title: F1_183

description: F1_183-2ndSUB_3114_TTACAGGA-TGACAAGC_S60_cat

data_processing:
Reads were quality checked with package FastQC (version 0.11.4,), then trimmed using Trimgalore (version 0.4.4) with default settings.
Trimmed reads were mapped to mouse genome annotation mm10 using STAR aligner (Dobin and Gingeras, 2015) with default settings.
Mapped reads were counted using RsubRead (version 1.32.4, (Liao et al., 2019)). Raw counts were then normalized using DESeq2 (version 1.16.1, (Love et al., 2014)).
Genome_build: ENSMBL mm10 release 98, Mus_musculus.GRCm38.98
Supplementary_files_format_and_content: txt matrix with log2 normalized values per sample.

source_name: CC F2 female_AB_lung

extract_protocol:
Whole liver RNA was extracted using Rneasy Midi kit from Qiagen. Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany).
The RNA sequencing library was generated from 1,000 ng of total RNA using the KAPA Stranded RNA-Seq Kit with RiboErase (HMR) (Roche Sequencing and Life Science; Wilmington, MA) and the manufacturer’s protocol was followed.
Libraries were sequenced on Illumina NovaSeq 6000 using NovaSeq 6000 S4 XP Reagent Kit 100 Nu, paired end, with an average of 30,000,000 reads per RNA sample

treatment_protocol: Livers were collected from mice

value: predictive

tag: strain background

value: a cross of two collaborative cross (CC) strains, CC011 x CC074

tag: genotype

value: AB

value: female

value: lung


title: Patient_69 SAMPLE_69

status: Public on Aug 31 2022

type: RNA

city: roskilde

first: Soraya

last: Naimy

state: Sjaelland

address: sygehusvej 9

department: department of pathology

country: Denmark

institute: zealand universityhospital

description: raw data were quality checked in the nSolver software by using default parameters, imaging QC, bibdng density, positive control linearity and positive control limit detection (set to 0.5 fM) was evaluated

hyb_protocol: From each sample, 100-200 ng of RNA was used for hybridization using the nCounter PanCancer IO 360 Gene Expression Panel, according to the manufacturer’s nCounter XT protocol (NanoString Technologies, Seattle, Washington, US).

scan_protocol: digitl detection and counting of the hybridized probes wer done one an epifluorescence microscope in the digital analyzer mode, NanoString Technologies, Seattle, Washington, US

data_processing: Data analysis was performed in nSover software version 4.0

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Primary Skin melanoma

label_protocol: biotinylated capture probe was used to pair withthe targit probe

extract_protocol: Total RNA was isolated from five 10-µm sections of whole FFPE tissue using Roche hi-pure FFPET kit (Roche Life Science, Mannheim, Germany) according to manufacturer`s protocol. NanoDrop™ Lite spectrophotometer (Thermo Fischer Scientific, Waltham, Massachusetts, US) was used to measure total RNA quality and quantity.

tag: tissue

value: Primary Skin melanoma

tag: histology

value: Superficial spreading melanoma

tag: status after 5 years

value: alive

tag: age

tag: Sex

value: man

tag: status

value: nonbrisk

tag: braf v600e ihc status

value: positive

tag: Stage


title: 18098D-02-28

type: SRA

city: Washington

first: Valerie

middle: Wailin

last: Hu

state: DC

department: Biochemistry and Molecular Medicine

country: USA

institute: The George Washington University School of Medicine and Health Sciences

library_source: genomic

data_processing:
Filtered raw fastq files using Illumina quality flag
Followed CpG_Me workflow which included the steps below.
Trimmed to remove adapters and 5' and 3' methylation bias with Trim Galore!
Aligned to hg38 reference genome with Bismark
Removed PCR duplicates with Bismark
Extracted CpG methylation counts at all covered sites to generate genome-wide cytosine methylation reports with Bismark
Genome_build: hg38
Supplementary_files_format_and_content: Bismark genome-wide cytosine methylation report for each sample with columns for chromosome, CpG position, strand, methylated count, unmethylated count, dinucleotide context, and trinucleotide context

molecule: genomic DNA

source_name: male from the Faroe Islands (Denmark)

extract_protocol:
Sperm was isolated from semen (which contains various cell types) using a published discontinuous gradient protocol (Wu, de Gannes, Luchetti, & Richard Pilsner, 2015). DNA was isolated from the purified sperm cells using a Qiagen AllPrep DNA/RNA mini kit following the manufacturer's protocol. Somatic cell contamination after sperm isolation never exceeded 1% of total cells.
The samples were sent to Admera Health (South Plainfield, NJ), a CLIA-certified laboratory, for WGBS analyses. The directional Illumina TruSeq DNA Methylation library kit was used for sample preparation following the manufacturer's protocol. WGBS was then performed on an Illumina HiSeq X sequencer resulting in 150 bp PE reads achieving roughly 4x coverage genome wide per sample. Raw FASTQ files were received from Admera Health for further analyses. All samples were processed blindly without the processors' knowledge of tertile level from sperm isolation through the WGBS analyses.

treatment_protocol: Genomic DNA was treated with bisulfite for downstream whole genome bisulfite sequencing analyses of DNA methylation as described below

tag: sample group

value: Validation

tag: tertile

value: First

value: male

value: sperm

tag: bmi

tag: storage (days)

tag: batch

tag: sperm motility (%)

tag: smoking

value: Yes

tag: pp'-dde    (mg/mg lipid)


title: Donor 3 SARS-CoV-2 Replicate 1

city: St. Louis

first: Stacey

middle: Lynn

last: Rentschler

state: Missouri

address: 660 S Euclid Ave

department: Medicine

institute: Washington University in St. Louis

library_source: transcriptomic

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Genome_build: Ensembl GRCm38.76 and GRCh38.76
Supplementary_files_format_and_content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Isolated primary cardiac pericytes

growth_protocol: Cardiac pericytes were plated at 8 x 103 cells/cm2 in flat-bottomed 24-well plates 2-4 days before the start of an experiment and cultured in Pericyte Medium (Sciencell cat#1201)

extract_protocol:
RNA was extracted using the 5X MagMax Pathogen RNA/DNA isolation kit (Thermo Scientific cat# 4462359) on the Kingfisher Flex extraction robot (Thermo Scientific).
Takara-Clontech SMARTer Ultra Low RNA

treatment_protocol: Cardiac pericytes were replated for the experiments and allowed to settle for at least 2 days before the infection. The SARS-CoV-2 mNeonGreen viral stock was diluted by the Pericyte Growth Medium at a multiplicity of infection (MOI of 1) and added onto cells instead of the growth medium for 3 hours to allow viral entry. After incubation, cells were washed with 1 mL of warm PBS three times and replaced with fresh culture medium.

tag: cell type

value: Primary cardiac pericytes

tag: treatment

value: SARS-CoV-2 mNeonGreen MOI=1

tag: tissue source

value: Non-failing Explanted Adult Left Ventricle


title: F1_182

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

country: Germany

institute: University Münster

description: F1_182-2ndSUB_3114_CCGTGAAG-CAGTGGAT_S59_cat

organism: Mus musculus

value: predictive

tag: strain background

value: a cross of two collaborative cross (CC) strains, CC011 x CC074

tag: genotype

value: AB

tag: tissue


title: 18098D-02-17

tag: Sex

tag: age


title: Patient_67 SAMPLE_67

value: Primary Skin melanoma

tag: histology

tag: status after 5 years

tag: status

value: brisk

tag: braf v600e ihc status

value: negative

tag: Stage


title: 18098D-02-16

tag: sample group

tag: tertile

tag: bmi

tag: storage (days)

tag: batch

value: No


title: 18098D-02-11

tag: sperm motility (%)

tag: smoking

tag: pp'-dde    (mg/mg lipid)


title: Patient_66 SAMPLE_66

value: Superficial spreading melanoma

value: alive

value: woman


title: Donor 3 Mock Replicate 2

tag: cell type

tag: treatment

value: Mock - Pericyte Growth Medium

tag: tissue source


title: F1_180

description: F1_180-2ndSUB_3114_CTTGGTAT-CCAAGTCC_S57_cat

tag: strain background

tag: genotype

tag: Sex

value: female

tag: tissue

value: lung


title: Donor 3 Mock Replicate 1


title: 18098D-02-09

value: Validation

value: First

value: male

value: sperm

tag: age


title: 18098D-02-06


title: F1_179

description: F1_179-2ndSUB_3114_GTCGGAGC-GGTTATAA_S56_cat

source_name: CC F2 female_AA_lung

value: predictive

value: AA


title: Patient_65 SAMPLE_65

tag: histology

tag: status after 5 years

value: dead

tag: status

value: absent

tag: braf v600e ihc status

value: positive

tag: Stage


title: Patient_64 SAMPLE_64

value: Primary Skin melanoma

value: brisk

value: negative


title: 18098D-02-52

tag: sample group

value: Discovery

tag: tertile

value: Third

tag: bmi

tag: storage (days)

tag: batch

value: Yes


title: Donor 2 SARS-CoV-2 Replicate 4

tag: cell type

value: Primary cardiac pericytes

tag: treatment

value: SARS-CoV-2 mNeonGreen MOI=1

value: Heart Failure Explanted Adult Left Ventricle


title: Patient_63 SAMPLE_63

value: Superficial spreading melanoma

value: alive

value: woman


title: F1_177

description: F1_177-2ndSUB_3114_ATGAGGCC-GTTAATTG_S54_cat

source_name: CC F2 female_NA_lung

value: predictive

tag: strain background

value: a cross of two collaborative cross (CC) strains, CC011 x CC074

value: female

value: lung


title: Donor 2 SARS-CoV-2 Replicate 3

tag: tissue source


title: Patient_68 SAMPLE_68

tag: Sex

value: man

value: absent


title: Patient_62 SAMPLE_62

tag: tissue

value: Primary Skin melanoma

value: brisk


title: Donor 2 SARS-CoV-2 Replicate 2


title: Donor 2 SARS-CoV-2 Replicate 5


title: F1_176

description: F1_176-2ndSUB_3114_GCAGAATT-ACCGGCCA_S53_cat

tag: genotype


title: F1_175

description: F1_175-2ndSUB_3114_AACGTTCC-GGAGTACT_S52_cat


title: F1_178

description: F1_178-2ndSUB_3114_ACTAAGAT-AACCGCGG_S55_cat


title: 18098D-02-49

value: Discovery

value: male

value: sperm

tag: age

tag: sperm motility (%)

tag: smoking

tag: pp'-dde    (mg/mg lipid)


title: Donor 2 SARS-CoV-2 Replicate 1

value: Primary cardiac pericytes


title: 18098D-02-03

value: Third

value: No


title: F1_181

description: F1_181-2ndSUB_3114_TCCAACGC-TTGGACTT_S58_cat

value: AB


title: 18098D-02-46

value: Yes


title: Patient_60 SAMPLE_60

tag: histology

value: Superficial spreading melanoma

tag: status after 5 years

value: alive

tag: status

tag: braf v600e ihc status

value: negative

tag: Stage


title: 18098D-02-45

tag: sample group

tag: tertile

tag: bmi

tag: storage (days)

tag: batch


title: F1_174

description: F1_174-2ndSUB_3114_GGTACCTT-AAGACGTC_S51_cat

value: predictive

tag: strain background

value: a cross of two collaborative cross (CC) strains, CC011 x CC074

value: AA

tag: Sex

value: female


title: Donor 2 Mock Replicate 3

tag: cell type

tag: treatment

value: Mock - Pericyte Growth Medium

tag: tissue source

value: Heart Failure Explanted Adult Left Ventricle


title: F1_173

description: F1_173-2ndSUB_3114_GCACGGAC-GTCTCGCA_S50_cat

tag: genotype

tag: tissue

value: lung


title: Donor 2 Mock Replicate 2


title: 18098D-02-44

value: Discovery

value: male

tag: age

tag: sperm motility (%)

