvested from biological duplicates using the NucleoSpin RNA kit (Macherey-Nagel)
Sequencing libraries were constructed using the NEBNext Ultra II Directional RNA Preparation Kit (New England Biolabs) and the NEBNext Multiplex Oligos for Illumina

treatment_protocol: The cells were harvested using Accutase

value: Liver

tag: cell line

value: Human embryonic stem cell line WA09 differentiated to hepatocyte-like cells (HLCs)


title: GCA081-Normal_CD-TI-Endoscopy

description:
7796-YX-9_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz

value: Terminal Ileum


title: GCA082-Control-TI-Endoscopy

description:
6778-YX-13_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: HLC differentiated day 18 Rep 1


title: Tumor biopsy 25


title: GCA083-Mild-TI-Endoscopy

description:
6778-YX-17_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: Tumor biopsy 24


title: 10T-PATZ1-OE3

data_processing:
cDNA libraries were single-end sequenced (50bp) on an Illumina HiSeq 2000 or 4000. Reads were aligned to the mouse genome (NCBI37/mm9) with TopHat v1.3.3 and allowed one alignment with up to two mismatches per read. mRNA RPKM values were calculated using Seqmonk’s mRNA quantitation pipeline. All FPKMs represent an average from three biological replicates for in-vitro studies for library construction. A gene was included in the analysis if it met all of the following criteria: The maximum FPKM reached 10 at any time point, the gene length was > 200bp as determined by the DESeq2 package in R Bioconductor. P values were adjusted using the Benjamini-Hochberg procedure of multiple hypothesis testing
Assembly: mm10 (GRCm38)
Supplementary files format and content: Gene count

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen). The aqueous phase containing the RNA was loaded onto a gDNA Eliminator Spin Column (Qiagen, USA) for elimination of genomic DNA, and RNA was isolated using the RNeasy Plus kit (Qiagen) according to manufacturer’s instructions. Total RNA (500 to 1000 ug) was reverse transcribed into cDNA using the M-MLV reverse transcriptase (Invitrogen),
Strand-specific libraries were generated from 500 ng total RNA using the TruSeq Stranded Total RNA Library Prep Kit (Illumina).  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.


title: Input


title: NPC_RING1ms/ms_Rep1_anti-RING1_CUT&RUN

city: Ann Arbor

first: Charles

middle: William

last: Ryan

state: Michigan

address: 1241 Catherine St, 4909 Buhl Building

department: Human Genetics

institute: University of Michigan

description: Sequencing performed by University of Michigan Advanced Genomics Core

data_processing:
For CUT&RUN, reads were aligned to hg38 using bwa-0.7.17 and filtered for map quality score >30 and converted to bam files using samtools/1.9. PCR duplicates were removed using picard-tools/2.8.1 (https://broadinstitute.github.io/picard/). Blacklist regions (ENCFF356LFX) were removed using the bedtools intersect function (bedtools2/2.30.0). Correlation between CUT&RUN signal at PRC1 target loci across biological replicates was determined using deepTools functions multiBamSummary and plotCorrelation (deeptools 3.5.2). Correlated replicates were merged using samtools/1.9. Merged BAM files were then converted to BIGWIG format for visualization using the coverage function in the R package rtracklayer. Peaks were called using MACS2 2.2.9.1. Peaks were then analyzed using R packages s GenomicRanges and rtracklayer.  Bedops -m was used to combine BED files containing the RING1 and RNF2 peaks (bedops/2.4.41). Bedtools merge function was then used to consolidate overlapping peaks (bedtools2/2.30.0).
Assembly: hg38
Supplementary files format and content: For files ending in SpikeNorm.bw, format is BigWig where data are normalized for an E. Coli spike in as described in the associated publication. For files ending in RPM.bw, format is BigWig where data are normalized as counts per 10,000,000 mapped and filtered reads. For files ending in .broadPeak, files contain peaks in BED-readable format and are the output of MACS2 broad peakcalling function. For the file called "ConsolidatedR1R2.bed", the format is BED file with columns chr start stop, and this file was made by taking peaks that were present in both biological replicates of RING1 and RNF2 CUT&RUN and merging them.
Library strategy: CUT&RUN

source_name: Neural progenitor cell monolayer

growth_protocol: N2/B27/FGF growth media at 37C 5%CO2

extract_protocol:
EpiCypher CUTANA™ ChIC/CUT&RUN kit v3 protocol (Epicypher, Durham NC)
Next Seq P2 100 cycle kit (Illumina)

treatment_protocol: CRISPR-cas9 genome editing was used to generate a RING1/RNF2 allelic series. Otherwise, NPCs were grown under normal growth conditions.