tag: smoking

tag: pp'-dde    (mg/mg lipid)


title: F1_172

description: F1_172-2ndSUB_3114_ATGTAAGT-ACTCTATG_S49_cat


title: Patient_57 SAMPLE_57

value: Primary Skin melanoma

tag: histology

tag: status after 5 years

value: dead

value: woman

tag: status

value: brisk

tag: braf v600e ihc status

value: positive

tag: Stage


title: Patient_58 SAMPLE_58

value: Superficial spreading melanoma

value: man

value: nonbrisk


title: Donor 1 SARS-CoV-2 Replicate 5

value: Primary cardiac pericytes

value: SARS-CoV-2 mNeonGreen MOI=1


title: Patient_61 SAMPLE_61

value: alive

value: absent


title: Donor 2 Mock Replicate 1

value: Mock - Pericyte Growth Medium


title: 18098D-02-36

tag: sample group

tag: tertile

value: Third

value: sperm

tag: bmi

tag: storage (days)

tag: batch

value: No


title: 18098D-02-32

value: Discovery

tag: Sex

value: male


title: F1_171

description: F1_171-2ndSUB_3114_CGGCGTGA-GCGCCTGT_S48_cat

source_name: CC F2 female_BB_lung

value: predictive

tag: strain background

value: a cross of two collaborative cross (CC) strains, CC011 x CC074

tag: genotype

value: BB

value: female

value: lung


title: F1_170

description: F1_170-2ndSUB_3114_TAATACAG-ATATTCAC_S47_cat

value: AB

tag: tissue


title: Patient_56 SAMPLE_56

value: Primary Skin melanoma

value: Superficial spreading melanoma

tag: age

value: woman

value: brisk

value: positive


title: Donor 3 SARS-CoV-2 Replicate 2

tag: cell type

value: Primary cardiac pericytes

tag: treatment

value: SARS-CoV-2 mNeonGreen MOI=1

tag: tissue source

value: Non-failing Explanted Adult Left Ventricle


title: Donor 1 SARS-CoV-2 Replicate 4

value: Heart Failure Explanted Adult Left Ventricle


title: F1_169

description: F1_169-2ndSUB_3114_AATCCGGA-CTACAGTT_S46_cat


title: Donor 1 SARS-CoV-2 Replicate 3


title: Donor 3 Mock Replicate 3

value: Mock - Pericyte Growth Medium


title: 18098D-02-26

value: Discovery

value: Third

value: male

value: sperm

tag: sperm motility (%)

tag: smoking

value: No

tag: pp'-dde    (mg/mg lipid)


title: Patient_59 SAMPLE_59

tag: histology

tag: status after 5 years

value: alive

tag: status

value: absent

tag: braf v600e ihc status

tag: Stage


title: F1_168

description: F1_168-2ndSUB_3114_GGCTTAAG-TCGTGACC_S45_cat

value: predictive

value: a cross of two collaborative cross (CC) strains, CC011 x CC074

value: BB

value: female

value: lung


title: Patient_54 SAMPLE_54

value: Primary Skin melanoma

value: Superficial spreading melanoma

value: woman

value: nonbrisk

value: positive


title: Donor 1 SARS-CoV-2 Replicate 2

value: Primary cardiac pericytes

value: SARS-CoV-2 mNeonGreen MOI=1

value: Heart Failure Explanted Adult Left Ventricle


title: 18098D-02-21

tag: sample group

value: Discovery

tag: tertile

value: Third

value: male

value: sperm

tag: bmi

tag: storage (days)

tag: batch

value: Yes


title: F1_167

description: F1_167-2ndSUB_3114_TTGGACTC-GGAAGCAG_S44_cat

value: predictive

tag: strain background

value: a cross of two collaborative cross (CC) strains, CC011 x CC074

tag: genotype

tag: Sex

tag: tissue


title: Patient_53 SAMPLE_53

description: raw data were quality checked in the nSolver software by using default parameters, imaging QC, bibdng density, positive control linearity and positive control limit detection (set to 0.5 fM) was evaluated

value: alive

tag: age


title: Donor 1 SARS-CoV-2 Replicate 1

tag: cell type

tag: treatment

tag: tissue source


title: 18098D-02-18

tag: sperm motility (%)

tag: smoking

value: No

tag: pp'-dde    (mg/mg lipid)


title: Patient_52 SAMPLE_52

value: Primary Skin melanoma

tag: histology

tag: status after 5 years

value: man

tag: status

value: brisk

tag: braf v600e ihc status

value: negative

tag: Stage


title: F1_166

description: F1_166-2ndSUB_3114_CCAAGTCT-AAGGATGA_S43_cat

value: AB

value: female

value: lung


title: Donor 1 Mock Replicate 3

value: Primary cardiac pericytes

value: Mock - Pericyte Growth Medium

value: Heart Failure Explanted Adult Left Ventricle


title: Patient_55 SAMPLE_55

value: Superficial spreading melanoma

value: woman

value: nonbrisk

value: positive


title: 18098D-02-27

tag: sample group

value: Discovery

tag: tertile

value: Third

value: male

value: sperm

tag: bmi

tag: storage (days)

tag: batch

value: Yes


title: Patient_51 SAMPLE_51

tag: tissue

value: Primary Skin melanoma

value: alive

tag: age

tag: Sex

value: brisk


title: 18098D-02-15


title: F1_165

description: F1_165-2ndSUB_3114_CTCTCGTC-TATAACCT_S42_cat

value: predictive

tag: strain background

value: a cross of two collaborative cross (CC) strains, CC011 x CC074

tag: genotype

value: AB

value: female


title: Donor 1 Mock Replicate 2

tag: cell type

value: Primary cardiac pericytes

tag: treatment

value: Mock - Pericyte Growth Medium

tag: tissue source

value: Heart Failure Explanted Adult Left Ventricle


title: Patient_50 SAMPLE_50

tag: histology

value: Superficial spreading melanoma

tag: status after 5 years

value: man


title: Donor 1 Mock Replicate 1


title: 18098D-02-14

value: Discovery

tag: sperm motility (%)

tag: smoking

tag: pp'-dde    (mg/mg lipid)


title: 18098D-02-01

tag: sample group

tag: tertile

value: Third


title: F1_164

description: F1_164-2ndSUB_3114_TCTCTACT-CGCGGTTC_S41_cat

value: lung


title: 24_MZ1_IAAHSR3

city: Bethesda

first: Dinah

middle: S.

last: Singer

state: MD

address: Building 10, Room 4B-17

department: Division of Cancer Biology

institute: National Cancer Institute

description: HCT116RmAC cells treated with MZ1+IAA under heat shock conditions replicate 3

data_processing:
RNA-seq reads were aligned to human reference genome (hg19) with STAR aligner. Raw read counts were obtained using htseq-count.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts of sequencing reads for each sample

source_name: HCT116RmAC_MZ1+IAA under heat shock conditions

growth_protocol: The HCT116 RmAC cells were grown in Maccoy's 5A (modified) media (Gibco) supplimented with 10% fetal bovine serum in 37 °C and 7.5% CO2

extract_protocol:
RNA was isolated from WT, RAD21 depleted, BRD4 depleted and BRD4 and RAD21 depleted HCT116 Rad21mAIDmClover cells using the Micro RNeasy-Plus Kit (Qiagen)
Libraries were prepared using  the Illumina TruSeq Stranded mRNA Library Prepaccording to manufacturers' instructions.

treatment_protocol: Depletion of BRD4 by 0.1 uM MZ1 was complete by 4 hours; IAA-induced degradation (500 uM) of RAD21 was complete by 1 hour. Subsequent co-depletion experiments were for 3 hours with 0.1uM MZ1, followed by the addition of 500uM IAA, for a total of 4 hours.

tag: cell line

value: human colorectal carcinoma cell line

value: MZ1+IAA under heat shock conditions


title: 18098D-02-07

value: male

value: sperm

tag: bmi

tag: storage (days)

tag: batch

value: Yes


title: F1_163

description: F1_163-2ndSUB_3114_GACCTGAA-TTGGTGAG_S40_cat

value: predictive

tag: Sex

tag: tissue


title: Patient_48 SAMPLE_48

value: Primary Skin melanoma

value: alive

tag: age

tag: status

value: absent

tag: braf v600e ihc status

value: positive

tag: Stage


title: F1_162

description: F1_162-2ndSUB_3114_AGTTCAGG-CCAACAGA_S39_cat

tag: strain background

value: a cross of two collaborative cross (CC) strains, CC011 x CC074

tag: genotype

value: AB

value: female


title: 23_MZ1_IAAHSR2

description: HCT116RmAC cells treated with MZ1+IAA under heat shock conditions replicate 2

tag: cell type

tag: treatment


title: 18098D-02-48

value: First

tag: sperm motility (%)

tag: smoking

value: No

tag: pp'-dde    (mg/mg lipid)


title: F1_161

description: F1_161-2ndSUB_3114_TGGATCGA-GTGCGATA_S38_cat


title: 22_MZ1_IAAHSR1

description: HCT116RmAC cells treated with MZ1+IAA under heat shock conditions replicate 1

tag: cell line


title: Patient_47 SAMPLE_47

tag: histology

value: Superficial spreading melanoma

tag: status after 5 years

value: man

value: negative


title: F1_160

description: F1_160-2ndSUB_3114_CAAGCTAG-ACATAGCG_S37_cat

value: BB

value: lung


title: 18098D-02-47

tag: sample group

value: Discovery

tag: tertile

value: male

value: sperm

tag: bmi

tag: storage (days)

tag: batch


title: Patient_46 SAMPLE_46

tag: tissue

value: Primary Skin melanoma

tag: age

tag: Sex

value: woman

tag: status

value: brisk

tag: braf v600e ihc status


title: Patient_45 SAMPLE_45

value: alive

value: nonbrisk

value: positive

tag: Stage


title: 18098D-02-41

tag: sperm motility (%)

value: Yes


title: F1_159

description: F1_159-2ndSUB_3114_GCTTGTCA-GAACATAC_S36_cat

value: predictive

tag: strain background

value: a cross of two collaborative cross (CC) strains, CC011 x CC074

tag: genotype

value: AB

value: female


title: 18098D-02-40

value: First

tag: smoking

tag: pp'-dde    (mg/mg lipid)


title: 18098D-02-37


title: F1_158

description: F1_158-2ndSUB_3114_ATCCACTG-AGGTGCGT_S35_cat


title: 20_IAAHSR2

description: HCT116RmAC cells treated with IAA under heat shock conditions replicate 2

source_name: HCT116RmAC_IAA under heat shock conditions

tag: cell line

tag: cell type

value: human colorectal carcinoma cell line

tag: treatment

value: IAA under heat shock conditions


title: Patient_43 SAMPLE_43

tag: histology

value: Superficial spreading melanoma

tag: status after 5 years

value: man

value: negative


title: Patient_44 SAMPLE_44

value: Primary Skin melanoma


title: Patient_49 SAMPLE_49

value: woman


title: 19_IAAHSR1

description: HCT116RmAC cells treated with IAA under heat shock conditions replicate 1


title: Patient_42 SAMPLE_42


title: 18098D-02-35

tag: sample group

value: Discovery

tag: tertile

value: male

value: sperm

tag: bmi

tag: storage (days)

tag: batch

value: No


title: 18098D-02-33

tag: Sex

tag: tissue

tag: age


title: 17_MZ1HSR2

description: HCT116RmAC cells treated with MZ1 under heat shock conditions replicate 2

source_name: HCT116RmAC_MZ1 under heat shock conditions

value: MZ1 under heat shock conditions


title: 18_MZ1HSR3

description: HCT116RmAC cells treated with MZ1 under heat shock conditions replicate 3


title: Patient_41 SAMPLE_41

description: raw data were quality checked in the nSolver software by using default parameters, imaging QC, bibdng density, positive control linearity and positive control limit detection (set to 0.5 fM) was evaluated

value: alive

tag: status

value: nonbrisk

tag: braf v600e ihc status

value: positive

tag: Stage


title: 16_MZ1HSR1

description: HCT116RmAC cells treated with MZ1 under heat shock conditions replicate 1


title: 21_IAAHSR3

description: HCT116RmAC cells treated with IAA under heat shock conditions replicate 3


title: F1_154

description: F1_154-2ndSUB_3114_CCGCGGTT-AGCGCTAG_S31_cat

value: predictive

tag: strain background

value: a cross of two collaborative cross (CC) strains, CC011 x CC074

tag: genotype

value: AB

value: female

value: lung


title: 18098D-02-30

value: First

tag: sperm motility (%)

tag: smoking

tag: pp'-dde    (mg/mg lipid)


title: Patient_40 SAMPLE_40

tag: histology

value: Superficial spreading melanoma

tag: status after 5 years

value: man

value: brisk

value: negative


title: 15_DMSOHSR3

description: HCT116RmAC cells treated with DMSO under heat shock conditions replicate 3

source_name: HCT116RmAC_DMSO under heat shock conditions

tag: cell line

tag: cell type

value: human colorectal carcinoma cell line

tag: treatment

value: DMSO under heat shock conditions


title: 18098D-02-29

tag: sample group

value: Discovery

tag: tertile

value: male

value: sperm

tag: bmi

tag: storage (days)

tag: batch

value: Yes


title: Patient_38 SAMPLE_38

tag: tissue

value: Primary Skin melanoma

value: alive

tag: age

tag: Sex

tag: status

value: absent

tag: braf v600e ihc status


title: 14_DMSOHSR2

description: HCT116RmAC cells treated with DMSO under heat shock conditions replicate 2


title: F1_156

description: F1_156-2ndSUB_3114_GGACTTGG-CGCAGACG_S33_cat

value: predictive

tag: strain background

value: a cross of two collaborative cross (CC) strains, CC011 x CC074

tag: genotype

value: AA


title: 18098D-02-24

value: First

tag: sperm motility (%)

tag: smoking

value: No

tag: pp'-dde    (mg/mg lipid)


title: F2_253

data_processing:
Reads were quality checked with package FastQC (version 0.11.4,), then trimmed using Trimgalore (version 0.4.4) with default settings.
Trimmed reads were mapped to mouse genome annotation mm10 using STAR aligner (Dobin and Gingeras, 2015) with default settings.
Mapped reads were counted using RsubRead (version 1.32.4, (Liao et al., 2019)). Raw counts were then normalized using DESeq2 (version 1.16.1, (Love et al., 2014)).
Genome_build: ENSMBL mm10 release 98, Genome: Mus_musculus.GRCm38.98
Supplementary_files_format_and_content: txt matrix with log2 normalized values per sample.

source_name: lung

value: control

value: BB

value: f


title: Patient_39 SAMPLE_39

tag: histology

value: Superficial spreading melanoma

tag: status after 5 years

value: man

value: brisk

value: positive

tag: Stage


title: F1_157

description: F1_157-2ndSUB_3114_AAGTCCAA-TATGAGTA_S34_cat

value: AB

value: female

value: lung


title: 13_DMSOHSR1

description: HCT116RmAC cells treated with DMSO under heat shock conditions replicate 1

tag: cell line

tag: cell type

value: human colorectal carcinoma cell line

tag: treatment

value: DMSO under heat shock conditions


title: Patient_36 SAMPLE_36

value: Primary Skin melanoma

value: alive


title: F1_155

description: F1_155-2ndSUB_3114_TTATAACC-GATATCGA_S32_cat

value: predictive

value: a cross of two collaborative cross (CC) strains, CC011 x CC074

value: AA


title: 18098D-02-22

tag: sample group

value: Discovery

tag: tertile

value: First

value: male

value: sperm

tag: bmi

tag: storage (days)

tag: batch

value: Yes


title: Patient_37 SAMPLE_37

tag: tissue

value: Superficial spreading melanoma

tag: age

tag: Sex

value: man

tag: status

value: brisk

tag: braf v600e ihc status


title: F2_244

value: control

tag: genotype

value: f


title: F2_242

value: AB


title: 12_MZ1_IAANHSR3

description: HCT116RmAC cells treated with MZ1+IAA under non heat shock conditions replicate 3

source_name: HCT116RmAC_MZ1+IAA under non heat shock conditions

value: human colorectal carcinoma cell line

value: MZ1+IAA under non heat shock conditions


title: 18098D-02-02

tag: sperm motility (%)

tag: smoking

value: No

tag: pp'-dde    (mg/mg lipid)


title: Patient_35 SAMPLE_35

value: Primary Skin melanoma

tag: histology

tag: status after 5 years

value: alive

value: woman

value: nonbrisk

value: positive

tag: Stage


title: F2_240

value: AA


title: 11_MZ1_IAANHSR2

description: HCT116RmAC cells treated with MZ1+IAA under non heat shock conditions replicate 2

tag: cell line

tag: cell type

tag: treatment


title: 10_MZ1_IAANHSR1

description: HCT116RmAC cells treated with MZ1+IAA under non heat shock conditions replicate 1


title: 18098D-02-20

tag: sample group

value: Discovery

tag: tertile

value: First

value: male

value: sperm

tag: bmi

tag: storage (days)


title: Patient_34 SAMPLE_34

tag: tissue

value: Superficial spreading melanoma

value: dead

tag: age

tag: Sex

value: absent

value: negative


title: 18098D-02-12

tag: batch

value: Yes


title: F2_238

value: control

tag: genotype

value: AB

value: f


title: 9_IAANHSR3

description: HCT116RmAC cells treated with IAA under non heat shock conditions replicate 3

source_name: HCT116RmAC_IAA under non heat shock conditions

value: human colorectal carcinoma cell line

value: IAA under non heat shock conditions


title: 18098D-02-10

tag: sperm motility (%)

tag: smoking

value: No


title: F2_237


title: F2_256

value: BB


title: Patient_33 SAMPLE_33

value: Primary Skin melanoma

tag: histology

value: alive

value: man

tag: status

value: brisk

tag: braf v600e ihc status

value: positive


title: 8_IAANHSR2

description: HCT116RmAC cells treated with IAA under non heat shock conditions replicate 2

tag: cell line


title: 18098D-02-04

value: Discovery

value: First

value: male

value: sperm

tag: pp'-dde    (mg/mg lipid)


title: Patient_32 SAMPLE_32

value: Superficial spreading melanoma

tag: status after 5 years

value: woman

value: negative

tag: Stage


title: F2_228

value: control

value: AA

value: f


title: T47D

city: Boston

first: Rinath

last: Jeselsohn

address: 450 Brookline Ave, D728

department: Medical Oncology

institute: DFCI

data_processing:
Library strategy: Whole Genome Sequencing
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For SNP/INDEL detection GATK was used.
For CNV detection control-FREEC was used.
For SV detection DELLY was used.
Genome_build: hg19

source_name: Breast carcinoma cell line

growth_protocol: Cells were grown in their original media

extract_protocol:
Total DNA isolation was performed using the QIAamp DNA Blood Mini Kit (Qiagen).
DNA-seq libraries were generated using a Thruplex DNA Seq Kit (Takara Bio USA)

treatment_protocol: Cells were maintained in their original media and harvested for DNA extraction.

value: T47D breast carcinoma cell line


title: F2_227


title: F1_147

value: high

value: AB


title: Patient_31 SAMPLE_31

value: Primary Skin melanoma

value: alive

value: absent


title: Patient_29 SAMPLE_29

value: dead

value: man


title: 4_MZ1NHSR1

description: HCT116RmAC cells treated with MZ1 under non heat shock conditions replicate 1

source_name: HCT116RmAC_MZ1 under non heat shock conditions

tag: cell type

value: human colorectal carcinoma cell line

tag: treatment

value: MZ1 under non heat shock conditions


title: 5_MZ1NHSR2

description: HCT116RmAC cells treated with MZ1 under non heat shock conditions replicate 2


title: 7_IAANHSR1

description: HCT116RmAC cells treated with IAA under non heat shock conditions replicate 1

value: IAA under non heat shock conditions


title: Patient_30 SAMPLE_30

description: raw data were quality checked in the nSolver software by using default parameters, imaging QC, bibdng density, positive control linearity and positive control limit detection (set to 0.5 fM) was evaluated

value: Superficial spreading melanoma

value: brisk

value: positive


title: MDA134

value: MDA_MB134 breast carcinoma cell line


title: F1_144


title: 3_DMSONHSR3

description: HCT116RmAC cells treated with DMSO under non heat shock conditions replicate 3

source_name: HCT116RmAC_DMSO under non heat shock conditions

value: DMSO under non heat shock conditions


title: Patient_27 SAMPLE_27

value: nonbrisk

value: negative


title: 2_DMSONHSR2

description: HCT116RmAC cells treated with DMSO under non heat shock conditions replicate 2


title: F1_129

value: low

value: f


title: P.aeruginosa_TBCF strain MTase cp KO, mid log phase, biol rep 3

city: Shenzhen

first: Yang

last: Liu

state: Guangdong

address: Liuxian

country: China

institute: Sustech Hospital

data_processing:
RSEM v1.3.1
Trimmed sequence reads were mapped to Pseudomonas aeruginosa TBCF using rsem-calculate-expression with unique mapping setting (--bowtie-m)
Read count extraction was performed using RSEM rsem-generate-data-matrix
Assembly: Pseudomonas aeruginosa TBCF
Supplementary files format and content: tab-delimited text files include reads counts for each Sample

organism: Pseudomonas aeruginosa

source_name: P.aeruginosa_TBCF strain MTase cp KO

growth_protocol: P. aeruginosa TBCF and mutants were grown in Luria-Bertani (LB) liquid media at 37°C with constant shaking at 220 rpm with aeration.

extract_protocol:
Total RNA extraction and purification was performed for 3 biological replicates of each strain using RNeasy Mini Kit (QIAGEN) and RNase-Free DNase Set (QIAGEN) according to the manufacturer’s protocol. 1μg of total RNA was used for the construction of sequencing libraries.
RNA sequencing was performed on Illumina NovaSeq 6000 sequencing platform generating 150 bp paired-end reads.

treatment_protocol: The in-frame deletion mutagenesis of methyltransferase ap or cp was performed through two-step allelic exchange. P. aeruginosa TBCF and mutants were cultured to mid log phase.