value: Neural progenitor cell monolayer

value: H9 Human Embryonic Stem Cel (WiCell Lot#WB0090)

value: neural progenitor cell

value: Homozygous RING1 R95Q missense (RING1 c.284G > A;p.R95Q)


title: GCA081-Normal_CD-AC-Endoscopy

description:
7796-YX-10_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz

value: Ascending Colon


title: GCA079-Control-AC-Endoscopy

description:
6778-YX-16_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz

value: Control


title: 10T-PATZ1-OE2


title: NPC_RING1ms/ms_Rep1_anti-IGG_control_CUT&RUN


title: GCA079-Control-TI-Endoscopy

description:
6778-YX-15_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: Tumor biopsy 22

value: Prostate tumor


title: HLC differentiated day 18 Rep 2


title: Tumor biopsy 27

value: Adeno carcinoma


title: GCA078-Control-AC-Endoscopy

description:
6778-YX-20_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: Tumor biopsy 21


title: GCA078-Control-TI-Endoscopy

description:
6778-YX-19_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: HLC differentiated day 17 Rep 1


title: 10T-Viral-Vector3


title: NPC_wildtype_Rep1_anti-RING1_CUT&RUN

value: wild type


title: NPC_wildtype_Rep1_anti-IGG_control_CUT&RUN


title: 10T-Viral-Vector2


title: Tumor biopsy 20


title: NPC_RING1ms/ms_Rep2_anti-RING1_CUT&RUN


title: Tumor biopsy 18


title: Tumor biopsy 23


title: GCA077-Mild-TI-Endoscopy

description:
6145-YX-23_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz

value: Mild


title: GCA076-Control-TI-Endoscopy

description:
6145-YX-19_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: Tumor biopsy 17


title: 10T-Viral-Vector1


title: Tumor biopsy 19


title: NPC_RING1ms/ms_Rep2_anti-IGG_CUT&RUN


title: NPC_wildtype_Rep2_anti-RNF2_CUT&RUN


title: GCA075-Quiescent-AC-Endoscopy

description:
6145-YX-22_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz

value: Quiescent


title: NPC_wildtype_Rep1_anti-RNF2_CUT&RUN


title: HFD 10

city: Zhengzhou

first: yu

last: dongsheng

state: He Nan

address: The First Affiliated Hospital of Zhengzhou University

country: China

data_processing:
Data quality control of raw data with fastp software; Removal of primers and adapter sequences (Adaptor)
Remove sequences with fragment length < 50 bp;
Remove N bases to a certain percentage of reads (default is set to 5 bp)
Removal of low-quality bases with mass values less than 20;
Calculate the base average mass value with a 4 base window, and excise it if the base average mass value is less than 20
Assembly: mm10
Supplementary files format and content: Data for each sample is included

source_name: liver

growth_protocol: After detissue, store in liquid nitrogen

extract_protocol: Trizol (Invitrogen) method was used to extract total RNA from tissues

treatment_protocol: C57BL/6 mice in chow group were fed with a standard laboratory rodent chow diet (Chow) (Xietong Organism, Nanjing, China), and the other three groups were fed with a high fat diet (HFD, 60% fat, 20% carbohydrate, 20% protein; Research Diets, New Brunswick, USA) for 12 weeks as previously described.