tag: strain

value: P.aeruginosa_TBCF strain MTase cp KO

tag: developmental stage

value: mid log stage

value: MTase cp KnockOut


title: SUM44

value: SUM44PE breast carcinoma cell line


title: Patient_26 SAMPLE_26

source_name: Primary Skin melanoma

tag: tissue

value: Primary Skin melanoma

value: alive

tag: age

value: woman


title: F1_141

value: high

value: AA

tag: Sex


title: 1_DMSONHSR1

description: HCT116RmAC cells treated with DMSO under non heat shock conditions replicate 1

value: human colorectal carcinoma cell line


title: F1_128

tag: genotype


title: Patient_25 SAMPLE_25

value: Superficial spreading melanoma

value: absent

value: positive


title: 6_MZ1NHSR3

description: HCT116RmAC cells treated with MZ1 under non heat shock conditions replicate 3

value: MZ1 under non heat shock conditions


title: P.aeruginosa_TBCF strain MTase cp KO, mid log phase, biol rep 1


title: Human colon cancer cells - clone WT_rep1

city: Stockholm

first: Anita

last: Göndör

address: Nobels väg 16, KI Solna Campus, Karolinska Institutet, Box 280

department: MTC

country: Sweden

institute: Karolinska Institutet

data_processing:
Basecalls performed using CASAVA version 1.8.2
Chip-seq data was performed by nf-core/chipseq pipeline (version 1.2.2)
Picard (v2.23.1) was used to mark duplicates. BEDTools (v2.29.2) and bedGraphToBigWig were used create normalized bigWig files.
MACS2 (v2.2.7.1) was used to call peaks with following parameter "callpeak --broad --broad-cutoff 0.1-f BAMPE  -g 2.7e9 "
Genome_build: hg19
Supplementary_files_format_and_content: peak text files

source_name: Human colon cancer cells

growth_protocol: Human colon cancer cells (HCT-116) were maintained in McCoy's 5A medium modified medium (Life Technologies, 16600-082) supplemented with 10% FBS, and 1% penicillin and streptomycin (Life Technologies)

extract_protocol:
Cells were fixed with 1% freshly prepared formaldehyde solution for 10min and then lysed with buffer containing: 50 mM Tris-HCl, pH 8; 10 mM EDTA; 1% SDS; x1 Proteinase inhibitor (Roche). Chromatin was sonicated and DNA–protein complexes were immune-purified with antibodies against CTCF (CS 2899S)
DNA sample was used for library by following the manufacturer’s recommendations of NEBNext® Ultra™ IIDNA Library Prep Kit (New England BioLabs, US). Index codes were added to each sample. Briefly, the genomic DNA was randomly fragmented to size of 350bp. DNA fragments were end polished, A-tailed, ligated with adapters, size selected and further PCR enriched. Then PCR products were purified (AMPure XP system), followed by size distribution by Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA), and quantification using real-time PCR. Library was then sequenced on NovaSeq 6000 S4 flow cell with PE150 strategy.

treatment_protocol: No treatment has been involved

value: Human colon cancer cells

tag: genotype/variation

value: wild type

tag: antibody


title: MCF7

value: MCF7 breast carcinoma cell line


title: F1_146

value: AB

value: f


title: Patient_28 SAMPLE_28

tag: histology

value: brisk


title: Patient_24 SAMPLE_24

value: man

tag: status


title: F1_126


title: P.aeruginosa_TBCF strain WT, mid log phase, biol rep 2

source_name: P.aeruginosa_TBCF strain WT

value: P.aeruginosa_TBCF strain WT

value: mid log stage


title: Human colon cancer cells - clone E4 no antibody_rep1

value: CTCF mutation


title: GES-1 cells, Trx1 low-3

city: Beijing

first: Xin

last: Guan

address: Peking University Third Hospital, 49 Huayuan North Road, Haidian District, Beijing

institute: Peking university Third Hospital

data_processing:
Differential expression analysis of three groups was performed using the DESeq2 R package (1.20.0) which provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution.
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Padj<0.05 and |log2(fold change)| > 1 were set as the threshold for significantly differential expression. We used cluster Profiler R package (3.8.1) to test the statistical enrichment of differential expression genes in KEGG pathways.
FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: HISAT2 v2.0.5
Supplementary_files_format_and_content: gene_count_fpkm.txt (represents FPKM values for each Sample), matrix.txt  (represents raw gene counts for each Sample)

source_name: Gastric epithelial cells co-cultured with H.pylori with Trx1 low expression

growth_protocol: GES-1 cells co-cultured with H.pylori mentioned above were collected at 12h and three biological repeats were performed for each group.

extract_protocol: Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA) and then prepared to structure library which was initially quantified by Qubit2.0 Fluorometer for Transcriptome sequencing and the insert size of the library is detected by Agilent 2100 bioanalyzer at the Novogene Bioinformatics Technology Co., Ltd.

value: Gastric epithelial cells


title: Patient_23 SAMPLE_23

value: Primary Skin melanoma

value: alive

tag: braf v600e ihc status

value: negative


title: F1_125

value: high


title: Patient_22 SAMPLE_22

value: Superficial spreading melanoma


title: Human colon cancer cells - clone D3 no antibody_rep1

tag: cell line


title: F1_124

value: low

value: BB


title: Human colon cancer cells - WT CTCF_rep1

value: Human colon cancer cells

value: wild type

value: CTCF


title: P.aeruginosa_TBCF strain MTase cp KO, mid log phase, biol rep 2

value: P.aeruginosa_TBCF strain MTase cp KO

value: MTase cp KnockOut


title: P. aeruginosa PAO1 (WT) treated by NV716_rep 2

city: Hanover

first: Susanne

last: Häußler

address: Feodor-Lynen-Str. 7

department: Molecular Bacteriology

institute: Twincore

data_processing:
Reads were were quality controlled (option “--nextseq-trim=20”) and clipped using cutadapt and mapped to the reference genome PAO1 (NC_002516.2) using bowtie2
Genome_build: NC_002516.2 (PAO1)
Supplementary_files_format_and_content: Processed data file is a data matrix that contains raw unique gene reads.

growth_protocol: PAO1 and daughter bacteria collected after the 52th passage in the presence of potentiators at ½ MIC were spread on TSA containing or not potentiators at ½ MIC and incubated overnight, after which 3 colonies were independently inoculated in 2mL MHB-CA containing or not ½ MIC of potentiators and incubated overnight at 37°C with shaking at 130 rpm

extract_protocol:
RNA was extracted from cell pellets using the InviTrap® Spin Cell RNA Mini Kit (INVITE) according to the manufacturer's instruction
Ribosomal RNA was removed using the Ribo-Zero Bacteria Kit (Illumina) and libraries for transcriptomics were generated according to Shishkin et al., 2015 and Bhattacharyya et al., 2019

treatment_protocol: Serial passage cultures in broth were performed by exposing to potentiators alone at ½ MIC, with daily 1/1000 dilution of the bacteria and readjustment of the concentration to ½ MIC of the previous day, during 52 days.

value: treated with NV716 after 52 passages


title: F1_123

value: f


title: P. aeruginosa PAO1 (WT) treated by NV716_rep 1


title: F1_121

value: AA


title: Patient_20 SAMPLE_20

value: woman

value: brisk


title: Human colon cancer cells - clone E4 CTCF_rep1

value: CTCF mutation


title: Human colon cancer cells - clone D3 CTCF_rep1


title: Patient_19 SAMPLE_19

value: Primary Skin melanoma

value: alive

value: nonbrisk

value: positive


title: P. aeruginosa PAO1 (WT) treated by alexidine_rep 3

value: treated with alexidine after 52 passages


title: F1_116

value: high

value: AB


title: P.aeruginosa_TBCF strain WT, mid log phase, biol rep 3

value: P.aeruginosa_TBCF strain WT

value: mid log stage

value: wild type


title: RNAseq of 4324_SPL_CB_XENO

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

description: RNAseq of 4324_SPL_CB_XENO

data_processing:
paired end reads mapped to hg38 for human samples and mm10 for mouse samples using STAR (v2.7)
gene quantification using RSEM v1.3.1
Genome_build: hg38 for human, mm10 for mouse
Supplementary_files_format_and_content: text file for gene counts, TPM and FPKM of each gene annotated in Gencode M22

source_name: cord blood CD34+

growth_protocol: Human CD34 cells were transplanted into NSG-SGM3 mice, harvested when the mice were sick, and GFP+ cells were sorted from the spleen. Wild type or ARF-null lineage negative cells were isolated from mouse bone marrow, transduced with lentivirus, transplanted into BL6 mice, harvested when mice were sick, and GFP+ cells were sorted from bone marrow or spleen.

extract_protocol:
RNA was harvested using the Qiagen AllPrep Kit (Qiagen AllPrep Micro Kit for Low input samples) and RNA was quantified using the Quant-iT RiboGreen RNA assay (ThermoFisher) and quality checked by the 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent) prior to library generation.
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20020599). For the low input samples, cDNA was generated using Tecan/NuGen Ovation RNA-Seq System V2 (catalog 7102) with 1ng RNA, sheared to 300bp using Covaris, and libraries were prepped using the Kapa Hyper kit/protocol (catalog KK8504) and using Illumina True Seq IDT DNA UD Indexes (20020178). Low input library quality was evaluated on a D1000 tape using Agilent’s Tape Station 4200.

tag: growth conditions

value: lentiviral transduction, transplant into NSG-SGM3 mice, harvest spleen and sort GFP+ cells

value: Spleen

tag: input

value: Low Input


title: Patient_18 SAMPLE_18

value: Superficial spreading melanoma

tag: status after 5 years

value: absent

tag: Stage


title: P. aeruginosa PAO1 (WT) treated by alexidine_rep 2

tag: treatment


title: F1_113

value: low

value: f


title: Patient_17 SAMPLE_17

value: Primary Skin melanoma

value: man

value: negative


title: P. aeruginosa PAO1 (WT) treated by alexidine_rep 1

tag: strain


title: F1_108

value: AA


title: P.aeruginosa_TBCF strain WT, mid log phase, biol rep 1

tag: developmental stage


title: RNAseq of 4626_SPL_KD032

description: RNAseq of 4626_SPL_KD032

value: lentiviral transduction, transplant into NSG-SGM3 mice, harvest spleen of sick mice and sort GFP+ cells

tag: tissue


title: RNAseq of 4630_SPL_KD032

description: RNAseq of 4630_SPL_KD032


title: F1_103

value: high


title: P. aeruginosa PAO1 (WT) treated by colistin_rep 3

value: treated with colistin after 52 passages


title: Patient_21 SAMPLE_21

value: alive

tag: age

value: woman

value: brisk

value: positive


title: RNAseq of 4622_SPL_KD032

description: RNAseq of 4622_SPL_KD032

value: Spleen


title: F1_093

value: AB

tag: Sex


title: RNAseq of 4624_SPL_KD032

description: RNAseq of 4624_SPL_KD032

tag: genotype

value: Low Input


title: P. aeruginosa PAO1 (WT) treated by colistin_rep 1

value: wild type


title: F1_092


title: Patient_14 SAMPLE_14

value: Superficial spreading melanoma

value: nonbrisk


title: P. aeruginosa PAO1 (WT) treated by colistin_rep 2


title: RNAseq of 4628_SPL_KD032

description: RNAseq of 4628_SPL_KD032


title: P. aeruginosa PAO1 (WT) non-treatment_rep 3

value: untreated


title: F1_091

value: f


title: Patient_12 SAMPLE_12

value: Primary Skin melanoma

value: man

value: negative


title: F1_086

value: low


title: iPSCMC2

city: Berlin

first: Yanyan

last: Luo

address: Luisenstrasse 2

institute: Department of Dermatology and Allergy Allergie-Centrum-Chari

data_processing:
2 × 150 bp sequencing configuration and 20–30 million reads per sample.
Sequence quality, reads trim and mapped to human genome (GRCh38.p7) .
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: counts

source_name: hiPSC derived mast cells

extract_protocol:
The total RNA was extracted with NucleoSpin RNA isolation Kit
RNA libraries were prepared for sequencing using standard illumina protocol

tag: cell type

value: hiPSC derived mast cells

value: on day 52 of differentiation


title: iPSCMC3


title: Patient_11 SAMPLE_11

value: alive


title: P. aeruginosa PAO1 (WT) non-treatment_rep 1


title: F1_081


title: iPSCMC1


title: Patient_16 SAMPLE_16

value: woman


title: Patient_15 SAMPLE_15

value: brisk


title: F1_077

value: AA


title: Patient_10 SAMPLE_10


title: 5A

source_name: hiPSC line

value: hiPSCs

value: no differentiation


title: F1_073

value: AB


title: 250A


title: Patient_8 SAMPLE_8

value: Superficial spreading melanoma

value: positive


title: F1_071

value: BB


title: Patient_9 SAMPLE_9

value: absent


title: Patient_7 SAMPLE_7

value: Primary Skin melanoma

value: nonbrisk


title: 1B


title: F1_066

value: f


title: hsMC3

source_name: skin

value: primary mast cells

value: 3d after isolation


title: Patient_5 SAMPLE_5

value: man


title: F1_070

value: low


title: Patient_13 SAMPLE_13

value: dead

value: negative


title: Patient_6 SAMPLE_6

value: alive


title: hsMC2


title: P. aeruginosa PAO1 (WT) non-treatment_rep 2

value: wild type

value: untreated


title: F1_065

value: AB


title: hsMC1


title: F1_064


title: F1_063


title: Patient_4 SAMPLE_4

value: Superficial spreading melanoma

value: brisk


title: HiChIP-T47D

data_processing:
library strategy: Hi-ChIP
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated using hic-pro and fithichip