value: liver

value: WT

value: high fat diet 12 weeks


title: HFD 9

institute: The First Affiliated Hospital of Zhengzhou University


title: 10T-PATZ1-OE1


title: NPC_wildtype_Rep2_anti-RING1_CUT&RUN


title: GCA075-Quiescent-TI-Endoscopy

description:
6145-YX-21_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: Tumor biopsy 15


title: HFD 7


title: NPC_wildtype_Rep2_anti-IGG_control_CUT&RUN


title: GCA076-Control-AC-Endoscopy

description:
6145-YX-20_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: GCA074-Control-AC-Endoscopy

description:
6145-YX-18_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: Tumor biopsy 14


title: GCA074-Control-TI-Endoscopy

description:
6145-YX-17_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: HFD 6


title: Tumor biopsy 13


title: HFD 5


title: NPC_RING1ms/ms_Rep2_anti-IGG_control_CUT&RUN


title: GCA073-Control-AC-Endoscopy

description:
6145-YX-16_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: Tumor biopsy 12


title: Tumor biopsy 11


title: Tumor biopsy 16


title: NPC_RING1-/-_Rep2_anti-H2AK119ub1_CUT&RUN

value: Homozygous RING1 Knockout (RING1 c.280delG; p.S96SFS10*)


title: HFD 3


title: GCA073-Control-TI-Endoscopy

description:
6145-YX-15_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: HFD 4


title: NPC_RING1-/-_Rep2_anti-IGG_CUT&RUN


title: HFD 8


title: GCA072-Control-TI-Endoscopy

description:
6145-YX-13_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: Tumor biopsy 9


title: HFD 1


title: GCA072-Control-AC-Endoscopy

description:
6145-YX-14_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: Tumor biopsy 10


title: NPC_wildtype_Rep2_anti-IGG_CUT&RUN

description: Sequencing performed by University of Michigan Advanced Genomics Core


title: HFD 2


title: GCA071-Mild-TI-Endoscopy

description:
6145-YX-6_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: chow 10

value: chow diet


title: Tumor biopsy 8


title: NPC_RING1ms/ms_Rep2_anti-H2AK119ub1_CUT&RUN


title: Tumor biopsy 7


title: NPC_RNF2ms/ms_Rep2_anti-H2AK119ub1_CUT&RUN

value: Homozygous RNF2 R98Q missense (RNF2 c.292_293AG > CA;p.R98Q)


title: GCA069-Normal_CD-TI-Endoscopy

description:
6145-YX-10_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz

value: Terminal Ileum


title: GCA069-Normal_CD-AC-Endoscopy

description:
6145-YX-9_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: chow 9


title: NPC_RNF2ms/ms_Rep2_anti-IGG_CUT&RUN

value: Neural progenitor cell monolayer

value: H9 Human Embryonic Stem Cel (WiCell Lot#WB0090)


title: Tumor biopsy 6


title: NPC_wildtype_Rep2_anti-H2AK119ub1_CUT&RUN

value: neural progenitor cell


title: chow 8


title: NPC_RING1+/ms_Rep2_anti-H2AK119ub1_CUT&RUN

value: Heterozygous RING1 R95Q missense (RING1 c.284G > A;p.R95Q)


title: chow 7


title: GCA068-Mild-AC-Endoscopy

description:
6145-YX-12_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz

value: Ascending Colon


title: chow 6


title: GCA068-Normal_CD-TI-Endoscopy

description:
6145-YX-11_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: Tumor biopsy 5

value: Prostate tumor


title: NPC_RING1+/ms_Rep2_anti-IGG_CUT&RUN


title: Tumor biopsy 4

value: Adeno carcinoma


title: chow 5


title: NPC_RING1+/ms_Rep1_anti-IGG_CUT&RUN


title: GCA066-Quiescent-AC-Endoscopy

description:
6145-YX-4_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: Tumor biopsy 3


title: Tumor biopsy 2


title: NPC_RING1+/ms_Rep1_anti-H2AK119ub1_CUT&RUN


title: GCA067-Mild-AC-Endoscopy

description:
6145-YX-24_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: NPC_RNF2ms/ms_Rep1_anti-H2AK119ub1_CUT&RUN


title: chow 4


title: GCA066-Quiescent-TI-Endoscopy

description:
6145-YX-5_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: Tumor biopsy 1


title: chow 3


title: NPC_RNF2ms/ms_Rep1_anti-IGG_CUT&RUN


title: GCA065-Normal_CD-TI-Endoscopy

description:
6145-YX-7_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: GCA065-Mild-AC-Endoscopy

description:
6145-YX-8_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: NPC_wildtype_Rep1_anti-IGG_CUT&RUN