growth_protocol: Cells were grown in estrogen deprived media for 3 days

extract_protocol:
After proximity ligation with biotin-dATP, nuclei were lysed and sonicated and chromatin immunoprecipitation with H3K27AC, followed by DNA purification and biotin capture of the Hi-C contacts
DNA library preparation was performed with Tn5 on beads, amplifying for 11 cycles total

treatment_protocol: Cells were treated with 10nM E2 for 45 minutes

value: T47D breast carcinoma cell line

tag: agent

value: Estrogen

tag: chip antibody

value: H3K27ac (C15410196, Diagenode)


title: Patient_3 SAMPLE_3

value: Primary Skin melanoma

tag: histology

value: woman

tag: status

value: nonbrisk


title: HiChIP-SUM44

tag: cell line

value: SUM44PE breast carcinoma cell line


title: Patient_1 SAMPLE_1

tag: braf v600e ihc status


title: Patient_2 SAMPLE_2

value: man


title: F1_031

value: high

value: AA

value: f


title: HiChIP-MDA134

value: MDA_MB134 breast carcinoma cell line


title: HiChIP-MCF7

value: MCF7 breast carcinoma cell line


title: F1_035

value: low


title: MpalsP197L_10, Treated, 24 hours, biol rep 2

status: Public on Aug 30 2022

city: Vienna

first: Alexandra

last: Casey

address: Dr.-Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

data_processing:
Raw reads were unzipped and viewed using FastQC v.0.11.7. Illumina adaptors and low quality tils were quality trimmed using Trimmomatic-0.38.
Paired-end reads were interleaved, and ribosomal RNA was removed using Sortmerna-2.1 and error corrected using BayesHammer (SPAdes-3.10.0) with setting-only-error-correction.
Clean reads were mapped to a reference transcriptome (JGI 3.1, obtained from https://marchantia.info/download/v31/) using Salmon.
Lanes were collapsed and normalized counts for each gene were obtained using the DESeq2 v.1.21.3 package.
Assembly: JGI 3.1
Supplementary files format and content: CSV file of a matrix table of normalised counts obtained for each gene from each sample using DESeq2.

organism: Marchantia polymorpha

source_name: whole plant

growth_protocol: Plants were grown on 100 x 21 mm round petri dishes on top of autoclaved cellophane discs (A.A. Packaging LTd, Preston, UK) placed on the surface of 30 mL Johnson's medium with 0.8% agar.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
Samples with RNA integrity (RIN) numbers provided by an Agilent 2100 BioAnalyser (Agilent Technologies) ≥8 were suitable for cDNA library preparation following the Illumina RNA prep protocols (Welcome Trust Oxford Genomics Centre)

treatment_protocol: 8 day old gemmae were moved onto chlorsulfuron-treated or untreated control medium and collected at different timepoints after transfer. Each sample represents 6 plants grown on the same media plate.

value: whole plant

tag: time

value: 24 hours

value: 5 nM Chlorsulfuron


title: MpalsP197L_10, Treated, 12 hours, biol rep 1

value: 12 hours


title: MpalsP197L_10, Control, 6 hours, biol rep 2

value: 6 hours

value: Untreated


title: MpalsP197L_10, Control, 2 hours, biol rep 2

value: 2 hours


title: MpalsP197L_10, Treated, 12 hours, biol rep 2


title: MpalsP197L_10, Control, 24 hours, biol rep 2


title: MpalsP197L_10, Control, 6 hours, biol rep 1


title: MpalsP197L_10, Treated, 6 hours, biol rep 2


title: MpalsP197L_10, Treated, 36 hours, biol rep 1

value: 36 hours


title: MpalsP197L_10, Treated, 24 hours, biol rep 1


title: MpalsP197L_10, Control, 36 hours, biol rep 1


title: MpalsP197L_10, Control, 12 hours, biol rep 1


title: MpalsP197L_10, Control, 12 hours, biol rep 2


title: MpalsP197L_10, Control, 36 hours, biol rep 2


title: MpalsP197L_10, Treated, 36 hours, biol rep 2


title: MpalsP197L_10, Control, 2 hours, biol rep 1


title: MpalsP197L_10, Control, 0 hours, biol rep 1

value: 0 hours


title: MpalsP197L_10, Control, 0 hours, biol rep 2


title: MpalsP197L_7, Treated, 48 hours, biol rep 2

value: 48 hours


title: MpalsP197L_7, Treated, 48 hours, biol rep 1


title: MpalsP197L_10, Control, 24 hours, biol rep 1


title: MpalsP197L_7, Control, 48 hours, biol rep 1


title: MpalsP197L_7, Control, 48 hours, biol rep 2


title: tarsal joint_exercised_prearthritic phase

city: Chihuahua

first: Susana

middle: Aideé

last: González-Chávez

state: Chihuahua

address: Circuito Universitario Campus II

department: Facultad de Medicina

country: Mexico

institute: Universidad Autónoma de Chihuahua

description: RNA equimolar pools from eight mice in each group were made.

hyb_protocol: Hybridization was performed using the M22K_01 (UNAM, Mexico City, Mexico) chip containing 23,232 genes from the mouse genome

scan_protocol: The scan and acquisition of the signal were developed using the ScanArray 4000 (Packard BioChips Technologies, Billerica, Massachusetts, USA).

data_processing: The analysis of the microarray scanning was done using GenArise Microarray Analysis Tool software (UNAM), and the lists of differentially expressed genes (DEGs) (Z-score ≥ 1.5 SD) were obtained

source_name: Tarsal joint, collagen-induced arthritis, no exercised

label_protocol: Reverse transcription-polymerase chain reaction (RT-PCR) was performed, and the resulting complementary DNA (cDNA) from CIA DBA1_ExePre were labeled with Cy5, while the cDNA from the CIA DBA1_No Exe group was labeled with Cy3

growth_protocol: No exercised mice with CIA

extract_protocol: Total RNA was purified using the RNeasy® Mini Kit (Qiagen, Hilden, Germany) extraction kit, following the manufacturer’s protocol

treatment_protocol: No exercised

tag: gender

value: male

tag: arthritis model

value: collagen-induced arthritis

value: Tarsal joint

source_name: Tarsal joint, collagen-induced arthritis, exercised, phase prearthritic

treatment_protocol: Exercised prearthritic phase


title: MpalsP197L_7, Control, 36 hours, biol rep 2

tag: treatment


title: MpalsP197L_7, Control, 36 hours, biol rep 1


title: MpalsP197L_10, Treated, 6 hours, biol rep 1


title: MpalsP197L_7, Treated, 36 hours, biol rep 2


title: MpalsP197L_10, Treated, 2 hours, biol rep 1


title: tarsal joint_exercised_postarthritic phase

label_protocol: Reverse transcription-polymerase chain reaction (RT-PCR) was performed, and the resulting complementary DNA (cDNA) from CIA DBA1_ExePost were labeled with Cy5, while the cDNA from the CIA DBA1_No Exe group was labeled with Cy3

tag: strain

source_name: Tarsal joint, collagen-induced arthritis, exercised, phase postarthritic

treatment_protocol: Exercised postarthritic phase


title: MpalsP197L_7, Control, 24 hours, biol rep 2


title: MpalsP197L_7, Treated, 24 hours, biol rep 2


title: MpalsP197L_7, Treated, 24 hours, biol rep 1


title: MpalsP197L_7, Treated, 6 hours, biol rep 2


title: MpalsP197L_7, Treated, 12 hours, biol rep 1


title: MpalsP197L_7, Control, 4 hours, biol rep 1

value: 4 hours


title: MpalsP197L_7, Treated, 12 hours, biol rep 2


title: MpalsP197L_7, Control, 4 hours, biol rep 2


title: MpalsP197L_7, Treated, 4 hours, biol rep 1


title: MpalsP197L_7, Control, 2 hours, biol rep 2


title: MpalsP197L_7, Control, 6 hours, biol rep 2


title: MpalsP197L_7, Treated, 36 hours, biol rep 1


title: MpalsP197L_7, Treated, 6 hours, biol rep 1


title: MpalsP197L_7, Treated, 2 hours, biol rep 1


title: MpalsP197L_7, Control, 12 hours, biol rep 1


title: MpalsP197L_7, Treated, 4 hours, biol rep 2


title: MpalsP197L_7, Control, 0 hours, biol rep 5


title: MpalsP197L_7, Control, 12 hours, biol rep 2


title: MpalsP197L_7, Control, 6 hours, biol rep 1


title: MpalsP197L_7, Treated, 2 hours, biol rep 2


title: MpalsP197L_7, Control, 2 hours, biol rep 1


title: MpalsP197L_7, Control, 0 hours, biol rep 4


title: MpalsP197L_7, Control, 0 hours, biol rep 1


title: MpalsP197L_7, Control, 0 hours, biol rep 2


title: Tak-2, Control, 48 hours, biol rep 2

value: Wild type


title: Tak-2, Control, 48 hours, biol rep 1


title: Tak-2, Treated, 48 hours, biol rep 2


title: Tak-2, Treated, 48 hours, biol rep 1


title: MpalsP197L_7, Control, 24 hours, biol rep 1


title: Tak-2, Control, 36 hours, biol rep 2


title: Tak-2, Treated, 36 hours, biol rep 2


title: Tak-2, Control, 36 hours, biol rep 1


title: Tak-2, Treated, 24 hours, biol rep 1


title: Tak-2, Treated, 24 hours, biol rep 2


title: Tak-2, Treated, 12 hours, biol rep 2


title: Tak-2, Control, 6 hours, biol rep 2


title: Tak-2, Treated, 6 hours, biol rep 2


title: Tak-2, Control, 24 hours, biol rep 2


title: Tak-2, Control, 24 hours, biol rep 1


title: Tak-2, Treated, 6 hours, biol rep 1


title: Tak-2, Control, 2 hours, biol rep 2


title: Tak-2, Control, 12 hours, biol rep 2


title: Tak-2, Treated, 4 hours, biol rep 2


title: Tak-2, Control, 4 hours, biol rep 1


title: Tak-2, Control, 12 hours, biol rep 1


title: Tak-2, Control, 6 hours, biol rep 1


title: Tak-2, Treated, 4 hours, biol rep 1


title: MpalsP197L_7, Control, 0 hours, biol rep 3


title: Tak-2, Treated, 2 hours, biol rep 1


title: Tak-2, Treated, 2 hours, biol rep 2


title: Tak-2, Control, 0 hours, biol rep 4


title: Tak-2, Control, 0 hours, biol rep 1


title: Tak-2, Control, 0 hours, biol rep 5


title: Tak-2, Control, 0 hours, biol rep 3


title: Tak-2, Control, 0 hours, biol rep 2


title: Tak-2, Treated, 36 hours, biol rep 1


title: porcine embryos  siL03

city: Changchun

first: Daoyu

last: Zhang

address: Xinzhu street 1977

institute: Jilin University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt genomic benchwork
Trimmed sequence reads were mapped to Sscrofa11.1 using bowtie2(v2.3.5)
Read count extraction and normalization were performed using stringTie(v2.1.7)
Supplementary files format and content: Sscrofa11.1
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Sus scrofa

source_name: 8-cell embryos

growth_protocol: Embryo culture medium

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: siRNA micromanipulation of cytoplasmic injection

value: 8-cell embryos

value: embryos

value: LncT KD

value: siRNA injection


title: Tak-2, Treated, 12 hours, biol rep 1

value: whole plant

value: 5 nM Chlorsulfuron


title: porcine embryos  siL02


title: porcine embryos  control03

value: Control


title: porcine embryos  siL01


title: Tak-2, Control, 2 hours, biol rep 1

value: Untreated


title: porcine embryos  control01


title: porcine embryos  control02


title: nhr-49(nr2041)_rep 2

city: Dallas

first: Peter

middle: M

last: Douglas

state: Texas

address: 6000 Harry Hines Blvd

department: Department of Molecular Biology

institute: University of Texas Southwestern Medical Center at Dallas

description: nhr-49(nr2041) biological replicate 2

data_processing:
Basecalling and trimming were performed using CLC Genomics Workbench ver. 9.5.
Sequences were mapped to the whole Caenorhabidits elegans genome using CLC Genomic Workbench ver. 9.5.
Expression values and Reads per kilobase million (RPKM) were calculated according to default CLC settings.
Assembly: WBcel235
Supplementary files format and content: excel file contains RPKM values for each transcript