value: wild type


title: chow 1


title: chow 2


title: NPC_wildtype_Rep1_anti-H2AK119ub1_CUT&RUN


title: Hi-C Pol3-depleted, DSB 4 hr

city: Lyon

first: Aurele

last: Piazza

address: 46 Allee d'Italie

institute: ENS Lyon

data_processing:
Reads alignement, contact filtering and PCR duplicate removal was performed using the hicstuff (v3.1.2) pipeline function with mapping quality set to 30 or 20. Hi-C contact matrices in sparse format were binned at 1 kb using hicstuff rebin function and converted to cooler format using hicstuff convert function.
For ssHi-C, sparse matrices generated by hicstuff pipeline function were processed with the sshicstuff pipeline function to isolate fragments of interest
Assembly: S. cerevisiae S288c-R64-2-1 (http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-2-1_20150113.tgz)
Supplementary files format and content: Hi-C and unfiltered ssHi-C contact data in cooler format, either per fragment (for ssHiC samples) or binned at 1kb (for HiC samples)
Supplementary files format and content: Unfiltered ssHi-C contact data in graal (sparse) format, per fragment
Supplementary files format and content: Tabulated ssHi-C contact data filtered with ssHiCstuff, binned at 1kb

source_name: Pol3-depleted, DSB 4 hr

growth_protocol: Cells were grown to exponential phase in YP-lactate media and synchronized in G1 with alpha-factor for 3 hours. Cells were washed 3 times in pre-warmed YP-lactate and released in S-phase in YP-lactate supplemented with 2% galactose. For Scc1-AID depletion experiment, 2 mM IAA were added at the time of release. For Pol3/Rfc1-AID depletion, 50 ug/mL doxycycline and  2 mM IAA were added 1 hour post-release.

extract_protocol:
Cells were spheroplasted with 0.25 mg/mL Zymolyase 100T at 37°C for 30 minutes, crosslinked with 3 mM EGS (ethylene glycol bis(succinimidyl succinate)) at 30°C for 40 minutes at 100 rpm, and quenched with 400 mM glycine for 5 minutes at 100 rpm.
Hi-C and ssHi-C library were generated using the Arima Hi-C+ kit following manufacturer instructions starting from 2-5x10^7 cells, with addition of the annealing oligonucleotide mix at 7 nM each in the lysis buffer prior to incubation at 62°C for 10 minutes.
DNA was fragmented in 300-400 bp DNA fragments using Covaris M220 sonicator. Illumina sequencing libraries were prepared using the Thermofisher Collibri ES DNA Library Prep Kit for Illumina Systems with UD indexes following manufacturer's instructions. For ssHi-C, two rounds of targeted capture using the IDT xGen Hybridization buffer and enhancer using biotinylated oligonucleotides at 0.6 uM each. The library was digested with MfeI and SspI in NEB cutsmart buffer prior to sequencing.

treatment_protocol: ~1.5x10^9 cells were crosslinked with 3% formaldehyde for 30 minutes at 120 rpm at room temperature, followed by quenching with 330 mM glycine for 30 minutes at 120 rpm.

value: S. cerevisiae culture


title: ssHi-C WT, DSB 4 hr replicate 4

data_processing:
Reads alignement, contact filtering and PCR duplicate removal was performed using the hicstuff (v3.1.2) pipeline function with mapping quality set to 30 or 20. Hi-C contact matrices in sparse format were binned at 1 kb using hicstuff rebin function and converted to cooler format using hicstuff convert function.
For ssHi-C, sparse matrices generated by hicstuff pipeline function were processed with the sshicstuff pipeline function to isolate fragments of interest
Assembly: S. cerevisiae S288c-R64-2-1 (http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-2-1_20150113.tgz)
Supplementary files format and content: Hi-C and unfiltered ssHi-C contact data in cooler format, either per fragment (for ssHiC samples) or binned at 1kb (for HiC samples)
Supplementary files format and content: Unfiltered ssHi-C contact data in graal (sparse) format, per fragment
Supplementary files format and content: Tabulated ssHi-C contact data filtered with ssHiCstuff, binned at 1kb
Library strategy: ssHi-C