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: All tissue

growth_protocol: Cultured at 20°C on HT115 bacteria and NGM plates supplemented with IPTG and Carbenicillin

extract_protocol:
Whole worm RNA was extracted using Trizol with freeze/thawing and vortexing. RNA was later enriched for mRNA using oligo(dt) beads.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Empty vector RNAi treatment for entirety of develpoment

value: L4 larvae

value: EV RNAi


title: wild-type_rep 3

description: empty vector RNAi biological replicate 3

value: wild type


title: nhr-49(nr2041)_rep 1

description: nhr-49(nr2041) biological replicate 1


title: nhr-49(nr2041)_rep 3

description: nhr-49(nr2041) biological replicate 3


title: wild-type_rep 2

description: empty vector RNAi biological replicate 2


title: THP1 cells

city: Hangzhou

first: Weina

last: Yun

address: yuhangtang road

institute: Zhejiang University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FRKM and count values for each sample

source_name: THP1 cells

growth_protocol: Cells were maintained in RPMI 1640 supplemented with 10% FBS and 1% penicillin- streptomycin.  All cells were kept at 37℃ in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: Ara-C resistant THP-1 cells obtained by gradually increasing the concentration of Ara-C from 5 nM to 10 μM. Cells were defined as Ara-C resistant cells once the duplicating speed equaling that of the untreated control group.

value: untreated

value: acute myeloid leukemia cells


title: Ara-C resistant THP1 cells

value: Ara-C resistant THP-1 cells obtained by gradually increasing the concentration of Ara-C from 5 nM to 10 μM.


title: MK3 cells, LV-Rik, biol rep3

city: Shanghai

first: Shanshan

last: Xue

address: 399 Wanyuan Road

institute: Children's Hospital of Fudan University

data_processing:
These libraries were sequenced on the Illumina NovaSeq 6000, and 125 bp/150 bp paired-end reads were generated.
Raw data (raw reads) were processed using Trimmomatic. The reads containing poly-N and the low-quality reads were removed to obtain clean reads.
Then, the clean reads were mapped to the reference genome using HISAT2.
The FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Differentially expressed genes (DEGs) were identified using the DESeq R package functions estimateSizeFactors and nbinomTest.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values and counts for all Samples

growth_protocol: MPTC cells were maintained in Dulbecco’s modified Eagle medium/Nutrient Mixture F-12 supplemented with 10% fetal bovine serum (FBS) and 1× penicillin–streptomycin in humidified atmosphere with 5% CO2 at 37C. MK3 cells were maintained in DMEM/HIGH GLUCOSE medium supplemented with 10% fetal bovine serum (FBS) and 1× penicillin–streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using TRIzol(Thermo, USA). RNA integrity was evaluated using the Agilent 2100 Bioanalyzer. The samples with an RNA integrity number (RIN) ≥ 7 were subjected to subsequent analysis.
The libraries were constructed using the TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s instructions.

treatment_protocol: LncRNA Rik cDNA was amplified by PCR and then cloned into the GV367-Ubi-MCS-SV40-EGFP-IRES-puromycin vector, and the correct sequence of lncRNA Rik was verified by sequencing. In short, when cell confluence reached 20%-30%, MPTC cells were infected in the presence of 1×10^6 TU/mL lentivirus, while MK3 cells were infected with 1×10^8 TU/mL lentivirus, and the media were supplemented with 5 mg/mL polybrene. The cells were washed with fresh complete medium after 16 h. All infection procedures were carried out in strict accordance with the experimental protocol. Three days after infection, the cells were screened with puromycin. After screening for at least one week, the efficiency of lncRNA Rik overexpression was verified by RT‒PCR. Cryopreservation and subsequent experimental studies were conducted on overexpressed cloned cell lines.

value: mesenchymal stem cells

value: Rik overexpression

value: lentivirus infection


title: MK3 cells, con238-Rik, biol rep3

value: WT


title: MK3 cells, con238-Rik, biol rep2


title: MK3 cells, LV-Rik, biol rep2


title: MK3 cells, LV-Rik, biol rep1


title: MPTC cells, LV-Rik, biol rep3

source_name: MPTC

value: MPTC


title: MK3 cells, con238-Rik, biol rep1


title: MPTC cells, LV-Rik, biol rep2


title: pancreatic tumor of xenograft mouse processed with SKOV3 cell, 1

first: Chunmei

last: Cui

state: Beijing

address: Xueyuan Road 38, Haidian district, eijing

institute: Peking University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
1. RNA degradation and contamination was monitored on 1% agarose gels.
2. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA)
3. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: pancreatic cancer cell line

value: injection with SKOV3 cell


title: pancreatic tumor of xenograft mouse processed with SKOV3 cell, 3


title: pancreatic tumor of xenograft mouse processed with SKOV3 cell, 2


title: MPTC cells, LV-Rik, biol rep1


title: MPTC cells, con238-Rik, biol rep2


title: MPTC cells, con238-Rik, biol rep3


title: MPTC cells, con238-Rik, biol rep1


title: pancreatic tumor of xenograft mouse, 3

value: normal saline solution


title: pancreatic tumor of xenograft mouse, 1


title: pancreatic tumor of xenograft mouse, 2


title: wild-type_rep 1

description: empty vector RNAi biological replicate 1


title: BMDMs, NLRC3_KO, RPMI 1640, rep3

city: Wuhan

first: You

last: Shang

state: Hubei

address: Jianghan district

department: Critical Care Medicine

institute: Wuhan Union Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample
Supplementary files format and content: Matrix table with raw counts for every gene and every sample

source_name: mice femurs and tibias

growth_protocol: BMDMs were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), recombinant M-CSF and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was isolated from 1.0 × 10^6 BMDMs and was extracted from macrophages using TRIzol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded RNA-Seq Kit following manufacturer's protocols.

treatment_protocol: BMDMs were treated with or without LPS.

value: mice femurs and tibias

value: BMDM

value: NLRC3 KO

value: RPMI 1640


title: CLIP_SHSY5Y-RA_rep2_CLIP

city: D

first: Kate

last: Meyer

state: NC

address: 307 Research Drive Box 3711

department: Biochemistry

institute: Duke University School of Medicine

description: RA replicate 2, CLIP RNA

data_processing:
adapter removal (SeqAn 2.3.2, flexbar 3.0.3)
demultiplexing (Python 2.7.11)
alignment (HISAT2) to hg19
paired sample peak-calling (MACS2 2.1.1.20160309)
overlap of replicate peaksets (Bedtools 2.25.0)
de novo motif analysis (homer 4.11.1, MEME 5.0.5)
peak annotation (homer 4.11.1, mm10)
bam to bigwig conversion (Python 2.7.11, deeptools 3.2.1)
Assembly: UCSC homo sapiens (hg19)
Supplementary files format and content: bigwig (.bw), peak files (.bed)

source_name: RA-treated SH-SY5Y +FLAG-HA-hRBM45

growth_protocol: 1:1 Eagle's Minimal Essential Medium (EMEM) and Ham's F12 Nutrient mix, 10% FBS, Penicillin/Streptamycin; cultured in vitro at 37˚C, 5.0% CO₂, humidified

extract_protocol:
CLIP RNA extraction performed according to iCLIP protocol (10.1016/j.ymeth.2013.10.011); size-matched input (SM input) RNA extraction performed in parallel as adapted from eCLIP protocol (10.1038/nmeth.3810)
libraries generated using iCLIP protocol with post-extraction input and CLIP RNA (10.1016/j.ymeth.2013.10.011)

treatment_protocol: cell lines transduced with lentivirus expressing FLAG-HA-tagged human RBM45 (SH-SY5Y), expression confirmed by WB and RT-qPCR  treated with exchange into differentiation media (DM: Neurobasal A medium +1x GlutaMAX, B27+ nutrient mix, Penicillin/Streptamycin) containing DMSO (control, 0.1% v/v) or 10 µM RA in DMSO (0.1% v/v), allowed to culture for seven days with media replenishment at days 3 and 5  crosslinked with UV irradiation using 2 doses of 150 mJ/cm2 prior to cell culture dissociation and collection for use in iCLIP library preparation protocol

value: cultured human neuroblastoma cell line

value: DM +10 uM RA (in DMSO 0.1% v/v) for 7 days

tag: antibody

value: Sigma-Aldrich HA-Tag (H3663) Mouse mAb

tag: molecule subtype

value: crosslinked immunoprecipitated RNA


title: CLIP_SHSY5Y-DMSO_rep2_input

description: DMSO replicate 2, paired input RNA

source_name: DMSO-treated SH-SY5Y +FLAG-HA-hRBM45

value: DM +DMSO (0.1% v/v) for 7 days

value: no antibody

value: input total RNA


title: CLIP_SHSY5Y-RA_rep1_CLIP

description: RA replicate 1, CLIP RNA


title: CLIP_SHSY5Y-DMSO_rep1_CLIP

description: DMSO replicate 1, CLIP RNA


title: CLIP_SHSY5Y-DMSO_rep2_CLIP

description: DMSO replicate 2, CLIP RNA


title: normal tissue

city: Nanchang

first: Dewu

address: 17 Yongwai Street

institute: Institute of Burn Injury, The First Affiliated Hospital of Nanchang University

description: adjacent normal skin tissues

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering.

source_name: adjacent normal skin tissues

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

extract_protocol: Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols.

tag: disease state

value: adjacent normal skin tissues

tag: age

value: Mixed sample:45–58 years


title: CLIP_SHSY5Y-RA_rep1_input

description: RA replicate 1, paired input RNA


title: BMDMs, NLRC3_KO, RPMI 1640, rep2

tag: tissue

tag: genotype


title: BMDMs, WT, RPMI 1640, rep2

tag: cell type

value: WT


title: BMDMs, WT, RPMI 1640, rep1


title: BMDMs, NLRC3_KO, RPMI 1640, rep1


title: CLIP_SHSY5Y-DMSO_rep1_input

description: DMSO replicate 1, paired input RNA


title: BMDMs, NLRC3_KO, LPS, rep3

value: LPS


title: human-overexpressing LINC00839-3

city: Guangzhou

first: Xiaoting

address: Baiyun District

institute: Southern Medical University

data_processing:
Trimmomatic-0.36
hisat2(version:2.1.0)
spliced mapping
Stringtie(version:1.3.3)
samtools
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: colorectal cancer

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: stably transfected cell lines with LINC00839

tag: transfection

value: stably expressing LINC00839


title: wound tissue

description: diabetic chronic wounds

source_name: diabetic chronic wounds

value: diabetic chronic wounds


title: human-control cells containing the empty vector-1

value: containing the empty vector


title: BMDMs, WT, RPMI 1640, rep3

value: mice femurs and tibias

value: BMDM


title: human-control cells containing the empty vector-3


title: BMDMs, NLRC3_KO, LPS, rep2

value: NLRC3 KO


title: BMDMs, NLRC3_KO, LPS, rep1


title: human-overexpressing LINC00839-2


title: CLIP_SHSY5Y-RA_rep2_input

description: RA replicate 2, paired input RNA

value: cultured human neuroblastoma cell line


title: human-overexpressing LINC00839-1


title: BMDMs, WT, LPS, rep3


title: BMDMs, WT, LPS, rep2


title: PB Mk  DMSO rep3

city: Charlottesville

first: Fujun

last: Qin

state: VA

address: 345 Crispell Dr.