source_name: WT, DSB 4 hr


title: Hi-C Pol3/Rfc1-depleted, DSB 4 hr

source_name: Pol3/Rfc1-depleted, DSB 4 hr


title: GCA062-Severe-TI-Endoscopy

description:
6145-YX-2_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz

value: Severe


title: NPC_RING1-/-_Rep1_anti-IGG_CUT&RUN


title: ssHi-C Scc1-depleted rad51D DSB 4 hr

source_name: Scc1-depleted rad51D DSB 4 hr


title: NPC_RING1-/-_Rep1_anti-H2AK119ub1_CUT&RUN


title: GCA061-Mild-TI-Endoscopy

description:
5314-YX-22_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz

value: Mild


title: ssHi-C chrIV-845464::RE(700 bp), DSB 2 hr


title: GCA060-Mild-AC-Endoscopy

description:
5314-YX-18_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: ssHi-C rad51D DSB 4 hr replicate 2

source_name: rad51D DSB 4 hr


title: NPC_RING1ms/ms_Rep1_anti-IGG_CUT&RUN

value: Homozygous RING1 R95Q missense (RING1 c.284G > A;p.R95Q)


title: ssHi-C WT, no donor, DSB 4 hr

source_name: WT, no donor, DSB 4 hr


title: GCA060-Normal_CD-TI-Endoscopy

description:
5314-YX-19_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: GCA059-Moderate-AC-Endoscopy

description:
5314-YX-21_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz

value: Moderate


title: GCA062-Normal_CD-AC-Endoscopy

description:
6145-YX-1_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: ssHi-C WT, no donor, DSB 2 hr

source_name: WT, no donor, DSB 2 hr


title: VP2.11_Input

city: Saint Louis

first: Meaghan

last: Creed

state: MO

address: 4370 Duncan Ave

department: Anesthesiology

institute: Washington University

data_processing:
Gene counts imported into the R/Bioconductor package EdgeR5 and TMM normalization size factors were calculated and imported to Limma.
Reads were aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a
Differential gene expression analysis with Benjamini-Hochberg false-discovery rate adjusted p ≤ 0.05
Assembly: Ensembl
Supplementary files format and content: Tab delimited files contain raw reads for each sample
Supplementary files format and content: CSV file contains summary of DGE comparing TRAP to Input Samples

source_name: 4 male, 6 female

extract_protocol:
The ventral pallidum from 7-10 adult mice was dissected into ice cold buffer (20 mM HEPES (pH 7.3), 150 mM KCl, 10 mM MgCl2, 0.5 mM dithiothreitol, 100 μ g/mL cycloheximide, EDTA-free protease inhibitor cocktail, 5 μL/mL RNasin and 2 μL/mL Superasin). Samples were homogenized and centrifuged for 10 min at 20,000g, 4°C. NP-40 and 1, 2-diheptanoyl-sn-glycero-3-phosphocholine were added to the supernatant at final concentrations of 1 % and 30 mM, respectively. 200 µL of the sample was removed and 500 µL of Trizol was added to constitute the Input fraction.
Streptavidin Dynabeads (300 µL, Invitrogen Cat#65601) pre-conjugated with Protein L (ThermoFischer Cat# 29997) and Anti-HA antibody (Biolegend Cat# 901513) in homogenization buffer were added to the remaining sample. Beads were collected on a magnet at 4°C and washed for 5 cycles with 1ml 350mM KCl buffer before resuspension in 700 µL of Trizol for the TRAP fraction.
RNA was isolated following the Zymo RNA Clean & Concentrator 5 protocol with on-column DNase digestion.
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovoSeq

value: Brain, ventral pallidum

value: All neurons, glia

value: VGluT2-Cre x Rpl22 (homozygous for VGluT2-Cre, heterozygous for Rpl22)

tag: Sex

value: pooled male and female

tag: age

value: 10-16 weeks


title: VP2.11_TRAP

tag: tissue

value: Glutamatergic neurons


title: VP2.6_TRAP

source_name: 4 male, 7 female


title: VP2.2_TRAP


title: VP2.6_Input


title: VP1.6_TRAP

source_name: 3 male, 4 female

value: 9-12 weeks


title: ssHi-C Scc1-depleted DSB 4 hr

source_name: Scc1-depleted DSB 4 hr


title: GCA058-Normal_CD-AC-Endoscopy

description:
5314-YX-15_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz

source_name: Ascending Colon

tag: patient


title: MCF7-MS-WA-repl2

city: Bathinda

first: Shashank

last: Kumar

state: Punjab

address: VPO Guddha

department: Biochemistry

country: India

institute: CENTRAL UNIVERSITY OF PUNJAB

description: Breast mammary epithelial cancer cell line MCF7 derived mammosphere treated with WA replicate 2

data_processing:
Illumina genrated raw reads were filtered (Adaptor removal and length filtering) using trimgalore and cutadapt
High quality trimmed reads were alligned to human genome (GRCh38.p7) using miRDeep2 software
Raw count expression for each miRNA condidate and sample was calculated using edgeR software
Genome_build: Human genome (GRCh38.p7)
Supplementary_files_format_and_content: Microsoft office excel worksheet (.xlsx) table matrix having raw expression count for each miRNA condidate and each sample
Supplementary_files_format_and_content: Microsoft office excel worksheet (.xlsx) table matrix having normalized expression count for each miRNA condidate and each sample

growth_protocol: MCF7 cells were seeded at density of 1x104 cells/well) in 6-well ultra-low-attachment plates (Corning, Tewksbury, MA, US) in serum-free DMEM Ham’s F12 nutrient mixture (1:1 v/v) supplemented with 2% B-27 supplement, 10 ng/ml fibroblast growth factor, and 20 ng/ml epidermal growth factor.

extract_protocol:
Small RNA was isolated from Withaferin A without treated (control group) and Withaferin A treated (experimenta group) MCF7 derived mammosphere (MS) samples
Libraries were prepared using a QIAseq® miRNA Library Kit (Qiagen, Maryland, U.S.A.) protocol.

treatment_protocol: Withaferin A (WA) treated (2 µM) concentration and without treated MCF7 cells were allowed to form mammosphere (MS) and incubated at 37 ºC under a 95 % humid environment in an incubator having 5% CO2 for five days.

value: Breast mammary gland


title: VP2.2_Input


title: GCA058-Normal_CD-TI-Endoscopy

description:
5314-YX-14_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz

source_name: Terminal Ileum

value: Terminal Ileum


title: ssHi-C Scc1-depleted DSB 2 hr

source_name: Scc1-depleted DSB 2 hr


title: MCF7-MS-WA-repl1

description: Breast mammary epithelial cancer cell line MCF7 derived mammosphere treated with WA replicate 1


title: VP1.6_Input


title: NPC_RING1ms/ms_Rep1_anti-H2AK119ub1_CUT&RUN

description: Sequencing performed by University of Michigan Advanced Genomics Core

value: Neural progenitor cell monolayer

value: H9 Human Embryonic Stem Cel (WiCell Lot#WB0090)

value: neural progenitor cell


title: Hi-C Scc1-depleted rad51D DSB 4 hr

value: S. cerevisiae culture


title: N2A_RNA_siCSB_rep2

city: La Jolla

first: Alon

last: Goren

state: CA

address: 9500 Gilman Drive

institute: University of California San Diego

description:
N2As were induced to differentiate into neurons through the addition of Retinoic acid.
N2A_RNA_counts.txt

data_processing:
The FASTQ reads underwent quality checking and adaptor trimming using Trim Galore. Subsequently, they were mapped to either the hg38 or mm10 reference genomes using STAR. The read counts per gene were then determined using featureCounts.
Assembly: hg38 or mm10
Supplementary files format and content: tab-delimited text files include read counts for each sample

extract_protocol:
RNA was extracted by TRIzol and then constructed into library.
RNA libraries for RNA-seq were prepared using NEBNext rRNA Depletion Kit v2 (E7400L) followed by NEBNext Ultra II RNA Library Prep kit (E7775S).

treatment_protocol: Human dermal fibroblasts were trans-differentiated into functional neurons by depleting the RNA-binding protein PTBP1.

value: siCSB


title: MCF7-MS-repl2

description: Breast mammary epithelial cancer cell line MCF7 derived mammosphere without WA treated replicate 2


title: GCA055-Quiescent-AC-Endoscopy-Rep2

description:
7796-YX-8_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz

value: Ascending Colon

value: Quiescent


title: N2A_RNA_siCSB_rep1


title: MCF7-MS-WA-repl3

description: Breast mammary epithelial cancer cell line MCF7 derived mammosphere treated with WA replicate 3


title: Hi-C rad51D DSB 4 hr replicate 2


title: MCF7-MS-repl1

description: Breast mammary epithelial cancer cell line MCF7 derived mammosphere without WA treated replicate 1