department: Pathology

institute: University of Virginia

data_processing:
The raw sequencing data underwent quality control analysis and filtering using the NG SQC Tool Kit version 2.3.3,
followed by alignment of high-quality reads to the hg38 genome using HISAT version 2.1.0,
Read count determination with StringTie version 1.3.3b.
Differential expression analysis was performed with Ballgown version 2.6.0
Gene set enrichment analysis was conducted using Enrichr

source_name: Adult peripheral blood CD34+ Cells

growth_protocol: Human CD34+ cells cultured for for 3 days in prestimulation medium (100 ng/ml human SCF, 100 ng/ml human TPO, 100 ng/ml FLT3 ligand and 20 ng/ml human IL-3)  followed by 4 days in megakaryocytic differentiation medium ( 25 ng/ml human SCF, 40 ng/ml human TPO, 100 ng/ml human SDF1⍶),then CD61+ cells were magnetically sorted using anti-CD61 microbeads (Miltenyi Biotec)

extract_protocol:
RNA isolation employed the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany)
The cDNA library was constructed using an NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA)
Sequencing was conducted on an NovaSeq 6000 SequencingSystem (Illumina, San Diego, CA).

treatment_protocol: Megakaryocytic cultures were treated with either solvent DMSO or Dyrk inhibitors harmine or EHT 1610 each 5 µM.

tag: cd61+ cells isolation

value: anti-CD61 microbeads (Miltenyi Biotec, Auburn,CA)

value: DMSO


title: PB Mk  DMSO rep2


title: CB Mk Harmine rep2

source_name: Umbilical cord blood CD34+ Cells

value: 5 uM Harmine


title: CB Mk Harmine rep1


title: PB Mk  DMSO rep1


title: BMDMs, WT, LPS, rep1


title: human-control cells containing the empty vector-2


title: CB Mk Harmine rep3


title: CB Mk EHT 1610 rep3

value: 5 uM EHT 1610


title: CB Mk EHT 1610 rep1


title: CB Mk EHT 1610 rep2


title: CB Mk DMSO rep3


title: primary human keratinocytes, shRNA-NC 3

city: shanghai

first: Ming

middle: zhe

last: Ma

email: mmz666@163.com, mmz666@shca.org.cn

address: Dongan Road 270

department: Department of gastric surgery

institute: Fudan university shanghai cancer center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome
Fragments per kilobase Million (FPKM) were calculated using the formula:(total exon reads)/[mapped reads(million)*exon length (kb)]
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary human keratinocytes

growth_protocol: We isolated primary human keratinocytes from fresh postoperative skin samples of children as described previously by Hildebrand et al. Primary human keratinocytes were cultured in EpiLife Medium (catalog No. MEPI500CA, GIBCO) supplemented with Human Keratinocyte Growth Supplement (catalog No. S0015, GIBCO). Keratinocytes were maintained in a humidified incubator at 37°C in the presence of 5% CO2. All keratinocytes have been passaged for fewer than 6 passages.

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary human keratinocytes were transfected with shRNA-NR037661 or shRNA-NC

value: primary human keratinocytes

value: 1.8 mM CaCl2 for 72 h

value: shRNA-NC


title: primary human keratinocytes, shRNA-NR037661 3

value: primary human keratinocytes from fresh postoperative skin samples of children

value: NR037661 knockdown


title: primary human keratinocytes, shRNA-NC 2

value: WT


title: primary human keratinocytes, shRNA-NR037661 1


title: primary human keratinocytes, shRNA-NR037661 2


title: Galea-

city: OMAHA

first: Meng

last: Niu

state: NE

address: 42nd and Emile

department: Department of Neurological sciences

institute: University of Nebraska Medical Center

library_source: transcriptomic single cell

data_processing:
Cellranger 6.0.1 was used for basecalling, demultiplexing and initial analyses to create the single cell count matrix.
In spedific, cellranger mkfastq and cellranger count were used for this purpose with default parameters.
Assembly: mm10
Supplementary files format and content: H5 files were created from cellranger count to store the matrix of UMI per gene per cell for each sample

source_name: Non-phagocytic cells (S. aureus-dsRed-) from the brain

extract_protocol:
CD45+, dsRed+ and dsRed- cells were collected from the brain and galea at day 3 post-infection for scRNA-seq processing. A total of 1,757 dsRed+ cells were analyzed in the brain and 2,878 in the galea, along with 2,563 dsRed- cells in the brain and 2,510 in the galea.
Cells were processed using a 10X Genomics instrument where single cells were lysed, RNA reverse-transcribed, and RNA barcoded using a Chromium Single-Cell 3´ Reagent Kit v3 (Cat# PN-1000075; 10X Genomics) according to the manufacturer’s instructions. Illumina compatible cDNA libraries were created and quantified by qPCR using the KAPA Library Quant Kit (Illumina) (Cat# KK4824; KAPA Biosystems) and were loaded at a concentration of 1.3 pM on an Illumina NextSeq550 instrument.
Samples were sequenced following the parameters suggested by 10X Genomics to an average depth of ~ 50,000 reads/cell.

treatment_protocol: Mice were infected with a S. aureus-dsRed strain using an established model of craniotomy infection.

value: Galea-

value: CD45+ cells

tag: days post infection

tag: infection

value: S. aureus-dsRed-


title: primary human keratinocytes, shRNA-NC 1

tag: cell line


title: Galea+

source_name: Phagocytic cells (S. aureus-dsRed+) from the galea

value: Galea+

value: S. aureus-dsRed+


title: ref1 vs. epl1-trunc-1:485-tag-flag-1-a

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: scanning of slides using Agilent G256BA Imagene feature extraction

data_processing: genes, no bg corr, dye corr

organism: Saccharomyces cerevisiae

source_name: refpool

label_protocol: robot amplification and labeling v1.0

extract_protocol:
yeast HTP RNA isolation for robot v2.0
yeast RNA isolation for robotic amplification v1.0

value: reference pool

tag: extract protocol

value: yeast HTP RNA isolation for robot v2.0


title: epl1-tag-flag-1-b vs. ref1

value: refpool

value: yeast RNA isolation for robotic amplification v1.0


title: Brain-

value: Brain-


title: ref1 vs. epl1-trunc-1:380-tag-flag-1-a


title: ref1 vs. eaf1-del-tag-HA-1-a


title: eaf1-ctrunc-1:982-tag-HA-1-b vs. ref1


title: ref1 vs. eaf1-ctrunc-1:982-tag-HA-1-a


title: epl1-trunc-1:485-tag-flag-1-b vs. ref1


title: CB Mk DMSO rep1

value: anti-CD61 microbeads (Miltenyi Biotec, Auburn,CA)

value: DMSO


title: eaf1-del-tag-HA-1-b vs. ref1


title: Brain+

source_name: Phagocytic cells (S. aureus-dsRed+) from the brain

value: Brain+


title: SY5Y_KORescue-2-gm_rep2

description: replicate 2, KO Rescue clone 2 SH-SY5Y GM (ribodepleted-RNA-seq)

data_processing:
adapter removal (SeqAn 2.3.2, flexbar 3.0.3)
alignment (HiSAT2 2.1.0) to UCSC genomes; hg19
bam to bigwig conversion (Python 2.7.11, deeptools 3.2.1)
read count measurements (Subread 1.6.3, featureCounts 1.6.5)
differential gene expression analysis (DESeq2 1.32.0, R 3.6.0)
differential exon usage analysis (DEXSeq 1.38.0, R 3.6.0)
annotation, de novo motif enrichment (homer 4.11.1, MEME 5.0.5)
downstream expression analyses (R 3.6.0, RStudio)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig (.bw), read counts (.output), alignment (.bam)

growth_protocol: 1:1 Eagle's Minimum Essential Medium + Ham's F12 Nutrient Mix, 10% heat-inactivated FBS, Penicillin/Streptamycin; cultured in vitro at 37˚C, 5.0% CO2, humidified

extract_protocol:
total RNA extraction performed using TRIzol, DNase-I treated, isolated by PCI extraction and EtOH precipitation
library generated using ribodepletion of total RNA (NEB #7870), followed by construction with NEBNext Ultra II non-directional RNA library prep kit (NEB #7770)

treatment_protocol: (1) no treatment, (2) control treatment with 0.1% DMSO in differentiation media (1x Neurobasal A, Penicillin/Streptamycin, 1x GlutaMax, 1x B27 supplement), (3) differentiation with 10 µM RA/0.1% DMSO in differentiation media

value: SK-N-SH neuroblastoma subline

value: Cas9-guided RBM45 KO +F-HA-tagged RBM45_mut{delta}gRNA, isogenic clonal isolate #2

value: no treatment, culture media only


title: SY5Y_KORescue-2-ra_rep2

description: replicate 2, KO Rescue clone 2 SH-SY5Y differentiated (ribodepleted-RNA-seq)

value: differentiation, 10 µM RA in 0.1% DMSO for seven days


title: SY5Y_KORescue-2-dmso_rep2

description: replicate 2, KO Rescue clone 2 SH-SY5Y control (ribodepleted-RNA-seq)

value: control treatment, 0.1% DMSO for seven days


title: epl1-trunc-1:380-tag-flag-1-b vs. ref1


title: IPSC-CM cells, Propofol 3

first: Yangyang

last: liu

address: Jin zun 115

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform.
Read count extraction and normalization were performed and 150 bp paired-end reads were generated.
Differential expression analysis was carried out using the DESeq Bioconductor package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Induced pluripotent stem cells (IPSC)

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). 1 ug of total RNA was used for the construction of sequencing libraries.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Induced pluripotent stem cells (IPSC)

value: iPSC-derived Cardiomyocytes(IPSC-CM)

tag: phenotype

value: dilated (DCM)

value: Duchenne Muscular Dystrophy (DMD)

value: Propofol

tag: time

value: Day 30


title: SY5Y_KORescue-2-gm_rep1

description: replicate 1, KO Rescue clone 2 SH-SY5Y GM (ribodepleted-RNA-seq)

tag: treatment


title: CB Mk DMSO rep2


title: ref1 vs. epl1-tag-flag-1-a

tag: strain

value: reference pool

value: yeast HTP RNA isolation for robot v2.0


title: SY5Y_KORescue-2-dmso_rep1

description: replicate 1, KO Rescue clone 2 SH-SY5Y control (ribodepleted-RNA-seq)


title: IPSC-CM cells, Propofol 2


title: SY5Y_KORescue-2-ra_rep1

description: replicate 1, KO Rescue clone 2 SH-SY5Y differentiated (ribodepleted-RNA-seq)


title: IPSC-CM cells, Etomidate 3

value: Etomidate


title: IPSC-CM cells, Propofol 1


title: BM, Female_Young_Old, Pool, HTO

city: Los Angeles

first: Helen

middle: S

last: Goodridge

state: CA

address: 8700 Beverly Boulevard

institute: Cedars-Sinai Medical Center

description:
hashtag1-hashtag10
Female_Young_Old_barcodes.tsv.gz
Female_Young_Old_matrix.mtx.gz
Female_Young_Old_features.tsv.gz
HTO_feature_reference_revised.csv

library_source: other

data_processing:
Libraries were sequenced on a NovaSeq 6000 (Illumina) as per the Single Cell 3′ v3.1 Reagent Kits User Guide, with a sequencing depth of ~40,000 reads/cell.
The demultiplexed raw reads were aligned to the transcriptome using STAR (version 2.5.1) (Dobin et al 2013) with default parameters and mouse mm10 transcriptome reference from Ensembl version 84 annotation, containing all protein coding and long non-coding RNA genes.
Expression counts for each gene in all samples were collapsed and normalized to unique molecular identifier (UMI) counts using Cell Ranger software version 4.0.0 (10X Genomics)
Assembly: mm10
Supplementary files format and content: CellRanger formated expression matrix and hashtags reference for sample demultiplexing

molecule: protein

source_name: Bone marrow

extract_protocol:
Bone marrow cells from young and old mice (5 mice in each group) were barcoded with TotalSeq hashtag antibodies (Table S1), pooled, and classical Ly6Chi monocytes (Ly6G-CD11b+CD115+Ly6Chi cells) were isolated by FACS sorting. Male and female mice were processed separately
RNA libraries were prepared for sequencing using standard 10X protocols.

value: Bone marrow

value: 2-6 months, 24-30 months

value: WT

tag: Sex

value: female


title: IPSC-CM cells, DSMO 1

value: DSMO


title: IPSC-CM cells, Etomidate 2


title: SY5Y_KORescue-1-dmso_rep1

description: replicate 1, KO Rescue clone 1 SH-SY5Y control (ribodepleted-RNA-seq)

value: SK-N-SH neuroblastoma subline

value: Cas9-guided RBM45 KO +F-HA-tagged RBM45_mut{delta}gRNA, isogenic clonal isolate #1


title: SY5Y_KORescue-1-gm_rep2

description: replicate 2, KO Rescue clone 1 SH-SY5Y GM (ribodepleted-RNA-seq)

value: no treatment, culture media only


title: IPSC-CM cells, Etomidate 1

value: Induced pluripotent stem cells (IPSC)


title: IPSC-CM cells, DSMO 3

value: iPSC-derived Cardiomyocytes(IPSC-CM)


title: SY5Y_KORescue-1-ra_rep1

description: replicate 1, KO Rescue clone 1 SH-SY5Y differentiated (ribodepleted-RNA-seq)

value: differentiation, 10 µM RA in 0.1% DMSO for seven days


title: IPSC-CM cells, DSMO 2

value: dilated (DCM)

value: Duchenne Muscular Dystrophy (DMD)


title: BM, Female_Young_Old, Pool, GEX


title: SY5Y_KORescue-1-ra_rep2

description: replicate 2, KO Rescue clone 1 SH-SY5Y differentiated (ribodepleted-RNA-seq)


title: DRBshRNA_rep2

city: Singapore

first: Xavier

last: ROCA

state: Singapore

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

data_processing:
We aligned the paired-end reads to human genome (UCSC-hg19) using Tophat2 with Bowtie2
We used Cufflinks, Cuffmerge and Cuffdiff for transcripts assembly.
We employed rMATS to analyze alternative splicing events.
Assembly: hg19

source_name: THP-1 cell line

growth_protocol: THP-1 (ATCC, TIB-202) cells were cultured in RPMI-1640 (ATCC, 30-2001), supplemented with 10% FBS (Gibco, LS26140079), 100 U/ml Penicillin and 100 μg/ml Streptomycin at 37 oC, and 5% CO2.

extract_protocol:
We isolated Total RNA using RNeasy Mini Kit (Qiagen), followed by DNase treatment (TURBO DNA-free Kit, Ambion) and RNA purification (RNA Clean and Concentrator, Zymo Research).
We prepared cDNA libraries using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: Only in drug treatment groups, knockdown cells were treated with 50 μM DRB or 1 μM CPT (camptothecin) for 7 h.

tag: shRNA

value: treated with 50 uM DRB for 7h


title: CPTshRNA_rep3

value: treated with 1 uM CPT for 7h


title: DRBshRNA_rep3


title: DRBscr_rep2

value: scramble


title: SY5Y_KORescue-1-dmso_rep2

description: replicate 2, KO Rescue clone 1 SH-SY5Y control (ribodepleted-RNA-seq)

value: control treatment, 0.1% DMSO for seven days


title: CPTshRNA_rep2


title: CPTshRNA_rep1


title: IgG

city: Moscow

first: Natalia

last: Klimenko

address: 34/5 Vavilova Street

country: Russia

institute: Institute of Gene Biology (IGB) of the Russian Academy of Sciences

description: Preimmune control

data_processing:
Adapters, poly-N, poly-A and low-quality read ends were removed using cutadapt software (Martin 2011) (quality threshold was set to 20, reads with the length less than 20 bp after trimming were discarded).
The remaining reads were aligned to build version mm10 (GRCm38, Ensembl release) of the Mus musculus genome using Bowtie version 1 (Langmead et al. 2009) (with enabling options -best, -strata, -tryhard). Only reads that aligned exactly one time were passed through for further analysis.
PCR duplication artifacts were removed using the Picard MarkDuplicates function (http://broadinstitute.github.io/picard/). In addition, peaks overlapping with blacklist regions were discarded (https://sites.google.com/site/anshulkundaje/projects/blacklists).
Peak calling was performed using MACS version 2 against preimmune control (IgG) (Zhang et al. 2008) with the suppression of model built and assignment the reads extension length to 200 bps. (https://sites.google.com/site/anshulkundaje/projects/idr).
NarrowPeak files contain peaks with MACS2 p values less than 1x10-5.
Assembly: mm10
Supplementary files format and content: Processed data was obtained by MACS2 and includes: extended bed (narrowPeak) peak calls regions

source_name: adult brain

growth_protocol: C57BL/6 mice (Jackson Laboratory, USA). Animals were kept in identical conditions (a standard light- and temperature-controlled environment, 12-hour light/dark cycle; light on at 7:00 AM; 21 °C, with access to food and water adlibitum)

extract_protocol:
DNA was eluted by Elution Buffer (50mM Tris-HCl (pH-8,0), SDS 1% and 1mM EDTA) and treated with RNase A for 30 min and protease K (Thermo Fisher Scientific) overnight, incubated at 65 degrees for 6 hours and extracted by phenol-chloroform method
For NGS library preparation, 30 ng of DNA and NEBNext Ultra II DNA library prep kit for Illumina was used according to the manufacturer’s protocol. Adaptor ligation was performed using NEBNext multiplex oligos for Illumina index primer set #1 (NEB). Quality of DNA was analyzed with Bioanalyzer DNA 1000 Chip kits (Agilent). DNA yields were assessed using Qubit assay kits (Thermo Fisher Scientific)

treatment_protocol: For chromatin immunoprecipitation one whole brain from P120 mouse was homogenized in ten volumes PBS supplemented with PIC (Roch) and PhIC (Sigma) on ice in Dounce Loose (Millipore). Then formaldehyde was added up to 1% and samples were incubated for 10 minutes on ice. After centrifuged at 4C, for 10 minutes at 1000g; washed three times by the same cold PBS and then resuspend in 1 ml of Sonication Buffer (50 mM HEPES-KOH pH 7.9; 140 mM NaCl; 1 mM EDTA; 1% Triton X-100; 0.1% Na deoxycholate; 0.1% SDS) supplemented with PIC and PhIC in Dounce Tight (Millipore) for nuclear destruction. Chromatin was sheared to ~ 500 bp by sonication at Covaris and precipitated by 10mkL anti-PHF10 antibodies purified and validated by us previously (Soshnikova, et.al., 2014; Soshnikova, et al., 2021) and 1mkg control rabbit IgG (Invitrogen) on Mab-select beads (GE Health). Then beads were washed by Sonication Buffer, Wash buffer A (Sonication buffer with 500mM NaCl), Wash Buffer B (20mM Tris-HCl (pH=8,0), 1mM EDTA, 250mM LiCl, 0,5% NP-40, 0,5% deoxycholate Na), TE subsequently

value: brain

tag: days postnatal

tag: antibody source

value: rabbit

tag: chip antibody

value: anti-IgG (Invitrogen)


title: DRBshRNA_rep1


title: ChIP_seq_PHF10_2

description: PHF10 replicate 2

tag: tissue

value: anti-PHF10 (non-commercial)


title: BM, Male_Young_Old, Pool, HTO

description:
hashtag1-hashtag10
Male_Young_Old_barcodes.tsv.gz
Male_Young_Old_matrix.mtx.gz
Male_Young_Old_features.tsv.gz
HTO_feature_reference_revised.csv

value: Bone marrow

tag: age

value: 2-6 months, 24-30 months

tag: genotype

value: WT

value: male


title: DRBscr_rep3


title: DRBscr_rep1


title: SY5Y_RBM45KO-2-ra_rep1

description: replicate 1, RBM45 KO clone 2 SH-SY5Y differentiated (ribodepleted-RNA-seq)

tag: cell type

value: SK-N-SH neuroblastoma subline

value: Cas9-guided RBM45 KO, isogenic clonal isolate #2


title: SY5Y_KORescue-1-gm_rep1

description: replicate 1, KO Rescue clone 1 SH-SY5Y GM (ribodepleted-RNA-seq)

value: Cas9-guided RBM45 KO +F-HA-tagged RBM45_mut{delta}gRNA, isogenic clonal isolate #1

value: no treatment, culture media only


title: SY5Y_RBM45KO-2-ra_rep2

description: replicate 2, RBM45 KO clone 2 SH-SY5Y differentiated (ribodepleted-RNA-seq)

value: differentiation, 10 µM RA in 0.1% DMSO for seven days


title: BM, Male_Young_Old, Pool, GEX


title: ChIP_seq_PHF10_1

description: PHF10 replicate 1


title: SY5Y_RBM45KO-2-dmso_rep2

description: replicate 2, RBM45 KO clone 2 SH-SY5Y control (ribodepleted-RNA-seq)


title: CPTscr_rep2


title: SRRM2_rep3

value: untreated


title: CPTscr_rep1

value: treated with 1 uM CPT for 7h


title: SY5Y_RBM45KO-2-gm_rep2

description: replicate 2, RBM45 KO clone 2 SH-SY5Y GM (ribodepleted-RNA-seq)


title: SRRM2_rep1


title: CD45- EpCAM+ IEC from Vil.Cre Maf.flox mice (replicate 1)

city: Berlin

first: Christian

last: Neumann

address: Hindenburgdamm 30

institute: Charité-Universitätsmedizin Berlin

data_processing:
Raw sequence reads were mapped to the mouse GRCm38/mm10 genome with Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene and differential gene expression analysis was performed using DESeq2
Assembly: mm10
Supplementary files format and content: counts, FPKM

growth_protocol: IECs were FACS-sorted from the small intestine. IECs were defined as viable CD45- EpCAM+ cells.

extract_protocol:
Total RNA was purified with miRNeasy Micro Kit (Qiagen) from FACS-sorted IECs isolated from small intestine. RNA quality was determined on a Bioanalyzer using the RNA 6000 Pico Kit (Agilent).
mRNA 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.

value: Small intestine

value: CD45- EpCAM+ IEC

tag: genotype/variation

value: Vil.Cre Maf.flox

tag: mouse background


title: SRRM2_rep2


title: SCR_rep1

value: scramble


title: SRRM1_rep1


title: CD45- EpCAM+ IEC from Maf.flox mice (replicate 2)

source_name: CD45- EpCAM+ IEC from Maf.flox mice


title: SCR_rep3


title: CD45- EpCAM+ IEC from Vil.Cre Maf.flox mice (replicate 3)


title: CPTscr_rep3


title: SRRM1_rep3


title: SY5Y_RBM45KO-2-gm_rep1

description: replicate 1, RBM45 KO clone 2 SH-SY5Y GM (ribodepleted-RNA-seq)


title: CD45- EpCAM+ IEC from Maf.flox mice (replicate 3)


title: SRRM1_rep2


title: SCR_rep2


title: SY5Y_RBM45KO-1-ra_rep2

description: replicate 2, RBM45 KO clone 1 SH-SY5Y differentiated (ribodepleted-RNA-seq)

value: Cas9-guided RBM45 KO, isogenic clonal isolate #1