title: GCA055-Quiescent-AC-Endoscopy-Rep1

description:
5222-YX-22_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: Hi-C rad51D DSB 2 hr replicate 2

source_name: rad51D DSB 2 hr


title: GCA055-Normal_CD-TI-Endoscopy

description:
5222-YX-21_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: N2A_RNA_siNC_rep1

value: siNC


title: GCA053-Quiescent-TI-Endoscopy

description:
5222-YX-7_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: FSF-TIM3/LysM-Cre #3

city: Goyang-si

first: Ki Sun

last: Kim

state: Gyeonggi-do

address: 323, Ilsan-ro, Ilsandong-gu

country: South Korea

institute: National Cancer Center

data_processing:
All data processing step flowed by MACROGEN corporation benchwork.
Sequence reads were filtered criteria (Exclude genes from the analysis if they have a value of 0 in any of samples).
Normalization : RLE Normalization (Using read count data, estimate size factors and perform normalization. Conduct statistical analysis using the DESeq2 R library).
Assembly: mm10
Supplementary files format and content: FPKM, TPM, raw read counts for each sample

source_name: lung tissue

extract_protocol:
Total RNA was isolated using Easy-Blue (iNtRON). 200 ng of total RNA was used for the construction of sequencing library.
Total RNA was subjected to a sequencing library construction using the Agilent SureSelect RNA Direct kit according to the manufacturer's protocol.

value: lung tissue

value: TIM3 overexpression


title: Hi-C WT, no donor, DSB 4 hr


title: Hi-C Scc1-depleted DSB 4 hr


title: Hi-C WT, no donor, DSB 2 hr


title: FSF-TIM3/LysM-Cre #2


title: MCF7-MS-repl3

description: Breast mammary epithelial cancer cell line MCF7 derived mammosphere without WA treated replicate 3


title: GCA045-Mild-AC-Endoscopy

description:
5314-YX-13_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz

value: Mild


title: GCA055-Quiescent-AC-Endoscopy-Rep3

description:
7796-YX-7_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: ssHi-C exo1D DSB 4 hr

source_name: exo1D DSB 4 hr


title: FSF-TIM3 WT #3

value: WT


title: GCA053-Normal_CD-AC-Endoscopy

description:
5222-YX-8_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: FSF-TIM3 WT #2


title: FSF-TIM3/LysM-Cre #1


title: ssHi-C exo1D DSB 2 hr

source_name: exo1D DSB 2 hr


title: GCA043-Normal_CD-AC-Endoscopy

description:
5222-YX-10_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: ssHi-C WT, DSB 4 hr + Noco

source_name: WT, DSB 4 hr + Noco


title: Hi-C Scc1-depleted DSB 2 hr


title: FSF-TIM3 WT #1


title: GCA041-Normal_CD-AC-Endoscopy

description:
5222-YX-4_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: GCA041-Normal_CD-TI-Endoscopy

description:
5222-YX-3_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: N2A_RNA_siNC_rep2


title: IMQ+N_rep2

city: Tainan City

first: Yi-Kai

last: Hong

state: Please select an option below

address: No.1, Daxue Rd., East Dist.

country: Taiwan

institute: National Cheng Kung University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChips Clariom D mouse arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip™ Scanner 3000 7G.

data_processing: Affymetrix GeneChip Command Console Software v4.0 (AGCC 4.0, Affymetrix®) and Transcriptome Analysis Console (TAC) Software v4.0.1 were used with default analysis settings, and expression values were processed with the signal space transformation and robust multichip average methods, which included log2 transformation and quantile normalization.

label: biotin

source_name: Skin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: After hair was removed from the back skin of C57BL/6J mice (8 weeks old), a traction device (Figure 1) was adhered to by quick-drying glue.

extract_protocol: Total RNAs extracted from the mouse skin were isolated by using RNeasy mini kit

treatment_protocol: Traction force was induced by elongating plastic device on the skin for a total 10 mm at first day. Thereafter, IMQ cream (5%) was topically applied on the stretched or non-stretched skin every day for total 7 days as previous experiments

tag: strain

value: IMQ-treated mouse without full-stretch (Non-stretch)


title: IMQ+N_rep4


title: IMQ+N_rep1